The "how to" of molecular modeling in education and research
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Figure 4.2. 0.002 au isodensity surface with superimposed electrostatic potential of (a) Li+, (b) Na+, and (c) K+ ion. The maximum potential value is 0.8 au, and the level of theory is B3LYP/6-31G(d).From Molecular Modeling Basics CRC Press, May 2010.Here is...
Figure 3.14. A solutesolvent boundary surface described by a set of interlocking atom-centered spheres. The surface is discretized by using triangular tesserae. Drawing graciously provided by Benedetta Mennucci.From Molecular Modeling Basics CRC Press, May...
Figure 3.8. (a) Adenine (C5H5N5) in a liquid drop of 246 water molecules. (b) Adenine in a periodic box of 511 water molecules.From Molecular Modeling Basics CRC Press, May 2010.Conceptually, the simplest way of simulating a molecule in solution is to place...
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linked to by 2Ever feel a tinge of guilt when you download a fantastic piece of software like Avogadro for free (). Me neither! Free software is my God-given right. Voluntary contributions? Upgrading to the expert version? Provide feedback? So long, suckers!That being said,...
linked to by 1Nick Greeves has made a wonderful website called ChemTube3D. And I mean this quite literally, the site is full of wonders: Jmol-animated reaction mechanisms for the most important organic reactions.I especially like the way the usual 2D representations of reactions...
(1)This is a useful equation. Remember it, and your life will change for the better. The equation comes from one of the fundamental equations of statistical mechanics,(2)as you can see hereBoth equations tell you how the energies of molecule A (EA) and B (EB)...
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Avogadro 0.9.7 was released on 18 July 2009. You can download Avogadro here. I have been less involved in the development of Avogadro in the last six weeks due to a major event in my personal life. Still this release has some great new features in it, several...
More on Avogadro and the Blue Obelisk.First, many apologies to Marcus Hanwell who is the real Doctor Who of Avogadro (but who has been temporarily transported through time and space due to his first child). It’s always great to see new people joining.Then...
