Theoretical Chemistry

Theoretical Chemistry

  • 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

  • Billy Wayne Mccann added an answer:
    How do I account for the energy difference between two spin states?

    Hi,

    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?

    Billy Wayne Mccann · Oak Ridge National Laboratory

    I concur with the answers given by Gerald and Debangu: DFT may not be the most reliable tool to *accutately* calculate the electronic energy differences between spin states. There's also the problem of 'spin contamination' when dealing with open-shell calculations.

    However, your question, in general, without regarding the issues of DFT, stems from the Hamiltonian operator and the anti-symmetric nature of the wavefunction tself. The Hamiltonian, as you know, comprises kinetic and potential energy terms. For now, we will neglect the kinetic term, and speak only in terms of the potential energy operator.

    Recall that the potential energy operator is composed of a classic electrostatic operator, usually denoted 'J', and a non-classical exchange operator, usually denoted 'K'. Also recall that the exchange energy is a stabilizing factor.

    Being fermions, electrons of the opposite spin can occupy the same spatial molecular orbital, but electrons of the same spin cannot. For ground state molecular hydrogen, the two electrons occupy the same molecular orbital, but different spin orbitals. But for the triplet state, i.e. an exited state (for molecular hydrogen, at least), the electrons cannot be in the same spatial orbital because they have the same spin.

    If one expresses the wavefunctions for singlet molecular hydrogen as a Slater determinant, one will find that, upon expansion of the integrals for solving the Schrodinger  equation, those integrals involved with the exchange integral are ZERO , due to the presence of a spin orthogonality which cancels those terms.  But in the case of the triplet, there is no spin orthogonality because the electrons have the same spin. 

    Now, the exchange term is a stabilizing term, that is, it reduces the overall energy of the wavefunction. Because there is no exchange stabilization for singlets, the triplet state may sometimes be LOWER in energy than the singlet state. This is especially seen in triplets whose valence orbitals are degenerate. Also, now that the electrons are in different molecular orbitals, their distance from one another is larger, leading to less electrostatic repulsion. See the 'triplet stabilization' phenomenon.

    However, one must consider that the kinetic energy term may also change energy due to the change in "shape" of the molecular orbital in which the electron is now located. For an electronic excited state, the energy is larger because, well, it takes energy to promote that electron.

    Hope that this answer is clear and that it answers your question.

  • 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

    I HAVE GAUSSIONS03 WITH CARRY OUT QM/MM CALCULATION

  • 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 :)

  • Tian Shi asked a question:
    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.

  • 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 ..is 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

    Moustafa,

    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 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.
    Thanks.

    Dzmitryi 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

    yes. 

    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... 

    thanks... 

    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..........

  • Mihai Surducan 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? 

    Mihai Surducan · Babeş-Bolyai University

    You can also try Chemcraft. It is pretty straightforward to use and the trial version is valid for 150 days.

    www.chemcraftprog.com

  • Emadeldin M Kamel added an answer:
    How can I optimize large transition states in which OH is moving from one molecule to another?

    I'm using Gaussian 09 and I'm trying to get a transition state in which the OH is transferring from cytochrome to a substrate, some of my calculations are normally terminated but I got a small imaginary frequency not related to the desired move of OH, while the remaining don't. 

    Emadeldin M Kamel · Beni Suef University

    At last , I got by changing the geometries of the reactants to a better position

  • Arumugam Dhandapani added an answer:
    Why does the second lone pair of electrons in an oxygen atom always show higher perturbation energy in NBO analysis?

    Why the second lone pair of LP2(O) oxygen atom always show higher perturbation energy than first lone pair of LP1(O) oxygen atom in NBO analysis. Dear experts please clarify this.........

    Arumugam Dhandapani · Government Arts College, Chidambaram.

    Dear sir,

       Absolutely my compound S and p% also shows the same. And thanks for your answer sir.......

  • Arumugam Dhandapani added an answer:
    How these transitions are possible π*-σ*, π*-π* and σ*-σ*?

    I get these transitions from my NBO analysis and how these transitions are possible. In some publications itself these transitions are listed and i am very much confused. In UV only four transitions are possible and how these type of transitions shown by NBO analysis. Please help me to clear about this.......

    Arumugam Dhandapani · Government Arts College, Chidambaram.

    Thanks a Lot Madam.....

  • Prashant Uday Manohar added an answer:
    How do the correlation interactions change with distance in moller plesset perturbation calculation?

    I am running one system containing two gold atoms in vacuum using mp2, mp3 method with changing the distance between two gold atoms. I tried many different basis set ( lanl2dz, lanl2mb, aug-cc-pvdz-pp, aug-cc-pvtz-pp, aug-cc-pvqz-pp). I got the lowest energy at 2.6 angstrom. After that upto 5.75-6.0 angstrom distance the energy is raising. Upto here it looks like a normal van der Waals energy plot. But after crossing 6 angstrom, again the total energy of the system is decreasing. But it should not be decreased. In case 15 angstrom distance separation b/w gold atoms, the energy is even lower than 2.6 angstrom distance b/w those atoms. According to the normal vdw energy plot, the energy graph should be flat after a certain distance. I can not understand what is the source of the problem here. I didn't observe this kind of problem in Hartree-Fock calculation.

    Prashant Uday Manohar · Birla Institute of Technology and Science Pilani

    Use multi-reference methods such as MRCC, MRCI or MRPT to get correct qualitative description during bond-breaking. You may try EOM-SF-CC as well. If you are not keen about quantitative accuracy, then SF-DFT or TD-DFT with suitable exchange-correlation functional (taking care of long-range interactions properly) may work in some cases.

  • Iresh Gallindawatte added an answer:
    How do I determine KPoint values for a molecule for DFTB+ calculations?

    I need to know how to determine KPointAndWeight to fill out the input .hsd file.Anybody know about this? your consideration is highly appreciated.

    Iresh Gallindawatte · PGIS,University of Peradeniya

    Eugene F Kislyakov, Sorry sir I can not  follow your statement since I am a novice who is using DFTB+ for the first time.I request to have it in little more descriptive .

  • Shobeir K. S. Mazinani added an answer:
    How can I calculate the individual atomic polarzabilities in a molecule using molpro/gaussian?

    I have a molecule containing two atoms I want to calculate polarizability tensor for each atom in the molecule @ ccsd(T).

    Shobeir K. S. Mazinani · Arizona State University

    It's all about partitioning of the molecular polarizability. In my paper, Electronic transport through hydrogen bond we have used this technique. Please look at the introduction and the relevant references.

  • Tarik Ömer Oğurtani added an answer:
    How do you calculate ΔG of adsorbed species?

    Dear all,

    I am trying to calculate  ΔG of adsorbed species by using VASP. For this I need to calculate Zero point energies and Entropy of absorbed species. But I am confused with that. What type of calculations do I need to get ZPE and Entropy. Please help me in this case.

    Thanks in advance.

    anjibabu

    Tarik Ömer Oğurtani · Middle East Technical University

    Dear Anji, All these prototype shortwaves no matter how sophisticated they are,  one would have heal of a time to adapt them to the specific problems one faces in materials science. Because of that I have always developed my own tailor made codes in first MatCad environment and then switch to  FORTRAN,    including the mathematical subroutines even though some of them are available in IMSL etc. 

    One easily organize 

  • Eugene F Kislyakov added an answer:
    Software to lower the symmetry of molecules?

    I am having difficulty in lowering the symmetry of a big molecule. My molecule has D3h symmetry, but I want to calculate it in C2v symmetry. Does anyone know the proper software with which to do that?

    Eugene F Kislyakov · Belarusian State University

    The same group can mean different geometries. It is more convenient to define geometry, than group. Standard procedure.

  • What does erroneous write stand for?

    Working with silicon two-layered clusters, I get an error message that goes like:

    Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00.
    Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00.
    End of G2Drv F.D. properties file 721 does not exist.
    End of G2Drv F.D. properties file 722 does not exist.
    End of G2Drv F.D. properties file 788 does not exist.
    IDoAtm=11111111111111111111111111111111111111111111111111
    IDoAtm=11111111111111111111111111111111111111111111111111
    IDoAtm=11111111111111111111111111111111111111111111
    Differentiating once with respect to electric field.
    with respect to dipole field.
    Differentiating once with respect to nuclear coordinates.
    CalDSu exits because no D1Ps are significant.
    There are 435 degrees of freedom in the 1st order CPHF. IDoFFX=6 NUNeed= 3.
    435 vectors produced by pass 0 Test12= 1.13D-12 1.00D-09 XBig12= 1.46D+04 1.75D+01.
    AX will form 72 AO Fock derivatives at one time.
    435 vectors produced by pass 1 Test12= 1.13D-12 1.00D-09 XBig12= 6.83D+03 2.12D+00.
    Erroneous write. Write -1 instead of 509295232.
    fd = 4
    orig len = 650011392 left = 509295232
    g_write

    I am using pbe0/6-31G** requesting a freq calc and adding the xqc on the scf, annexed are my files. It's not the first time I get this message for I've adjusted the system several times with no result

    Thanks!

    Best regards

    Juan-Sebastián Gómez-Jeria · University of Chile

    Use the option int=nofofcou and tell me it it worked or not. Regards, Juan

  • Bojidarka B. Ivanova added an answer:
    What is the difference between AM1 and PM3 methods?

    What is the difference between AM1 and PM3 methods in computational chemistry and when is it better to use one over the other?

    Bojidarka B. Ivanova · Technische Universität Dortmund

    Mr./Miss/Mrs. Albar,

    The formalism is the same, but the parameters are different.
    Please find in this topic the following refs:

    [1] M. Dewar, W. Thiel, Ground States of Molecules. 38. The MNDO Method.
    Approximations and Parameters, J. Am. Chem. Soc. 99 (1977) 4899 - 4907
    [2]M. Dewar, E. Zoebisch, E. Healy, J. Stewart, AM1: A New General Purpose Quantum Mechanical
    Molecular Model, J. Am. Chem. Soc. 107 (1985) 3902 - 3909

    [3] J. Stewart, Optimization of Parameters for Semiempirical Methods
    I. Method, J. Comput. Chem. 10 (1989) 209-220

    In addition you can find their application in vibrational spectroscopy and the correlations obtained for few examples (attachment).

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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