Questions tagged [computational-chemistry]

A field which employs computers to model and study chemical systems and chemical behavior, using various models, from approximations of the Schrödinger equation to Monte-Carlo simulations, to modeling with differential equations.

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How to propose reaction mechanism [closed]

my question is related to the computational method/technique to predict intermediate products of a reaction. For example, I have initial compound A (such as Fe3O4) and I know the final product B (such ...
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Open shell TDDFT excitaion contribution

If I have a open shell system (10 alpha electrons and 9 beta electrons) and running TDDFT calculations, is it possible to have a 9a→10b transition? Or does it have to be 9b→10b? Because both exciation ...
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How to define a chemical bond computationally?

I'm working with an amorphous system. With oxygen, my system has both covalent and ionic bond forming cations. I utilise the Wannier centre to define a covalent bond, and my theory is that if the ...
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Smarts string for querying two N substitutions at any place along bicyclic ring

I'm a newbie to SMARTs string representation and have been stuck on generating the structure that I want. I have a pattern of chemical scaffold of interest which I'd use as a query to screen a library....
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Are there tools or algorithms to detect organic molecules from 3D crystal structures?

The task I'm thinking of is to detect entire molecules from structures, such as in a crystallographic information file (CIF) or from the XYZ file generated in a molecular dynamics simulation. ...
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Interpair vs. intrapair nondynamic correlations

What is the difference between interpair and intrapair nondynamic correlations? What would an example of each “look” like in the context of the $\ce{H4}$ system [1]? Reference Ramos-Cordoba, E.; ...
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ORCA finished by error termination in SCF gradient [migrated]

I try to optimize and compute frequencies for the system built up from C, O, H, and Co atoms in the following functionals: B2PLYP, B2PLYP-D3, B3LYP, B3LYP-D3, BLYP, BLYP-D3, DSD-PBEP86, PBE, PBE-D3, ...
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Shannon Ionic Radii and Coordination number

So I have been struggling to find the Goldschmidt paramter for a couple of layered double perovskite as it requires the knowledge of shannon ionic radii. Now shannon ionic radius for a particular ...
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How to calculate <ab|ab> integrals to carry out Schwarz pre-screening of molecular integrals

During writing my own two-electron integration library I faced an issue of dealing with integrals that have very small values beyond the C/C++ double data type. ...
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Charge Transfer and Multireference Methods

I have read in literature that systems that exhibit "high charge-transfer character" are best treated using multireference/multiconfigurational methods. Why is that? What makes such a system ...
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If you are doing an ONIOM calculation in Gaussian, how do you add both custom MM parameters and a custom basis set using GEN and Amber=SoftFirst?

I am trying to calculate a biological system using AMBER forcefields as my low-layer in ONIOM3. I also want to use a non-native basis set (aug-pc-1 for opt+freq, aug-pc-2 for SPE) that requires custom ...
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STO-1G in Gaussian

I don't see the STO-1G basis set in the available sets on the Gaussian website and the software (g16) throws an error if I try. I see how it seems possible to use a custom basis but I'm not entirely ...
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Validating Resultant Structures of Computational Quantum Chemistry Optimisations

I have tried finding sources (publications, websites, blogs) that outline the logic of accepting the resultant structure of optimisation. I understand using a Hessian to determine if the structure is ...
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How significant is the effect of pi stacking on substituent bond dissociation in an enzyme?

Let there be a system of phenylalanine in a T-shaped pi-stacking configuration with a tyrosine. Both are part of a longer peptide (~40 amino acid separation in the chain). In this system, an oxonium-&...
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What does it mean by pruning and enrichment in the case of Rosenbluth method?

As far as I understand: Pruning means deleting something. Enrich means to enhance/increase weight. Now my question is, in the case of PERM algorithm, Are we deleting some polymers chains? Or, are ...
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6-31G basis set of Silicon and the p-orbitals

Following is the 6-31G basis set of silicon. The numbers in the bracket denotes power raised to 10, e.g. $1.231(+3)=1.231 * 10^3$ Now silicon is $1s^22s^22p_x^22p_y^22p_z^23s^23p_x^13p_y^1$. Now I am ...
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Gaussian type orbitals and p-type orbital

The Gaussian orbital for $p_x$ is defined as: $$\psi_{p_x}=C(x-x_A)e^{-(\vec r - \vec R_A)^2}$$ Where $C$ is a constant. Now if we multiply two such orbitals with two different centers, then $$C_1(x-...
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Why do DFT calculations output molecular orbitals?

My understanding is that DFT finds the electron density which minimizes some energy functional. How does it make the connection from this optimized density to molecular orbitals?
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How do computational programs decide how many virtual orbitals to compute?

How do computational programs decide how many virtual orbitals to compute? For example, a Gaussian job of benzene at the TD-DFT B3LYP/3-21G level of theory calculates from 42 electrons a total of 66 ...
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What is the physical significance of the damping function in calculation of vdW interaction energy?

In order to take care for the singularity (also removing the double counting of exchange-correlation) obtained with this expression, $$E_\mathrm{vdW} = \frac{C^6}{R^6}$$ many type of damping functions ...
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Van der Waals Parameters (non-bonded parameter) in Amber? [duplicate]

I have a complex that contains transition metals. I am doing parametrization and building the force field. I have one question about the frcmod file. In the file, ...
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Variational (Rayleigh-Ritz) method and multielectron wavefunction

I am studying Rayleigh-Ritz method and I have some problem to understand what the final wavefunction looks like. Suppose that we have a system with $N$ electrons, atom or molecule. We are interested ...
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Adhesion energy vs free energy of solvation

I am looking to compute the solvation free energy of Pt(111). Experimental data are still rare because the entropic term is hard to measure. I have found a paper where they use a QM/MM approach to ...
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Using 3 layer ONIOM(M06-2X:PM7:UFF) over 2 layer ONIOM(M06-2X:AMBER) or 2 layer ONIOM(M06-2X:OPLS) to study enzymatic aldehyde reduction

I'm trying to model the reaction mechanism of an enzymatic steroid reduction. Experimental research proposes a large variety of intermediates, which I believe would each require separate ...
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Can AMBER as low-layer be used to model reaction mechanisms using ONIOM? If yes, do you need to parameterize the intermediates and Transition states?

I'm debating moving from (M06-2X:PM7:UFF) to (M06-2X:PM7:AMBER) for modelling a reaction mechanism in an enzyme. I've already examined the errors introduced by my partitioning and whether they cancel ...
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Schrodinger operator with matrix potential and Green's function

Clearly Schrodinger operators with matrix potentials appear very naturally in molecular dynamics/quantum chemistry, particularly when considering a crude adiabatic basis or diabatic basis for an ...
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Given a CIF (crystallographic interchange format) file (and thus cartesian atomic coordinates), how can you find the bonds between atoms?

Applications like Vesta show bonds when viewing a CIF file; how could one algorithmically find all bond pairs? Here is an example CIF file: ...
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What are advantages and drawbacks of using different orders of Møller-Plesset perturbation theory?

I am about to do some research in computational chemistry, however, I do not understand one method: What is the difference between second order and third order, etc, Møller-Plesset perturbation theory?...
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Is there an error at page 138, 4.4 of Introduction of Computational Chemistry 3rd Edition?

Firstly, I found the RHF expansion of $\Phi_2$ and $\Phi_3$ is not symmetric at equation (4.29). Then I expand $\Phi_2$ by myself, the results showed it's $ \Phi_2 = (\chi_A\chi_A-\chi_B\chi_B)(\alpha\...
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Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules? [closed]

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
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Troubleshooting an Autodock Vina Error on Chimera: "Could not find an atomic number for Hn Hn"

After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply ...
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Exploiting 8-fold symmetry of ERI tensor for building Coulomb and Exchange matrices

I'm trying to write a restricted Hartree Fock code in Fortran that reads in a file of zeroth-iteration 1 and 2 electron integrals (FCIDUMP format) and uses them to do the SCF procedure from an initial ...
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Physical origin of induction and dispersion energies

I am reading this book on non-covalent interactions. Chapter 1 states that there are 3 types of non-covalent interactions: Electrostatic interactions, which are just the coulomb interactions between ...
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Matrix elements evaluation in Hartree-Fock method

In Roothaan's matrix formulation of the Hartree-Fock method, we eventually must evaluate the elements in the Fock matrix in the form: $$F_{\mu\nu} = \langle \mu | {-\frac{1}{2}}\nabla^2 | \nu \rangle ...
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What material properties are unpredictable (not reproducible) but can be measured consistently and at a low cost?

I'm looking for a process to create a material which has some easy to measure properties. These properties should be consistent over a long period. It should be very hard (expensive) to predict/...
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What molecules other than N$_2$ have wrong orbital ordering when calculated using Hartree-Fock?

N$_2$ is a canonical example of this aspect of the failure of HF method, for instance, see table 4.9 in "Modern Quantum Chemistry" by Szabo and Ostlund. Here it is shown that in HF, the HOMO ...
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Listing all possible structures for a given Markush structure automatically

I have Markush formulas described as mol blocks, v3000, even if that does not matter that much because I could convert it into another format if needed. I need the possibility to automatically list ...
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Handling of tautomerism in QSAR modelling

This article from 2009: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776169/ mentions the potential impact of tautomerism on QSAR modelling, and concludes that more work is needed to address it. 12 ...
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How to give different color to each type of heteroatom during substructure matching in RdKit

Substructure matching in RdKit generally highlights the matched component in red color over the original molecule. The code for achieving the same is as follows. ...
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5 votes
1 answer
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On the definition of eigenframe

While reading the following article, Elizaveta A. Suturina, Kevin Mason, Carlos F. G. C. Geraldes, Ilya Kuprov, David Parker, Beyond Bleaney's theory: experimental and theoretical analysis of ...
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Why SCF procedure in Hartree-Fock doesn't keep returning the same coefficients?

In the context of Hartree-Fock theory, using Roothaan formalism, we write: FC=SCE where F is the matrix of the Fock operator, C are the coefficients to be used in the construction of the wave function ...
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The MOs computed with HF method by programs like Gaussian are symmetry adapted orbitals?

I know that some molecules have symmetry elements, and that we can associate operators to them. These operaors commute with the molecular electronic hamiltonian $H$, so the wavefunction can be chosen ...
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How does the electronic structure Hamiltonian scales with basis sets and the number electrons?

Given a chemical system with $N$ electrons and a basis set $S = \{\phi_i\}$ with $K$ basis functions. If one to discretize the Hamiltonian with this basis sets, what is the dimension? The electronic ...
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6 votes
1 answer
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How can I formally justify the description of an electronic excitation that includes only the relevant orbitals?

I am writing a small program to animate electronic transitions. To do this, I am animating a Rabi cycle for a single electron as it moves from an occupied into a virtual orbital. The on-resonance ...
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1 vote
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What are the initial experiments to hypothesize or decide the method of protein degradation?

For a protein of interest, How to determine it’s degrading method— protease or proteasome? Is it possible through bioinformatics? What are the initial experiments to hypothesize or decide the method ...
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6 votes
1 answer
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Why are MD simulations necessary for obtaining Boltzmann populations?

Given that MD simulations converge to the Boltzmann distribution $\rho \sim \exp(-\beta \epsilon)$ after sufficiently long times, and all the macroscopic quantities can be computed from the Boltzmann ...
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How can I understand if my system has degenerate electronic configuration?

How can I understand if my system has degenerate electronic configuration? I'm running some post-HF methods and in the meanwhile try to understand which is the most accurate method for my system. ...
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2 votes
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How to compare the Leonard-Jones potential energy curves of diatomic molecules?

The graph shows the dependence of potential energy on internuclear or intermolecular distance according to the L-J model, but how to compare lennard-jones potential energy curves of diatomic molecules,...
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Preparing a surface with two different compounds in computational chemistry

I need to perform QM calculation on a surface built up by a junction of a Palladium surface with an cerium (IV) oxide one. I have the xyz file of both the surfaces, but the calculation should be ...
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How to find the appropriate isovalue with given probability to plot atomic orbitals

As far as I know, a plot of orbitals is drawn by taking region with 90% probability for an electron to be found. Meanwhile, the program which can plots orbitals, such as VMD, gets isovalue (...
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