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.

Chemically selective imaging of subcellular structure in human hepatocytes with coherent anti-stokes raman scattering (CARS) near-field scanning optical microscopy (NSOM)

Abstract: We demonstrate the combination of coherent anti-Stoke Raman scattering (CARS) with near-field scanning optical microscopy (NSOM) for chemically selective imaging via intrinsic vibrational resonances with spatial resolution below the diffraction limit. Femtosecond, near-IR pulses are used to produce CARS signals from human hepatocytes, and by tuning the CARS signal to be resonant with C−H stretching frequencies, image contrast is observed with an optical spatial resolution of ∼128 nm.

Isotope Fractionation of Water during Evaporation without Condensation

Abstract: The microscopic events engendering liquid water evaporation have received much attention over the last century, but remain incompletely understood. We present measurements of isotope fractionation occurring during free molecular evaporation from liquid microjets and show that the isotope ratios of evaporating molecules exhibit dramatic differences from equilibrium vapor values, strong variations with the solution deuterium mole fraction, and a clear temperature dependence. These results indicate the existence of an energetic barrier to evaporation and that the evaporation coefficient of water is less than unity. These new insights into water evaporation promise to advance our understanding of the processes that control the formation and lifetime of clouds in the atmosphere.

Effects of vibrational motion on core-level spectra of prototype organic molecules

Abstract: Effects of vibrational motion on core-level spectra of prototype organic molecules Janel S. Uejio 1∗ and Craig P. Schwartz 1∗ and Richard J. Saykally 1 and David Prendergast 2 Department of Chemistry, University of California, Berkeley, California 94720-1460, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720. Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720. These authors contributed equally. (Dated: October 22, 2008) A computational approach is presented for prediction and interpretation of core-level spectra of complex molecules. Applications are presented for several isolated organic molecules, sampling a range of chemical bonding and structural motifs. Comparison with gas phase measurements indicate that spectral lineshapes are accurately reproduced both above and below the ionization potential, without resort to ad hoc broadening. Agreement with experiment is significantly improved upon inclusion of vibrations via molecular dynamics sampling. We isolate and characterize spectral features due to particular electronic transitions enabled by vibrations, noting that even zero-point motion is sufficient in some cases. PACS numbers: Unknown When applied to molecular systems, core level spec- troscopies are powerful probes of both occupied and un- occupied electronic states, uniquely revealing intimate details of both intra- and inter-molecular interactions [1]. Methods involving x-ray absorption (XAS, NEXAFS, XANES) or x-ray photo-electron spectroscopy (XPS) are increasingly being applied to complex molecular sys- tems, including nucleotides, peptides and large organic molecules [2]. However, a major limitation of this tech- nology is the fact that extraction of molecular informa- tion from these experiments often depends explicitly on comparisons with theoretical calculations, which are ex- tremely challenging to perform at experimental accuracy. In this Letter, we describe the extension of a recently de- veloped method for predicting core-level spectra of con- densed phases [3] to isolated organic molecules – pyrrole, s-triazine, pyrrolidine and glycine – which demonstrates qualitative improvements over existing methods [4–6] in comparison with experiment and provides new insights into the origins of particular spectral features in terms of coupling of electronic and vibrational degrees of freedom. The challenges for simulating gas phase core-level spec- tra are maintaining accuracy in the following areas: (1) description of the core-hole excited state; (2) represen- tation of both bound excitonic states below the ioniza- tion potential (IP) and resonance states in the continuum above the IP; and (3) inclusion of vibrational effects, ei- ther due to experiments being performed near room tem- perature, or from intrinsic zero-point motion. Density functional theory (DFT) [7, 8] has proved ac- curate in reproducing the excitation energies associated with core-level spectra via total energy differences (so- called ∆SCF or ∆KS) [9]. Accordingly, we model the lowest energy core-level excited state self-consistently us- ing a full core-hole and excited electron (XCH) [3]. This is particularly important for molecular systems, where screening of the core-hole excitation is greatly enhanced by the presence of the excited electron, which can be strongly bound to the core-hole in the lowest energy ex- cited state. In contrast, for non-molecular condensed phases, such as covalent and ionic crystalline solids, the inherent dielectric screening of the valence charge den- sity often dominates, and so, explicit inclusion of the ex- cited electron may not be necessary in such cases [5]. We use the PBE form of the generalized gradient approxi- mation to the exchange-correlation potential [10]. Tran- sition amplitudes are estimated in the single-particle and dipole approximations and excitations to states above this first excited state are approximated using the unoc- cupied Kohn-Sham eigenstates computed from the XCH self-consistent potential. This is in contrast to the closely related full core hole (FCH) approximation [5, 6], which ignores the excited electron, or replaces it with a uniform background charge density, and the half core hole (HCH) approach [4] related to Slater’s transition-state potential (TP) [11]. The HCH (or TP) approach has been applied extensively to molecular and cluster models of materials using linear combinations of atomic orbitals (LCAO) to describe the electronic structure. These have included applications to isolated molecules [9], molecules on sur- faces [12], and condensed phase molecular liquids [13]. In our XCH implementation [3] we use norm-conserving pseudopotentials. Core-hole matrix elements with va- lence electrons are calculated by reconstructing the core region of the pseudostates within an atomic frozen core approximation. Other approaches often treat the core- excited atom at the all-electron level, while using effective core potentials for the surrounding unexcited atoms.

Quantitative characterization of the (D2O)3 torsional manifold by terahertz laser spectroscopy and theoretical analysis

Abstract: We report the measurement of two new perpendicular (D2O)3 torsional bands by terahertz laser vibration–rotation–tunneling (VRT) spectroscopy of a planar pulsed supersonic expansion. The first (28.0 cm−1) band corresponds to the k=±2l←0 transition, and is the lowest frequency vibrational spectrum observed for a water cluster. The second (81.8 cm−1) band originates in the first excited torsional state, and has been assigned as k=3u←±1l. An effective three-dimensional Hamiltonian is derived to describe the rotational structure of each torsional state. Degenerate torsional levels with k=±1 and k=±2 exhibit a Coriolis splitting linear in K implying the presence of vibrational angular momentum, and a second-order splitting from off-diagonal coupling between degenerate sublevels with +|k| and −|k|. With this effective Hamiltonian we fit a total of 554 rovibrational transitions in five different bands connecting the lowest nine torsional states, with a rms residual of 1.36 MHz. The data set comprises the two new ...

Extended X-Ray absorption fine structure from hydrogen atoms in water

Abstract: We report the first quantitative measurement of extended x-ray absorption fine structure (EXAFS) from hydrogen atoms. A single oscillation is observed from gaseous water consistent with the location of the covalently bonded hydrogen in H 2O. The experimental phase and amplitude of the oscillation are in excellent agreement with curved wave multiple scattering calculations for isolated water molecules. With this determination of the O-H scattering phase shift we have quantified the covalent hydrogen bond distance (0.95+/-0.03 A) in liquid water, thus demonstrating that hydrogen EXAFS can become a valuable complement to existing structural methods in chemistry and biology.

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.