Computational Chemistry

Computational Chemistry

  • Michal Kolář added an answer:
    What are the principle papers describing the basis sets listed below.

    I'm not 100% sure about the convention that computational chemists use in regards to publications and new basis sets. I was wondering if there were papers published with regards to each quantum chemical basis set (even say between two similar pople basis sets. e.g.  631-g vs 631++g) as a sort of explanation/introduction to each basis. I was looking on ESML basis set exchange hoping to find relevant literature but so far that has led to no avail.

    I'm looking for literature pertaining to:

    6-31g

    6-31g++(d)

    def2-TZVP

    cc-pVTZ

    also if anyone has the literature introducing qst2 or qst3 those would be greatly appreciated.

    Michal Kolář · German Research School for Simulation Sciences

    If you wish to learn the basics about basis sets, I'd suggest to check some textbooks rather than the original papers. I recommend Molecular modelling by A. Leach or Introduction to computational chemistry by F. Jensen.

  • Massimiliano Arca added an answer:
    Can you tell me how I can create the Group.txt file from the Gausssum directory?

    For the COOP function I get a message that indicates the program cannot find my Group.txt file even though I have systematically placed a copy in every folder within the Gaussum directory. Can you tell me how I can create the Group.txt file. I have attached the Gaussian output file also below. Secondly, I like to know that, from the DOS image in gausssum, how can I understand one peak is belongs to which orbital state. I also like to know how I draw the DOS in origin from the Gausssum?

    Massimiliano Arca · Università degli studi di Cagliari

    I've used Gausssum seldom for analyzing electronic transitions calculated at TD-DFT level. In those cases, I've followed the worked example reported here:

    http://gausssum.sourceforge.net/GaussSum2.2/Example/index.html

    Please pay attention to the following points:

    - the file must be named "groups.txt" (with lower case "g" and final "s"

    - it must be placed in a "gausssum2.x" subdirectory of the folder containing your output gaussian file (x depending on your version). 

    Hope this may help.

  • Wim Buijs added an answer:
    Collaboration on sucrose derivative computational project?

    I'm looking to collaborate on a sucrose derivative computational project that predicts relative sweetness values using relatively simple FMO theory.  I have done preliminary calculations, have gotten a positive correlation, and I'm willing to share the data.  I'd like some assistance with the computational chemistry, preferably someone with experience calculating MO energies while taking into account conformational effects.

    Any takers?

    Wim Buijs · Delft University Of Technology

    I am interested in sucrose/carbohydrate chemistry from a food and thermo dynamical perspective, till the description of the enzymatic conversion as well. Predicting sweetness might fit into that as well, and we can discuss what level of theory would already be appropriate to answer this question. Please mail me at w.buijs@tudelft.nl

  • Masood Ahmad Rizvi asked a question:
    Is B3LYP TZVP level of theory ideal to optimize an organoselenium compound?

    Please suggest a reference.

  • Sayed Muktar Hossain added an answer:
    Can someone advise on the Error l914 in TD-OPT calculation with gaussian?
    I do TD-opt calculations for geometry optimization in excited state, and I get this error: You need to solve for more vectors in order to follow this state.
    Error termination via Lnk1e in /..../.../g09/l914.exe.
    How can I fix this error?
    Sayed Muktar Hossain · Indian Institute of Technology Bhubaneswar

    Dear Hamed Haghshenas sir,

     I also got the same error messege during excited state calculation in solvent in G09. My input was # td b3lyp/6-31g(d) scrf=(solvent=methanol). please help me I'm new in this field.

  • Fatemeh Sepehr added an answer:
    Gaussian09, scrf=smd or scrf=pcm?
    I actually have a general question about the differences between SCRF=PCM and SCRF=SMD in G09. As far as I know, in theory SMD includes corrections for CDS (cavitation, dispersion and solvent structure effects) while PCM does not. In practice, SMD distorts and reorients the gas optimized structures much more than PCM does and also SMD gives more accurate solvation energies compared to PCM ( though SMD has been parameterized more carefully on a large number of input solvation free energies, so its success over PCM may be just as a result of its optimized parameters for delta G and not because of its more realistic structure !?). So, is the more distorted SMD optimized geometry more reliable than PCM? In fact, I have not seen many papers using SMD??

    The other question is that are vibrational IR frequencies calculated with SCRF optimized geometry reliable or preferable over vacuum frequencies? And if yes, since the normal mode vibrational frequencies calculated at SMD differs with those obtained by PCM, which one is more reliable?
    Fatemeh Sepehr · University of Tennessee

    Yes, I have tried COSMO in ADF code and it gives similar results to SMD.

    I am more towards SMD too.

  • Pankaz K. Sharma added an answer:
    Why am I getting error while using IOp(3/107 and 3/108) with wb97 functional in gaussian?

    I'm trying to use IOp(3/107=0400100000,3/108=0400100000) with wb97 functional in gaussian 09, but I get error termination every time.

    nThT2=3 NYI in PrismS.
    Error termination via Lnk1e in /home/jahir/g09/l502.exe at Fri Sep 12 18:46:39 2014.

    I'm attaching my log file. Please help

    Pankaz K. Sharma · Ewha Womans University

    Could it be that you are using too many digits for the IOp values?

    From the Gaussian IOp reference manual:

    http://www.gaussian.com/g_tech/g_iops/iops2.pdf

    IOp(3/107):  Omega for short/long range Hartree-Fock exchange.
    0 Standard HF exchange
    MMMMMNNNNN Short range HF exchange with NNNNN/10000 and long range exchange with MMMMM/10000.

    IOp(3/108): Omega for short/long range DFT exchange.
    0 Standard DFT exchange or default from functional.
    MMMMMNNNNN Short range DFT exchange with NNNNN /10000 and long range DFT exchange  with MMMMM/10000.

  • Jacek Martynow added an answer:
    Is there any software to calculate the enantiomeric or diastereomeric excess in organic molecules?
    As we have been involved in docking, SAR, QSAR and DFT calculation using Schrödinger software, I started thinking about possibility of using any software for theoretical calculation of stereoselectivity in organic molecules. It can be helpful to organic chemists to check the probabilities/optimization of conditions for the formation "ee" and "de" in product before doing experiments. If you have any idea, please comment on this.
    Jacek Martynow · Melinta Therapeutics

    Imre - exactly! Reaction kinetics is everything in majority of asymmetric syntheses. It is a function not only of the reactant structures, but multiple other factors come into play, like the effects of concentration, pH, temperature, pressure, complex catalytic interactions with trace components, etc. A practicing chemist might just not feel that such calculations have practical value... until proven convincingly, of course :)

  • Skyler Saleebyan added an answer:
    Can somebody please provide an example IRC calculation in MolPro?

    I've been trying to read through the molpro website and their relevant material for (what i at least think is) intrinsic reaction coordinate calculations but for some reason nothing I read there is settling in.

    If I could just see an example file for running an intrinsic reaction coordinate calculation, I think it'd all make more sense. In terms of the basis I will be using it's DEF2-TZVP but if I can see an example file I think I can adjust parameters just fine. Even if you want to propose alternate software molpro is still greatly preferred in this case thanks to certain limitations involving the computing system I am running calculations on in the time limit I have.

    Also, a small side question. Any rough estimates on the time an IRC calculation needs with 48 cores (2 nodes) for compounds between 10 and 20 atoms numerous? I'd like to give them a generous amount of time to run without having to wait a week for my turn in the queue to come up from long walltimes.

    Skyler Saleebyan · University of California, Santa Barbara

    Thank you Saeedreza

    Initially I was trying to do IRC calculations with Gaussians, but had a lot of bad luck with errors. Feel free to post your example.

  • Anupam Singh added an answer:
    How to get Cartesian coordinates for united atoms given the Cartesian coordinates for all atoms?
    I have a PDB file for triglyceride which contains Cartesian coordinates for all atoms (C,H,O) but I need coordinates for united atoms. How can I modify this file?
    Anupam Singh · Jawaharlal Nehru Centre for Advanced Scientific Research

    Hi Prerana,

    You can open your PDB in VMD. And try commands mentioned in below link.

    https://sites.google.com/site/akohlmey/software/topotools

    Cheers!!

  • Allen Clabo added an answer:
    How can I run a NMR job using Solvent - Deuterated Chloroform in Gaussian 09's latest version of D 01?

    I am trying to run NMR gaussian calculation of my compound using Deuterated Chloroform as solvent with b3lyp/6-31g** methodology using Gaussian 09 package version of D.01. The job was not at all running stating error in the input line. When I go through manuals I understood that versions later than A 01 will run that job but even when using the D 01 version it was not running. Can anyone give me suggestions in this regard?

    Allen Clabo · Francis Marion University

    Show us your input file! We can't help you with an input error if we don't know exactly what your input is!!

  • Mahendra Gaur added an answer:
    Which software is best to design a homology model of an unknown protein?
    Homology modelling at low alignment
    Mahendra Gaur · Siksha O Anusandhan University

    Swiss Model and Phyre2 is best automated homology modeling tool which give all information about predicted model...further u can use InterPro,Protparam,Protscal,QMEAN server,Energy minimization of model etc for refinement and checking model quality.

  • Saman Alavi added an answer:
    Can anybody guide me to calculate Spatial distribution function?
    I would like to calculate SDF (Spatial distribution function) around solutes in aqueous solution. I have molecular dynamics trajectory of this mixture (x,y,z coordinates at each time). I know the concept of RDF. But in case of SDF I am not sure about (r , theta, phi) space and its visualization.

    I want to write a code for this kindly help me to clear this point how to reach from (x,y,z) coordinates to SDF.
    Saman Alavi · University of British Columbia - Vancouver

    I would also recommend TRAVIS. You can see their website: http://www.travis-analyzer.de/gal.php

    Our recent paper has another example: https://www.researchgate.net/publication/265243798_Molecular_dynamics_and_ab_initio_studies_of_the_effects_of_substituent_groups_on_thermodynamics_and_structure_of_four_selected_imidazolium-based_Tf2N-_ionic_liquids?ev=prf_pub

  • Michał Henryk Jamróz added an answer:
    Can anyone help with geometry optimization in Gaussian09 -bond breakage?

    Sometimes when I try to do a geometry optimization in Gaussian, the bonds to an atom end up broken and it acts essentially as a free atom - or at least that's what it seems to me. It ends up in weird locations, not to mention how much slower computation is. Last time this happened was with a benzofurazan derivative. The oxygen atom from the small heterocyclic ring was abstracted from the molecule and ended up moving freely. I was trying to make a TD-DFT optimization of the first excited state in vacuum. The ground state was optimized successfully. Is there a way to fix this problem?

    Michał Henryk Jamróz · Instytut Chemii i Techniki Jądrowej

    Visit our web page: smmg.pl and download my Hauusian program.

    May be Hauusian can help you in generation of proper . gjf file

    Michal

  • Chin-Hung Lai added an answer:
    How to interpret ETS-NOCV results?

    Dears all:

    Recently, I did two bond energy decomposition analyses using ETS-NOCV in ADF. However, I was really confused with the results. The analyses show that the total orbital interaction energy is   ********************. What does it mean?

    Chin-Hung Lai · Chung Shan Medical University

    Thanks for asking. Yes, I have already figure out what went wrong. 

  • Vladimir Potemkin added an answer:
    How does one find important residues?

    I have two proteins that interact with each other. Now I want to dock these two proteins but I don't know about their important residues that are involved in interactions. No experimental studies are available for these proteins. Is there any computational method to identify potent residues and regions in protein?

    Vladimir Potemkin · Chelyabinsk State Medical Academy

    You can on-line evaluate atom-atom electron overlaps at www.chemosophia.com using "Electron properties: Fast integration of atomic basins" or compute properties of critical points of electron density using "Electron properties calculation (Search for critical points of electron density)". Both programs are available for large systems up to 10 000 atoms. The computations are free now.

  • Vladimir Potemkin added an answer:
    What method is employed to check the structure/molecule stability?

    Recently I was encountered with a problem where structure shown in figure is not able to get converted to any product. May be possibly due to its resonance effect or any other effect between the neighboring groups (cyano and amino). Neither cyano group is reactive nor amino group is reactive. Do I have any alternative option to prove this hypothesis via any computational software/webserver/informatics/molecular modeling, that the concern molecule is highly stable or inert for any reaction  Even I don't know which software is better for these calculations.

    Any other relevant information regarding the query will be helpful.

    Please suggest me a way to solve this problem.

    Vladimir Potemkin · Chelyabinsk State Medical Academy

    You can calculate on-line Gibbs free energy, Heat of formation, Entropy, Enthalpy of molecules at www.chemosophia.com now for free. It can be done using “Physicochemical properties calculation” software after registration.

  • Mohammed Saber Gad added an answer:
    Calculation of emission spectrum in gaussian-09 software

    Hi,to all

    can anyone please tell me the steps i.e; all the commands in calculating emission spectra using gaussian-09 software and also the interpretation of the result?

    Regards

    Barsha

    Mohammed Saber Gad · National Research Center, Egypt

    follow this link

    www.gaussian.com/g_prod/g09b.htm

  • Abolfazl Noorjahan added an answer:
    Why in today's force fields do we not consider explicitly 1-3 van-der-Waals interactions?

    Such interactions are explicitly considered in the force fields of the 70s.

    Abolfazl Noorjahan · University of Alberta

    To make a long story short:

    1) in organic chemistry, using bonded potentials are common due to limited type of bonds that one needs to define and parametrize.

    2) in material (non-organic) field people are mostly using non-bonded potentials (pair potentials) as atoms can change their neighbors by jumps (without any chemical reaction).

    I suggest you watch first couple of lectures from this course and you will find the answer to you question by an expert:

    MIT 3.320 Atomistic Computer Modeling of Materials (available on youtube)

  • Vladimir Potemkin added an answer:
    Is there a procedural method to finding many ground state conformations?

    I have been performing numerous gs/ts optimizations on an ensemble of small (n=15 +/- 5) compounds, and I was interested in trying to map out all the possible conformations of the ground state one could reasonably expect.

    With the number of compounds I'm dealing with, I wanted to find see if there were any methods that can set up a large amount of guesses for ground states instead of having to try and manually guess states. I kind of am envisioning something like a breadth based search that uses a very cheap algorithm like UFF to find a large collection of guesses. Am I being overly optimistic or is there something out there that can help me.

    Vladimir Potemkin · Chelyabinsk State Medical Academy

    You can perform on-line conformational search with evaluation of probability of existence of each conformer at www.chemosophia.com now for free. It can be done using “Extended Global Minimum Search + Construction of Multi-Conformational Molecular Model (4D-Structure)” or “Extended Global Minimum Search + Construction of Multi-Conformational Molecular Model for Chiral Molecules (4D-Structure)” software after registration.

  • Tayyibe Bardakçı 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?

    Tayyibe Bardakçı · Fatih University

    Dear all, I appreciate for your suggestions.

    Firstly, as Allen Clabo mentioned, I have been searching for a minimum energy structure, instead of a transition state. As I mentioned in the question, after visualizing imaginary frequencies,  some small changes around the coordinates of imaginary frequencies solved the problem in many cases. But my problem was after doing those changes in the coordinates, still I couldn't get correct minima. 

    But, the job with "opt=calcall" keyword finished yesterday (I had given it on 24th July)  with normal termination, and I have a smaller value of energy than the previous calculations. So I have given the frequency job, I hope I wont get imaginary frequencies this time.

    @Zygmunt Flisak; in some cases, the jobs with more strict convergence criteria was ok, but most of the time it failed. 

    @Francesco Muniz-Miranda: 37 atoms.

    Thank you again for you answers.

    Tayyibe.

    p.s. Sorry for the late response, I wanted to reply the question after trying some of yours' suggestions, and I have been waiting for their results.

  • Daniele Tedesco added an answer:
    How can I design a gaussian calculation for optical rotation calculation using TDDFT?
    Many people report it but when I run such a calculation its ended.

    # td b3lyp/6-31g scrf=(solvent=chloroform) geom=connectivity polar=optrot

    Here is the command for the calculation but it terminates abnormally giving a severe error message. Please help me in setting up such a calculation.
    Also some people report that they calculated [Alpha]D values using GIAO with TD DFT but it cannot be set up using Gauss View.
    Daniele Tedesco · University of Bologna

    In your command line, you are missing to define the frequency at which optical rotation should be calculated: this is done by using the CPHF=RdFreq keyword and an additional input line after the molecule specification to define the desired frequency or wavelength (eg 589.3nm for the sodium D line).
    Moreover, you don't need the TD keyword for this calculation.

    ---
    [...]
    # b3lyp/6-31g geom=connectivity polar=optrot cphf=rdfreq scrf=(solvent=chloroform)

    [molecule specification]

    589.3nm

    ---

    http://www.gaussian.com/g_tech/g_ur/k_polar.htm

  • Andrea Mauri added an answer:
    How to use E-Dragon to calculate molecular descriptors?

    Hello, I used E-Dragon to calculate the molecular descriptors, but when I used some SMILES of chemicals, it showed errors, for example, I succeeded to get the molecular descriptor data of O=[Cr](=O)=O, but I couldn't get the data for O=S1(=O)O{-}.[Fe]{2+}.O{-}1 or Cl{-}.[Cd]{2+}.Cl{-}. Does anyone also use E-Dragon or Dragon, do you know why I had this kind of problem? 

    Andrea Mauri · Università degli Studi di Milano-Bicocca

    E-Dragon accepts SMILES as input file format. You can directly use CORINA to convert 2D SMILES structures to 3D molecular strucures.

    You can always inspect the dragon.log ('Result as text' menu). dragon.log reports warnings and errors occured during calculation.

    The O=S1(=O)O{-}.[Fe]{2+}.O{-}1 or Cl{-}.[Cd]{2+}.Cl{-} SMILES has several problems:

    - it is not a standard SMILES: {and } are not allowed in standard SMILES, charged atoms should be reported as [Fe2+] and not as [Fe]{2+} (see daylights SMILES tutorial );

    - it is a disconnected structure. Disconnected structures are not allowed.

  • Alexander Galstyan added an answer:
    Where can I find the computational chemistry basis set in analytical form?

    If I use the basis set in gaussian for the computation of a molecule geometry, let it be 6-31G and some simple molecule, I keep in mind that I have an analytical representation of the result of my calculation (I got coefficients for some gaussian terms).

    Where I can find this analytical terms?

    Alexander Galstyan · Lomonosov Moscow State University

    Thank you very much, Matteo! This is really helpful.

  • Saba niaz Theoretician added an answer:
    What are diffuse functions, & p or d or f type of functions included in Gaussian calculations?

    I'm conducting my undergraduate research work using Gaussian09 software package in Linux Operating System.
    I'm using the B3LYP method and 6-311G basis set for my calculations.
    All tutorials and guide lines say that putting (d), (d,p) after the basis set naming will add polarizable functions to molecule.
    & putting + or ++ (6-311+G/ 6-311++G) will add diffuse functions to the molecule.

    I want to know exactly,
    1. What are these polarizable and diffuse functions....??  
    2. What are 'f' type, 'd' type or 'p' type polarizable fuctions.....??
    3. I'm working only with 2nd row elements (Li-Ne), so should I add above functions to my  calculations...??

    Any help will be appreciated.
    Thank you.

    Saba niaz Theoretician · University of Kashmir

    i suggest you to use b3lyp 6311++dp  for second row elements if this doesnt work  then try  these combinations with b3lyp

    6311+d,p 

    6311+d

    but if u r having a transition metal try using b3lyp with lanl2dz or b3lyp with lanl2mb combination. i hope it helps.

    try reading cramer for computational chemistry its a good book and i hope this will prove helpful to u . 

  • Niyaz Safarov added an answer:
    How to make the procedure of molecules overlay comfortable ?
    I would like to write a convenient overlay procedure. What features should it have to be really comfortable for everyone?
    Niyaz Safarov · Baku State University

    Dear Alexey,

    It depends on the OS you are going to explore under and what kind of molecules are to be overlayed.. Practically,  for an averaege user,  GUI and mouse clicks are convenient to use. If protein molecules are concerned automated generating of  Ramachandran plots would be of advantage.

  • Anatoly V Berezkin added an answer:
    How does one convert forcefield parameter from pcff to oplsaa ?

    I got some useful parameter in PCFF form. I need to convert them in OPLSAA. How do I do that? As I see the functional form of these two for bond and angle is same. What about lenard jones? PCFF use 9-6 lenard jones, how to get 12-6 form in oplsaa?

    Thanks in advance.

    Anatoly V Berezkin · Technische Universität München

    Repulsive part of VdW potential is just introduced to reproduce short-range repulsion, and because of that can be defined nearly arbitrary (by exp(r), r9, r12). One can try to extract attractive dipole-dipole "long-range" part from 6-9 and directly transfer it to 6-12 potential. The repulsive part in that case can be chosen to keep the same position of energy minima (sigma) and its depth (epsilon) as in 6-9 version. An alternative solution could be to build potential energy curve for 6-9 in Origin and find corresponding parameters of 6-12 by fitting. Of course people usually write, that force-fields are not transferable. But we should take into account, that all these FF are derived from QM. VdW interactions in "cheap" QM realizations are poorely reproduced, the concept of partial charges is questionable in itself, and charges can be very different depending on method of calculations.  Thus, original FF normally requires modifications for really accurate simulations, anyway. By my experience, density is more sensitive to bond lengths, vaporization energy mostly depends on partial charges. VdW parameters are of secondary importance, because they vary not so strong from one compound to another. And, in principle, why not to use VdW parameters of OPLS?

  • Mudar Ahmed Abdulsattar added an answer:
    Is that possible to have negative charge (based on Mulliken Population Analysis) on a metal center of an anionic complex?
    Is that possible to have negative charge (based on Mulliken Population Analysis) on a metal center of an anionic complex?
    Mudar Ahmed Abdulsattar · Ministry of Science and Technology, Iraq

    Mullikan charges are only mathematical abstracts that do not represent the exact experimental charges. Using other methods like NBO with advanced basis sets can give charges that match the experiment.

  • Mudar Ahmed Abdulsattar added an answer:
    If Gaussview has re-generated the atomic labeling system for a z-matrix, is there any way to change the numerically-assigned atomic labels?
    I.e. Change each atom's numeric label whether it be by selecting a sequence of atoms in a specified order, or manually changing each one separately, etc.
    Mudar Ahmed Abdulsattar · Ministry of Science and Technology, Iraq

    You can also change the atomic labels without the use of gaussview by interchanging there coordinates in Gaussian input file

  • Abdallah Sayyed-Ahmad added an answer:
    Which are the differences between the AMBER and the CHARMm Force fields?

    Hi to all,

    AMBER and CHARMm are among the force fields used for computate protein properties.

    I'd like to know Which are the differences between the AMBER and the CHARMm Force fields, and when AMBER or CHARMm should be used for.

    Thank you

    Abdallah Sayyed-Ahmad · Birzeit University

    Hi Alexey, 

    That is why I said "better" not better and the first reference I mentioned reflect your point about folding. But I am not sure that from limited number of examples one can make a final judgment.

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