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Questions related to Computational Chemistry
Suppose we consider the binding of a ligand L to a metal M, M+L=ML and M+2L=ML2 . We compute the Gibbs free energy change for two reaction using DFT. But can we compare this two free energies to...
13 January 2021 6,491 4 View
Hi all, There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result. This is concerning Raccoon(1) original, not Raccoon2. The original...
18 December 2020 4,819 2 View
Hi all, Please imagine this to be a brand new machine with the latest installation of: Autodock Vina Autodock AutodockTools (MGLTools). I'm following a Nature Protocol for the prediction of...
15 December 2020 2,764 3 View
Hello Is it possible to compute intermolecular interactions in a mixture of solvent using DFT tools in Gaussian-09 or GAMESS US, DMOl3 or any other computational chemistry code? For example we...
06 December 2020 7,796 3 View
It is well known that for a closed shell (all electrons are paired up) molecule, the HOMO-LUMO gap is related to its stability. However, I often see that the same argument is used for open-shell...
02 December 2020 7,317 4 View
Hi all, I guess there are probably several ways of doing this. I'm looking to get access to every Pubchem CID. All compounds are published for download, but the files are quite large in size and...
02 November 2020 9,206 3 View
The molecule in question is a molecule with 3 non-equivalent hydrogens. Am I going to have to run the calculations in all of the transition states?
19 October 2020 2,061 3 View
Hello, I have trouble with transitional state calculation in gaussian 16 program. I started with the first frequency calculation with cartesian coordination and it ends up normally. the input...
16 October 2020 2,092 1 View
I am trying to use the FMO (Fragment Molecular Orbital) method which works to make large (thousands of atoms) molecules more palatable for ab initio computational quantum-chemical calculations on...
30 September 2020 5,385 2 View
I'm doing TDDFT calculation. I have calculated excited state calculation for n=20 states. The first state (lowest in energy) showing negative wavelength and oscillator strength. How we can explain...
12 August 2020 7,290 4 View
I am trying to calculate van der Waals radius for silver atoms and ions. Could anyone explain the steps required to perform accurate calculations.
04 August 2020 3,220 3 View
Dear Expertise I want to apply the strain in some unusal directions like [105] [113] or even [11 100], it is easily to get the strain tensor, but how can I apply it in the input file of QE and...
28 July 2020 3,292 3 View
I would appreciate if you can answer some of these questions: 1) Can you suggest some good resources from which I can learning computation from scratch? 2) Are ORCA and GAMESS free tools? 3) Are...
15 July 2020 5,407 2 View
I did TD-DFT calculation of a dimer containing radical anion. Here, charge=-1 and multiplicity=2 in the Gaussian input file. After TD-DFT of that dimer containing two different molecules (let's...
12 July 2020 8,768 3 View
In frequency calculations in Gaussian09 using DFT-B3LYP and 6-311+G(d) functional and basis set, we know that scaling factor is applied to correct the obtained frequencies. But is there any...
27 June 2020 3,580 4 View
Hello, I calculated a cation molecule with gaussian 09. Based on the output file, how can I determine which atom has a charge? In Gaussian view, N atom has 4 bonds, so it might have + charge. What...
10 April 2020 9,906 4 View
Hi dear all, I just carrying out a computational run of a single point energy at MP2/6-31g++(2p,2d)//B3LYP/6-31g++(d,p), but when I tried to do the refinement at MP2/6-31g++(2p,2d) the next error...
28 March 2020 6,217 3 View
I am designing a gas molecule-limonene using Quantum ESPRESSO. In the input file for Quantum ESPRESSO, I have to define the choice of bravais lattice and cell dimension and cell parameters. But...
26 March 2020 9,500 4 View
Say, a concerted transition state involves the breaking of two bonds and the associated making of two new bonds. Does each bond making/breaking has a corresponding imaginary frequency, so in total...
20 March 2020 5,827 4 View
In detail, I want to know whether the HOMO of my molecule is either bonding or anti-bonding in nature? Please suggest me the software or code that can give the percentage of the antibonding...
16 March 2020 7,097 3 View
computational chemistry: I want to make the base overlap corrections for the dichloroacetyl chloride dimer. I put the following sentence to run the calculation in Gaussian: frec B3LYP/6-311++G**...
28 February 2020 6,784 3 View
Hello, I am working on the detection of pesticides with the help of Surface Enhanced Raman Spectroscopy (SERS) and I want to simulate an organic molecule along with the cluster of silver atoms....
24 February 2020 1,661 5 View
Hi. I am working on some organic molecules and performing simulations with the help of Gaussian software. But my jobs are not getting converged within 24 hours of walltime. I am producing a...
14 February 2020 5,735 4 View
Dear all, I made a semiempirical orbital calculation (using MOPAC) of a fairly large complex of a ligand and a protein binding site. Now I am trying to find the highest occupied orbital with a...
12 February 2020 8,147 4 View