Computational Chemistry Highlights: April issue

The April 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 this issue features contributions from CCH editors Steven Bachrach and Jan Jensen:

All Five Forms of Cytosine Revealed in the Gas Phase

Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design

The Melatonin Conformer Space: Benchmark and Assessment of Wave Function and DFT Methods for a Paradigmatic Biological and Pharmacological Molecule

Zwitterions and Unobserved Intermediates in Organocatalytic Diels–Alder Reactions of Linear and Cross-Conjugated Trienamines

Interested in more? There are many ways to subscribe to CCH updates.

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 this issue features contributions from CCH editors Steven Bachrach, Ric Baron and Jan Jensen:

Anharmonic Vibrational Frequency Calculations Are Not Worthwhile for Small Basis Sets

Calculation of Molecular Entropies Using Temperature Integration

Free Fructose is Conformationally Locked

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

The Fold-In Approach to Bowl-Shaped Aromatic Compounds: Synthesis of Chrysaoroles

Musings about C2

Interested in more? There are many ways to subscribe to CCH updates.

DFT-D, DFT-D2 and DFT-D3: Density functional dispersion correction

Dispersion-corrected DFT, such as B3LYP-D3, are not new functionals but a mix of conventional functionals and an add-on energy term.  For example, B3LYP-D3 denotes a calculation with the usual B3LYP functional plus a D3 dispersion correction energy term.  The dispersion correction energy term is a relatively simply function of interatomic distances and contain adjustable parameters that are fitted to conformational and interaction energies computed using CCSD(T)/CBS.  The fitting is done for a given functional. DFT-D and DFT-D2 energy corrections consider all pairs of atoms while DFT-D3 also consider triplets of atoms to account for three-body effects.

Because the dispersion correction is an add-on term it does not directly alter the wavefunction or any other molecular property.  However, geometry optimizations with dispersion correction will lead to a different geometry than without because the dispersion correction contributes to the forces acting on the atoms.

Dispersion corrections can lead to significant improvements in accuracy and the computational cost associated with dispersion corrections are negligible, so if your favorite code supports dispersion corrections for your functional of choice there is little reason not to use it.

Similar (but not identical) dispersion corrections have also been developed for semi-empirical methods such as PM6, usually in combinations with analogous add-on energy terms to improve hydrogen bonding, e.g. PM6-DH+ and PM6-DH2.

Further reading:
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
Dispersion corrections and bio-molecular structure and reactivity


This work is licensed under a Creative Commons Attribution 3.0 

Computational Chemistry Highlights: February issue

The February 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 this issue features contributions from CCH editors Steven Bachrach, Gemma Solomon and Jan Jensen:

Assessing the Accuracy of Density Functional and Semiempirical Wave Function Methods for Water Nanoparticles: Comparing Binding and Relative Energies of (H2O)16 and (H2O)17 to CCSD(T) Results

Using Orbital Symmetry to Minimize Charge Recombination in Dye-Sensitized Solar Cells

Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory

Bowl-Shaped Fragments of C70 or Higher Fullerenes: Synthesis, Structural Analysis, and Inversion Dynamics

Interested in more? There are many ways to subscribe to CCH updates.

The Molecule Calculator v.1.1

+Jimmy Charnley Kromann has put a new version of the Molecule Calculator online.  The main new features are:

1. JSmol instead of Jmol.  This means that MolCalc now works on iPhones and iPads.  The only thing that doesn't seem to work there is measuring distances and angles.  This also means that the load button had disappeared.

2. New starting points for molecule building: the default starting structure is still methane, but this can now now be changed to benzene or the water dimer.  It is also possible to search for other structures using common names or SMILES.

3. One can now compute other thermodynamic properties in addition to the heat of formation.

The guts of the calculations are still the same as for version 1.0 except that the MMFF force field is used for pre-optimization instead of the UFF force field.

As always the source code is available on Github

The development of MolCalc is supported by the University of Copenhagen through the Education at its Best initiative (Den gode uddannelse).

This work is licensed under a Creative Commons Attribution 3.0 Unported License.  

Getting started with JSmol

Readers of this blog will know I am quite fond of Jmol. But Jmol uses Java, which has some securities issues and doesn't work on iOS.  Luckily, Jmol has been converted to JavaScript to create a program called JSmol.

JSmol accepts all the same commands as Jmol, but setting up a webpage with JSmol is a little bit different.  Here is a very simple page to help get you started and the HTML code and be found below.

The location of the jsmoltest.html is in my home directory while the jsmol code is in a folder called "jsmol" also sitting in my hope directory.  The jsmol folder is created when you unzip the JSmol zip file you can download here.

The JSmol distribution also includes a simple example of having two JSmol windows on one webpage.  You can find that file here.


This work is licensed under a Creative Commons Attribution 3.0 

Computational Chemistry Highlights: January issue

The January 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 this issue features contributions from CCH editors Steven Bachrach, Dmitri Fedorov and Jan Jensen:

Synthesis, Characterization, and Computational Studies of Cycloparaphenylene Dimers

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

FixSol solvation model and FIXPVA2 tessellation scheme

Graphene-derived nanorings of electronic power

Extreme oxatriquinanes and a record C–O bond length

Interested in more? There are many ways to subscribe to CCH updates.