35 votes

Resources for learning Chemistry

Books about Inorganic Chemistry General texts Housecroft, C. E.; Sharpe, A. G. Inorganic Chemistry, 4th ed.; Prentice Hall: Upper Saddle River, NJ, 2012. Weller, M.; Overton, T.; Rourke, J.; ...
27 votes

Resources for learning Chemistry

Video Resources (online) The University of Nottingham's Periodic Videos The periodic table of videos includes introductions to all elements. The molecular videos section focuses on interesting ...
22 votes

Resources for learning Chemistry

Online Courses Chemistry LibreTexts This collection was formerly known as UC Davis' ChemWiki: The Dynamic Chemistry Hypertext. It is a collaborative approach toward chemistry education where an Open ...
21 votes

Resources for learning Chemistry

Books about Analytical Chemistry Schwarzenbach, G.; Flaschka, H. A. Complexometric Titrations; Methuen: London, 1957 (translated by H. Irving in 1969). Skoog, D. A.; West, D. M.; Holler, F. J.; ...
20 votes
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How do Quantum Software Packages Work?

There are many tricks. Since I'm not a developer, I'm not privy to all of them, but there are some simple things to start. Some integrals are predictably close to zero: Even in fully first-principals ...
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20 votes

Resources for learning Chemistry

Software ChemOffice Professional Commercial software for drawing molecular structures, 3D models and many more. High price but most higher education institutes will provide students/staff with free ...
19 votes
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Creating energy profile diagrams for publication

PyEnergyDiagrams I use my own script. I have posted it on GitHub now. This is the final result: It is quite easy to use, on the GitHub readme there is a small tutorial. You have to create an ...
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18 votes

Resources for learning Chemistry

Books about General Chemistry Atkins, P. W.; Jones, L. L.; Laverman, L. E. Chemical Principles: The Quest for Insight, 6th ed.; W. H. Freeman: New York, 2012. Silberberg, M.; Amateis, P. Chemistry: ...
17 votes
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Structure that breaks InChI

Okay, let's tackle at least one problem here. Consider the rotation of 1,2-dichloroethane (BP86/cc-pVDZ): These conformational changes can be further rationalised: C and C' are the same ...
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17 votes

Generating neat orbitals/surfaces from molden/wfn-files

Often different quantum chemical programs require different analysing tools. Unfortunately there is no universal standard (program), that can do it all. If there were, someone would come along and ...
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16 votes
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Python package for modelling chemical reactions

This is not really my area of expertise, but a quick search for "python chemical reactions" revealed three hits I've never seen before that may be of interest, the first one being closest to what you ...
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15 votes
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What are GAMESS and Gaussian?

There exist a physical theory called quantum mechanics which describes the Universe at atomic and subatomic length scales. Chemical systems, such as, for instance, molecules, are one types of systems ...
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15 votes
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How to visualise the total electron density from a Gaussian 16 calculation?

When GaussView gives you the error Surface build failed! Processing mesh, No data to plot. IsoValue may be out of range it means that the data in your .cube ...
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14 votes
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Methods for Determining Partial Charges

There are lots, and I mean lots of methods and software programs to produce partial charges. See Wikipedia for a small (incomplete list) Let's start with the basics. The idea of a partial atomic ...
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14 votes
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How to calculate Lennard-Jones potential with quantum mechanical methods

Yes, this is technically possible. A basic tutorial for this is in the excellent Psi4Numpy project, which I'll reproduce here with minor modifications. Their example fits the counterpoise-corrected ...
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14 votes

How can I draw alpha helices in ChemDraw?

I use ChemDraw Professional 19.1.1.32. If you follow File>Open Templates>Advanced BioDraw, you will find the black helix that I have reoriented from horizontal to vertical. The red helix was ...
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13 votes

Generating neat orbitals/surfaces from molden/wfn-files

for completeness, gmolden can actually produce high quality pictures like these: You need to click the button in the top right in density mode to get the opengl rendering. It is also fully rotatable. ...
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13 votes

Is Orca wrongly breaking bonds? Why can it only optimize the molecule with COPT activated?

It seems to be a bug with optimization in internal coordinates. As I already mentioned in comments, ORCA couldn't converge at geometry relaxation step when optimization is done in internal coordinates....
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13 votes
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What does the format nF10.8 mean?

It is a Fortran format specifier. It means $n$: repeat the input $n$ times, once for each weight F: input is a floating-point number 10.8: the number is of total width 10 (including the decimal ...
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12 votes
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How to simulate chemical reactions in GAMESS?

As in geometry optimization, you are searching for stationary point on the potential energy surface (PES). Not for local minimum, but for saddle point, therefore in GAMESS, you specify ...
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12 votes

How can I draw alpha helices in ChemDraw?

This illustration may be a combination of two images, or simply a program I don't know about. However, there are many (3D) protein visualisation programs that can show alpha-helices such as PyMol, VMD ...
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11 votes
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Software for viewing a structure and altering bond angles

Have a look at Avogadro! build your own structures or import files in various formats. optimize the geometry using different force fields change and measure bond length, bond angles and dihedral ...
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11 votes
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How to specify a different isotope in the ORCA quantum chemistry program?

ORCA cannot read isotope information from XYZ files -- the OpenBabel specification does not include it and so ORCA doesn't look for it in the geometry file. You need to copy-paste the geometry into ...
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11 votes

How do I perform a partial optimisation in GAMESS?

Unfortunately GAMESS is not as user friendly as other quantum chemistry packages, so when it comes to running non-standard calculations a little bit more effort is necessary. First of all I recommend ...
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11 votes
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Discrepancy when calulating mol weights with ChemSketch and Python RDKit

In first place, you must clarify with the users of the database the purpose of the entries about molecular weight because average molecular weight and exact molecular weight differ in their meaning ...
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10 votes

How to find a transition state for an electrophilic addition with Gaussian and map the reaction pathway?

I would like to build on LordStryker's well-written guide by providing some elementary examples of input file formatting for these calculations. Now that I've re-read the question, I see that my ...
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10 votes
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What free software exists to view molecule pictures within a file explorer?

I found this tool named thumbfish (Windows only). It can display thumbnails for variety of formats and is free
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10 votes

How do Quantum Software Packages Work?

First things first, I would check your code: there is no reason 400 unique integrals should take an hour, even with the most naive implementation. You are computing at a rate of an integral every ten ...
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10 votes

How do Quantum Software Packages Work?

To further reduce storage requirement, integrals may be calculated on the fly, emplpoying different caching strategies. For some methods storing all the integrals is plainly impossible.
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