Questions tagged [theoretical-chemistry]

For questions seeking answers deduced from or composed of theories regarding the chemical substances and about models and methods of theoretical chemistry.

78 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
14
votes
0answers
2k views

How to Calculate Transition Dipole Moment from Two Known Wavefunctions

I am 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 ...
12
votes
0answers
145 views

Calculating Triplet-Triplet Spin-Orbit Coupling

According to the Q-Chem manual [1], the singlet-triplet spin-orbit couplings between a singlet excited state $I$ and a triplet excited state state $J$ is: $$\langle\Phi_\text{singlet}^I|\hat{\mathrm H}...
11
votes
0answers
266 views

What is the largest coupled cluster calculation that has ever been done (as of March 2019)?

I am doing some research and trying to make sure the numbers I am reporting are accurate. I found that the paper by Sylvetsky et. al. says:[1] We were, however, able to complete a ...
7
votes
0answers
99 views

Is the 9H-fluoren-9-ylium cation aromatic?

In this cation, there are two individual benzene rings which are aromatic. But in the entire π system, there are 12 π-electrons which should make it antiromatic. Which is correct?
6
votes
0answers
130 views

Where to find experimental spin-orbit coupling constants?

I am searching for experimental spin-orbit coupling constants, particularly for main group elements and Cr(0) to calculate correlation consistent Composite Approach (ccCA) energetics. This method ...
6
votes
0answers
130 views

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 ...
6
votes
0answers
76 views

Do “random” “2D” polymers constrained to a box actually form “space filling” curves?

Background: The self avoiding walk model is (allegedly) a reasonable model for polymers, at least with respect to certain "universal" (i.e. lattice independent) constants -- see section 1.1. in this ...
6
votes
0answers
191 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 ...
6
votes
0answers
135 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 ...
6
votes
0answers
270 views

Canonical vs localized orbitals - stationary towards changes?

So regarding Koopman's theorem I found the the explanation that you should not use it to find the ionization potential of localized orbitals because, much unlike canonical orbitals they will not be ...
6
votes
0answers
337 views

Workflow for many-molecule/many-conformer calculations in Spartan, GAMESS, AND Gaussian

I wish to investigate the antioxidant properties of several hydrocarbon compounds, which are each mono- or polyhydroxylated, specifically at the phenyl ring. I wish to gain insight into my workflow ...
6
votes
0answers
1k views

What does Molecular Orbital Theory get wrong?

I am learning about MO theory in my advanced inorganic chemistry course and am starting to realize that it is truly the most accurate representation of how molecular orbitals look like, where they are ...
6
votes
0answers
2k views

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 ...
5
votes
0answers
71 views

Laplacian of the Hartree Fock second-order reduced density matrix

I am attempting to replicate and understand the Colle-Salvetti method for approximating the electron correlation energy.[1] I have successfully replicated the method, but there is one part of the ...
5
votes
0answers
40 views

Why are the OV and VO blocks of the CIS 1RDM zero?

I know the reduced density matrix has the form: $$ \gamma(\alpha,\beta) = \langle\Psi_N|c^{\dagger}_{\alpha} c_{\beta}|\Psi_n \rangle $$ but when $\Psi_N$ is the configuration interaction singles (CIS)...
5
votes
0answers
164 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 ...
5
votes
0answers
70 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 ...
5
votes
0answers
63 views

What theoretically is the smallest cyclic trans hydrocarbon to correspond to a local potential energy minimum?

Trans-cyclooctene is isolatable at room temperature. Trans-cycloheptene is also known at low temperature. Ab Initio Conformational Analysis of trans-Cyclohexene (1995) says that there is ...
5
votes
0answers
169 views

Why isn't CASPT2 used in surface hopping simulations?

I will write what I think the answer is. I'd like someone to confirm and maybe explain in detail. I think that since surface hopping dynamics simulates movements on PES, it has to calculate gradients ...
4
votes
0answers
56 views

Is there any publicly available software that can do deterministic CCSDTQP other than MRCC?

MRCC can do arbitrary order coupled cluster but much of the code is computer-generated (not hand-coded by a human) so it can be slow. There are some stochastic codes for high-order coupled cluster, ...
4
votes
0answers
103 views

Variational method: Hydrogen atom ground state in STO-3G basis expansion

I computed numerically the ground state energy of hydrogen by variational procedure, firstly expanding the wave function over the s-wave basis set STO-3G $$\psi(r)=\sum_{i=0}^3 C_{i} e^{-\alpha_ir^2}$$...
4
votes
0answers
360 views

What is the ANO-RCC basis set and how does it work?

On the basis set exchange, the ANO-RCC basis looks huge, even for hydrogen: ...
4
votes
0answers
97 views

Number of configurations/states for electrons in orbitals

I'm performing complete active space calculations for the prediction of X-ray absorption L edge spectra. This involves an excitation from 2p orbitals to the 3d orbitals of the metal. For the ...
4
votes
0answers
137 views

Evaluating Franck-Condon factors

Franck-Condon overlap integrals are given by $\langle\psi^e_{v_e}|\psi^g_{v_g}\rangle$, where $\psi^e_{v_e}$ and $\psi^g_{v_g}$ are the vibrational functions for the $v^{th}$ vibrational states of the ...
4
votes
0answers
52 views

Is there a model for (quality of) two-component-polymerization (dependent on e.g. concentration)?

Sadly my chemistry background is only from high school (I'm a roboticist), but I try my best to explain the problem: Situation: Lets say I have two water based solutions/suspensions. One contains ...
4
votes
0answers
91 views

Molecular (infrared) vibrations: General relationship between molecular mechanics force constants and harmonic frequencies (in internal coordinates)?

In molecular mechanics method simple molecules, say symmetrical tri-atomics (H$_2$O), have potential energy surface governed by distances $r_1,r_2$ and angle $a$ like $V (r_1,r_2,a_{121}) = K (r_1 - ...
4
votes
0answers
340 views

Examples of intramolecular hydrogen bonding closing bond angles

Okay, we've established that intramolecular hydrogen bonding can exist in molecules, and doesn't always serve the purpose of closing the bond angle at least relative to other stereoisomers of the same ...
3
votes
0answers
30 views

Can Hartree-Fock be considered the quantum mechanical “Monopole” term in a quantum mechanical multipole expansion?

From what I understand, Hartree-Fock simplifies the exact electron-electron interaction with its two electron integrals. It reminds me of the classical energy of a charge distribution combined with ...
3
votes
0answers
75 views

What is the largest known zero-point energy for a molecule?

I was surprised to find out that the zero-point energy (ZPE) for the ground state of $\ce{BH3}$ is a few thousand $\pu{cm-1}$, because for molecules I usually work with, it's much smaller. Does anyone ...
3
votes
0answers
70 views

Modelling the Oregonator

Assuming this is the correct place for a post like this, I need to write a piece of code to show the oscillations in the Oregonator. I have successfully done so for the Brusselator, but have been ...
3
votes
0answers
116 views

Explaining hypervalency in the framework of molecular orbital theory

In preparing for teaching duties in an introductory course in inorganic chemistry, I seem to have made a digression into how we understand the hypervalent molecules. Just to re-iterate what this ...
3
votes
0answers
172 views

Good software/module in python to determine nuclear attraction integral in Slater type orbital basis sets

I am trying to solve a Hamiltonian of one electron and 10 stationary nuclear centers. here, the electron is treated quantum mechanically and nuclear centers are treated classically objects. The ...
3
votes
0answers
39 views

Calculate the Magnitude of Nonadiabatic Coupling

I'm in the great position to be able to calculate nonadiabatic couplings with TDDFT. The result of such a calculation is a displacement for every atom in x, y and z. ...
3
votes
0answers
287 views

Crystal Field Theory - Operator Equivalent Methods

I am a bit confused by some of the points of operator equivalent methods in crystal field theory. I would appreciate any help I could get with any of my questions. First, I am confused as to the ...
3
votes
0answers
96 views

What proof is there that the “Island of Stability” exists?

Often I see people talking about an "Island of Stability" existing for super-heavy elements on the periodic table, but I don't see any reason to thinks this exists? Surely the heavier you go the more ...
3
votes
0answers
173 views

How to derive the electron density of Hooke's atom?

Hooke's atom has the following wave function: $$\Psi( \boldsymbol{r_1}, \boldsymbol{r_2}) \propto \left( 1 + \frac{|\boldsymbol{r_1} - \boldsymbol{r_2}|}{2} \right) \exp\left(-\frac{(r_1^2+r_2^2)}{4}\...
3
votes
0answers
116 views

Coordinates for molecules except cartesian and zmatrix

Every program in theoretical chemistry that I know uses different ways of writing their input. The same holds true for writing the geometry of the molecules of interest. But they can all be reduced to ...
3
votes
0answers
98 views

What closure relations can we use in molecular modelling?

Following my question here about the BBGKY hierarchy I was wondering does anyone have any experience in using the method outlined. In particular how would I take an equation off the page and for some ...
2
votes
0answers
37 views

Can the Belousov-Zhabotinsky reaction be simulated with the Brusselator?

I'm trying to simulate the Belousov-Zhabotinsky reaction mathematically, with a system of ODEs. I know how to do this with the Oregonator and now I'm looking for another model to simulate the BZ-...
2
votes
0answers
51 views

Explosive reaction based on reaction rate

Question We have the following chemical reactions: $$ \begin{align} \ce{A + B^* &-> C + D^*}\tag{1}\\ \ce{D^* &-> B^* + B^*}\tag{2}\\ \ce{B^* &-> B}\tag{3} \end{align} $$ ...
2
votes
0answers
83 views

How to formulate the 1 dimensional time-dependent Schrodinger’s equation from a given function?

Assuming $f(t) =e^{−iωt}$, formulate the 1 dimensional time-dependent Schrodinger’s equation. I started solving the problem as \begin{align} E &= hf, \tag1\label{eq:1}\\ E &= ħw, \tag2\...
2
votes
0answers
81 views

Antisymmetrized Product of Strongly Orthogonal Geminal (APSG) method

To get a deeper understanding of electronic structure methods, like Hartree-Fock, MP2, and Coupled Cluster method, there are many small programs (codes) available in Python, C++ or Fortran, for ...
2
votes
0answers
28 views

GVP(PP) orbital energies?

Hartree-Fock orbital energies can be interpreted physically, e.g. in Koopmans theorem, while one cannot assign active MCSCF orbitals to energies in general. What about GVB, say for example GVB(PP) ...
2
votes
1answer
302 views

Whats the symmetric, anti-symmetric and non-symmetric part of the direct product of irreducible representations?

I am trying to understand how to see if a vibrational mode is Jahn-Teller active or not. According to the group theoretical description of the Jahn-Teller effect one needs to check if the symmetric ...
2
votes
0answers
123 views

How to obtain the distance of maximum probability of finding an electron on x axis

I have the radial component of the wavefunction $R_{nl}(r)=r^2e^{-2r/3a_{0}}$ so to obtain the maximum distance on x axis I do not know if I have to compute the second derivative of $R_{nl}^2(r)$ or $...
2
votes
0answers
96 views

Problem with understanding the transformation of Hessian in primitive internal coordinates to Hessian in delocalized internals

I am currently working out the theory of Hessians in different coordinate systems. Using the Wilson B matrix $\mathbf{B}=B_{ij}=\frac{\partial q_i}{\partial x_j}$, where $q_i$ denotes the $i$th ...
2
votes
0answers
48 views

Dexamethasone radius of gyration source

I am looking for a source for the radius of gyration of dexamethasone in aqueous solution. Does anyone know where I could get it from? Even better would be an estimation of the Stokes radius, but the ...
2
votes
0answers
1k views

Why is conjugation not possible if there is not present alternate $\pi$ molecules according to MO theory?

I was reading this page at Chemwiki; there they were discussing conjugated-$\pi$ bond. In order to show that conjugation requires alternate double bonding, they cited the example of 1,3,6-...
2
votes
0answers
299 views

kinetic reaction rate greater than extent of reaction for equilibrium

I'm comparing a model with chemistry at equilibrium versus a kinetic one. I take a network of two reactions: methane steam reforming (MSR) and water gas shift (WGS) at 700°C. I calculated extent of ...
2
votes
0answers
245 views

Graph theory, isomer enumeration and chemical graph theory

Where could we find a good description of graph theory applied to the general problem of isomer enumeration and chemical graph theory?