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If you are using MS Word 2007 or newer, use the equation feature. It is designed for math but works okay for chemistry.
Go to the insert tab. (For shortcut you can press Alt+= sight together)
Click on the equation button on the far right.
Type in your equation. Use the buttons in the ribbon to do superscripts and subscripts. Alternatively you can use _ ...
28
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.; 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.
Miessler, ...
25
These illustrations are by David Goodsell, and carry his famous look. Whilst I was not able to determine what specific software he uses, this page suggests that he probably creates his illustrations as a composite of renders and that the outlines and depth cueing are achieved by running a 'find edges' filter over the z-buffer of the scene, which can be ...
22
Video Resources (online)
The University of Nottingham's Periodic Videos
The periodic table of videos includes introductions to all elements. The molecular videos section focusses 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 ...
20
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 ...
19
Disclaimer
This is not for the faint-hearted.
If you are not interested in using LaTeX, stop reading now, as this uses the media15 or movie9 packages to embed U3D in a pdfLaTeX generated PDF. This answer assumes basic familiarity with LaTeX. I have tested this with pdfLaTeX and it should work fine in XeLaTeX.
One of the tools I have used (DAZ Studio) is ...
18
Even though your question has already been answered (and this is not an alternative answer), but if you're open to it, switching from Word to LaTeX with the chemmacros package (PDF) will benefit you greatly in the long run.
17
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.
Preliminaries
Suppose you ...
17
Alas, the problem of course is that you need both position q and momentum p to get an accurate picture of the overall electron state.
This is not true in quantum mechanics; it is sufficient to characterize the wavefunction $\left\langle x |\psi\right\rangle$ in position space or $\left\langle k|\psi\right\rangle$ in momentum space. Which is chosen is ...
17
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.
Books about Biochemistry and Chemical Biology
Voet, D.; Voet, J. ...
17
In the first step, separately draw the individual ring structures. ChemDraw comes with an template library of predrawn structures, including some suitable cyclopentadienyl rings.
You can place the ring structures anywhere in your document.
Select one ring structure. On the Structure menu, click Add Multi-Center Attachment. This adds a multi-center node as ...
16
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 ...
16
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 ...
16
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 instance of ED class and then add the energy levels to it.
from energydiagram import ED
diagram = ED()
diagram.add_level(0,'Separated Reactants')
diagram.add_level(-5....
15
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 ...
15
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 ...
15
Online Courses
UC Davis' ChemWiki: The Dynamic Chemistry Hypertext
The ChemWiki 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 conventional paper-based books.
Jim Clark's Chemguide
An ...
15
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 ...
13
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. ...
13
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 ...
13
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 institutional licenses.
MarvinSketch
Freeware (closed-source) for drawing molecular structures with a wide feature set. In addition to just being able to draw ...
13
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 ...
13
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 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 ...
12
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 ...
12
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.
chempy
from chempy import ReactionSystem # The rate constants below are arbitrary
rsys = ReactionSystem.from_string("""2 Fe+2 + H2O2 -> 2 Fe+3 + 2 ...
12
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 psi4
import numpy as np
import matplotlib as mpl
...
11
ChemEQL is pretty nice in some instances and free, but it looks like it has been mostly abandoned.
I'm aware of Titrator, but it only runs on Windows and I've never had a chance to run it. It's also free.
I've heard good things about Visual MINTEQ, but it is Windows only and I've never had a chance to run it. Supposedly well maintained.
There is also ...
11
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 (...
11
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.
Another ...
11
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 ...
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