Theoretical Chemistry

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2 Which DFT method is suitable and publishable for organic-inorganic hybrid molecules?
By G. S. Suresh Kumar · Manonmaniam Sundaranar University

Marawan Ahmed · Swinburne University of Technology

Could you please be more clear. in most cases, DFT is the best option at least to start but this can be very tricky depending on the molecule you are ... [more]

Could you please be more clear. in most cases, DFT is the best option at least to start but this can be very tricky depending on the molecule you are working with. I encourage you to read the literature for similar molecules like your and what are the properties you are looking for. For sure you are not the first one.

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7 Scan Bond Length - Transition State
By Meilani Wibowo · National Taiwan University of Science and Technology

Christof Walter · Universität Würzburg

The problem might also lie in the methodology: A bond dissociation (especially a homolytic one) can lead to near degeneracies and if this is the case ... [more]

The problem might also lie in the methodology: A bond dissociation (especially a homolytic one) can lead to near degeneracies and if this is the case RHF or RMP2 are definitely not the right choice and a UDFT approach might be much more sensible. If one assumes a heterolytic bond dissociation, than solvent effects are tremendously important. Since charge separation is highly unfavourable in the gas phase, barriers and theromdynamic data derived form gas phase calculations of ionic reactions are almost meaningless. I would assume that the potential energy curve for an ionic dissociation in the gas-phase would converge to the 1/r-behaviour of coulomb's law and thus never go down.

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13 How to fix the direction of atoms in Gaussian?
By Chong Liu · Lanzhou University

kalyan Dhar · Politecnico di Milano

C -1 0.00 0.00 0.00 C -1 0.00 0.00 1.52 H -1 1.02 0.00 -0.39 H -1 -0.51 -0.88 -0.39 H -1 -0.51 0.88 -0.39 H -1 -... [more]

C -1 0.00 0.00 0.00 C -1 0.00 0.00 1.52 H -1 1.02 0.00 -0.39 H -1 -0.51 -0.88 -0.39 H -1 -0.51 0.88 -0.39 H -1 -1.02 0.00 1.92 H -1 0.51 -0.88 1.92 H -1 0.51 0.88 1.92 Now if you want to relax C then put 0 , instead of -1 . Finally input code #p b3lyp/gen opt freq nosym pseudo=read . put all Cartesian co-ordinate that i paste it in first C C 0 6-311++G(d,p) *** H H 0 6-31+G(d,p) ***** you can use multiple's sets (basis) . P,S . its also depends what you wanna do ? the purpose of your study . hope everything is clear .

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30 How to calculate percentage contribution of a particular excitation from TDDFT output of Gaussian09?
By Soumen Ghosh · Indian Institute of Technology Bombay

Christof Walter · Universität Würzburg

I had the same problem and in my opinion (although I am not 100% sure), the solution lies in the fact, that in a TDDFT framework, the norm is not def... [more]

I had the same problem and in my opinion (although I am not 100% sure), the solution lies in the fact, that in a TDDFT framework, the norm is not defined exactly as in a CIS expansion, where the sum over all coefficients squared gives one (or 0.5 in gaussian), since there are also deexcitations, which are not present in the CIS. In fact the sum over all the coefficients of the excitations squared MINUS the sum over all the coefficients of the deexcitations squared is normalized to one: (O,O)=XX-YY=1, see Annu. Rev. Phys. Chem. 2012. 63:287–323 page 291. That means that the coefficient of a certain excitation has to be bigger than one, if it dominates the state and if the corresponding deexcitation has a significant contribution (as in the example discussed above).

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Question:
Open How can I find out the DNA interaction of a molecule, theoretically?
With the help of Gaussian software one can find out the DNA interaction of molecule theoretically. Can anyone help me perform the calculation?

With the help of Gaussian software one can find out the DNA interaction of molecule theoretically. Can anyone help me perform the calculation?

By Manas Sarma · Gauhati University

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5 Eigen vector following algorithm to find saddle points.
By Suresh kn · Ruhr-Universität Bochum

Yutaka Nagahata · Hokkaido University

This is the best method so far as I know http://kmweb.fukui.kyoto-u.ac.jp/~smaeda/GRRM_PR000.html author's page https://sites.google.com/site/satoshi... [more]

This is the best method so far as I know http://kmweb.fukui.kyoto-u.ac.jp/~smaeda/GRRM_PR000.html author's page https://sites.google.com/site/satoshimaedahokkaidouniv/

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6 Search for transition states in a dicopper complex.
By Lucas Esteves · Universidade Federal de Juiz de Fora

Frerich Keil · Technische Universität Hamburg-Harburg

The suugestions given above are ok. In case you use Qchem, you could also try our Dimer method, in particular close to the TS. The growing string meth... [more]

The suugestions given above are ok. In case you use Qchem, you could also try our Dimer method, in particular close to the TS. The growing string method (JCP 120(204),7877 might be also useful.

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Answer added to:
27 When calculating with gaussian 09, if the frequency becomes negative what should be done?
By Razieh Dashtpeyma ·

C.Yohannan Panicker · TKM College of Arts and Science

Add the coordinates of imaginary frequency value to the coordinates of standard output . Then optimize and calculate frequency yohannanpanicker

Add the coordinates of imaginary frequency value to the coordinates of standard output . Then optimize and calculate frequency yohannanpanicker

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6 Materials Studio 6.1 problem
By Tanmoy Chakraborty · Indian Institute of Technology Guwahati

Stephen Todd · Accelrys Inc

The problem that you are facing is that you have a cyclopentadienyl ring which has a dummy atom representing the Pi system. This is not recognised by ... [more]

The problem that you are facing is that you have a cyclopentadienyl ring which has a dummy atom representing the Pi system. This is not recognised by Forcite or Discover as a valid particle for molecular dynamics because it has no mass associated with it and hence the program gives an error. I think that it is pretty hard to study MD of organometallics using classical simulations techniques. I did a quick search for "organometallics" on http://references.accelrys.com This turned up many hits but publications were nearly all using DMol3. I guess you could potentially delete the Pi system and create bonds between the cyclopentadienyl fragment and the metal atom but I am not convinced this would give good results (picking a forcefield might be challenging!)

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2 What is the best manner to theoretically model the ionic liquid effects on Diels Alder reactions?
By Hafida Chemouri · Abou Bakr Belkaid University of Tlemcen

Americo Lemos · Universidade do Algarve

First of all you should anticipate if the IL will coordinate/interact preferentially with the diene or with the dienophile. Let’s suppose you are do... [more]

First of all you should anticipate if the IL will coordinate/interact preferentially with the diene or with the dienophile. Let’s suppose you are doing a “normal electron demand” DA, so it would be better if the IL could make the dienophile more electrophilic or enhance the electron rich character of the diene. If you are trying an “inverse electron demand” DA its just the opposite. For example if you are trying a cyclo-addition between cylopentadiene and methyl vinyl ketone, an IL which will coordinate with C=O will be favourable… If you attempting a cycloaddition for example between an electron deficient diene (or usually an heterodiene electron poor and furan other electron rich dienophiles, for example ethyl vinyl ether, an IL which may coordinate preferentially with the oxygen of the dienophiles will be prejudicial; by the other hand if it will coordinate preferentially with the diene making it more electron deficient it will be beneficial. Summarizing, if the IL can lower the energy gap between HO MO and LUMO of the reactants it may help, if not it will be bad. Always a proper balance between stability and reactivity must be attained. Hope I helped in some way. Good luck and good work.

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15 What information can be obtained from the calculation of frequencies what was obtaned?
By Razieh Dashtpeyma ·

Dan Maftei · Universitatea Alexandru Ioan Cuza

If you are interested in electronic spectra, performing frequency calculations at equilibrium ground and excited state geometries would allow a "physi... [more]

If you are interested in electronic spectra, performing frequency calculations at equilibrium ground and excited state geometries would allow a "physical sound" picture (vibronic shape) of the simulated absorption/fluorescence band. See works of F. Santor and V. Barone published in 2007-2008 in JCP and also more recent case studies of D. Jacquemin for details on Franck-Condon computations. Be prepared to spend months of CPU time to compute vibrational frequencies in excited state (even for medium sized molecules) as compared to hour(s) for the same runs in ground state.

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6 What software can I use to compute the conceptual-DFT Fukui function?
By Ramón Miranda-Quintana · University of Havana

George Fitzgerald · Accelrys Inc

The program DMol3 from Accelrys, Inc can do this, as described in https://www.researchgate.net/publication/200612981_On_the_use_of_fractional_charges_... [more]

The program DMol3 from Accelrys, Inc can do this, as described in https://www.researchgate.net/publication/200612981_On_the_use_of_fractional_charges_for_computing_Fukui_functions?ev=prf_pub

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1 Can someone suggest a not-too-complicated way to predict (computationally) if a polymer has a tendency to crystallize?
By Ekaterina Badaeva · University of Washington Seattle

Unmesh Vibhute · College of Engineering, Pune

Dear friend just go to below links http://www.sump4.com/publications/book003.pdf

Dear friend just go to below links http://www.sump4.com/publications/book003.pdf

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Question:
Open Has anyone used upack (Utrecht Crystal Packer)? If so is there a simple reference document for the atom codes and their meaning?
I have been reading through the extensive manual for upack which is generally very helpful but am having difficulties interpreting what all of the ato... [more]

I have been reading through the extensive manual for upack which is generally very helpful but am having difficulties interpreting what all of the atom codes refer too. Is there another document somewhere, which I have missed, that lists the codes and there meaning side by side? I am also hoping to use this on a fairly large dataset, and wondered if anyone knew if there was a script or program already out there that automated the creation of the subst.con file?

By James Mcdonagh · University of St Andrews

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6 How to calculate free energy change (Gibbs free energy) during phase-transition using GAUSSIAN?
By Tanmoy Chakraborty · Indian Institute of Technology Guwahati

Ranylson Marcello Savedra · Universidade Federal de São Carlos

Free Energy is answer of molecular interactions, where the effect is mostly derived from electrostatic forces, Hellmann-Feynman Theorem. But the main ... [more]

Free Energy is answer of molecular interactions, where the effect is mostly derived from electrostatic forces, Hellmann-Feynman Theorem. But the main problem is "during phase-transition", I think it is not a equilibrium state, so to estimate assembled in this conditions is a rare event and the population is small and will produce large errors.

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1 Helium subatomic structure
By Marc Inberg · University of Western Sydney

Daniel Sadowsky · University of Minnesota Twin Cities

There are wikipedia articles on the two main pathways through which this can happen: http://en.wikipedia.org/wiki/Proton–proton_chain_reaction ht... [more]

There are wikipedia articles on the two main pathways through which this can happen: http://en.wikipedia.org/wiki/Proton–proton_chain_reaction http://en.wikipedia.org/wiki/CNO_cycle In all the processes that I know of, decay by positron emission happens *before* the nuclei reaches a mass of 4, not after (the resulting particle would be very high in energy, even by the standards of stellar chemistry).

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25 How can we define symmetry in calculated vibrational modes.
By Vikas Baboo · University of Lucknow

Oday Hamadi · University of Baghdad

Atkins explained all about molecular symmetry with good ranging from basics to advanced concepts

Atkins explained all about molecular symmetry with good ranging from basics to advanced concepts

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3 How can we derive the transmission probability of a charged particle in a parabolic barrier?
By Mojdeh Banafsheh · University of Geneva

Giovanni Villani · National Research Council

I am not a specialist of this field, but I remembered that Truhlar had done some papers on this subject and I found on line the paper "Parabolic Tunne... [more]

I am not a specialist of this field, but I remembered that Truhlar had done some papers on this subject and I found on line the paper "Parabolic Tunneling Calculations", J. Phys. Chem. 1981, 85, 624-628, with a similar expression. I hope that this paper can help you. Giovanni Villani

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28 What is the standard length of time for abinitio w/ MP2, 250 basis sets(6-311++G**), 441 primitives to reach convergance?
By Linda Grabill · Western Washington University

Linda Grabill · Western Washington University

Filip, Thank you for your reply. We were able to get a grant to upgrade our software (GaussView//Gauss 09) and computer. I have had the opportunity ... [more]

Filip, Thank you for your reply. We were able to get a grant to upgrade our software (GaussView//Gauss 09) and computer. I have had the opportunity to work with current basis sets and functionals with trial software (which takes advantage of multiprocessing). We were pleased with the quality of the results and thrilled with the time saving! All of the suggestions made here sure helped get us on the right track for finding inavluable research papers. I feel like a kid at Christmas waiting for our new lab to be up and running!! Thank you all again.....

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5 Is a noncovalent interaction a type of weak interaction?
By Razieh Dashtpeyma ·

Mohanned Al-anber · University of Basrah

The weak interaction like the dispersion forces

The weak interaction like the dispersion forces

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6 Without kinetic experiment is it possible to predict which intermediate is forming?
By Sayan Ghosh · Indian Institute of Technology Bombay

Moisés Canle López · University of A Coruña

If you have enough data to perform good Linear Free Energy Relationships (LFER, of which you may use several depending on the process you are studying... [more]

If you have enough data to perform good Linear Free Energy Relationships (LFER, of which you may use several depending on the process you are studying), then you might be able to use the so-obtained data into a reaction map (More O'Ferrall-Albery-Jencks map). This procedure is relatively long and need good previous training... The results can be, however, spectacular...!

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Question:
Open Interpretation of spin-orbit calculations
Dear RG members! I'm trying to calculate the transition probality between the 2nd doublet and the 1st quadruplet terms of HO2 system. In accordance w... [more]

Dear RG members! I'm trying to calculate the transition probality between the 2nd doublet and the 1st quadruplet terms of HO2 system. In accordance with Landau-Zener model I must obtain the matrix element of SOC between these terms. I've used effective charge (Zeff) model for single set MOs. The output fragment for the states of interest is following: < (S=0.5,MS= 0.5)//(S=1.5,MS= 1.5) > = 16.1124 + 59.9051I < (S=0.5,MS= 0.5)//(S=1.5,MS= 0.5) > = 0.0000 + 0.0000I < R > = 0.000000 < (S=0.5,MS= 0.5)//(S=1.5,MS=-0.5) > = 9.3025 -34.5862I < (S=0.5,MS=-0.5)//(S=1.5,MS= 0.5) > = 9.3025 + 34.5862I < (S=0.5,MS=-0.5)//(S=1.5,MS=-0.5) > = 0.0000 + 0.0000I < R > = 0.000000 < (S=0.5,MS=-0.5)//(S=1.5,MS=-1.5) > = 16.1124 -59.9051I My question concerns the interpretation of these results. (What value must be used in Landau-Zener equation?) 1. Am I supposed to calculate the absolute values of these complex numbers? 2. What pair of Ms1//Ms2 can be chosen? Maybe the simple avaraging is assumed. 3. The pairs (MS=+0.5//Ms=-1.5) and (MS=-0.5//Ms=+1.5) are absent in table. Why? Thank you in advance for the layman's questions.

By Alexander Sharipov · Baranov Central Institute of Aviation Motor Development

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20 NMR calculations using GIAO approach and different temp. condition at B3LYP/6-31G**, results show same values in two or more calculated results.
By Vikas Baboo · University of Lucknow

Dan Maftei · Universitatea Alexandru Ioan Cuza

I would recommend starting with a conformational analysis on your molecule, either in a systematic MM approach or following an educated guess and scan... [more]

I would recommend starting with a conformational analysis on your molecule, either in a systematic MM approach or following an educated guess and scanning the potential energy surface along the dihedral angle between the substituent and the pyrrole ring. Then, geometry optimizations initiated from energy minima should and frequency calculations should yield multiple conformations. Keep al the conformers within about 2 kcal/mol of free energy difference wrt. the most stable one and perform GIAO NMR computations on each conformer. Plot the shielding tensors (or the computed chemical shifts e.g. wrt TMS) against experiment. Check for deviations from a linear dependence. See if other conformers have similar (reversed) deviations from linearity. Perform a Boltzmann average on chemical shifts (based on free energies computed in the previous frequency runs) and check the linearity, again. Depending on the energetics of conformational isomerism and the vicinity of the incriminated protons in each conformation, you may evidence a conformational equilibrium.

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Question:
Open How to simulate an explicit solvation of Diels-Alder reaction by Monte Carlo method in Sybyl-X 1. 1 of windows?
I want to simulate a solvation by Monte Carlo method using sybyl program, please give me the procedure and how can I obtain the radial distribution fu... [more]

I want to simulate a solvation by Monte Carlo method using sybyl program, please give me the procedure and how can I obtain the radial distribution function?

By Hafida Chemouri · Abou Bakr Belkaid University of Tlemcen

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Answer added to:
5 What is the procedure for making a Monte Carlo simulation of solvent effects?
By Hafida Chemouri · Abou Bakr Belkaid University of Tlemcen

Adriano Santos ·

I'm sending to you a classic paper about Monte Carlo method. In this paper you will find the main ideas about this. I think that it will help you, ver... [more]

I'm sending to you a classic paper about Monte Carlo method. In this paper you will find the main ideas about this. I think that it will help you, very much.

Metropolis & Ulam - The MC Method.pdf ×

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Question:
Open I need help to compute magnetic properties by ADF programe
The magnetizability is important in many applications,

The magnetizability is important in many applications,

By Aqeel Ali · University of Basrah

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9 Does anyone know how to generate a multiple peak gaussian curve?
By Mehboob Alam · University of Calcutta

Ragini Raman · Bharathidasan University

explain about diluted magnetic semiconductor quantum dot.how it is related to Zinc oxide quantum dot.from this how to create zinc oxide cluster in gau... [more]

explain about diluted magnetic semiconductor quantum dot.how it is related to Zinc oxide quantum dot.from this how to create zinc oxide cluster in gaussian 09.

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7 Regarding Computational Chemistry Software
By Ravi Kumar Venkatraman · Indian Institute of Science

Ravi Kumar Venkatraman · Indian Institute of Science

Thank you folks

Thank you folks

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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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