Richard J. Saykally

Bio: Richard J. Saykally is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Spectroscopy & Absorption spectroscopy. The author has an hindex of 94, co-authored 457 publications receiving 40997 citations. Previous affiliations of Richard J. Saykally include University of California & Lawrence Berkeley National Laboratory.

Characterization of hydrogen bond acceptor molecules at the water surface using near-edge x-ray absorption fine-structure spectroscopy and density functional theory

Abstract: We present a combined experimental/computational study of the near-edge x-ray absorption fine structure of the liquid water surface which indicates that molecules with acceptor-only hydrogen bonding configurations constitute an important and previously unidentified component of the liquid/vapour interface.

Evidence for water rings in the hexahydrated sulfate dianion from IR spectroscopy.

Abstract: Whereas isolated SO42- is unstable, hydrated clusters of this dianion have been formed and investigated using a variety of different methods. Several structures of [SO4(H2O)6]2- have been proposed that account for its high stability in the gas phase. Zhou et al. [J. Chem. Phys. 2006, 125, 111102] recently reported infrared spectra of [SO4(H2O)n]2- in the 540−1850 cm-1 region and assigned the spectrum of the hexahydrated ion to a Td symmetry structure in which all six water molecules donate two hydrogen bonds to the sulfate core. Here, an infrared spectrum of this ion in the hydrogen stretch region (2620−3840 cm-1) and B3LYP/AUG-cc-pVDZ calculations indicate that a significant population of these ions correspond to lower symmetry structures containing water rings in which each water molecule donates hydrogen bonds to both the sulfate dianion and a neighboring water molecule. These calculations indicate that inter-water hydrogen bonds are slightly favored over additional solvation of the dianion core. These...

Determination of the intermolecular potential energy surface for (HCl)2 from vibration–rotation–tunneling spectra

Abstract: An accurate and detailed semiempirical intermolecular potential energy surface for (HCl)2 has been determined by a direct nonlinear least‐squares fit to 33 microwave, far‐infrared and near‐infrared spectroscopic quantities using the analytical potential model of Bunker et al. [J. Mol. Spectrosc. 146, 200 (1991)] and a rigorous four‐dimensional dynamical method (described in the accompanying paper). The global minimum (De=−692 cm−1) is located near the hydrogen‐bonded L‐shaped geometry (R=3.746 A, θ1=9°, θ2=89.8°, and φ=180°). The marked influence of anisotropic repulsive forces is evidenced in the radial dependence of the donor–acceptor interchange tunneling pathway. The minimum energy pathway in this low barrier (48 cm−1) process involves a contraction of 0.1 A in the center of mass distance (R) at the C2h symmetry barrier position. The new surface is much more accurate than either the ab initio formulation of Bunker et al. or a previous semiempirical surface [J. Chem. Phys. 78, 6841 (1983)].

Mechanism of ion adsorption to aqueous interfaces: Graphene/water vs. air/water.

Abstract: The adsorption of ions to aqueous interfaces is a phenomenon that profoundly influences vital processes in many areas of science, including biology, atmospheric chemistry, electrical energy storage, and water process engineering. Although classical electrostatics theory predicts that ions are repelled from water/hydrophobe (e.g., air/water) interfaces, both computer simulations and experiments have shown that chaotropic ions actually exhibit enhanced concentrations at the air/water interface. Although mechanistic pictures have been developed to explain this counterintuitive observation, their general applicability, particularly in the presence of material substrates, remains unclear. Here we investigate ion adsorption to the model interface formed by water and graphene. Deep UV second harmonic generation measurements of the SCN- ion, a prototypical chaotrope, determined a free energy of adsorption within error of that for air/water. Unlike for the air/water interface, wherein repartitioning of the solvent energy drives ion adsorption, our computer simulations reveal that direct ion/graphene interactions dominate the favorable enthalpy change. Moreover, the graphene sheets dampen capillary waves such that rotational anisotropy of the solute, if present, is the dominant entropy contribution, in contrast to the air/water interface.

Water Dimers in the Atmosphere: Equilibrium Constant for Water Dimerization from the VRT(ASP-W) Potential Surface

Abstract: The equilibrium constant for water dimerization (KP) was determined as a function of temperature via rigorous calculation of the canonical (H2O)2 partition function using the recently developed split Wigner pseudo-spectral method and the VRT(ASP-W) pair potential. Our KP(T) values are significantly larger than those from previous theoretical treatments but somewhat smaller than literature experimental values, which exist, however, only over a very limited temperature range. These results indicate that water dimers can exist in sufficient concentrations (e.g., 1016 cm-3 at 40 °C and 100% relative humidity) to affect physical and chemical processes in the atmosphere.

Fast parallel algorithms for short-range molecular dynamics

Abstract: 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.

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

Abstract: 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。

The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment

Abstract: The optical properties of metal nanoparticles have long been of interest in physical chemistry, starting with Faraday's investigations of colloidal gold in the middle 1800s. More recently, new lithographic techniques as well as improvements to classical wet chemistry methods have made it possible to synthesize noble metal nanoparticles with a wide range of sizes, shapes, and dielectric environments. In this feature article, we describe recent progress in the theory of nanoparticle optical properties, particularly methods for solving Maxwell's equations for light scattering from particles of arbitrary shape in a complex environment. Included is a description of the qualitative features of dipole and quadrupole plasmon resonances for spherical particles; a discussion of analytical and numerical methods for calculating extinction and scattering cross-sections, local fields, and other optical properties for nonspherical particles; and a survey of applications to problems of recent interest involving triangula...

Dye-Sensitized Solar Cells

Abstract: Dye-sensitized solar cells (DSCs) offer the possibilities to design solar cells with a large flexibility in shape, color, and transparency. DSC research groups have been established around the worl ...

Quantum Dot Bioconjugates for Ultrasensitive Nonisotopic Detection

Abstract: Highly luminescent semiconductor quantum dots (zinc sulfide-capped cadmium selenide) have been covalently coupled to biomolecules for use in ultrasensitive biological detection. In comparison with organic dyes such as rhodamine, this class of luminescent labels is 20 times as bright, 100 times as stable against photobleaching, and one-third as wide in spectral linewidth. These nanometer-sized conjugates are water-soluble and biocompatible. Quantum dots that were labeled with the protein transferrin underwent receptor-mediated endocytosis in cultured HeLa cells, and those dots that were labeled with immunomolecules recognized specific antibodies or antigens.