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.

Significant research efforts, mostly experimental, have been devoted to finding high-performance anode materials for lithium-ion and potassium-ion batteries; both graphitic carbon-based and carbon nanotube-based materials have been generating huge interest. Here, first-principles calculations are performed to investigate the possible effects of doping defects and the varying tube diameter of carbon nanotubes (CNTs) on their potential for battery applications. Both adsorption and migration of Li and K are studied for a range of pristine and nitrogen-doped CNTs, which are further compared with 2D graphene-based counterparts. We use detailed electronic structure analyses to reveal that different doping defects are advantageous for carbon nanotube-based and graphene-based models, as well as that curved CNT walls help facilitate the penetration of potassium through the doping defect while showing a negative effect on that of lithium.

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First-principles computational investigation of nitrogen-doped carbon nanotubes as anode materials for lithium-ion and potassium-ion batteries

Halogen bonds between I2 and ion pairs: Interpreting the ability of ionic liquids in efficient capture of radioactive iodine

The ionic-liquid/graphite interface is important in understanding the behaviors of the ionic-liquid electrolyte in carbon-based supercapacitors and Li-ion batteries. A row-like cation–anion structure of the 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide ([BMP][TFSA]) ionic liquid (a popular choice for interfacial studies) on the graphite surface has been suggested on the basis of scanning tunneling microscopy images, but it is unclear if this structure is the most stable one. Herein, we explore alternative models of the [BMP][TFSA] monolayer on graphite basal plane with first-principles density functional theory. We find that the checkerboard type of structure is in fact more stable than the row-like structure. We further use simulated annealing based on classical molecular dynamics simulations to obtain more stable conformations of ions on the surface. Both charge-density-difference and noncovalent-interaction analyses show that the higher stability of the checkerboard structure than the...

Structure and Interaction of Ionic Liquid Monolayer on Graphite from First-Principles

The interplay between halogen bonding and hydrogen bonding has caused recent interest in the formation of 2D self-assembled molecular arrays on solid surfaces. Herein we present a first-principles density functional theory study of the self-assemblies of two brominated anthraquione molecules on Au(111) and Au(110). The possible binding sites of these two compounds on the facets were first explored, and then various self-assembled patterns involving different halogen and hydrogen bonds were examined both in the gas phase and on the gold surface. To visually investigate the nature of lateral adsorbate–adsorbate and vertical adsorbate–substrate interactions, the atoms in molecules, noncovalent interaction index, and electron density difference analyses were undertaken. The molecules tend to be self-assembled by means of triangular binding motifs with simultaneous halogen and hydrogen bonds. Upon the formation of the dimers in the gas phase as well as on the gold surface, significant band shifts around the Fe...

Interplay between Halogen and Hydrogen Bonds in 2D Self-Assembly on the Gold Surface: A First-Principles Investigation

Considering the excessive ingestion of fluoride ion (F−) may result in many diseases, herein, by introducing 2-hydroxy-1-naphthaldehyde azine framework to 1,8-naphthalimide derivatives, we have developed a unique colorimetric/fluorometric probe (NYL) for detection of fluoride. The response of NYL toward F− is an integration of ESIPT and PET processes with a large stokes’ shift (173 nm). The striking color change from yellow to light-purple and fluorescent quenching of probe NYL can be observed only in the presence of fluoride ions. Furthermore, 1H NMR titration indicates the probe undergoes the deprotonation of hydroxyl through the Hydrogen-bond interaction between phenolic O H and F− ions.

Yunxiang Lu

Papers

First-principles computational investigation of nitrogen-doped carbon nanotubes as anode materials for lithium-ion and potassium-ion batteries

Halogen bonds between I2 and ion pairs: Interpreting the ability of ionic liquids in efficient capture of radioactive iodine

Structure and Interaction of Ionic Liquid Monolayer on Graphite from First-Principles

Interplay between Halogen and Hydrogen Bonds in 2D Self-Assembly on the Gold Surface: A First-Principles Investigation

A novel naphthalimide-based probe for highly sensitive and selective recognition of ﬂuoride ion