Unanswered Questions
496 questions with no upvoted or accepted answers
27
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answers
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How to calculate transition dipole moment from two known wavefunctions
I'm interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment ...
- 6,801
24
votes
0
answers
1k
views
What is d-orbital collapse?
When I was perusing the works of Schwarz on atomic structure, I came across the unfamiliar term of d-orbital collapse.
He describes it as a variation in energetic sequence from group 1 to 3 elements ...
- 60k
15
votes
0
answers
358
views
Rotation around CC bond in 1,2-dioxetane: transition states and local minimum structures
TLDR:
What: Potential energy surface associated with rotation around CC bond in the ring-opened version of 1,2-dioxetane.
How: State average(4)-CASSCF(12,10)/VTZP constrained geometry optimizations ...
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12
votes
0
answers
309
views
Accuracy of quantum chemistry calculations on iodine neglecting relativistic effects
Triiodothyronine is a molecule with three iodine atoms. If we attempted to calculate its properties with ab initio methods like Hartree-Fock or more complicated ab initio methods which included ...
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11
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0
answers
1k
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Understanding two-electron integrals in Gaussian 09
I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in ...
- 9,881
10
votes
0
answers
141
views
Using symmetry and group theory arguments to explain iron(II) in a tetrahedral crystal field
I am trying to figure out how to explain $1s \rightarrow 3d$ spectroscopic transitions for $\ce{Fe^{2+}}$ in $T_\mathrm{d}$ symmetry. These transitions make up the pre-edge region in K edge X-ray ...
- 101
10
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0
answers
2k
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Why is the bond angle of N-N-N in hydrogen azide not 180 degrees?
Chen and Wang (2009) have reported an $\ce {N-N-N}$ bond angle in the hydrazoic acid molecule of $171.5$ degrees using B3LYP/6-311G** model. The wikipedia page for the molecule also reports a similar ...
- 10.7k
9
votes
0
answers
196
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Is there a reliable chemical theory that predicts pKa based on structure?
Obviously, there are general stability arguments that can be made to estimate relative pKas, such as evaluating the stability of the conjugate base of an acid, or thinking about how polarized the bond ...
- 38.4k
9
votes
0
answers
430
views
Vanishing integral rule for two-electron integrals
I understand the vanishing integral rule for a one-electron integral to be:
$$\langle i | \hat{O} | j \rangle = 0 \hspace{1cm} \mathrm{if} \hspace{0.2cm} \Gamma_O \neq \Gamma_i \otimes \Gamma_j$$
...
- 11.8k
9
votes
0
answers
514
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multielectron spin-orbit coupling and energy level
For multi-electron atoms for which the Hamiltonian (including the spin-orbit coupling) reads
$$H=\sum_i T_i-Z\sum_i V_i+\sum_i V_i^{\text{s.o.}}+\sum_{i>j}V_{ij}$$
The $T_i$ are the kinetic ...
- 281
8
votes
0
answers
207
views
Where is bifurcation situated on cyclohexane isomerisation PES?
I am wondering what does PES for cyclohexane isomerisation looks like.
I have two possibilities in mind but each has some kind of vagueness.
1) Starting from boat conformation minimum, followed by ...
- 534
8
votes
1
answer
3k
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Geometries of SCl2(OCH3)2 and SF2(OCH3)2
I am not able to understand the difference between structure of $\ce{SCl_{2}(OCH_{3})_{2}}$ and $\ce{SF_{2}(OCH_{3})_{2}}$.
I am already well versed with Molecular Orbital and VSEPR theories. I found ...
CommunityBot
- 1
7
votes
0
answers
101
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Why do nuclei move considerably slower than electrons
I've been trying to learn quantum chemistry at an introductionary level. While reading I've found out that the Born-Oppenheimer approximation seems to be the reason for the basic and crucial model of ...
- 79
7
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0
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124
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Additional example determining Marcus parameters searched
Background / theory: The electron transfer in organic materials was formalized by the Marcus theory, introducing $|H_{ab}|$ to describe the how molecules (or more generally: sites) are coupled with ...
- 30.4k
7
votes
0
answers
3k
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Warning during geometry optimization via Gaussian
I have some recurrent problem with my DFT calculations [functional: hseh1pbe; basis:6-31+g(d,p), object: porphyrin derivative]. During the MO setting I get:
**** Warning!!: The largest alpha MO ...
7
votes
0
answers
214
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Interstitial sites: edge and face sharing?
In close packed structures there is one octahedral hole per close packed atom. In a HCP unit cell these octahedra form a chain of face sharing polyhedra. Is this this universal in close packing or ...
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7
votes
1
answer
3k
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Beer's law: UV-Vis absorbance values exceeding 2
In classical analytical chemistry, absorbance values in Beer's law can theoretically range from 0 to infinity.
As general rule of thumb neither high, nor very low absorbance are used for ...
- 29.2k
7
votes
1
answer
4k
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Geometry of AsF5 molecule
Which of the following is the best description of the arragement of fluorine atoms around the arsenic atom in a molecule of $\ce{AsF5}$?
(a) trigonal bipyramid
(b) octahedron
(c) tetrahedron
(...
- 38.4k
6
votes
0
answers
78
views
Why SCF-MO methods fail when treating bond-breaking processes?
I'm currently studying the EVB(Empirical Valence Bond) approach. While reading on this article (https://pubs.acs.org/doi/10.1021/ja00224a011), the author mentioned about the usage of SCF-MO formalism ...
- 221
6
votes
0
answers
103
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Obtaining transition density matrix
I'm trying to assemble a transition density matrix on quantum computer using one-body excitation $\widehat{E}$ operator on 2 active spatial orbitals, i.e. on 4 spin-orbitals. The problem is, I need to ...
- 4,606
6
votes
0
answers
71
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Are there examples of publications using DFT instead of HF as a coupled-cluster reference?
I have been searching for a while, and only managed to find an article by M. Saitow,[1] where CAM-B3LYP orbitals are used. I was wondering if this has been done elsewhere.
It was recommended to me by ...
- 44.3k
6
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0
answers
201
views
Why are the unsaturated fatty acids usually unconjugated?
My textbook gives the structures of the unsaturated fatty acids in food including oleic acid, linoleic acid, linolenic acid and docosatetraenoic acid. I figure that when two or more $\ce{C=C}$ double ...
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6
votes
0
answers
192
views
Hund's rule for comparing term symbol energies in excited state
This question was asked in an exam:
The lowest energy electronic state for excited state carbon atom is,
a. $^1D_2$
b. $^3D_1$
c. $^3D_3$
d. $^3D_2$
Although we have been taught Hund's rule for ...
- 7,030
6
votes
0
answers
357
views
Geometry of a free radical at the bridgehead carbon
With reference to J. Am. Chem. Soc. 1968, 90 (19), 5266–5267, they state:
The most favorable geometry of aliphatic free radicals remains an unsolved problem, since existing data are consistent with a ...
- 7,030
6
votes
0
answers
114
views
Solving the Schrödinger equation for a rotating triatomic linear molecule
This source is showing that solving the Schrödinger equation for a triatmoic linear molecule yields the same formula for the rotationaI quantum states $BJ(J+1)$ as for dipoles.
For dipoles, the total ...
- 647
6
votes
0
answers
109
views
Why does BCF (boron carbofluoride) not exist?
$\ce{BCF}$ (boron carbofluoride, or carbon borofluoride, not to be confused with another so-called BCF molecule that has nothing to do with it) should exist as a vapor molecule with the bonds $\ce{B≡C-...
- 61
6
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0
answers
90
views
How long would it take for a tank of same-spin hydrogen atoms to become a tank of H₂?
In the question
Is there an energy cost associated with flipping the spin of an electron?, it is shown that it is very unlikely for two hydrogen atoms to bond if their electrons have the same spin. ...
- 2,242
6
votes
0
answers
573
views
How to extract force constants for normal modes from ORCA?
I am following the computational method described in Scientific Reports.[1] Where the authors analyze the contribution of each excited state normal-modes to the shift of the transition energy. For ...
- 44.3k
6
votes
0
answers
383
views
How to evaluate the expectation value of the Hamiltonian for a three electron Slater determinant?
I'm having trouble with a few concepts dealing with slater determinants and many electron systems. In particular, when dealing with 3 electron systems, I know that
$$
\psi_0 = \frac{1}{\sqrt{6}} \det
...
- 11.8k
6
votes
0
answers
201
views
Vibrational Self-Consistent Field
There are a few things about VSCF that I don't understand:
Which coordinates do you work in? If you work in normal mode coordinates, how do you evaluate the effect of the average of one normal mode ...
- 11.8k
6
votes
0
answers
972
views
Platt's Notation/Nomenclature for transitions
How do you read Platt's Notation / Nomenclature? Where can I learn this?
Some examples where I've seen this mentioned:
In Platt's notation the transitions are designated as $\ce{A -> B}$ and $\ce{...
- 1
6
votes
0
answers
113
views
Program to compute multipoles of water at CCSD(T)-F12 accuracy
I want to compute traceless cartesian electrostatic multipole moment tensors up to fourth order (hexadecapole), at CCSD(T)-F12 accuracy using a large basis set. I'd like to be able to choose the ...
- 181
6
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0
answers
333
views
How to define the initial guess for the electron density?
This is a technical question. If I have a one-dimensional box of length L, and an electron density existing in the box and integrating to N electrons. And if I want to determine the electron density ...
5
votes
0
answers
157
views
N2 HOMO-LUMO Gap calculation
I am thinking about calculating the HOMO-LUMO energy gap for $\ce{N2}$ molecule.
I thought I could model this as a particle in a box problem to find $E_\text{HOMO}$ and $E_\text{LUMO}$.
The formula I ...
- 151
5
votes
0
answers
156
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Combining two overlapping wavefunctions
Let's assume that we solved the many-body Schrödinger equation for two molecules and we can now write their wave functions as
$$
|\Psi_1\rangle = O_1|\operatorname{vac}\rangle\,,\\
|\Psi_2\rangle = ...
- 217
5
votes
0
answers
70
views
Do disulfide bonds determine the 3-dimensional structure of a protein or do they just stabilise the 3D structure?
I noticed that most disulfide bonds occur when two cysteine side chains exist in close proximity to each other. Do those cysteine side chains "look out" for each other during folding, that ...
- 41.2k
5
votes
0
answers
120
views
Meaning of $^2[\,1/2]$ terms in atomic spectroscopy
I was trying to analyze some atomic emission spectroscopy data and I encountered unfamiliar notation of the terms for me.
Commonly, the electronic states of the atoms can be described by quantum ...
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5
votes
0
answers
223
views
Splitting of atomic orbitals due to Stark effect
I am performing graduate level research on ZEKE Photoelectron Spectroscopy and central to this form of spectroscopy is Rydberg states and the Stark effect. The Stark effect is caused by an electric ...
- 71.6k
5
votes
0
answers
178
views
Stress-Strain Graph Under Uniaxial and Biaxial Strain
I was going through a recently published journal paper by ACS (Applied Nano Materials) about gas separation using nanoporous Graphene.
DOI No. - https://dx.doi.org/10.1021/acsanm.0c02340
Supporting ...
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5
votes
0
answers
117
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Type of chirality in polycyclic compounds
Ignoring whether or not this molecule could exist, is there a name for this type of chirality? This molecule's mirror image cannot be superimposed on itself but there are no chiral centres.
Even ...
- 4,606
5
votes
0
answers
58
views
On the localized screening of cerium (when compared to iron)
I was reading the paper 'A linear response approach to the calculation of the effective interaction parameters in the LDA+U method' by Cococcioni - (Paper here) .
Quoting from the first paragraph on ...
- 101
5
votes
0
answers
103
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Is there a mistake in diagramatic representation of RS perturbation theory described in Szabo and Ostlund textbook?
I'm trying to understand rules of the diagrammatic representation of the many body perturbation theory that described in Szabo and Ostlund "Modern Quantum Chemistry" textbook. One of the ...
CommunityBot
- 1
5
votes
0
answers
88
views
Does a [B4O8]4- anion really exist?
I am currently collecting information for an abstract and therefore I wanted to discuss different $\ce{[BO3]^3-}$ and $\ce{[BO4]^5-}$ connectivities. I also found a book on crystallography and the ...
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5
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0
answers
116
views
Can you use a photon's torque to change a molecule?
Can you use the torque of a photon to change bond angles, etc.? 11-Cis-Retinal to the all trans version, in the eye, is a good illustration [1].
Note: This phenomenon can be observed by closing ...
- 477
5
votes
0
answers
428
views
What is the theoretical justification for state averaging in SA-CASSCF?
According to the molpro manual, section 7.3:
In order to compute excited states it is usually best to optimize the
energy average for all states under consideration. This avoids
root-flipping ...
- 44.3k
5
votes
0
answers
226
views
How to derive a state symmetry in D2h point group from its wavefunction?
Let's have an atomic carbon with the following electron configuration:
$$
1s^2 2s^2 2p^2
$$
One of it's levels is ${}^1S_0$, which is corresponding with the following state:
$$
\begin{align}
\left| ...
- 1,267
5
votes
0
answers
74
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Identifying principal quantum numbers in natural population analysis
Following a Hartree-Fock calculation, I would like my program to perform some kind of Natural Bond Orbital (NBO) analysis. Preceding this I would like to output a list of atomic orbitals, along with ...
- 1,271
5
votes
0
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321
views
Why is spin-contamination undesirable?
Why is spin-contamination, introduced by e.g. Unrestricted Hartree Fock, undesirable, and to which problems further on can it lead?
The only problem I currently see myself is that spin-contamined ...
- 1,696
5
votes
0
answers
168
views
How to calculate a molecule's oscillator strength?
I was wondering how to calculate a molecule's (e.g. biphenyl) oscillator strength using a very simplified model.
If I want to calculate a molecule's excited states a good start is something like a ...
- 369
5
votes
0
answers
93
views
MCSCF Hessian transformation
I have tried doing the transformation of the Hessian in MCSCF following the notation that is used in Molecular Electronic-Structure Theory (MEST). Here I try to show what steps I have taken (to get ...
- 2,242