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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57 views

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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Is there a way to set different special bonds for different atom groups in the same structure in LAMMPS? [migrated]

I am running some simulations on a metal organic framework and I need to set different 1-4 coul and lj parameters for different components on my MOF. I need to set it to be 0 1 for the inorganic part ...
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35 views

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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Autodock Vina Error on Chimera: Service "local" unavailable [migrated]

I was confronted with an error, upon trying to dock a minimized ligand to a target protein, that the "service 'local' [is] unavailable". I then realized that one must have an executable file ...
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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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77 views

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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1answer
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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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1answer
208 views

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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45 views

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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45 views

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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114 views

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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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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1answer
218 views

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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25 views

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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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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47 views

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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387 views

Why is chemistry based on rules and exceptions when everything can be simulated? [closed]

I am a 10+1 student, currently preparing for JEE. It requires me to prepare for Maths, Physics and Chemistry. I particularly enjoy logic related subjects and application, so I find maths and physics ...
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1answer
105 views

Practical use of the partition function in molecular simulations

In the second chapter of Understanding Molecular Simulation, Frenkel and Smit derive an equation for the partition function and the thermal average of the generic observable A, stating that these ...
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52 views

What is the exact Hamiltonian core of the Fragment Molecular Orbital Method?

My major is not chemistry and I am trying to understand the Hamiltonian core of the Fragment Molecular Orbital (FMO) method. I think it should be the normal Hamiltonian core of the restricted Hartree-...
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73 views

Relation of partial charge with wavefunction

Suppose we have an one electron system. The probability $P$ that electron's position is in some interval $x + dx$ is given by: $$P = \int_x^{x+dx}|Ψ(x)|^2 dx$$ So if we measure $N$ times the electron'...
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1answer
43 views

Obtaining orbitals from a many-body wave function

I have seen how sometimes people talk of orbitals obtained from a CAS or DMRG calculation. I haven't found any explanation of how this is possible. Given the many body wave function (obtained from ...
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Classification model from biological assays with different compounds

If I want to use an undersampling approach to construct the machine learning model (classification model predicting whether the target compounds are active or inactive, using chemical fingerprint as ...
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1answer
81 views

What is the format of mol2vec featurize?

When I use the featurize command in mol2vec, I get a .csv file as an output with about 300 columns. But these columns are simply labelled by their number. What feature does each column represent? ...
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1answer
56 views

How do I find an atom in VMD by using its index

For my work I was asked to run a computational NMR of a mostly water structure and then asked to show which hydrogen in this structure correspond to what chemical shifts I am visualizing the structure ...
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Rotating orbitals and parameters for a many-body calculation

I am confused with some results I am getting. Given a molecule (In particular, I was toying with triangulenes, some benzenoids and things like that, but this is not very important), I perform first a ...
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45 views

Exact nature of HOMO of square planar isomer of tetraamminemagnesium(0)

I need to calculate information about the (hypothetical) square-planar form of the tetraamminemagnesium(0) molecule as a reference to my personal QC research project; everything goes fine until we go ...
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Comparing geometries and substrates calculated with DFT for different pathways

As DFT calculation is an excellent tool for confirming and understanding experimental results, I got deep into this field as organic chemist. I successfully isolated interesting transition states (TS) ...
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59 views

What are the references in multi-reference methods? [closed]

There is this question: What exactly is meant by 'multi-configurational' and 'multireference'? But I still don't understand what the multiple "references" are. I understand ...
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1answer
219 views

Hessian matrix and mass-weighted Hessian eigenvalues

If I have the Hessian matrix and the mass-weighted Hessian matrix for a system, I can find the normal modes from the mass-weighted Hessian and the force constants from the Hessian. I have a list of ...
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1answer
62 views

Computational determination of the diagram of molecular orbitals of a polyatomic chemical species

A diagram of molecular orbitals for $\ce{H2O}$ would be as follows: The above diagram has been constructed qualitatively following the steps that I have been instructed in various classes on this ...
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How to transform 'Cartesian gradient' taken from the formatted checkpoint file into the input orientation?

I would like to extract the energy gradient at a particular geometry with many digits from the formatted checkpoint file. However, Gaussian prints the gradient components related to the standard ...
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Linear algebra and Hess's law?

I am a high school student taking chemistry who was tasked to solve a large set of Hess's Law problems. Naturally I tried to find a way to get my computer to carry out this repetitive piece of work ...
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2answers
709 views

How to estimate the temperature needed to overcome an activation energy barrier?

Trying to elucidate a reaction pathway, I calculated the energies for different transition states possible for that reaction (computational chem. DFT). I found activation free energies ranging from 29 ...
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1answer
39 views

Association constant calculation in 3:1 complexes

I have a question about calculating the association constant related to 3:1 host-guest complexes. I am using the UV-vis titration method, I know the stoichiometry from the molar fraction method which ...
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49 views

Gibbs free energy of mixing in a control volume

I'm trying to model the amount of energy lost due to mixing of a $\mathrm{HCl}$ solution using the Gibbs free energy of mixing. However, I really like a second opinion on the model and the results, ...
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1answer
276 views

Why don't the MO energies sum up to Hartree-Fock SCF value?

I would like to calculate Hartree-Fock energy of $\ce{H3^+}$ ion from orbital energies. So I performed the following calculation in Gaussian 16: ...
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1answer
103 views

Quantum chemistry Python package to solve the Coupled-Perturbed Hartree–Fock equations

Two of the most well-known Python quantum chemistry pakcages, PySCF and Psi4, can solve the Hartree–Fock equations. However, I am interested in finding analytic derivatives of the electron integrals: $...
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52 views

How to model a molecule of benzene surrounded by 100 molecules of water with molecular dynamics?

I have experience calculating molecular properties (mostly DFT). However, I would like to spend some time on molecular dynamics methods. I would like to ask your advice to direct me towards a program ...
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64 views

Linear equations for constructing molecules with covalent bonds

(By training I am a math-guy and my knowledge of chemistry is restricted to school level) I have read a little bit about the electron spheres and sub-spheres, the Aufbau principle and covalent bonds ...
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1answer
61 views

Could Gaussian or Spartan software determine stereoisomers from conformational landscape of a molecule alone?

I read that, on some papers, conformers were generated by stereoconfiguration of the molecules and from there, they evaluated stability of each stereoisomer in terms of free energy differences between ...

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