Theoretical Chemistry

Theoretical Chemistry

  • Mohammadreza Dorvash added an answer:
    4
    How can I measure "Solubility Product Constant (Ksp)" of a protein?

    There is a term in chemistry called Solubility Product Constant or Ksp which is:

    when a chemical compound in the solid state is in chemical equilibrium with a solution of that compound, we can write an equilibrium constant named Ksp.

    aA(s)⇌cC(aq)+dD(aq)

    Ksp=[C]c[D]d

    (this is the link to wikipedia and chemwiki for anyone who wants to read more about it)

    Q: is it possible to measure such value for a protein? how is it possible?

    + 1 more attachment

    Mohammadreza Dorvash

    well

    the thing is that I have a hypothesis:

    we know that:

    protein "X" in the cell has specific solubility and when it is produced more than its solubility, it will be aggregated. Researchers observed this phenomenon for decades. they even used it to improve production of pharmaceutical products. for example when you express a recombinant protein (such as interferon) in E.coli you can make it to form aggregates or some forms of inclusion bodies by changing the temperature etc. 

    my hypothesis is:

    the cell itself, can actively change the solubility of its proteins by post translational modifications. So it may increase the solubility or reduces it whenever required.

    now I want to measure this specific solubility of protein "X" and its modified form in the physiologic state of the cell (without changing temperature or anything else).

  • Pablo Labra-Vázquez added an answer:
    3
    Does the CAMB3LYP functional include by default dispersion corrections such as D3 or does it have to be specified as a keyword in Gaussian 09W?

    I'm running a calculation for which non covalent interactions are important. I've tried B3LYP, PBE0 and B3PW91 with the LANL2DZ basis set but all fail to acurately predict the energy of the molecule's vibrations. I'm starting to use dispersion-corrected functionals, however I don't know which of them already contain dispersion corrections, particularly CAMB3LYP. 

    Pablo Labra-Vázquez

    CAM-B3LYP has actually overcome the problem and predicted really well the molecular vibrations. I'll try other long-range corrected functionals anyways. Thank you both. 

  • Philip James Hasnip added an answer:
    8
    Softwares for Theoretical chemistry?

    What do you recommend for computational chemistry ?

    Philip James Hasnip

    Dear Nora,

    To answer this question properly we need a bit more information about what you actually want to model. Without this information, people are likely to just tell you what they use and/or develop, and you won't know whether it's useful for you or not because you won't know what they are using it for!

    For myself, I develop a plane-wave-based density functional theory program called CASTEP [1], and naturally I recommend it to everyone! However it really is only useful if you want ab initio simulations ("quantum chemistry"), and the requirement for periodicity (because of the plane-wave basis set) is either desirable (materials chemistry, surface chemistry etc) or at least not a problem (e.g. using a supercell approach).

    CASTEP will optimise simulation geometry, perform MD/path-integral MD and compute a variety of spectra (optical/EELS/IR/NMR) but it is an ab initio program, so if a classical forcefield is good enough it would be much quicker to use that (e.g. with DL_POLY, LAMMPS, GROMACS or AMBER).

    Even if you do want ab initio simulations, CASTEP is far from the only program capable of performing them. There are many other ab initio  programs, some also plane-wave-based (e.g. ABINIT, Quantum Espresso, VASP), some with localised basis sets (e.g. FHI-AIMS, CRYSTAL, GAUSSIAN) and some with mixed basis sets (e.g. CP2k). Localised basis sets generally make it harder to get accurate forces and stresses, but are much more efficient for applying the Fock operator in (e.g. Hartree-Fock or hybrid functionals) and of course you don't have to have a periodic simulation if you don't want one.

    Hope that helps,

    Phil Hasnip

    (CASTEP developer)

    [1] http://www.castep.org

  • Vishal Adhav added an answer:
    20
    How to fix the direction of atoms in Gaussian?
    I want to fix the entire model except the boundary H atoms at the optimization procedure by Gaussian 09. The direction of the H atoms are also needed to fix. Only the bond distances are optimized. If the H atoms are restricted by fixing both the angle and dihedral angle, it can make sense. However, there are many atoms to fix, it is cumbersome. Is there an easy way? Thank you.
    Vishal Adhav

    Hi

    i am doing PES scan using  ModRedundant but my file got terminate so how can i restart it?

  • Bojidarka B. Ivanova added an answer:
    4
    Which is better on MP2, Dunning's triple zeta vs Pople's 6-311 G ?

    Hello there. 

    I am a student. 

    I am working with a system which involves mapping PES with a system that has multiple rings,  with MP2 and MO6-2X.

    Does Dunning triple zeta better than the conventional Pople's triple split basis? 

    Thank you in advance for your ideas. 

    Bojidarka B. Ivanova

    Mr. Cuyacot ,

    Yes it is, but it is slower as computtional cost.

  • Ashar J Malik added an answer:
    1
    Can anyone explain the algorithm for the calculation of change in energy by Ewald sum method?

    I am having problem with ewald sum energy calculation part.

    I have written the code and validated it with NIST data for total coulomb potential, it is matching well. But when i am trying to calculate  change in coulomb potential (new configuration - old configuration), i am confused with this part.

    Ashar J Malik

    Hi, 

    It is not clear from what you have written - to completely grasp what the problem is. Could you please add some more information?

    What is the system you are studying - values will depend on that.

    When you say you wrote some code - does that mean you wrote it yourself - or put together libraries? What language are you using?

    What exactly is confusing you? Are the values not what you are expecting?

    If you add the above information you will be better able to get a coherent answer.

    Best,
    /A 

  • Christopher Xiaoquan Sun added an answer:
    3
    What things should be take into account, when building structure for CASTEP calculations in material Studio?

    I want to Calculate band structures and phonon calculations by using CASTEP, so kindly guid that what things are important for building the crystal structures for such calcualtion in Material Studio?

    Christopher Xiaoquan Sun

    Agree with Otto, reading through those document is like studying simulation throughly.

  • Christopher Xiaoquan Sun added an answer:
    2
    What does CPU time stand for in the OUTCAR of VASP?

    The CPU time in at the end of OUTCAR is very much different for the time it take in reality.

    I want to know from where I will got the exact time of calculation?

    As I am checking the same file on different number of nodes so I can compare the time of calculation? 

    Christopher Xiaoquan Sun

    I know the computing time in Gaussian is real time * the number of core

  • Yasaman Jami added an answer:
    3
    Can anyone suggest a reliable force field for Cd++?
    Can anyone suggest a reliable force field for Cd++?
    Yasaman Jami

    Amber should work,

  • Parmendra Kumar Bajpai added an answer:
    5
    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? 

    Parmendra Kumar Bajpai

    I can suggest you books that deals with this problem. Apart from Wilson, Decius and Cross, already suggested by someone, You may consult, Infrared and Raman Spectra by G.Turrel, and similar title by S. Califano. 

  • Ben Joseph Cuyacot added an answer:
    17
    Are der instances that theoretical catching of a TS is impossible even if experiment suggests it exist (LFER) for some "very concerted" reactions?

    Good.day,

    I've been calculating and searching a TS 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 TS 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...  

    Thanks...

    Ben Joseph Cuyacot

    Thank you guys. 

    Live long and prosper. :)

  • A. M. Verma added an answer:
    7
    Should ZPVE also be added in the result of SPE?

    Dear all,

    I got confused.

    I have optimized the geometry and calculated the SPE also on the optimized geometry. I think it's right (correct me if I'm wrong. I'm beginner). I saw one paper in which ZPVE was added to SPE. However, SPE doesn't calculate ZPVE but frequency calculation does.

    So am I right or wrong?

    Thanks

    A. M. Verma

    Thanks Bartosz 

    That was quite helpful and elaborated reply. Even Gaussian guys didn't elaborate this much.

    Thanks once again

  • Mohamad Johari Abu added an answer:
    4
    How do I create an equation from two projection point in the ternary system?

    The tie line between basis point to solid solution. for example, in CaO-CuO-TiO2 ternary system; the projection tie line from CaO (1,0,0) to solid solution type (12.75, 37.25, 50), so how to create an equation from this line.

    tqvm

    Mohamad Johari Abu

    Thank you. very helpful for my understanding.

  • Anthony Nash added an answer:
    4
    Are there cases of protonation of a nitrogen (schiff base), which do not have transition states using DFT?

    From an earlier question I was grateful to learn about the two step process for the movement of a double bond from a Schiff base (-N=C) down the backbone of a glucose molecule to form C=C. This involved 1) the protonation of the nitrogen, then 2) the removal of a hydrogen from the further carbon involved in the eventual C=C.

    If I start from my schiff base, should the protonation of the nitrogen be considered as an intermediate step with OR without a transition state? For example, I cannot optimise a starting structure with H3O, it converges to be a protonated schiff base plus H2O. Equally I can't optimise the protonated intermediate having first used H2O (the intermediate N+ .... OH-, always reverts back to N .... H2O). 

    As a protonation is simply the acceptance of a proton from the environment, is there a transition step for it? Or is it just a further intermediate step before the transition step which would be the removal of the hydrogen from the carbon chain with the shift of -HN+=C-C to -HN-C=C?

    Many thanks

    Anthony 

    Anthony Nash

    Hi Bojidarka,

    Many thanks for the response. That is a lot of information. I am currently reading through the attachment and going through your reference. 

    With regards to you final question, this is not a process of organometallic intermediates. This is a compound which we have isolated in the lab in a solution of lysine, arginine and glucose. The product is glucosepane. I am currently working on defining the possible reaction pathway. Unfortunately, there is no quantum mechanical data to use. 

    Thanks again for the material. 

  • Bojidarka B. Ivanova added an answer:
    4
    How do I optimize a Pi state using Gaussian?

    I am looking to optimize doublet Pi state of LiNO+ using gaussian by ccsd(t). Every time I optimize it is optimizing doublet Sigma state. How do I optimize the Pi state? Thanks in advance.

    Bojidarka B. Ivanova

    Mr.  Anusuri,

    Please follow the discussion below and the shown sub-link:

    https://www.researchgate.net/post/Any_advice_on_excited_state_density_from_GAMESS_US#568782215dbbbda9b98b45df

  • Joaquim Mª Rius Bartra added an answer:
    9
    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!

    V.R.,

    Eric Z

    Joaquim Mª Rius Bartra

    Dear Eric,

    I suggest you to take a look in my guide and maybe could help you,

    I hope it helps you,

    Joaquim

  • Mk Amshumali added an answer:
    4
    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?

    Mk Amshumali

    Thank you Joaquim Rius,

    I Think I have to depend on Guassian.

    Muchas Gracias!!

  • Jacques Lavau added an answer:
    4
    Does anyone know of a proof, that the divergence of a vector field exists?

    Does anyone know how to prove, that the defining limit, is actually well defined?

    Please see attachment.

    Roger

    Jacques Lavau

    There is at least an inferior horizon limiting the validity and competence of the scholar geometry we were taught. Unlimited extrapolation from our macroscopic habits into the microphysics domain has never been validated.

  • Sadeem Fadhil added an answer:
    17
    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

    http://www.nature.com/nmat/journal/v6/n3/full/nmat1846.html

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

    Sadeem Fadhil

    Dear Eugene

    Sure I will disseminate to you and to public when its ready, but still I need to confirm through calculations before anything.

  • Manimaran D added an answer:
    13
    What software can I use to compute the conceptual-DFT Fukui function?
    Im interested in the Fukui function of conceptual-DFT, but I dont know how to compute it.
    Manimaran D

    Hello Ramón Alain,

    I hope Dr. Tian Lu - Multiwfn program may HELP you to compute Fukui function from the Gaussian Output file. Kindly find one more similar program.

    UCA-FUKUI

    Introducing “UCA-FUKUI” software: reactivity-index calculations

    http://link.springer.com/article/10.1007%2Fs00894-014-2492-1

    Download Link: http://www2.uca.es/dept/quimica_fisica/software/UCA-FUKUI.zip

    Hope it's HELP : )

    regards,
    Mani

  • Ali Nasir Imtani added an answer:
    15
    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 ? 

    Ali Nasir Imtani

    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 ?

    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:
    4
    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:
    7
    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

    Well,

    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:
    3
    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,

    Rafik

  • Manohar Sehgal added an answer:
    2
    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:
    17
    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 'http://www.gaussian.com/g_tech/g_ur/k_scrf.htm' 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:
    12
    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:
    7
    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:
    3
    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: http://homepage.univie.ac.at/mario.barbatti/papers/review/worth_ann_rev_phs_chem_55_127_2004.pdf

    And in this paper you can find an example on the quality of the surface hopping in comparison to more precise methods: http://scitation.aip.org/content/aip/journal/jcp/138/9/10.1063/1.4793274

  • Jerzy Hladyszowski added an answer:
    2
    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

    or

    #P pm3 opt=Z-Matrix nosymm order

    I found the "order" command in this websites.

    http://www.lct.jussieu.fr/manuels/Gaussian03/g_ur/u_newzmat.htm

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

    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

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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