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 extract transition density cube from .fch file in Gaussian? [migrated]

I have been trying to extract the transition density cube of a simple molecule, $H_2O$. I did a regular geometry optimization and then TD-DFT calculation with a keyword Density=Transition=1, which is ...
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I want to scan 1 atom moving away from 2 atoms simultaneously while using the opt=modredundant option on the bond length between the 2 atom bonds [duplicate]

Using gaussian i want to scan one atom moving away from two atoms while optimizing the bond length between the other two atoms. I have been attempting to use a dummy atom to scan moving the two bonds ...
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33 views

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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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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34 views

What are the references in multi-reference methods?

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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72 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
42 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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1answer
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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
581 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
32 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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42 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
193 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
62 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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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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61 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
44 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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2answers
114 views

Significance of the ground state energy in quantum chemistry?

In quantum mechanics, quantum chemistry, and condensed matter physics courses, it seems like finding the ground state energy of a Hamiltonian is incredibly important. I can understand why having the ...
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2answers
73 views

To which extent is protein folding conserving subprotein structures?

I am actually a pure mathematician, who stumbled over this paper «Protein-Folding Analysis Using Features Obtained by Persistent Homology» by Ichinomiya et al. (Biophys. J. 118, 2020, 2926-2937; link),...
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Spin Multiplicities of Ions

The multiplicity is fundamentally defined as $2S + 1$ where $S$ is the total spin. From what I understand, the multiplicity corresponds with the number of unpaired/paired electrons. For example, in ...
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1answer
22 views

How to Build Hydrogen Atoms in MOE using SVL

I'm working on automating a process in MOE using SVL commands. I've got pretty much everything worked out, except I can't seem to find anything for building hydrogen atoms using an SVL command (...
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1answer
114 views

Confusion regarding DFT basics, i.e. the connection between Hohenberg–Kohn theorems, external potentials and the Kohn-Sham method

I have a question on the basics of DFT, which bases on the Hohenberg-Kohn theorem: there exist an unique mapping between the external potential, the electronic wave function and thus also the ...
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Changing the level of theory for organometallic compounds

I'm finishing my Ph.D. in Inorganic Chemistry and having a debate with my supervisor. The work in question have two organometallic compounds A and B. The structures are based on X-Ray Diffraction, so ...
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105 views

Disambiguate molecule's bonds, angles or dihedral angles selection

I am working on a project where one of the goals is to store data from computational quantum chemistry calculations for later retrieval. Currently, we are trying to store the outcomes of simple bond (...
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28 views

Is an element's “atomic electron configuration” EXACTLY equal to the term with the largest coefficient in the CI series of the neutral atom?

For atoms and molecules with more than one electron, the wavefunction cannot be written as a single Slater determinant, so the ground-state configuration of (the atom or molecule in question) is ...
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47 views

How to identify multiple molecules in a single xyz file?

I wonder if there exists a tool/script/algorithm to identify multiple molecules and/or atoms in a single XYZ or gaussian log file. As an example, imagine one does a single point calculation for the ...
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32 views

High symmetry points and x-coordinates

Is it possible to work out the x-coordinates related to high symmetry points? The software I'm using doesn't provide me with that, so I was wondering if there is a way to manually figure it out, as I ...
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19 views

small negative frequencies in DF T optimizations with organic molecules containing CF3 groups [duplicate]

When optimizing by DFT medium-sized organic molecules containing aromatic CF3 groups (for example, adducts involving takemoto's catalyst), the frequency calculation on optimized structures have always ...
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1answer
57 views

What is an appropriate way to write a recursive SMARTS that excludes trifluoromethyl groups as a potential R group?

C[CX4&!$(C(F)(F)F)] is the smarts I've tried. It does not exclude the trifluoride in CC(F)(F)F.
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Measuring energy required or generated in gasification

The typical equation used to measure heat is as follows: $q = mcΔT\\ \text{Where, }\\ q = \text{heat} (\pu{J}) \\ m = \text{mass} (\pu{g}) \\ c = \text{specific heat capacity} (\pu{J g^-1 K^-1})\\ ΔT ...
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1answer
61 views

How to carry out basis set fitting and extrapolation

I am playing around with basis set extrapolations, and i would like to perform some simple tests by doing some parameter fitting and checking the errors. The functional form of the fitted curve is ...
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55 views

CCSD and CISD size consistency problem

I have performed a Gaussian16 calculation to explore the size-consistency problem for the CISD and CCSD methods. The system I am studying is the water dimer and the results are not what I expected at ...
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2answers
51 views

How to model 98% ethanol solution concentration graph over time

İ want to plot a graph of ethanol solution concentration over time .So we know that alcohol evaporates quickly in open air but is there a time when the rate of evaporation mathces that of water and ...
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1answer
117 views

How does the application of Schrödinger equation to model a particle in a box explain the origin of degeneracy of atomic orbitals?

Is the particle in a box concept analogous to an electron in an orbital? If so, can we apply the equation for the allowed energies of a particle in a box $$E = \frac{h^2n^2}{8mL^2}$$ to the allowed ...
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2answers
51 views

Milliliters of NaBr when changing molarity [closed]

I was very confused by this problem. I was able to get the molarity, but I wasn’t certain how to go from there: If $\pu{2.60 g}$ of $\ce{NaBr}$ is dissolved in enough water to make $\pu{160.0 mL}$ of ...
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Calculating nanocluster's Lewis acidity

In general, fluoride ion affinity, ammonia binding energy, photoacoustic IR spectra of adsorbed species (pyridine, CO) are used to measure the Lewis acidity of a material. But in the computer ...
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62 views

TD-DFT transition dipole moment vector does not align with experimental data

I have been modelling excited states of some molecules with similar stucture using TD-DFT theory, however, I have encountered an issue that sometimes transition dipole moment does not align with the ...
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43 views

Computing optimized 3D structures in python that take solvent into account

I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows: ...
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38 views

How to choose the parameter to scan in finding transition state by using Gaussian 16?

I have problems in finding the TS of reaction dehydrogenation of an organic compound. I read many tricks to find the TS and see scan is an effective method. As I know we can use the product of the ...
4
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1answer
152 views

Potential Energy Curve from Hartree-Fock Calculations

I am currently working on some quantum chemical calculations, in particular looking at dissociation energy curves generated from Hartree-Fock, CI, CCSD and MP2 methods for diatomic molecules. Now, I ...
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0answers
40 views

Interpreting data on molecular orbitals in GaussView 6.0 [duplicate]

Introduction I have been trying to use computational software to gain more insight into how molecular orbitals are formed, as well as their shapes and sizes in accordance with Molecular Orbital Theory....
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43 views

Physical interpreation of coulomb and exchange integral

When trying to solve the Schrodinger equation for the electronic hamiltonian: $$H_{el} = \sum_{i=1}^{N} \bigg( - \frac{1}{2}\nabla_i^2 - \sum_A \frac{Z}{r_{i_A}} \bigg) + \sum_{i>j=1}^{N}\frac{1}{...
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27 views

How to retrieve excited state molecular orbital coefficients in Gaussian?

Currently I am doing TD-DFT calculations in Gaussian and want to calculate transition dipole moment for $S_1$ transition manually. However, I do not manage to retrieve molecular orbital coefficients ...
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26 views

How much should I scan an aromatic dihedral?

Suppose I have a napthalene-like molecule (attached), and I would like to scan (relaxed) its aromatic dihedral (highlighted atoms). I used CGENFF to obtain its dihedral parameters as follows, HGA4 ...
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1answer
43 views

Aluminum electrodes for NaCl [duplicate]

Upon using aluminium Electrodes for a concentrated solution of NaCl, i conducted electrolysis on the solution for nearly 4-5 hours. There was definitely a gas possibly hydrogen being evolved at the ...
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86 views

How to use dispersion correction with M06-2x in Gaussian 09 or 16?

I would like to perform an optimization calculation using the functional M06-2x using the BJ dispersion correction in Gaussian 0.9. However, I can't find the parameters for this functional as I found ...
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48 views

Virtual screening lib

I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
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16 views

Sticking coefficents for dissociative adsorption

I am trying to simulate the decomposition of Hydrogen Peroxide ($\ce{H2O2}$) on $\ce{Pt}$ using Chemkin Pro. I am using a two step global reaction model for the reaction which is as follows- $$\ce{...

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