Theoretical Chemistry

The use of mathematical and computational methods to build theories explaining observations of chemical reactions, such as quantum chemistry. | Contact experts in Theoretical Chemistry to get answers

2,456 views 620 posts

Questions related to Theoretical Chemistry

What are the possible reasons for the catalytic activity of transition metal especially as a bi-functional catalyst?

I want to know about the fundamental theoretical chemistry of the catalyst nature of the transition metal, metal-oxide/phosphide/boride etc.

07 October 2019 1,435 3 View

Is there any software/chemoinformatics toolkit which can generate rxn files from reaction smarts?

I'm trying to generate CGR and in order to do so I want to use the Marvin Sketch auto mapper function on a bunch of reactions, stored as reaction smarts. But in order to use the auto mapper...

09 September 2019 716 3 View

How to increase the number of optimisation steps in ORCA?

What is the keyword to increase the number of optimisation steps (not the number of SCF steps) in an ORCA optimisation calculation? The warning is suggesting I increase the "number of...

09 September 2019 2,090 2 View

Are these QC DFT settings appropriate?

I'm picking up quantum chemistry after a three year break. I've forgot a lot and I'm now using ORCA (version 4.0.1.2). My system is a non-enzymatic chemical reaction between lysine, arginine...

31 August 2019 4,135 2 View

Which basis set should I use for Cysteine metal complexes in Gaussian?

I am trying to work with some metal (Fe,Zn,Pb,Hg,Cd) complexes of Cysteine in Gaussian16. I tried B3LYP/6-311++G for Fe & Zn and B3LYP/LanL2DZ for other complexes. Am I in the right track?...

30 August 2019 3,418 5 View

How to displace a molecule along a particular normal mode?

I am using gaussian09. I want to calculate triple derivative at the minimum of potential energy surface of acetone to get the cubic anharmonicity constant. For that I need to do energy...

14 August 2019 731 6 View

How to batch import the Raman spectrum of several log files in gaussian09?

I have dozens of log files and I will like to know if there is a way to batch import their Raman spectrum files from their log file. I know how to import the Raman spectrum of each file by using...

08 August 2019 4,531 3 View

Which basis set should I use for Cysteine metal complexes in Gaussian?

I am trying to work with some metal (Fe,Zn,Pb,Hg,Cd) complexes of Cysteine in Gaussian16. I tried B3LYP/6-311++G for Fe & Zn and B3LYP/LanL2DZ for other complexes. Am I in the right track?...

08 August 2019 3,348 6 View

Are these QC DFT settings appropriate?

I'm picking up quantum chemistry after a three year break. I've forgot a lot and I'm now using ORCA (version 4.0.1.2). My system is a non-enzymatic chemical reaction between lysine, arginine...

08 August 2019 1,845 3 View

How to displace a molecule along a particular normal mode?

I am using gaussian09. I want to calculate triple derivative at the minimum of potential energy surface of acetone to get the cubic anharmonicity constant. For that I need to do energy...

08 August 2019 8,560 6 View

How to get anharmonicity constant value from gaussian? Also what theory is encoded in software to calculate anharmonic frequencies?

I have done anharmonic frequency calculations in Gaussian09.(for acetone). At the end of the output file I can see the anharmonic frequencies. I do not see anharmonicity constant value(for...

22 July 2019 4,220 5 View

Why there is no change in energy of Hydrogen(atom) when field is applied using gaussian software compared to when no field is applied?

I have done SCF calculation for hydrogen atom and in the second job I did the SCF calculation on hydrogen atom with field of 0.05 a.u in a particular direction, but there is no change in energy...

12 July 2019 1,678 2 View

How to quantify total non-covalent interactions in a transition state?

I have two transition states for the same reaction (oxidative addition), in which one transition state is more stable compared to the other because of the higher number of non-covalent...

09 July 2019 6,086 22 View

Is there any instance where local electrophilicity index fails to reproduce expected results?

Local electrophilicity index, a significant parameter of conceptual dft can be utilized to predict electrophilic or nucleophilic sites of attacks. Are there any instance where this model fails to...

07 July 2019 8,156 2 View

Why there is no change in energy of Hydrogen(atom) when field is applied using gaussian software compared to when no field is applied?

I have done SCF calculation for hydrogen atom and in the second job I did the SCF calculation on hydrogen atom with field of 0.05 a.u in a particular direction, but there is no change in energy...

07 July 2019 3,460 2 View

Why does the ghost atom give error in NICS calculation with the basis set Def2ztvp in Guassian 09?

I am trying to calculate NICS (0 and 1) values for heterocyclic compounds using Gaussain 09. I am placing the ghost atom (Bq or 0) at the center of the ring. I am using the method/basis set...

07 July 2019 5,808 3 View

In NAMD, should the flexible cell option turned on during NPT simulation ?

I am confused about setting the cell basis in NAMD. Initially, I set the cell basis according to my solvation box dimensions + 2 or 3A to separate the unit cells in the PBC. This is fine during ...

11 May 2019 6,331 4 View

How to calculate intermolecular electrostatic interaction energies using mopac?

Hi, I hope someone can help me. I have a system of two radical species, and I would like to approximate the energy associated with non-covalent interaction. The molecules are ions, one is...

03 April 2019 6,532 1 View

How can I optimise transition state (QST3) in Gaussian ?

Facing problem regarding TS (QST3) optimisation.

20 February 2019 7,677 4 View

Why should we use the universal gas constant R when dealing with liquids?

The universal/molar/ideal gas constant R is given by R=PV/nT; this however, on an average, is considered true for gases (H2, O2, N2 are excluded). Involving R in chemical expressions dealing with...

22 January 2019 251 11 View

How to computationally perform conformer generation of radicals?

Is there an automatic way to generate conformers for radical like systems in general (a doublet spin multiplicity)? My current system for study is a substituted fullerene with a missing H atom...

21 January 2019 1,902 2 View

How to check if an internal coordinate is totally symmetric with the help of the molecular structure?

I would like to decide whether a given internal coordinate (angle or dihedral angle) is totally symmetric, i.e., E(y1,y2,...,yi+delta,y[3N-5/6])=E(y1,y2,...,yi-delta,y[3N-5/6]) for any delta,...

15 January 2019 3,060 3 View

How to check if an internal coordinate is totally symmetric with the help of the molecular structure?

I would like to decide whether a given internal coordinate (angle or dihedral angle) is totally symmetric, i.e., E(y1,y2,...,yi+delta,y[3N-5/6])=E(y1,y2,...,yi-delta,y[3N-5/6]) for any delta,...

01 January 2019 9,710 4 View

How to computationally perform conformer generation of radicals?

Is there an automatic way to generate conformers for radical like systems in general (a doublet spin multiplicity)? My current system for study is a substituted fullerene with a missing H atom...

01 January 2019 4,816 3 View

Badges
Science topic