Biomedical subjects

R J Saykally

Publications and source records attributed to R J Saykally.

At least 19 recordsLinked to original sources

PubMed2006

Water dimers in the atmosphere III: equilibrium constant from a flexible potential.

We present new results for the water dimer equilibrium constant K(p)(T) in the range 190-390 K, using a flexible potential energy surface fitted to spectroscopical data. The increased numerical complexity due to explicit consideration of the monomer vibrations is handled via an adiabatic (6 + 6)d decoupling between intra- and intermolecular modes. The convergence of the canonical partition function of the dimer is ensured by computing all energy levels up to dissociation for total angular momentum values J = 0-5 and using an extrapolation scheme to higher values. The newly calculated values for K(p)(T) are in very good agreement with available experimental data at room temperature. At higher temperatures, an analysis of the convergence of the partition function reveals that quasi-bound states are likely to contribute to the equilibrium constant. Additional thermodynamical quantities (deltaG, deltaH, deltaS, and C(p)) have also been determined and fit to quadratic expressions a + bT + cT2.

Journal Article↗

PubMed2005

Local hydration environments of amino acids and dipeptides studied by X-ray spectroscopy of liquid microjets.

The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s --> sigma(NH) preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s --> pi(CN) resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the alpha amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.

Glycine↗

PubMed2005

X-ray absorption spectroscopy of liquid methanol microjets: bulk electronic structure and hydrogen bonding network.

We have measured the X-ray absorption (XA) spectrum of liquid (298 K) methanol at the oxygen and carbon K edges. The 4a(1) orbital at the O K edge exhibits a pronounced sensitivity to the formation of intermolecular hydrogen bonds, with significant differences observed between the vapor and bulk spectra, whereas the C K edge reveals only subtle corresponding spectral changes. Comparison with DFT computed spectra of model methanol clusters indicates that the bulk liquid comprises long chains (n > 6) and rings of hydrogen-bonded monomers.

Journal Article↗

PubMed2005

pH dependence of the electronic structure of glycine.

The carbon, nitrogen, and oxygen K-edge spectra were measured for aqueous solutions of glycine by total electron yield near-edge X-ray absorption fine structure (TEY NEXAFS) spectroscopy. The bulk solution pH was systematically varied while maintaining a constant amino acid concentration. Spectra were assigned through comparisons with both previous studies and ab initio computed spectra of isolated glycine molecules and hydrated glycine clusters. Nitrogen K-edge solution spectra recorded at low and moderate pH are nearly identical to those of solid glycine, whereas basic solution spectra strongly resemble those of the gas phase. The carbon 1s --> pi*(C=O) transition exhibits a 0.2 eV red shift at high pH due to the deprotonation of the amine terminus. This deprotonation also effects a 1.4 eV red shift in the nitrogen K-edge at high pH. Two sharp preedge features at 401.3 and 402.5 eV are also observed at high pH. These resonances, previously observed in the vapor-phase ISEELS spectrum of glycine, have been reassigned as transitions to sigma* bound states. The observation of these peaks indicates that the amine moiety is in an acceptor-only hydrogen bond configuration at high pH. At low pH, the oxygen 1s --> pi*(C=O) transition exhibits a 0.25-eV red shift due to the protonation of the carboxylic acid terminus. These spectral differences indicate that the variations in electronic structure observed in the NEXAFS spectra are determined by the internal charge state and hydration environment of the molecule in solution.

Glycine↗

PubMed2005

A 'first principles' potential energy surface for liquid water from VRT spectroscopy of water clusters.

We present results of gas phase cluster and liquid water simulations from the recently determined VRT(ASP-W)III water dimer potential energy surface (the third fitting of the Anisotropic Site Potential with Woermer dispersion to vibration-rotation-tunnelling data). VRT(ASP-W)III is shown to not only be a model of high 'spectroscopic' accuracy for the water dimer, but also makes accurate predictions of vibrational ground-state properties for clusters up through the hexamer. Results of ambient liquid water simulations from VRT(ASP-W)III are compared with those from ab initio molecular dynamics, other potentials of 'spectroscopic' accuracy and with experiment. The results herein represent the first time to the authors' knowledge that a 'spectroscopic' potential surface is able to correctly model condensed phase properties of water.

Computer Simulation↗

PubMed2004

Elucidating the role of many-body forces in liquid water. I. Simulations of water clusters on the VRT(ASP-W) potential surfaces.

We test two new potentials for water, fit to vibration-rotation tunneling (VRT) data by employing diffusion quantum Monte Carlo simulations to calculate the vibrational ground-state properties of water clusters. These potentials, VRT(ASP-W)II and VRT(ASP-W)III, are fits of the highly detailed ASP-W (anisotropic site potential with Woermer dispersion) ab initio potential to (D(2)O)(2) microwave and far-infrared data, and along with the SAPT5s (five-site symmetry adapted perturbation theory) potentials, are the most accurate water dimer potential surfaces in the literature. The results from VRT(ASP-W)II and III are compared to those from the original ASP-W potential, the SAPT5s family of potentials, and several bulk water potentials. Only VRT(ASP-W)III and the spectroscopically "tuned" SAPT5st (with N-body induction included) accurately reproduce the vibrational ground-state structures of water clusters up to the hexamer. Finally, the importance of many-body induction and three-body dispersion are examined, and it is shown that the latter can have significant effects on water cluster properties despite its small magnitude.

Journal Article↗

PubMed2004

Shape control of near-field probes using dynamic meniscus etching.

Dynamic etching methods for fabricating fibre optic tips are explored and modelled. By vertically translating the fibre during etching by an HF solution under an organic protective layer, a variety of tip shapes were created. The probe taper lengths, cone angles and geometrical probe shapes were measured in order to evaluate the dynamic meniscus etching process. Fibre motion, etching rate, meniscus distortion and etching time were all found to be important variables that can be used to control the final probe shape.

Equipment Design↗

PubMed2003

Poled polymer thin-film gratings studied with far-field optical diffraction and second-harmonic near-field microscopy.

Electrical poling induces polar ordering of molecules in a grating that has been holographically inscribed on a thin film of polymer with azobenzene side chains. The resulting chi2 grating, seen by second-harmonic-generation (SHG) near-field scanning optical microscopy, can have a periodic structure that is significantly different from the topographical image. The far-field linear and SHG diffration patterns correlate well with the grating structures. Poling of the thin-film grating, which presumably has photodriven nonuniform material properties within each period, leads to the more complex structure of the chi2 grating.

Journal Article↗

PubMed2003

An enhanced cosmic-ray flux towards zeta Persei inferred from a laboratory study of the H3+-e- recombination rate.

The H3+ molecular ion plays a fundamental role in interstellar chemistry, as it initiates a network of chemical reactions that produce many molecules. In dense interstellar clouds, the H3+ abundance is understood using a simple chemical model, from which observations of H3+ yield valuable estimates of cloud path length, density and temperature. But observations of diffuse clouds have suggested that H3+ is considerably more abundant than expected from the chemical models. Models of diffuse clouds have, however, been hampered by the uncertain values of three key parameters: the rate of H3+ destruction by electrons (e-), the electron fraction, and the cosmic-ray ionization rate. Here we report a direct experimental measurement of the H3+ destruction rate under nearly interstellar conditions. We also report the observation of H3+ in a diffuse cloud (towards Persei) where the electron fraction is already known. From these, we find that the cosmic-ray ionization rate along this line of sight is 40 times faster than previously assumed. If such a high cosmic-ray flux is ubiquitous in diffuse clouds, the discrepancy between chemical models and the previous observations of H3+ can be resolved.

Journal Article↗

PubMed2001

High spatial resolution imaging with near-field scanning optical microscopy in liquids.

The mechanism of tuning fork-based shear-force near-field scanning optical microscopy is investigated to determine optimal experimental conditions for imaging soft samples immersed in liquid. High feedback sensitivity and stability are obtained when only the fiber probe, i.e., excluding the tuning fork prongs, is immersed in solution, which also avoids electrical shorting in conductive (i.e., buffer) solutions. Images of MEH-PPV were obtained with comparable spatial resolution in both air and water. High optical resolution (approximately160 nm fwhm) was observed.

Ethylenes↗

PubMed2001

Water clusters: untangling the mysteries of the liquid, one molecule at a time.

Extensive terahertz laser vibration-rotation-tunneling spectra and mid-IR laser spectra have been compiled for several isotopomers of small (dimer through hexamer) water clusters. These data, in conjunction with new theoretical advances, quantify the structures, force fields, dipole moments, and hydrogen bond rearrangement dynamics in these clusters. This new information permits us to systematically untangle the intricacies associated with cooperative hydrogen bonding and promises to lead to a more complete molecular description of the liquid and solid phases of water, including an accurate universal force field.

Hydrogen Bonding↗

PubMed2001

Hydrogen bond breaking dynamics of the water trimer in the translational and librational band region of liquid water.

The effect of exciting each of the three classes of intermolecular vibrations on the hydrogen bond lifetime (tau(H)) of the isolated water trimer is investigated by far-infrared laser spectroscopy. Single excitation of a librational vibration decreases tau(H) by 3 orders of magnitude to tau(H) = 1-6 ps, comparable to the time scale of a number of important bulk water dynamical relaxation processes. In contrast, excitation of translational or torsional vibrations has no significant effect (tau(H) = 1-2 ns). Although such a dependence of tau(H) on intermolecular motions has also been proposed for liquid water via computer simulations, these are the first experiments that provide a detailed molecular picture of the respective motions without extensive interpretation.

Hydrogen Bonding↗

PubMed2001

Single photon infrared emission spectroscopy of the gas phase pyrene cation: support for a polycyclic aromatic hydrocarbon origin of the unidentified infrared emission bands.

We report the first observation of infrared emission from a gaseous ionic polycyclic aromatic hydrocarbon (PAH), the pyrene cation, over the range of wavelengths spanned by the ubiquitous interstellar unidentified infrared emission bands (UIRs). The complete set of pyrene cation IR emissions is observed, with relative intensities consistent with astrophysical observations, supporting the proposal that ionized PAHs are major contributors to the UIR bands. Additionally, unidentified features possibly arising from dehydrogenated PAH species are noted in the spectrum.

Journal Article↗

PubMed2001

Complete characterization of the (D2O)2 ground state: high Ka rotation-tunneling levels.

We report the observation of extensive a- and c-type rotation-tunneling (RT) spectra of (D2O)2 for Ka = 0-4. These data allow quantification of molecular constants and tunneling splittings for a number of previously unobserved RT states of (D2O)2. The vibrational ground state has thus been characterized to energies as high as those of some of the intermolecular vibrations, and we present the first test of the VRT(ASP-W) potential at these high Ka states.

Journal Article↗

PubMed2000

Peripherally hydrogenated neutral polycyclic aromatic hydrocarbons as carriers of the 3 micron interstellar infrared emission complex: results from single-photon infrared emission spectroscopy.

Infrared emission spectra of five gas-phase UV laser-excited polycyclic aromatic hydrocarbons (PAHs) containing aliphatic hydrogens are compared with the main 3.3 microns and associated interstellar unidentified infrared emission bands (UIRs). We show that neutral PAHs can account for the majority of the 3 microns emission complex while making little contribution to the other UIR bands; peripherally hydrogenated PAHs produce a better match to astrophysical data than do those containing methyl side groups; 3.4 microns plateau emission is shown to be a general spectral feature of vibrationally excited PAHs containing aliphatic hydrogens, especially those containing methyl groups; and finally, hot-band and overtone emissions arising from aromatic C-H vibrations are not observed in laboratory emission spectra, and therefore, in contrast to current assignments, are not expected to be observed in the UIRs.

Astronomy↗

PubMed2000

Nonlinear chemical imaging microscopy: near-field third harmonic generation imaging of human red blood cells.

Third harmonic generation (THG) imaging using a near-field scanning optical microscope (NSOM) is demonstrated for the first time. A femtosecond, tunable near-infrared laser was used to generate both nonresonant and resonantly enhanced third harmonic radiation in human red blood cells. We show that resonantly enhanced THG is a chemically specific bulk probe in NSOM imaging by tuning the excitation source onto and off of resonance with the Soret transition of oxyhemoglobin. Additionally, we provide evidence that tightly focused, nonresonant, far-field THG imaging experiments do not produce contrast that is truly surface specific.

Algorithms↗

PubMed1999

Spectroscopic determination of the water pair potential.

A polarizable water pair potential was determined by fitting a potential form to microwave, terahertz, and mid-infrared (D2O)2 spectra through a rigorous calculation of the water dimer eigenstates. It accurately reproduces most ground state vibration-rotation-tunneling spectra and yields excellent second viral coefficients. The calculated dimer structure and dipole moment are very close to those determined from microwave spectroscopy and high-level ab initio calculations. The dimer binding energy and acceptor switching and donor-acceptor interchange tunneling barriers are in excellent agreement with recent ab initio theory, as are cyclic water trimer and tetramer structures and binding energies.

Algorithms↗

PubMed1998

Single photon infrared emission spectroscopy: a study of IR emission from UV laser excited PAHs between 3 and 15 micrometers.

Single-photon infrared emission spectroscopy (SPIRES) has been used to measure emission spectra from polycyclic aromatic hydrocarbons (PAHs). A supersonic free-jet expansion has been used to provide emission spectra of rotationally cold and vibrationally excited naphthalene and benzene. Under these conditions, the observed width of the 3.3-micrometers (C-H stretch) band resembles the bandwidths observed in experiments in which emission is observed from naphthalene with higher rotational energy. To obtain complete coverage of IR wavelengths relevant to the unidentified infrared bands (UIRs), UV laser-induced desorption was used to generate gas-phase highly excited PAHs. Lorentzian band shapes were convoluted with the monochromator-slit function in order to determine the widths of PAH emission bands under astrophysically relevant conditions. Bandwidths were also extracted from bands consisting of multiple normal modes blended together. These parameters are grouped according to the functional groups mostly involved in the vibration, and mean bandwidths are obtained. These bandwidths are larger than the widths of the corresponding UIR bands. However, when the comparison is limited to the largest PAHs studied, the bandwidths are slightly smaller than the corresponding UIR bands. These parameters can be used to model emission spectra from PAH cations and cations of larger PAHs, which are better candidate carriers of the UIRs.

Argon↗