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The thermochemistry of the conversion of glucose to levulinic acid through fructofuranosyl intermediates is investigated using the high-level ab initio methods G4 and G4MP2. The calculated gas phase reaction enthalpies indicate that the first two steps involving water molecule elimination are highly endothermic, while the other steps, including additional water elimination and rehydration to form levulinic acid, are exothermic. The calculated gas phase free energies indicate that inclusion of entropic effects makes the dehydration steps more favorable, although the elimination of the first water is still endothermic. Elevated temperatures and aqueous reaction environments are also predicted to make the dehydration reaction steps thermodynamically more favorable. On the basis of these enthalpy and free energy calculations, the first dehydration step in conversion of glucose to levulinic acid is likely a key step in controlling the overall progress of the reaction. An assessment of density functional theories and other theoretical methods for the calculation of the dehydration and hydration reactions in the decomposition of glucose is also presented.

The coupled cluster (CC) ansatz is generally recognized as providing one of the best wave function-based descriptions of electronic correlation in small- and medium-sized molecules. The fact that the CC equations with double excitations (CCD) may be expressed as a handful of dense matrix-matrix multiplications makes it an ideal method to be ported to graphics processing units (GPUs). We present our implementation of the spin-free CCD equations in which the entire iterative procedure is evaluated on the GPU. The GPU-accelerated algorithm readily achieves a factor of 4-5 speedup relative to the multithreaded CPU algorithm on same-generation hardware. The GPU-accelerated algorithm is approximately 8-12 times faster than Molpro, 17-22 times faster than NWChem, and 21-29 times faster than GAMESS for each CC iteration. Single-precision GPU-accelerated computations are also performed, leading to an additional doubling of performance. Single-precision errors in the energy are typically on the order of 10(-6) hartrees and can be improved by about an order of magnitude by performing one additional iteration in double precision.

The static dipole polarizabilities of water clusters (2

Long-range dispersion interactions have a critical influence on physical quantities in simulations of inhomogeneous systems. However, the perceived computational overhead of long-range solvers has until recently discouraged their implementation in molecular dynamics packages. Here, we demonstrate that reducing the cutoff radius for local interactions in the recently introduced particle-particle particle-mesh (PPPM) method for dispersion [Isele-Holder et al., J. Chem. Phys., 2012, 137, 174107] can actually often be faster than truncating dispersion interactions. In addition, because all long-range dispersion interactions are incorporated, physical inaccuracies that arise from truncating the potential can be avoided. Simulations using PPPM or other mesh Ewald solvers for dispersion can provide results more accurately and more efficiently than simulations that truncate dispersion interactions. The use of mesh-based approaches for dispersion is now a viable alternative for all simulations containing dispersion interactions and not merely those where inhomogeneities were motivating factors for their use. We provide a set of parameters for the dispersion PPPM method using either ik or analytic differentiation that we recommend for future use and demonstrate increased simulation efficiency by using the long-range dispersion solver in a series of performance tests on massively parallel computers.

The completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] has proven to be a reliable tool in describing vertical excitation energies in small and medium size molecules. In order to reduce the high numerical cost of the genuine CR-EOMCCSD(T) method and make noniterative CR-EOMCCSD(T) approaches applicable to large molecular systems, two active-space variants of this formalism [the CR-EOMCCSd(t)-II and CR-EOMCCSd(t)-III methods], based on two different choices of the subspace of triply excited configurations employed to construct noniterative correction, are introduced. In calculations for green fluorescent protein (GFP) and free-base porphyrin, where the CR-EOMCCSD(T) results are available, we show good agreement between the active-space CR-EOMCCSD(T) (variant II) and full CR-EOMCCSD(T) excitation energies. For the oligoporphyrin dimer (P(2)TA) active-space CR-EOMCCSD(T) results provide reasonable agreement with experimentally inferred data. For all systems considered we demonstrated that the active-space CR-EOMCCSD(T) corrections lower the EOMCCSD (iterative equation-of-motion coupled-cluster method with singles and doubles) excitation energies by 0.2 and 0.3 eV, which leads to a better agreement with experiment. We also discuss the quality of basis sets used and compare EOMCC excitation energies with excitation energies obtained with other methods. In particular, we demonstrate that for GFP and FBP Sadlej's TZP and cc-pVTZ basis sets lead to a similar quality of the EOMCC results. The performance of the CR-EOMCCSD(T) implementation is discussed from the point of view of timings of iterative parts and scalability of the most expensive, N(7), part of the calculation. In the latter case the scalability across 34 008 processors is reported.

DFT calculations have been performed with the B3LYP and MPW1K functional on the hydrogen atom abstraction reactions of ethenoxyl with ethenol and of phenoxyl with both phenol and α-naphthol. Comparison with the results of G3 calculations shows that B3LYP seriously underestimates the barrier heights for the reaction of ethenoxyl with ethenol by both proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms. The MPW1K functional also underestimates the barrier heights, but by much less than B3LYP. Similarly, comparison with the results of experiments on the reaction of phenoxyl radical with α-naphthol indicates that the barrier height for the preferred PCET mechanism is calculated more accurately by MPW1K than by B3LYP. These findings indicate that the MPW1K functional is much better suited than B3LYP for calculations on hydrogen abstraction reactions by both HAT and PCET mechanisms.Many hydrogen atom abstraction reactions proceed by a classical hydrogen-atom transfer (HAT) mechanism, involving three electrons distributed among three atomic orbitals. 1 As shown schematically in Figure 1a, the proton and one of the electrons in the X-H bond being broken are both transferred to the singly occupied orbital on radical Y · .However, in recent years both experimental and computational studies have found that, when the abstracting radical center carries at least one unshared pair of electrons and the hydrogen to be abstracted is bonded to an atom that also has an unshared pair of electrons, a protoncoupled electron transfer (PCET) mechanism may be preferred to a HAT mechanism. 2 As illustrated in Figure 1b, such a PCET mechanism involves a total of five atomic orbitals. The proton in the X-H bond is transferred to a lone pair of electrons on radical Y · ; and, simultaneously, an electron is transferred from a lone pair on X to the singly occupied orbital on Y. Thus, unlike the case in HAT, where the proton and the electron of the hydrogen atom are transferred from X to the same AO on Y, in PCET the proton is transferred between one pair of AOs on X and Y, and the electron is transferred between another pair of AO on these two atoms.We have reported the results of unrestricted (U)B3LYP calculations on the preferred mechanism for the degenerate hydrogen abstraction reactions of benzyl radical with toluene, methoxyl radical with methanol, and phenoxyl radical with phenol. 3 Our calculations found that for the first two of these reactions, a HAT mechanism is favored. However, for the reaction of phenoxyl with phenol, our (U)B3LYP calculations found a PCET mechanism to be ‡ showed that MPW1K --a modified version of the Perdew-Wang gradient-corrected exchange functional, with one parameter optimized to give the best fit to the kinetic data for these 40 radical reactions, --reduced the mean signed error in the barrier heights for these reactions to -1.3 kcal/mol.It is not known whether B3LYP makes similar or, perhaps, even larger errors for PCET reactions, as for these 40 HAT reactions. It is a...

Green tea polyphenol epigallocatechin gallate (EGCG) is a strong anti-oxidant that has previously been shown to reduce the number of plaques in HIV-infected cultured cells. Modified EGCG palmitoyl-EGCG (p-EGCG), is of interest as a topical antiviral agent for Herpes Simplex Virus (HSV-1) infections. This study evaluated the effect of p-EGCG on HSV-infected Vero cells. Results of cell viability and cell proliferation assays indicate that p-EGCG is not toxic to cultured Vero cells and show that modification of the green tea polyphenol epigallocatechin gallate (EGCG) with palmitate increases the effectiveness of EGCG as an antiviral agent. Furthermore, p-EGCG is a more potent inhibitor of Herpes Simplex Virus 1 (HSV-1) than EGCG and can be topically applied to skin, one of the primary tissues infected by HSV. Viral binding assay, plaque forming assay, PCR, real-time PCR, and fluorescence microscopy were used to demonstrate that p-EGCG concentrations of 50 µM and higher block the production of infectious HSV-1 particles. p-EGCG was found to inhibit HSV-1 adsorption to Vero cells. Thus, p-EGCG may provide a novel treatment for HSV-1 infections.