pentavalentcarbon
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What are complete active space methods and how are such spaces defined for molecules?
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7 votes

Multiconfigurational self-consistent field (MCSCF) calculations can be further categorized. What you are referring to is a complete active space SCF (CASSCF) calculation. In CASSCF, the 1-particle ...

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Calclulation of MP2 first order wave function
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8 votes

The main problem with the last statement, $$ \begin{align} C^{MP2} &= c\cdot c^T \\ \Rightarrow P^{MP2}_{ij} &= \sum_{a}C^{MP2}_{ia}(C^{MP2}_{ja}), \end{align} $$ is that one never has "MP2 ...

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Notation for excited states
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7 votes

As has already been mentioned in comments, those letters and numbers for each state correspond to their symmetry, specifically the symmetry of the (purely electronic) wavefunction. For more ...

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How is a counterpoise corrected geometry optimization done?
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5 votes

Background For a system consisting of two molecules (monomers or fragments are also used) X and Y, the binding energy is $$ \Delta E_{\text{bind}} = E^{\ce{XY}}(\ce{XY}) - [E^{\ce{X}}(\ce{X}) + E^{\...

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What causes energy peaks during a molecular dynamics energy minimization?
3 votes

At the top of your config file, you imply that you want to perform an NVE calculation, but you’re actually doing NVT, because you have the Langevin thermostat turned on. Langevin works by giving the ...

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Differences between Liquid and Solid Infrared Spectrometry
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2 votes

Some basic comments can be found in Spectrometric Identification of Organic Compounds. Although it is primarily concerned with interpretation, it has some notes on the types of instrumentation and ...

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Can visible light or infrared radiation excite electrons?
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7 votes

Different regions of the electromagnetic spectrum correspond to different atomic and molecular processes, each with one or more associated spectroscopies. Here is a general summary, with decreasing ...

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Which intermolecular interaction is dependent on the inverse cube of distance?
6 votes

2 The ion-ion or charge-charge interaction is given by $$ V_{\text{cc}} = \frac{Z_{i}Z_{j}e^{2}}{4\pi\epsilon_{0}} \frac{1}{|\mathbf{R}_{i} - \mathbf{R}_{j}|} $$ and is therefore proportional to $R^...

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Two electron integral evaluation over primitive Gaussians without recurrence relations
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5 votes

As you mentioned, most implementations such as Obara–Saika (OS), McMurchie–Davidson (MD), Head-Gordon–Pople (HGP), and many others use a series of horizontal and vertical recurrence relations to build ...

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Is there an upper limit on the coordination number of a coordination compound?
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3 votes

I don't see why not. It is a matter of having enough of an interaction between the center and the ligands, usually in the form of donor/acceptor orbital pairs, and enough space around the ...

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Accuracy benchmarks for atomic multipole moments
5 votes

To the best of my knowledge, there is no definition of "chemical accuracy" for higher-order (electric) multipole moments, in part because they are difficult to measure experimentally, with relatively ...

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Reporting reaction energies calculated using electronic energies rather than enthalpies
2 votes

In the case of atoms or molecules in a vacuum, at $0~\mathrm{K}$, and infinitely apart, the "reaction energy" of $$ \ce{A + B -> A \bond{....}\bond{....}\bond{....} B}, $$ where $\ce{A \bond{....}...

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Library / function for computation of molecular mass / molecular weight in C
1 votes

If you download AmberTools, under the AmberTools/src/sff directory, there is atomic_number.{h,c}. Note that this code is under the GPL. atomic_number.h: #ifndef ATOMIC_NUMBER_H #define ...

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Molecular orbital diagram and irreducible representations for dinitrogen
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13 votes

Because this is a diatomic molecule, there are no group orbitals. Put another way, the group orbitals are the molecular orbitals. Knowing the nitrogen atomic orbitals (AOs) and their irreducible ...

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How do you calculate the dipole moment of larger molecules?
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10 votes

The total dipole of a molecule can be thought of as the sum of dipoles of individual functional groups: $$ \vec{\mu}_{\text{total}} = \sum_{i}^{N_\text{groups}} \vec{\mu}_{i} $$ Because each dipole ...

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How large an energy difference in Hartree can be used to distinguish two different structures?
6 votes

That's a pretty incredible threshold. To put things in perspective, if $1 E_{\mathrm{h}} \approx \pu{627 kcal/mol}$, then $\pu{0.0000001 a.u.} = \pu{6.27e-5 kcal/mol}$. Energy differences between ...

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Analytical gradient of the Hartree-Fock nuclear-electronic repulsion term
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9 votes

There are a few points to discuss: Since there are $3N$ possible $\{X_{A}\}$, each term where an $X_{A}$ appears will result in $3N$ matrix elements. In your first equation, that will be $S$, $T$, $V$...

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Distinguishing propan-2-ol from ethanol using IR spectroscopy
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2 votes

Here is the spectrum for ethanol: Here is the spectrum for propan-2-ol: Here are the tabulated peak positions ($\pu{cm^{-1}}$) and percent transmittance (%T) for the two. I've tried to match the ...

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How to unify all the subunits in a PDB file?
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3 votes

If you don't care about residue and atom numbering, which you probably do, then sed '/^TER/d' < 1A3N.pdb > 1A3N_combined.pdb will do. Since atom entries must be reordered, it looks like ...

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How to write an entire trajectory into a single PDB file?
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4 votes

#!/usr/bin/env python2 import MDAnalysis # file formats are automatically deduced; this is a standard topology and binary # (NetCDF) trajectory from AMBER topology = 'peptide_1.prmtop' trajectory = '...

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What does the format nF10.8 mean?
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13 votes

It is a Fortran format specifier. It means $n$: repeat the input $n$ times, once for each weight F: input is a floating-point number 10.8: the number is of total width 10 (including the decimal ...

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How to do Lowdin symmetric orthonormalisation?
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9 votes

Your first question has already been answered, but in words: to find $f(A)$ for some matrix $A$, you diagonalize it to obtain the eigenvalues $a$ and eigenvectors $U$, apply $f$ to the diagonalized ...

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Finding CML files for small molecules
3 votes

Another location, if you're ok with the mol2 format (which Avogadro can open), PQR has links to download structures on every page. For example, on the cadaverine page: This will trigger a browser ...

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O-H infrared band dependence of alcohol concentration in water
4 votes

The easiest thing to do is look at some example spectra. All of them are taken from the Spectral Database for Organic Compounds. This is 1-propanol, first as a liquid film and then in $\ce{CCl4}$. ...

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Polarity of symmetric Lewis structure
5 votes

The problem is that the first Lewis diagrams you learn to draw don't take 3D structure into account. A more realistic structure for dichlorodifluoromethane looks like where the dashed wedged bond is ...

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Calculating dipole moments from atomic partial charges
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11 votes

From a theoretical standpoint, that approach is correct: $$ \mu_i = \sum_{a}^{N_{\text{atoms}}} \sum_{i\in\{x,y,z\}} r_{ia}q_{a}, $$ where the set of atomic partial charges $\{q\}$ could come from ...

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How do I show that a transition is magnetic dipole allowed with group theory/symmetry?
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12 votes

For a state-to-state transition coupled by an operator to be allowed, the direct product of the irreducible representations (irreps) of all three components must contain the completely symmetric irrep ...

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Ionisation Energy vs First Ionisation Energy
4 votes

There is no difference between "ionization energy" and "first ionization energy". Another definition from Wikipedia: The ionization energy (IE) is qualitatively defined as the amount of energy ...

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How to determine conformation using IR
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3 votes

This is perhaps my biased view as a theorist, but I've collaborated quite a bit with a condensed-phase 2D-IR group and a little with a UV resonance Raman group, so I have some understanding of the ...

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Are "gas phase" calculations the same as "vacuum" calculations?
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10 votes

I don't know the etymology of the phrase, but yes, "gas phase" calculations are the same as "vacuum" calculations. There is no difference. Think of it this way: the only option other than a "gas ...

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