1. Manual
1.1. Overview
1.1.1. Methods
XMVB provides an ab initio computing platform for various VB approaches, including classical VB methods, such as VBSCF, BOVB, VBCI, VBPT2, modern VB methods, such as SCVB and GVB, and molecular orbitals based VB method, BLW. Combined with solvation models, it can perform VBPCM, VBEFP, and VBSMD to account for solvent effects. Incorporating XMVB with KS-DFT code, it can be applied to hybrid DFVB calculation. In this manual, only a brief introduction to classical VB methods is provided. Please read the following references for details:
Articles:
Book Chapters:
1.1.1.1. The VBSCF method
The wave function of Valence Bond Self Consistent Field (VBSCF) method is the linear combination of VB structures, as shown below.
In VBSCF method, All VB structures share the same set of VB orbitals, and both sets of the structure coefficients and VB orbitals are optimized simultaneously to minimize the total energy. This is comparable to the MCSCF method in the MO theory. VBSCF method takes care of the static electron correlation and gives equivalent results to the MO-based CASSCF calculations. It should be noted that the dynamic electron correlation is not accounted for in the VBSCF method. In XMVB, VBSCF method is the default method, thus this keyword can be ignored.
1.1.1.2. VB Methods including Dynamic Correlation
The VBSCF result includes only static correlation energy, which makes VBSCF results not accurate enough for quantitative researches. The purpose of post-VBSCF methods is to take dynamic correlation into account as much as possible to get accurate enough results. There are several post-VBSCF methods developed so far and will be introduced in this section. It is strongly recommended to perform post-VBSCF calculations with initial guesses from a pre-proceeded VBSCF calculation. As to VBCI and VBPT2, this is enforced.
1.1.1.2.1. The BOVB method
The orbitals of Breathing Orbital Valence Bond (BOVB) method are also optimized by SCF procedure, as VBSCF does. The difference between VBSCF and BOVB methods is that BOVB provides an extra degree of freedom during orbital optimization. In BOVB method, each VB structure has its own set of orbitals and are optimized independently
Thus, the orbitals adopt themselves to the instantaneous field of the VB structures, rather than to the mean field of all the structures in VBSCF. This degree of freedom makes the orbitals in BOVB “breathing” in different structures, introduces dynamic correlation, and thereby improves considerably the accuracy of VB computations.
1.1.1.2.2. The VBCI method
The VBCI method is based on localized VB orbitals. In this method VB orbitals are divided to several blocks (occupied and virtual orbitals). Excited VB structures are generated by replacing occupied VB orbitals with virtual orbitals that are localized on the same block. The wave function of VBCI is the linear combination of all reference and excited VB structures
where \(\Phi^i_K\)is CI structure coming from VBSCF structure K, including reference and excited structures, and the coefficients \({C_{Ki}}\) are obtained by solving the secular equation. The VBCI weight can be given either with equation
which gives weights of all CI structures, or in a more compact way as
where \(W_K\) is the contracted weights of reference structure K, including weights of all CI structures coming from structure K.
Allowing for different excitations for different electronic shells, currently the VBCI method consists of the following calculation levels:
VBCI(S,S): only single excitations are involved in either active electron or inactive electron. In brief, this is a VBCIS procedure.
VBCI(D,S): the active shell is treated by single and double excitations, whereas the inactive shell by single excitations only. Also included in this level are double excitations which consist of a single excitation from each shell.
VBCI(D,D): single and double excitations are involved for both active and inactive electrons, in short, VBCISD.
1.1.1.2.3. The VBPT2 Method
Another post-VBSCF method is Valence Bond second-order Perturbation Theory (VBPT2) method. The wave function of VBPT2 can be separated into 2 parts as
where VBSCF wave function is taken as the zeroth-order wave function \(\Psi^0\), and the first-order part is the combination of singly and doubly excited wave functions
To enhance the efficiency of VBPT2, the virtual orbitals are delocalized and orthogonal to the occupied space, and the excitations include all virtual orbitals. In this manner, the excited structures in VBPT2 don’t belong to any fundamental structure, and the matrix elements can be calculated easily with Coulson-Slater rules.
1.1.2. Installation
Both distributions of XMVB are currently available for LINUX platform. 1.5GB RAM is required. Followings are the instructions for installation. Note that the source code will NEVER be released to the users. Only compiled object file or executable files are available for users.
1.1.2.1. Module distribution
Tip
This is an installation guidance for GAMESS-XMVB,whose functions are not provided on the XACS cloud computing platform.
To build the module distribution, the user may need a library file libgamess-xmvb.a
which can be found in the package they obtained. The user may also need to prepare LIBCINT library file libcint.a
which is needed for some functions in XMVB. After that, copy these two library files to object
directory in GAMESS-US. The user also need to make the following modifications to linke XMVB into GAMESS-US package. We assume that the user will run GAMESS-XMVB with AMD-64 Linux, which corresponds to linux64
architecture of GAMESS-US, and the target is sockets
. All operation is proceeded in the root directory of GAMESS-US.
Open
ddi/compddi
and modifyif($COMM == sockets) then set DDI_COMM = '-DDDI_SOC' endif
to
if($COMM == sockets) then set DDI_COMM = '-DDDI_SOC -mcmodel=large' endif
then run
cd ddi && ./compddi
to recompile DDI.
Open
comp
, find the entry forlinux64
, then modifyset EXTRAOPT=" "
to
set EXTRAOPT="-mcmodel=large"
in the branch of
gfortran
, then run./compall
to recompile all modules.
Open
lked
, modifyset XMVB=false
to
set XMVB=true
to activate linking XMVB, then modify
set VBOBJ='xmvb.o'
to
set VBOBJ='libgamess-xmvb.a libcint.a /path/to/lapack /path/to/blas'
where
/path/to/lapack
is the location (absolute path) of LAPACK library file, and/path/to/blas
is the location of BLAS library file. If MKL is used for GAMESS-US, LAPACK and BLAS library files may be omitted.Open
lked
, find the entry forlinux64
, then modifyset LDOPTS=' '
to
set LDOPTS='-fopenmp -mcmodel=large'
in the branch of
gfortran
, then run./lked gamess xmvb
to start linking. After that, an executable file
gamess.xmvb.x
including the whole capability of XMVB will be generated.Before running GAMESS-XMVB, don’t forget to append a line
setenv VBINP $USERSCR/$JOB.xmi
in the file
gms-files.csh
. The varialbe$USERSCR
can be replaced with other values such as$SCR
which is defined inrungms
.
1.1.2.2. Stand-alone distribution
The stand-alone distribution is released as a package of compiled executable files. To install the stand-alone distribution, the users should:
Unpack the compressed tar file by using the following command,
tar xvfz xmvb.tar.gz
Once the file is unpacked successfully, a new directory xmvb/ will be created.
Set the VBDIR environment variable to the location of XMVB package and append xmvb/ to your
$PATH
. The variable VBDIR is essential for PPD algorithm and utility PREINT.
1.1.3. Running a job
A typical XMVB job consists of the following two steps:
Prepare the integrals of primitive basis functions and the MO orbitals of the system. An input file including molecular information and basis set information is needed. Files “1e.tem”, “2e.tem” and “orb.mo” will be generated after this step.
Run XMVB calculation. A file with extension name “.xmi”(XMI file, see section Input ) is needed here.
The programs, utilities and files needed in these 2 steps differ in different distributions. The details are shown below.
1.1.3.1. For module distribution
The two steps of an XMVB job in module distribution are done in one shot with command
rungms job [VERNO] [1]
after all files are prepared.
Step 1 is done in GAMESS program with a GAMESS input file including line
$CONTRL VBTYP=XMVB $END
XMVB calculation will be proceeded automatically following the completion of step 1.
Tip
By default, XMVB guess and input files will not be copied into the $SCR directory, which is the real directory where GAMESS- US is doing the calculation. Please copy these files into your $SCR directory BEFORE the calculation. Otherwise an error may occur.
After the calculation, the integral files and XMVB outputs will also be left in $SCR. Integral files may be used for XMVB calculations with stand-alone XMVB program. Please remember to get them if you need them later for stand-alone XMVB.
1.1.3.2. For stand-alone distribution
With stand-alone distribution used, step 1 is done with program PREINT. After obtaining the integral, create an input file file.xmi for your job (for details, see section Input). Then run the XMVB job by typing command
xmvb file.xmi
Then an output file with name file.xmo will be obtained. For use XMVB in parallelization, see below.
1.1.3.3. Parallelization in stand-alone XMVB
MPI and OpenMP are two popular protocols for parallelization. MPI will create a bunch of processes and the data is synchronized by message-passing, and is useful for multi-node parallelization in distributed systems, e.g. clusters. OpenMP creates a bunch of lightweight threads under a process and is useful for parallelization in single node. The MPI+OpenMP strategy may take the advantages of both protocols to provide a highly-efficient parallelization with multiple nodes. With \(N_\textrm{MPI}\) MPI processes and \(N_\textrm{OMP}\) OpenMP threads for each process, the total number of CPU cores consumed for a parallel job \(N_\textrm{CPU}\) is
Currently such strategy is supported only by stand-alone XMVB. To use MPI in XMVB, the user may have MPICH installed in the computer. The version of MPICH to compile XMVB is 3.3.2.
1.1.3.3.1. MPI parallelization
To run XMVB with MPI parallelization, the user need to type the command
mpirun -np N xmvb file.xmi
to start a computation with N processes. For more information about running parallel computation with MPICH, please refer to the MPICH documentation.
1.1.3.3.2. OpenMP parallelization
The OpenMP parallelization does not need to change the command of running XMVB jobs, as shown in 3.2. The number of CPU cores for the parallelization can be controlled by setting the variable OMP_NUM_THREADS
export OMP NUM THREADS=N
if you just need a certain number N of CPUs for your job. If the variable is abesent, OpenMP parallelizes the XMVB computation with ALL processors in your computer.
For large systems, OpenMP parallelzation may proceed a strange “segmentation fault”. This is because the stack size of threads is not large enough. This can be avoided by setting the stack size to a certain number to avoid this error. In OpenMP parallelization, the stack size of master and slave threads are set in different ways. The stack size of master thread is set by command ulimit as shown
ulimit -s stack_size
The default stack size is 8192. Setting a larger value or simply
ulimit -s unlimited
The stack size of slave threads are controlled by environment variable $OMP_STACKSIZE. Following command will set the stack size of each slave threads to 1GB
export OMP_STACKSIZE=1G
1.1.4. Utilities
Tip
This utilities in this section is not provided on the XACS cloud computing platform.
1.1.4.1. Viewing VB orbitals: Moldendat
Viewing VB orbitals is available. To do that, you need to run a utility, called “moldendat”:
moldendat.exe MOfile vbdat [denfile] >&vbfile
where MOfile is an output file of Gaussian or GAMESS-US, or formatted Gaussian checkpoint file (.fchk); vbdat is a XMVB xdat file; if .fchk file is inputted, an optional XMVB density file with extension “.den” is also supported. The program will produce an NEW output file (vbfile) with the same format as input MO files, with which you can view VB orbitals with MOLDEN or MacMolPlt (for GAMESS-US only) packages.
1.1.4.2. Preparing integrals: PREINT
This utility is developed to prepare integrals and MO orbitals for XMVB. To run PREINT, simply type the command as following:
preint input >&output
where input is the input file (see below) and output is the user-defined output file. A typical input file for F2 molecule is shown below:
hf cc-pVTZ libcint spher
0 1
F 0.000000 0.000000 0.000000
F 0.000000 0.000000 1.400000
Here keyword libcint
means the integrals will be generated by external library LIBCINT and spher
means spherical integrals will be generated. Both keywords are optional. Currently “spher” can only be used with “libcint”.
The program provides three files for standalone XMVB jobs:
x1e.int containing 1-e integrals and MO orbitals
x2e.int storing 2-e integrals
INFO storing basis function information and coordinate of the molecule
The Basis sets and elements supported by current PREINT are:
STO-2G H-Ca,Sr
STO-3G H-Xe
STO-6G H-Kr
3-21G H-Cs
3-21G* H-Ar
3-21++G H-Ca
3-21++G* H-Ar
4-31G H-Cl
6-31G H-Zn
6-31G* H-Kr
6-31G** H-Zn
6-31+G H-Ca
6-31+G* H-Ca
6-31+G** H-Ca
6-31++G H-Ca
6-31++G* H-Ca
6-31++G** H-Ca
6-311G H-Ca,Ga-Kr,I
6-311G* H-Ca,Ga-Kr,I
6-311G** H-Ca,Ga-Kr,I
6-311+G H-Ca
6-311+G* H-Ca
6-311+G** H-Ca
6-311+G(2d,p) H-Ca
6-311++G H-Ca
6-311++G* H-Ca
6-311++G** H-Ca
6-311++G(2d,2p) H-Ca
cc-pVDZ H-Kr
cc-pVTZ H-Ca
aug-cc-pVDZ H-Kr
cc-pCVDZ H-Ca
cc-pCVTZ H-Ca
aug-cc-pCVDZ H-Ar
aug-cc-pCVTZ H-Ar
DZP H-Ba,La,Hf-Rn
TZP H-Ca
PREINT can also proceed DFT calculations. Currently supported DFT functionals are:
Exchange functionals: Slater, B88.
Correlation functionals: VWN1, VWN5, LYP.
Exchange-correlation functionals: SVWN1, SVWN5, BLYP.
Hybrid functionals: BHHLYP, B3LYP
More functionals will be implemented and supported in the future. All functionals support R-, U-, and RO-type calculations. To enable DFT calculations, just replace “hf” in the exmaple with functional names, for instance
ub3lyp cc-pVTZ libcint spher
0 1
F 0.000000 0.000000 0.000000
F 0.000000 0.000000 1.400000
1.1.4.3. Cartesian to spheric integral transformation: 6D25D
This utility transforms integrals from cartesian type to spheric (harmonic) type. Currently the utility supports D and F transformation only and not available for higher basis functions.
To run the utility, typing the command as following:
6d25d.exe [-if gau/gms/lib] [-of gau/std]
where option “-if” defines the sequential of cartesian F functions. Argument “gau” means the sequential in Gaussian and PREINT, “gms” means the sequential in GAMESS-US. Option and “lib” means the sequential by LIBCINT; -of” defines the output format of spheric F basis functions. Argument “gau” means the spheric F functions used in Gaussian package and “std” means standard spheric F function, which is different from the definition in Gaussian. By default, 6d25d will use Gaussian type for both input and output format.
After running 6d25d, the original cartesian integral files x1e.int, x2e.int and INFO will be overwritten by the spheric integrals. Make a backup of your cartesian integral files if you need them later.
1.1.4.4. Use NBOs as XMVB initial guess: NBOPREP
This utility read the NBOs obtianed from a previous GAMESS/Gaussian calculation, and transfer them to the XMVB readable formats so that user may use them as initial guess in later XMVB calculations with keyword GUESS=NBO
.
The user need to run a GAMESS/Gaussian calculations with keyword
$NBO PLOT $END
to get files with name FILE.36 and FILE.37 which stores NBOs and PNBOs. Then run NBOPREP as following:
nboprep.exe outfile [NBO/PNBO]
where “outfile” refers to the output file of GAMESS/Gaussian program, and “NBO/PNBO” tells the program which kind of NBOs should be prepared for later XMVB calculation. The user may be able to use keyword GUESS=NBO
by copying file “orb.nbo” generated by NBOPREP to the directory where the XMVB job will be proceeded.
1.1.4.5. Generate cube file for XMVB computation: vbcubegen
This utility generates cube grid file to visualize VB orbitals with other programs. It supports module distribution or stand-alone XMVB with keyword INT=CALC
or INT=LIBCINT
since basis function information is essential for generating grids. The syntax of this utility is
vbcubegen.exe xmofile
where xmofile refers to the XMO output file of the XMVB computation. After that, a cube grid file with the same file name as the xmo file will be generated, with which the user may visualize VB orbitals with programs such as GaussView, Multiwfn etc.
1.2. Input
The extension name of XMVB input file is “xmi”. All the contents is organized in sections and case insensitive. The input file is structured in sections with following rules:
The first line of an xmi file is the job title or description of the job and should not be replaced or omitted.
A section start with a line includnig only the section name and ends with a line with only “$END”.
All contents after “#” is recognized as a comment and will not be parsed.
Commonly used sections are:
manual/input:VB structure description ($STR)
An example of XMVB input file is shown below:
H2 L-VBSCF # Job title
$CTRL # Start of $CTRL section
NSTR=3 # 3 VB structures in this computation
NAO=2 NAE=2 ISCF=5 # VBSCF algorithm for RDM-based algorithm
IPRINT=3 # Printing level
ORBTYP=HAO FRGTYP=SAO # VB orbitals are HAO with symmetrized atomic orbital fragments (SAO)
INT=LIBCINT # Integrals are evaluated with LIBCINT library
BASIS=CC-PVTZ # Basis set is cc-pVTZ
GUESS=READ # Initial guess read from $GUS section
$END # End of $CTRL section
$STR # Start of $STR section for structure description with NSTR defined in $CTRL
1 2 # covalent structure H-H
1 1 # ionic structure H- H+
2 2 # ionic structure H+ H-
$END # End of $STR section
$FRAG # Start of $FRAG section since SAO fragment is requested
1*2 # 2 fragments, 1 atom included in each
SPZDXXDYYDZZ 1 # Fragment 1, basis functions s, pz, dxx, dyy and dzz on atom 1
SPZDXXDYYDZZ 2 # Fragment 2, basis functions s, pz, dxx, dyy and dzz on atom 2
$END # End of $FRAG section
$ORB # Start of $ORB section for orbital description
1*2 # 2 VB orbitals, each includes 1 fragment (since fragments defined in $FRAG)
1 # orbital 1, with only fragment 1
2 # orbital 2, with only fragment 2
$END # End of $ORB section
$GEO # Start of $GEO section since INT=LIBCINT requested
H 0.0 0.0 0.0 # H2 coordinate given in Cartesian
H 0.0 0.0 0.74
$END # End of $GEO section
$GUS # Start of $GUS section since GUESS=READ requested, pasted from previous computation result
15 15
# ORBITAL 1 NAO = 15
-0.3532245024 1 -0.5363311264 2 -0.2343104477 3 -0.0000000000 4
0.0000000000 5 -0.0199961314 6 -0.0000000000 7 0.0000000000 8
-0.0192894825 9 -0.0003896018 10 0.0000000000 11 -0.0000000000 12
-0.0003896018 13 0.0000000000 14 -0.0020820012 15
# ORBITAL 2 NAO = 15
0.3532245024 16 0.5363311264 17 0.2343104477 18 0.0000000000 19
-0.0000000000 20 -0.0199961314 21 0.0000000000 22 -0.0000000000 23
-0.0192894825 24 0.0003896018 25 -0.0000000000 26 -0.0000000000 27
0.0003896018 28 0.0000000000 29 0.0020820013 30
$END
1.2.1. Global control ($CTRL)
The $CTRL section contains the information of how a job is performed. The input format is name=value or name=option, except for the keywords which need no values or options. <enter> and <space> are used to separate keywords. If a keyword accepts several options in a time, the options are separated with “,”.
1.2.1.1. Keywords for Global Control
1.2.1.1.1. BPREP
This keyword initiates an integral transformation from primitive basis functions to VB basis functions with $BFI (see our offline manual) needed. The transformation may freeze core orbitals, remove some primitive basis functions which are not involved in VB calculation, and hybridize basis functions. XMVB will use primitive basis functions without transformation if this keyword is missing.
Note
This keyword cannot be used together with ORBTYP=HAO
or GUESS=MO
(see descriptions for keywords ORBTYP=option and GUESS=option)
1.2.1.1.2. EPG=n
Set the convergent criterion of energy to \(10^{-n}\). Default value is 7.
1.2.1.1.3. GPG=n
Set the convergent criterion of gradient. Floating point number is inputted. Default value is 2.D-3 for ISCF=1/3, 1.D-3 for ISCF=2/5, and 1.D-4 for ISCF=6.
1.2.1.1.4. ITMAX=n
n is the maximum number of iterations. Default value is 200.
1.2.1.1.5. NMUL=n
n is the spin multiplicity (2S + 1) of system. Default value is 1, which means singlet state.
1.2.1.1.6. NAO=m
m is the number of active VB orbitals whose occupation number varies in the structures. NAO
is required if keywords STR
or ISCF=5
(see below) is specified.
1.2.1.1.7. NAE=n
n is the number of active VB electrons which occupy the active orbitals. NAE is required if keywords STR
or ISCF=5
(see below) is specified.
1.2.1.1.8. NSTR=n
n is the number of VB structures (or determinants). This keyword can be omitted if STR
(see below) is assigned.
1.2.1.1.9. STR=options
This keyword generates VB structures automatically and hence NSTR
and the $STR
section are not needed. This keyword requires NAO
and NAE
to declare the active space. Users may use one or several of the following options:
COV: Covalent structures will be generated.
ION[(n-m)]: Ionic structures will be generated. A simple ION will generate all ionic structures; ION(n,m) will generate only the \(n^\textrm{th}\) and \(m^\textrm{th}\) order ionic structures and ION(n-m) will generate ionic structures from the \(n^\textrm{th}\) to the \(m^\textrm{th}\) order.
FULL: All VB structures will be generated.
1.2.1.1.10. FIXC
Request to fix structure coefficients for VB structures. In VB theory, the coefficients are obtained by solving the secular equation
For some special purposes, one may want to fix the coefficients. In such situation, the coefficients are inputted following the corresponding VB structures and the energy will be obtained directly by
For example, the following input will constrain the coefficients of the three VB structures to be 1.0:0.5:0.5
$STR
1 2 1.0
1 1 0.5
2 2 0.5
$END
The corresponding wave function will in the expression
where N is the normalization coefficient.
1.2.1.1.11. GROUP=EXP
Divide VB structures into groups according to the expression EXP. An expression with n structures divided into m groups can be expressed as:
Here \(S_{i1} \ldots S_{nm}\) are the structure numbers, a comma “,” is used to separate the structures numbers in the same group, and two commas “,,” is used to separate different groups. Coefficients of structures should be given in Global control ($CTRL), similar to FIXC. The ratio of VB structures within the same group will be fixed, as introduced in FIXC. The coefficients of VB structures in different groups will not be fixed and shall be optimized by solving secular equation. Following is an example:
$CTRL
NSTR=3
GROUP=1„2,3
$END
$STR
1 2 1.0 # S1
1 1 0.5 # S2
2 2 0.5 # S3
$END
The above example devide 3 VB structures into 2 groups:
Group 1. \(G_1 = S_1\)
Group 2. \(G_2 = 0.5(S_2 + S_3)\)
Hence a 3 structure problem becomes a 2 “structure” problem:
where \(C_1\) and \(C_2\) are coefficients of \(G_1\) and \(G_2\) obtained by solving secular equation. The finalwave function can be expressed as
1.2.1.1.12. NSTATE=n
Energy, coefficients and weights of structures for the \(n^\textrm{th}\) excited state, rather than for the ground state, will be calculated and printed out. The values of n can be:
0: The ground state.(Default)
n: The \(n^\textrm{th}\) excited state.
Note
VB orbitals are optimized by minimizing the energy of required state. When the \(n^\textrm{th}\) excited state is requested, the \((n+1)^\textrm{th}\) root will be chosen as the \(n^\textrm{th}\) excited state when solving the secular equation. Thus, n must be smaller than the number of structures.
For VBCI calculaitons, NSTATE can be only 0 or 1.
1.2.1.1.13. IPRINT=n
Printing levels for XMVB. The available levels are:
1: Initial guess, energy, coefficients, weights, and orbitals will be printed. This is the default printing level.
2: All contents in IPRINT=1, Hamiltonian and overlap matrices in terms of VB structures, and population analysis will be printed.
3: All contents in IPRINT=2, density matrix and orbital overlap matrix will be printed.
1.2.1.1.14. SORT
Sort the VB structures in descending order according to coefficients.
1.2.1.1.15. CTOL=tol
Set the Coefficient TOLerance when printing coefficients and weights of VB structures.
Only the coefficients and weights of VB structures whose absolute values of coefficients are not smaller than tolerance tol will be printed. The default tolerance is 0, which means all structures will be printed.
Note
The tolerance tol is a real parameter. For instance,
CTOL=0.01
means that only structures whose absolute values of coefficients larger than or equal to 0.01 will be printed. For VBCI this keyword is not functioning
1.2.1.1.16. CICUT=n
Set cut threshold to \(10^{-n}\) for CI configurations. The contribution of a CI configuration is estimated by perturbation theory. If the contribution is less than the threshold, the configuration will be discarded. This will reduce the computational effort for CI calculations. Recommended values are 5 or 6. Default value is 0 (no cut).
1.2.1.1.17. NCOR=m
In VBCI or VBPT2 calculations, the first m orbitals (2m electrons) will be frozen in the VBCI or VBPT2 calculation. In BOVB caluclations, the first m orbitals will be kept as VBSCF orbitals. The default value is 0, which means all orbitals will be counted in VBCI, VBPT2 or BOVB.
1.2.1.1.18. GUESS=option
This keyword describes the way to generate or read the initial guess for a VB computation.
Valid options can be:
AUTO: The program automatically provides guess orbitals by diagonalizing a fragmant-localized Fock matrix. This is the default option.
UNIT: The first basis function of an orbital in $ORB is set to be the guess for the orbital.
NBO: Initial guess will be obtained from NBOs.
READ: Guess orbitals are read from external file, which should be provided by user. MO: Initial guess of VB orbitals will be obtained directly from molecular orbitals.
RDCI: Initial guess in VBCI type will be given by users.
Note
GUESS=MO
cannot be used with BPREP
.
GUESS=NBO
cannot be used with BPREP
and needs an extra preparation by NBOPREP
.
GUESS=AUTO
cannot be used when some orbitals contain only one basis function (see Orbital description ($ORB) section).
1.2.1.1.19. WFNTYP=option
Options for the way to expand the many-electron wave functions of system.
STR: VB structures are used. (Default)
DET: VB determinants are used for state functions, instead of VB structures.
1.2.1.1.20. VBFTYP=option
Options for the way to expand VB structures.
PPD: paired-permanent-determinant algorithm is used.
DET: Slater determinant algorithm is used.
By default, the program will decide which one to use according to the system, method, or algorithm the users choose.
Note
PPD expansion can be used only with
ISCF=1
orISCF=3
.ISCF=5
,VBPT2
,VBCI
,DFVB
, solvation VB methods, DEN, and IPRINT \(\ge\) 2 will use DET expansion automatically.All systems with multiplicity larger than 2 will be calculated with DET expansion.
Systems with electrons in VB calculation larger than 14 will be calculated with DET expansion.
1.2.1.1.21. ORBTYP=option
Specify the type of VB orbitals. Valid options are:
HAO: Hybrid Atomic Orbitals are used.
BDO: Bond Distorted Orbitals are used.
OEO: Overlap Enhanced Orbitals are used.
GEN: VB orbitals are defined by users. (Default)
Note
Fragments definition ($FRAG) is needed if
ORBTYP=HAO
is specified. The Fragments definition ($FRAG) section will specify the fragments based on atoms or basis functions and orbitals will be assigned in Orbital description ($ORB) section based on the fragment definitions in Fragments definition ($FRAG).ORBTYP=OEO
does not need Fragments definition ($FRAG) and Orbital description ($ORB) sections since the OEOs are delocalized in the whole system.ORBTYP=GEN
does not need Fragments definition ($FRAG) section, and orbitals will be described in terms of VB basis functions explicitly in Orbital description ($ORB) section.ORBTYP=HAO
cannot be used withBPREP
.ORBTYP=BDO
can be used with other orbital types, such asORBTYP=HAO,BDO
.ORBTYP=BDO
is equivalent toORBTYP=GEN,BDO
.
1.2.1.1.22. FRGTYP=option
Specify the type of fragments when ORBTYP=HAO
.
ATOM: The fragments of system will be defined with atoms. This is the default.
SAO: The fragments of system will be defined with symmetrized atomic orbitals.
Note
Fragments definition ($FRAG) is required for FRGTYP=SAO
. For FRGTYP=ATOM
, each atom is considered as a fragment if no FRAG section appears in the input file.
1.2.1.2. Keywords for Computational Methods and Algorithms
1.2.1.2.1. HF/RHF/UHF/ROHF
A Hartree-Fock calculation will be proceeded. RHF/UHF/ROHF represent the restricted, unrestricted and restricted open-shell Hartree-Fock calculations respectively. When only “HF” is assigned, RHF will be proceeded when system is singlet and UHF for other cases.
1.2.1.2.2. Density Functional Theory
A DFT calculation will be proceeded. Currently supported keywords and corresponding functionals are listed below:
- LDA Functionals
Slater Slater exchange functional
VWN/VWN5 Vosko-Wilk-Nusair correlation functional
VWN1 Another Vosko-Wilk-Nusair correlation functional
SVWN/SVWN5 Slater + VWN5 XC functional
SVWN1 Slater + VWN1 XC functional
- GGA Functionals
B88 Beck88 exchange fuctional
LYP Lee-Yang-Parr correlation functional
BLYP Becke88 + Lee-Yang-Parr XC functional
- Hybrid Functionals
BHHLYP 0.5 B88 + 0.5 HFX + LYP hybrid functional
B3LYP Becke’s 3 parameter hybrid functional, with VWN1 involved
B3LYP5 Becke’s 3 parameter hybrid functional, with VWN5 involved
The users may use “R”, “U”, and “RO” ahead of the name of functional to specify restricted, unrestricted or restricted open-shell calculations, the same as HF method. For example, “RB3LYP” will run the restricted B3LYP calculation. If only the name of functional is specified, restricted calculation will be run for singlet and unrestricted for others.
1.2.1.2.3. VBSCF
A VB Self-Consistent Field computation is requested. This is the default method for the XMVB program.
1.2.1.2.4. BOVB
Ask for a Breathing Orbital VB (BOVB) calculation.
Note
BOVB method cannot be used with VBCI.
BOVB method is usually more difficult to converge than VBSCF. Thus, it is recommended to run a BOVB job with a good initial guess. It is recommended to run a VBSCF calculation first, followed by the BOVB calculation with optimized VBSCF orbitals as the initial guess.
1.2.1.2.5. ABOVB
Ask for an Approximate Breathing Orbital VB (A-BOVB) calculation.
1.2.1.2.6. BLW
Block Localized Wavefunction (BLW) method is requested. With this keyword specified, Global control ($CTRL) will not be read and the structure will be generated automatically. The users only need specify the type of VB orbitals (see FRGTYP=option and ORBTYP=option above).
Note
The implementation of the BLW method in the program is not optimized. Users are recom mended to run GAMESS-BLW for a BLW calculation.
1.2.1.2.7. VBCIS:
Ask for a VBCIS calculation.
1.2.1.2.8. VBCISD
Ask for a VBCISD calculation.
1.2.1.2.9. VBCIDS
Ask for a VBCIDS calculation.
1.2.1.2.10. VBPT2
A VBPT2 computation will be performed.
1.2.1.2.11. DFVB
Ask for a DFVB calculation.
1.2.1.2.12. SCC
Size-Consistent Correction in DFVB computations will be switched on.
1.2.1.2.13. VBEFP
Ask for a VBEFP calculation.
1.2.1.2.14. VBPCM
Ask for a VBPCM calculation.
1.2.1.2.15. VBEFPPCM
Ask for a VBEFP/PCM calculation.
1.2.1.2.16. TBVBSCF
Activate tensor-based VBSCF. Currently TBVBSCF is valid only when:
ISCF=5
,NAO=m
andNAE=n
are selected.Structures are generated automatically with STR=options.
Number of active electrons should be at least 4, in which 2 for both \(\alpha\) and \(\beta\) parts.
1.2.1.2.17. VMAX=n
The maximum number of \(\sigma\) kept in Davidson diagonalization. The default value is 10. Only for TBVBSCF.
1.2.1.2.18. READCOEF
Read a file “coef” (see File with coefficients for the structures/determinants (.coeff)) with coefficients of the first n structures as the initial guess of Davidson diagonalization. The file may be obtained from a previous TBVBSCF. Only for TBVBSCF.
1.2.1.2.19. ISCF=n
ISCF specifies orbital optimization algorithm. The value n currently can be:
1: Numerical gradients with forward-difference approximation are used with the DFP-BFS algorithm. This is the default option of XMVB.
2: Analytical gradients in terms of basis functions with the L-BFGS algorithm. This algorithm involves only the first-order density matrix and is not suitable in cases displaying structures that are orthogonal to each other.
3: Numerical gradients with central-difference approximation are used with the DFP-BFS algorithm.
4: Optimization with Generalized Brillium Theory(GBT) is requested.
5: Analytical gradients in terms of VB orbitals with the L-BFGS algorithm. This is the most efficient algorithm so far. This option needs
NAO
andNAE
.6: VBSCF with full hessian matrix.
NAO
andNAE
are needed for this option. This algorithm is potentially faster and more robust than ISCF=5, but it is still under development and thus is not recommended in the current version of the program.
1.2.1.2.20. EIGMTHD=option
Specify the way to solve the secular equation and get the energy and coefficients. The available options can be:
FULL: Solving secular equation in the traditional way.
ITER: An iterative algorithm will be used to solving secular equation. This will be helpful for VBCI or VBSCF with large number of structures.
1.2.1.2.21. WSTATE=EXP
Activate the state-average VBSCF calculation for ISCF=1-5. WSTATE may provide an array containing non-zero weights of the specific states. Following is the example for
$CTRL
NSTR=10 WSTATE(3)=0.5,0.0,0.3,0.0,0.0,0.2
$END
1.2.1.3. Keywords for Integrals
1.2.1.3.1. INT=option
Read integrals from file or calculate them directly. The valid options can be:
READ: Read integrals from existing file “x1e.int” and “x2e.int”. This is the default option.
CALC: Calculate integrals directly. Section Geometry description ($GEO) is essential.
LIBCINT: Integrals are calculated directly by an external library LIBCINT. Section Geometry description ($GEO) is essential.
1.2.1.3.2. BASIS=basis_set
Assigning the basis set when INT=CALC is requested. Basis sets are expressed the same way as Gaussian, i.e. 6-31G*, aug-cc-pVTZ etc. The supported basis sets can be found in Preparing integrals: PREINT.
1.2.1.3.3. NCHARGE=n
Charge of the system in current XMVB calculation. Default is 0, which means the neutural system. Positive numbers denote a cation system and negative numbers mean the system is anion. This keyword will also specify the number of electrons in current calculation, NEL is not needed anymore in such case.
1.2.1.3.4. ERI=CD
This keyword activates the Cholesky decomposotion for ERIs. Only valid with ISCF=5
and INT=CALC
.
1.2.1.3.5. CDTOL=float
The tolerance of Cholesky decomposition. Default is \(1 \times 10^{-10}\). Float may be expressed like 1.d-6, 0.001 etc.
1.2.1.4. Keywords for Wave Function Analysis
1.2.1.4.1. BOYS
Boys localization is requested for the final VB orbitals.
Note
It is strongly recommended to use this keyword for VBSCF. This makes VB orbitals easier to be interpreted and more physically meaningful.
Boys localization is available only for VBSCF method.
Boys localization can be only used in cases in which orbitals are separated into blocks, and there is no common basis function between blocks.
1.2.1.4.2. DEN
First-order density matrix is requested. The result will be written to a file with extended name “den”.
1.2.1.4.3. OUTPUT=AIM
WFN file for AIM2000 program will be printed. This is available only in module distribu- tion. A $AIM
with WFN filename is relevant for this keyword. Without $AIM
, the content of WFN file will be stored in “.dat” file of GAMESS-US.
1.2.1.5. Keywords for Symmetry
1.2.1.5.1. SYMM=option
Options for the point group used in VB computation. Currently only Abelian groups are supported. More details are shown in the table.
Note
The main axis of the molecule should be put along the Z-axis when \(C_\textrm{2}\), \(C_\textrm{2v}\), \(C_\textrm{2h}\), \(D_\textrm{2}\)and \(D_\textrm{2h}\) are applied.
This keyword cannot be used together with OEO type of VB orbitals(see keyword ORBTYP=option) and MO type of initial guess.
1.2.1.5.2. IRRP=option
Options for the irreducible representation used in VB computation. Valid options are shown in the table.
SYMM Option |
Point Group |
IRRP Option |
Irreducible Representation |
---|---|---|---|
CS |
\(C_\textrm{s}\) |
AP, APP |
\(A'\), \(A''\) |
CI |
\(C_\textrm{i}\) |
AG, AU |
\(A_\textrm{g}\), \(A_\textrm{u}\) |
C2 |
\(C_\textrm{2}\) |
A, B |
\(A\), \(B\) |
C2V |
\(C_\textrm{2v}\) |
A1, A2, B1, B2 |
\(A_\textrm{1}\), \(A_\textrm{2}\), \(B_\textrm{1}\), \(B_\textrm{2}\) |
C2H |
\(C_\textrm{2h}\) |
AG, AU, BG, BU |
\(A_\textrm{g}\), \(A_\textrm{u}\), \(B_\textrm{g}\), \(B_\textrm{u}\) |
D2 |
\(D_\textrm{2}\) |
A1, A2, B1, B2 |
\(A_\textrm{1}\), \(A_\textrm{2}\), \(B_\textrm{1}\), \(B_\textrm{2}\) |
D2H |
\(D_\textrm{2h}\) |
AG, AU, B1G, B2G, B3G, B1U, B2U, B3U |
\(A_\textrm{g}\), \(A_\textrm{u}\), \(B_\textrm{1g}\), \(B_\textrm{2g}\), \(B_\textrm{3g}\), \(B_\textrm{1u}\), \(B_\textrm{2u}\), \(B_\textrm{3u}\) |
1.2.1.6. Keywords for Previous Version
The following keywords appear in the previous version and are not available since version 2.0. This part is important only for those who are used to the previous version.
1.2.1.6.1. CIG
This keyword has been modified as GUESS=RDCI
.
1.2.1.6.2. DET
This keyword has been replaced by WFNTYP=DET
.
1.2.1.6.3. EXC
This keyword has been replaced by NSTATE=1
.
1.2.1.6.4. IOPT=n
This keyword has been replaced by keyword ISCF=n.
1.2.1.6.5. IOUT=n
1.2.1.6.6. NODIIS
1.2.1.6.7. VBXM=n
This keyword has been replaced by keywords WFNTYP=option and VBFTYP=option.
1.2.2. Required for BPREP($BFI)
The BFI section specifies how to transform primitive basis function to VB basis functions.The primitive basis functions are those used in GAMESS, Gaussian or PREINT and VB basis functions are used in XMVB. The Syntax of $BFI
section is:
$BFI
NFROZ NBAS
List of frozen MOs
List of basis functions
$END
Here NFROZ is the number of frozen MOs and NBAS is the number of VB basis functions used in XMVB. Then frozen MOs and basis functions will be listed respectively. If there is no MO to be frozen, place a blank line there. The VB basis functions may be reordered according to how users list them. This new order will be used in $ORB
section for the orbital description VB structure.
Following are two examples for the BFI section. The first example comes from the HF molecule with 6-31G basis set, where basis functions are not hybridized:
$BFI
3 6
1 4 5
1 2 4 7 8 11
$END
In this example, three MOs 1, 4 and 5 are frozen and 6 VB basis functions are kept for the XMVB calculation. Primitive basis functions 3, 5, 6, 9 and 10 are removed from the list as the corresponding MOs are frozen. Note that the fourth VB basis function is the primitive basis function 7 according to the list, not primitive basis function 4 anymore. The second example comes from the CH4 molecule with 6-31G basis set, showing the orbital freezing and the hybridization of basis functions:
$BFI
3 8
1 3 4
1 1 1 1 1 1 3 3
1.0 1
1.0 2
1.0 4
1.0 7
1.0 8
1.0 11
0.5 12 0.5 14 0.5 16
0.5 13 0.5 15 0.5 17
$END
Here MOs 1, 3 and 4 are frozen and 8 hybrid VB basis functions are used in XMVB calculation. Line “1 1 1 1 1 1 3 3” specifies the number of primitive basis function in each VB basis function. Following lines specifies how the VB basis functions are hybridized. In this example,the 7-th VB basis function is a hybrid basis function composed of 3 primitive basis functions 12, 14 and 16
1.2.3. description ($STR)
The $STR
section describes the information of VB structures or VB determinants if DET of $CTRL
section is specified. For VB structures, paired electrons, which may be lone pairs or covalent bonds, should be written first followed by unpaired electrons. The number of unpaired electrons depends on the spin multiplicity. For example: For a structure with three lone pairs (orbitals 1, 2, and 3), one covalent bond (orbitals 4 and 5), and one unpaired electron (orbital 6), the structure is expressed as,
1 1 2 2 3 3 4 5 6
For determinants, all alpha orbitals are listed first, followed by beta orbitals. For example: A determinant of alpha orbtials 1, 2, 3, 4, and 6 and beta orbtials 1, 2, 3, and 5 is expressed as
1 2 3 4 6 1 2 3 5
Note that it is strongly recommended to write the most important structure as the first one.
This can avoid potential problems in VBCI.
If BOVB is specified in $CTRL
section, the program will try to convert the VB orbitals into breathing orbitals. It uses automatically different orbitals for different structures. For example: If the initial VB structures are:
1 1 2 3
1 1 2 4
1 1 3 5
The program will convert them to:
1 1 2 3
6 6 7 4
8 8 9 5
Note that the VB structures should be independent. VB structures are recommended to be written in the following orders:
Inactive Active
where “Inactive” stands for the inactive orbitals which keep doubly occupied in all structures; “active” stands for the active orbitals whose occupation varies in the structures. The singly occupied orbitals in high-spin systems should always be put in the tail of the structures.
Following are the examples of typical bonding patterns and their corresponding manual/input:VB structure description ($STR) and Global control ($CTRL) sections, in which only active orbitals are labeled:
System of 2-electrons on 2-centers
$CTRL nstr=3 nmul=1 $END $STR 1 2 ; S1 1 1 ; S2 2 2 ; S3 $END
System of 3-electrons on 2-centers
$CTRL nstr=2 nmul=2 $END $STR 1 1 2 ; S1 2 2 1 ; S2 $END
System of 3-electrons on 3-centers
$CTRL nstr=8 nmul=2 $END $STR 1 2 3 ; S1 2 3 1 ; S2 1 1 3 ; S3 3 3 1 ; S4 2 2 3 ; S5 2 2 1 ; S6 1 1 2 ; S7 3 3 2 ; S8 $END
System of 4-electrons and 3-centers
6 VB structures (3 VB orbitals with 4 electrons, singlet)
$CTRL nstr=6 nmul=1 $END $STR 1 1 2 3 ; S1 1 1 2 2 ; S2 1 1 3 3 ; S3 1 2 3 3 ; S4 2 2 3 3 ; S5 2 2 1 3 ; S6 $END
1.2.4. Fragments definition ($FRAG)
Generally, the $FRAG
section is required if ORBTYP=HAO
. In this section, fragments in which VB orbitals are localized will be defined and the orbitals will be generated with the basis functions specified in the fragments.
The syntax of $FRAG
is:
$FRAG
nf(1), nf(2), . . . nf(N)
[basis function description(1)] lf(1,1), lf(2,1), . . . lf(nf(1),1)
[basis function description(2)] lf(1,2), lf(2,2), . . . lf(nf(2),2)
. . .
[basis function description(N)] lff(1,N), lf(2,N), . . . lf(nf(N),N)
$END
Here the system is separated into N fragments. nf(i) means the number of atoms or basis functions in the \(i^\textrm{th}\) fragment, and lf(j,i) is the atom or basis function j in the \(i^\textrm{th}\) fragment. Basis function description is needed only when FRGTYP=SAO
is chosen. Following is an example of H2 molecule with FRGTYP=ATOM
:
$CTRL
NSTR=3 ORBTYP=HAO
FRGTYP=ATOM
$END
$STR
1 2
1 1
2 2
$END
$FRAG
1 1
1
2
$END
$ORB
1 1
1
2
$END
The above $FRAG
specifies two fragments, where one atom is in each fragment. Fragment 1 includes the first H atom and fragment 2 includes the second H atom. With this definition, users only need to specify fragment in which an orbital is located in Orbital description ($ORB) section. With FRGTYP=SAO
, the fragments are specified by the type of basis functions. Following is an example of HF molecule with 6-31G basis set:
$CTRL
NSTR=3 VBFTYP=DET DEN
ISCF=5 NAO=2 NAE=2
ORBTYP=HAO FRGTYP=SAO
$END
$STR
1:4 5 6
1:4 5 5
1:4 6 6
$END
$FRAG
1 1 1 1
S 1
SPZ 2
PX 2
PY 2
$END
$ORB
1 1 1 1 1 1
2
2
3
4
2
1
$END
For the second fragment, “1” in the first line of $FRAG
means that the block contains basis functions located on one atom; “SPZ 2” means that the fragment includes the \(s\) and \(p_z\) basis functions in the second atom. The basis functions are described by groups of \(s\), \(p\), \(d\), \(f\), etc. For example, a fragment including \(s\), \(p_z\), \(d_{xx}\), \(d_{yy}\), \(d_{zz}\), \(f_{zzz}\), \(f_{xxz}\) and \(f_{yyz}\) basis functions in atoms 1 and 2 should be described as
$FRAG
2
spzdxxyyzzfzzzxxzyyz 1 2
$END
or
$FRAG
2
spzdxxdyydzzfzzzfxxzfyyz 1 2
$END
Here “s” means basis function \(s\), “pz” means basis function \(p_z\), “dxxyyzz” means \(d_{xx}\), \(d_{yy}\) and \(d_{zz}\), and “fzzzxxzyyz” means \(f_{zzz}\), \(f_{xxz}\) and \(f_{yyz}\). The ordering of basis functions are not compulsively defined, but the basis functions with the same type of \(s\), \(p\), \(d\) and \(f\) should be written together. For example, the above description can be written equivalently as
$FRAG
2
spzfzzzfxxzfyyzdxxdyydzz 1 2
$END
or
$FRAG
2
spzfxxzfyyzfzzzdxxdyydzz 1 2
$END
as users like.
1.2.5. Orbital description ($ORB)
Required When ORBTYP=HAO
or ORBTYP=GEN
.
The first line describes the number of basis functions (or fragments) that are used for VB orbitals. For instance, max(i) means that the \(i^\textrm{th}\) orbital is expanded as max(i) functions (fragments), which are specified in the following lines. If the value of max(i) is 1, it means that the corresponding orbital will not optimized. From the second line, the indices of basis functions are listed, where one orbital begins with one new line. Following is example:
4 4 2
3 4 5 6 ; orbital 1 is expanded with 4 basis functions (fragments)
4 3 5 6 ; orbital 2 is expanded with 4 basis functions (fragments)
1 2 ; orbital 3 is expanded with 2 basis functions (fragments)
Note
It is important to emphasize again that the \(n^\textrm{th}\) VB basis function in
$ORB
section is NOT necessarily the \(n^\textrm{th}\) primitive basis function, but the \(n^\textrm{th}\) VB basis function specified in the BFI section.It is suggested to write the most important basis function as the first one, as the program takes the first function as the “parent” function for the orbital if
GUESS=UNIT
. This can avoid potential problems in convergence.If
ORBTYP=OEO
is chosen, the$ORB
is not needed. All the orbitals will be delocalized in the whole system, which means orbitals will use all basis functions.If the users want to freeze (not optimize) some orbitals in the calculation, simply assigning the number of basis functions (fragments) of the corresponding orbital to “0”. For example, “0*5 2 2” means that there are totally 7 VB orbitals and the first 5 will be frozen during SCF iterations. In this case, an initial guess should be provided either by
GUESS=READ
orGUESS=MO
.
1.2.6. AIM Section($AIM)
This section is relevant if OUTPUT=AIM
is specified. The content of this section is an optional file name specified by users. This file name will be used as the WFN file name. By default, the content of WFN file will be stored in ".wfn"
file with the same name as input for standalone distribution and in ".dat"
file for module distribution.
1.2.7. Initial guess description ($GUS)
Required when GUESS=MO
or GUESS=READ
or GUESS=RDCI
.
When GUESS=MO
is required in manual/input:VB structure description ($STR) section, $GUS
describes how VB orbital guess comes from MOs. An example of $GUS
from H2 calculation is shown below:
$GUS
1 1
2 1
$END
The example shows that both VB orbitals 1 and 2 will get the initial guess from MO 1. All orbitals should be specified in this section.
If GUESS=READ
or GUESS=RDCI
is required, orbitals from previous computation will be read from $GUS
section. Thus, this section now contains the orbitals provided as the initial guess. The content is the same as the ORB file
of the previous computation. See File with optimized VB orbitals (.orb) and orbital guess (.gus) for details of the content.
1.2.8. Required when SCF=n ($SCF)
The section contains n columns of structure coefficients, each denotes a state. Following is the example for SCF=2
with 2 structures:
$SCF
1.0 1.0
2.0 -2.0
$END
Thus the result of \(\langle S_1+2S_2|\hat{H}|S_1-2S_2\rangle\)will be calculated, where \(\ S_1\)and \(\ S_2\)denote the 2 structures.
1.2.9. Geometry description ($GEO)
Required when INT=CALC
or INT=LIBCINT
.
section contains the geometry of the system in cartesian coordinates, and the unit is Angstrom. Both Gaussian and GAMESS-US format are supported. Here both examples of the same geometry are given:
Gaussian Format:
$GEO
F 0.0 0.0 -0.7
F 0.0 0.0 0.7
$END
GAMESS-US Format:
$GEO
F 9.0 0.0 0.0 -0.7
F 9.0 0.0 0.0 0.7
$END
The users may choose their favorite.
1.3. Output
1.3.1. Main XMVB output file (.xmo)
The output of XMVB is stored in a file with extesion “xmo”. The following is an example for stand-alone XMVB:
*************************************************************
M M MM MM M M MMMM MMMM M
M M M M M M M M M M M
M M M M M M MMMM MMM MMMM M
M M M M M M M M M M
M M M M M MMMM MMMM M M
*************************************************************
Released on Jun 14, 2015
Cite this work as:
(a) Z. Chen, F. Ying, X. Chen, J. Song, P. Su, L. Song, Y.
Mo, Q. Zhang and W. Wu, Int. J. Quantum. Chem., 2015, 115,
737 (b) L. Song, Y. Mo, Q. Zhang, W. Wu, J. Comput. Chem.
2005, 26, 514.
Job started at Mon Jun 8 14:36:17 2015
Work Directory at /home/fmying/VB_Workshop/Tutorial/lesson1/ex1 PID = 18199
---------------Input File---------------
H2 VBSCF FRAG BY ATOM
$ctrl
str=full nao=2 nae=2 # generate all VB structures with 2 active orbitals and 2 active electrons
orbtyp=hao frgtyp=atom # Construct VB orbitals with HAOs, fragmented by atom
iscf=5 # VBSCF algorithm with reduced density matrix
iprint=3 # Full print level
itmax=2000 # Maxinum number of iterations is set to 2000.
$end
$frag
1 1 # 2 fragments, each contains 1 atom
1 # First fragment, containing atom 1
2 # Second fragment, containing atom 2
$end
$orb
1 1 # 2 orbitals, each contains 1 fragment
1 # Orbital 1, containing fragment 1
2 # Orbital 2, containing fragment 2
$end
---------------End of Input--------------
Number of 0th ion structures is: 1 from 1 to 1
Number of 0th ion determinants is: 2 from 1 to 2
Number of 1th ion structures is: 2 from 2 to 3
Number of 1th ion determinants is: 2 from 3 to 4
Total number of structures is: 3
Total number of determinants is: 4
READING INTEGRALS...
Reading 2-e Integrals...
Done
OPTIMIZATION METHOD: LBFGS WITH ANALYTICAL ORBITAL GRAD IENT
Number of Structures: 3
The following structures are used in calculation:
1 ***** 1 2
2 ***** 1 1
3 ***** 2 2
Nuclear Repulsion Energy: 0.715104
Diagonalize Fock Matrix...
--------------Initial Guess--------------
5 5
0.5388052224 1 0.5354436033 2 0.0000000000 3 0.0000000000 4
0.1668081998 5
0.5388052224 6 0.5354436033 7 0.0000000000 8 0.0000000000 9
-0.1668081998 10
--------------End of Guess--------------
VBDET is applied
10 Coefficients 10 Independent
ITER ENERGY DE GNORM
1 -1.0806051993 -1.0806051993 0.3355377748
2 -1.0995681133 -0.0189629140 0.2387997424
3 -1.1308761698 -0.0313080566 0.1539314497
4 -1.1420399230 -0.0111637531 0.1093622053
5 -1.1465763955 -0.0045364726 0.0120926244
6 -1.1466054202 -0.0000290247 0.0001989203
VBSCF converged in 6 iterations
Total Energy: -1.14660543
First Excited: -0.256277
The Last Change in Energy: -0.000000
Number of Iteration: 6
****** MATRIX OF OVERLAP ******
1 2 3
1 1.000000 0.820727 0.820727
2 0.820727 1.000000 0.507832
3 0.820727 0.507832 1.000000
****** MATRIX OF HAMILTONIAN ******
1 2 3
1 -1.857032 -1.547823 -1.547823
2 -1.547823 -1.558228 -1.080145
3 -1.547823 -1.080145 -1.558228
****** COEFFICIENTS OF STRUCTURES ******
1 0.83675 ****** 1 2
2 0.09850 ****** 1 1
3 0.09850 ****** 2 2
****** COEFFICIENTS OF DETERMINANTS ******
a
b
1 0.48184 ****** 2
1
2 0.48184 ****** 1
2
3 0.09850 ****** 1
1
4 0.09850 ****** 2
2
****** WEIGHTS OF STRUCTURES ******
1 0.83545 ****** 1 2
2 0.08228 ****** 1 1
3 0.08228 ****** 2 2
Lowdin Weights
1 0.53757 ****** 1 2
2 0.23121 ****** 1 1
3 0.23121 ****** 2 2
Inverse Weights
1 0.94072 ****** 1 2
2 0.02964 ****** 1 1
3 0.02964 ****** 2 2
****** OPTIMIZED ORBITALS ******
1 2
1 0.763386 0.000000
2 0.307544 0.000000
3 0.000000 0.000000
4 0.000000 0.000000
5 0.032894 0.000000
6 0.000000 0.763386
7 0.000000 0.307544
8 0.000000 0.000000
9 0.000000 0.000000
10 0.000000 -0.032894
****** ORBITALS IN PRIMITIVE BASIS FUNCTIONS ******
1 2
1 S 0.763386 0.000000
2 S 0.307544 0.000000
3 X 0.000000 0.000000
4 Y 0.000000 0.000000
5 Z 0.032894 0.000000
6 S 0.000000 0.763386
7 S 0.000000 0.307544
8 X 0.000000 0.000000
9 Y 0.000000 0.000000
10 Z 0.000000 -0.032894
****** ORBITAL OVERLAP ******
1 2
1 1.000000 0.712623
2 0.712623 1.000000
****** DENSITY MATRIX ******
1 2 3 4 5
1 S 0.360753
2 S 0.145336 0.058551
3 X 0.000000 0.000000 0.000000
4 Y 0.000000 0.000000 0.000000 0.000000
5 Z 0.015545 0.006262 0.000000 0.000000 0.000670
6 S 0.311533 0.125507 0.000000 0.000000 0.013424
7 S 0.125507 0.050563 0.000000 0.000000 0.005408
8 X 0.000000 0.000000 0.000000 0.000000 0.000000
9 Y 0.000000 0.000000 0.000000 0.000000 0.000000
10 Z -0.013424 -0.005408 0.000000 0.000000 -0.000578
6 7 8 9 10
6 S 0.360753
7 S 0.145336 0.058551
8 X 0.000000 0.000000 0.000000
9 Y 0.000000 0.000000 0.000000 0.000000
10 Z -0.015545 -0.006262 0.000000 0.000000 0.000670
ISCF = 5 currently does not support VB orbital densities
===============================================
XMVB ATOMIC POPULATION ANALYSIS
===============================================
****** POPULATION AND CHARGE ******
ATOM MULL.POP. CHARGE LOW.POP. CHARGE
1 H 1.000000 0.000000 1.000000 0.000000
2 H 1.000000 -0.000000 1.000000 -0.000000
****** ATOMIC SPIN POPULATION ******
ATOM MULL.POP. LOW.POP.
1 H 0.000000 0.000000
2 H 0.000000 0.000000
****** BOND ORDER ******
ATOM 1 ATOM 2 DIST BOND ORDER
1 H 2 H 0.740 0.952
****** VALENCE ANALYSIS ******
TOTAL BONDED FREE
ATOM VALENCE VALENCE VALENCE
1 H 1.000 0.952 0.048
2 H 1.000 0.952 0.048
****** DIPOLE MOMENT ANALYSIS ******
DX DY DZ TOTAL
0.000000 0.000000 -0.000000 0.000000
****** ENERGY DECOMPOSITION ANALYSIS ******
TOTAL VB ENERGY : -1.146605431571
NUCLEAR REP. ENERGY : 0.715104335541
KINETIC ENERGY : 1.134053760016
POTENTIAL ENERGY : -2.280659191588
VARIAL THEOREM VALUE: 2.011067968731
Cpu for the Job: 0.38 (sec)
Job Finished at Mon Jun 8 14:36:17 2015
1.3.2. File with optimized VB orbitals (.orb) and orbital guess (.gus)
A file with extension “orb” is an output file of XMVB, which stores the optimized VB orbitals. The format is as follows:
max(1), max(2), . . . , max(val3)
# comment for orbital 1
cvic(1,1), nvic(1,1), cvic(1,1), nvic(2,1), . . . , cvic(max(1),1), nvic(max(1),1)
# comment for orbital 2
cvic(1,2), nvic(1,2), cvic(2,2), nvic(2,2), . . . , cvic(max(2),2), nvic(max(2),2)
. . .
# comment for orbital n
cvic(1,val3), nvic(1,val3), cvic(2,val3), nvic(2, val3), . . . , cvic(max(val3), val3), nvic(max(val3), val3)
where max(i) stands for the number of basis functions in \(i^\textrm{th}\) VB orbital, nvic(j,i) is the \(j^\textrm{th}\) basis function in \(i^\textrm{th}\) VB orbital and cvic(j,i) is the coefficient of nvic(j,i). The lines starting with “#” are treated as comments.
For VBSCF and BOVB calculations, a file of orbital guess may be provided. For VBCI calculations, the guess from a previous VBSCF calculation is required with the extension “gus”. The format of orbital guess file is exactly the same as ORB file. Initial guess files with or without comments are both supported by XMVB.
Note
The initial guess from previous computation with GUESS=READ
or GUESS=RDCI
now is recommended to be provided in Initial guess description ($GUS) section rather than in an external file to make the computation simpler. The support for GUS file remains mainly for the compatibility.
1.3.3. File with additional information (.xdat)
The file with extension “xdat” is an output file of XMVB. It keeps some other information such as the orbitals in original basis form. Using utility overview:viewing vb orbitals: moldendat can read this file and put the VB orbitals to Gaussian and GAMESS output files and Gaussian fchk files.
1.3.4. One-electron density file (.den)
If keyword DEN
of Global control ($CTRL) section, hybrid VB methods (DFVB, VBEFP, VBPCM and VBEFPPCM), or printing level larger than 1 are specified, one-electron density is saved to a file with “den” extension.
1.3.5. File with basis functions information (.info)
This file stores the information of basis functions for the current system, including number of atoms, number of primitive basis functions, basis functions for each atom, and the type of each basis function. This file is essential for stand-alone distribution to carry out FRGTYP=ATOM
or FRGTYP=SAO
and population analysis.
1.3.6. File with coefficients for the structures/determinants (.coeff)
This file will be obtained after a required TBVBSCF
calculation. The coefficients for the structures/determinants are stored in the file and it may be used for later TBVBSCF to accelerate solving secular equation which is proceeded by Davidson Diagnolazation. If the number of structures is larger than the number stored in “coef”, they will be treated as coefficients of the first N structures and the rest will be set to zero.
1.4. Theory and Methodologies
In this appendix, a brief introduction to VB theory and methodologies will be given to the users. For more detailed information, it is recommended to the users to read our reviews and research papers.
1.4.1. Introduction to VB Theory
In quantum chemistry, the many-electron wave function for a system is expressed as a linear combination of state functions:
In spin-free quantum chemistry, state functions \(\Phi_{K}\) should be a spin eigenfunction with anti-symmetry with respect to permutation of electron indices.The wave function is of the form
where \(\hat{A}\) is an antisymmetrizer, \(\Omega_0\) is an orbital product as
where \(\phi_i\) is the set of VB orbitals which can be purely localized hybrid atomic orbitals (HAOs), bond distorted orbitals (BDOs, delocalized along the bonding direction), and totally delocalized overlap enhanced orbitals (OEOs), and \(\Theta_{K}\) is a spin function. For VB methods, the state functions are VB functions, and their spin functions may be taken as the Rumer basis sets
where \(\left(ij\right)\) runs over all bonds and k over all unpaired electrons. Given an orbital product \(\Omega_0\) a complete set of VB functions is constructed by choosing all independent spin functions \(\Theta_{K}\) .
The coefficients \(C_{K}\) in Eq. (A.1) are determined by solving the conventional secular equation \(\mathbf{HC}=E\mathbf{MC}\) , where Hamiltonian and overlap matrices are defined as follows:
and
Structural weights are given by the Coulson-Chirgwin formula
Eqs. (A.5) and (A.6) involve N! terms due to antisymmetrizer \(\hat{A}\) . If one-electron functions are orthogonal, only a few terms are non-zero and make contributions to the matrix elements, and consequently the matrix elements can be conveniently evaluated. However, in VB methods, non-orthogonal orbitals are generally used, and thus all N! terms make contributions to the matrix elements. Although it is not necessary to expand all N! terms to evaluate a determinant, the computational demanding in VB calculations is in general much more than that in MO calculations.
1.4.2. The Evaluation of Hamiltonian and Overlap Matrices
In the XMVB package, two algorithms are implemented to compute the Hamiltonian and overlap matrices: one based on the Slater determinant expansion method, and the other based on the paired-permanent-determinant method.
1.4.2.1. Slater determinant expansion algorithm
Traditionally, an HLSP function is expressed in terms of \(2^{m}\) Slater determinants (m is the number of covalent bonds of structure),
where \(D(\Omega_K)\) is a Slater determinant corresponding to Eq. (A.3), \(P_{i}\) is an operator that exchanges the spins of the two electrons forming the i-th bond.
Example: An HLSP function corresponding to a Kekulé structure of benzene is written as
The Hamiltonian matrix element is expressed as
where \(f_{rs}\) and \(g_{rs,ut}\) are one-electron and two-electron integrals respectively, and \(D(S_r^s)\) and \(D(S_{ru}^{st})\) are the first and the second order cofactors of the overlap matrix between the two determinants respectively. Cofactors are computed by the Jacobi ratio theorem. The costs are of the order \(N^3\) for the first order and \(N^4\) for the second order cofactors at most.
1.4.2.2. Paired-permanent-determinant approach
Paired-permanent-determinant (PPD) approach is based on the spin-free form of VB theory. In the spin-free VB theory, the Hamiltonian and overlap matrix elements are now written as
and
respectively, where is the first diagonal element of the standard irreducible representation of permutation P of the symmetric group \(S_{N}\). In the PPD approach, a function, called PPD, is defined as follow:
Given an N × N square matrix
the PPD of \(\mathbf{A}\) for the irreducible representation [λ] is the number
The evaluation of a PPD function is performed by a procedure similar to the Laplacian expansion algorithm for determinant. Hamiltonian and overlap matrix elements are computed by multiplying electronic integrals with their corresponding cofactors of PPDs. Evaluation of a PPD is more complicated than that of a determinant. But it can be beneficial when there are many bonded pairs in system. In that case there are only a few PPDs rather than numerous determinants to be evaluated.
1.4.3. Orbital Optimization
The gradient vectors of energy are evaluated in four ways: the first is the numerical approximation by differential method; the second is analytical gradient based on Fock matrices, using only the first order density matrix; the third is analytical based on the first and the second order orbital density matrices; and the third is based on generalized Brillouin theorem. The first three methods are fitted for all-type orbitals, and the later one is only available for strictly localized and delocalized orbitals. The second one is suitable only when there is no orthogonality between VB functions. There are two orbital optimization methods adopted in the package. The optimization with numerical gradient is based on the Davidson-Fletcher-Powell (DFP) family of variable metric methods, and the optimization with analytical gradient is proceeded with limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) method.
1.4.4. The VBSCF Methods
The wave function of Valence Bond Self Consistent Field (VBSCF) method is the linear combination of VB structures, as shown in eq.(A.1). In VBSCF method, All VB structures share the same set of VB orbitals, and both sets of the structure coefficients and VB orbitals are optimized simultaneously to minimize the total energy. This is comparable to the MCSCF method in the MO theory. VBSCF method takes care of the static electron correlation and gives equivalent results to the MO-based CASSCF calculations. It should be noted that the dynamic electron correlation is not accounted for in the VBSCF method. In XMVB, VBSCF method is the default method, thus this keyword can be ignored.
1.4.5. Post-VBSCF Method
The VBSCF result includes only static correlation energy, which makes VBSCF results not accurate enough for quantitative researches. The purpose of post-VBSCF methods is to take dynamic correlation into account as much as possible to get accurate enough results. There are several post-VBSCF methods developed so far and will be introduced in this section. It is strongly recommended to perform post-VBSCF calculations with initial guesses from a pre-proceeded VBSCF calculation. As to VBCI and VBPT2, this is enforced.
1.4.5.1. The BOVB Method
The orbitals of Breathing Orbital Valence Bond (BOVB) method are also optimized by SCF procedure, as VBSCF does. The difference between VBSCF and BOVB methods is that BOVB provides an extra degree of freedom during orbital optimization. In BOVB method, each VB structure has its own set of orbitals and are optimized independently
Thus, the orbitals adopt themselves to the instantaneous field of the VB structures, rather than to the mean field of all the structures in VBSCF. This degree of freedom makes the orbitals in BOVB “breathing” in different structures, introduces dynamic correlation, and thereby improves considerably the accuracy of VB computations.
1.4.5.2. The VBCI Method
The VBCI method is based on localized VB orbitals. In this method VB orbitals are divided to several blocks (occupied and virtual orbitals). Excited VB structures are generated by replacing occupied VB orbitals with virtual orbitals that are localized on the same block. The wave function of VBCI is the linear combination of all reference and excited VB structures
where \(\Phi^i_K\) is CI structure coming from VBSCF structure K, including reference and excited structures, and the coefficients \({C_{Ki}}\) are obtained by solving the secular equation. The VBCI weight can be given either with eq. (A.7), which gives weights of all CI structures, or in a more compact way as
where \(W_K\) is the contracted weights of reference structure K, including weights of all CI structures coming from structure K.
Allowing for different excitations for different electronic shells, currently the VBCI method consists of the following calculation levels:
VBCI(S,S): only single excitations are involved in either active electron or inactive electron. In brief, this is a VBCIS procedure.
VBCI(D,S): the active shell is treated by single and double excitations, whereas the inactive shell by single excitations only. Also included in this level are double excitations which consist of a single excitation from each shell.
VBCI(D,D): single and double excitations are involved for both active and inactive electrons, in short, VBCISD.
1.4.5.3. The VBPT2 Method
Another post-VBSCF method is Valence Bond second-order Perturbation Theory (VBPT2) method. The wave function of VBPT2 can be separated into 2 parts as
where VBSCF wave function is taken as the zeroth-order wave function \(\Psi^0\), and the first-order part is the combination of singly and doubly excited wave functions
To enhance the efficiency of VBPT2, the virtual orbitals are delocalized and orthogonal to the occupied space, and the excitations include all virtual orbitals. In this manner, the excited structures in VBPT2 don’t belong to any fundamental structure, and the matrix elements can be calculated easily with Coulson-Slater rules.
1.4.5.4. The DFVB Method
Density functional valence bond (DFVB) method is a VB computational method which combines VBSCF and DFT correlation functional. In DFVB method, the wave function, density and static correlation energy is provided by VBSCF method, while the dynamic correlation energy is obtained by DFT correlation functional. The total energy formalism of DFVB is expressed as:
where \(E^\textrm{VBSCF}\) is the VBSCF part, including static correlation energy, and \(E_\textrm{C}\left[\rho^\textrm{VB}\right]\) is the DFT correlation energy obtained by a functional according to current VB density \(\rho^\textrm{VB}\) . The total energy and wave function is optimized through a SCF procedure. In practice, GGA correlation functionals, such as LYP, PW, PBE correlation functional, are recommended functionals.
1.4.6. Solvation VB Methods
1.4.6.1. The VBPCM Method
The VBPCM method is an ab initio solvation VB method that is based on implicit solvation model PCM in which the state wave function is expressed in the usual terms as a linear combination of VB structures. The Schrödinger equation of VBPCM is expressed as
where \(\hat{H}^0\) is the Hamiltonian operator in vacuum and \(\hat{V}^{\textrm{PCM}}\) is the solvation potential obtained by PCM. The VBPCM wave function and energy are optimized simultaneously in an SCF procedure. VBPCM is now available for VBSCF and BOVB.
VBPCM has been used in several researches. VBPCM has been rewritten in XMVB 2.0 and is capable for hetero-PCM and EFP/PCM calculations.
1.4.6.2. The VBEFP Method
The VBEFP method is an QM/MM method in which the QM part is expressed as a VB wave function and the MM part is expressed with EFP1, which is a polarized water model proposed by Gordon et al. The VBEFP energy is obtained by following equation
where \(\hat{H}^0\) is the Hamiltonian operator in vacuum and \(\hat{V}^{\textrm{EFP}}\) is the solvation potential obtained by EFP method. An SCF procedure is used to optimize the wave function and energy of VBEFP simultaneously.
Currently, VBEFP is available only in module distribution and is only available for VBSCF. With the use of EFP, VBEFP is very useful to take strong and short solvent-solute interactions into account.
2. Tutorial
2.1. BDE and RE of F2
2.1.1. Introduction
F2 is a typical diatimic molecule which is simple enough for the users as a starting point. There is only 1 chemical bonding in the molecule. The 3 structures of the bonding is shown below.
Here S1
denotes the covalent structure in which two active electrons are shared between both F atoms while S2
and
S3
denote 2 quivalent ionic structures in which two active eletrons doubly occupy orbital on certain F atom.
In this exercise, we will try to proceed computations for the bond dissociation energy (BDE) and resnance energy (RE) of F2. This takes computations at stationary point and dissociation limit with various sets of VB structures. This exercise will provide a first glance at VB computation. The users will learn the struct and syntax of XMVB input, how to build a simple input file, how to run the job and what we will get from the output.
Note
This exercise just shows the users how to proceed a VBSCF computation for a specific molecule, what we can get from the output and how to analyze the results. The accurate computation of BDE of F2 requires higher level computational methods with delocalized inactive \(\pi\) orbitals.
2.1.2. Computations with 3 Structures at Stationary Point
The computations are proceeded with F-F bond length 1.4 Angstrom, and the basis set is cc-pVDZ. For simplicity, F atoms are located in the Z axis.
2.1.2.1. Input File
Here shows the XMVB input file for all 3 structures at stationary point:
F2 VBSCF with 3 structures
$CTRL
STR=FULL NAO=2 NAE=2 ISCF=5 IPRINT=3
ORBTYP=HAO FRGTYP=SAO
INT=LIBCINT BASIS=CC-PVDZ
$END
$FRAG
1*6
SPZDXXDYYDZZ 1
SPZDXXDYYDZZ 2
PXDXZ 1
PXDXZ 2
PYDYZ 1
PYDYZ 2
$END
$ORB
1*10
1
2
1
2
3
4
5
6
1
2
$END
$GEO
F 0.0 0.0 0.0
F 0.0 0.0 1.4
$END
The global keywords listed in $CTRL
section are explained below:
STR=FULL
XMVB generates all VB structures automatically according to a specific active space.ISCF=5
VBSCF computation with RDM-based algorithm.IPRINT=3
XMVB will print most information.NAO=2
andNAE=2
Specify the active space with 2 active orbital and 2 active electrons respectively.ORBTYP=HAO
andFRGTYP=SAO
The VB orbitals are described with fragments.INT=LIBCINT
Integrals are evaluated by XMVB withLIBCINT
library.BASIS=CC-PVDZ
The basis set is cc-pVDZ.
Note
The orbitals of a molecule can be devided into “inactive” and “active” parts. The inactive orbitals are always doubly occupied in all VB structures, while the occupation numbers of active orbitals can be 0, 1 or 2 in each VB structure.
$FRAG
section describes the fragments used to construct VB orbitals. In this case, the first line 1*6
means that there are 6 fragments built and each fragment include only 1 atom. The details of fragments are described in the following lines. For example, SPZDXXDYYDZZ 1
means that the fragment includes s, pz, dxx, dyy and dzz basis functions on atom 1, which is the first F atom in this case.
$ORB
section describes VB orbitals. The first line 1*10
means that there are 10 orbitals in this case, each consisting of only 1 fragment. Each line below describes one orbital. For example, the first orbital includes only fragment 1, meaning that this orbital locates on the first F atom and belongs to the \(\sigma\) space since the F-F lies on Z axis. Also, orbital 6 with fragment 4 shows that the orbital describes the \(\pi_x\) orbital on the first F atom.
$GEO
section shows the geometry of F2 molecule. Both Cartesian and internal coordinates are supported.
Note
Since NAO=2
is specified in $CTRL
section, the last 2 orbitals in $ORB
should be the active orbitals.
It is highly recommended that active orbitals are always palced after the inactive ones. This may make the input file more readable and less possible to get error.
2.1.2.2. Computational Results
In this case, 3
VB structures are generated with 1 covalent structure (0th ion structure) and 2 ionic structures (1th ion structures). These structures can be expaned into 4
determinants.
Number of 0th ion structures is: 1 from 1 to 1 Number of 0th ion determinants is: 2 from 1 to 2 Number of 1th ion structures is: 2 from 2 to 3 Number of 1th ion determinants is: 2 from 3 to 4 Total number of structures is: 3 Total number of determinants is: 4 . . . Number of Structures: 3 The following structures are used in calculation: 1 ***** 1:8 9 10 2 ***** 1:8 9 9 3 ***** 1:8 10 10
The user may find from the output file that the VBSCF converged after 25
iterations and the final energy is -198.75115493
hartree.
VBSCF converged in 25 iterations
Total Energy: -198.75115493
First Excited: -197.880879
The coefficients and weights shows the importance of each structure. Following are the coefficients and weights of generated VB structures. Both coefficients and weights show that the covalent structure is the dominant one. So the F-F bond should be a covalent bond.
****** COEFFICIENTS OF STRUCTURES ****** 1 -0.80579 ****** 1:8 9 10 2 -0.21326 ****** 1:8 9 9 3 -0.21326 ****** 1:8 10 10 . . . ****** WEIGHTS OF STRUCTURES ****** 1 0.77586 ****** 1:8 9 10 2 0.11207 ****** 1:8 9 9 3 0.11207 ****** 1:8 10 10
Finally, the bond order value (0.773) in atomic population analysis shows that F-F bond should be a single bond.
****** BOND ORDER ****** ATOM 1 ATOM 2 DIST BOND ORDER 1 F 2 F 1.400 0.773
2.1.3. Computations with 3 Structures at Dissociation Limit
2.1.3.1. Input File
The input file for such computation can be easily obtained by modifying the corresponding one at stationary point. As shown below, one just needs to modify the coordinate of the second F atom to change 1.4
to 10.0
. This will increase the F-F bond distance to 10.0 Angstrom.
$GEO
F 0.0 0.0 0.0
F 0.0 0.0 10.0
$END
2.1.3.2. Computational Results
After SCF procedure, the user will get the final energy as shown below. The computational energy of dissociated F2 is -198.74386524
hartree.
Total Energy: -198.74386524
First Excited: -197.850852
Both coefficients and weights of VB structures show that the wave function includes only covalent structure, indicating that the molecule is dissociated to 2 F\(\cdot\) radicals.
****** COEFFICIENTS OF STRUCTURES ****** 1 1.00000 ****** 1:8 9 10 2 0.00000 ****** 1:8 9 9 3 0.00000 ****** 1:8 10 10 . . . ****** WEIGHTS OF STRUCTURES ****** 1 1.00000 ****** 1:8 9 10 2 0.00000 ****** 1:8 9 9 3 0.00000 ****** 1:8 10 10
By substracting energies at stationary point and dissociation limit, the BDE can be obtained as 4.4
kcal/mol.
2.1.4. Computations with Covalent Structure at Stationary Point
2.1.4.1. Input File
The input file can be obtained by replacing STR=FULL
with STR=COV
in the input file of 3 structures at stationary point, as shown below.
$CTRL
STR=COV NAO=2 NAE=2 ISCF=5 IPRINT=3
ORBTYP=HAO FRGTYP=SAO
INT=LIBCINT BASIS=CC-PVDZ
$END
2.1.4.2. Computational Results
The structure information is shown below. It can be seen that only 1 covalent structure is generated for this computation.
Number of 0th ion structures is: 1 from 1 to 1 Number of 0th ion determinants is: 2 from 1 to 2 Total number of structures is: 1 Total number of determinants is: 2 . . . Number of Structures: 1 The following structures are used in calculation: 1 ***** 1:8 9 10
The final energy after SCF iteration is -198.67485969
hartree.
Total Energy: -198.67485969
The Last Change in Energy: -0.000000
The bond order result in atomic population analysis shows that the bond order with only covalent structure is 0.324
, which is much smaller than computations with 3 structures.
****** BOND ORDER ****** ATOM 1 ATOM 2 DIST BOND ORDER 1 F 2 F 1.400 0.324
The RE value, 47.6 kcal/mol, can be obtained from energies by covalent and 3 structure computations at stationary point. Compared with the computational BDE 4.4, RE is much larger than BDE, indicating that the chemical bonding in F2 is an charge-shifting bond. The much smaller bond order data with only covalent structure also indicates that resonance plays an important role in the F-F bonding.
2.2. Resonance in C6H6
2.2.1. Introduction
Benzene (C6H6) is a classical aromatic molecule in which electrons in \(\pi\) space are delocalized. The covalent valence bond structures are shown in the following table.
The 5 covalent structures can be classified as 2 types: the first 2 structures are Kekulé structures and the others are regarded as Dewar structures. In this exercise, the resonance energy in the benzene molecule will be computed to show how resonance stabilize the aromatic molecule.
2.2.2. Computations with 5 Covalent Structures
First, we will compute the energy with all 5 covalent structures.
2.2.2.1. Input File
The input file is shown below.
C6H6
$ctrl
str=cov nao=6 nae=6 iscf=5 iprint=3
orbtyp=hao frgtyp=sao
int=libcint basis=cc-pvdz
$end
$frag
12 2*6
spxpydxxdyydzzdxy 1-12
pzdxzdyz 1 2
pzdxzdyz 3 4
pzdxzdyz 5 6
pzdxzdyz 7 8
pzdxzdyz 9 10
pzdxzdyz 11 12
$end
$orb
1*18 1*6
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
3
4
5
6
7
$end
$geo
C 0.6995000584 1.2115696411 0.0000000000
H 1.2460106991 2.1581538376 0.0000000000
C -0.6995000584 1.2115696411 0.0000000000
H -1.2460106991 2.1581538376 0.0000000000
C -1.3990001169 0.0000000000 0.0000000000
H -2.4920213982 0.0000000000 0.0000000000
C -0.6995000584 -1.2115696411 0.0000000000
H -1.2460106991 -2.1581538376 0.0000000000
C 0.6995000584 -1.2115696411 0.0000000000
H 1.2460106991 -2.1581538376 0.0000000000
C 1.3990001169 0.0000000000 0.0000000000
H 2.4920213982 0.0000000000 0.0000000000
$end
In this input file, the molecule lays in the XY plane. The fragments specified in $FRAG
section are defined according to the symmetries. Since we concern on the resonance in \(\pi\)space, electrons locating in \(\sigma\)space is not in the interest. Thus eletrons in the \(\sigma\)orbitals can be treated as inactive ones and make them delocalized in all structures. To this reason, the first fragment is defined to include all basis functions in \(\sigma\) space in the molecule. The remained fragments denote \(\pi\) orbitals locates on each CH group.
2.2.2.2. Computational Results
5 VB structures will be generated in the computation and can be found in the output:
Number of Structures: 5 The following structures are used in calculation: 1 ***** 1:18 21 22 20 23 19 24 2 ***** 1:18 20 21 22 23 19 24 3 ***** 1:18 20 21 19 22 23 24 4 ***** 1:18 19 20 22 23 21 24 5 ***** 1:18 19 20 21 22 23 24
Final energy can be found after the VBSCF iteration as -230.63450
hartree.
Total Energy: -230.63449533
Both coefficients and weights of VB structures show that structures are in 2 groups. Structure 2 and 5 correspond to the Kekulé structures, which are the dominant ones, and the others denote Dewar structures.
****** COEFFICIENTS OF STRUCTURES ****** 1 0.14537 ****** 1:18 21 22 20 23 19 24 2 -0.40098 ****** 1:18 20 21 22 23 19 24 3 0.14537 ****** 1:18 20 21 19 22 23 24 4 0.14537 ****** 1:18 19 20 22 23 21 24 5 -0.40098 ****** 1:18 19 20 21 22 23 24
****** WEIGHTS OF STRUCTURES ****** 1 0.11245 ****** 1:18 21 22 20 23 19 24 2 0.33132 ****** 1:18 20 21 22 23 19 24 3 0.11245 ****** 1:18 20 21 19 22 23 24 4 0.11245 ****** 1:18 19 20 22 23 21 24 5 0.33132 ****** 1:18 19 20 21 22 23 24
The atomic population analysis shows that the bond orders of all CC bondings are the same as 1.188, showing the effect of conjugation.
****** BOND ORDER ****** ATOM 1 ATOM 2 DIST BOND ORDER 1 C 2 H 1.093 0.979 1 C 3 C 1.399 1.188 3 C 4 H 1.093 0.979 3 C 5 C 1.399 1.188 5 C 6 H 1.093 0.979 5 C 7 C 1.399 1.188 7 C 8 H 1.093 0.979 7 C 9 C 1.399 1.188 9 C 10 H 1.093 0.979 1 C 11 C 1.399 1.188 9 C 11 C 1.399 1.188 11 C 12 H 1.093 0.979
2.2.3. Computations with 2 Kekulé Structures
2.2.3.1. Input File
The input file is shown below.
C6H6
$ctrl
nstr=2 nao=6 nae=6 iscf=5 iprint=3
orbtyp=hao frgtyp=sao
int=libcint basis=cc-pvdz
guess=read
$end
$str
1:18 19-24
1:18 19 24 20 21 22 23
$end
$frag
12 2*6
spxpydxxdyydzzdxy 1-12
pzdxzdyz 1 2
pzdxzdyz 3 4
pzdxzdyz 5 6
pzdxzdyz 7 8
pzdxzdyz 9 10
pzdxzdyz 11 12
$end
$orb
1*18 1*6
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
3
4
5
6
7
$end
$geo
C 0.6995000584 1.2115696411 0.0000000000
H 1.2460106991 2.1581538376 0.0000000000
C -0.6995000584 1.2115696411 0.0000000000
H -1.2460106991 2.1581538376 0.0000000000
C -1.3990001169 0.0000000000 0.0000000000
H -2.4920213982 0.0000000000 0.0000000000
C -0.6995000584 -1.2115696411 0.0000000000
H -1.2460106991 -2.1581538376 0.0000000000
C 0.6995000584 -1.2115696411 0.0000000000
H 1.2460106991 -2.1581538376 0.0000000000
C 1.3990001169 0.0000000000 0.0000000000
H 2.4920213982 0.0000000000 0.0000000000
$end
$gus
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 5 5 5 5 5 5
# ORBITAL 1 NAO = 90
-0.4085807072 1 -0.0018715270 2 0.0001649808 3 0.0000999746 4
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0.0000833088 11 0.0010378240 13 0.0011389938 15 -0.0001957425 16
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0.0010378340 33 0.0011390026 35 -0.0001957414 36 -0.0001334204 37
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0.0001488619 43 -0.0002148556 44 0.0000001381 45 -0.0000988751 47
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0.0009574723 70 0.0000839012 71 0.0010378364 73 0.0011390336 75
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0.0000988788 107 0.0000000209 108 0.0010810705 110 0.0000001777 111
0.0009153543 113 0.0011399863 115 -0.0002143672 116 -0.0001372134 117
0.0000966809 118 0.0000001629 119
# ORBITAL 2 NAO = 90
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0.0000791296 17 0.0000125324 18 -0.0000788689 19 -0.2888931497 21
-0.0012304753 22 0.0002562013 23 0.0001337942 24 0.0001566737 25
0.0001915140 27 0.0001494777 28 0.0008219804 30 -0.0001516843 31
0.0005907316 33 0.0007979421 35 -0.0001550608 36 -0.0000790540 37
0.0000136909 38 0.0000800072 39 -0.5781904466 41 -0.0024581181 42
0.0005050109 43 -0.0001390292 44 0.0000000205 45 -0.0000746810 47
0.0000000140 48 0.0015287631 50 -0.0000000553 51 0.0012982685 53
0.0015971801 55 -0.0003048222 56 -0.0001585226 57 -0.0001238936 58
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0.0001337970 64 -0.0001566499 65 0.0001915245 67 -0.0001494674 68
0.0008219645 70 0.0001517465 71 0.0005907569 73 0.0007979557 75
-0.0001550484 76 -0.0000790645 77 0.0000136980 78 -0.0000799949 79
0.2888931500 81 0.0012304673 82 -0.0002563957 83 0.0001337007 84
0.0001561303 85 0.0001914997 87 0.0001482011 88 -0.0008221145 90
0.0001556889 91 -0.0005906834 93 -0.0007980414 95 0.0001543768 96
0.0000791346 97 0.0000125801 98 0.0000788956 99 0.5781904449 101
0.0024591332 102 -0.0005052562 103 -0.0001393968 104 0.0000000109 105
-0.0000739491 107 -0.0000000104 108 -0.0015297884 110 -0.0000000183 111
-0.0012968826 113 -0.0015966043 115 0.0003041670 116 0.0001581403 117
-0.0001241023 118 -0.0000000148 119
# ORBITAL 3 NAO = 90
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-0.0000528411 5 -0.0001543791 7 0.0000142568 8 -0.0010905424 10
-0.0000444470 11 -0.0013582539 13 -0.0013824483 15 0.0002505625 16
0.0001341232 17 -0.0000778672 18 -0.0000745639 19 0.5006118515 21
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0.0001543481 27 0.0000142554 28 -0.0010905019 30 0.0000444391 31
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0.0000778110 38 -0.0000745770 39 -0.0000000362 41 0.0000000221 42
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0.0002704667 48 -0.0000000212 50 0.0002206198 51 0.0000000294 53
0.0000000132 55 -0.0000000141 56 -0.0000000081 57 0.0000000045 58
0.0000602462 59 -0.5006118875 61 -0.0021171392 62 0.0004445257 63
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0.0010904959 70 0.0000442655 71 0.0013583140 73 0.0013824713 75
-0.0002505931 76 -0.0001341382 77 -0.0000777637 78 -0.0000746227 79
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0.0000000315 113 0.0000000132 115 -0.0000000150 116 -0.0000000085 117
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# ORBITAL 4 NAO = 90
-0.2891567875 1 -0.0011788380 2 0.0006696401 3 0.0001162136 4
-0.0000434029 5 0.0000569096 7 -0.0002181218 8 0.0005581052 10
-0.0000173221 11 0.0007001594 13 0.0007639834 15 -0.0000761592 16
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0.0007001375 33 0.0007639670 35 -0.0000761610 36 -0.0000306572 37
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0.0005581117 70 -0.0000174532 71 0.0007001480 73 0.0007639674 75
-0.0000761793 76 -0.0000306569 77 -0.0000221958 78 -0.0000003814 79
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0.0000433741 85 0.0000569103 87 0.0002181062 88 0.0005581088 90
0.0000174178 91 0.0007001487 93 0.0007639740 95 -0.0000761773 96
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0.0024208558 102 -0.0012969285 103 0.0000049612 104 -0.0000000253 105
0.0003380902 107 -0.0000000083 108 -0.0013033682 110 -0.0000000436 111
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# ORBITAL 5 NAO = 90
-0.5007497195 1 -0.0020926701 2 0.0011274729 3 -0.0000664898 4
0.0000686296 5 -0.0002263515 7 -0.0001918806 8 0.0011015128 10
0.0000674501 11 0.0010736729 13 0.0013237329 15 -0.0001590050 16
-0.0000498765 17 0.0000054571 18 0.0000298585 19 0.5007496847 21
0.0020926790 22 -0.0011275085 23 -0.0000664796 24 -0.0000685616 25
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0.0000056242 38 -0.0000296943 39 0.0000000348 41 0.0000000890 42
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0.0002002088 48 -0.0000000915 50 0.0000942443 51 0.0000001220 53
0.0000000504 55 -0.0000000578 56 -0.0000000328 57 0.0000000176 58
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0.0000664970 64 -0.0000686556 65 0.0002263560 67 0.0001918646 68
0.0011015108 70 0.0000673487 71 0.0010736709 73 0.0013237272 75
-0.0001590238 76 -0.0000498723 77 -0.0000054290 78 -0.0000298875 79
0.5007496855 81 0.0020926723 82 -0.0011275078 83 0.0000664707 84
0.0000685365 85 0.0002263476 87 -0.0001921026 88 -0.0011015386 90
0.0000681438 91 -0.0010736605 93 -0.0013237484 95 0.0001588863 96
0.0000498882 97 -0.0000056552 98 0.0000296659 99 0.0000000336 101
0.0000000883 102 -0.0000000217 103 -0.0000000323 104 -0.0001852396 105
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0.0000001203 113 0.0000000496 115 -0.0000000565 116 -0.0000000328 117
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# ORBITAL 6 NAO = 90
0.4091251475 1 0.0018241997 2 -0.0036592202 3 0.0000020694 4
-0.0000011859 5 0.0007741716 7 0.0013387077 8 -0.0007515405 10
0.0000812994 11 -0.0006732113 13 -0.0009930082 15 -0.0000359553 16
-0.0002099914 17 0.0000257544 18 0.0000416529 19 -0.4091251464 21
-0.0018242229 22 0.0036594107 23 0.0000019865 24 0.0000007218 25
0.0007741606 27 -0.0013398977 28 0.0007516717 30 0.0000776616 31
0.0006731473 33 0.0009930840 35 0.0000365738 36 0.0002099303 37
0.0000247332 38 -0.0000426613 39 0.4088400900 41 0.0018185067 42
-0.0036610579 43 -0.0000000395 44 0.0000000662 45 -0.0015467853 47
0.0000000329 48 -0.0006312514 50 -0.0000001499 51 -0.0007924283 53
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0.0000001297 59 -0.4091251455 61 -0.0018241642 62 0.0036594070 63
0.0000019879 64 -0.0000006481 65 0.0007741792 67 0.0013399307 68
0.0007516425 70 -0.0000774650 71 0.0006732027 73 0.0009931240 75
0.0000366093 76 0.0002099034 77 0.0000247197 78 0.0000427155 79
0.4091251465 81 0.0018241721 82 -0.0036592195 83 0.0000021021 84
0.0000012118 85 0.0007742169 87 -0.0013386734 88 -0.0007514874 90
-0.0000814990 91 -0.0006732734 93 -0.0009930272 95 -0.0000359181 96
-0.0002099801 97 0.0000258758 98 -0.0000415851 99 -0.4088400890 101
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0.0007910987 113 0.0009920653 115 0.0000386489 116 0.0002101309 117
-0.0000504971 118 -0.0000000437 119
# ORBITAL 7 NAO = 90
-0.0107819418 1 0.1790782666 2 0.0924284475 3 -0.0318865151 4
-0.0553049355 5 -0.0062977525 7 -0.0109401070 8 0.0108331095 10
-0.0038054399 11 0.0070287849 13 -0.0063313721 15 0.0455977157 16
0.0036387887 17 -0.0036035054 18 -0.0062459698 19 -0.0107819418 21
0.1790782665 22 0.0924284475 23 0.0318865153 24 -0.0553049354 25
0.0062977526 27 -0.0109401069 28 0.0108331095 30 0.0038054400 31
0.0070287847 33 -0.0063313720 35 0.0455977157 36 0.0036387887 37
0.0036035054 38 -0.0062459697 39 -0.0107755990 41 0.1791237848 42
0.0924406313 43 0.0638465961 44 -0.0000000002 45 0.0126243430 47
0.0000000000 48 0.0051202404 50 0.0000000002 51 0.0127397005 53
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0.0318865153 64 0.0553049352 65 0.0062977526 67 0.0109401069 68
0.0108331095 70 -0.0038054405 71 0.0070287846 73 -0.0063313721 75
0.0455977156 76 0.0036387886 77 0.0036035055 78 0.0062459696 79
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0.0553049354 85 -0.0062977525 87 0.0109401069 88 0.0108331095 90
0.0038054404 91 0.0070287849 93 -0.0063313722 95 0.0455977156 96
0.0036387887 97 -0.0036035055 98 0.0062459696 99 -0.0107755990 101
0.1791237842 102 0.0924406314 103 -0.0638465970 104 -0.0000000002 105
-0.0126243426 107 0.0000000000 108 0.0051202413 110 -0.0000000001 111
0.0127397007 113 -0.0063317099 115 0.0456056422 116 0.0036342781 117
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# ORBITAL 8 NAO = 90
0.0080809826 1 -0.1247496483 2 -0.0702559576 3 -0.0784948406 4
0.0639689094 5 -0.0281707685 7 0.0270146479 8 0.0056247890 10
0.0119191820 11 -0.0144007347 13 0.0039111625 15 -0.0517266720 16
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-0.0281707673 27 -0.0270146491 28 -0.0056247882 30 0.0119191787 31
0.0144007344 33 -0.0039111628 35 0.0517266760 36 0.0069585494 37
0.0014215110 38 -0.0074905056 39 -0.0161618860 41 0.2495029330 42
0.1404967375 43 0.0323045190 44 0.0000000022 45 0.0186150565 47
0.0000000009 48 0.0009097151 50 0.0000000004 51 0.0166398753 53
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0.0000000000 59 -0.0080809826 61 0.1247496481 62 0.0702559577 63
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-0.0056247889 70 -0.0119191785 71 0.0144007345 73 -0.0039111625 75
0.0517266726 76 0.0069585489 77 0.0014215107 78 0.0074905052 79
0.0080809832 81 -0.1247496565 82 -0.0702559623 83 -0.0784948381 84
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-0.0119191823 91 -0.0144007346 93 0.0039111629 95 -0.0517266754 96
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-0.2495029327 102 -0.1404967374 103 0.0323045205 104 0.0000000024 105
0.0186150551 107 0.0000000008 108 -0.0009097149 110 -0.0000000002 111
-0.0166398772 113 0.0078227354 115 -0.1034460320 116 -0.0139150025 117
0.0143938213 118 0.0000000001 119
# ORBITAL 9 NAO = 90
0.0139974362 1 -0.2160783634 2 -0.1216786927 3 0.0639676065 4
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0.0179215924 70 -0.0022068304 71 -0.0027201814 73 -0.0067737896 75
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0.0120431584 97 -0.0074907426 98 0.0100672461 99 0.0000000003 101
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0.0000000004 107 -0.0437801767 108 -0.0000000001 110 0.0184419877 111
-0.0000000003 113 0.0000000001 115 -0.0000000020 116 -0.0000000003 117
0.0000000003 118 -0.0029035175 119
# ORBITAL 10 NAO = 90
-0.0051440589 1 0.1005718952 2 0.0845638529 3 -0.1397337895 4
0.1141834782 5 -0.0457303867 7 0.0234939964 8 0.0117656669 10
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0.0770087429 76 0.0164532290 77 0.0072726817 78 0.0060307742 79
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-0.0056709073 91 -0.0100493797 93 -0.0019026432 95 0.0770087402 96
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0.0049551210 107 0.0000000006 108 0.0006914310 110 -0.0000000001 111
-0.0041279019 113 0.0038040170 115 -0.1542612996 116 -0.0329629888 117
0.0177440529 118 0.0000000001 119
# ORBITAL 11 NAO = 90
-0.0088998256 1 0.1742799331 2 0.1465089246 3 0.1142486920 4
-0.0078131644 5 0.0235313039 7 -0.0185720459 8 -0.0034227095 10
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0.0285120656 17 -0.0060359574 18 -0.0142465448 19 0.0088998257 21
-0.1742799344 22 -0.1465089259 23 0.1142486881 24 0.0078131605 25
0.0235313028 27 0.0185720448 28 0.0034227096 30 -0.0060473293 31
-0.0064037026 33 0.0032944147 35 -0.1334935795 36 -0.0285120659 37
-0.0060359581 38 0.0142465441 39 -0.0000000001 41 0.0000000021 42
0.0000000018 43 -0.0000000007 44 -0.2057016988 45 0.0000000001 47
-0.0593097208 48 -0.0000000000 50 -0.0158714988 51 0.0000000000 53
-0.0000000001 55 0.0000000016 56 0.0000000003 57 0.0000000002 58
-0.0037832706 59 -0.0088998256 61 0.1742799323 62 0.1465089241 63
-0.1142486911 64 0.0078131629 65 -0.0235313036 67 0.0185720454 68
-0.0034227098 70 -0.0060473291 71 0.0064037028 73 -0.0032944147 75
0.1334935779 76 0.0285120654 77 0.0060359579 78 0.0142465442 79
0.0088998257 81 -0.1742799352 82 -0.1465089263 83 -0.1142486891 84
-0.0078131618 85 -0.0235313029 87 -0.0185720453 88 0.0034227093 90
-0.0060473274 91 -0.0064037028 93 0.0032944141 95 -0.1334935796 96
-0.0285120659 97 0.0060359576 98 -0.0142465449 99 -0.0000000001 101
0.0000000020 102 0.0000000018 103 0.0000000006 104 0.2057016950 105
-0.0000000001 107 0.0593097217 108 0.0000000001 110 -0.0158715011 111
-0.0000000001 113 -0.0000000000 115 0.0000000017 116 0.0000000004 117
-0.0000000002 118 0.0037832703 119
# ORBITAL 12 NAO = 90
-0.0037231920 1 0.0111150627 2 0.0324659518 3 0.0947657341 4
0.1639019892 5 0.0324226748 7 0.0560650241 8 0.0004508783 10
-0.0049970547 11 -0.0045275601 13 0.0010122333 15 0.1490787651 16
0.0353865179 17 -0.0067083649 18 -0.0116265648 19 -0.0037231920 21
0.0111150626 22 0.0324659517 23 -0.0947657340 24 0.1639019892 25
-0.0324226745 27 0.0560650241 28 0.0004508780 30 0.0049970544 31
-0.0045275597 33 0.0010122332 35 0.1490787652 36 0.0353865178 37
0.0067083650 38 -0.0116265647 39 -0.0037179973 41 0.0112563382 42
0.0325136599 43 -0.1892984480 44 -0.0000000001 45 -0.0647516749 47
-0.0000000000 48 -0.0070415813 50 0.0000000001 51 0.0029723742 53
0.0010156547 55 0.1491231283 56 0.0353714222 57 0.0134368381 58
-0.0000000001 59 -0.0037231920 61 0.0111150627 62 0.0324659517 63
-0.0947657339 64 -0.1639019894 65 -0.0324226745 67 -0.0560650241 68
0.0004508780 70 -0.0049970546 71 -0.0045275596 73 0.0010122332 75
0.1490787651 76 0.0353865177 77 0.0067083651 78 0.0116265647 79
-0.0037231920 81 0.0111150627 82 0.0324659518 83 0.0947657342 84
-0.1639019894 85 0.0324226748 87 -0.0560650241 88 0.0004508784 90
0.0049970549 91 -0.0045275602 93 0.0010122333 95 0.1490787649 96
0.0353865178 97 -0.0067083650 98 0.0116265649 99 -0.0037179973 101
0.0112563375 102 0.0325136602 103 0.1892984469 104 -0.0000000001 105
0.0647516758 107 -0.0000000000 108 -0.0070415822 110 -0.0000000002 111
0.0029723750 113 0.0010156554 115 0.1491231290 116 0.0353714232 117
-0.0134368367 118 -0.0000000001 119
# ORBITAL 13 NAO = 90
-0.0077795017 1 0.1114492677 2 0.1676977293 3 0.0636506129 4
0.1102407267 5 0.0070910121 7 0.0122634165 8 -0.0147424044 10
0.0206787210 11 0.0059331824 13 0.0000881382 15 0.1838685648 16
0.0693750950 17 -0.0071295317 18 -0.0123503755 19 0.0077795017 21
-0.1114492677 22 -0.1676977292 23 0.0636506129 24 -0.1102407270 25
0.0070910126 27 -0.0122634173 28 0.0147424042 30 0.0206787185 31
-0.0059331821 33 -0.0000881383 35 -0.1838685644 36 -0.0693750951 37
-0.0071295320 38 0.0123503750 39 -0.0077800331 41 0.1114379546 42
0.1677056671 43 -0.1272989969 44 0.0000000000 45 -0.0141745507 47
-0.0000000000 48 0.0162731269 50 0.0000000000 51 -0.0250837618 53
0.0000883276 55 0.1838681097 56 0.0693765065 57 0.0142627162 58
0.0000000000 59 0.0077795017 61 -0.1114492678 62 -0.1676977292 63
0.0636506129 64 0.1102407272 65 0.0070910126 67 0.0122634172 68
0.0147424042 70 -0.0206787184 71 -0.0059331821 73 -0.0000881382 75
-0.1838685642 76 -0.0693750950 77 -0.0071295322 78 -0.0123503751 79
-0.0077795017 81 0.1114492677 82 0.1676977293 83 0.0636506130 84
-0.1102407268 85 0.0070910120 87 -0.0122634164 88 -0.0147424044 90
-0.0206787211 91 0.0059331824 93 0.0000881382 95 0.1838685647 96
0.0693750949 97 -0.0071295317 98 0.0123503756 99 0.0077800331 101
-0.1114379543 102 -0.1677056673 103 -0.1272989948 104 0.0000000001 105
-0.0141745525 107 0.0000000000 108 -0.0162731262 110 0.0000000001 111
0.0250837603 113 -0.0000883285 115 -0.1838681106 116 -0.0693765078 117
0.0142627144 118 0.0000000001 119
# ORBITAL 14 NAO = 90
0.0000011888 1 -0.0000428122 2 -0.0000193406 3 -0.2396559405 4
0.1383212588 5 -0.0833040860 7 0.0480780537 8 0.0081916407 10
0.0054632598 11 -0.0081940522 13 0.0000021430 15 -0.0000568495 16
-0.0000165189 17 -0.0045591993 18 0.0026388067 19 0.0000011888 21
-0.0000428110 22 -0.0000193401 23 0.2396559394 24 0.1383212571 25
0.0833040855 27 0.0480780535 28 0.0081916411 30 -0.0054632601 31
-0.0081940519 33 0.0000021439 35 -0.0000568498 36 -0.0000165188 37
0.0045591989 38 0.0026388061 39 -0.0000000000 41 -0.0000000000 42
-0.0000000000 43 -0.0000000000 44 -0.2767352102 45 -0.0000000000 47
-0.0961986294 48 -0.0000000001 50 -0.0109202542 51 0.0000000000 53
-0.0000000001 55 -0.0000000000 56 -0.0000000000 57 -0.0000000000 58
-0.0052745169 59 -0.0000011888 61 0.0000428110 62 0.0000193401 63
-0.2396559396 64 0.1383212572 65 -0.0833040854 67 0.0480780534 68
-0.0081916410 70 -0.0054632601 71 0.0081940518 73 -0.0000021439 75
0.0000568498 76 0.0000165188 77 -0.0045591989 78 0.0026388060 79
-0.0000011888 81 0.0000428123 82 0.0000193406 83 0.2396559404 84
0.1383212588 85 0.0833040860 87 0.0480780537 88 -0.0081916407 90
0.0054632598 91 0.0081940523 93 -0.0000021429 95 0.0000568495 96
0.0000165189 97 0.0045591993 98 0.0026388067 99 -0.0000000000 101
0.0000000001 102 -0.0000000000 103 -0.0000000000 104 -0.2767352058 105
-0.0000000000 107 -0.0961986304 108 -0.0000000000 110 0.0109202573 111
0.0000000000 113 -0.0000000001 115 -0.0000000000 116 -0.0000000000 117
0.0000000000 118 -0.0052745165 119
# ORBITAL 15 NAO = 90
-0.0006266032 1 -0.0382787571 2 -0.0483997291 3 0.1633248653 4
0.1961580581 5 0.0509526263 7 0.0877847417 8 -0.0121775015 10
0.0001460825 11 0.0084420611 13 0.0009659969 15 0.1928592179 16
0.0682975466 17 -0.0044975288 18 -0.0126684488 19 -0.0006266032 21
-0.0382787568 22 -0.0483997291 23 -0.1633248656 24 0.1961580581 25
-0.0509526265 27 0.0877847418 28 -0.0121775014 30 -0.0001460827 31
0.0084420612 33 0.0009659972 35 0.1928592182 36 0.0682975468 37
0.0044975286 38 -0.0126684491 39 -0.0000000000 41 -0.0000000001 42
-0.0000000001 43 -0.0000000005 44 -0.0865394535 45 -0.0000000003 47
-0.0003977750 48 -0.0000000001 50 -0.0204636857 51 0.0000000000 53
-0.0000000000 55 0.0000000003 56 0.0000000001 57 0.0000000000 58
-0.0048836154 59 0.0006266032 61 0.0382787567 62 0.0483997289 63
0.1633248656 64 0.1961580577 65 0.0509526263 67 0.0877847414 68
0.0121775015 70 -0.0001460828 71 -0.0084420614 73 -0.0009659972 75
-0.1928592177 76 -0.0682975466 77 -0.0044975287 78 -0.0126684492 79
0.0006266032 81 0.0382787572 82 0.0483997292 83 -0.1633248655 84
0.1961580588 85 -0.0509526262 87 0.0877847417 88 0.0121775015 90
0.0001460827 91 -0.0084420611 93 -0.0009659969 95 -0.1928592181 96
-0.0682975467 97 0.0044975289 98 -0.0126684490 99 0.0000000000 101
0.0000000001 102 0.0000000001 103 -0.0000000005 104 -0.0865394521 105
-0.0000000001 107 -0.0003977754 108 -0.0000000001 110 0.0204636868 111
0.0000000001 113 -0.0000000000 115 -0.0000000004 116 -0.0000000001 117
0.0000000000 118 -0.0048836154 119
# ORBITAL 16 NAO = 90
-0.0003586348 1 -0.0220988824 2 -0.0279910890 3 0.0076641824 4
0.1632676821 5 0.0290045303 7 0.0509421160 8 0.0106923614 10
0.0119090275 11 -0.0128503064 13 0.0005575567 15 0.1113324509 16
0.0394219179 17 -0.0074820090 18 -0.0044959757 19 0.0003586348 21
0.0220988823 22 0.0279910887 23 0.0076641819 24 -0.1632676811 25
0.0290045293 27 -0.0509421154 28 -0.0106923611 30 0.0119090285 31
0.0128503057 33 -0.0005575565 35 -0.1113324506 36 -0.0394219177 37
-0.0074820091 38 0.0044959755 39 0.0007213416 41 0.0441838214 42
0.0558579175 43 0.2904548744 44 -0.0000000001 45 0.1171902403 47
0.0000000000 48 -0.0039203318 50 -0.0000000002 51 0.0082203577 53
-0.0011142396 55 -0.2227104062 56 -0.0788656304 57 -0.0152767920 58
0.0000000001 59 0.0003586348 61 0.0220988824 62 0.0279910889 63
0.0076641824 64 0.1632676819 65 0.0290045295 67 0.0509421156 68
-0.0106923610 70 -0.0119090285 71 0.0128503057 73 -0.0005575565 75
-0.1113324512 76 -0.0394219179 77 -0.0074820092 78 -0.0044959756 79
-0.0003586348 81 -0.0220988822 82 -0.0279910888 83 0.0076641819 84
-0.1632676816 85 0.0290045301 87 -0.0509421157 88 0.0106923615 90
-0.0119090275 91 -0.0128503065 93 0.0005575567 95 0.1113324502 96
0.0394219176 97 -0.0074820090 98 0.0044959758 99 -0.0007213416 101
-0.0441838220 102 -0.0558579171 103 0.2904548721 104 -0.0000000001 105
0.1171902421 107 -0.0000000000 108 0.0039203305 110 -0.0000000001 111
-0.0082203568 113 0.0011142407 115 0.2227104073 116 0.0788656318 117
-0.0152767901 118 -0.0000000001 119
# ORBITAL 17 NAO = 90
-0.0012911822 1 -0.0067578701 2 0.0010641979 3 0.2465963959 4
-0.0149150249 5 0.1010029777 7 -0.0041486050 8 -0.0213705643 10
0.0047272710 11 0.0206865037 13 0.0003120959 15 0.1092296435 16
0.0566451247 17 0.0032481770 18 -0.0081643699 19 -0.0012911822 21
-0.0067578703 22 0.0010641980 23 -0.2465963959 24 -0.0149150244 25
-0.1010029782 27 -0.0041486050 28 -0.0213705640 30 -0.0047272709 31
0.0206865033 33 0.0003120959 35 0.1092296434 36 0.0566451249 37
-0.0032481772 38 -0.0081643701 39 0.0025873290 41 0.0136123011 42
-0.0020704704 43 0.2206386849 44 0.0000000000 45 0.0937752162 47
0.0000000000 48 -0.0274275908 50 -0.0000000002 51 0.0288047866 53
-0.0006225099 55 -0.2183274679 56 -0.1132505770 57 -0.0108749007 58
0.0000000001 59 -0.0012911822 61 -0.0067578702 62 0.0010641980 63
-0.2465963960 64 0.0149150247 65 -0.1010029780 67 0.0041486050 68
-0.0213705641 70 0.0047272710 71 0.0206865034 73 0.0003120959 75
0.1092296434 76 0.0566451248 77 -0.0032481771 78 0.0081643701 79
-0.0012911822 81 -0.0067578700 82 0.0010641980 83 0.2465963959 84
0.0149150247 85 0.1010029776 87 0.0041486049 88 -0.0213705644 90
-0.0047272711 91 0.0206865038 93 0.0003120960 95 0.1092296435 96
0.0566451247 97 0.0032481769 98 0.0081643700 99 0.0025873290 101
0.0136123017 102 -0.0020704709 103 -0.2206386828 104 0.0000000001 105
-0.0937752175 107 0.0000000001 108 -0.0274275902 110 0.0000000002 111
0.0288047861 113 -0.0006225107 115 -0.2183274690 116 -0.1132505784 117
0.0108748991 118 0.0000000001 119
# ORBITAL 18 NAO = 90
-0.0022422568 1 -0.0117861316 2 0.0017961586 3 -0.0149685697 4
0.2293271422 5 -0.0041574297 7 0.0961923012 8 -0.0046743391 10
0.0297488877 11 0.0035011315 13 0.0005353083 15 0.1890734811 16
0.0980836424 17 -0.0081565837 18 -0.0061626988 19 0.0022422568 21
0.0117861306 22 -0.0017961592 23 -0.0149685686 24 -0.2293271406 25
-0.0041574294 27 -0.0961923006 28 0.0046743386 30 0.0297488899 31
-0.0035011317 33 -0.0005353092 35 -0.1890734813 36 -0.0980836425 37
-0.0081565829 38 0.0061626996 39 0.0000000000 41 -0.0000000000 42
0.0000000000 43 0.0000000001 44 0.2552406577 45 0.0000000001 47
0.1034033602 48 0.0000000001 50 0.0215474843 51 -0.0000000000 53
0.0000000001 55 -0.0000000000 56 -0.0000000000 57 0.0000000000 58
0.0079649290 59 -0.0022422568 61 -0.0117861306 62 0.0017961592 63
0.0149685685 64 -0.2293271407 65 0.0041574294 67 -0.0961923005 68
-0.0046743388 70 0.0297488900 71 0.0035011319 73 0.0005353091 75
0.1890734813 76 0.0980836425 77 0.0081565830 78 0.0061626997 79
0.0022422568 81 0.0117861315 82 -0.0017961586 83 0.0149685698 84
0.2293271424 85 0.0041574298 87 0.0961923012 88 0.0046743391 90
0.0297488876 91 -0.0035011315 93 -0.0005353084 95 -0.1890734810 96
-0.0980836423 97 0.0081565838 98 -0.0061626989 99 0.0000000000 101
0.0000000000 102 -0.0000000000 103 -0.0000000000 104 -0.2552406531 105
-0.0000000000 107 -0.1034033615 108 -0.0000000001 110 0.0215474869 111
0.0000000001 113 -0.0000000001 115 -0.0000000001 116 -0.0000000000 117
-0.0000000000 118 -0.0079649287 119
# ORBITAL 19 NAO = 5
-0.6069137242 6 -0.5288219485 9 0.0160778803 12 0.0278520511 14
-0.0182054019 20
# ORBITAL 20 NAO = 5
-0.6069137241 26 -0.5288219486 29 -0.0160778803 32 0.0278520509 34
-0.0182054020 40
# ORBITAL 21 NAO = 5
-0.6069128657 46 -0.5288236221 49 -0.0321586274 52 0.0000000002 54
-0.0182031846 60
# ORBITAL 22 NAO = 5
-0.6069137243 66 -0.5288219484 69 -0.0160778802 72 -0.0278520508 74
-0.0182054020 80
# ORBITAL 23 NAO = 5
-0.6069137243 86 -0.5288219484 89 0.0160778802 92 -0.0278520511 94
-0.0182054019 100
# ORBITAL 24 NAO = 5
-0.6069128633 106 -0.5288236244 109 0.0321586294 112 0.0000000002 114
-0.0182031848 120
$end
In the input file, VB structures are specified by the users rather than automatically generated. The keyword NSTR=2
in $CTRL
section specifies 2 VB structures in the computation, and the 2 Kekulé structures are described in section $STR
. The keyword GUESS=READ
means that the initial guess is obtained by the user in $GUS
section. The initial guess comes from the optmized orbitals of previous computation, stored in corresponding ORB file.
2.2.3.2. Computational Results
The final energy of the computation can be found after VBSCF iterations as -230.62995
hartree. Compared with the energy including 5 covalent structures, the corresponding resonance energy from Dewar structures can be obtained as 2.8 kcal/mol.
****** BOND ORDER ****** ATOM 1 ATOM 2 DIST BOND ORDER 1 C 2 H 1.093 0.979 1 C 3 C 1.399 1.186 3 C 4 H 1.093 0.979 3 C 5 C 1.399 1.186 5 C 6 H 1.093 0.979 5 C 7 C 1.399 1.186 7 C 8 H 1.093 0.979 7 C 9 C 1.399 1.186 9 C 10 H 1.093 0.979 1 C 11 C 1.399 1.186 9 C 11 C 1.399 1.186 11 C 12 H 1.093 0.979
The atomic population analysis also shows that the bonder orders of CC bondings are the same as 1.186. Compared with the bond order from 5 covalent structures and the resonance energy from Dewar structures, the conjugation and stability mainly come from the resonance of Kekulé structures.
2.2.4. Computations with 1 Kekulé Structure
Finally, the computation including only 1 Kekulé structure, which represents a cycloalkene, will be proceeded to check the resonance from Kekulé structures.
2.2.4.1. Input File
The input file of this computation is shown below. The initial guess comes from the optimized orbitals of the computation including 2 Kekulé structures.
C6H6
$ctrl
nstr=1 nao=6 nae=6 iscf=5 iprint=3
orbtyp=hao frgtyp=sao
int=libcint basis=cc-pvdz
guess=read
$end
$str
1:18 19-24
$end
$frag
12 2*6
spxpydxxdyydzzdxy 1-12
pzdxzdyz 1 2
pzdxzdyz 3 4
pzdxzdyz 5 6
pzdxzdyz 7 8
pzdxzdyz 9 10
pzdxzdyz 11 12
$end
$orb
1*18 1*6
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
3
4
5
6
7
$end
$geo
C 0.6995000584 1.2115696411 0.0000000000
H 1.2460106991 2.1581538376 0.0000000000
C -0.6995000584 1.2115696411 0.0000000000
H -1.2460106991 2.1581538376 0.0000000000
C -1.3990001169 0.0000000000 0.0000000000
H -2.4920213982 0.0000000000 0.0000000000
C -0.6995000584 -1.2115696411 0.0000000000
H -1.2460106991 -2.1581538376 0.0000000000
C 0.6995000584 -1.2115696411 0.0000000000
H 1.2460106991 -2.1581538376 0.0000000000
C 1.3990001169 0.0000000000 0.0000000000
H 2.4920213982 0.0000000000 0.0000000000
$end
$gus
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 5 5 5 5 5 5
# ORBITAL 1 NAO = 90
-0.4085796783 1 -0.0018719283 2 0.0001665818 3 0.0001010685 4
0.0001981258 5 0.0000450438 7 0.0000863179 8 0.0009553396 10
0.0000836069 11 0.0010374634 13 0.0011387900 15 -0.0001957720 16
-0.0001340753 17 0.0000469703 18 0.0000827563 19 -0.4085796727 21
-0.0018719292 22 0.0001665812 23 -0.0001010727 24 0.0001981248 25
-0.0000450425 27 0.0000863186 28 0.0009553426 30 -0.0000836019 31
0.0010374618 33 0.0011387887 35 -0.0001957726 36 -0.0001340767 37
-0.0000469715 38 0.0000827567 39 -0.4090835453 41 -0.0018962542 42
0.0001483676 43 -0.0002144425 44 0.0000004419 45 -0.0001064444 47
0.0000000620 48 0.0010795224 50 -0.0000005324 51 0.0009089949 53
0.0011398054 55 -0.0002140828 56 -0.0001424123 57 -0.0000967357 58
0.0000004933 59 -0.4085796762 61 -0.0018717962 62 0.0001665571 63
-0.0001012559 64 -0.0001976491 65 -0.0000451304 67 -0.0000860262 68
0.0009554043 70 0.0000853899 71 0.0010374754 73 0.0011388868 75
-0.0001954373 76 -0.0001341537 77 -0.0000475649 78 -0.0000822130 79
-0.4085796747 81 -0.0018717874 82 0.0001665574 83 0.0001012488 84
-0.0001976456 85 0.0000451252 87 -0.0000860254 88 0.0009553937 90
-0.0000853972 91 0.0010374881 93 0.0011388931 95 -0.0001954365 96
-0.0001341565 97 0.0000475538 98 -0.0000822115 99 -0.4090835098 101
-0.0018962560 102 0.0001483691 103 0.0002144405 104 0.0000004455 105
0.0001064418 107 0.0000000681 108 0.0010795349 110 0.0000005509 111
0.0009089845 113 0.0011398035 115 -0.0002140768 116 -0.0001424127 117
0.0000967353 118 0.0000005091 119
# ORBITAL 2 NAO = 90
0.2888921826 1 0.0012283761 2 -0.0002515233 3 0.0001334436 4
-0.0001583616 5 0.0001866742 7 -0.0001486589 8 -0.0008194761 10
-0.0001545655 11 -0.0005903612 13 -0.0007993769 15 0.0001561841 16
0.0000815611 17 0.0000143387 18 -0.0000796338 19 -0.2888922723 21
-0.0012282896 22 0.0002516068 23 0.0001334933 24 0.0001581461 25
0.0001866825 27 0.0001482790 28 0.0008195384 30 -0.0001557097 31
0.0005903305 33 0.0007993976 35 -0.0001560171 36 -0.0000815893 37
0.0000140002 38 0.0000793106 39 -0.5781886874 41 -0.0024517953 42
0.0004960627 43 -0.0001410124 44 0.0000000144 45 -0.0000703152 47
0.0000000565 48 0.0015346481 50 -0.0000001631 51 0.0013051183 53
0.0016011118 55 -0.0003076892 56 -0.0001586915 57 -0.0001240234 58
0.0000001386 59 -0.2888922230 61 -0.0012282282 62 0.0002515995 63
0.0001335274 64 -0.0001581270 65 0.0001867496 67 -0.0001482931 68
0.0008194516 70 0.0001556375 71 0.0005904439 73 0.0007994395 75
-0.0001560266 76 -0.0000816204 77 0.0000141380 78 -0.0000793592 79
0.2888922537 81 0.0012283054 82 -0.0002515181 83 0.0001334812 84
0.0001583237 85 0.0001867191 87 0.0001486497 88 -0.0008194148 90
0.0001546034 91 -0.0005904524 93 -0.0007994211 95 0.0001561754 96
0.0000815940 97 0.0000144233 98 0.0000796423 99 0.5781886588 101
0.0024515577 102 -0.0004959802 103 -0.0001409979 104 -0.0000000307 105
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# ORBITAL 3 NAO = 90
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# ORBITAL 4 NAO = 90
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# ORBITAL 5 NAO = 90
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# ORBITAL 6 NAO = 90
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# ORBITAL 7 NAO = 90
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# ORBITAL 8 NAO = 90
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# ORBITAL 9 NAO = 90
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# ORBITAL 10 NAO = 90
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# ORBITAL 11 NAO = 90
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# ORBITAL 12 NAO = 90
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# ORBITAL 13 NAO = 90
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# ORBITAL 14 NAO = 90
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0.0000000001 43 0.0000000000 44 -0.2767109921 45 0.0000000000 47
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-0.0000000002 55 0.0000000000 56 0.0000000000 57 0.0000000000 58
-0.0052653392 59 0.0000243486 61 -0.0000211336 62 -0.0000197401 63
-0.2396956060 64 0.1383354959 65 -0.0832832749 67 0.0480626415 68
-0.0082077198 70 -0.0054692758 71 0.0082072205 73 0.0000008342 75
0.0000306102 76 0.0000082652 77 -0.0045627709 78 0.0026348913 79
0.0000243167 81 -0.0000211335 82 -0.0000197398 83 0.2396956060 84
0.1383354953 85 0.0832832746 87 0.0480626416 88 -0.0082077199 90
0.0054692764 91 0.0082072205 93 0.0000008337 95 0.0000306105 96
0.0000082651 97 0.0045627706 98 0.0026348910 99 0.0000000566 101
0.0000000007 102 -0.0000000000 103 -0.0000000000 104 -0.2767109937 105
0.0000000000 107 -0.0961484638 108 -0.0000000005 110 0.0109288338 111
0.0000000001 113 -0.0000000005 115 0.0000000001 116 -0.0000000001 117
-0.0000000000 118 -0.0052653392 119
# ORBITAL 15 NAO = 90
-0.0009983767 1 -0.0386214684 2 -0.0485455904 3 0.1633421841 4
0.1962473237 5 0.0509807373 7 0.0877733678 8 -0.0121832761 10
0.0001162009 11 0.0084147730 13 0.0010223542 15 0.1927411229 16
0.0682210653 17 -0.0045132574 18 -0.0126863282 19 -0.0009983769 21
-0.0386214683 22 -0.0485455906 23 -0.1633421842 24 0.1962473245 25
-0.0509807372 27 0.0877733679 28 -0.0121832762 30 -0.0001162008 31
0.0084147732 33 0.0010223542 35 0.1927411233 36 0.0682210653 37
0.0045132578 38 -0.0126863281 39 0.0000000963 41 0.0000000005 42
0.0000000001 43 -0.0000000002 44 -0.0868168628 45 -0.0000000004 47
-0.0005743185 48 -0.0000000005 50 -0.0204836282 51 0.0000000001 53
-0.0000000004 55 0.0000000002 56 0.0000000002 57 0.0000000001 58
-0.0048842722 59 0.0009985499 61 0.0386214692 62 0.0485455904 63
0.1633421850 64 0.1962473253 65 0.0509807366 67 0.0877733671 68
0.0121832762 70 -0.0001162013 71 -0.0084147740 73 -0.0010223547 75
-0.1927411227 76 -0.0682210647 77 -0.0045132580 78 -0.0126863286 79
0.0009985050 81 0.0386214693 82 0.0485455908 83 -0.1633421847 84
0.1962473254 85 -0.0509807370 87 0.0877733675 88 0.0121832760 90
0.0001162015 91 -0.0084147736 93 -0.0010223547 95 -0.1927411232 96
-0.0682210651 97 0.0045132576 98 -0.0126863286 99 0.0000001212 101
0.0000000009 102 -0.0000000000 103 -0.0000000009 104 -0.0868168632 105
0.0000000001 107 -0.0005743183 108 -0.0000000006 110 0.0204836287 111
0.0000000000 113 -0.0000000004 115 -0.0000000005 116 -0.0000000001 117
-0.0000000000 118 -0.0048842716 119
# ORBITAL 16 NAO = 90
-0.0005894251 1 -0.0223088039 2 -0.0280654665 3 0.0075643177 4
0.1633898810 5 0.0288954659 7 0.0510111520 8 0.0106960596 10
0.0118868073 11 -0.0128757602 13 0.0005926770 15 0.1112764638 16
0.0393823208 17 -0.0074782289 18 -0.0045126110 19 0.0005894222 21
0.0223088033 22 0.0280654662 23 0.0075643166 24 -0.1633898807 25
0.0288954662 27 -0.0510111513 28 -0.0106960596 30 0.0118868066 31
0.0128757604 33 -0.0005926768 35 -0.1112764634 36 -0.0393823205 37
-0.0074782291 38 0.0045126111 39 0.0011830149 41 0.0446313651 42
0.0560606696 43 0.2905583224 44 0.0000000000 45 0.1172071367 47
0.0000000000 48 -0.0038785631 50 -0.0000000003 51 0.0082267364 53
-0.0011834653 55 -0.2225345572 56 -0.0787777804 57 -0.0152898732 58
0.0000000001 59 0.0005894244 61 0.0223088033 62 0.0280654664 63
0.0075643175 64 0.1633898819 65 0.0288954663 67 0.0510111514 68
-0.0106960595 70 -0.0118868065 71 0.0128757604 73 -0.0005926768 75
-0.1112764638 76 -0.0393823205 77 -0.0074782294 78 -0.0045126114 79
-0.0005894255 81 -0.0223088036 82 -0.0280654663 83 0.0075643174 84
-0.1633898808 85 0.0288954658 87 -0.0510111516 88 0.0106960598 90
-0.0118868073 91 -0.0128757604 93 0.0005926770 95 0.1112764630 96
0.0393823204 97 -0.0074782290 98 0.0045126113 99 -0.0011830119 101
-0.0446313639 102 -0.0560606692 103 0.2905583232 104 -0.0000000002 105
0.1172071362 107 -0.0000000001 108 0.0038785629 110 -0.0000000005 111
-0.0082267365 113 0.0011834651 115 0.2225345571 116 0.0787777798 117
-0.0152898742 118 -0.0000000002 119
# ORBITAL 17 NAO = 90
-0.0014020326 1 -0.0068956525 2 0.0009658087 3 0.2467463560 4
-0.0150840636 5 0.1010428983 7 -0.0041186505 8 -0.0213912436 10
0.0047152733 11 0.0207049577 13 0.0003249521 15 0.1090368977 16
0.0565120453 17 0.0032595528 18 -0.0081550919 19 -0.0014020678 21
-0.0068956523 22 0.0009658091 23 -0.2467463563 24 -0.0150840638 25
-0.1010428983 27 -0.0041186508 28 -0.0213912436 30 -0.0047152734 31
0.0207049580 33 0.0003249521 35 0.1090368981 36 0.0565120453 37
-0.0032595527 38 -0.0081550918 39 0.0028093586 41 0.0137482733 42
-0.0019741520 43 0.2207188322 44 -0.0000000000 45 0.0939446698 47
0.0000000001 48 -0.0274316281 50 -0.0000000006 51 0.0288061575 53
-0.0006463540 55 -0.2181730829 56 -0.1130340303 57 -0.0108702108 58
0.0000000003 59 -0.0014020302 61 -0.0068956520 62 0.0009658091 63
-0.2467463568 64 0.0150840636 65 -0.1010428979 67 0.0041186509 68
-0.0213912440 70 0.0047152734 71 0.0207049583 73 0.0003249522 75
0.1090368979 76 0.0565120450 77 -0.0032595523 78 0.0081550920 79
-0.0014020296 81 -0.0068956524 82 0.0009658087 83 0.2467463565 84
0.0150840633 85 0.1010428980 87 0.0041186504 88 -0.0213912437 90
-0.0047152733 91 0.0207049580 93 0.0003249522 95 0.1090368978 96
0.0565120452 97 0.0032595526 98 0.0081550920 99 0.0028092657 101
0.0137482731 102 -0.0019741520 103 -0.2207188329 104 0.0000000001 105
-0.0939446697 107 0.0000000002 108 -0.0274316280 110 0.0000000006 111
0.0288061582 113 -0.0006463534 115 -0.2181730832 116 -0.1130340301 117
0.0108702120 118 0.0000000003 119
# ORBITAL 18 NAO = 90
-0.0023749933 1 -0.0118884368 2 0.0017334005 3 -0.0150505701 4
0.2293750064 5 -0.0041065876 7 0.0962994757 8 -0.0046652132 10
0.0297409795 11 0.0034826782 13 0.0005612091 15 0.1889435721 16
0.0978899218 17 -0.0081612949 18 -0.0061659303 19 0.0023750060 21
0.0118884365 22 -0.0017334006 23 -0.0150505706 24 -0.2293750071 25
-0.0041065875 27 -0.0962994755 28 0.0046652135 30 0.0297409784 31
-0.0034826783 33 -0.0005612086 35 -0.1889435720 36 -0.0978899215 37
-0.0081612954 38 0.0061659300 39 0.0000000032 41 0.0000000001 42
-0.0000000001 43 0.0000000002 44 0.2554222892 45 0.0000000000 47
0.1034266384 48 0.0000000003 50 0.0215760829 51 -0.0000000002 53
0.0000000002 55 -0.0000000000 56 -0.0000000001 57 -0.0000000001 58
0.0079574230 59 -0.0023750295 61 -0.0118884363 62 0.0017334008 63
0.0150505703 64 -0.2293750078 65 0.0041065877 67 -0.0962994753 68
-0.0046652137 70 0.0297409788 71 0.0034826785 73 0.0005612087 75
0.1889435718 76 0.0978899212 77 0.0081612957 78 0.0061659304 79
0.0023750118 81 0.0118884367 82 -0.0017334007 83 0.0150505701 84
0.2293750071 85 0.0041065877 87 0.0962994753 88 0.0046652134 90
0.0297409792 91 -0.0034826785 93 -0.0005612092 95 -0.1889435718 96
-0.0978899216 97 0.0081612954 98 -0.0061659305 99 0.0000000018 101
0.0000000003 102 0.0000000001 103 0.0000000001 104 -0.2554222907 105
0.0000000000 107 -0.1034266382 108 -0.0000000003 110 0.0215760822 111
0.0000000001 113 -0.0000000004 115 0.0000000000 116 -0.0000000001 117
0.0000000000 118 -0.0079574229 119
# ORBITAL 19 NAO = 5
-0.6051361517 6 -0.5306934722 9 0.0161429500 12 0.0279606935 14
-0.0181292011 20
# ORBITAL 20 NAO = 5
-0.6051361519 26 -0.5306934721 29 -0.0161429499 32 0.0279606936 34
-0.0181292011 40
# ORBITAL 21 NAO = 5
-0.6051369321 46 -0.5306928695 49 -0.0322859902 52 0.0000000004 54
-0.0181286009 60
# ORBITAL 22 NAO = 5
-0.6051361524 66 -0.5306934715 69 -0.0161429500 72 -0.0279606933 74
-0.0181292011 80
# ORBITAL 23 NAO = 5
-0.6051361522 86 -0.5306934717 89 0.0161429499 92 -0.0279606934 94
-0.0181292011 100
# ORBITAL 24 NAO = 5
-0.6051369320 106 -0.5306928697 109 0.0322859897 112 0.0000000007 114
-0.0181286008 120
$end
2.2.4.2. Computational Results
The final energy can be found as -230.59097
hartree, and the resonance Kekulé structures is 24.5 kcal/mol, which is the stablization energy to delocalize the \(\pi\) orbitals in a cycloalkene.
****** BOND ORDER ****** ATOM 1 ATOM 2 DIST BOND ORDER 1 C 2 H 1.093 0.980 1 C 3 C 1.399 1.425 3 C 4 H 1.093 0.980 3 C 5 C 1.399 1.011 5 C 6 H 1.093 0.980 5 C 7 C 1.399 1.425 7 C 8 H 1.093 0.980 7 C 9 C 1.399 1.012 9 C 10 H 1.093 0.980 1 C 11 C 1.399 1.011 9 C 11 C 1.399 1.425 11 C 12 H 1.093 0.980
The bond orders show that the CC bondings are not equivalent now, there are 3 CC bondings with bond order 1.425, close to double bonding, and 3 bondings with 1.011, close to single bonding. The computational results suggest that the resonance from Kekulé structrues mainly stabilizes the molecule and makes all CC bondings equivalent. Both resonance from Kekulé structures and equalization of CC bonds thus present the aromaticity in C6H6.
2.3. Menshutkin Reaction NH3 + CH3Cl \(\rightarrow\) [NH3CH3]+ + Cl-
2.3.1. Chemical question to be addressed
The last exercise is the Menshutkin reaction NH3 + CH3Cl \(\rightarrow\) [NH3CH3]+ + Cl-. The reaction is exothermic in solution. In this example, the reaction barrier in gas phase will be calculated with L-VBSCF and L-BOVB. For more information of the reaction and the computations in solution, please refer to:
2.3.2. Active/inactive electrons and orbitals
The reaction involves the breaking of the CH3-Cl bond and building of an NH3-CH3 bond. As such, the lone pair on NH3 and the CH3-Cl bond in the reactants constitute the active space, which involves 4 electrons on 3 orbitals. The remaining 32 electrons and 16 orbitals constitute the inactive space, including the core orbitals of N, C and Cl, 3 N-H bonds, 3 C-H bonds, and 3 s, 3 px and 3 py orbitals on Cl.
2.3.3. Fragmentation and important VB structures
The reaction involves 3 fragments: NH3, CH3 and Cl. The reactants include non-interacting NH3 and CH3Cl moieties while the product includes non-interacting [NH3CH3]+ and Cl- moieties. Following figure shows the important VB structures in reactant (a) and product (b).
2.3.4. Basis set and its subsets based on orbital symmetry
6–31G* is the basis set used in this example. The basis functions are simply separated into subsets according to the atoms. The basis functions on each atom will be treated as a subset and the VB orbitals will be built with these subsets.
2.3.5. Structures
There are 6 VB structures involved in the active space as shown in the figure. Structures S1-S3 describe the reactant, and S3-S5 describe the product. S6 describes the electron transfer between NH3 and Cl, and will appear in the TS region.
2.3.6. Input File
The input files of L-VBSCF for reactant and TS are given below:
Reactant:
NH3CH3cl reactant
$ctrl
nmul=1 nstr=6 iprint=3 iscf=5 nao=3 nae=4
orbtyp=hao frgtyp=atom
int=libcint basis=6-31G*
guess=read
$end
$stru
1:16 17 17 18 19
1:16 17 17 18 18
1:16 17 17 19 19
1:16 18 18 17 19
1:16 19 19 17 18
1:16 18 18 19 19
$end
$orb
1*5 4 4 1*3 4*3 4*3 4 4 1
6
6
6
6
6
1 7 8 9
2 3 4 5
6
6
6
1 7 8 9
1 7 8 9
1 7 8 9
2 3 4 5
2 3 4 5
2 3 4 5
1 7 8 9
2 3 4 5
6
$end
$geo
N 0.000000 0.000000 0.000000
C 0.000000 0.000000 10.000000
H -1.029985 0.000000 9.647297
H 0.514992 0.891993 9.647297
H 0.514992 -0.891993 9.647297
Cl 0.000000 0.000000 11.778400
H 0.939678 0.000000 -0.389227
H -0.469839 0.813785 -0.389227
H -0.469839 -0.813785 -0.389227
$end
TS:
NH3CH3cl
$ctrl
nmul=1 nstr=6 iprint=3 nao=3 nae=4 iscf=5 itmax=300
guess=read orbtyp=hao frgtyp=atom
int=libcint basis=6-31G*
$end
$stru
1:16 17 17 18 19
1:16 17 17 18 18
1:16 17 17 19 19
1:16 18 18 17 19
1:16 19 19 17 18
1:16 18 18 19 19
$end
$orb
1*5 4 4 1*3 4*3 4*3 4 4 1
6
6
6
6
6
1 7 8 9
2 3 4 5
6
6
6
1 7 8 9
1 7 8 9
1 7 8 9
2 3 4 5
2 3 4 5
2 3 4 5
1 7 8 9
2 3 4 5
6
$end
$geo
N 0.0000000000 0.0000000000 -2.4403680000
C 0.0000000000 0.0000000000 -0.6327610000
H 1.0651490000 0.0000000000 -0.4753840000
H -0.5325745000 -0.9224460928 -0.4753840000
H -0.5325745000 0.9224460928 -0.4753840000
CL 0.0000000000 0.0000000000 1.8067450000
H -0.9550790000 0.0000000000 -2.8031240000
H 0.4775395000 0.8271226766 -2.8031240000
H 0.4775395000 -0.8271226766 -2.8031240000
$end
The input files are almost the same except the initial guess and geometry. The initial guess of reactant is given here
. The initial guess of TS can be obtained from the computational results of reactant. For L-BOVB computations, the user may simply change ISCF=5
to ISCF=2
and append BOVB
in $CTRL
section. The initial guess of L-BOVB computations are from the computational results of correpsonding L-VBSCF computation.
2.3.7. Computational Results
2.3.7.1. The VB structures
Following table shows the VB structures involved in the calculation. The first 16 doubly occupied orbitals are inactive ones, orbital 17 corresponds to the lone pair on NH3, and orbitals 18 and 19 are singly occupied orbitals on CH3 and Cl respectively. The correspondence to the structures is also listed.
VB structure |
Structure |
---|---|
1 ***** 1:16 17 17 18 19 |
S1 |
2 ***** 1:16 17 17 18 18 |
S2 |
3 ***** 1:16 17 17 19 19 |
S3 |
4 ***** 1:16 18 18 17 19 |
S6 |
5 ***** 1:16 19 19 17 18 |
S4 |
6 ***** 1:16 18 18 19 19 |
S5 |
2.3.7.2. Energies
Following table shows the total energies (in a.u.) and reaction barrier at the L-VBSCF and L-BOVB levels. Compared with the reference value 33.0 kcal mol -1 (138.1 kJ mol -1) by Webb and Gordon, L-VBSCF overestimates the reaction barrier due to the lack of dynamic correlation, and L-BOVB significantly improves the result. Compared with the energies obtained by L-VBSCF and L-BOVB, L-BOVB decreases the energy at the TS geometry much more than in the reactants. The results show that dynamic correlation plays an important role in reaction barrier calculations.
L-VBSCF |
L-BOVB |
|
---|---|---|
\(E^{react}_{tot}\) |
-555.27775 |
-555.29156 |
\(E^{TS}_{tot}\) |
-555.21152 |
-555.24558 |
\(\Delta E^\neq\) |
41.6 |
28.8 |
2.3.7.3. VB wavefunction and weights
Table shows the weights of VB structures in the reactant and TS geometries. It is clear that the most important contribution comes from S1 in the reactant geometry and S3 in the TS geometry. In the TS, S4 represents the “covalent” structure of product and S3 represents the major “ionic” structure in both reactant and product. Thus, S3 represents the “bond breaking” of C-Cl and S4 shows the “bond forming” of N-C. Similar to the previous examples, L-BOVB provides larger weights for the secondary ionic structures as compared with L-VBSCF weights, which indicates that dynamic correlation plays a more important role for ionic structures than covalent ones, as already explained.
Reactant |
TS |
|||
---|---|---|---|---|
L-VBSCF |
L-BOVB |
L-VBSCF |
L-BOVB |
|
S1 |
0.663 |
0.621 |
0.091 |
0.178 |
S2 |
0.105 |
0.120 |
-0.001 |
0.002 |
S3 |
0.232 |
0.259 |
0.532 |
0.487 |
S4 |
0.000 |
0.000 |
0.364 |
0.286 |
S5 |
0.000 |
0.000 |
-0.004 |
0.010 |
S6 |
0.000 |
0.000 |
0.017 |
0.037 |
2.4. Potential Energy Surface of LiF (Optional)
2.4.1. Introduction
LiF is a simple hetero diatomic molecule with a single bond between atoms Li and F. The dissociation of LiF is always in the interest of chemists. The so-called “Harpoon effect” makes electron transfer when the distance between Li and F even larger than the sum of their van der Waals radius, indicating an electron transfer due to the crossing of diabatic states. For details, please refer to the reference.
In this optional exercise, the user should compute a series of points along the dissociation of LiF, get the energies of total wave function and each VB structure, and plot the potential energy surface. This exercise should be done by the users themselves. Only essential clues will be given. The basis set in this exercise is cc-pVDZ, and the active space is the minimal space.
2.4.2. Computations near equilibrium
The distance RLi-F is set to 1.5 Angstrom.
2.4.2.1. Computation with all VB structures
Note
There is only a single bond in the molecule, so the minimal active space should be (2,2).
VB structures can be automatically generated as we have seen in the example of F2.
Use keywords
ORBTYP=HAO
andFRGTYP=SAO
with proper definition of fragmenets in$FRAG
to build the orbitals.The active orbitals should always be placed at the last in
$ORB
section.
2.4.2.2. Computation with all possible covalent structures
Note
The covalent VB structures can be either picked from all VB structure computation, or generated automatically.
Orbitals obtained in previous computation can be used as initial guess.
2.4.2.3. Computation for all possible Li+F- ionic structures
Note
VB structures can be picked from all VB structure computation.
Initial guess can be obtained from the orbitals of previous computation.
2.4.2.4. Computation for all possible Li-F+ ionic structures
Note
VB structures can be picked from all VB structure computation.
Initial guess can be obtained from the orbitals of previous computation.
2.4.3. Computations for Other distances
Repeat the above computations at RLi-F= 1.1, 1.3, 1.7, 2.0, 2.6, 2.8, 3.0, 4.0, 7.0 Angstrom, get the energies and plot the potential energy surface. See at which distance the diabatic states cross. Following is the example of the potential energy surface.
3. Citation
You need to cite the references of XMVB as following formats:
A) J. Chem. Phys. format: The ab initio Valence Bond calculations are performed with the XMVB program.
B) American Chemical Society format: The ab initio Valence Bond calculations are performed with the XMVB program.