Cover Image, Volume 37, Issue 11doi: 10.1002/jcc.24353pmid: N/A
On page 1030 (DOI: 10.1002/jcc.24300), the Software News and Update from Richard Dronskowski and co‐workers features LOBSTER (Local‐Orbital Basis Suite Towards Electronic‐Structure Reconstruction), a tool to extract chemical‐bonding information from plane‐wave based DFT. LOBSTER processes the output of periodic density‐functional simulations, performs projection onto a local, auxiliary basis set, and so gives the user easy access to chemical‐bonding indicators such as projected densities‐of‐states and crystal orbital Hamilton population curves. LOBSTER is used in diverse fields, from solid‐state chemistry to surfaces and nanoscale materials, and is freely available for any non‐commercial research.
Cover Image, Volume 37, Issue 11doi: 10.1002/jcc.24365pmid: N/A
Polarizable QM/MM simulations allow quantum nuclei (small blue spheres) and electron density (diffuse green cloud) to interact with the static force field (transparent spheres) and induced‐dipole moments (blue and green bars) in the classical environment. The new software package LICHEM from G. Andrés Cisneros and co‐workers, discussed on page 1019 (DOI: 10.1002/jcc.24295), can perform QM/MM simulations with multipolar/polarizable force fields via interfaces to unmodified QM and MM packages.
Cover Image, Volume 37, Issue 11doi: 10.1002/jcc.24364pmid: N/A
The fast Fourier transform (FFT) algorithm enables extremely fast evaluation of energy functions. On page 961 (DOI: 10.1002/jcc.24273), Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov, and co‐workers apply this algorithm to protein‐protein docking, as well as to refine the results by focused resampling on the regions of interest using finer grids, in order to better explore protein interaction energy landscape. The cover image illustrates near‐native low energy translational subspace of protein‐protein interaction, obtained by focused FFT resampling around a near native complex model, given a single orientation of the ligand.
Effects of an electric field on interaction of aromatic systemsYoun, Il Seung; Cho, Woo Jong; Kim, Kwang S.
doi: 10.1002/jcc.24284pmid: 26696236
The effect of uniform external electric field on the interactions between small aromatic compounds and an argon atom is investigated using post‐HF (MP2, SCS‐MP2, and CCSD(T)) and density functional (PBE0‐D3, PBE0‐TS, and vdW‐DF2) methods. The electric field effect is quantified by the difference of interaction energy calculated in the presence and absence of the electric field. All the post‐HF methods describe electric field effects accurately although the interaction energy itself is overestimated by MP2. The electric field effect is explained by classical electrostatic models, where the permanent dipole moment from mutual polarization mainly determines its sign. The size of π‐conjugated system does not have significant effect on the electric field dependence. We found out that PBE0‐based methods give reasonable interaction energies and electric field response in every case, while vdW‐DF2 sometimes shows spurious artifact owing to its sensitivity toward the real space electron density. © 2015 Wiley Periodicals, Inc.
Effective protein conformational sampling based on predicted torsion anglesYang, Yuedong; Zhou, Yaoqi
doi: 10.1002/jcc.24285pmid: 26696379
Protein structure prediction is a long‐standing problem in molecular biology. Due to lack of an accurate energy function, it is often difficult to know whether the sampling algorithm or the energy function is the most important factor for failure of locating near‐native conformations of proteins. This article examines the size dependence of sampling effectiveness by using a perfect “energy function”: the root‐mean‐squared distance from the target native structure. Using protein targets up to 460 residues from critical assessment of structure prediction techniques (CASP11, 2014), we show that the accuracy of near native structures sampled is relatively independent of protein sizes but strongly depends on the errors of predicted torsion angles. Even with 40% out‐of‐range angle prediction, 2 Å or less near‐native conformation can be sampled. The result supports that the poor energy function is one of the bottlenecks of structure prediction and predicted torsion angles are useful for overcoming the bottleneck by restricting the sampling space in the absence of a perfect energy function. © 2015 Wiley Periodicals, Inc.