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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Note: Times Cited: 875 Reference EPFL-ARTICLE-206025doi:10.1021/cr0501846View record in Web of Science URL: ://WOS:000249839900009 Record created on 2015-03-03, modified on 2017-05-12

Complex Hydrides for Hydrogen Storage

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Triggered by the resounding success of cisplatin, the past decades have seen tremendous efforts to produce clinically beneficial analogues. The recent achievement of oxaliplatin for the treatment of colon cancer should, however, not belie the imbalance between a plethora of investigated complexes and a very small number of clinically approved platinum drugs. Strategies opening up new avenues are increasingly being sought using complexes of metals other than platinum such as ruthenium or gallium. Based on the chemical differences between these metals, the spectrum of molecular mechanisms of action and potential indications can be broadened substantially. Other approaches focus on complexes with tumour-targeting properties, thereby maximizing the impact on cancer cells and minimizing the problem of adverse side effects, and complexes with biologically active ligands.

Antitumour metal compounds: more than theme and variations

Modulation of an Anagostic Interaction in SiPSi-Type Pincer Platinum Complexes

The successful synthesis of different polyacenes including theoretical assessment on the stability of larger acenes are dis- cussed. The existence of favorable aromaticity criterion in polyacenes is understood in terms of different aromaticity indicators like nu- cleus independent chemical shift (NICS), harmonic oscillator model of aromaticity (HOMA), bond resonance energy (BRE). Clar's � - sextet rule is also very much effective in explaining their aromaticity. By virtue of low HOMO-LUMO gap, the probable application of polyacenes in the field of organic electronics is also highlighted. The polyacene analogues of inorganic ring compounds, viz., BN-acenes, CN-acenes, BO-acenes, BS-acenes, AlN-acenes and of alkali ring compounds, viz., Na-acenes and K-acenes also have polyacene-like aromaticity although in few cases the origin of aromaticity and qualitative nature of aromaticity differ significantly.

Aromaticity in Polyacenes and Their Structural Analogues

We report a comprehensive assessment of Lewis acidity for a series of carbone-stibenium and -bismuthenium ions using the Gutmann-Beckett (GB) method. These new antimony and bismuth cations have been synthesized by halide abstractions from (CDC)PnBr3 and [(pyCDC)PnBr2][Br] (CDC = carbodicarbene; Pn = Sb or Bi; py = pyridyl). The reaction of (CDC)SbBr3 (1) with one or two equivalents of AgNTf2 (NTf2 = bis(trifluoromethanesulfonyl)imide) or AgSbF6 gives stibaalkene mono- and dications of the form [(CDC)SbBr3-n][A]n (2-4; n = 1,2; A = NTf2 or SbF6). The stibaalkene trication [(CDC)2Sb][NTf2]3 (5) was also isolated and collectively these molecules fill the gap among the series of cationic pnictaalkenes. The Sb cations are compared to the related CDC-bismaalkene complexes 6-9. With the goal of preparing highly Lewis acidic compounds, a tridentate bis(pyridine)carbodicarbene (pyCDC) was used as a ligand to access [(pyCDC)PnBr2][Br] (10, 12) and trications [(pyCDC)Pn][NTf2]3 (Pn = Sb (11), Bi (13)), forgoing the need for a second CDC as used in the synthesis of 5. The bonding situation in these complexes is elucidated through electron density and energy decomposition analyses in combination with natural orbital for chemical valence theory. In each complex, there exists a CDC-Pn double bonding interaction, consisting of a strong σ-bond and a weaker π-bond, whereby the π-bond gradually strengthens with the increase in cationic charge in the complex. Notably, [(CDC)SbBr][NTf2]2 (4) has an acceptor number (AN) (84) that is comparable to quintessential Lewis acids such as BF3, and tricationic pnictaalkene complexes 11 and 13 exhibit strong Lewis acidity with ANs of 109 (Pn = Sb) and 84 (Pn = Bi), respectively, which are among the highest values reported for any antimony or bismuth cation. Moreover, the calculated fluoride ion affinities (FIAs) for 11 and 13 are 99.8 and 94.3 kcal/mol, respectively, which are larger than that of SbF5 (85.1 kcal/mol), which suggest that these cations are Lewis superacids.

Lewis Superacidic Heavy Pnictaalkene Cations: Comparative Assessment of Carbodicarbene-Stibenium and Carbodicarbene-Bismuthenium Ions.

The occurrence of planar hexacoordination is very rare in main group elements. We report here a class of clusters containing a planar hexacoordinate silicon (phSi) atom with the formula SiSb3M3+ (M = Ca, Sr, Ba), which have D3h (1A1′) symmetry in their global minimum structure. The unique ability of heavier alkaline-earth atoms to use their vacant d atomic orbitals in bonding effectively stabilizes the peripheral ring and is responsible for covalent interaction with the Si center. Although the interaction between Si and Sb is significantly stronger than the Si–M one, sizable stabilization energies (−27.4 to −35.4 kcal mol−1) also originated from the combined electrostatic and covalent attraction between Si and M centers. The lighter homologues, SiE3M3+ (E = N, P, As; M = Ca, Sr, Ba) clusters, also possess similar D3h symmetric structures as the global minima. However, the repulsive electrostatic interaction between Si and M dominates over covalent attraction making the Si–M contacts repulsive in nature. Most interestingly, the planarity of the phSi core and the attractive nature of all the six contacts of phSi are maintained in N-heterocyclic carbene (NHC) and benzene (Bz) bound SiSb3M3(NHC)6+ and SiSb3M3(Bz)6+ (M = Ca, Sr, Ba) complexes. Therefore, bare and ligand-protected SiSb3M3+ clusters are suitable candidates for gas-phase detection and large-scale synthesis, respectively.

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Bare and ligand protected planar hexacoordinate silicon in SiSb3M3+ (M = Ca, Sr, Ba) clusters

Developing effective structure-activity/property/toxicity relationships (QSAR/QSPR/QSTR) is very helpful in predicting biological activity, property, and toxicity of a given set of molecules. Regular change in these properties with the structural alteration is the main reason to obtain QSAR/QSPR/QSTR models. The advancement in making different QSAR/QSPR/QSTR models to describe activity, property, and toxicity of various groups of molecules is reviewed in this chapter. The successful implementation of Conceptual Density Functional Theory (CDFT)-based global as well as local reactivity descriptors in modeling effective QSAR/QSPR/QSTR is highlighted.

Sudip Pan

Papers

Modulation of an Anagostic Interaction in SiPSi-Type Pincer Platinum Complexes

Aromaticity in Polyacenes and Their Structural Analogues

Lewis Superacidic Heavy Pnictaalkene Cations: Comparative Assessment of Carbodicarbene-Stibenium and Carbodicarbene-Bismuthenium Ions.

Bare and ligand protected planar hexacoordinate silicon in SiSb3M3+ (M = Ca, Sr, Ba) clusters

Quantitative Structure-Activity/Property/Toxicity Relationships through Conceptual Density Functional Theory-Based Reactivity Descriptors