62
votes
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How do organic chemistry mechanisms become accepted?
Great question!
When I was teaching, Anslyn and Dougherty was a decent text for this. Here are some general comments:
First, please note that you cannot be sure about a mechanism. That's the real ...
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45
votes
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Why is FORTRAN so commonly used in computational chemistry?
I don't think that's really true anymore.
Some Fortran use is historical (i.e., early codes were developed in FORTRAN because that was the best programming language for number crunching in the 70s ...
- 27k
41
votes
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DFT Functional Selection Criteria
What's up with all that magic? (A chapter formerly known as Introduction)
The hunt for for the holy grail of density functional theory (DFT) has come a long way.[1] Becke states in the introduction of ...
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37
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How do organic chemistry mechanisms become accepted?
This doesn’t exactly concern the actual mechanism you asked for, but as part of my PhD thesis, I performed an amide alkyne coupling the mechanism of which had been researched by Arndt et al.[1] ...
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35
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Why not simulate every particle properties and interactions?
Forty electrons is tiny. Even if we limit ourselves to just the valence electons, cyclohexane already has 36 electrons. Anything drug-like has way more electrons that 40. For example, viagra has 178 ...
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32
votes
Why is FORTRAN so commonly used in computational chemistry?
I think it does make sense to provide a somewhat alternative view and to clarify the matter.
FORTRAN vs. Fortran
First off, one has to distinguish the old FORTRAN from the new Fortran, where, by ...
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27
votes
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Dipole moment of cis-2-butene
Mini Research Project Time
Updates
Added CCSD(T) $n_i$ and dipole moments and tweaked discussion (the delay was caused by a system-wide storage upgrade on the machines which took nearly a week to ...
- 4,559
26
votes
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Is there an energy cost associated with flipping the spin of an electron?
I will try to describe what happens when two hydrogen atoms approach each other from infinity. At infinite separation the hydrogen atoms don't feel their mutual presence and each atom has one electron ...
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26
votes
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Why is chemical accuracy defined as 1 kcal/mol?
Short answer: the goal of "thermochemical accuracy" for computational chemistry is to match or exceed experimental accuracy. Thus, ~1 kcal/mol comes from the typical error in thermochemical ...
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25
votes
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What are typical runtimes for CASSCF calculations?
There is nothing trivial about MCSCF calculations because it is hard to predict a priori how long a calculation will take. There are well-defined equations for calculating how many determinants
$$
D(...
- 7,284
24
votes
How to calculate molecular dipole moment from a known wavefunction?
The necessary formal derivation has already been nicely done by AngusTheMan. I'll start from the last equation:
$$
\langle \mu_{z} \rangle = \langle \Psi | \hat{\mu}_{z} | \Psi \rangle
$$
where $\...
- 7,284
24
votes
Accepted
Canonical MOs vs. Localized MOs: Do both represent reality in the same way?
NOTE: In the below, I'm implicitly discussing a ground-state, closed-shell wavefunction, where all occupied orbitals are doubly occupied. The discussion would be similar for open-shell wavefunctions, ...
- 16.9k
24
votes
Linear algebra and Hess's law?
To convert this into a generic linear algebra problem you'd rewrite it in the form $Ax=b$ where $A$ is a matrix of stoichiometric coefficients of size $m \times n$; $x$ is a vector of length n of ...
- 18.9k
23
votes
Does chemistry need machine learning?
The short answer is yes. Machine learning, data mining, AI and other techniques are highly useful in chemistry.
I completely agree with Fred's answer that lots of machine learning, expert systems and ...
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21
votes
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There are no wavefunctions in DFT
There are no wavefunctions in DFT.
I don't like that "wave function" is used here in the plural form and I feel like it reflects OP's misconception. The right way to say this is
There is no wave ...
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21
votes
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What exactly is meant by 'multi-configurational' and 'multireference'?
Your problem seems to be with the terminology used in CI methods, so let me go through the different terms you mentioned:
A configuration is a certain occupation of (molecular) orbitals. ...
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20
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Difference between Coupled Cluster and Full CI
Full Coupled Cluster (FCC) vs. Full Configuration Interaction (FCI)
The main theoretical difference is the way excitations are used. "Excitation" refers to putting one or more electrons in higher ...
- 6,758
19
votes
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How to calculate molecular dipole moment from a known wavefunction?
The dipole moment $\mu$ of a molecule is a measure of charge distribution in the molecule and the polarity formed by the nuclei and electron cloud.
We can perturb our system with an external ...
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19
votes
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How to evaluate the heat of formation with computational chemistry?
Your approach is quite correct, but as Jan already pointed out, it is incomplete. What you calculated is the difference in the electronic energy of the reaction $$\ce{H2 (g) + 1/2 O2 (g,\,{}^1\Delta_{...
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19
votes
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Is there a formula to tell how many conformers of a molecule to generate?
I haven't seen any rigorous benchmarking or guidelines.
Consider that the total number of conformers goes up like $3^n$, where $n$ is the number of rotatable bonds, and ~3 is the approximate number ...
- 27k
19
votes
A comprehensive list of theoretical approximations that are used in computational chemistry
The goal of computational chemistry is to obtain the properties of a system. This is done by solving Dirac's Equations.
Treating particles as point particles with mass
In most computational software, ...
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19
votes
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How are the atomic orbitals for multi electron atoms obtained?
Already in year 1928 Hartree proposed an approximate method of solving the Schrödinger equation for a many-electron atom that became known as the Hartree method (1, 2, 3). The Hartree method is based ...
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18
votes
Symmetrize nearly symmetric molecule
I've done some work in both symmetry detection and in distance matrix methods. I think it's a great idea in concept, but the devil will be in the details for large, more complex molecules.
The first ...
- 27k
18
votes
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How important is it that geometry be optimized at a high level of theory?
Method
Most of the time CCSD(T) would indeed be a huge overkill for geometry optimisation. DFT and MP2 have way better performance/cost ratio. Note that I said DFT and MP2 above, not or MP2; this is ...
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17
votes
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Structure that breaks InChI
Okay, let's tackle at least one problem here. Consider the rotation of 1,2-dichloroethane (BP86/cc-pVDZ):
These conformational changes can be further rationalised:
C and C' are the same ...
- 42.4k
17
votes
When using Gaussian to calculate NMR, what's the default solvent and frequency?
While Greg's answer describes sufficiently what the program does, I would like to extend a little on his remark. (This should have been a comment, but it was too long.)
The ...
- 42.4k
17
votes
Why is FORTRAN so commonly used in computational chemistry?
FORTRAN used to have an edge when it came to speed due to having much better optimizing compilers, in part due to its relative simplicity. Now that C and C++ compilers are nearly on par (and ...
- 809
17
votes
Generating neat orbitals/surfaces from molden/wfn-files
Often different quantum chemical programs require different analysing tools. Unfortunately there is no universal standard (program), that can do it all. If there were, someone would come along and ...
- 42.4k
17
votes
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PBE vs. PBEPBE functional
The designation PBEPBE is an actual terrible artefact from researchers using Gaussian. The actual publication[1, 2] only refers to it as PBE, and most other program packages (I know) implement it as ...
- 42.4k
16
votes
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How can you manage SCF convergence problems?
There can be many reasons for the SCF to not converge.
The initial guess wasn't great, and the convergence is slow. Increasing the number of SCF iterations can help here.
The SCF oscillates. This can ...
- 27k
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