Theoretical Chemistry

Theoretical Chemistry

  • 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

  • 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

  • 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

    you welcome..hopefully the things going well with you.

  • Sayyed Jalil Mahdizadeh added an answer:
    How one can theoretically calculate the electrical conductivity of materials?
    I'm going to calculate the electrical conductivity of some materials (like graphene) theoretically. Do you have any recommendations about suitable theoretical methods or can you suggest good references?
    Sayyed Jalil Mahdizadeh · Ferdowsi University Of Mashhad

    Thank you so much guys.

  • 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.

  • Thomas La Cour Jansen added an answer:
    How do you calculate dipole moment of an anion?

    I want to calculate potential energy curve and change in dipole moment for F- (fluorine anion) approach to the H2 molecule. Since, dipole moment of ionic molecule depends on the choice of reference, which reference is more convenient: center of mass of H2F- or center of charge or simply calculate at the center of mass of only H2 molecule?

    Thomas La Cour Jansen · University of Groningen

    @Carlos, Imagine that you have a system with just one point charge! If you now place the origin of your multipole expansion on the position of this charge (which is then also the centre of charge) you will get that the charge of the system equals to that charge and all higher multipoles will be zero. This is the most convenient situation. Of course you can use other points mathematically, but it does not give much sense to say that a system with a single point charge has higher multipole moments. In systems with real charge distributions you essentially remove the contribution to the multipole moments from the overall charge by using the centre of charge as origin. The overall charge then only contributes to the first (the charge) term. Reporting the origin you use is of course still a good idea as obviously not every know that the centre of mass is the best.

  • 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.

  • Viorel Chihaia added an answer:
    When calculating with gaussian 09, if the frequency becomes negative what should be done?
    I am interested in calculating & calculate frequency with gaussian 09
    Viorel Chihaia · Jülich Supercomputing Centre

    A way to avoid the transition state in the optimization is to rescale the system geometry (I recommend the expanding of the system). Thus the collective low frequency modes are "excited" and the system will avoid the TS during the geometry optimization.

  • Debabrata Singha added an answer:
    How can I optimize a dimerization of dye by using gaussian 09?

    How should I find the input geometry for the dye that undergoes H-type aggregation? I start with optimization of monomer by DFT and TDDFT. I have experimental IR, UV, NMR data. So I want to compare my expt with theory, so I need input geometry of dimer. So how should I find the input geometry?

    Debabrata Singha · Indian Institute of Technology Guwahati

    Thanks Mariano,

    I am using coumarin as chromophore.I placed two monomers at parallel and anti parallel orientation and starting to optimizing the ground state. But the problem is that when optimized ground state structure is very different than input i.e.making an angle of 40 degree to each other. . So if i change suppose the distance between monomers and optimize the geometry so how much accurate is this, as ultimately i will get optimized structure of 40 degree.

  • Melchor Sanchez-Martinez added an answer:
    Is it possible to know computationally that a compound can be activated by solar energy or not?

    Dear all, theoretical chemistry now a day has been found to be very promising in giving us ideas about reaction mechanism involved in a certain reaction. I want to know is it possible to know about how much energy can possibly activate a compound by theoretical calculation..Is it the HOMO-LUMO energy gap calculation..

    Melchor Sanchez-Martinez · Spanish National Research Council

    Sure that this prediction is possible. You can calculate the Homo-Lumo gap with a lot of QM programs like Gaussian, Orca, Gamess....(Use the cclib python library is a useful way to extract data from the QM program outputs http://cclib.sourceforge.net/wiki/index.php/Main_Page).

    In fact, and active research line is the  Charge and energy transfer in DNA and proteins ( some groups work on it : Voytiuk, Curutchet...) that try to measure the effect of the solar radiation and so on.

  • Subrat Kumar Pattanayak asked a question:
    How can I run g_vanhove function in GROMACS 4.6.3 version

    How can I get the graph like self part of van Hove function ? I ran g_vanhove -f .trr -s .tpr -n index.ndx -or vanhove _r.xvg but not getting graph.I tested for both 100ns and I ns ,any changes required in my .mdp file

  • Mudar Ahmed Abdulsattar added an answer:
    Automatically put data into Excel file from Gaussian 09 output files?
    Has anyone developed a program to take the enthalpy, entropy, and free energy from a Gaussian opt+freq output file and automatically plug it into an Excel file such that these values are listed in kj/mol in a table with appropriate headings? Any thoughts if not? I picture something where you can drag and drop the file into the program and it automatically populates your Excel file with your data to help speed things along. Thanks in advance!
    Mudar Ahmed Abdulsattar · Ministry of Science and Technology, Iraq

    Dear Ziegler

    You can do this by your self by (copy and past) from Gaussian output to excel. You can also use (text to column) in Data command to transform the Gaussian output exact columns you want. Finally, you can use the sorting facility in excel to sort the output in a descending or alphabetic order.

  • Debabrata Singha added an answer:
    How can I get AOT reverse micellar structure for theoretical chemistry?

    I need a input file for optimization of AOT reverse micellar system by Gaussian or Molecular mechanics. I would like to know is there any possibility getting .pdb or .cif file of AOT reverse micellar system.  

    Debabrata Singha · Indian Institute of Technology Guwahati

    Dear Stephane,

    Thanks for providing me AOT structure. We used to do gaussian calculation  and time resolved spectroscopy, recently we done a some work on synthesis of AgNPs in AOT RM and how the environment of RM perturb when nano particle generated in its core by experimentally doing photophysical study. So, now our aim is how a dye molecule behave in AOT RMs. Lots of work experimently done on this topic to understand the dynamics of RMs assembly but very less work done on perturbation of RMs interface by NPs theoretically. So we would like to have your advice, how should we progress.

  • Venkatesan Ragavendran added an answer:
    How do I choose the best exchange correlation functional for running a DFT calculation?

    Any recommendations on options for exchange correlation functionals ground and excited state DFT computations for single point as well as optimization jobs.

    Venkatesan Ragavendran · Sri Chandrasekharendra Saraswathi Viswa Mahavidyalaya University

    Hi manohar,

    My suggestion to your problem is that first optimize your compound with am1, then use it for hf optimization then check its suitability with dft optimization if not runs go for M06-2x an M05-2x. This will help you definitely. While you computing using M06 or M05 use this keyword

    #m062X/6-31+G(d,p) integral=ultrafine

    You can get your results fruitfully soon.

    Best wishes........

  • Mehdi Brahim added an answer:
    When XRD analyzed, what does it mean when a shifted peak is either left hand or right hand?
    XRD graph has a shifted peak when vary contents materials or vary temperature. The peaks on plane changed such as transfer to another degree, higher intensity, lower intensity. What do these indicate?
    Mehdi Brahim · Welding an NDT Research Center (CSC) Algeria

    When XRD peak moves either right or left ca mean there are constraints or machining, either residual stresses, therefore, they are positive or negative, depending on the displacement peaks

  • Avery Sader added an answer:
    Is it okay if my calculation frequency criteria it has not fulfilled in transition state optimization?

    I made a transition state optimization and the four convergence criteria are met, opt = (TS, CalcFC, Noeigentest), but calculating frequencies separately only three criteria for the convergence of the frequencies were met but I got the normal mode of vibration that I was looking for. It left me no error in the calculation of frequencies. Is it okay if my calculation frequency criteria it has not fulfilled?

  • Rina Dao 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?

    Rina Dao · Zhejiang University

    thank you Ramón Alain Miranda-Quintana, I understand your first point, (that electronecativity of whole molecule equals the E.N. of the substituent group). 

    but I don't understand the second idea. what you talk about seems the origin of DFT, but how does it relate to the density of an unpaired electron ? could you be more specific on that ?

  • Kapil Dhaka added an answer:
    I am having problems calculating hardness; is it (ionization potential - electron affinity) or 1/2(ionization potential - electron affinity)?
    I found these two formulas in different articles, which one is better to use and reasonable?
    Kapil Dhaka · Birla Institute of Technology and Science Pilani

    Ideally  its (I-A)/2 but if one is interested in behavior of graphs, You can use (I-A) too. Both are correct.

  • Florent Di Meo added an answer:
    Theoretical study of DPPH radical scavenging activity - can anyone provide suggestions for further improvements?

    We have studied the self-catalyzed Knoevenagel condensation, spectral characterization, DPPH radical scavenging activity, cytotoxicity, and molecular properties of 5-arylidene-2,2-dimethyl-1,3-dioxane-4,6-diones using single crystal XRD and DFT techniques. In the absence of any catalyst, a series of novel 5-arylidene-2,2-dimethyl-1,3-dioxane-4,6-diones were synthesized using Meldrum’s acid and formylphenoxyaliphatic acid(s) in water. These molecules are arranged in the dimer form through intermolecular H-bonding in the single crystal XRD structure. Compounds have better DPPH radical scavenging activity and cytotoxicity against A431 cancer cell line. The optimized molecular structure, natural bond orbital analysis, electrostatic potential map, HOMO–LUMO energies, molecular properties, and atomic charges of these molecules have been studied by performing DFT/B3LYP/3-21G(*) level of theory in gas phase.

    Florent Di Meo · Linköping University

    Hey, 

    For theoretical studies, I would suggest you to read this paper and especially references herein about HAT mechanism. 

    Many theoretical studies have been done about such mechanism, however, DPPH appears a bit more tricky. 

    My 2 cents, 

    Florent

  • Tarak Karamakar added an answer:
    Can someone comment on covalently bound ligand parametrization?

    I have a protein, where one of the reaction intermediate is covalently attached with a residue inside the active site. I need to parametrize this part of the protein. I used standard RESP calculations to get the charges and for the covalent bond I took the help of GAFF parameters. Is it a right way of dealing with this type of problem?

    Tarak Karamakar · Jawaharlal Nehru Centre for Advanced Scientific Research

    Thanks Dr. Kirschner, Dr. Christofferson, and Dr. Çelebi-Ölçüm for valuable suggestions and directing me towards a nice protocol.

  • Manohar Sehgal added an answer:
    Does anybody know where I can find the dielectric constant of fluoroantimonic acid (HSbF6)?

    We are currently studying protonation of carbonyl compounds in superacid media. Fluorantimonic acid is the strongest superacid known which reacts even with hydrocarbons producing carbocations and H2. For modeling of interactions of HSbF6 with subsrares we use COSMO, therefore we need to know the dielectric constant.

    Manohar Sehgal · DAV College Jalandhar

    Sir,
    Though your good self is better informed,but will it not be better to use OPTICAL dielectric constant instead of  the dielectric constant especially in COSMO?

  • Mudar Ahmed Abdulsattar added an answer:
    What is the best personal computer for use in ab initio calculations?
    Ab initio calculations takes a very long time and resources. Is there anyone who can advise me on the best computer to be used in performing such tasks?
    Mudar Ahmed Abdulsattar · Ministry of Science and Technology, Iraq

    Dear Dipayan Sen

    I tried i7 computer but I did not try AMD processors. My previous information is that Intel processors are faster than AMD (apart from the number of cores).

  • Cristian Vidal 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.
    Cristian Vidal · University of Oviedo

    You can use another option:

    Using cartesian coordinates, put  "opt=ModRedundant" keyword and then after blank line write numbers of fixed atoms and wildcart "F".

    E.G

    H x y z
    B x y z
    O x y z
    C x y z
    N x y z
    <blank line>
    1 2 F
    <blank line>

    With this keyword you fix atom H and B.

  • Fernando Jesús Tun added an answer:
    What is the best method of calculation to find transition state?
    I am calculating the transition state for tautomerization processes with opt = (TS,CalcAll,Noeigentest) with the method of calculation M062X/6-31 + g (d, p), but I cannot find it and QST2 does not work. Could someone tell me what is the best level of calculation to locate transition states because DFT fails in some cases?
    Fernando Jesús Tun · Universidad Autónoma de Yucatán

    I would like to thank everyone, especially Peter and Francesco for their comments and suggestions!. And yes I am looking at a proton transfer and we decided to use this functional and basis, as in previous studies at this university, where this combination gives a good description.
    After a change in calculation method was able to converge to the TS, I did:
    1) I did a Opt = (TS, CalcAll, Noeigentest, MaxCycle = 500, MaxStep = 500) PM6 geom = connectivity, obtaining only one imaginary frequency.
    2) Then I refine the calculation with Opt = (TS, CalcFC, Noeigentest, MaxCycle = 500, MaxStep = 500) M06-2X/6-31 + (d, p) geom = connectivity at the end of the TS optimization converged well .
    3) Finally, the final structure obtained was made ​​a calculation of frequencies (Freq M06-2X/6-31 + (d, p)), obtaining the desired imaginary frequency.
    Thank you for your help!

  • Chanchal Haldar 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.
    Chanchal Haldar · Indian School of Mines

    Got your point. thankx.

  • Pinaki Saha added an answer:
    I have synthesized a organic ligand which is EPR active in low temperatures, but why are no any spectra obtained in SQUID experiment?
    It is a tetradentate para imino quinone ligand (NNNO).
    Pinaki Saha · Ramakrishna Mission Residential College

    Thank you Sir....

  • Tarak Karamakar added an answer:
    How comparable is the interaction energies from B3LYP/aug-cc-pVTZ and SAPT2+3/aug-cc-pVTZ?

    We calculated the interaction energy of a system in two methods, B3LYP/aug-cc-pVTZ (Gaussian) and SAPT2+3/aug-cc-pVTZ (PSI4) and got an energy difference of about 8 kcal/mol. How reliable this is?

    Tarak Karamakar · Jawaharlal Nehru Centre for Advanced Scientific Research

    Thanks Dr. Korona

  • Behnam Farid 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

    You are welcome Xin-Yu. And thank you for the paper which I have just received. Incidentally, as I wrote in my first message on this page, to appreciate superexchange one cannot bypass appreciating direct exchange and kinetic exchange; the effective exchange Jeff that one obtains in dealing with superexchange, is to be understood in the light of direct exchange.

  • Matthew R Ryder added an answer:
    How can I represent the MP2 density?

    I can do the calculation with Gaussian09, GAMESS, NWChem,
    but do not know how to represent the  MP2 density

    Matthew R Ryder · University of Oxford

    With Gaussian09, you can simply put 'Density' in the command line and it will default to the current density. If your calculation is at the MP2 level of theory, this will give you what you are after.

    You can also put 'Density=Current' or 'Density=MP2' but they will give you the same result, as current is the default if no option is given to density and MP2 forces the density to be calculated at that level, regardless of the level of theory specified for the optimisation etc.

  • Michael S Deleuze added an answer:
    In the unrestricted B3LYP optimization, which MO is better to use? Alpha or beta?
    Someone said that change the unrestricted keyword to restricted in the output of MOs,but when i do that it select just alpha MOs, I don't know if it is the correct way and when compared with beta one its HOMO and LUMO energy is higher, please help me.
    Michael S Deleuze · Universiteit Hasselt

    Dear all,

    I essentially agree with the latest comment by Hamidreza Simchi - without however any reference to Islam and to the Saint Coran.

    One should pay the greatest attention in this discussion on the meaning of singlet "open-shell" wave functions. For many researchers (eg Houk), this implies a spin-polarized solution, with spin-alpha and spin-beta orbitals localized in different parts of the molecules. For many other researchers (eg Hans Lichka), singlet open-shell wave functions refer to strong deviations from 0 and 2 of natural orbital occupation numbers in multi-reference (eg CASSCF) calculations. Obviously, these two definitions are not equivalent, hence a lot of disputes in the scientific literature on for instance the electronic structure of graphene nanoflakes, which are essentially semantic in origin.

    In this context, it is worth reminding that for singlet states, spin-densities must be identically zero at everypoint in space. Symmetry-breakings of spin-densities otherwize imply a spin contamination (i.e. deviation of the expectation value of the S^2 operator), which in some cases may take absolutely catastrophic proportions. It is well-known that strong spin-contampinations indicate a too approximate treatment of electronic correlation, in particular static correlation (multi-reference effects). I recommend everyone to have a look at works we published in  J. Chem. Phys. 135 (2011), 104704, Chem. Phys. Lett. 553 (2012), 6.,   J. Mol. Mod., 417 (2013), 17-25 for detailed discussions of these issues.When electron pairs dissociate in biradical (or multiradical) systems (as for instance in dissociating H2) one cannot , with single-reference (HF or DFT) treatments, recover both the exact (symmetry-adapted) wave function and the exact energy. This is the essence of the famous "symmetry-dilemma" by Per-Olov Löwdin. Unrestricted SR treatments give the right dissociation energies for the wrong symmetries, whereas restricted SR treatments give wrong dissociation energies for the right wave function. To get everything exact, one has to go to the full-CI limit. See also: J. Chem. Phys., 131 (2009), 224321, a work which among others prove that correct treatments of correlation restore the correct symmetries in symmetry-breaking situations.

    With best regards,

     

                       Michael S. Deleuze,

    Prize Winner 2005 of the Royal Academy 

    of Belgium for the Sciences and the Arts.

     

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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