A field which implements computers to model and study chemical systems and chemical behavior, usually by approximating the Schrodinger equation for a given chemical system.

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Calculate redox potential and free energies based on structure of chemical molecules? [closed]

How to do it? And are there any programmes or softwares can do such thing? For example, in metabolic networks, I can have the very basic structure of the chemicals. Then I want to calculate the free ...
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0answers
17 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
197 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
91 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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1answer
94 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
57 views

Ordinary differential equation for molecule collision

My knowledge in 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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2answers
70 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
70 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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2answers
127 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
104 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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1answer
74 views

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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1answer
48 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 ...
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1answer
36 views

Visualizing PDB file in VMD, how to upload molecules?

Problem: When I load PDB-file of my protein of interest in VMD, nothing happens. The molecules is uploaded, but when I push "D" the screens with with big "VMD" letter freezes instead of presenting the ...
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1answer
74 views

Reference value for two-electron repulsion integral over GTO's

I am currently trying to implement a Full CI program from scratch. The energies I get are a bit too high, so I'm looking for the mistake. One possibility is my implementation of the two-electron ...
9
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1answer
124 views

Initial guess for Unrestricted Hartree-Fock calculation

I am implementing an Unrestricted Hartree-Fock calculation, following Ref. [1]. It works fine for a odd number of electrons ($N_\alpha\neq N_\beta$) since, despite the same initial guess for $\alpha$ ...
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1answer
197 views

Gaussian09 vs home made Hartree-Fock implementation

I implemented a restricted Hartree-Fock (RHF) calculation in the STO-3G basis set, as described in Szabo and Ostlund's book [1]. I managed to reproduce the energies of all their calculations ...
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1answer
114 views

Suggestions for simulating transport through membranes with Molecular Dynamics (MD) and Monte Carlo (MC)?

I'm intending to perform a simulation of the transport of simple ions or water through perm-selective membranes, using Molecular Dynamics (MD) and/or Monte Carlo (MC). I've read around that, in ...
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1answer
57 views

Computing accurate vibrational and rotational contributions to the free energy of transition states and loosely bound complexes

Recently I have been dealing with a lot of transition states and relatively loosely bound ion-dipole complexes and I have some trouble figuring out how to make sure that the rotational and vibrational ...
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1answer
118 views

How important is it that geometry be optimized at a high level of theory?

I've been doing research with a computational chemist for a little while now and in one of our projects we are dealing with a rather large system and because I go to a relatively small university, our ...
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1answer
38 views

How to save the force on a molecule in GROMACS?

I am a new student of molecular dynamics. I have started using GROMACS since one month. I have a small box of 8192 molecules each with 3 atoms. I have frozen the last molecule and run the simulation. ...
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1answer
149 views

Boys function for Gaussian integrals in ab-initio calculations

A few days ago I mentioned a problem with an Hartree-Fock program I am writing (HF using cartesian Gaussian STO-3G basis set). I can reproduce overlap and kinetic integrals of some references for ...
3
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1answer
85 views

How many basis functions used in STO-3G and 6-31+G** for the water molecule?

I am a little confused about how to decide how many basis functions that are used in a particular basis set for a given molecule. STO-3G is a so-called "minimal basis set", meaning that only one ...
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1answer
291 views

Can PBE (and LDA) actually be a better choice sometimes?

Part of my work as an inorganic chemist is to investigate the magnetic coupling between metallic centers in coordination compounds. After some time, I've noticed that the classic PBE functional is the ...
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3answers
156 views

Computing two-electron integrals with an STO-3G basis set

I am trying to implement a restricted Hartree-Fock calculation using an STO-3G basis set, for fun. I managed to perform this calculation where only $\mathrm{1s}$ orbitals are present ($\ce{H2}$ and ...
2
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1answer
81 views

Geometry optimization of a small molecule inside of a larger one

I'm very new to this and trying to optimize the structure of a larger molecule that "wraps" around a smaller molecule. I'm using ORCA. I'm having two issues with the task: a) I've attempted to use ...
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16 views

What can one learn from a plot of calculated molecular orbitals? [duplicate]

What can one learn from the plots of the various iso-probability surfaces/orbitals of a given molecule/system? Can any predictions be made about bonding or kinetics by looking at these plots? Can an ...
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1answer
92 views

What is the purpose of calculating other orbitals than HOMO and LUMO?

In this video of benzene orbitals, a lot of different orbitals are presented. Even orbitals that, I assume, could never be occupied. So what is the purpose of calculating all these orbitals? Isn't all ...
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2answers
170 views

Why large basis sets give better approximations to the exact solution of the Schrödinger equation?

The variational principle states that the energy of any approximate wave function will always be equal to or greater than the energy of the exact solution. Therefore the energy is minimized when ...
14
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1answer
209 views

Symmetrize nearly symmetric molecule

In the overall good paper of Beruski et. al.,[1] an algorithm of how to symmetrize an "almost symmetric" molecule by symmetrizing the distance matrix is given for the example of Methane. The ...
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2answers
136 views

What's the role of chemistry in computer science/engineering? [closed]

I am a student in computer science & engineering. I'm taking chemistry for non-majors. I know all subjects (not directly related to chemistry) have influence on other subjects. I want to know ...
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0answers
42 views

Are there any free pharmacophore modelling software?

I would like to know if there is any free and relatively updated software to getting started in pharmacophore modelling.
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0answers
47 views

Books on theoretical computational chemistry [closed]

I have read "Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory" and I am wondering which other books to read afterwards. I am leaning towards to theoretical rather than ...
5
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1answer
65 views

Custom-defined functionals in Gaussian 09

As stated before I want to try out custom-defined functionals. Besides the question about B3LYP itself, there is another related question. Short excerpt: $$\text{XC-Functional}=a ...
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1answer
107 views

Alternative Program for Orbital Population Analysis

Gaussian has Orbital-by-Orbital Population Analysis. From the manual: ...
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105 views

Definition of the B3LYP functional in common QC programs

I wanted to use custom functionals with Gaussian and came up with some interesting definitions of the B3LYP functional within Gaussian, Orca and Turbomole, ... $$\small\begin{array}{lcccccc} \hline ...
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0answers
21 views

If I want to sample rate constants of chemical reactions, what the distribution will be appropriate?

For example, I have a (chemical) reaction systems, I want to sample the parameter space. What will be the best and validated distribution for sampling? And why?
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1answer
37 views

Best way to prepare reference crystal structure with a given force field

I was wondering if somebody could give me some insight into best ways to produce crystal structures, with a given force field, at 0 K. I am interested specifically in glycine, and have obtained the ...
2
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2answers
115 views

Constrain bond angle In Gaussian molecular structure optimization

I am computing the optimized molecular structure in the Gaussian 09 computational chemistry package. As I have it now, I do not think that the optimized structure that I am getting from Gaussian is ...
3
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1answer
110 views

Is there a quantum chemistry package which calculates a second-order wavefunction?

I am trying to generate a change in density which corresponds to a second-order wave-function in standard Rayleigh-Schrodinger perturbation theory. I would like to try out a simple test on an atomic ...
2
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1answer
30 views

Do you know a simple fast front-end MD software for OS X

I need a GUI front-end simple MD software for OS X, something similar to ascalaph maybe. What I need to do is a rigid optimization of waters around a protein. I don't have many water molecules ...
2
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2answers
71 views

What do the molecular orbitals of a single water molecule look like?

Some time ago, (a few years back) I heard that the orbitals of a single water molecule were solved analytically (or was it just numerically). What do they look like? I am interested in the shape ...
5
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1answer
71 views

Non-bonded orbitals in water

General Chemistry perspective: Looking at the molecular orbitals of water, we can see that the oxygen is $sp^3$ hybridized. Oxygen forms two sigma bonds with hydrogens, and there are two lone pair ...
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1answer
509 views

Definition of Electronic energy

Using Born-Oppenheimer approximation, we separate the nuclear and electronic parts of the wavefunction, and treat them separately. We include the terms that have direct dependence on the electronic ...
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0answers
23 views

The Krieger-Li-Iafrate Approximation

I am having trouble understanding what this approximation is. Could someone explain it to me in an intuitive/simple way? Thank you.
4
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2answers
180 views

Converting a PDB file to XYZ file

I am trying to convert a pdb file of gold nanoparticle to the xyz file format to get the atomic coordinates. But when I try to use openbabel to do this, I get the following error. ...
4
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1answer
71 views

How to connect proteins via disulfide bonds computationally?

I want to connect proteins together to form a dimer. As seen in the picture, the monomers come close to each other along the edge of the higher-order structure (forget about the sulfate there). How ...
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1answer
45 views

How do I calculate the color of a compound? [closed]

I know this is complicated, but I'll ask. How do you calculate the color of a compound with pen and paper? Everyone knows that iron(II) sulfate is yellowish. How do I know without looking at it?
3
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1answer
133 views

Is there any molecule visualizing software for Python?

I am looking for a free and open-source software written or wrapped for Python that would simply allow me to generate bunch of figures (in eps, jpg, or pdf format) from a set of xyz files, e.g. water ...
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0answers
23 views

Internal treatments of gas cylinders for toxic gas mixture

The values of toxic components like $\ce{H2S}$, $\ce{NO}$, $\ce{SO2}$, etc. [in ppm level] get decreased after a while due to adsorption phenomenon. Manufacturers design some internal treatments in ...
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45 views

Probablity distribution of bend angle in gromacs

In an analysis I got the probability distribution of a bend angle $P(\theta)$ with respect to time. However, I need to plot $P(\theta)$ with respect to $1- \cos(\theta)$ where $\theta$ refers to the ...