The effect of hydrogen bonding on the diffusion of water in n-alkanes and n-alcohols measured with a novel single microdroplet method.

While the Stokes-Einstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that for small solutes, the diffusion coefficient is inversely proportional to the viscosity to a fractional power, and that solutes actually diffuse faster than SE predicts. For other solvent systems, attractive solute-solvent interactions, such as hydrogen bonding, are known to retard the diffusion of a solute. Some researchers have interpreted the slower diffusion due to hydrogen bonding as resulting from the effective diffusion of a larger complex of a solute and solvent molecules. We have developed and used a novel micropipette technique, which can form and hold a single microdroplet of water while it dissolves in a diffusion controlled environment into the solvent. This method has been used to examine the diffusion of water in both n-alkanes and n-alcohols. It was found that the polar solute water, diffusing in a solvent with which it cannot hydrogen bond, closely resembles small nonpolar solutes such as xenon and krypton diffusing in n-alkanes, with diffusion coefficients ranging from 12.5x10(-5) cm(2)/s for water in n-pentane to 1.15x10(-5) cm(2)/s for water in hexadecane. Diffusion coefficients were found to be inversely proportional to viscosity to a fractional power, and diffusion coefficients were faster than SE predicts. For water diffusing in a solvent (n-alcohols) with which it can hydrogen bond, diffusion coefficient values ranged from 1.75x10(-5) cm(2)/s in n-methanol to 0.364x10(-5) cm(2)/s in n-octanol, and diffusion was slower than an alkane of corresponding viscosity. We find no evidence for solute-solvent complex diffusion. Rather, it is possible that the small solute water may be retarded by relatively longer residence times (compared to non-H-bonding solvents) as it moves through the liquid.

FANTASIO: a versatile experimental set-up to investigate jet-cooled molecules

The design of a new apparatus, named FANTASIO, for studying jet-cooled molecules is described. It includes, around the same supersonic expansion cell, a high resolution Fourier transform spectrometer with single or multipass optics, a tunable diode laser spectrometer with optional cavity ring-down facilities, and a quadrupole mass spectrometer. Performance and operational procedures are illustrated.

A discrete time-dependent method for metastable atoms and molecules in intense fields

The full-dimensional time-dependent Schrodinger equation for the electronic dynamics of single-electron systems in intense external fields is solved directly using a discrete method. Our approach combines the finite-difference and Lagrange mesh methods. The method is applied to calculate the quasienergies and ionization probabilities of atomic and molecular systems in intense static and dynamic electric fields. The gauge invariance and accuracy of the method is established. Applications to multiphoton ionization of positronium, the hydrogen atom and the hydrogen molecular ion are presented. At very high laser intensity, above the saturation threshold, we extend the method using a scaling technique to estimate the quasienergies of metastable states of the hydrogen molecular ion. The results are in good agreement with recent experiments. (C) 2004 American Institute of Physics.

Charge exchange and dissociative processes in collisions of slow He2+ ions with H2O molecules

Experimental and theoretical studies of one-electron capture in collisions of He2+ ions with H2O molecules have been carried out in the range 0.025-12 keV amu(-1) corresponding to typical solar wind velocities of 70-1523 km s(-1). Translational energy spectroscopy (TES), photon emission spectroscopy (PES), and fragment ion spectroscopy were employed to identify and quantify the collision mechanisms involved. Cross sections for selective single electron capture into n=1, 2, and 3 states of the He+ ion were obtained using TES while PES provided cross sections for capture into the He+(2p) and He+(3p) states. Our model calculations show that He+(n=2) and He+(n=3) formation proceeds via a single-electron process governed by the nucleus-electron interaction. In contrast, the He+(1s) formation mechanism involves an exothermic two-electron process driven by the electron-electron interaction, where the potential energy released by the electron capture is used to remove a second electron thereby resulting in fragmentation of the H2O molecule. This process is found to become increasingly important as the collision energy decreases. The experimental cross sections are found to be in reasonable agreement with cross sections calculated using the Demkov and Landau-Zener models.

Isolation and cloning of exendin precursor cDNAs from single samples of venom from the Mexican beaded lizard (Heloderma horridum) and the Gila Monster (Heloderma suspectum)

Reptile venoms are complex cocktails of bioactive molecules, including peptides. While the drug discovery potential of most species remains unrealized, many are endangered and afforded protection under international treaties. In this study, we describe how potential clinically important bioactive peptides and their corresponding mRNAs can be structurally characterized from single, small samples of reptile venom. The potential type-2 diabetes therapeutics, exendin-3 and exendin-4, from the Mexican beaded lizard (Heloderma horridum) and the Gila monster (Heloderma suspectum), respectively, have been characterized at both protein and nucleic acid levels to illustrate the efficacy of the technique and its contribution to biodiversity conservation.

X-ray emission from charge exchange of highly-charged ions in atoms and molecules

Charge exchange followed by radiative stabilization are the main processes responsible for the recent observations of X-ray emission from comets in their approach to the Sun. A new apparatus was constructed at JPL to measure, in collisions of HCIs with atoms and molecules, (a) absolute cross sections for single and multiple charge exchange, and (b) normalized X-ray emission cross sections. The ions are produced by the JPL HCI Facility and passed through a neutral-gas target cell. The product charge states are analyzed by a retarding potential difference technique. Results are made absolute by measuring target pressure, and incident and product ion currents. X-rays emitted from the product ions are detected with a Ge solid-state detector having a resolution of approximately 100 eV. X-ray astronomy has taken major steps forward with the recent launch of the high-resolution satellites Chandra and Newton. The cross sections reported herein are essential for the development of the solar wind comet interaction models inspired by these observations.

Atom cooling using the dipole force of a single retroreflected laser beam

We present a mechanism for cooling atoms by a laser beam reflected from a single mirror. The cooling relies on the dipole force and thus in principle applies to arbitrary refractive particles including atoms, molecules, or dielectric spheres. Friction and equilibrium temperatures are derived by an analytic perturbative approach. Finally, semiclassical Monte-Carlo simulations are performed to validate the analytic results.

In Situ Single-Crystal Diffraction Studies of the Structural Transition of Metal-Organic Framework Copper 5-Sulfoisophthalate, Cu-SIP-3

The flexibility of the metal-organic framework Cu-2(OH)(C8H3O7S)(H2O)center dot 2H(2)O (Cu-SIP-3) toward reversible single-crystal to single-crystal transformations is demonstrated using in situ diffraction methods at variable temperature. At temperatures below a dehydration-induced phase transition (T < 370 K) the structure is confirmed as being hydrated. In the temperature range where the transition takes place (370 K < T < 405 K) no discrete, sharp Bragg peaks can be seen in the single-crystal X-ray diffraction pattern, indicating significant loss of long-range order. At temperatures higher than 405 K, the Bragg peaks return and the structure can be refined as dehydrated Cu-SIP-3. The loss of guest water molecules can be followed at temperatures below the phase transition giving insight into the mechanism of the dehydration. Addition of nitric oxide gas to the material above the gating opening pressure of 275 mbar also leads to loss of Bragg scattering in the diffraction pattern.

Information Gathering and Processing with Fluorescent Molecules

Molecular information gathering and processing – a young field of applied chemistry - is undergoing good growth. The progress is occurring both in terms of conceptual development and in terms of the strengthening of older concepts with new examples. This review critically surveys these two broad avenues. We consider some cases where molecules emulate one of the building blocks of electronic logic gates. We then examine molecular emulation of various Boolean logic gates carrying one, two or three inputs. Some single-input gates are popular information gathering devices. Special systems, such as ‘lab-on-a-molecule’ and molecular keypad locks, also receive attention. A situation deviating from the Boolean blueprint is also discussed. Some pointers are offered for maintaining the upward curve of the field.

Electron-impact ionization of diatomic molecules using a configuration-average distorted-wave method

Electron-impact ionization cross sections for diatomic molecules are calculated in a configuration-average distorted-wave method. Core bound orbitals for the molecular ion are calculated using a single-configuration self-consistent-field method based on a linear combination of Slater-type orbitals. The core bound orbitals are then transformed onto a two-dimensional (r,θ) numerical lattice from which a Hartree potential with local exchange is constructed. The single-particle Schrödinger equation is then solved for the valence bound orbital and continuum distorted-wave orbitals with S-matrix boundary conditions. Total cross section results for H2 and N2 are compared with those from semiempirical calculations and experimental measurements.

Targeting Heme with Single Domain Antibodies

Heme, i.e. iron (Fe) protoporphyrin IX, functions as a prosthetic group in a variety of hemoproteins that participate in vital biologic functions essential to sustain life. Heme is a highly reactive molecule, participating in redox reactions, and presumably for this reason it must be sequestered within the heme pockets of hemoproteins, controlling its reactivity. However, under biological stress conditions, hemoproteins can release their prosthetic groups, generating “free heme”, which binds loosely to proteins or to other molecules and presumably acquires unfettered redox activity. Moreover, a growing body of evidence supports the notion that “free heme” can act in a vasoactive, pro-inflammatory and cytotoxic manner when released from a subset of these hemoproteins, such as extracellular hemoglobin, generated during hemolytic conditions. (...)

In situ evaluation of single-cell lysis by cytosol extraction observation through fluorescence decay and dielectrophoretic trapping time

We present a new method for lysis of single cells in continuous flow, where cells are sequentially trapped, lysed and released in an automatic process. Using optimized frequencies, dielectrophoretic trapping allows exposing cells in a reproducible way to high electrical fields for long durations, thereby giving good control on the lysis parameters. In situ evaluation of cytosol extraction on single cells has been studied for Chinese hamster ovary (CHO) cells through out-diffusion of fluorescent molecules for different voltage amplitudes. A diffusion model is proposed to correlate this out-diffusion to the total area of the created pores, which is dependent on the potential drop across the cell membrane and enables evaluation of the total pore area in the membrane. The dielectrophoretic trapping is no longer effective after lysis because of the reduced conductivity inside the cells, leading to cell release. The trapping time is linked to the time required for cytosol extraction and can thus provide additional validation of the effective cytosol extraction for non-fluorescent cells. Furthermore, the application of one single voltage for both trapping and lysis provides a fully automatic process including cell trapping, lysis, and release, allowing operating the device in continuous flow without human intervention.

Investigation of single tryptophan proteins encapsulated in TEOS-derived sol-gel matrices by fluorescence spectroscopy /

In the work reported here, optically clear, ultrathin TEOS derived sol-gel slides which were suitable for studies of tryptophan (Trp) fluorescence from entrapped proteins were prepared by the sol-gel technique and characterized. The monitoring of intrinsic protein fluorescence provided information about the structure and environment of the entrapped protein, and about the kinetics of the interaction between the entrapped protein and extemal reagents. Initial studies concentrated on the single Trp protein monellin which was entrapped into the sol-gel matrices. Two types of sol-gel slides, termed "wet aged", in which the gels were aged in buffer and "dry-aged", in which the gels were aged in air , were studied in order to compare the effect of the sol-gel matrix on the structure of the protein at different aging stages. Fluorescence results suggested that the mobility of solvent inside the slides was substantially reduced. The interaction of the entrapped protein with both neutral and charged species was examined and indicated response times on the order of minutes. In the case of the neutral species the kinetics were diffusion limited in solution, but were best described by a sum of first order rate constants when the reactions occurred in the glass matrix. For charged species, interactions between the analytes and the negatively charged glass matrix caused the reaction kinetics to become complex, with the overall reaction rate depending on both the type of aging and the charge on the analyte. The stability and conformational flexibility of the entrapped monellin were also studied. These studies indicated that the encapsulation of monellin into dry-aged monoliths caused the thermal unfolding transition to broaden and shift upward by 14°C, and causedthe long-term stability to improve by 12-fold (compared to solution). Chemical stability studies also showed a broader transition for the unfolding of the protein in dry-aged monoliths, and suggested that the protein was present in a distribution of environments. Results indicated that the entrapped proteins had a smaller range of conformational motions compared to proteins in solution, and that entrapped proteins were not able to unfold completely. The restriction of conformational motion, along with the increased structural order of the internal environment of the gels, likely resulted in the improvements in themial and long-term stability that were observed. A second protein which was also studied in this work is the metal binding protein rat oncomodulin. Initially, the unfolding behavior of this protein in aqueous solution was examined. Several single tryptophan mutants of the metal-binding protein rat oncomodulin (OM) were examined; F102W, Y57W, Y65W and the engineered protein CDOM33 which had all 12 residues of the CD loop replaced with a higher affinity binding loop. Both the thermal and the chemical stability were improved upon binding of metal ions with the order apo < Ca^^ < Tb^"^. During thermal denaturation, the transition midpoints (Tun) of Y65W appeared to be the lowest, followed by Y57W and F102W. The placement of the Trp residue in the F-helix in F102W apparently made the protein slightly more thermostable, although the fluorescence response was readily affected by chemical denaturants, which probably acted through the disruption of hydrogen bonds at the Cterminal end of the F-helix. Under both thermal and chemical denaturation, the engineered protein showed the highest stability. This indicated that increasing the number of metal ligating oxygens in the binding site, either by using a metal ion with a higher coordinatenumber (i.e. Tb^*) which binds more carboxylate ligands, or by providing more ligating groups, as in the CDOM33 replacement, produces notable improvements in protein stability. Y57W and CE)OM33 OM were chosen for further studies when encapsulated into sol-gel derived matrices. The kinetics of interaction of terbium with the entrapped proteins, the ability of the entrapped protein to binding terbium, as well as thermal stability of these two entrapped protein were compared with different levels of Ca^"*^ present in the matrix and in solution. Results suggested that for both of the proteins, the response time and the ability to bind terbium could be adjusted by adding excess calcium to the matrix before gelation. However, the less stable protein Y57W only retained at most 45% of its binding ability in solution while the more stable protein CDOM33 was able to retain 100% binding ability. Themially induced denaturation also suggested that CDOM33 showed similar stability to the protein in solution while Y57W was destabilized. All these results suggested that "hard" proteins (i.e. very stable) can easily survive the sol-gel encapsulation process, but "soft" proteins with lower thermodynamic stability may not be able to withstand the sol-gel process. However, it is possible to control many parameters in order to successfully entrap biological molecules into the sol-gel matrices with maxunum retention of activity.

Photothermal Investigations on Certain Plasma Polymerized Thin Films and Near IR Overtone Studies of Some Organic Molecules

Photothermal effect refers to heating of a sample due to the absorption of electromagnetic radiation. Photothermal (PT) heat generation which is an example of energy conversion has in general three kinds of applications. 1. PT material probing 2. PT material processing and 3. PT material destruction. The temperatures involved increases from 1-. 3. Of the above three, PT material probing is the most important in making significant contribution to the field of science and technology. Photothermal material characterization relies on high sensitivity detection techniques to monitor the effects caused by PT material heating of a sample. Photothermal method is a powerful high sensitivity non-contact tool used for non-destructive thermal characterization of materials. The high sensitivity of the photothermal methods has led to its application for analysis of low absorbance samples. Laser calorimetry, photothermal radiometry, pyroelectric technique, photoacoustic technique, photothermal beam deflection technique, etc. come under the broad class ofphotothermal techniques. However the choice of a suitable technique depends upon the nature of the sample, purpose of measurement, nature of light source used, etc. The present investigations are done on polymer thin films employing photothermal beam deflection technique, for the successful determination of their thermal diffusivity. Here the sample is excited by a He-Ne laser (A = 6328...\ ) which acts as the pump beam. Due to the refractive index gradient established in the sample surface and in the adjacent coupling medium, another optical beam called probe beam (diode laser, A= 6500A ) when passed through this region experiences a deflection and is detected using a position sensitive detector and its output is fed to a lock-in amplifier from which the amplitude and phase of the deflection can be directly obtained. The amplitude and phase of the signal is suitably analysed for determining the thermal diffusivity.The production of polymer thin film samples has gained considerable attention for the past few years. Plasma polymerization is an inexpensive tool for fabricating organic thin films. It refers to formation of polymeric materials under the influence of plasma, which is generated by some kind of electric discharge. Here plasma of the monomer vapour is generated by employing radio frequency (MHz) techniques. Plasma polymerization technique results in homogeneous, highly adhesive, thermally stable, pinhole free, dielectric, highly branched and cross-linked polymer films. The possible linkage in the formation of the polymers is suggested by comparing the FTIR spectra of the monomer and the polymer.Near IR overtone investigations on some organic molecules using local mode model are also done. Higher vibrational overtones often provide spectral simplification and greater resolution of peaks corresponding to nonequivalent X-H bonds where X is typically C, N or O. Vibrational overtone spectroscopy of molecules containing X-H oscillators is now a well established tool for molecular investigations. Conformational and steric differences between bonds and structural inequivalence ofCH bonds (methyl, aryl, acetylenic, etc.) are resolvable in the higher overtone spectra. The local mode model in which the X-H oscillators are considered to be loosely coupled anharmonic oscillators has been widely used for the interpretation of overtone spectra. If we are exciting a single local oscillator from the vibrational ground state to the vibrational state v, then the transition energy of the local mode overtone is given by .:lE a......v = A v + B v2 • A plot of .:lE / v versus v will yield A, the local mode frequency as the intercept and B, the local mode diagonal anharmonicity as the slope. Here A - B gives the mechanical frequency XI of the oscillator and B = X2 is the anharmonicity of the bond. The local mode parameters XI and X2 vary for non-equivalent X-H bonds and are sensitive to the inter and intra molecular environment of the X-H oscillator.

Infrared and polarized Raman spectra of Cu(HSeO3)2 • H20 single crystal

Infrared and polarized Raman spectra of Cu(HSeO3) 2 - H20 single crystal have been recorded and analysed. The appearance of non-degenerate Se-OH stretching vibrations in the ~x: and ~y: polarizations of Raman spectra indicate distortion of the HSeO~- ion in the Cu(HSeO3)2 - H20 crystal. The low wavenumber values obtained for the symmetric and asymmetric stretching vibrations of the HSeO 3 ion are consistent with the strong hydrogen bonding and the influence of Jahn-Teller distortion as predicted in X-ray diffraction data. The shifting of the stretching and bending vibrations of the hydroxyl groups and water molecules from the free state values also confirms the strong hydrogen bonding in this crystal. Broad bands observed for both stretching and bending regions become sharp in the Raman spectrum recorded at 77 K. A doublet appears for the Se-OH stretching mode at this temperature indicating the settling of protons in an ordered position and the absence of intrabond proton tunnelling