Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

The Halogen Bond

A σ-hole bond is a noncovalent interaction between a covalently-bonded atom of Groups IV–VII and a negative site, e.g. a lone pair of a Lewis base or an anion. It involves a region of positive electrostatic potential, labeled a σ-hole, on the extension of one of the covalent bonds to the atom. The σ-hole is due to the anisotropy of the atom's charge distribution. Halogen bonding is a subset of σ-hole interactions. Their features and properties can be fully explained in terms of electrostatics and polarization plus dispersion. The strengths of the interactions generally correlate well with the magnitudes of the positive and negative electrostatic potentials of the σ-hole and the negative site. In certain instances, however, polarizabilities must be taken into account explicitly, as the polarization of the negative site reaches a level that can be viewed as a degree of dative sharing (coordinate covalence). In the gas phase, σ-hole interactions with neutral bases are often thermodynamically unfavorable due to the relatively large entropy loss upon complex formation.

Halogen bonding and other σ-hole interactions: a perspective

Halogen Bonding in Supramolecular Chemistry.

Halogen bonding has been known in material science for decades, but until recently, halogen bonds in protein–ligand interactions were largely the result of serendipitous discovery rather than rational design. In this Perspective, we provide insights into the phenomenon of halogen bonding, with special focus on its role in drug discovery. We summarize the theoretical background defining its strength and directionality, provide a systematic analysis of its occurrence and interaction geometries in protein–ligand complexes, and give recent examples where halogen bonding has been successfully harnessed for lead identification and optimization. In light of these data, we discuss the potential and limitations of exploiting halogen bonds for molecular recognition and rational drug design.

Principles and applications of halogen bonding in medicinal chemistry and chemical biology.

Recent years have seen many specific applications of polyhalide ionic liquids (ILs) such as oxidizing solvents for metals and alloys, immersion fluids for optical mineralogy, and electrolyte components for dye-sensitized solar cells. In this work, interhalogen interactions in a set of polyhalide ILs composed of polyhalide anions, [X3]−, [X5]−, and [X7]− (X = I or Br), with two typical cations, tetramethylammonium [NMe4]+ and 1,3-dimethylimidazolium [DMIM]+, were thoroughly studied from a computational point of view. In addition, a halogen-bonded supramolecular anion, [C6F13-I∙∙∙I∙∙∙I-C6F13]−, was also taken into account for comparison. Unlike those in bare polyhalide ions, halogen-halogen interactions in ionic pairs for the investigated ILs are somewhat asymmetric caused by the interactions between the cations and the anions. In general, there are two classes of interhalogen bonds in ionic pairs: one class with longer X∙∙∙X distances and smaller bond energies can be recognized as strong halogen bonds, while the other with shorter distances and much larger bond energies exhibits a significantly enhanced strength.

Computational Study of Halogen-Halogen Interactions in Polyhalide Ionic Liquids

Cationic and neutral halogen bonding (XB) donors use two types (I and II) of intramolecular hydrogen bonding (HB) to preorganize structures and increase the efficiency of halide anion recognition. Herein, several XB donors with and without preorganization function were studied. The amine group was introduced to form type I intramolecular HBs (inside of the binding site) for cationic XB donors, and the hydroxyl group was employed to provide type II intramolecular HBs (outside of the binding site) for neutral XB donors. From energetic prospective, the complexation between the receptors and halide anions was enhanced with the preorganization function, which is mainly contributed by the improved coplanarity of the donor geometries. The type II intramolecular HBs are predicted to be much stronger than the type I intramolecular HBs, and the coplanarity of the preorganization structures including type II intramolecular HBs would be further improved with the binding of halide anions. We hope that the results reported herein will assist in the application of preorganization in anion recognition process.

Yunxiang Lu

Papers

Computational Study of Halogen-Halogen Interactions in Polyhalide Ionic Liquids

Preorganization-enhanced halogen bonding via intramolecular hydrogen bonding: a theoretical study