There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

cclib: A library for package‐independent computational chemistry algorithms

The ground-state energy, electron density, and related properties of ordinary matter can be computed efficiently when the exchange-correlation energy as a functional of the density is approximated semilocally. We propose the first meta-GGA (meta-generalized gradient approximation) that is fully constrained, obeying all 17 known exact constraints that a meta-GGA can. It is also exact or nearly exact for a set of appropriate norms, including rare-gas atoms and nonbonded interactions. This SCAN (strongly constrained and appropriately normed) meta-GGA achieves remarkable accuracy for systems where the exact exchange-correlation hole is localized near its electron, and especially for lattice constants and weak interactions.

Strongly Constrained and Appropriately Normed Semilocal Density Functional

New designs of donor polymers yield organic solar cells with fill factors approaching 80%, significantly higher than those of conventional cells. This enhanced performance is attributed to the close-packed and highly ordered structure of the polymers PTPD3T and PBT13T, which leads to efficient charge extraction and suppressed recombination.

Polymer solar cells with enhanced fill factors

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although χOL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χOL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χOL force field is compared with sev...

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

The trifluoromethyl group can dramatically influence the properties of organic molecules, thereby increasing their applicability as pharmaceuticals, agrochemicals, or building blocks for organic materials. Despite the importance of this substituent, no general method exists for its installment onto functionalized aromatic substrates. Current methods either require the use of harsh reaction conditions or suffer from a limited substrate scope. Here we report the palladium-catalyzed trifluoromethylation of aryl chlorides under mild conditions, allowing the transformation of a wide range of substrates, including heterocycles, in excellent yields. The process tolerates functional groups such as esters, amides, ethers, acetals, nitriles, and tertiary amines and, therefore, should be applicable to late-stage modifications of advanced intermediates. We have also prepared all the putative intermediates in the catalytic cycle and demonstrated their viability in the process.

http://science.sciencemag.org/content/sci/328/5986/1679.full.pdf

J. Burant

Papers

Gaussian 03, Revision E.01.