Tagged Questions

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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1answer
94 views

Born-Oppenheimer Approximation reloaded

I'm an undergraduate Chemistry student and I'm currently writing my Final Dissertation. I've written a form of the Born-Oppenheimer approximation with the only initial assumption of parametric ...
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1answer
32 views

Gaussian Calculations - What is the Basis?

What am I actually changing when I click 631G(d) or 631G(d,p), etc. when I choose a "basis" in restricted Hartree Fock calculations? What is the difference between using an alternative basis? Many ...
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1answer
26 views

How can I estimate reaction rates in water with computational chemistry?

I want to estimate rates of substitution reaction of esters with nucleophiles in water. How can I estimate them with a computational chemistry software (preferably GAMESS(US))? Or is it practically ...
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2answers
28 views

What is the official file extension for SMILES and SMARTS files

I want to know what is the officially used file extension for files containing SMILES and SMARTS strings. Somewhere I see .SMI/.SMA and somewhere its the full .SMILES/.SMARTS.
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3answers
152 views

How is the bond length calculated from the total electronic energy?

In the quantum chemistry course that I currently attend, it was said several times that one of the key quantities derived from molecules by means of computation is the total electronic energy ...
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0answers
97 views

How to Locate the Excited State Dipole Moment in Turbomole Output (TD-DFT)

I want to calculate the dipole moment for the first excited state with a Q.C. program (TURBOMOLE: TD-DFT). The calculation lists the following output: ground state total dipole moment: ...
3
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1answer
101 views

Representation of chemical formulas as strings?

Is there a standard manner of representing chemical formulas as linear strings? For example, $H_2O$ can be represented with the string H2O. Isotopes are usually ...
2
votes
1answer
29 views

CMAP layout of data

I would like to use the charmm CMAP correction in another program (PyRosetta). I have looked at parmfile.doc and io.doc and this discussion, but nowhere is it distinctly written how the CMAP is laid ...
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2answers
125 views

Methods for Determining Partial Charges

I want to run classical molecular dynamics simulations of a periodically replicated surface (rutile $\ce{TiO2}$ with grooves). In order to do so, I first need to solve for the partial charges residing ...
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3answers
9k views

Why is gold golden?

Bulk gold has a very characteristic warm yellow shine to it, whereas almost all other metals have a grey or silvery color. Where does this come from? I have heard that this property arises from ...
1
vote
1answer
79 views

GAMESS crash course?

I'm still learning about MO theory – and I thought that I would do some calculations with GAMESS to become more familiar with the concept. Even though I look forward to delving into the realm of ...
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2answers
249 views

Dipole moment of cis-2-butene

I need someone to back me up on this before I go confront my teacher: I was doing some analysis of the dipole moment of cis-2-butene. Let's say that the alkyl groups are both on top. Would the dipole ...
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0answers
27 views

Book recommendations for protein structure refinement

I’m an undergraduate Chemistry student and I’m currently writing my dissertation about semi-empirical methods, particularly PM7, applied to protein structure refinement from X-ray structure. Could you ...
2
votes
1answer
57 views

Can you calculate the properties of a substance based soley on its atomic properties?

I'm trying to write some software that I can use to determine, roughly, what the physical properties of a pure substance are. I know I could just use a database of the known properties of each ...
2
votes
3answers
76 views

Which software is suitable to calculate the root mean square deviation between two protein structures?

I need to compute the root mean square deviation (RMSD) between two protein structures: the X-ray determined protein structure and the MOPAC optimized structure. Which software do you suggest?
3
votes
1answer
50 views

When it comes to bond energy or molecular binding energy, do people mean enthalpy?

When calculating bond energy or molecular binding energy, which value should I use, enthalpy or total energy? For example, A+B=C Should it be C's enthalpy of formation minus (A's+B's)enthalpies of ...
2
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1answer
125 views

Which one, Mulliken charge distribution and NBO, is more reliable?

Sometimes the Mulliken and NBO turn out to be so different that I can't decide which one I can trust. I've heard that Mulliken is inaccurate, but is NBO always accurate? And should I use Gaussian or ...
3
votes
1answer
74 views

Coefficients and Parameters for contracted Gaussian basis sets

I'm trying to write a program to calculate fixed-point Hartree-Fock level energies of molecules (for my amusement) and everything makes sense but this. I've been agonizing over this for almost 3 hours ...
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1answer
35 views

Using water model in a computer program

I am writing a small simulator for situations where water is the medium of all reactions. A quick googling confirmed that there are water models available in computer readable formats. Being a ...
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0answers
79 views

Structure of fluoroalkylsilane

I want to use FAS (fluoroalkylsilane) in my molecular dynamics study. How can I find it's real structure? So that I can find proper forcefield for simulating the molecule. It would be very nice if you ...
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vote
1answer
44 views

Writing Topology file for Ligand for Gromacs

Is there any tutorial for how to manually write the topology file for any Ligand file(PDB for mol2)? There are so many sites which provides it like ProDrug or ATB but no where the actual process is ...
1
vote
1answer
71 views

Two-electron Integrals over Gaussian Plane Waves [closed]

Is there an efficient method to compute the two-electron integrals over the basis set represented by a product of a Gaussian function $g(r)$ and plane wave: $\psi(r)=g(r)e^{ikr}$ where $\lambda=1/k$ ...
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vote
2answers
131 views

When using Gaussian to calculate NMR, what's the default solvent and frequency?

If I choose GIAO HF/STO-3G, is the default solvent $\ce{CD3Cl}$? Is the default frequency for $\ce{^1H-NMR}$ 500 MHz? What about the frequency for $\ce{^13C-NMR}$?
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1answer
65 views

“Electrwd” group?

The Amber force field parameters describe hydrogen atoms in various states: ...
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2answers
267 views

Are there any full worked examples of DFT calculations?

I just started learning DFT and now I am totally confused. Assuming I want to use B3LYP: \begin{align} v_s\left(\textbf{r}\right) &= v_\text{ext}\left(\textbf{r}\right) + \int d^3r\frac{n\left( ...
0
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1answer
75 views

molecular connectivity index

I would like to know about (question related to computational chemistry): what is valence molecular connectivity index of 3rd order cluster. Please provide an example? Thanks for your help.
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1answer
42 views

how are the frequencies at a local maximum of PES like?

On the potential energy surface, if you find a local maximum and calculate its frequencies in Gaussian or something like that, will you get all negative frequencies or all positive frequencies? I know ...
2
votes
1answer
96 views

How can a chemical structure be stored in a matrix?

How do I represent a chemical structure in a matrix format in Matlab? Can I input a chemical structure into Matlab using the S.M.I.L.E.S notation? I have to specify the connectivity of different ...
7
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1answer
95 views

Structure that breaks InChI

I am currently testing a piece of software that generates the InChI for a given structure. I also want to test error situations as end users will also deliver the mol files that will be used as input ...
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0answers
14 views

Simulating enzymatic change rates of Carbonic anhydrase

I'm trying to simulate effects of carbonic anhydrase on cellular pH as caused by changes in bicarbonate. I assume a bicarbonate homeostatic mechanisms which replenishes intracellular conenctrations ...
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1answer
47 views

Number of orbitals in full configuration interaction

I am using one quantum chemistry package where I am supposed to assign a number of active orbitals I want to be included in the FCI (full configuration interaction) calculation. For example if I have ...
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2answers
78 views

Theoretical principles of molecular simulations

I am pharmacy student and would like to work in the field of drug design. We learn to work with the programs but thats not enough for me. I want to learn the theoretical principles of computational ...
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0answers
37 views

Making a reasonable slab of alpha quartz

I want to perform a molecular dynamics simulation with alpha-quartz as my mineral surface. I want to study adsorption of water on alpha-quartz. The most dominant error that I came up with is the ...
5
votes
1answer
72 views

Magical reaction tanks

I would be interested to know people's opinion on the following matter. Background Often, when the far-from equilibrium behaviour of a chemical reaction system is analysed mathematically (in papers ...
5
votes
1answer
194 views

What's the difference between PBE and B3LYP methods?

I can't find an answer to that question. I was told that in B3LYP, more variables implemented in the method are empirical, but I can't find anywhere if it's true, and I'm sure it's not the only ...
5
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0answers
327 views

Natural Bond Orbital (NBO) analyses: Physical significance/interpretation of E(2) 'stabilization energy'?

PREFACE: I am no expert on this topic. My questions at the bottom may be off base. I have some experience with symmetry-adapted perturbation theory (SAPT) when it comes to analyzing intermolecular ...
0
votes
1answer
29 views

Controlling the shape of metal

Is there a way to control the shape of metal? Suppose I have a fast melting metal, is there a way to make it take a specific shape? Of course I don't mean to like put it in a template to take the ...
2
votes
2answers
188 views

Animate molecular vibrations as multiple xyz coordinate files

I have a frequency calculation by Gaussian09. Now I would like to extract vibrational modes as a set of xyz coordinate files. I would like to manually recompute numerically the points along a ...
2
votes
0answers
92 views

Are multiple transition states possible? Criteria to choose the correct one?

I am studying a reaction using electronic structure methods using various software packages (ORCA,GAMESS, G09) and have found two possible transition structures between product and reactant. Both have ...
4
votes
2answers
217 views

Reaction Pathways: What to do when IRC geometries are relaxed (optimized) and the energy changes significantly

The Story: Reaction pathways can be difficult things to deal with using electronic structure methods. Intrinsic reaction coordinates (IRCs) can be determined a number of ways (a discussion of these ...
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0answers
72 views

How to model iso-surface of molecular orbitals of singlet and triplet excited states

I've modelled the iso-surface of the highest occupied molecular orbital of a molecule with DFT in Gaussian.If I were to model the iso-surface of the molecular orbital of the singlet and triplet ...
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1answer
419 views

Is there an energy cost associated with flipping the spin of an electron?

THE STORY: A common example used to illustrate the limitations of restricted Hartree-Fock (RHF) theory is the H$_2$ dissociation energy ($D_e$) curves. RHF enforces electrons to be paired into spin ...
3
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1answer
55 views

Remove empty space from structures with R and S groups

We receive structures from a server within our company. Those structures are transferred as MOL files. Some of these structures contain R and/or S groups. Some of the creators of these structures ...
5
votes
1answer
306 views

Why are excited Slater determinants used to describe electron correlation?

Usually the first step in describing the electronic wave function of a molecule or atom is to describe it with a single Slater determinant. I get that this is an independent particle approximation, ...
2
votes
2answers
146 views

How to properly denote imaginary magnitudes of vibrational frequencies

Vibrational frequency computations provide the magnitudes of vibrational frequencies for each vibrational mode of a molecule ($3N-6$ degrees of freedom for non-linear molecules and $3N-5$ for linear ...
2
votes
1answer
441 views

Software for predicting chemical reactions

I wondered if it was possible to predict the product(s) of a reaction (or even the equilibrium) based on the reactants and the temperature/pressure. I found an answer to a similar question here: ...
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votes
4answers
142 views

Defining and testing custom made DFT functionals?

What is a good and free software for this endeavor? Any recommended articles on the subject? I want to design dft functionals, trying out different parametrizations and optimizing mixing constants for ...
2
votes
0answers
202 views

DFT optimization of a molecule in gaussian and find electrophilic sides [closed]

I am not a pro, but I have some experience with gaussian. For example, I can optimize a structure, calculate the frequency and rotational energies. In the lab I made a nucleophilic substitution ...
1
vote
1answer
92 views

Excited states and electron addition/removal energies within Hartree-Fock, CI, etc

Coming from a DFT background, I'm used to the concept that the DFT eigenvalues do not correspond to excitation energies (i.e., the band gap, ionization potentials, etc.). To correct for these it's ...
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1answer
275 views

Suggest methods and basis sets for a variety of systems

Please help me with any/all of the cases below. In the following cases, the named method and basis set are not suitable for the chemical systems. Why aren't they? Could you suggest a suitable ...