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.

Is arginine zwitterionic or neutral in the gas phase? results from ir cavity ringdown spectroscopy

Abstract: It is commonly thought that amino acids and peptides exist in a neutral configuration (protonated carboxylic acid and deprotonated amine) in the gas-phase1,2 because zwitterionic charge separation is unfavorable in the absence of solvation However, a recent report suggested that the most stable form of gaseous arginine is actually zwitterionic3 In this proposed configuration, the guanidine in the side chain serves as an intramolecular proton acceptor, whereas the carboxylic acid serves as the donor (cf Figure 1) We know of no previous direct experimental evidence that can support this intriguing claim and have accordingly performed a spectroscopic study of jet-cooled arginine using the novel technique of infrared cavity ringdown laser absorption spectroscopy (IR-CRLAS) Our results confirm that arginine indeed exists in the neutral configuration in a supersonic molecular beam The characterization of isolated gas-phase zwitterions is an important objective that has thus far proved elusive Detailed spectroscopic information would facilitate understanding of the structure and energetics of these systems, providing data that could be used to better parametrize biomolecular potential models4 Moreover, such studies constitute an essential starting point for investigating salient details of biomolecular solvation In infrared spectroscopy experiments, one could unambiguously identify the neutral form of arginine by the presence of carbonyl stretch bands at ca 1700 cm-1 and the zwitterion by carboxylate asymmetric and symmetric stretches at ca 1500-1600 cm-1 IR-CRLAS is a new ultrasensitive direct absorption technique that has recently been used to study a variety of molecular systems5-7 The method employs a set of highly reflective mirrors that form an optical cavity into which an absorbing sample can be placed The sample absorption is determined by monitoring the exponential intensity decay of laser radiation coupled into the cavity Resonant absorption will attenuate more light on each pass than does the passive cavity, leading to a faster decay of the light intensity By measuring the time constant of the exponential decay, one can directly extract the absolute absorbance of the sample Tuning the light over a given frequency range will thus produce an absorption spectrum Ultrahigh sensitivity results from the combination of a large path length and insensitivity to fluctuations in the total intensity Gas-phase arginine was produced using a heated, pulsed, 4-inch-slit molecular beam source, described previously8 The free base form of L-arginine (CAS 74-79-3) was obtained from Sigma No additional sample preparation was used Maintaining the source at a temperature ca 170 °C optimized the arginine signal After the experiment was run, a mass spectrum and FTIR spectrum (taken in a KBr pellet) of the sample remaining in the source as well as the residue collected on a microscope slide downstream of the source confirmed that the sample in the molecular beam did not undergo significant decomposition The IR-CRLAS spectrum of arginine in the 1550-1750 cm-1 region revealed two peaks near 1700 cm-1 (cf Figure 2; 1666 cm-1, 1693 cm-1), corresponding to a carbonyl stretch of a carboxylic acid and confirming that neutral arginine was present in our molecular beam The fact that several peaks were observed in this region can be explained by the presence of several nearly isoenergetic conformers Different structures led to distinct local environments and vibrational frequencies Similar patterns have been found in matrix isolation studies of other amino acids9 Scans near 1600 cm-1 showed no peaks Consequently, a significant population of zwitterions cannot be present in our molecular beam, assuming that the carboxylate mode intensity of the zwitterionic form of arginine is comparable to the carbonyl mode intensity of the neutral (1) Reva, I D; Plokhotnichenko, A M; Stepanian, S G; Ivanov, A Yu; Radchenko, E D; Sheina, G G; Blagoi, Y P Chem Phys Lett 1995, 232, 141-148 (2) Locke, M J; McIver, R T J Am Chem Soc 1983, 105, 4226-4232 (3) Price, W D; Jockusch, R A; Williams, E R J Am Chem Soc 1997, 119, 11988-11989 (4) Gregurick, S K; Fredj, E; Elber, R; Gerber, R B J Phys Chem B 1997, 101, 8595-8606 (5) Scherer, J J; Voelkel, D; Rakestraw, D J; Paul, J B; Collier, C P; Saykally, R J; O’Keefe, A Chem Phys Lett 1995, 245, 273-280 (6) Paul, J B; Collier, C P; Saykally, R J; Scherer, J J; O’Keefe, A J Phys Chem A 1997, 101, 5211-5214 (7) Paul, J B; Saykally, R J Anal Chem 1997, 69, A287-A292 (8) Liu, K; Fellers, R S; Viant, M R; McLaughlin, R P; Brown, M G; Saykally, R J ReV Sci Instrum 1997, 67, 410-416 (9) Reva, I D; Stepanian, S G; Plokhotnihenko, A M; Radchenko, E D; Sheina, G G; Blagoi, Yu P J Mol Struct 1994, 318, 1-13 Figure 1 Zwitterionic form of arginine Notice that this is not the standard zwitterion associated with biomolecules For this system, the guanidine in the side chain is the base, as opposed to the backbone amine of the amino acid

Femtosecond spectroscopy of carrier relaxation dynamics in type II CdSe/CdTe tetrapod heteronanostructures

Abstract: Branched nanocrystal heterostructures synthesized from CdSe and CdTe exhibit a type II band structure alignment that induces separation of charge upon photoexcitation and localizes carriers to different regions of the tetrahedral geometry The dynamics of carrier relaxation examined with femtosecond pump-probe spectroscopy showed heterostructures having rise times and biexponential decays longer than those of nanorods with similar dimensions This is attributed to weaker interactions with surface states and nonradiative relaxation channels afforded by the type II alignment

Raman thermometry measurements of free evaporation from liquid water droplets.

Abstract: Recent theoretical and experimental studies of evaporation have suggested that on average, molecules in the higher-energy tail of the Boltzmann distribution are more readily transferred into the vapor during evaporation. To test these conclusions, the evaporative cooling rates of a droplet train of liquid water injected into vacuum have been studied via Raman thermometry. The resulting cooling rates are fit to an evaporative cooling model based on Knudsen's maximum rate of evaporation, in which we explicitly account for surface cooling. We have determined that the value of the evaporation coefficient (gamma(e)) of liquid water is 0.62 +/- 0.09, confirming that a rate-limiting barrier impedes the evaporation rate. Such insight will facilitate the formulation of a microscopic mechanism for the evaporation of liquid water.

Probing the Interfacial Structure of Aqueous Electrolytes with Femtosecond Second Harmonic Generation Spectroscopy

Abstract: The existence of polarizable anions at the outermost layer of electrolyte solutions has received much recent attention from both theory and experiment, but remains controversial. Anions can be probed directly in the UV via their strong charge-transfer-to-solvent (CTTS) transitions. We have recently described experimental characterizations of enhanced concentrations of several anions at the air−water interface, using the surface-specific technique of second harmonic generation. Here we present a detailed description of the experimental design and methodology used in these experiments, as well as a proof of principle experiment with the known surfactant tetrabutylammonium iodide (TBAI), yielding surface enhancements in excellent agreement with surface tension measurements. Furthermore, we analyze the observed increase in the nonresonant contribution to the SHG response from the water background of alkali halide solutions. The observed change in the water structure of alkali halide (except iodide) solutions ...

Surface relaxation in liquid water and methanol studied by x-ray absorption spectroscopy

Abstract: X-ray absorption spectroscopy is a powerful probe of local electronic structure in disordered media. By employing extended x-ray absorption fine structure spectroscopy of liquid microjets, the intermolecular O–O distance has been observed to undergo a 5.9% expansion at the liquid water interface, in contrast to liquid methanol for which there is a 4.6% surface contraction. Despite the similar properties of liquid water and methanol (e.g., abnormal heats of vaporization, boiling points, dipole moments, etc.), this result implies dramatic differences in the surface hydrogen bond structure, which is evidenced by the difference in surface tension of these liquids. This result is consistent with surface vibrational spectroscopy, which indicates both stronger hydrogen bonding and polar ordering at the methanol surface as a consequence of “hydrophobic packing” of the methyl group.

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.