Theoretical Chemistry

Theoretical Chemistry

  • Can anyone tell me what is the best basis set to run polycarbonate samples?

    I am working on the polycarbonate compound. I would like to know which basis set will give me good data closer experimental values of frequency, geometrical parameters, reactivity details and other related values.

    Juan José Gamboa-Carballo · Instituto Superior de Tecnologías y Ciencias Aplicadas

    You should try with a TZV Pople's basis set, some times they are more accurate and lighter than Dunning's. I sugest not to use MP2 if you want termodinamics, rather use CCSD(T)

  • Robert J Paruch added an answer:
    How do you output the trajectory file in MD simulation?

    Sorry about the confusing title. 

    I am talking about the output frequency to write the trajectory file. Normally, the time-step in MD simulation is 1 or 2fs. And I am using 1ps/frame to output the trajectory file. The file size is big. And when I analysis these files. I choose 10ps/frame. I found it's hard to find difference to analyze the file between 1ps/frame and 10ps/frame. So should I change the frequency to write the trajectory file to 10ps/frame to save space? 

    How often do you guys store the trajectory files?

    Robert J Paruch · Pennsylvania State University

    One can also think of a variable output frequency if this is appropriate for the system and kind of simulation. For example, output frequency has to be high during the high energy stage of the simulated proces, when particles move quickly. Then, as the system equilibrates, the output frequency can be reduced. It helps to decrees the size of the output file, keeping the relevant information.

  • Ron Shepard added an answer:
    How do we calculate energies with multireference configuration interaction method in Gaussian 09?

    I try to calculate the energy with multireference configuration interaction method of certain system using gaussian 09 packet, but I do not know what is the keyword.

    Ron Shepard · Argonne National Laboratory

    COLUMBUS does MRCI, and it is also free.

  • Eric B. J. Harris added an answer:
    Why carboxyl group is inactive in Diels-Alder reaction?

    Are there any examples of Diels-Alder reaction in which carboxyl group (in acids or esters) acts as a part of a dien or a dienophile? What are the reasons of its inactivity in this reaction?

    Eric B. J. Harris · Australian National University

    Yes, there are examples of methylene barbituric acid derivatives and methylene meldrum's acid derivatives undergoing hetero Diels Alder reactions as a diene component. These systems are strongly electronically activated and sterically fixed in cisoid conformation.

    Cinnamates and similar systems have also been used but often require an electron rich dienophile and sometimes occur via step-wise rather than concerted process.

    The major limitation for the use of esters and carboxyl groups is that they are not electrophilic enough to make good dienophiles and possess poor orbital overlap on the carbon atom in addition to suffering from higher steric requirements.

  • Mihai Surducan added an answer:
    Has anybody had problems with IRC calculations within a PCM model?

    Dear Coleagues,

    I am investigating the hydrolysis process of phosphate esters using PCM model to simulate the surroundings of the reactive system. The process is completely described in gas phase, however in aqueous phase I have had some problems with the Intrinsic Coordinate Reaction (IRC) analysis. The behaviour of the curve was not normal and two main problems were observed:
    1 – When I try to obtain the IRC in two outputs, by specifying the forward and reverse keywords in the calculation line, what I get is the same path, i.e., the reactants reach the transition state (in the forward calculation) and after that the transition state reach the reactants once again (in the reverse calculation).
    2 – After this problem I tried to change the IRC parameters and I put a different stepsize and a diferent maxpoints. In this situation the change of step size were not regular and in one extremity of the curve the IRC points accumulate in the same region, where the stepsize remained practically unchanged.
    The set of keywords were:
    # irc=(calcfc,maxpoints=60,forward,stepsize=20,maxcyc=200) scf=(maxcycle=200) b3lyp/gen gfinput pseudo=read scrf=(pcm,read)
    At the end of input:
    Has anybody here had a similar problem in IRC calculations using the continuum approach?
    I really appreciate any help you can provide.

    Mihai Surducan · Babeş-Bolyai University

    Ok. So my opinions related to these matters:

    - for the concerted mechanism, based on the gradient graph, it seems like you located your TS. I usually saw the accumulation that you talk about in calculations which ended with an error. Try restarting the calculation or decreasing the step size.

    - for the "normal mechanism", I can see that the transition state is at a maximum on the gradient graph, which is completely wrong. For the TS: you should have a minimum on the gradient graph and a maximum on the relative energy graph, so the TS is incorrect.

    -if I understood correctly, you said these are results for the "reverse" IRC, right? Well, to be best that I can judge from all the graphs that you showed me, the IRC is followed in both directions (aka both in the reverse and forward directions, because the TS should always be at point 0). Why is that?

  • Partha Sarathi Sengupta asked a question:
    By which methods can we get data on Fe(II) -C bonds in [Fe(CN)6](4-), and whether it is longer than that in [Fe(CN)6](3-).

    Fe(II) -C bonds in [Fe(CN)6](4-) is longer than that in [Fe(CN)6](3-). By which methods we get these data?

  • Sai Siddhardha R. S. added an answer:
    How can I do proton adsorption studies on Metal nanoparticles in Materials Studio software?

    Can you please give me the details of the  parameters involved in it....

    Sai Siddhardha R. S. · Sri Sathya Sai Institute of Higher Learning

    Thanks Saeed Kazemiabnavi, I'm studying electrochemical reduction of  proton by applying a cathodic reduction potential.(Hydrogen eveolution reaction)

    I would like to study the proton adsorption energy on different nano particle surface computationally, before going on to do a real experiment.

    This helps me to nail down the right system for the reaction.

    Can you please suggest me in this regard on how to screen the materials for Hydrogen evolution reaction using Materials studio Software.

    What kinda parameters involved in  it?

  • How do I evaluate the behavior of ring structure of a polymer?

    Dear all,

    I am running a MD simulation of polystyrene with AMBER. It looks the benzene ring on the backbone distribute evenly. My advisor asked me to find a way to evaluate the behavior of the change of ring structure on the polymer. Does anyone have any idea about this? 


    X Sun.

    Aldo Fabrizzio Combariza Montañez · Universidad de Sucre

    Check this out, you will find this paper useful:

    The FF is not a problem, AMBER is optimized for Hydrocarbons, so your pretty safe using this FF. 

  • Veliyana Londong Allo added an answer:
    Can someone help me solve the reason for why I'm getting negative frequencies?
    I'm calculating a Fischer Tropsch process metals involved but I do not like the cluster as the unit cell is repeated. I get nine negative frequency values with the value of 90 cm-1 - 400 cm-1. I am using Gaussian 09.
    Veliyana Londong Allo · Bandung Institute of Technology

    thanks for help...

  • Karl Sohlberg added an answer:
    What is the spectroscopic technique used to differentiate between sp2 and sp3 bondning of carbon?

    The production from carbon arc plasma produce a mixture of carbon nanostructure including nanorods, nanofiber, nanotube, graphene,diamondlike carbon etc,so how to differentiate between the product of sp2 and sp3 bonding carbon?

    Karl Sohlberg · Drexel University

    EELS will give chemical identification, and with the right instrument can be done with atomic resolution. Here are some references from a forthcoming review:

    • Browning, N.D., Chisholm, M.F., & Pennycook, S.J., Atomic-resolution chemical analysis using a scanning transmission electron microscope. Nature 366 (6451), 143-146 (1993)
    • Allen, L.J., Findlay, S.D., Lupini, A.R., Oxley, M.P., & Pennycook, S.J., Atomic-Resolution Electron Energy Loss Spectroscopy Imaging in Aberration Corrected Scanning Transmission Electron Microscopy. Physical Review Letters 91 (10), 105503 (2003)
    • Pennycook, T.J., Beck, M.J., Varga, K., Varela, M., Pennycook, S.J., & Pantelides, S.T., Origin of Colossal Ionic Conductivity in Oxide Multilayers: Interface Induced Sublattice Disorder. Physical Review Letters 104 (11), 4.
    • 10.1103/PhysRevLett.104.115901
    • Pennycook, T.J., Oxley, M.P., Garcia-Barriocanal, J., Bruno, F.Y., Leon, C., Santamaria, J., Pantelides, S.T., Varela, M., & Pennycook, S.J., Seeing oxygen disorder in YSZ/SrTiO3 colossal ionic conductor heterostructures using EELS. Eur. Phys. J.-Appl. Phys 54 (3), 11 (2011).
    • 10.1051/epjap/2011100413
    • Garcia-Barriocanal, J., Rivera-Calzada, A., Varela, M., Sefrioui, Z., Iborra, E., Leon, C., Pennycook, S.J., & Santamaria, J., Colossal ionic conductivity at interfaces of epitaxial ZrO2: Y2O3/SrTiO3 heterostructures. Science 321 (5889), 676-680 (2008).
    • Varela, M., Findlay, S.D., Lupini, A.R., Christen, H.M., Borisevich, A.Y., Dellby, N., Krivanek, O.L., Nellist, P.D., Oxley, M.P., Allen, L.J., & Pennycook, S.J., Spectroscopic imaging of single atoms within a bulk solid. Phys. Rev. Lett. 92, 095502 (2004)
    • Varela, M., Gazquez, J., & Pennycook, S.J., STEM-EELS imaging of complex oxides and interfaces. MRS Bulletin 37 (1), 29 (2012)

  • Saeideh Hosseini added an answer:
    Is it possible to break chemical bonds in a cl2 molecule using photolysis?

    if we search about bond energy of cl2 reach to 243 kJ/mol ( and by convert unit and mathematical calculation and convert to nm of light ( find the 493 nm and this wavelength is Related "bluish green" (493–498 nm) light. 
    if this light radiate to the cl2 gas what react is predictable for this conditions .

    Saeideh Hosseini · University of Zanjan

    you can see the attached links

  • Naiwrit Karmodak added an answer:
    How can I calculate magic numbers (Au nanoparticles) for Cubic, Icosahedron, cubo-octahedron Truncated octahedron clusters?

    I want to know magic numbers and its outer diameter, (1 nm to 3 nm) surface area. 

    Naiwrit Karmodak · Indian Institute of Science

    Behind this concept of magic numbers for clusters, can you give some logic from electronic structures or molecular orbitals.  

  • Jose Jimenez added an answer:
    What might cause persistently inflated (>1.1) values of r-hat in a community occupancy analysis?

    Hi all, I'm trying to fit a couple of community occupancy models and am noticing that r-hat values for certain parameters are well above 1.1 (in the 1.3 - 1.6 range) even with fairly long runs (like, 200,000 iterations w/ 100,000 burn-in).  The model structure includes Bernoulli inclusion parameters associated with all beta parameters.  At any rate, the problematic r-hat values are consistently associated with the precision hyper-parameters for the betas.  Covariates with essentially no model support seem to converge slightly better (or at least have lower r-hats for the precision hyperparameter) than covariates with some support.   Strangely, these r-hat values also seem to stabilize pretty quickly (like, the difference between 15,000 iterations and 50,000 iterations is minimal). I'm curious to hear if anybody else has encountered this.  My kind of desperate explanations are

    1. The model just needs to be run out longer.
    2. I should increase the thinning rate (the trace-plots indicate that the tau chains will occasionally make pretty massive leaps that might be inconsequential if culled by thinning).
    3. This is related to the Bernoulli inclusion parameters turning the betas on and off, and r-hat wouldn't be expected to approach convergent values unless the inclusion probability were very close to 0 or 1.
    4. This is related to tau hyper-parameters themselves, which might not be expected to be distributed roughly normally.
    5.  The taus are derived nodes based upon stochastic sigma hyperparameters, and I should be tracing the latter instead.

    Sorry for the book.  Thanks for any help!

    Jose Jimenez · Spanish National Research Council

    Hi John:

    - Did you use covariates? Did you scaled them?
    - Consider changing the parametrizacion. Sometimes you can improve the convergence .
    - What's the magnitude of p? As you know, with very low p values, the results would be inconsistent.


  • Eugene F Kislyakov added an answer:
    What is the spin only and spin plus orbital magnetic moment of (CrCl6)3- ?

    What is the spin only and spin plus orbital magnetic moment of (CrCl6)3- ?

    Eugene F Kislyakov · Belarusian State University

    Orbital magnetic moment exists only for sphericaly symmetric systems, dear Atul.

  • Pardis Td added an answer:
    What does the error "Warning -- assumption of classical behavior for rotation may cause significant error" in Gaussian mean?

    this statement is included in the log file when I do frequency calculations by gaussian 09

    this warning can be neglected ?????
    what this mean about the accuracy of enthalpy and other parameter ?????
    the output is :

    Atom 25 has atomic number 17 and mass 34.96885
    Molecular mass: 698.55788 amu.
    Principal axes and moments of inertia in atomic units:
    1 2 3
    Eigenvalues -- ******************************
    X 0.99976 0.00000 -0.02175
    Y 0.00000 1.00000 0.00000
    Z 0.02175 0.00000 0.99976
    This molecule is an asymmetric top.
    Rotational symmetry number 1.
    Warning -- assumption of classical behavior for rotation
    may cause significant error
    Rotational temperatures (Kelvin) 0.00639 0.00417 0.00340
    Rotational constants (GHZ): 0.13324 0.08698 0.07086
    Zero-point vibrational energy 369763.0 (Joules/Mol)
    88.37547 (Kcal/Mol)
    Warning -- explicit consideration of 33 degrees of freedom as
    vibrations may cause significant error

    Thank you 

  • Milagros Avendaño added an answer:
    How can we prove the mechanism of DA reactions with Gaussian?

    I have Gaussian output data and I want to prove mechanism of Diels Alder 

    Milagros Avendaño · Central University of Venezuela

    If you have experimental data from your reaction you can run the simulation to find the transition state, compute the theorethical values and see how close the proposed mechanism is from the real one.

  • Saba Niaz Theoretician added an answer:
    What is the work function and electron affinity of FeS2 and FeSiS4?

    Does any one has any data about work function and electron affinity of FeS2 and FeSiS4

    Saba Niaz Theoretician · University of Kashmir

    u can get the electron affinity from quantum mechanical descriptors try reading a theoretical paper and use koopmans theorm . plus if u r well versed with gaussian 03 . then get the molecule optimised and from the results of the output u will get ur electron affinity.

  • Tamás Beke-Somfai added an answer:
    What is the experimental estimate for the intramolecular hydrogen bonding in the catechoxyl radical (1,2-dihydroxybenzene semiquinone radical)?

    I want to evaluate whether the available literature experimental bond dissociation energy (BDE) values of the O-H bond of catechoxyl radical potentially incorporated the magnitude of the intramolecular hydrogen bonding in the ground state of the radical.

    Tamás Beke-Somfai · Chalmers University of Technology

    Hi Ameha,

    I think it is hard to give a direct answer for such a specific question with little factual info. However, in case you found some experimental studies for this problem, then the values should incorporate all the interactions which stabilizes the H on the O and thus your experimental value will include stabilizing value of the O-H---O  bond as well (you have to break this one too in order to remove that H). Note, that mechanism-wise it could be that actually the H which is not in the above H-bond dissociates, this seems at first more likely, that is the second hydrogen dissociates here: -O-H---O-H . In this case the intremolecular bond "catalyses" the dissociation as it sucks e- from the second O, weaking its O-H bond.

    In case you want to get an estimate for the overall contribution for the intramolecular bond, you might look for experiments which performed the same but with e.g. 1-hydroxy 2-metoxy benzene, or similar compound where intramolecular H-bonds are more limited.

    Hope this helps, let me know if I misunderstood your question.


  • Michael Nazarkovsky added an answer:
    How do we plot Harkins Jura isotherm and Frenkel Halsey Hill Isotherm for adsorption?

    what parameters go in x-axix and y-axis?

    adsorption studies

    Michael Nazarkovsky · Chuiko Institute of Surface Chemistry, Kiev, Ukraine

    Why "dislike"?

  • Felipe Schneider added an answer:
    How do I define FRAGOCCUPATIONS in ADF 2013?

    How should one define the FRAGOCCUPATIONS keyword within a ADF 2013 input file? I am using an all-electron basis set.

    Felipe Schneider · Federal University of Santa Catarina

    Thanks Paul!

  • Bernhard Schäfer added an answer:
    How can I exchange a PF6- anion for Cl- in a ruthenium(II) complex?

    Is there any simple method to exchange PF6- counterion for some smaller group (as Cl-)? I need to increase water solubility of ruthenium(II) polypyridyl complex.

  • Grant Hill added an answer:
    Can you recommend a good overview of halogen bonding?


    Grant Hill · The University of Sheffield

    You might also find this perspective interesting, it is focused on experimental results of small gas-phase complexes, but I find it helps with understanding the fundamentals. 

  • Rachida Fodil added an answer:
    How can I calculate the interaction energies of some complexes without using the BSSE-CP correction?

    I have optimized the κappa-carrabiose in presence of 1, 2 and 3 water molecules (complex 1, complex 2 and complex 3) and I need to compute their interaction energies. To obtain the energy of each monomer should I optimize each monomer alone?

    Thank you in advance .

    Rachida Fodil · University of Sidi-Bel-Abbes

    Tanks a lot Ali Hamed.

  • Kurt A Kistler added an answer:
    How can one find the nature of excited states (both singlet & triplet) using DFT?

    I want to know the nature of excited states (n,pi* or pi,pi*) and their relative ordering in polar and non polar solvents

    Kurt A Kistler · Pennsylvania State University

    Indeed, Jorge.  "Bright" = high osc strength = long transition dipole vector.  Generally the oscillator strength is given by "f", while magnitude of trans dipole is in Debye or e-bohr. 

  • Elder Mota added an answer:
    Why is the bonding capability of Platinum 4 if It has 2 unpaired electrons?

    I am doing a theoretical study of Platinum and I don't understand why It can do 4 bonds, If your electron configuration is 5d86s1. I need to understand because of the paramethers of charge and spin multiplicity.

    Elder Mota · Federal University of Pará

    Thanks Joaquim and Orlando for help me!

  • Massimiliano Arca added an answer:
    Can anyone help me find out the MO composition in a metal complex?
    How can I find out the % of metal character and % of ligand character in a particular MO of a metal complex?I have done a few NBO calculation but It only gives the bonding composition.
    Massimiliano Arca · Università degli studi di Cagliari

    GaussSum is a very good tool for this aim. You have to specify the fragment composition, and you get the % of each fragment in each MO.



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

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

    Maxim Tafipolski · University of Wuerzburg

    just to add to my previous answer. The issue on two alternatives (Urey-Bradley term vs stretch-bend cross-term) is nicely explained in the book of Norman Allinger (p. 66):

    Molecular Structure: Understanding Steric and Electronic Effects from Molecular Mechanics:

  • Subrata Tewary added an answer:
    Can anybody help me how to calculate transition moment between ground to excited state in CASSF calculation using G09?


    Subrata Tewary · Indian Institute of Technology Bombay

    u mean CASSCF right? If its then MOLCAS is best module, since its paid; better use ORCA (open source) than Gaussian. 

  • Francesco Muniz-Miranda added an answer:
    How can I solve an imaginary frequency problem in transition metal complexes in gaussian?

    I have optimized various transition metal complexes at b3lyp/def2-tzvp level in gaussian 03, but when I attempt to do frequency calculations, in some of them I have one or two imaginary frequencies. I solved the problem by changing dihedral or bond distance/angle of that imaginary frequency in gaussview, but in a few of them, especially in cobalt complex I couldn't solve the problem. I have tried to optimize the complex using keywords such as "opt=tight int=grid=ultrafine", using different checkpoint file with guess=read, changing dihedral, starting to optimize with a smaller basis set, etc., all of these didn't work. Finally in one of the related questions on researchgate, one suggests "opt=calcall" keyword, and I have given the job with that keyword on 24th july, however it's still running. What else should I do to overcome this problem?

    Francesco Muniz-Miranda · Università degli Studi di Modena e Reggio Emilia

    There's an even stricter criterion than Opt=Tight, and it's Opt=VeryTight.
    Maybe it can be useful.

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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