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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64
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4k views

How do organic chemistry mechanisms become accepted?

Now I have been learning chemistry for five years. I remember when I started organic chemistry, it was fun to draw arrows between molecules to show, as if in a mathematical demonstration, how the ...
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Striking examples where Kohn-Sham orbitals clearly have no physical meaning

In Density Functional Theory courses, one is often reminded that Kohn-Sham orbitals are often said to bear no any physical meaning. They only represent a noninteracting reference system which has the ...
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Why is FORTRAN so commonly used in computational chemistry?

I've been using Ruby to write scripts for research, but I want to get into some heavier stuff that Ruby is just too slow for. I noticed there are a few things written in C and C++, but there is an ...
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How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
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Generating neat orbitals/surfaces from molden/wfn-files

I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's Kohn-Sham-...
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1answer
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Natural Bond Orbital analysis: Significance of stabilization energy determined by 2nd order perturbation

PREFACE: I am no expert on this topic. My questions at the bottom may be off base. I have some experience with symmetry-adapted perturbation theory (SAPT) when it comes to analyzing intermolecular ...
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1answer
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Is there an energy cost associated with flipping the spin of an electron?

THE STORY: A common example used to illustrate the limitations of restricted Hartree-Fock (RHF) theory is the H$_2$ dissociation energy ($D_e$) curves. RHF enforces electrons to be paired into spin ...
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DFT Functional Selection Criteria

I have a very very general question: In DFT functional selection , mostly people speak about the most recent ones. For example my professor always asks: " which DFT Functional did you select ? " ...
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1answer
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Suggest methods and basis sets for a variety of systems

Please help me with any/all of the cases below. In the following cases, the named method and basis set are not suitable for the chemical systems. Why aren't they? Could you suggest a suitable method/...
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Pros and cons of Cartesian vs. Z-matrix representations of molecules?

Over the course of my studies, I have switched largely from using Z-matrix representations of molecular geometries in calculations to Cartesian representations. The software that I use now makes it ...
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How should I go about picking a functional for DFT calculations?

I've been looking to use time-dependent density functional theory, but reading the literature I keep getting overwhelmed by how many different functionals there are. How should I go about selecting ...
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Is hybridization used in ab initio valence bond calculation?

Many general chemistry textbooks introduced the concept "hybridization" to construct a symmetry-adapted VB-type wavefunction. In the textbooks, usually the minimal basis is used and without optimizing ...
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Overlap between computer science and chemistry?

This isn't particularly a question about chemistry itself, but more-so the prospect of chemistry. What kind of opportunities arise when you overlap chemistry and computer science? I'm a computer ...
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A comprehensive list of theoretical approximations that are used in computational chemistry

I am having trouble recognizing all the approximations that are used in computational chemistry. I would like to start an answer list (similar as to the list of resources for learning chemistry) that ...
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Does chemistry need machine learning? [closed]

In many fields of science (e.g. biology, medicine, psychology, statistics, physics), machine learning and artificial intelligence techniques are becoming more and more popular to analyze data. Is it ...
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1answer
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Canonical MOs vs. Localized MOs: Do both represent reality in the same way?

In my understanding localized molecular orbitals (LMOs) are equivalent to "standard" molecular orbitals, often called canonical orbitals (CMOs—by the way, why are they called canonical?). We can ...
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Why is chemical accuracy defined as 1 kcal/mol?

"Chemical accuracy" in computational chemistry, is commonly understood to be $1~\mathrm{kcal\over mol}$, or about $4~\mathrm{kJ\over mol}$. Spectroscopic accuracy is $1~\mathrm{kJ\over mol}$, and that ...
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Where does computational chemistry overlap with organic chemistry?

I was wondering what research exists that combines computational chemistry and organic chemistry. For the past three years, I've been using Amber and Gaussian (in hopes) to identify and understand ...
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What is natural bond orbital theory used for?

My understanding is that the NBO methodology transforms the molecular orbital picture of a molecule into a collection of pairwise interactions (bond orbitals). This is obviously handy for didactic and ...
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Structure that breaks InChI

I am currently testing a piece of software that generates the InChI for a given structure. I also want to test error situations as end users will also deliver the mol files that will be used as input ...
22
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1answer
297 views

How dependent are computed charges using the quantum theory of atoms in molecules on the used level of theory?

The quantum theory of atoms in molecules is based on the topology of the electron density. This mathematical analysis allows to find critical points and hence has a unambiguous way of separating a ...
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DFT Code for Atoms : Sources

Some time ago I implemented the restricted and unrestricted Hartree-Fock methods. I had a lot of fun and I learned a lot. It goes without saying that Szabo and Ostlund's book "Modern Quantum Chemistry"...
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How to calculate wavenumbers of normal modes from the eigenvalues of the Cartesian force constant matrix?

I would like to get the wavenumbers (Frequencies -- in Gaussian) from the eigenvalues of the force constant matrix (...
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1answer
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What's the difference between PBE and B3LYP methods?

I can't find an answer to that question. I was told that in B3LYP, more variables implemented in the method are empirical, but I can't find anywhere if it's true, and I'm sure it's not the only ...
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1answer
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Is the Springborg 6D phase space model used in modern molecular orbital modeling?

In a series of papers in the early 1980s, Michael Springborg explored an interpretation of the Wigner phase space function as an electron density in a six-dimensional $(q,p)$ phase space. He applied ...
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1answer
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Is it possible to compute the colour of *any* molecule?

Above are some spectral emission lines for hydrogen, helium and neon. Using the Schroedinger equation, it's possible to derive the colours that hydrogen will emit when light is fired at it. A little ...
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Why not simulate every particle properties and interactions?

Today we have huge computational power (which is even significantly larger with supercomputers). I know that computational chemistry is used sometimes to predict particle properties. As I read on ...
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Modern open-source tools for simulation of NMR spectra

I am interested in predicting the NMR spectrum of small organic compounds. It doesn't matter to me if the prediction is very accurate. I'll eventually be comparing the prediction to experimental ...
19
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1answer
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Symmetrize nearly symmetric molecule

In the overall good paper of Beruski et. al.,[1] an algorithm of how to symmetrize an "almost symmetric" molecule by symmetrizing the distance matrix is given for the example of Methane. The ...
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How to calculate molecular dipole moment from a known wavefunction?

Say I have a molecular wavefunction as a set of molecular orbitals and want to calculate the molecule's dipole moment, but don't know how! I searched a lot but couldn't find any practical example. $$\...
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How to evaluate the heat of formation with computational chemistry?

I'm sorry if this is a stupid question, but since I'm a beginner with computational chemistry, please, be patient. Let's consider the reaction of formation of water: $$\ce{1/2 O2(g) + H2(g) -> ...
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1answer
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Difference between Coupled Cluster and Full CI

I'm looking at some high precision quantum chemistry methods like Coupled Cluster (CC) and FULL CI (FCI). It seems both CC and FCI start from Hartree-Fock and then excite the electron to higher ...
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2answers
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Do modern dispersion-corrected DFT methods give more accurate molecular geometries?

I was discussing with a colleague the use of modern dispersion-corrected density functionals. I take it almost as a given that the methods generally produce "better" (for some definition) geometries, ...
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1answer
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What exactly is meant by 'multi-configurational' and 'multireference'?

Some topics here have touched on this before (see 1, 2, 3), but I haven't found a clear definition yet. I would like to know what exact property of the wave function these terms refer to. It would ...
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1answer
731 views

When simulating spectral line broadening, which convolution is preferred?

Many computational chemistry packages permit the calculation of vibrational and electronic spectra. These spectra are obtained as a set of discrete eigenvalues however they are often convolved with ...
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(Computationally) finding similarity between two organic compounds

I have been struggling to find an acceptable answer for this question for my purposes. There are many ways to find similarity between two organic compounds - some of which are particularly popular ...
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Ambimodal transition states in some organic reaction pathways

In many computational studies, mechanisms appear to have so-called ambimodal transition states, i.e. a transition state which can lead to multiple products, in conflict to the common undergraduate ...
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2answers
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Dipole moment of cis-2-butene

I need someone to back me up on this before I go confront my teacher: I was doing some analysis of the dipole moment of cis-2-butene. Let's say that the alkyl groups are both on top. Would the dipole ...
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4answers
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Is there a formula to tell how many conformers of a molecule to generate?

Let's say we want to generate conformers of molecules (e.g., ligands for docking in a protein pocket). Is there a formula, like a function of the number of rotatable bonds, to decide how many ...
17
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2answers
893 views

Do bare protons exist, even transiently, in aqueous solution?

Generally $\ce{H^+}$ ions in water remain in the form of hydronium ions ($\ce{H3O+}$), and not as "free" aqueous protons, as far as I've been taught. My question: is this always the case, even when ...
17
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1answer
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Why is MP2 failing to calculate proper IR frequencies for [Co(CO)4]- and [Fe(CO)4]2-?

I was doing some IR calculations on different 3d transition metal carbonyl complexes during some practical courses where we were introduced to effective core potentials. While doing this we found that ...
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Hierarchy of electronic wavefunctions

The previous question contained too much unnecessary information and was edited. I am wondering about the "hierarchy" of wavefunctions. If one can combine atomic orbitals (AO) into molecular orbitals ...
16
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3answers
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Computing two-electron integrals with an STO-3G basis set

I am trying to implement a restricted Hartree-Fock calculation using an STO-3G basis set, for fun. I managed to perform this calculation where only $\mathrm{1s}$ orbitals are present ($\ce{H2}$ and $\...
16
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2answers
961 views

How to compute 2-electron integral for Hartree-Fock code?

I'm working on writing my own code for $\ce{H2}$ in an STO-3G basis set using Hartree-Fock (HF), and I am currently stuck on how to construct the two-electron integral matrix. I know how to evaluate ...
16
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2answers
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Practical differences between storing 2-electron integrals and calculating them as needed?

Some texts that I read suggest calculating all of the 2-electron integrals at once (taking into account permutational symmetry) and some suggest calculating them on demand when building the Fock ...
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3answers
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Modern alternatives to Gaussian [closed]

Specifically, I'm curious if there are any programs which come close to Gaussian in breadth but also take advantage of things such as GPU processing. There's a page on wikipedia that goes through ...
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3answers
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Are there any full worked examples of DFT calculations?

I just started learning DFT and now I am totally confused. Assuming I want to use B3LYP: \begin{align} v_s\left(\textbf{r}\right) &= v_\text{ext}\left(\textbf{r}\right) + \int d^3r\frac{n\left( \...
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1answer
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Hellmann-Feynman Forces with Hartree-Fock

The energy in the Hartree-Fock approximation is given as: $$E_{HF}=\left<\psi_{HF} \left| \hat{H} \right| \psi_{HF} \right>=\sum_{i,j}P_{i,j}H_{i,j}^{core}+\frac{1}{2}\sum_{i,j,k,l}P_{i,j}P_{l,...
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1answer
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Why is the 2-position of pyridine electron richer than the 4 position

I am wondering about the electronic structure of pyridine. If we look at nucleophilic substitution, which favored on electron poor centers, for 2-chloro and 4-chloro pyridine we see that the ...
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2answers
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What are typical runtimes for CASSCF calculations?

I'm doing single point energy calculations of FeS using ORCA. I originally used DFT with a variety of functionals, and these calculations all took less than a minute. Now I'm attempting to run CASSCF ...

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