Sunday, April 15, 2012

Virtual Molecular Modeling Kit

I recently came across a very interesting resource called the Virtual Molecular Modeling Kit.  It looks like it can do an awful lots of things and I have only scratched the surface myself.

Very commendably, the authors Otis Rothenberger and Thomas Newton, have created a set of instructional videos.  The video below highlights the fact Jmol 12.2 and later versions now have a molecular editor, which I somehow had completely missed.

These, and related sites such as this one and this one, are examples of what I call chemical calculators.  In analogy with conventional calculators, they allow effortless computations for certain quantities that, before, we would have to laboriously compute by hand, or approximate, or memorize.

Students are no longer required to manually compute square roots or take logarithms.  We now have these calculators that can compute dipole moments, electrostatic potentials and orbitals, with roughly the same effort it takes to use a calculator.  Perhaps we should stop requiring students to memorize nomenclature and perform trivial computations and start teaching them how to solve more interesting chemical problems using these tools. 

Monday, April 2, 2012

Computational Chemistry Highlights: March issue

The March issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years.  CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists.  You can read more about it here.

Table of content for the March issue featuring contributions from CCH editors Patrik Rydberg, Steven Bachrach, and Jan Jensen:

Finding Density Functionals with Machine Learning

Synthesis and Properties of [9]Cyclo-1,4-naphthylene: A π-Extended Carbon Nanoring

Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase
Effects of Ethynyl Substitution on Cyclobutadiene

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

Numerical Errors and Chaotic Behavior in Docking Simulations

Regiolone and Isosclerone, Two Enantiomeric Phytotoxic Naphthalenone Pentaketides: Computational Assignment of Absolute Configuration and Its Relationship with Phytotoxic Activity

The Energy Computation Paradox and ab initio Protein Folding

Entropic Intermediates and Hidden Rate-Limiting Steps in Seemingly Concerted Cycloadditions. Observation, Prediction, and Origin of an Isotope Effect on Recrossing

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

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