A field which implements computers to model and study chemical systems and chemical behavior, using various models, from approximations of the Schrodinger equation to Monte-Carlo simulations to modeling with differential equations.

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Binding energy of organic molecules/small peptides on the surface of SiO2 [on hold]

Technically, I am not from a chemistry background. I am trying to run MD simulation of silicon dioxide where I am looking for calculating binding energy of small organic molecules on the surface of ...
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1answer
24 views

Making sense of J coupling data for Hydronium

I found J coupling data for hydronium using DFT and GIAO but I need help making sense of the data. Can someone with help?
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1answer
76 views

What is the correct way to verify a structure's geometry? (example: 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 ...
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25 views

Considerations when calculating band offsets

I am trying to calculate band offsets of interfaces with the superlattice method: I create a large periodic conventional unit cell. At the bottom of the cell, there are layers of crystal A. At the top ...
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40 views

Software for Chemistry + Electrochemistry Workflow

I am working on a project (can't talk about it), but essentially we have a list of compounds which includes catalysts for electrochemical reactions (those that release energy), metals like Ti, Mn, Zn, ...
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51 views

What are the unsolved problems in quantum chemistry? [closed]

The question is not necessarily limited in quantum, but also computational and theoretical chemistry. Wikipedia listed a few https://en.wikipedia.org/wiki/List_of_unsolved_problems_in_chemistry ...
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29 views

How obtain mass-weighted coordinates used to plot intrinsic reaction coordinates

I have obtained the energies from an IRC calculation. Usually these are plotted in papers vs the mass weighted coordinates; often something like this is labeled on the x axis: $Å \times ...
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1answer
621 views

There are no wavefunctions in DFT

I have seen this phrase several times across DFT textbooks. However, I am not sure if it still holds. Was there a change or a theorem that proved it otherwise? Several programs display wavefunctions ...
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72 views

Estimating stability and mean life of anomalous tautomers

A pair of bases in the DNA, say, A-T, have a tautomerized form A*-T* (resulting from switching the sides of both protons along the hydrogen bridges). I have studied how, by means of DFT computations, ...
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1answer
49 views

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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1answer
93 views

How to find chemical similarity between two compounds using Tanimoto method

I came across a paper named "Chemical Similarity Searching" by Peter Willett John M. Barnard and Geoffrey M. Downs, 1998. At one place, this paper talks of finding chemical structure similarity ...
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1answer
68 views

Why is the CASSCF method multi-configurational, while the CI method is not?

The CASSCF method is perhaps the most commonly used theoretical method for studying difficult chemical systems exhibiting multi-reference character or non-dynamical/static/strong correlation. CASSCF ...
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228 views

DFT Code for Atoms : Sources

Some time ago I implemented the restricted and unrestricted Hartree-Fock methods. I had a lot of fun and I learned a lot. It goes without saying that Szabo and Ostlund's book "Modern Quantum ...
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29 views

Compute minimum energy paths from arbitrary positions on the potential energy surface

The minimum energy path is a useful concept in understanding chemical reaction paths. As I understand it, such MEP's are most often computed to verify that a transition state structure connects two ...
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29 views

What should I use as the starting structure for stacking interaction energy calculation using Gaussian?

I have a crystal structure (single crystal, organic molecule- pyranone carboxamide derivative) that shows pi-pi stacking, and I want to do theoretical calculations. I am using Dispersion-correcting ...
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3answers
51 views

How is mean square displacement defined in Brownian motion?

I am trying to calculate mean square displacement (MSD) of water in a simulation to calculate its diffusion coefficient. However I am little confused on its exact form. Can anyone please explain it in ...
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1answer
49 views

Raman Spectrum of carbon chains: How to identify the vibrational modes

So I am using NWChem to calculate the raman spectra of C2H2 and C4H4. For example for the first I obtained the following frequencies: ...
3
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1answer
191 views

What is the purpose of Gaussian, itself?

I have been doing some research into computational chemistry, having never looked into the area before, and have read about a popular, paid-for software "Gaussian", and free alternatives such as ...
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25 views

Conical intersection using GAMESS

I would like to know how to locate conical intersection using a GAMESS calculation. I really appreciate an example alone with this since I am a novice I do not have a clear idea among bunch of ...
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11 views

Predicting Dissociation Energy in I_2 via orca

In one of my classes we used orca with three different functionals BP86, B3LYP, and M-06L all with the basis set def2-SVP. In addition to predicting via orca we did it experimentally by a deslandres ...
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1answer
127 views

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 ...
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1answer
77 views

Software for visualizing molecular force vectors

I would like to visualize molecular normal modes as vectors sitting on each atom, and not as actual vibrations. I am able to do this, in part, with Molden by copying in the vector into a file readable ...
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2answers
122 views

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 ...
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1answer
48 views

How does Gaussian 09 normalize the excitation coefficients?

When I did excited state calculations with Gaussian 09, I was asking me on how those values are normalized because a simple sum over the squared of the coefficients did not yield 1. So ... how are ...
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1answer
117 views

How to treat pressure in computational chemistry?

I have a reaction where a gas at high pressure and a solution with all kinds of species is involved. How do I take pressure correctly into account to get reasonable values for $G$? Do I calculate ...
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57 views

Is it possible to “brute-force” material creation through algorithms?

I know its a bit of a soft question, but lately I've wondered what important properties and calculations would a program that iterates through certain types of molecules and atoms need in order to ...
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65 views

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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70 views

Isotropic Fermi Contact Couplings vs. Dipolar Coupling Constant

I need to calculate a Dipolar Coupling Constants for some fancy triplet molecule that has been measured by EPR spectroscopy. My "normal" output from Gaussian gives me the following: Isotropic Fermi ...
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2answers
514 views

The time scale of calculations in computational chemistry

Is it possible to determine or get a range of the time required for a specific calculation with knowledge of the type (MM or QM), class (semi-empirical, ab initio or DFT), the degree of theory (MP, ...
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1answer
42 views

Determine rate equations for entire kinetic scheme

I am working with the following kinetic scheme that represents pyrolysis of a biomass particle: The paper that discusses this scheme provides the following rate constants: K1 for the pathway of ...
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2answers
141 views

Single Point Energy in Gaussian software

I used Gaussian software to determine the single point energy (SPE) of 3 molecules namely ethane, ethene and phenol. The SPE for the molecules are -79.83, -78.59 and for phenol it is quite large at ...
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1answer
108 views

How to get 3D molecular structures for 270 compounds?

I need to calculate 10 properties for 270 molecules using Gaussian 09. Could you please suggest me what is the best and shortest way to have the structure of 270 molecules (in the format .com or ...
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51 views

Metal Carbonyl Bonding

I am really struggling with this question we have been set in class: Metal-carbonyl bonding: Conceptionally, one can build up $[Fe(CO)_5]$ from the $Fe(CO)_4$ fragment plus free CO in order to ...
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35 views

Creating Molecular Orbital and Walsh Diagrams

Does anyone know of a good website to create your own MO and Walsh diagrams? Could you potentially make them on a software package such as excel? Any advice on this would be greatly appreciated.
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116 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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1answer
123 views

Ab initio effective potentials

I have been reading a journal on ab-initio pseudopotentials, and I need some help understanding it. The journal is http://journals.aps.org/pra/abstract/10.1103/PhysRevA.10.1528 A summary of the ...
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1answer
43 views

Is there an algorithm that counts Joback groups in a structure?

So I was wondering, there are a lot of cheminformatics tools (eg Babel) out there, to analyze and convert representations. I also saw some codes which counts certain groups, but ignores the carbon ...
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0answers
100 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 ...
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1answer
119 views

Why does bond length decrease with increased basis set quality for SCF methods?

From Reviews in Computational Chemistry Vol. 5, for $\ce{H2O}$ using HF, MP2, CCSD, and CCSD(T), all lengths in angstroms: $$ \small \begin{array}{rcccc} \text{Basis} & \text{HF} & ...
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2answers
58 views

Software for creating the QSAR model?

There is the .csv file with a large amount of descriptors and known experimental activity. Which software can find and describe model for prediction. Most important - numerical representation of ...
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1answer
78 views

Nuclear zero-point energy and quantum delocalization effects of water molecules

What do we mean by "Nuclear zero-point energy" and "quantum delocalization effects" of water molecules ? It's said that without these effects "water" becomes somewhat unbounded, which is not very well ...
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14 views

Is there a published list of adsorption vibrational frequencies of different mocules on different substrates?

Calculating vibrational adsorption frequencies of adsorbed molecules on substrates can be a very difficult task involving solving the vibrational Schrodinger equation. Some published Journals in the ...
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2answers
115 views

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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1answer
81 views

pka from molecular dynamics

How can one calculate pKa values from first principle calculations, static or dynamics? I have encountered some works using CPMD where people try to find pKa values from -(i) constrained Molecular ...
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0answers
72 views

Programs for chemical structure visualisation and drawing 2d and 3d [duplicate]

I want to create list of simple and useful software to draw molecules 2d and 3d with small description. Not necessary only freeware software. Also web-based services are interesting. Your help in ...
7
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2answers
79 views

Free chemical database to search for physical properties?

I am looking for an Open-access tool that can search "backwards", eg. give me all the structures corresponding to a given heat of formation, critical pressure, etc. It would be even better if the ...
2
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1answer
131 views

What is the Franck-Condon region

What precisely is the Franck-Condon region? My understanding is that the FC region is the "bonding" or "equilibrium" region in a potential energy surface, i.e. near the minimum. But when a transition ...
3
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0answers
68 views

Wavefunction convergence error and keywords. (Spartan)

I am currently working with Spartan software and am calculating MOs. My problem is that when I try to do calculations SCF error occures. And every time I try to put some keywords (like CONVERGE, ...
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70 views

How big is the influence of basis set and functional on ZPE and thermal corrections?

Most quantum chemistry packages are capable of computing ZPE and thermal corrections for a given temperature. But how big is the influence of the basis set chosen and the functional used? Is it ...
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21 views

Why is equilibrium constant unitless? [duplicate]

Why is equilibrium constant like kp and kc unitless? It should be unitless when the number of product and reactant molecules are equal but why is it so in other cases?