37
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 ...
23
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.; ...
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 ...
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
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: ...
19
votes
Accepted
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 ...
- 9,049
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 ...
- 43.7k
16
votes
Accepted
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 ...
- 7,378
16
votes
Accepted
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 ...
- 7,378
15
votes
Accepted
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 ...
- 2,090
15
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 ...
- 15.9k
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.
...
- 199
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....
- 18.8k
13
votes
Accepted
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 ...
- 7,378
13
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 ...
- 898
11
votes
Accepted
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 ...
- 17.2k
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 ...
- 43.7k
11
votes
Accepted
ORCA: How to plot an adiabatic potential in dihydrogen H2 molecule?
By adiabatic, I presume you mean the Born-Oppenheimer approximation (which is usually used). If you need a plot of potential against H-H distance, then you need to do a relaxed potential energy ...
- 5,607
11
votes
Accepted
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 ...
- 27.7k
10
votes
Accepted
Trying to understand SMILES(?) patterns
First off this is SMARTS not SMILES.
Think of SMARTS as like a regular expression language for molecules (e.g., SMILES).
So let's break down some of those characters:
...
- 27.6k
10
votes
Generating neat orbitals/surfaces from molden/wfn-files
VMD is my current go-to for molecular visualization. As with any software, it takes some getting used to, but the wealth of options, what seems to be a robust feature set, and generally flexible ...
- 17.2k
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 ...
- 2,324
10
votes
Accepted
Software for compound database creation\enumeration
This is typically called library (or scaffold) enumeration. Doing it in SMILES is usually pretty easy by script, but there are a few other options:
KNIME
SMILIB
But it's very easy to write a script ...
- 27.6k
10
votes
How to run a B2PLYP-D3 calculation in Gaussian 09?
Search for B2PLYP on the Moller-Plesset page:
B2PLYPD3 requests the same but with Grimme's D3BJ dispersion [Grimme11, Goerigk11].
The correct D3 parameters will be set for you automatically.
<...
- 7,378
10
votes
Gaussian Error: Zero Point Energy Calculation on Fluoroform fails
As you can see in the error message
#T B3LYP/6â€311+G(3df,2p)
there is some Unicode garbage in your input file; the dash between the 6 and 3 isn't an ASCII dash. ...
- 7,378
10
votes
Accepted
ChemDraw: how to change the default aromatic ring style for drawing from SMILES
From pp. 91–92 ChemDraw 20.0 User Guide, PDF version shipped with the ChemOffice suite:
Toggle Aromatic Display
An aromatic structure can be displayed either as an alternating double and single bond ...
- 37.3k
10
votes
Accepted
Software to draw one-dimensional PES including vibrational energy levels
I have made this basic python 3 script which runs in a Jupyter notebook (or in Visual Studio Code). With different molecules you will need to adjust the plot scale. The first 10 levels are plotted ...
- 29.8k
9
votes
How should elements be colored? And how many bonds does an atom have?
To extend on Philipp's excellent answer, I'd like to offer some advice on judging bond orders. Pekka Pyykkö and Michiko Atsumi published covalent (single-, double-, triple-) bond radii for (almost) ...
- 43.7k
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