NCIPLOT: a program for plotting non-covalent interaction regions

Non-covalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these non-covalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define non-covalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their van der Waals radii. We recently developed an alternative perspective, derived from the electronic density: the Non-Covalent Interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of non-covalent interactions is of great potential value. Here, we describe the NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities. A wide range of options for tuning the range of interactions to be plotted is also presented. To demonstrate the capabilities of our approach, several examples are given from organic, inorganic, solid state, and macromolecular chemistry, including cases where NCI analysis gives insight into unconventional chemical bonding. The NCI code and its manual are available for download at http://www.chem.duke.edu/~yang/software.htm.     

IDSite: An accurate approach to predict P450-mediated drug metabolism

Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets.     

Thermochemistry of Alane Complexes for Hydrogen Storage: A Theoretical and Experimental Investigation

Knowledge of the relative stabilities of alane (AlH(3)) complexes with electron donors is essential for identifying hydrogen storage materials for vehicular applications that can be regenerated by off-board methods; however, almost no thermodynamic data are available to make this assessment. To fill this gap, we employed the G4(MP2) method to determine heats of formation, entropies, and Gibbs free energies of formation for 38 alane complexes with NH(3-n)R(n) (R = Me, Et; n = 0-3), pyridine, pyrazine, triethylenediamine (TEDA), quinuclidine, OH(2-n)R(n) (R = Me, Et; n = 0-2), dioxane, and tetrahydrofuran (THF). Monomer, bis, and selected dimer complex geometries were considered. Using these data, we computed the thermodynamics of the key formation and dehydrogenation reactions that would occur during hydrogen delivery and alane regeneration, from which trends in complex stability were identified. These predictions were tested by synthesizing six amine-alane complexes involving trimethylamine, triethylamine, dimethylethylamine, TEDA, quinuclidine, and hexamine and obtaining upper limits of ΔG° for their formation from metallic aluminum. Combining these computational and experimental results, we establish a criterion for complex stability relevant to hydrogen storage that can be used to assess potential ligands prior to attempting synthesis of the alane complex. On the basis of this, we conclude that only a subset of the tertiary amine complexes considered and none of the ether complexes can be successfully formed by direct reaction with aluminum and regenerated in an alane-based hydrogen storage system.     

Effect of tellurium promoter on vanadium phosphate catalyst for partial oxidation of n-butane

Te-promoted (1%) vanadium phosphate catalyst (VPDTe) was prepared via VOPO4·2H2O by calcining its precursor VOHPO4·0.5H2O in a flow of n-butane/air.VPDTe catalyst has resulted a higher existence of V5+ phase with V5+/V4+ ratio of 0.23.SEM micrographs show that Te addition altered the arrangement of the platelets from "rose-like" clusters to layer with irregular shape.Te addition has also markedly lowered the reduction activation energies of the vanadium phosphate catalyst as revealed by TPR profile.The amount of active oxygen species associated with V4+ phase of the Te promoted catalyst was significantly higher than those of the unpromoted catalyst.These observations suggest that high mobility and availability of reactive oxygen species contributed to the enhancement of n-butane conversion up to 80% at 673 K,while only 47% over unpromoted catalyst (2400 h-1,1.7% n-butane in air).     

Structural and micro structural studies of PbO-doped SnO2 sensor for detection of methanol,propanol and acetone

In the present work the structural information of PbO-doped SnO2 thick film sensor has been investigated with X-ray diffractometer (XRD) and scanning electron microscope (SEM). Initially, SnO2 powder was derived using sol-gel process and was subsequently doped with PbO and ground up to nanosized particles. A suitable gas sensor structure was fabricated on 1′′×1′′ alumina substrate using thick film technology. The necessary paste for screen printing was also developed. SEM results showed sol-gel derived powder gets more agglomerated in the thick film form. The sensitivity of the sensor has been investigated at different temperatures (150 ?C?350 ?C) upon exposure to methanol, propanol and acetone, yielding a maximum at 250 ?C for acetone with 1 wt% PbO-doping while at 350 ?C for propanol with 3 wt% PbO-doping of the sensor. The reduction of particle size to nanometers (validated through XRD) leads to a dramatic improvement in sensitivity of sensors for the chosen organic vapors. The results also correlate well with the microstructural properties of the material and the dopant.     

Chin.J.Chem.设立“NHU-CJC Innovation Award”

新和成控股集团有限公司着力于中国学术期刊的大发展,提升我国期刊的国际影响力,与中国科学院上海有机化学研究所于2018年1月签署协议,自2018年至2022年,每年捐赠人民币二十万元,对投稿给Chin.J.Chem.原创性非常强的工作,由主编或副主编提名,经主编和副主编全体投票,获2/3同意,授予"新和成《中国化学》创新奖"(NHU-CJC Innovation Award),每位作者均将获得证书和奖金,相关工作将在Breaking Report栏目发表。     

Photo-induced Synthesis and Characterization of Poly（methyl methacrylate） Grafted Sodium Salt of Partially Carboxymethylated Guar Gum

Photo-induced graft copolymerization of methyl methacrylate（MMA） onto sodium salt of partially carboxymethylated guar gum（Na-PCMGG, DS = 0.291） was carried out in an aqueous medium using ceric ammonium nitrate（CAN） as photoinitiator to synthesize a novel graft copolymer, Na-PCMGG-g-PMMA, which may find its potential application as a metal adsorbent. The influences of synthesis variables such as concentrations of photoinitiator（CAN）, nitric acid and monomer（MMA） as well as reaction time, temperature and amount of substrate on the grafting yields were studied and the reaction conditions for optimum photo-grafting were evaluated. At optimum concentration, the maximum values of the grafting yields achieved were G = 271.61% and GE = 63.89%. The experimental results were found to be in very good agreement with the proposed kinetic scheme. The photo-graft copolymerization of MMA onto Na-PCMGG（ DS = 0.291） was also carried out in the presence and absence of ultraviolet radiation for studying the efficiency of the photoinitiator. The influence of carboxymethyl groups introduced onto the guar gum molecules with regard to its behavior towards ultra-violet radiation induced grafting with MMA was also investigated. Photo-grafting process was confirmed and the products were characterized with the help of the spectroscopic（1H-NMR and FTIR） and SEM techniques.     

Advances towards using finger/toenail dosimetry to triage a large population after potential exposure to ionizing radiation

Rapid and accurate retrospective dosimetry is of critical importance and strategic value for the emergency medical response to a large-scale radiological/nuclear event. One technique that has the potential for rapid and accurate dosimetry measurements is electron paramagnetic resonance (EPR) spectroscopy of relatively stable radiation-induced signals (RIS) in fingernails and toenails. Two approaches are being developed for EPR nail dosimetry. In the approach using ex vivo measurements on nail clippings, accurate estimation of the dose-dependent amplitude of the RIS is complicated by the presence of mechanically-induced signals (MIS) that are generated during the nail clipping. Recent developments in ex vivo nail dosimetry, including a thorough characterization of the MIS and an appreciation of the role of hydration and the development of effective analytic techniques, have led to improvements in the accuracy and precision of this approach. An in vivo nail dosimetry approach is also very promising, as it eliminates the problems of MIS from the clipping and it has the potential to be an effective and efficient approach for field deployment. Two types of EPR resonators are being developed for in vivo measurements of fingernails and toenails.     

Structural behaviour of fibre metal laminates subjected to a low velocity impact

Structural impact tests were first presented to cover typical fibre metal laminates (FMLs) subjected a low velocity projectile impact,which produced the corresponding load-displacement traces and deformation/failure modes for the validation of numerical models.Finite element (FE) models were then developed to simulate the impact behaviour of FMLs tested.The aluminium (alloy grade 2024-0) layer was modelled as an isotropic elasto-plastic material up to the on-set of post failure stage,followed by shear failu...     

A diffuse-interface method for two-phase flows with soluble surfactants

A method is presented to solve two-phase problems involving soluble surfactants. The incompressible Navier-Stokes equations are solved along with equations for the bulk and interfacial surfactant concentrations. A non-linear equation of state is used to relate the surface tension to the interfacial surfactant concentration. The method is based on the use of a diffuse interface, which allows a simple implementation using standard finite difference or finite element techniques. Here, finite difference methods on a block-structured adaptive grid are used, and the resulting equations are solved using a non-linear multigrid method. Results are presented for a drop in shear flow in both 2D and 3D, and the effect of solubility is discussed.