Books about Inorganic Chemistry
Housecroft, C. E.; Sharpe, A. G. Inorganic Chemistry, 4th ed.; Prentice Hall: Upper Saddle River, NJ, 2012.
Weller, M.; Overton, T.; Rourke, J.; Armstrong, F. Inorganic Chemistry, 6th ed; Oxford UP: Oxford, U.K., 2014.
This is the latest version of the textbook commonly known as Shriver & Atkins.
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 chemical reactions. Apart from having quite some entertaining value, they visualise a lot of reactions that can only safely be carried out in a laboratory environment....
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 calculations, there are parts of the code that prune out integrals that will clearly be negligible. This cuts out a lot of work. Consider, for example, overlap ...
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.; Crouch, S. R. Fundamentals of Analytical Chemistry, 9th ed.; Brooks/Cole: Pacific Grove, CA, 2013.
Elgrishi et al., A Practical Beginner’s Guide to Cyclic ...
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 instance of ED class and then add the energy levels to it.
from energydiagram import ED
diagram = ED()
Mapping a Reaction Pathway: A Simple Guide
There are various ways to go about determining a reaction pathway using electronic structure theory. This post is to serve as a brief guide, highlighting a few useful techniques that may make this process more efficient. I will restrict this guide to a simple reaction mentioned below.
Suppose you ...
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 conformation, since these are mirror images.
The same applies to B and B'.
A and C are local minima and can be referred to as conformes in the above given way
B and D ...
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 just invent something new.
I personally prefer ChemCraft for producing publication ready images. It is a commercially distributed program. It mainly supports any ...
For the coloring part I would suggest you look at the CPK coloring convention.
As for the decision whether a bond is a single or a double bond: You could make this decision based on the bond length between two atoms. But you will need to find typical values for single, double and triple bonds for every combination of elements which seems a bit too much ...
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: The Molecular Nature of Matter and Change, 7th ed.; McGraw-Hill: New York, 2014.
Oxtoby, D. W.; Gillis, H. P.; Campion, A. Principles of Modern Chemistry, 8th ...
This collection was formerly known as UC Davis' ChemWiki: The Dynamic Chemistry Hypertext. It is a collaborative approach toward chemistry education where an Open Access textbook environment is constantly being written and re-written by students and faculty members resulting in a free Chemistry textbook to supplant ...
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 one encounter at this level, and as such, they can in principle be completely described by quantum mechanics. What is meant by a "complete description" is that ...
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 file doesn't have values of density at that isovalue. So when it tries to plot a surface, it cannot plot anything.
The IsoValue (default is 0.00040, I believe) means that you construct a surface at ...
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 charge, while useful for concept, can not be defined uniquely. Quantum chemical methods (whether wavefunction or DFT) produce some sort of electron density. ...
Commercial software for drawing molecular structures, 3D models and many more. High price but most higher education institutes will provide students/staff with free institutional licenses. The molecular sketcher now has a free online version (built using HTML$5$ and JS): ChemDraw online
MarvinSketch (desktop) & MarvinJS (...
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 want.
from chempy import ReactionSystem # The rate constants below are arbitrary
rsys = ReactionSystem.from_string("""2 Fe+2 + H2O2 -> 2 Fe+3 + 2 ...
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 MP2/aug-cc-pVDZ total interaction energy of the helium dimer.
from __future__ import print_function
import numpy as np
import matplotlib as mpl
I use ChemDraw Professional 184.108.40.206. 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 enlarged and colored red. I hope this is of help.
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. Switching to optimization in Cartesian coordinates (coordsys cartesian) or old internal ones (coordsys redundant_old) in the %geom section of the input, or ...
It is a Fortran format specifier.
$n$: 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 point), and has 8 digits to the right of the decimal point
This means the number cannot have more than one digit to the left of the decimal point, which makes ...
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 RUNTYP=SADPOINT. You would also need the correct (non-guess) Hessian matrix, which you can calculate separately with RUNTYP=HESSIAN. In transition state (TS), you should have ...
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.
While i really like molden for its quick response opening structure files, usability is not its strength. Also it is slow to generate the orbitals.
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 or Yasara. Here you can ray-trace the image (i.e. transparent background) and then combine the illustration with something else, e.g. an illustration from ...
For predicting chemical reaction you should use classical mechanics to take in account the simple interactions between the molecules and quantum mechanical for all the aspects concerning the molecule itself and complex interactions.
Knowing the principal parameter such as temperature and pressure that could describe the system with the classical mechanics (...
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 angles
Once you've used it, you don't want to miss it again.
Geoff Hutchison, who cannot be praised enough for his child Avogadro, has given the right ...
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 your input file:
* xyz 0 1
H 0.55630745024474 -2.41808278363585 -1.72738492075924 M 2
Alternatively, if you are only interested in the ...
As you mentioned, there've been quite some attempts on CAOS (Computer-Assisted Organic Synthesis), such as
WODCA from the Gasteiger group
CHIRON from the Hanessian group
LHASA from the Corey group
I might be awfully wrong, but I think they were/are all closed source.
But you might want to have a look at OSET, an open source Java project on which Ivan ...