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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questions with no upvoted or accepted answers
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What are energies in computational methods relative to?
As per my understanding, in molecular mechanics (MM) the computed strain energy is based off the strain inherent in the molecule under study relative to an idealized form. For example, cyclobutane to ...
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Simulation of electronic potential from nanoparticles interacting with molecules
I work with SERS, where the Raman signal gets enhanced by the electric field of the nanoparticles. Now I like to simulate this kind of spectrum with Gaussian. I found a paper[1], where it looks very ...
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What is the definition of energy-independent basis?
I am reading this article by Zatsarinny and Fischer [1].
At some point they span a wave function $\Psi_{E}$ in terms of energy independent basis
$$\Psi_{E}=\sum_{k} A_{E k} \Psi_{k}$$
For example, The ...
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Illegal valence meaning
I'm using the rdkit package to process some molecules.
I noticed that when creating a molecule from a SMILES string the library does some syntactic and some semantic checks. This question regards the ...
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Covering conformers in a molecular modelling; consider them as a static entity or work with modelling shifts as well?
I am currently working with a molecular docking project, examining potential affinities of a solvent on a protein in an assay to evaluate potential error margin. The solvent is cyclohexanol (referred ...
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51 views
How do STO-based computer programs implement the STO integral formulae?
In most cases, STO integrals are evaluated assuming that the orbitals are directed towards each other, using spherical harmonics; however, in GTO-based software Cartesian GTOs are used, with the ...
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37 views
Curtin-Hammett principle to evaluate alkene insertion
Given an unsymmetrical alkene in a simple non-stereoselective catalytic hydrogenation reaction. If one would want to investigate the nuances in the catalytic cycle of a dihydride complex leading to ...
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65 views
Calculating the energy of a molecule using probability distributions
I wish to calculate the energy for a protein where the position of all the C-alpha atoms is known.
One way is to calculate the pairwise distances between the atoms and then look up a probability ...
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68 views
GAMESS(US) Polarizable Continuum Model frequency calculations are giving me what seems to be garbage
I'm trying to run Polarizable Continuum Model (PCM) calculations using the GAMESS(US) software. I'm not that well versed in what exactly these calculations are doing (beyond the whole, 'gas within a ...
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72 views
Tight binding model with Extended Huckel Approximation
I've been reading Albright's Orbital Interactions in Chemistry. In the chapter on solids, he provided a general approach to find the band structure of a solid state system
Now if we are to model a ...
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59 views
Is there any publicly available software that can do deterministic CCSDTQP other than MRCC?
MRCC can do arbitrary order coupled cluster but much of the code is computer-generated (not hand-coded by a human) so it can be slow. There are some stochastic codes for high-order coupled cluster, ...
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79 views
Chirality as atom feature
I have been reading some literature on molecular energy prediction using machine learning techniques and I have noticed that one of the input parameters in many of the available models is "chirality". ...
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118 views
Variational method: Hydrogen atom ground state in STO-3G basis expansion
I computed numerically the ground state energy of hydrogen by variational procedure, firstly expanding the wave function over the s-wave basis set STO-3G
$$\psi(r)=\sum_{i=0}^3 C_{i} e^{-\alpha_ir^2}$$...
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71 views
How can I save and read the CI vector during CASSCF calculations in Gaussian?
I have searched through the GAUSSIAN 16 manual and have not been able to solve these two related issues:
(1) I want to be able to save the CI vector and load it as an initial guess for a different ...
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67 views
Factorizing Slater determinant into product of spin-up and spin-down slater determinant
I am reading the book on MONTE CARLO METHODS IN AB INITIO QUANTUM CHEMISTRY by Hammond and Lester. (Chapter 5-Variational Trial Functions, Section 5.3-Hartree Fock and Beyond, Sub-Section 5.3.3 ...
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462 views
What is the ANO-RCC basis set and how does it work?
On the basis set exchange, the ANO-RCC basis looks huge, even for hydrogen:
...
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218 views
What algorithm is GaussView using for the clean function?
A colleague showed me GAUSSIAN 09 which comes with GaussView 5
for drawing structures. What impressed me was the snappiness of the
Clean function.
What algorithm is used for the Clean function?
The ...
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141 views
What computational methods are available for predicting nanoparticle structure?
I'm a quantum chemist, and nearly every system I've ever cared about has been studied by DFT. However, I am currently trying to model the surface interactions on a nanoparticle around 100 nm in ...
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How to calculate the resonance energy of thiophene?
How to calculate the Resonance energy of Thiophene?
I know how to calculate the resonance energy of Benzene. I am applying same procedure for thiophene, too. (Wikipedia: Resonance energy)
The values ...
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129 views
Geometry optimization: energy not lowered in every cycle
I am performing geometry optimizations of an enzyme active site, covalently bonded to a substrate. I have a total of 122 atoms, of which 7 are fixed in space during the optimizations. I am using ORCA ...
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44 views
Getting Molecular Orbital contributions to the ESP fitted charges
For a single determinant wavefunction, the electron density is the sum of the densities arising from each molecular orbital. The molecular Electrostatic potential $\phi_{mol}$ is calculated from the ...
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86 views
DFT: Can the calculated enthalpy of two systems that aren't isoelectronic be compared?
As a simple example, say I wish to calculate the product of a reaction between methyl iodide and triethylamine, then compare it with the product of benzyl iodide and triethylamine. My goal is to ...
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90 views
Briggs-Rauscher numerical model
I want to use the Briggs-Rauscher experiment to demonstrate oscillating reactions, and then explain it using a numerical model. How much is known about this reaction? Is it possible to write down a ...
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195 views
How to solve the Schrödinger equation of 1D hindered rotor?
I have the following equation:
$$-\frac{{{\hbar }^{2}}}{2I{}_{r}}\frac{{{d}^{2}}\psi }{d{{\theta }^{2}}}+V\left( \theta \right)\psi =E\psi, $$
with
$$V\left( \theta \right)=a+\sum\limits_{n=1}^{...
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212 views
Multidimensional potential energy scans - picking the ideal dimensions to scan
I am relatively new to electronic structure calculations, and I am trying to figure out the most appropriate way of scanning a potential energy surface (PES) to locate an appropriate transition state.
...
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441 views
Semi-numeric or analytic Hessian for DFT (GAMESS)
I'm trying to understand what parameter in the $FORCE group is better to use in computing vibrational frequencies (NVIB=2) of ...
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96 views
Molecular (infrared) vibrations: General relationship between molecular mechanics force constants and harmonic frequencies (in internal coordinates)?
In molecular mechanics method simple molecules, say symmetrical tri-atomics (H$_2$O), have potential energy surface governed by distances $r_1,r_2$ and angle $a$ like
$V (r_1,r_2,a_{121}) = K (r_1 - ...
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90 views
Computing van der Waals constants from molecular structure
How can van der Waals constants be computed from molecular structure?
Is there software that already does this?
Is there software that can design a molecule with specified van der Waals constants?
...
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68 views
Glycine nucleation simulations
I am trying to run nucleation simulations of glycine in water. To generate a supersaturated solution, a solution that will crystallize, I need to know the solubility. Luckily for me, this data exists. ...
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696 views
How to Locate the Excited State Dipole Moment in Turbomole Output (TD-DFT)
I want to calculate the dipole moment for the first excited state with a Q.C. program (TURBOMOLE: TD-DFT). The calculation lists the following output:
ground state total dipole moment:
...
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21 views
Best way of studying protonation in non-polar solutions with ~100ppm of water present using computational methods?
I am currently looking at the mechanism of the formation of storage deposits in jet fuel. Interestingly, the concentration of acids in the fuel correlates strongly with the total insolubles formed ...
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51 views
Mechanism of decomposition of alkali metal halides in flames
A student recently asked an interesting question What happens when KCl is introduced in the Bunsen flame?. This apparently simply question led me to an interesting debate. We all know that emission of ...
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What are the cheapest basis sets able to model intermolecular dipole interactions inside a metal complex and give good relative energies, with DFT?
As a example, If I have a square planar complex of a cation with both a weakly polar ligand (X) and strongly polar ones, like ammonia and water I expect a bit of stabilization due to formation of a ...
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38 views
How does one calculate the electronic difference density in practice?
I am interested in calculating electronic difference density maps. These have been described for quite a long time by Bader and others. For example, below is the fourth of a series of papers which ...
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83 views
Tight binding model for nanoparticles as finite systems
I'm still trying to calculate the band structure ab initio for some hypothetical nanoparticles. It seems that I can directly build a tight-binding model by forming Bloch functions, numerically ...
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82 views
Simple sandbox software for an interactive molecular dynamics simulation
I'm not sure if this is the right site to ask a such question. But I'm getting to learn the world of the small.
I know there is software out there like NAMD, and LAMMPS. But these tools are very ...
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52 views
Overlap matrix for finite sized square lattice of hydrogen atoms
So I'm trying to use the LCAO method to calculate molecular orbitals on a square lattice of hydrogen atoms. To this end, I need to compute the Hamiltonian matrix. With the nearest neighbor interaction ...
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49 views
CNDO/2 clarification
I wrote a piece of code on RHF using Python a while back, and figured I'd extend it to also implement CNDO/2 (yes, I know it's old but I figured it'd be easier for me.)
The approximated Fock matrix ...
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46 views
IRC analogue of conical intersections and minimum energy crossing points?
In my project, there are some spin forbidden organometallic reactions that involves both the triplet minima and singlet transition state (TS). Using the penalty method in qchem as well the method of ...
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323 views
Calculating bond length in VMD (Visual Molecular Dynamics)
Is there a way to calculate bond length in VMD (Visual Molecular Dynamics)?
I have a lot of trajectory files of water molecule, and I need to calculate the bond length of $\ce{O-H}$ bond, and find the ...
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203 views
Software for conformational search
I need a free software to perform a conformational search on molecules with 10 to 16 rotational bonds. What software would you recommend me? Where can I download it? Where can I find a manual of this ...
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173 views
relaxed dihedral PES scan: symmetry of the system not reflected
Using G16 and performing a relaxed PES scan on a dihedral angle, I performed 72 steps where one phenyl group of a symmetric terphenyl is rotated about the C(aryl)-C(phenyl) bond by 5° in every step. I'...
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199 views
Good software/module in python to determine nuclear attraction integral in Slater type orbital basis sets
I am trying to solve a Hamiltonian of one electron and 10 stationary nuclear centers. here, the electron is treated quantum mechanically and nuclear centers are treated classically objects. The ...
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417 views
Restarting a Gaussian partially constrained relaxed surface scan using GICs
I am Using Gaussian 16 rev D.01, and I want to perform relaxed surface scans where I vary a bond distance. At the same time I constrain seven atom coordinates during the entire optimization (this is ...
3
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62 views
Does a constrained wave function method exist similar to constrained density functional theory?
I am trying to find out if a constrained wave function method exists for running quantum chemistry calculations. I know that constrained DFT exists and can be used to constrain the charge density to ...
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173 views
Total SCF Energy with Pseudopotentials
Is there a physical meaning to the SCF energy of a molecule obtained using pseudopotentials to represent the core electrons of heavy atoms (for example gold)?
I've been running calculations in ...
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119 views
Bond order analysis in molpro
I'm trying to compute bond orders in a molecule, let's consider S2 as an example. I'm not entirely sure what's the right way to do that, but I assume NBO (Natural Bond Orbital) should give me what I ...
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505 views
Failure to Locate Stationary Point in GAMESS
I'm currently trying to optimize the geometry of a complex using GAMESS at the B3LYP level. However, I keep failing to converge the SCF. I've already tried the following:
increasing the number of ...
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186 views
calculate SPE using dummy/ghost atoms in NWChem
I have been making some failed attempts to calculate interaction energy of 2 monomers using a dummy/ghost atom in NWChem6.5.
The code I was using to calculate the interaction energy is:
...
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39 views
Calculate the Magnitude of Nonadiabatic Coupling
I'm in the great position to be able to calculate nonadiabatic couplings with TDDFT.
The result of such a calculation is a displacement for every atom in x, y and z.
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asked Feb 17 '18 at 11:18
pH13 - Yet another Philipp
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