Theoretical Chemistry

Theoretical Chemistry

  • Ben Joseph Rubiato Cuyacot added an answer:
    How effective are the optimization (and sadpoint) searchs with solvent effects to give good results compared to the vacuum models?

    Hello there noble science people...

    i am doing equilibrium geometries and saddle point searchs in gaseous phases. but the experiments in which the mechanism were based, used polar solvent and the substances involved were charged particles (although closed shell species).

    does this mean i have to emulate these solvent effects for better elucidation and results ? or it'll just make calculation more expensive with little positive gain.

    if so,,, is the PCM compatible with geometry and sadsearch? or is there any other alternative approach?

    Thank you all. Live long and prosper. 

    Ben Joseph Rubiato Cuyacot

    Thanks Dr. Tamura

    may I ask why is CPCM not suitable for anhydrous alcohol solvent?.

  • Bruno Cramer added an answer:
    Any thoughts about the accuracy of Gaussian Composite methods (G1,G2,G3,G4) when applied to calculation of ionization potential of TM complexes?
    I'm thinking of using high level ab initio methods in calculating the ionization energy of first row transition metal complex. I am also concerned by the possible computational resources that would be required to carry out such calculation. Say, one have only an access to an HPC not a supercomputer. How realistic or practical would this be? And are there any free software package that is equipped with this method?
    Bruno Cramer

    I recommend that you read the article "A study of the rotational barriers for some organic compounds using the G3 and G3CEP theories"-J Mol Model (2014) 20:2199.Douglas Henrique Pereira et al.

    Maybe this approach meets your task  requiring less computational cost. With the method G3CEP they got 1.29 kcal.mol-1 deviation against 1.16 kcal.mol-1 deviation with the G3 method. The study contemplates enthalpy of formation, atomization
    energy, electron affinity, ionization potential, and proton affinity. Computational costs were reduced from 7% to 70% depending on the molecule's size. 

    Try the method out repeting the procedure with a couple of molecules so you get  some feeling about  it in order to proceed with the method or not. Good luck.


  • Yusuke Tamura added an answer:
    How can I run ADMP jobs at various temperature and how can I assign temperatures to the system?

    How to run ADMP job at various temperature and how to assign temperature to the system? thanks in advance

    Yusuke Tamura

    you're welcome.

  • Nikita Medvedev added an answer:
    What are the most efficient methods to study electronic transitions semiclassically?

    I am currently using surface hopping method to study electronic transitions involving 2 states. Please let me know what are the other techniques used to study such systems with more accuracy. 

    Nikita Medvedev

    Here is an overview you might find useful:

    And in this paper you can find an example on the quality of the surface hopping in comparison to more precise methods:

  • T. P M Goumans added an answer:
    Are there instances that theoretical search of a TST is impossible even if experiment suggests it exist (LFER) for some "very concerted" reactions?,

    I've been calculating and searching a TST structure of this "Sn2 concerted reaction" (as suggested by experiment through LFER) for months

    the experimental energy barrier  is about 21kcal/mol which rather small

    my first initial runs involves minimization (optimization) calculation showed that the nucleophile is really attacking the center  and the simultaneous detaching of the leaving group...from frame 1 to the end, IT SUGGESTS THAT SN2 reaction really happens... 

    but when I chose some frames in THE CRUCIAL POINTS (NSERCHS) of the attack and subject it to SADPOINT searches.. THe search goes to the product side as if the reaction is fast that the TST is very difficult to catch... 

    another thing is that frequencies of this frames that I examine contains very small imaginary values as if it is stable which is contradictory...

    Im using DFT and MP2 for these searches using appropriate basis sets for the system which were based on the previous studies)...

    Can anyone enlighten me with Localization of TST in concerted reactions with small energy barriers...  


    T. P M Goumans

  • Jerzy Hladyszowski added an answer:
    How can I implement the "order" command in gaussian 03?

    I can implement the "nosymm" command of this mode:

    #P pm3 opt=Z-Matrix nosymm

    but i can't implement the "order" command of this mode:

    #P pm3 opt=Z-Matrix order


    #P pm3 opt=Z-Matrix nosymm order

    I found the "order" command in this websites.

    My problem occurs because the gaussian execute one reordering in the atoms of the input z matrix and the scan of energy don't works.

    someone help me?

    Jerzy Hladyszowski

    Hi, You may use Opt(redundant,addredundant) ; please read the manual how to specify scan variables in redundant coordinates,  I wish you success, Jerzy

  • Harry ten Brink added an answer:
    Why is n-pi* transition band of equal intensity to that of pi-pi* transition band in absorption spectra for naphthalimide derivatives?

    Even though n-pi* transition is a forbidden transition why does its intensity (OD) comparable to the pi-pi* transition for naphthalimide derivatives? I am getting the the above observation along with red shift for the latter and blue shift for the former transitions. I want to know the reason behind such an observation.

    Is the comparable intensity (O.D.) related to any solvent effect or something else and why?

    Harry ten Brink

    First question / remark:

    Which derivatives and what are the spectra you mention. There is a very large literature on naphtalamide derivates: did you search that for your answer?

  • Thorsten Stolper added an answer:
    How can I obtain the analytic derivative of B matrix?

    As we know that elements in B matrix are the dq/dx, in which q is the internal coordinates, and x is the cartesian coordinates. Does anyone know where we can get the analytic first derivative of B matrix? 

    Thorsten Stolper

    You should take everything into account of the above mentioned points. As an additional note, I liked the attached reference which lists the first and second derivatives of primitive stretches, bends and torsions.

    However, there are some small mistakes in some derivatives, as far as I remember so you should check them yourself.

    • Source
      [Show abstract] [Hide abstract]
      ABSTRACT: The optimization of ab initio molecular geometries is discussed. Based on comparisons of 30 minimizations and 15 saddle-point optimizations, the most efficient combination of coordinate system, approximate and exact Hessians, and step control is determined. Use of a proposed set of extra-redundant internal coordinates is shown to reduce the number of geometry steps significantly relative to the use of redundant coordinates. Various update schemes are tested for minimum and saddle-point optimizations, including combination formulas. The complete expressions for the first and second derivatives of the Wilson B matrix are presented, thereby avoiding the need to calculate this by finite-difference methods. The presented scheme appears to be the most efficient, robust and generally applicable scheme to date. © 2002 American Institute of Physics.
      The Journal of Chemical Physics 11/2002; 117(20). DOI:10.1063/1.1515483
  • Manuel Hochheim added an answer:
    Is there a cost efficient way to calculate ground- and excited-state vibrational frequencies of adsorbed molecules?

    Dear colleagues,

    I'm trying to calculate the ground- and excited-state vibrational frequencies of a molecule (PTCDA) adsorbed on NaCl and KCl surfaces. For larger and stepped surfaces the usage of TD-DFT with a range separated hybrid (CAM-B3LYP) is already too time demanding. Because of this I'm looking for a cost efficient method. I already tried different semi empirical methods implemented in the MOPAC package. A non-periodic cluster approach was used. Unfortunately, I was not able to converge the scf of the excited state calculation properly.

    I hope you can help me by proposing suitable methods.

    Manuel Hochheim

    Dear Oleg,

    sorry that it took so long to respond. Thank you for your suggestions.

    1) As far as I know there are no range separated hybrids in TURBOMOLE and no analytic derivatives for range separated hybrids in ORCA.

    Now I'm trying GAMESS and it looks quite promising.

    2) I'm using the Energy-consistent Pseudopotentials of the Stuttgart/Cologne Group + the related valence functions.

    3) I agree. There are other range-separated hybrids. I'm just trying to use CAM-B3LYP because it has shown to be very suitable for my purposes and to be as consistent as possible.

  • Gangotri Dey added an answer:
    How can I find the IR data at high temperature?

    Hello all!

    I am interested to know how can I compute the IR freq at room temperature. I have already computed the data with DFPT using the phonon calculations. I assume it is for 0K calculations. 

    Thanks for the help in advance.

    Gangotri Dey

     Alexander P. Litvinchuk. Many thanks for your kind reply. It is certainly very helpful. 

  • Choutipalli Venkata Surya Kumar added an answer:
    How can I construct a concerted transition state?

    For any reaction say for 1,3 dipolar cycloaddition reaction, if i construct a TS, how can i computationally prove that TS is concerted???

    Choutipalli Venkata Surya Kumar

    Thank you all for valuable suggestions...i got it now....

  • Ibrahim Khan added an answer:
    Are there any programs to automatically sort frequencies from a Gaussian output file to a table in Excel?

    Gaussian output files from frequency calcualtion are very messy and cannot easily be copy and pasted into a table because there are a lot of useless characters between the frequencies. Does anyone know of a computer program to easily sort data from Gaussian output files to tables in Excel? 

    Ibrahim Khan

    Gausssum program is straight forward simple program for this purpose...If you have any difficulty in using, inbox me....

  • Fortunatus Jacob added an answer:
    Computational Chemistry on Organic Molecules
    I'm interesterd in quantum chemistry,
    Fortunatus Jacob

    Great, have GAMESS US software at your hands

  • Diego Cortés-Arriagada added an answer:
    How can I plot the reaction force and reaction force constant?

    Can someone provide me with the steps to follow in other to obtained the reaction force and reaction force constant plot following an IRC calculation?

    Diego Cortés-Arriagada

    The reaction force is obtained as the negative derivative of the total energy (E) with respect to the reaction coordinate (several papers describe the method). You need the energy and the reaction coordinate values in the R-->TS-->P direction, which are obtained, for instance, at final of the .log file.

    The gradient can be obtained from a exel work by resolving a simple equation in the form of: Reaction_force=-(E{n+1}-E{n})/(RC{n+1}-RC{n}), where E{n} is the energy in the n step, and RC{n} is the reaction coordinate at the step n. Moreover, the reaction works are obtained as the energy diference between the critical points in the reaction force profile.

  • Renjith Raveendran Pillai added an answer:
    How do electron affinity and ionization potential values from DFT differ from HF calculations if one uses Koopmann theorem?

    I calculated electron affinity and ionization potential for a compound using Koopmann theorem.One of my friends told me that Koopmann theorem is valid only for HF calculations.But the values EA and IP,  that i got from DFT and HF calculations are almost same. deviation is about 0.2 eV. Can anyone say why I got almost same values from the DFT and HF, eventhough Koopmann theorem is valid only for HF?

    Renjith Raveendran Pillai

    Hi Lokesh,

    My molecule is not a simple one. It contains 56 atoms.

  • Amber Jain added an answer:
    How can I get the average populations of excited states from Molecular Dynamics simulations (ES-NAMD)?

    I'm new to excited state non-adiabatic molecular dynamics. I'm wondering if there're techniques to get average population of different excited states from hundreds of trajectories. If there are some references, give me some advice. Thanks a lot.

    Amber Jain

    For most purposes average over populations should suffice. That being said, the other approach sometimes people use is the average over quantum amplitudes squared.

    In a recent paper, an attempt was made to combine these two methods - Landry, Falk, Subotnik JCP 139, 211101 (2013).

  • Alexander V. Belyakov added an answer:
    How do I calculate NICS ISO, NICS(0), NICS(0)zz, NICS(0)π, and NICS(0)πzz for a planar molecule, such as Benzene, using Gaussian 09?

    Right now I am trying to figure out how to calculate NICS values for benzene and other benzene-like molecules such as borazine. Specifically, I would like to know how to interpret the output/log file of the NMR for benzene and other molecules. Here is what I have done so far...

    1. I have run the NMR calculation for benzene and various benzene analogs (e.g., azaborines). In all of these molecules, I have employed a ghost atom (Bq) in the center of the planar ring (for NICS0), as well as an atom 1 Angstrom perpendicularly above the ring center (for NICS1). 

    2. I have referred to the literature, but I can't seem to find any information on how to interpret the NMR log files to find these NICS values. Some of my values for benzene match up to those reported in other papers but I'm not completely confident if I'm even looking at the right numbers or adding the correct numbers up. I'm particularly having trouble with finding/calculating NICS(0)πzz.

    Any help would be very much appreciated. In case anyone would like to know, I'm using Gaussia 09 and the following computational parameters for my jobs: DFT, b3lyp, 6-311+G(d,p).


    Alexander V. Belyakov

    To calculate NICS ISO, NICS(0), NICS(0)zz, NICS(0)π, and NICS(0)πzz for a planar molecule, such as Benzene, using Gaussian see:

    Which NICS Aromaticity Index for Planar π Rings Is Best? / H. Fallah-Bagher-Shaidaei, C. S. Wannere, C. Corminboeuf, R. Puchta, P. v. R. Schleyer // Organic Letters. - 2006. - Vol. 8, N 5. - P. 863-866.

    and Manual for evaluating dissected NICS in Supporting Information

  • Kiana kh added an answer:
    How can one use gaussian to deduce PET process occuring in any molecule?

    Also is there any difference in electron transfer and charge transfer mechanism

    Kiana kh

    No, there is no difference between these two mechanisms

    Charge transfer and electron exchange are two difference mechanism

  • Hamidreza Simchi added an answer:
    How do I account for the energy difference between two spin states?


    I have calculated energies of two spin states of a compound by DFT with unrestricted spin. They gave two different energies after optimization. Can any one suggest what are the ways to account the energy difference between the two spin states?

    Hamidreza Simchi


    Any cluster has two important parameters: charge and spin. Spin degree of freedom, S,  is shown in multiplicity, 2S+1. For finding the optimized structure, you should change multiplicity when charge is fixed and find the cohesive energy of each state. The spin configuration of the lowest cohesive energy is the ground state of your system. Of course based on the Hond's rule  if e.g., S=1, you have two spin up 1/2 electrons in your system and if e.g., S=2, you have four spin up 1/2 electrons in your system.

    Best Regards

  • Saeid Farsadpour added an answer:
    How can I obtain B in calculations of frequency-dependent hyperpolarizability from its tensors?

    I am using cam-b3lyp/6-31g(d) POLAR cphf=rdfreq in gaussian 09 to
    calculate the frequency-dependent hyperpolarizability. Finally I got 18 beta tensor elements.
    Do you know exactly what these 18 tensors are?
    and how i can obtain B(-2w,w,w) from these 18 tensor?
    thank you very much

  • S. Manivarman added an answer:
    Regarding Computational Chemistry Software
    Has anybody interfaced Gaussian09 with GROMACs software for carrying out the QM/MM calculations?
    S. Manivarman


  • G. Santosh added an answer:
    What is the origin of Soret and Q bands in porphyrin spectra?

    In the absorption spectrum of porphyrins, the intense soret band is attributed to the S0 to S2 transition whereas the q bands are attributed to the S0 to S1 transition. It is clearly understandable why there is one Soret band but not so intuitive to understand why there are 4 Q bands. Very often the Gouterman's four orbital model is invoked to explain the number of bands, but can anyone explain this four orbital model in very simple terms, without dragging into the complex jargons of computational/theoretical chemistry? 

    From what do these additional HOMO LUMO states arise that we end up having 4 Q bands and not just one? 

    Anyone please!

    G. Santosh

    Thanks Debangsu, for your replies. Will get back for more querries :)

  • Saba Niaz added an answer:
    How can I calculate the polarizability of a carbon atom?

    one work shows random phase approximation based theory by Benedict et al. PRB, 1998

    Saba Niaz

    if u r using gaussian software read the optimised carbon atoms output file u will find polarisablity of carbon .

    1.  if u r unable to find do let me know i will send u the polarisablity of carbon.

    2. plus r u talking about a single carbon atom or a molecule that comprises of carbon .send me its molecular formula and let me know that what basis set and functional  u r using . 

    i hope ur querie is answered.

  • Paul G. Ellis added an answer:
    Why the wave function is needed to be orthonormal in quantum chemistry and what is that mean?

    for obtaining the solution of schrodinger equation and utilizing it in MO calculations its always needed that the integral of the eignfunction of electron to be equal to 1 that mean that the probability of finding the electron is equal 1 (i.e 100% prediction ) otherwise it would not be the eignfunction ? 

    Paul G. Ellis


    As Wikipedia says (1st link below):

    "A molecular orbital describes the behavior of one electron in the electric field generated by the nuclei and some average distribution of the other electrons. In the case of two electrons occupying the same orbital, the Pauli principle demands that they have opposite spin. Necessarily this is an approximation, and highly accurate descriptions of the molecular electronic wave function do not have orbitals (see configuration interaction)." {NB: This also clarifies, a little more, the answer I gave previously.)

    Putting it simply (and I hope correctly): the electrons interact, in a theoretical chemistry calculation, as such calculations are usually based on an approximation to the Schrodinger equation, which includes a potential energy term V (for e-e and e-nuc etc interactions) in the hamiltonian H. As you probably know already, finding the best LCAO representation of (approximate) MO wavefunctions via the energy-minimisation approach leads to terms of the type <ψ|H|ψ> and <ψ|ψ>, which get expanded in terms of the AOs, with the latter yielding the overlap matrix about which you've enquired.

    As for the meaning of the overlap matrix, you might find the 2nd link, below, to be as good an explanation as you'll get.

    I have to sign off from this whole conversation now. However, from the more recent questions you've been asking, it seems to me that you'll learn more from searching the web and textbooks yourself (almost all the answers are out there if you're prepared to work at it). Only raise questions here when you're really stuck.

    Best of luck - Paul

    + 1 more attachment

  • Matúš Dubecký added an answer:
    Can I do simulations on GAMESS using different basis sets for different atoms in a large system?

    Can I do simulations on GAMESS using different basis sets for different atoms in a large system?

    thus indicating a computational run which basis set is use for an specific atom?

    If so, is this specified in the manual? a tip or something... 

  • Dzmitryi V. Ushakou added an answer:
    How I can find the matrix of binding energies between pairs of atoms in my molecule in Gaussian 09?

    Hello everyone.
    Maybe anyone could help me with one problem in Gaussian 09. How I can find matrix of binding energy between pairs of atoms in my molecule? I had found distance matrix in log-file, but I cannot find binding energy for all pairs of atoms.

    Dzmitryi V. Ushakou

    Thank you for the answers

  • Swapnali Dhanayat added an answer:
    What are the Bohr radii of Al2O3 and NiAl2O4?

    I hv prepared Al2O3 and NiAl2O4 nanopartical having partical size 2.5 nm so I wish to know the quantum confinement region of both material ,can anyone tell me plz what is Bohr radius of Al2O3 and NiAl2O4????

    Swapnali Dhanayat

    Thank you Alexander


    as per my knowledge  each material having bohr radius so i wanted to know the bohr radii of Al2O3 and NiAl2O4 or after which size we say its a quantum dot or its in quantum confinement region

  • Oleg Gromov added an answer:
    How can I calculate charge transfer spectra?

    I need to calculate some UV-vis spectra, where most interesting transitions are due to intermolecular charge transfer. Size of a problem might scale up to hundred of second and third row elements atoms, hence CCSD(T), which is as I know the best way, isn't applicable,  DFT is preferable, but I understand its drawbacks.Currently thinking about CAM-B3LYP, for example, but have some doubts. Will be grateful for any good benchmark references.

    Oleg Gromov

    Thank you very much, Dr. Dubecky, I noticed similar thing. I compared CASSCF/NEVPT2 with B3LYP and CAM-B3LYP for simplified version of my system and found, that results are in the same order as in reference you given. B3LYP with lowest, CAM-B3LYP with highest energies.

  • Joaquim Mª Rius Bartra added an answer:
    Any thoughts about structural studies and TST searchs involving sulfur?

    I've been trying to solve this problem for weeks now...

    this problem involves an SN2 reaction with sulfur as the centerpiece (a sulfonyl)... 

    the delima is that in all my TST searchs, it suggest  the proposed TST has no imaginary frequency  and the sulfur appears to  have accepted the additional bonds and just rearranging... making the SN2 impossible... this is contrary to the experiment that says substitution is possible on sulfur...

    what are the appropriate basis functions to be used for this type of problem? a help would mean a lot... 


    Joaquim Mª Rius Bartra

    Hello Ben,

    First think of see is the method. With HF it is difficult to see something. In the calculus use a dft, b3lyp or better B3PW91 (only changing the name in input DFTTYP=B3PW91 ). Try it if it works and you can locate the TS.

    Also could help me if you add the commands of input, because for TS search, some configurations are needed. Example Nvib, etc..

About Theoretical Chemistry

The use of mathematical and computational methods to build theories explaining observations of chemical reactions, such as quantum chemistry.

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