Theoretical Chemistry

Theoretical Chemistry

  • 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.

    Regards,

    M.

  • 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:

    http://books.google.de/books?id=SzpeidfI8MwC&printsec=frontcover&hl=de#v=onepage&q&f=false

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

    thanks

    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.

  • Ali Ghiami-Shomami added an answer:
    To purchase suitable gaussian version?

    I  want to  minimize the energy of organic molecules that are used in my study, I have checked on internet and found that the gaussian 09 rate is $1150. It is expensive, Please tell me how I can purchase a cheaper version suitable for my studies?

    Ali Ghiami-Shomami · University of Guilan

    Hi Dear Shama

    Here, you can see lists of computational chemistry software from this website:

    http://www.ccl.net/chemistry/links/software/index.shtml

    Also, I attached this picture that compares many common computational chemistry programs together with their prices.

    I hope it helps.

  • Can someone help me run an Energy Decomposition Analysis (EDA)?

    I'm trying to identify the types of interactions that take place between a Surface Group in an Activated Carbon and a pollutant, to determine what fraction of this interaction energy is dispersive, covalent, etc. Any help (software, methods, etc.) will be welcomed.
    Thanks in advance.

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

    Thanks everybody, always a pleasure

  • M. Farooq Wahab added an answer:
    What do you understand by the signs on the electrode potentials as used in electrochemistry?

    Dear readers, I am doing a short academic survey on some concepts in electrochemistry for educational purposes. The question is simple: What do you understand by the negative and positive signs for the half reactions as they appear in standard electrode potentials. Textbooks often use a sweeping statement by stating that these are merely sign conventions. However, there is perfect logic behind using the signs. Kindly answer number-wise.

    1) What do you understand with special reference to the sign for the half cell?

    Zn2+ + 2e ---> Zn,   E = -0.76 V vs. SHE

    2) Do you agree that the negative sign is a "electrostatic" sign, which simply means that the zinc electrode is "negatively charged" in an electrostatic sense when a zinc rod is dipped in a zinc sulfate solution? Whereas the hydrogen electrode is positively charged, again in electrostatic sense. This implies that it is incorrect to write the following equation, because the electrostatic sign is invariant. 

    Zn --> Zn2+ + 2e   E = +0.76 V, which is often shown in textbooks?

    Thank you.

    M. Farooq Wahab · University of Texas at Arlington

    Thanks Prof. Ybarra. It is indeed a useful theoretical treatment. Please continue. With that, we should also be able to find an experimental way for case II in your notes. Your case II proves that a potential difference develops when the metal is dipped in an electrolyte. The ideas of double layers were known a century ago. What experimental and observations did these people have which made them think about the double layers at the metal-electrolyte interface and consequently how did they determine the sign of the electrode wrt to the electrolyte? I will also try to find more about it.

  • Solomon Jacobson added an answer:
    How to get the potential energy surface (PES) for adenine interacting with graphene using DFT?
    I want to calculate the minimum energy geometries (mutiple minima) of adenine on surface of graphene
    Solomon Jacobson · Henkel AG & Co
    It depends on how much computer time you have available. I would start with a model of the graphene surface. You can use a 2-d periodic model or a small cluster model. If you use the small cluster model it should be 2 or 3 time larger than the adenine. Next I would generate several random configurations for adenine-grahene pair. Then minimize with DFT and use a Monte-Carlo accept/reject criteria. I would also fix the graphene geometry at this point, buf you can do a complete miniziation for the best few conformations.
  • Ferhati Azedine added an answer:
    How do I install the Gaussrate interface for Polyrate?

    I received the following message:

    Welcome to GAUSSRATE 2009-A!

    ... installing
    grep: ../src/Makefile: No such file or directory

    Do you want to use GAUSSRATE to perform VTST for
    barrierless association reaction with varaible reaction
    coordinate and multifacted dividing surface?
    Note: only MPI version available and this executable is only for VRC-VTST [ yes ]: no
    .... creating Makefile
    .... done with Makefile
    ehook:
    Compiler error line 349 of common.inc: Too many names.
    Table limit now 802.
    Try rerunning with the -Nn1604 option.

    /usr/bin/f77: aborting compilation
    gmake[1]: *** [hooks_gr.o] Error 255
    gmake: *** [GRS] Error 2

    ---- GAUSSRATE INSTALLATION COMPLETE ----

    Have a nice day! :)

    Ferhati Azedine · The University of Batna

    it seems there is some file missed : mpif.h  one of them

    so the problem is resolved

    many thanks to Anouar Rekik  for his kind availability

  • Bartłomiej Gostyński added an answer:
    Can I switch my GD2 dispersion model to a GD3 dispersion model in the wB97xD functional in Gaussian 09?

    In DFT calculations, the wB97xD potential uses the built-in GD2 dispersion model.

    Is there any way to "switch" it to the GD3 model, either by manipulating e.g. IOp(3/124) or by defining proper parameters e.g. S6 = 1.00, D = 6.00 and so on?

    Bartłomiej Gostyński · Centre of Molecular and Macromolecular Studies in Łódź

    The information was very helpful, thanks you all.

  • Adedapo Adeyinka added an answer:
    Does anyone know a protocol to measure the intramolecular interactions energy between two oxygen atoms?

    We have crystallized some bioactive organic molecules. On the basis of van der Waals radius of oxygen we found them to possess remarkably short intramolecular oxygen...oxygen interaction. Further, the molecular orbital diagram showed pear shaped orbital overlap between two oxygen atoms.

    The characterization of the electron density of such O…O interactions is not common in the literature. But a learned gentlemen tells me that the vdW-radius is a poor descriptor for covalently bonded atoms.

    Another idea was to conduct theoretical analysis by Bader theory (AIM—‘‘Atoms in Molecules’’) to support the experimental observation. I hope it is capable of detection of weak interactions of any type such as hydrogen bonds, van der Waals, dihydrogen bonds, oxygen-oxygen interactions etc.

    However, for that I’m told that any two overlapping spherical electron densities will yield a bond critical point. A pre-requisite for a BCP as an eigenvalue of the diagonalised Hessian matrix of the total electron density is a local maximum in the Laplacian of the density. No rearrangement of the electrons is required for this purely geometrical effect.

    In short I’m confused how to go about. I’m an Organic synthetic chemist, who knows Synthesis, characterisation by spectroscopy and crystallography. I’ve also some experience in deterring themal behavior using DSC, TGA and DTA. I know that whether geometric electronic or any other effect, an interaction between O-O if not repulsive is remarkable. However, the theoretical aspect is beyond me, kindly help!!

    Adedapo Adeyinka · University of Pretoria

    Dear Chiranjeev,

                                   This is just to allude to what Sergio said, for your kind of investigation the Interacting Quantum atoms method is  probably your best option in this case. As Sergio said its only constraint is its long computation times (due to the fact that originally one could only use Hatree-Fock or MP2 wavefunctions to calculate interaction eneegies and given that HF level of theory is not good enough to obtain accurate informations on most molecular systems) . However recently with the AIMALL program of Todd Keith it is possible to carry out IQA calculations on B3LYP optimized structures and that is much faster. Maybe you should explore this option.

    Best Regards,

    Adedapo

  • Elbay Malikmammadov added an answer:
    How are the weights of potassium dihydrogen phosphate and dipotassium hydrogen phosphate obtained when preparing phosphate buffer?

    The preparation of buffer requires you to dissolve 1.816g of potassium dihydrogen phosphate in water, and dilute to 200mL with the same solvent.

    Then you dissolve  2.322g of dipotassium hydrogen phosphate in water, and dilute to 200mL with the same solvent.

    Then you mix 188.8mL of the first solution and 11.2mL of the second solution. If necessary, you adjust the pH to 5.6 using the first or second solution.

    However, how are the weights of potassium dihydrogen phosphate and dipotassium hydrogen phosphate obtained? What is the theoretical basis for obtaining these values?

    Elbay Malikmammadov · Middle East Technical University

    It is actually quite easy. You have to use Handerson-Hasselbach equations (as mentioned above) and have some Analytical Chemistry knowledge such as:

    To prepare a buffer, best method is to calculate how much of each ion you are required to put by Handerson-Hasselbach equation (before that you of course should know how much volume of the solution you are required to use to prepare at least some more of the required volume). Let's solve a small example of preparation of a 1 liter of buffer of phosphoric acid solution having pH=6: (explanations are written in bold)

    Firstly you need to do the calculations via Handerson Hasselbach equation. pKa's of phosphoric acid are 2.3, 7.21 and 12.35. If required pH is 6, then, 7.21 will be used, since it is more near to the needed pH. This means, monopotassium dihydrogen phosphate and dipotassium monohydrogen phosphate (diprotic (H2PO4-) and monoprotic (HPO4--) potassium salts) will be used.

    pH = pKa + log ([A-]/[HA])                 HANDERSON-HASSELBACH EQUATION

    Now, for A- you put K2HPO4 concentration, and for HA you put KH2PO4 concentration:     BECAUSE IN K2HPO4 THERE IS ONE H+ LESS THAN KH2PO4

    6 = 7.21 + log(A/HA)
    log(A/HA)=-1.2
    A/HA = 0.063

    So, now you know the fold difference between these salts, and the Molarity of the solution would be given to you, and you can calculate the required amount:

    HA+A=0.05
    A/HA=0.063

    HA=0.047M
    A=0.003M

    This means, you need to put 0.047 moles of KH2PO4 and 0.003 moles of K2HPO4 salts into 1 liters of solution (molecular weights: KH2PO4= 39+2+31+4*16=136amu; K2HPO4= 39*2+1+31+4*16=174amu)

    Thus, 0.047*136=6.392g of KH2PO4 and 0.003*174= 0.522g of K2HPO4 should be added.

    But, you should also note that, if |pH-pKa| >1 , then buffer capacity of solution decreases. In this case, it is equal to 1.2   WHICH MEANS IT WOULD BE HARDER FOR BUFFER SOLUTION TO RESIST AND KEEP THE pH OF SOLUTION STABLE

    I hope the calculations are clear. If you still have any questions you can ask by commenting.

    Best Regards.

  • Matthew D. Miller added an answer:
    Anybody familiar with the freezing of atoms in gaussian software?

    If we use -1 for freeze the atoms all the direction of the atoms are freezes  but I want freeze atoms particularly one Cartesian axis just say Z-direction remaining two direction relaxes. Is it possible in Gaussian?

    Matthew D. Miller · Semichem Inc.

    I have performed calculations with a limited number of atoms frozen using cartesian coordinates (truncated protein with a ligand).  I suggest testing the file format shown by Dr. Ruangpornvisuti above.  The column flagged with 0 for atom optimization and -1 for atom freezing does work.  Upon completion of the calculation, files can opened and the frozen atoms will align correctly on top of each other.  This column is not required in an input file by default and is assumed to be 0 when not included.  This is described in the oniom section of the manual (search for freeze).

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

    It is possible to use z-matrix coordinates to freeze atoms, although I am uncertain why this would be preferable to do.  If it is desirable to use z-matrix (use the readfreeze option), it is very important to list atoms that are frozen at the top because atoms which shift in position during optimization will be used as a reference point for the frozen atoms and the frozen atoms will not actually remain in the same position.  However, if the frozen atoms are listed first, each frozen atom will reference frozen atoms and it works.  The "notatoms" and list of atom numbers to be frozen should be included in the input file.  I had some challenges using the z-matrix and suggest using the cartesian coordinates.  Readfreeze is described in the following section:

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

    I suggest you confirm the atom positions do not move by viewing the input and output files overlaid. 


    Good luck,

    M

  • Tatiana Korona added an answer:
    What quantum-chemical method is preferable to determine the dispersion interaction between the low-polar molecules?

    What quantum-chemical method is preferable to determine the dispersion interaction between the low-polar molecules?

    Tatiana Korona · University of Warsaw

    @Alexey Nikitin

    It cannot be true that SCS-CCSD is not cheaper than CCSD(T). SCS-CCSD is just a CCSD code with the final energy calculated as a weighted sum of SS and SO components. For CCSD(T) you need to calculate CCSD first (cost: o^2v^4 times number of iterations, where o,v are numbers of occupied,virtual orbitals), and then the perturbative (T) correction (cost: o^3v4). For large molecules (large "o") this is much more expensive than CCSD (or SCS-CCSD).

    Returning to the original question: SAPT(DFT) vel DFT-SAPT is a good method to calculate intermolecular interaction energies, including the dispersion contribution.

  • Ferhati Azedine added an answer:
    How to convert Gauusian 09 file to .xml using babel or obabel?

    this conversion is needed for Mesmer3.0  (kinetics)

    Ferhati Azedine · The University of Batna

    many thanks to Reinaldo Molina-Ruiz and
    Aristotelis Zaras 

    the problem is over  both Babel and Obabel work for me

  • Tatiana Korona added an answer:
    How to calculate the bond polarizability in a molecule?
    I want to calculate the value of polarizability of the bond in the presence and absence of external field for a molecule
    Tatiana Korona · University of Warsaw

    Atom-atom, atom-bond, bond-bond "polarizabilities" can be defined within the Hueckel model, see e.g. Quantum Chemistry, 3rd ed. by J.P.Lowe and K.A.Peterson, pp. 406-408. The atom-atom polarizability lk shows how the electron density at atom l will change if the Coulomb integral at atom k changes etc.

  • Paul Fleurat-Lessard added an answer:
    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.
    Paul Fleurat-Lessard · Claude Bernard University Lyon 1

    Hi,

    If you want to fix only one cartesian direction, then the easiest is to use Opt=Z-mat and then define the variables to be optimized and those to be fixed. For example, let's consider the water optimization with the z-direction fixed for the second hydrogen atom.

    #P B3LYP 6-31G(d,p) Opt=Z-mat

    Optimization one OH distance.

    0,1

    O xO yO zO

    H xH1 yH1 zH1

    H xH2 yH2 zH2

     xO 0.

     yO 0.

     zO 0.

     xH1 0.

     yH1 1.

    zH1 0.

     xH2 0.

     yH2 0.

     zH2 1.

     Regarding the example of Christian Vidal, one example would be (still H2O):

    #P B3LYP 6-31G(d,p) Opt=ModRedundant

    Optimization one OH distance.

    0,1

    O 0. 0. 0.

    H  0. 0. 1.

    H  0. 1. 0.

     2 F

    This would freeze the second H atom.

    Hope this helps,

    Paul.

  • Ahsan Z Rizvi added an answer:
    How can I initialize a covariance matrix in Kalman filter based backpropagation algorithm?
    We are using Kalman for ANN training.
    Ahsan Z Rizvi · Indian Institute of Technology Indore

    @ Leonard Kramer, Thanks 

    I also did the same. And it is working :)

  • Tatiana Korona added an answer:
    Why do I have an error message in qcisd calculation?
    I am trying to do a frequency calculation using TZVP basis set at QCISd method in Gaussian 09 version, but I have an error message.
    ....................................................

    DD1Dir will call FoFDir 1 times, MxPair= 552
    NAB= 276 NAA= 0 NBB= 0 NumPrc= 6.
    DE(Corr)= -1.2204516 E(CORR)= -563.35323981 Delta=-1.16D-09
    NORM(A)= 0.12234534D+01
    *************
    *MAX. CYCLES*
    *************
    Largest amplitude= 3.70D-02
    Error termination via Lnk1e in /home/rameswar/g09/l913.exe at Sun Aug 25
    14:27:37 2013.
    Job cpu time: 36 days 4 hours 3 minutes 14.3 seconds.
    File lengths (MBytes): RWF= 34915 Int= 0 D2E= 0 Chk= 48
    Scr= 1

    ..........................................................................
    Can I restart the job again? What are the keywords I need to include in
    the root section to get a normal termination?
    Tatiana Korona · University of Warsaw

    Delta=-1.16D-09 denotes that your energy is practically converged, so if you just want the QCISD energy, you can use E(CORR)= -563.35323981 as your final result.

  • Tatiana Korona added an answer:
    How to run SCAN in gaussian software ?
    The bond angle changes when the molecule have more than one structure eg. tautomeric form...
    Tatiana Korona · University of Warsaw

    You can also use webmo.net to produce input scripts for you: go to working demo, build your molecule and select Tools-> Edit Z-matrix, where you have a possibility to select  a bond, angle etc. to be scanned.

  • Xin-Yu Wang added an answer:
    What's the differences of "hopping", "tunneling" and "superexchange"?
    In such as "Electron Tunneling Pathways and Role of Adenine in Repair of Cyclobutane Pyrimidine Dimer by DNA Photolyase",
    J. Am. Chem. Soc. 2012, 134, 8104 − 8114
    Xin-Yu Wang · Nankai University

    Oh. Finally I found the exact answer in this great TUTORIAL REVIEW

    Electron transfer in peptides and proteins

    by

    Meike Cordes and Bernd Giese 

    @

    http://pubs.rsc.org/en/content/articlehtml/2009/cs/b805743p

    The keypoints are

    "that an overlap between donor and acceptor orbitals allows electron tunneling or super-exchange between the redox partners"

    "the separating matrix is regarded as a bridge between the two redox partners, with bridge orbitals involved in electronic communication between donor and acceptor,
    thereby lowering the potential barrier and facilitating electron tunneling"

    "Since ET rates drop exponentially with increasing distance, a practical upper limit for reasonably fast ET through proteins exists"

    "Distances that exceed the upper limit for fast electron tunneling reactions can be overcome in a multistep hopping process"

    "the main characteristics of sequential ET (hopping) are the occurrence of chemical intermediates"

    "superexchange ET shows a strong exponential distance dependence, whereas electron hopping exhibits only weak distance dependence"

  • Behnam Farid added an answer:
    Can we consider the reduced mass of free particles equal to the yielded mass from combining these particles?

    Its well known that the yielded mass from combining two particles is lesser than the summation of their free masses. The reduced mass is also lesser than the summation of their individual masses. I want to know, experimentally, is the reduced mass equal to the mass yielded from the combining particles?

    Stam Nicolis is right.

  • M. K. Dwivedi added an answer:
    How can I partially optimize the molecular geometry by freezing atoms coordinates using GAMESS?

    The ifreez/iactat option in GAMESS doesn't working when I performed runtype=optimize. The structure is getting optimized to E_minimum with all atoms.   

    In addition to above, you can use FMO method also. Which allow to use IFREEZ (1)=1, 2,...

  • Rosa Al-noor added an answer:
    Can anyone help with an error message (convergence failure) in Gaussian 09?
    I'm working in Zr cluster system using DFT B3LYP calculation in Gaussian 09. I get an error message convergence failure. I tried simple basis set sto-3g basis set calculation checkpoint file moving to larger basis set DFT B3LYP but also get the same error. Any suggestions?
    Rosa Al-noor · Al-Mustansiriya University

    Great!! that’s good news Sk Jahiruddin.

  • Closed account added an answer:
    I was wondering if it is possible to perform a calculation in Gaussian 09 using MMFF94 forcefield?
    In the manual only Amber, Dreiding, and UFF Molecular Mechanics Methods are described.

    Any ideas if this is possible?
    Deleted · University of Cincinnati

    The L402 link reads in IOp(4/20=N). According to the IOp manual, N=18 is MMFF. IOp(4/33=3) may be used to print all information about the force field being used for testing purposes. I'm not entirely sure that route will work though. But it may be a shortcut to the implementation you are pursuing using BUF94, VDW94, etc.

    --

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

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

  • Alexey Nikitin added an answer:
    Is the hydrogen bond directed?
    In some force fields, the hydrogen bond is described not only by the electrostatic term, but the angle one. Does this have any justification other than the crystallographic statistics?
    Alexey Nikitin · Институт молекулярной биологии им. В.А. Энгельгардта Российской академии наук

    This article contains references to the history of the directionality:

  • Elie Kawerk added an answer:
    Is anyone an expert in electro-negativity and single electron density?

    In organic radicals, is there a relationship between the single electron density and electronegativity of the substituent on the atom possessing single electron?

    Elie Kawerk · Università degli Studi di Trieste

    Dear Rina, 

    I suggest that you read the following publication: https://www.researchgate.net/publication/232248885_A_new_method_to_derive_electronegativity_from_resonant_inelastic_x-ray_scattering 

    in which the authors derive the electronegativity of a radical from a spectroscopic parameter related to the electronic density of the excited electron. 

    Best regards

  • 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 :)

  • Devarajan Thangamani added an answer:
    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.
    Devarajan Thangamani · Bharathiar University

    Sir what software used to calculate the fugi function....

  • Antonio Del Zoppo added an answer:
    How can we derive the transmission probability of a charged particle in a parabolic barrier?
    How can we derive the transmission probability of a charged particle in a parabolic barrier?
    Antonio Del Zoppo · INFN - Istituto Nazionale di Fisica Nucleare

    The exact solution of the problem of quantum transmission through an inverted parabolic barrier is given by the formalism in Physical Review 89, 1102 (1953), the so-called Hill-Wheeler formula.

    Antonio Del Zoppo

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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