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 Pharmacological Basis of Therapeutics A Textbook of Pharmacology, Toxicology and Therapeutics for Physicians and Medical Students. By Prof. Louis Goodman and Prof. Alfred Gilman. Pp. xiii + 1383. (New York: The Macmillan Company, 1941.) 50s. net.

The Pharmacological Basis of Therapeutics

Exposure to even very low levels of lead, cadmium, and mercury ions is known to cause neurological, reproductive, cardiovascular, and developmental disorders, which are more serious problems for children particularly. Accordingly, great efforts have been devoted to the development of fluorescent and colorimetric sensors, which can selectively detect lead, cadmium, and mercury ions. In this critical review, the fluorescent and colorimetric sensors are classified according to their receptors into several categories, including small molecule based sensors, calixarene based chemosensors, BODIPY based chemosensors, polymer based chemosensors, DNA functionalized sensing systems, protein based sensing systems and nanoparticle based sensing systems (197 references).

Fluorescent and colorimetric sensors for detection of lead, cadmium, and mercury ions

: 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

In the wide area of supramolecular chemistry, cucurbit[n]urils (CBn) present themselves as a young family of molecular containers, able to form stable complexes with various guests, including drug molecules, amino acids and peptides, saccharides, dyes, hydrocarbons, perfluorinated hydrocarbons, and even high molecular weight guests such as proteins (e.g., human insulin). Since the discovery of the first CBn, CB6, the field has seen tremendous growth with respect to the synthesis of new homologues and derivatives, the discovery of record binding affinities of guest molecules in their hydrophobic cavity, and associated applications ranging from sensing to drug delivery. In this review, we discuss in detail the fundamental properties of CBn homologues and their cyclic derivatives with a focus on their synthesis and their applications in catalysis.

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Cucurbiturils: from synthesis to high-affinity binding and catalysis

Activation and Stabilization of Drugs by Supramolecular pKa Shifts: Drug‐Delivery Applications Tailored for Cucurbiturils

The growing realization that photoinduced bending of slender photoreactive single crystals is surprisingly common has inspired researchers to control crystal motility for actuation. However, new mechanically responsive crystals are reported at a greater rate than their quantitative photophysical characterization; a quantitative identification of measurable parameters and molecular-scale factors that determine the mechanical response has yet to be established. Herein, a simple mathematical description of the quasi-static and time-dependent photoinduced bending of macroscopic single crystals is provided. This kinetic model goes beyond the approximate treatment of a bending crystal as a simple composite bilayer. It includes alternative pathways for excited-state decay and provides a more accurate description of the bending by accounting for the spatial gradient in the product/reactant ratio. A new crystal form (space group P21/n) of the photoresponsive azo-dye Disperse Red 1 (DR1) is analyzed within the cons...

Model for photoinduced bending of slender molecular crystals.

Azo dyes account for 60–70% of all dyes known to date. Understanding the factors that affect the direction of keto–enol tautomerism in azo dyes through spectral measurements is crucial to their potential applications. This review encompasses the most important spectroscopic studies of different azo dyes categorized by their structures within the last few years (2010–2014). It is concluded that the stability of the keto and enol forms largely arises from the ability to establish intra-molecular and inter-molecular hydrogen bonding, respectively. There are many factors that affect the keto or enol form, for example, polar solvent, high temperature, neutral pH and electron withdrawing substituents favor the keto form through intramolecular hydrogen bonding, whereas, nonpolar solvent, low temperature, high pH and electron donating groups favor the enol form through intermolecular hydrogen bonding. Encapsulation inside nanocaged microheterogenous systems creates a rigid environment that stabilizes the enol form mostly, while in the solid state, most of the tautomeric equilibrium lies in favor of the keto form. Understanding of keto–enol tautomerism in azo dyes helps to probe solvation dynamics, to tune the pKa values in chemical sensing, and to explain proton transfer in the excited state.

Spectroscopic studies of keto–enol tautomeric equilibrium of azo dyes

Covalent organic nanosheets (CONs) have attracted much attention because of their excellent physical, chemical, electronic, and optical properties. Although covalent organic nanosheets have widely been used in many applications, there are only a few CONs that have been tested for bio-medical applications. Nanometer sized triazine-based nanosheets were obtained by exfoliating their bulk counterparts in water. The obtained nanosheets were dispersible and stable in water with enhanced photoluminescence properties compared to the bulk material. The nanosheets were biocompatible and non-toxic and showed ability to stain HeLa cell nuclei without additional assistance of an external targeting agent.

/pdf/covalent-organic-nanosheets-for-bioimaging-3o149kh0rn.pdf

Covalent organic nanosheets for bioimaging

The potential increase in fluorescence of a benzimidazole-type fungicide (carbendazim) due to complexation with cucurbit[6]uril is reported The fluorescence of the probe carbendazim in aqueous Na2SO4 solution (pH=761) at room temperature is found to increase by a maximum factor of ∼100 and blue-shifted up to ∼11±1 nm with the increase in cucurbit[6]uril concentration up to ∼5 mM This fluorescence enhancement is the result of formation of a 1:1 guest-host inclusion complex, in which the guest carbendazim is incorporated inside the hydrophobic cavity of the host curbit[6]uril through the amido-ester part Such mode of inclusion is supported by NMR spectral measurements, in which upon encapsulation, the resonance of the methyl-protons of the amido-ester moiety is shifted significantly to upfield in the 1H NMR spectrum Also, to assess the formation of inclusion complex, solid samples prepared by co-evaporation have been studied, using differential scanning calorimetry (DSC) Measurement of the enhancement as a function of cucurbit[6]uril concentrations yielded a value of the equilibrium constant (K
 a
 ) of 271±10 M−1 at 25°C From the temperature dependence of the equilibrium constants, ΔH and ΔS values have been negative in sign, indicating the dipole-dipole interactions and the steric factors associated with the formation of this inclusion complex It might be proposed that the spectral changes due to the inclusion of carbendazim are the result of decrease in the polarity of the surrounded media rather than the loss of carbendazim rotational mobility

Na’il Saleh

Papers

Activation and Stabilization of Drugs by Supramolecular pKa Shifts: Drug‐Delivery Applications Tailored for Cucurbiturils

Model for photoinduced bending of slender molecular crystals.

Spectroscopic studies of keto–enol tautomeric equilibrium of azo dyes

Covalent organic nanosheets for bioimaging

Fluorescence Enhancement of Carbendazim Fungicide in Cucurbit[6]uril