Theoretical Chemistry

Theoretical Chemistry

  • Sadeem Fadhil added an answer:
    Why the adiabatic Born–Oppenheimer approximation (BOA) is broken down in graphene?

    I want to know is the broken down of BOA in graphene has been solved or not yet,

    See the link

    what are the other cases where the BOA is also broken down in them and Why

    Sadeem Fadhil

    Yes dear Eugene you got my point.

    Thank you

  • Renjith Bhaskaran added an answer:
    How do I use QST2 in Gaussian to find Transition State?

    I'm trying to re-create the results from (Theoretical Chemistry Accounts 125(3): 269-278) where the authors determined the transition state and activation energies for DNA-nucleobase alkylation by sulfur mustard/ mustard gas.

    When I try and run these calculations, I get a termination error (/export/software/GaussianNew//g09/l101.exe). I was wondering if anyone could offer insight or try and recreate the results from this paper and maybe give a walk through of how this is done. Admittedly, I am not a computational chemist - I try and stick to synthesis but am working on an independent proposal for my PhD program and wanted to learn more about this field.

    Thanks in advance for your help!


    Eric Z

    Renjith Bhaskaran

    Dear Eric,

    for your query on " the activation barrier is about 10 kcal/mol off from the result obtained using the Gaussian 98 package. Between packages, is it normal for energies to differ by this value?"

    An energy difference of ~0.5 eV between packages seems to be unusual. My suggestion is to verify the TS geometry and the imaginary frequency that you got with the published data, if available. If you find this is within the error limit, then you should further confirm it by performing an IRC calculation. If IRC ended in the reactant and product direction, then (in this case) you can confirm TS is actually a first order saddle point.

    regards, renjith

  • Joaquim Mª Rius Bartra added an answer:
    For geometry optimization of larger molecules, avagadro software is not supporting; why?

    in theoretical chemistry for geometry optimization of larger molecules avagadro software is not supporting why?

    Joaquim Mª Rius Bartra

    Dear Amshumali,

    With this information I suppose three different situations:

    1) Avogadro is a specific "visualising program" with the "extra tool" of the perform a optimization with a force field. The results obtained with this method are not too much reliable in a study but it is very useful to build a very complex structures (i.e with gaussview is much more complex draw some type of compounds). This tool has a consumption of RAM and CPU and a possibility of error is that the system do not has enough resources if the molecule is too much large.

    2)If using the program only to build inputs, then maybe you has a problem reading the outputs or preparing the inputs. If you use this software in this way, please report it with more technical details.

    3) Also, some kind of system, such crystals, can give error depending where you read the file or if the crystal structures is not properly introduced. For example, a common "bug" happens when you try to add cells to your crystal. This happens because some crystal file only has a portion of the unit cell that Avogadro interpret.

    In general, if Avogadro gives you a problem, you could change to other program such Molden or MacMolPLT (which this last one is particular very useful to prepare inputs to gamess software).

    I hope it helps you,

    Joaquim Rius

  • Ali Nasir Imtani 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 ? 

    Ali Nasir Imtani

    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 ?

    answer: if not equal to 1 we must normalize the wave function by multiplying the function by constant and then we must find this constant> the constant call normalization constant.

  • Bartosz Trzaskowski added an answer:
    What to do with G09 when displacement is high whereas force is low and predicted change in energy low?

    Dear All,

    I optimize a structure with M06 / 6-311+g(d,p).

    After a lot of optimisation step , the predicted energy is low -1.7 D-07 and forces very low.

    However the calculation do not converge as the displacement stay very strong.

    Have you got any suggestion to finish the optimisation?

    All default with keyword   #p opt=(calcall,verytight)

    Here the conclusion of a step:

                      Item               Value             Threshold       Converged?
    Maximum   Force            0.000006        0.000002        NO
    RMS          Force             0.000000        0.000001       YES
    Maximum  Displacement 0.106470        0.000006        NO
    RMS          Displacement 0.016269        0.000004        NO
    Predicted change in Energy=-1.767915D-07

    I know the threshold is low but it is not changes the fact that displacement value is very hight!

    Else with the loose keyword and B3LYP I have the same problem.

    Thanks for your suggestions.

    Bartosz Trzaskowski

    As suggested above, you're most likely stuck in a geometry that is not the minimum you're looking for and gaussian optimized can't move in any reasonable direction. Modify the geometry slightly and try reoptimizing - if it doesn't help modufy the geometry more and try reoptimizing.

    SCF(qc) or SCF(xqc) also helps in some cases. Other ideas: you can try also opt=z-matrix or opt=cartesian - these have usually completely different convergence process that the redundant coordinates (it doesn't matter how our input geometry is specified - this is a completely different problem). 

    Finally, make sure you;re using Int=Ultrafine (for any DFT), adding opt=tight is also usually a good idea. 

    If none of these (try different combinations of the keywords above) help, change the DFT functional to a similar one.

  • Ali Ahmadi Peyghan added an answer:
    How do we know formation energy is reasonable for any system or reaction ?

    What is indicating negative (-ve) and positive (+ve) formation energy. I have calculated formation energy of La(1-x)EuxVO4 from DFT by using formula total energy of product-total energy of reactant

    Formation energy = La15EuV16O64-15(La)-Eu-16(V)-32O2

    I got formation energy = -307.01 eV. I want to know this is reasonable formation energy for this reaction.

    Ali Ahmadi Peyghan


    1) In eq. 1, (- ∆Hr) is atomization energy (enthalpy)

    2) Entropy terms are available in the output of the freq analysis (see the attachment)

  • Rafik Karaman added an answer:
    Can I do an ellipsoid fitting on my molecule with Ballview?

    I want to calculate the diameter of a molecule. Can I do an ellipsoid fitting with Ballview. Or is there any other user friendly software that can do this job? Or also measuring distances etc?

    Rafik Karaman

    Dear Maria,

    The best approach to get the three dimensions of a molecule is to draw it in ArgusLab program (free download), minimize it with molecular mechanics, then with semi-empirical method such as AM1. Once done, you can view it using the same program (ArgusLab) and there is a key for giving you the three dimensions of the molecule (x, y and z). Using the same program you can click any two atomes connected or not connected to get the interatomic distance between them.

    Another program called MOLDEN (free download); you can view your optimized structure from Gaussian or ArgusLab in MOLDEN then you click in any two atoms to get the interatomic distance.

    It does not matter if the atoms are shown as, balls, sticks or ellipsoid, always you get the same value.

    Hoping this will be helpful,


  • Manohar Sehgal added an answer:
    Is it necessary for electrons to hop from lower oxidation states to higher oxidation states in double exchange mechanism?

    In Mn-O-Mn system, electron hop from Mn3+ to Mn4+ via O 2p orbitals.

    I want to know, vice versa is possible or not i.e. from Mn4+ to Mn3+.

    Manohar Sehgal

    I try to explain in my own humble way:applying as less  mathematics  as is possible.

    [1]The term 'hopping' deals with a lattice model, where the direct space contains a set of  points where the movement of an electron over the lattice points can be “seen” as a number of 'jumps' called 'hops'.

    [2] In a specific case of super exchange, there lies O^-2 between the two metal ions which differ in their charges.

    [3] We want to transmit[or transfer or shift- your choice to  speak this word  in a simple way] an electron  from one metal ion to the other which has to happen through O^-2.

    [4] Whatever way you may think, but the basic concept one has to remembered is that:

     “ For an electron to hop from an atomic orbital to an atomic orbital of the neighbouring atom, the two orbitals should  overlap to a very large extent.”

    [5] After having discussed this basic point  , we first tryMn^4 to Mn^3.And then  possibility for Mn^3 to Mn^4 and then the DE mechanism-  in fact all need to discuss together.

      In the basic process of the mechanism of hopong is that  in Mn^4(t2g^3; vacant eg set ( dx2-y2& dz^2),  a “d” hole from Mn^4 overlaps with with filled “p” orbitals of O^-2 because   the vacant  dz^2   of Mn^4 and filled “p” orbitals are  analogous ( pls. note I have not used the word same) and would overlap-meanng that there should be  hopping and Mn^4 and Mn^3 ion change takes places

       Mn^3O^-2Mn^4 {I}  ----------- Mn^4O^-2Mn^3{II} .

    [6] Now  think of Mn^3[ t2g3. eg^1] which still possesses vacant dz^2. Thus it would involve the transfer of an electron from the Mn^3 to the central oxide ion  and simultaneously the transfer of an electron from the oxide ion  to the Mn^4 site. 

    [7] Since, every discussion looks incomplete without involving rigorous mathematics, I,  very humbly, try  to simply and would restrict only to :

     Hopping integral “t”  which is=  - 1/2 of the expectation value of the Hamiltonian wrt two specific configurations of atomic orbitals of  two neighbouring ions.

    [8]When t = 0, the  orbitals of the neighboring ions do not overlap. And thus no hopping.

  • Yusuke Tamura 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. 

    Yusuke Tamura

    If you are using GAMESS current version of Dec 5, 2014, SMD is available in it. Refer the documents, INPUT.DOC (section2. Input Description) and REFS.DOC (section 4. Further Information on GAMESS document page).

    I'm not sure whether GAMESS works as same as G09. I'm afraid you have done TS search with PCM in only one shot. The example 'Fluorescence example' given in the page '' shows a multistep procedure.
    Let M(GS) and C(GS) be the energy of solute and the cavity energy, respectively. Geometry optimization for searching M(TS) starts, but C(GS) keeps unchanged. Then optimization of C(TS) is needed until SCF is achieved for both M(TS) and C(TS).?

  • 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 :)

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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