Theoretical Chemistry

Theoretical Chemistry

  • 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 · Energy Research Centre of the Netherlands

    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 · Georg-August-Universität Göttingen

    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.

  • 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 · University of Bonn

    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 · George Washington University

     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 · Central Leather Research Institute

    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 · King Fahd University of Petroleum and Minerals

    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 · The Nelson Mandela African Institute of Science and Technology

    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 · Pontifical Catholic University of Chile

    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 · TKM College of Arts and Science, University of Kerala, Trivandrum, India

    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 · University of Pennsylvania

    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 · Saint-Petersburg State Institute of Technology

    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 · Kharazmi University

    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 · Iran University of Science and Technology


    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 · Government Arts College, C-Mutlur, Chidambaram


  • 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 · Goa University

    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 · University of Kashmir

    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 · London Business School


    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

  • 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 · Akademia Pomorska w Slupsku

    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 · Dr. Babasaheb Ambedkar Marathwada University

    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 · Lomonosov Moscow State University

    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 · Autonomous University of Barcelona

    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..

  • Yaopeng Li added an answer:
    Why is Gibbs free energy lower than its lower heating value for CO or H2?

    Fuel exergy estimates the inherent chemical energy in the fuel that is actually available to do work.

    LHV is the actually released energy of fuel measured in the experiment during combustion.

    For most fuels, the exergy is always larger than the LHV. However, for CO or H2, it is on the contrary. So why the practical value of released energy can be larger than the theoretical value? Is it related to the combustion process?

    Thanks for your attention, and your explanation.

    Yaopeng Li · Dalian University of Technology

    Thank you for all your kind help.  I suppose that the reason is associated with the reduced molecule from reactants to productions for H2 or CO reaction process. However,  increased molecule during reaction is obtained for the other fuels, which leads to the increase of entropy.

  • Patrick K Tamukong asked a question:
    How can I restore translational symmetry in DFT-in-DFT (or WFT-in-DFT) embedding theory?

    Partitioning a large molecule for easy computation through DFT-in-DFT (or WFT-in-DFT) embedding theory poses no issues with translational symmetry since one is in the molecular frame. However, for extended systems such as molecular wires, translational symmetry breaking becomes an issue not to be ignored in embedding. Does anyone working on this subject know how to address the problem of restoring translational symmetry in a partitioned system?

  • Elder Mota added an answer:
    How can I use the command "Add=N" in a "TD" calculation in Gaussian 09W?

    I am doing a theoretical study about graphene and I have to run a "td" caulculus in Gaussian 09W, but my molecular structure is big, and my computer is not very good. So I found this command in Gaussian's manual, but I am not getting to use it. I ran the cauculus to 25 states, and I am  trying to add more 20 states. I read that I can use the command "Add=N" and "Read", and to use the ".chk" file of the first 25 states, but I don't know how to write the input file.

    Elder Mota · Federal University of Pará

    Thank you Bartosz TrzasKowsky for help me!

  • Kenno Vanommeslaeghe added an answer:
    Why Urey-Bradley term largely abandoned in modern force fields?

    Why Urey-Bradley term largely abandoned in modern force fields?

    Kenno Vanommeslaeghe · University of Maryland, Baltimore

    Sorry for resurrecting a long-dead thread - just wanted to add my 2 cents. As pointed out before, the computational cost is not a significant consideration in favor or against UB terms. With that out of the way, the only *advantage* of UB terms is the better reproduction of subtleties in the vibrational spectrum, as explained in Maxim Tafipolski's post. *However*, this advantage is not as big as it seems, as the phenomena a UB term is expected to capture are largely inconsequential for the overall conformational sampling in a typical biomolecular/organic simulation. Conversely, the disadvantages are:
    (1) Encumbering the force field parametrization process and making it more underdetermined (as mentioned before).
    (2) Poorly transferable! (Because the 1-3 distance can be very different for the same central atom (2) in the same hybridization state.)

    For a general force field for organic molecules, disadvantage (2) trumps all other considerations; therefore, we have a standing order not to introduce any new UB terms in the CHARMM General Force Field (CGenFF). It does contain a good number of existing UB terms that were transfered from biomolecular model compounds and would be prohibitively laborious to re-optimize, but I consider them a liability. To be clear, the impact of a poorly transfered UB term is expected to be modest compared to a badly guessed charge or dihedral, but I still would be happier without them.

    Of course, in a highly specialized force field for biomacromolecules, disadvantage (2) is much less of an issue, though there's still disadvantage (1), and the fact that the advantage is modest...

  • Bojidarka B. Ivanova added an answer:
    How do I evaluate the magnitude of error of energies calc. by Gaussian?

    I have a hard time finding comprehensive reviews discussing and compare the error of reaction gibbs energy, activation energy, etc, for different methods/basis, especially for organic or organometallic compounds. Only pieces of it lying here and there.

    For example, if I calculate a Diels-Alder reaction catalyzed by Jogenson-Hayashi catalyst using simple, small substrate. How accurate is the energy difference between substrate and product, as well as the intermediates / transition states. Will it be like 1 kcal/mol, 5 kcal/mol, 20 kcal/mol or something for like B3LYP/6-31++G(d,p)?

    I seen someone claim the origin of a 3.5:1 selectivity (calc. 0.74 kcal/mol) is the energy difference of two different TS, using M06/6-31++G(d,p) methods. Can it be that accurate?

    Bojidarka B. Ivanova · Technische Universität Dortmund

    Mr. Li,

    Please find as attachment the accuracy towards thermodynamics prediction of some of the methods and the references

  • Arumugam Dhandapani added an answer:
    How can I scale down the unscaled frequencies using proper scale factor?

    I am using single scale factor to scale down the whole frequencies of the molecule depend on their basis set. It is good one or there is any list of scale factor applicable for particular frequency ranges. Please send me the proper scale factors for the pople basis sets.

    Arumugam Dhandapani · Government Arts College, Chidambaram.

    Dear sir,

       I am using Gaussian 03 for my quantum calculations and my clarification is whether one scale factor is enough for entire frequency or more than one scale factor is good to scale down. Especially this scale factor is better for C-H and this One is better for some other vibrations like this..........

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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