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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32
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4answers
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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 ? " ...
22
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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 ...
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3answers
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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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Why is no dynamical correlation recovered in the CASSCF method?

Configuration interaction is the only certain way to get a calculation to converge toward the exact solution of the many-body Schrödinger equation (within the approximations used for the framework of ...
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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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2answers
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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 ...
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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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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 ...
21
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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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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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Definition of the B3LYP functional in common QC programs

I wanted to use custom functionals with Gaussian and came up with some interesting definitions of the B3LYP functional within Gaussian, Orca and Turbomole, ... $$\small\begin{array}{lcccccc} \hline ...
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U- or RO-method for Singlet-Triplet Gap?

When I want to compare the energy between two different spin states of the same molecule, i.e. singlet-triplet-gap, do I better use unrestricted or restricted open formalism to compare the energies ...
16
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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 $\...
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1answer
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Software for predicting chemical reactions

I wondered if it was possible to predict the product(s) of a reaction (or even the equilibrium) based on the reactants and the temperature/pressure. I found an answer to a similar question here: ...
16
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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 ...
5
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2answers
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How to obtain the Raman spectrum along every coordinate of a scan in Gaussian?

I am doing a scan calculation using Gaussian09 and adding the Freq=Raman keyword to my input file. My objective is to obtain the ...
33
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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 ...
21
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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 ...
18
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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 ...
19
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3answers
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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 ...
23
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1answer
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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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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 ...
7
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1answer
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How to obtain the radial probability distribution function from a quantum chemical calculation?

In the book "Quantum Chemistry" by Ira Levine I found a plot of the radial probability distribution function of argon: The figure appears in the context of the following section: Electron ...
13
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What is the purpose of calculating other orbitals than HOMO and LUMO?

In this video of benzene orbitals, a lot of different orbitals are presented. Even orbitals that, I assume, could never be occupied. What is the purpose of calculating all these orbitals? Isn't all ...
13
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1answer
526 views

Why do post-Hartree-Fock methods fail to predict the direction of the dipole moment of carbon monoxide?

In carbon monoxide the dipole moment (negative to positive) points towards the oxygen, as I explained it in How can the dipole moment of carbon monoxide be rationalised by molecular orbital theory? A ...
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1answer
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how are the frequencies at a local maximum of PES like?

On the potential energy surface, if you find a local maximum and calculate its frequencies in Gaussian or something like that, will you get all negative frequencies or all positive frequencies? I know ...
5
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2answers
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What is the correct way to verify a structure's geometry, for example for benzene?

My goal is to compare a calculated bond length with experimental data. Benzene is obviously common enough to expect sufficient experimental data to be available for it on the internet. I have found ...
5
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1answer
781 views

GAMESS crash course?

I'm still learning about MO theory – and I thought that I would do some calculations with GAMESS to become more familiar with the concept. Even though I look forward to delving into the realm of ...
3
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1answer
357 views

Solving two electron integral numerically

Is there any software package in python or C to evaluate two electron integral repulsion integral in quantum chemistry of atoms. I am trying to solve the helium atom by constructing many body basis....
14
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2answers
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Software for viewing a structure and altering bond angles

Does anyone know of any good software that would allow me to view the structure of a compound while also allowing me to change the bond angles in the structure (and give me numeric values for those ...
13
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2answers
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Gaussian: Relaxed scan with modredundant optimization and dummy atoms

I would like to perform a relaxed scan in Gaussian09 on my molecule using the modredundant optimization. Because I want to scan over two bond lengths simultaneously,...
5
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1answer
155 views

Quotable Literature for the Enthalpy of a Proton

A proton obviously has no electronic energy, no vibrational and no rotational degrees of freedom. Therefore I think it is fair to assume, that $$H(\ce{H+})=\frac32\cdot \mathcal{R}\cdot T$$ holds for ...
18
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1answer
733 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 ...
10
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What is the dipole moment direction in the nitrosonium ion?

In the recent question about the molecular orbitals of $\ce{NO^{$x$}};\ x\in\{-1,0,+1\}$ the follow-up title question arose: Just a random side-question: What’s the dipole moment’s negative and ...
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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/...
24
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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 ...
15
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How to find a transition state for an electrophilic addition with Gaussian and map the reaction pathway?

I aim for two things with this post – on the one hand to produce a manual for other people to use, but also to verify what I obtained via searching, asking a more experienced user as well as receiving ...
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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 ...
20
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1answer
488 views

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 ...
18
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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 ...
14
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2answers
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What do short-range and long-range corrections mean in DFT methods?

Currently I am looking for the most accurate calculation method for a simple non-conjugate molecule consist of C, N, O and H. Normally I would try each method for a similar and known molecule then ...
11
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2answers
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Why are excited Slater determinants used to describe electron correlation?

Usually the first step in describing the electronic wave function of a molecule or atom is to describe it with a single Slater determinant. I get that this is an independent particle approximation, ...
11
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4answers
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Defining and testing custom made DFT functionals?

What is a good and free software for this endeavor? Any recommended articles on the subject? I want to design dft functionals, trying out different parametrizations and optimizing mixing constants for ...
10
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1answer
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Calculating pKa's using Gaussian

I've been learning to use Gaussian recently and I found a question here that seemed like a good opportunity for me to practice. I know that I can obtain $K_a$ from $$\Delta G=-RT\ln(K_a)$$ using the ...
7
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1answer
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What are complete active space methods and how are such spaces defined for molecules?

I am new to computational chemistry and would like to know about the active space and inactive space terminologies in MCSCF type calculations. For understanding this I have four systems: $\ce{H2O}$ ...
15
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3answers
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Why are basis sets needed?

I am not sure whether this question is even reasonable, but here it goes. We are taught about the different types of basis sets (extended, minimal, double-zeta, plane wave), but I do not think it is ...
16
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1answer
924 views

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 are the total energies of transition states so commonly corrected for zero-point vibrational energy?

So often I see total energies of transition states corrected for zero-point vibrational energy which always confuses me. Zero point energy is the lowest energy that a ground state minimum energy ...
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Is it reasonable to use natural orbitals of an unrestricted HF calculation as a basis to start a CASSCF calculation for a radical

Let's say we want to run a CASSCF calculation of a radical, for example the cation of a neutral closed-shell molecule (therefore, we calculate an open-shell radical cation). MOLCAS, as well as ...
6
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1answer
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How to calculate Lennard-Jones potential with quantum mechanical methods

I want to know the procedure to calculate the Lennard-Jones potential for a metal-halogen pair (specifically vanadium-chlorine). Is it possible to calculate using any QM packages like Mopac, NWChem, ...