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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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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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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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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43 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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39 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: ...
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177 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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21 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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10 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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97 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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66 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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118 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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42 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
103 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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63 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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58 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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502 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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37 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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139 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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96 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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50 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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31 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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111 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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119 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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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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90 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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115 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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55 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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74 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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31 views

Excitation using TDDFT GAMESS [closed]

I would like to know the value for the NSTATE for photochromic molecular excitation using GAMESS. Also how to decide that..?
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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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109 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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75 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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71 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 ...
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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 ...
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106 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 ...
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58 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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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?
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1answer
240 views

Is there any software package for quantum chemistry that includes CAMB3LYP?

I want to do calculations on systems with photoinduced electron transfer, and I've read that the Coloumb Attenuating Method is a modification of the functionals that makes calculations including ...
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2answers
155 views

Diagonalization of Hessian H= PkP$^{-1}$: what do the elements of P matrix physically mean?

This is quoted from Computational Chemistry by Errol J. Lewars' chapter 2's Stationary Points & Normal-Mode Vibrations: ZPE: \begin{align}\mathbf H &=\begin{bmatrix} \dfrac{\partial ^2 ...
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195 views

Why is Hessian Matrix called 'force-constant' matrix?

Hessian Matrix is a square matrix containing the elements as the second-order partial derivatives of energy-function of a molecule; the derivative is done with respect to geometric coordinates of the ...
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1answer
77 views

Ordinary differential equation for molecule collision

My knowledge is 0 in chemistry. But, I have a good background in mathematics and computer programming. I have planed to simulate the collision of two simple molecules $\ce{Br2}$ and $\ce{H2}$ just ...
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105 views

Negative LUMO Energy

During the (DFT-)computations that I have done over the last years, it happened quite often that I got negative energies for the LUMO and many times also for a bunch of virtual orbitals. Is there a ...
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1answer
77 views

How to calculate hydrogen from SMILES string?

How to calculate the number of hydrogen atoms from SMILES string? For example, SMILES String: C1=CC(=C(C=C1C(CN)O)O)O The known result is C8H11NO3
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158 views

Molecular mechanics force fields for metals?

I know of several general molecular mechanics methods suitable for metals, including Dreiding and UFF. I know it's difficult to get many things right for such classical treatment of inorganic / ...
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1answer
127 views

How to determine the best computational method for energy calculation of a molecule?

In computational or quantum chemistry text books comparing between various methods for energy calculation of a molecule (e.g geometry optimization) such as Semi-empirical, Ab-initio or DFT and also ...
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83 views

How does CASSCF yield a more-negative total energy from less-negative orbital energies?

When comparing single-configurational Hartree-Fock computations with corresponding CASSCF results, it appears that the CASSCF calculation is somehow able to generate more-negative total energies from ...
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Should I include solvation in quantum chemical calculations of a simplified protein-ligand interactions?

I am running a B3LYP-D3/6-31+G geometry optimization of a protein-ligand interaction. Well, not quite, I have simplified the protein to four amino acids surrounding the active site, but I keep the ...
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54 views

Horizons of a bachelor degree in chemistry [closed]

If I have a bachelor degree in chemistry, what master programmes can I apply for ? In other words, are the choices limited in chemical engineeirng, biochemistry,etc? Is it possible to apply for a ...