Computational chemistry for graphene-based energy applications: progress and challenges.

Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.

Parallelization of the discrete gradient method of non-smooth optimization and its applications

We investigate parallelization and performance of the discrete gradient method of nonsmooth optimization. This derivative free method is shown to be an effective optimization tool, able to skip many shallow local minima of nonconvex nondifferentiable objective functions. Although this is a sequential iterative method, we were able to parallelize critical steps of the algorithm, and this lead to a significant improvement in performance on multiprocessor computer clusters. We applied this method to a difficult polyatomic clusters problem in computational chemistry, and found this method to outperform other algorithms.

Parallel I/O scheduling in the presence of data duplication on multiprogrammed cluster computing systems

The widespread adoption of cluster computing as a high performance computing platform has seen the growth of data intensive scientific, engineering and commercial applications such as digital libraries, climate modeling, computational chemistry, computational fluid dynamics and image repositories. However, I/O subsystem performance has not been keeping pace with processor and memory performance, and is fast becoming the dominant factor in overall system performance.  Thus, parallel I/O has become a necessity in the face of performance improvements in other areas of computing systems. This paper addresses the problem of parallel I/O scheduling on cluster computing systems in the presence of data replication.  We propose two new I/O scheduling algorithms and evaluate the relative performance of the proposed policies against two existing approaches.  Simulation results show that the proposed policies perform substantially better than the baseline policies.

Challenges of continuous global optimization in molecular structure prediction

The molecular geometry, the three dimensional arrangement of atoms in space, is a major factor determining the properties and reactivity of molecules, biomolecules and macromolecules. Computation of stable molecular conformations can be done by locating minima on the potential energy surface (PES). This is a very challenging global optimization problem because of extremely large numbers of shallow local minima and complicated landscape of PES. This paper illustrates the mathematical and computational challenges on one important instance of the problem, computation of molecular geometry of oligopeptides, and proposes the use of the Extended Cutting Angle Method (ECAM) to solve this problem.

ECAM is a deterministic global optimization technique, which computes tight lower bounds on the values of the objective function and fathoms those part of the domain where the global minimum cannot reside. As with any domain partitioning scheme, its challenge is an extremely large partition of the domain required for accurate lower bounds. We address this challenge by providing an efficient combinatorial algorithm for calculating the lower bounds, and by combining ECAM with a local optimization method, while preserving the deterministic character of ECAM.

Computational investigations on periodic trends in Group 14 chemistry

Describes the use of computer-aided molecular modelling to investigate trends in the chemistry of the Group 14 elements, namely carbon, silicon, germanium, tin and lead. The chemical behaviour of two classes of molecules containing Group 14 elements was related to trends in the fundamental properties of these elements.

Single enatiomer free-radical chemistry - Lewis acid-mediated reductions of racemic halides using chiral non-racemic stannanes

Additions of one to two equivalents of Lewis acids that include magnesium salts to free-radical reduction reactions involving ester functionalized radicals and (1R,2S,5R)-menthyldiphenyltin hydride 4, bis((1R,2S,5R)-menthyl)phenyltin hydride 5, tris((1R,2S,5R)-menthyl)tin hydride 6, bis((1R,2S,5R)-menthyl)-[8-(N,N-dimethylamino)naphthyl]tin hydride 12, bis((1R,2S,5R)-menthyl)-[1-((S)-N,N-dimethylaminoethyl)phenyl]tin hydride 13 or 3α-dimethylstannyl-5α-cholestane 14 result in remarkable enantioselectivities. Examples include (S)-naproxen ethyl ester 16, produced in 74% yield and greater than 99% ee at −78°C from the bromide and 5 in the presence of MgBr₂, and ethyl (R)-N-trifluoroacetyl-_D-phenylglycinate 18, obtained in 78% yield and 99% ee under identical conditions. Kinetic and computational studies provide insight into the origins of these observations.

Spectroscopic and computational characterizations of alkaline-earth- and heavy-metal-exchanged natrolites

Synchrotron infrared (IR) and micro-Raman spectra of natrolites containing alkaline-earth ions (Ca2+, Sr2+, and Ba2+) and heavy metals (Cd2+, Pb2+, and Ag+) as extra-framework cations (EFCs) were measured under ambient conditions. Complementing our previous spectroscopic investigations of natrolites with monovalent alkali metal (Li+, Na+, K+, Rb +, and Cs+) EFCs, we establish a correlation between the redshifts of the frequencies of the 4-ring and helical 8-ring units and the size of the EFCs in natrolite. Through ab initio calculations we have derived structural models of Ca2+- and Ag+-exchanged natrolites with hydrogen atoms, and found that the frequency shifts in the H - O - H bending mode and the differences in the O - H stretching vibration modes can be correlated with the orientations of the water molecules along the natrolite channel. Assuming that the members of a solid solution series behave as an ideal mixture, we will be able to use spectroscopy to probe compositions. Deviation from ideal behavior might indicate the occurrence of phase separation on various length scales. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A computational search for lipases that can preferentially hydrolyze long-chain omega-3 fatty acids from fish oil triacylglycerols

Consumption of long-chain omega-3 fatty acids is known to decrease the risk of major cardiovascular events. Lipases, a class of triacylglycerol hydrolases, have been extensively tested to concentrate omega-3 fatty acids from fish oils, under mild enzymatic conditions. However, no lipases with preference for omega-3 fatty acids selectivity have yet been discovered or developed. In this study we performed an exhaustive computational study of substrate-lipase interactions by docking, both covalent and non-covalent, for 38 lipases with a large number of structured triacylglycerols containing omega-3 fatty acids. We identified some lipases that have potential to preferentially hydrolyze omega-3 fatty acids from structured triacylglycerols. However omega-3 fatty acid preferences were found to be modest. Our study provides an explanation for absence of reports of lipases with omega-3 fatty acid hydrolyzing ability and suggests methods for developing these selective lipases.

Single layer lead iodide : computational exploration of structural, electronic and optical properties, strain induced band modulation and the role of spin-orbital-coupling

Graphitic like layered materials exhibit intriguing electronic structures and thus the search for new types of two-dimensional (2D) monolayer materials is of great interest for developing novel nano-devices. By using density functional theory (DFT) method, here we for the first time investigate the structure, stability, electronic and optical properties of monolayer lead iodide (PbI2). The stability of PbI2 monolayer is first confirmed by phonon dispersion calculation. Compared to the calculation using generalized gradient approximation, screened hybrid functional and spin-orbit coupling effects can not only predicts an accurate bandgap (2.63 eV), but also the correct position of valence and conduction band edges. The biaxial strain can tune its bandgap size in a wide range from 1 eV to 3 eV, which can be understood by the strain induced uniformly change of electric field between Pb and I atomic layer. The calculated imaginary part of the dielectric function of 2D graphene/PbI2 van der Waals type hetero-structure shows significant red shift of absorption edge compared to that of a pure monolayer PbI2. Our findings highlight a new interesting 2D material with potential applications in nanoelectronics and optoelectronics.