bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron stimulated oxidation of the Ni(111) surface: Dependence on substrate temperature and incident electron energy
Authors: Stirniman M. J. , Li Wei , Sibener S. J.
Published: July 2002

The effect of surface temperature on the rate of oxidation of the Ni(111) surface with and without electron irradiation has been determined for temperatures between 120 and 340 K. The oxidation rate in the presence of an electron beam demonstrates an inverse dependence on the substrate temperature, while without an electron beam we observe a decrease in oxidation rate with decreasing substrate temperature, decreasing almost to zero at 120 K. Similar rates are observed near room temperature for the two cases. We have found that oxidation of this surface can be well described by either of two rate expressions: one that relates the oxide growth rate to the rate of lateral growth of two dimensional oxide islands, and another that is first order in oxide and oxygen coverages at the surface. The physical implications of each model are discussed in terms of the nucleation sites created by the electron beam, and the rate constants for oxidation at these nucleation sites. We present evidence that the nucleation sites created by the electron beam are metastable, with an unusually long half-life of about 600±150 s. We have also investigated the dependence of the cross section for nucleation center creation as a function of incident electron energy at constant electron flux and constant oxygen exposure. The energy dependencies of the cross section for nucleation center creation and the yield of secondary electrons produced by irradiation from the incident electron beam are compared, leading to consideration of the role that such secondary electrons may have in the creation of nucleation centers. The results presented herein delineate the correct low temperature oxidation kinetics for Ni(111) in the absence of perturbing electrons. They also provide a cautionary note for experiments which use electron-based probes, or optical probes which generate intense swarms of electrons, for studying the oxidation kinetics of metals, and perhaps other classes of interfacial reactions.
Fragmentation of fullerenes in collisions with atomic and molecular targets
Authors: Ehlich R. , Westerburg M. , Campbell E. E. B.
Published: July 2002

Fragmentation cross sections of fullerene cations have been measured as a function of collision energy under single collision conditions. The ions are produced by laser desorption from a C60/C70 substrate. Collision products are analyzed with a linear time of flight mass spectrometer. The collision energy ranges from 5 eV up to more than 150 eV in the center of mass reference frame. A combination of molecular dynamics calculations and statistical RRKM theory has been applied to help understand the nature of the fragmentation dynamics. The results of collisions using different fullerenes as projectiles (C+56, C+58, C+60, C+70) as well as collisions with a range of target gases (Ne, Ar, O2, CO2, (CH2)3, C3H6, SF6) give additional insight into the fragmentation mechanisms. The energy dependence of the fragmentation cross sections can be used to identify exothermic reactions between projectile and target as is shown for the case of molecular oxygen.
The oxidation induced formation of metallocarbohedrene ions
Authors: Deng H. T. , Kerns K. P. , Castleman A. W.
Published: July 2002

Oxidation reactions of titanium metallocarbohedrenes (Met–Cars) and their derivatives are studied using a SIDT–LV (selected ion drift tube with laser vaporization source) and a triple quadrupole mass spectrometer, both operated at near thermal energies. A surprising finding is the selective and sole production of Ti8C+12 in the reactions of neutral metal–carbon species with oxygen. However, no Met–Car ions are formed when these neutral Met–Cars derivatives are interacted with other potentially reactive neutral molecules, including N2O and Cl2. The mechanisms for this oxidation induced ionization are discussed in light of oxidation induced excitation and thermionic emission.
Size dependence of mobility on the surface of metal clusters: Ammonia on Ag10 and Ag16
Authors: Lian Li , Mitchell Steven A. , Hackett Peter A. , Rayner David M.
Published: July 2002

Equilibrium constants for the reactions of NH3 with the silver clusters, Ag10 and Ag16, have been measured in the gas phase as a function of temperature using a cluster flow reactor. The binding enthalpies, ΔH300°=−9.8±1.0 and −15.9±1.0 kcal mol−1, and entropies, ΔS300°=−10.3±3.0 and −23.5±3.0 cal mol−1 K−1, have been obtained for the complexes Ag10NH3 and Ag16NH3, respectively. Statistical mechanics modeling indicates that NH3 is mobile on the surface of Ag10NH3. In contrast, it is locally bound on Ag16. The implication is that the binding mechanism involves only electrostatic interaction on Ag10 and that Ag16 provides a site favorable to a stronger classical chemical lone-pair bond. Thus ammonia may diffuse on Ag10 and be localized on Ag16.
Single and multiple photon ionization of triethylamine
Authors: Mathis J. E. , Compton R. N.
Published: July 2002

Single and multiple photon ionization photoelectron spectroscopy of triethylamine (TEA) was studied using a newly developed high-resolution electron spectrometer which utilizes position sensitive detection. The adiabatic ionization potential of TEA was accurately determined using both single (7.47±0.04 eV) and multiphoton (7.53±0.10 eV) ionization photoelectron spectroscopy. Although excitation to both the S1 and S2 states can occur, multiphoton ionization always occurs out of the S1 state. When the cation dissociates, the distribution of photoelectron energies similarly reflects this partitioning between S1 and S2.
Calculation of free-energy differences from computer simulations of initial and final states
Authors: Hummer Gerhard , Szabo Attila
Published: July 2002

A class of simple expressions of increasing accuracy for the free-energy difference between two states is derived based on numerical thermodynamic integration. The implementation of these formulas requires simulations of the initial and final (and possibly a few intermediate) states. They involve higher free-energy derivatives at these states which are related to the moments of the probability distribution of the perturbation. Given a specified number of such derivatives, these integration formulas are optimal in the sense that they are exact to the highest possible order of free-energy perturbation theory. The utility of this approach is illustrated for the hydration free energy of water. This problem provides a quite stringent test because the free energy is a highly nonlinear function of the charge so that even fourth order perturbation theory gives a very poor estimate of the free-energy change. Our results should prove most useful for complex, computationally demanding problems where free-energy differences arise primarily from changes in the electrostatic interactions (e.g., electron transfer, charging of ions, protonation of amino acids in proteins).
Icosahedra of icosahedra: The stability of (C60)13
Authors: Hansen K. , Hohmann H. , Müller R. , Campbell E. E. B.
Published: July 2002

The relative stability of clusters of fullerenes has been investigated. By heating the clusters before ionization we have obtained mass spectra where only the monomer and (C60)13 are present in significant amounts. An approximately 20% increase of the activation energy for evaporation of a monomer from (C60)13 compared to that from (C60)14 explains the experimental results.
Characterization of CdSe nanocrystallite dispersions by small angle x-ray scattering
Authors: Mattoussi H. , Cumming A. W. , Murray C. B. , Bawendi M. G. , Ober R.
Published: July 2002

We use x-ray scattering at small angles (SAXS) to study interparticle interactions in dilute dispersions of CdSe nanocrystallite particles. In particular, we probe the dependence of these interactions on a few key parameters, including the nature of the cap molecules attached to the surface of the particles and the solvent. Alkyl capped nanocrystallites with relatively long hydrocarbon chains are stable in a range of solvents. Nanocrystallites capped with smaller molecules show attractive interparticle interactions. Existence of association (e.g., dimers and trimers) in dispersions characterized by attractive interactions is observed in the scattering data for pyridine capped particles.
Phase transitions in molecular clusters
Authors: Acevedo Anita J. , Caballero Linnette M. , López Gustavo E.
Published: July 2002

Using classical Monte Carlo techniques, anomalies in the constant volume heat capacity as a function of temperature are observed for (CO)5 and (N2)5. These anomalies have been related to cluster phase transitions. The usual solid–liquid coexistence region is observed for both systems. However, for (CO)5 a low-temperature phase transition is observed that is associated with an orientational change in the molecular components of the system. Root-mean-square bond fluctuations and distribution of potential energies are used to characterize the various phase transitions.
A reexamination of the hydrophobic effect: Exploring the role of the solvent model in computing the methane–methane potential of mean force
Authors: Young William S. , Brooks III Charles L.
Published: July 2002

Molecular dynamics simulations are used to examine the role of explicit electronic polarization on the computed potential of mean force (PMF) for methane–methane association in water. Calculations were performed using the same simulation protocol with three different water models: the TIP3P model [J. Chem. Phys. 79, 926 (1983)], the TIP4P model [J. Chem. Phys. 79, 926 (1983)], and a polarizable version of the TIP4P model [J. Chem. Phys. 95, 7556 (1988)]. By computing the PMF for methane–methane association in three different water models, we are able to isolate effects that arise from the inherent structure of the water model versus those that are a result of adding explicit electronic polarization to the water model. We observe links between the structuring of the solvent and the computed PMF for methane–methane association. These results suggest that for the water models used, the inherent structure of the water model has a greater effect on the methane–methane PMF than does solvent polarizability.
Excited state dynamics with nonadiabatic transitions for model photoinduced proton-coupled electron transfer reactions
Authors: Fang Jian-Yun , Hammes-Schiffer Sharon
Published: July 2002

Photoinduced proton-coupled electron transfer is investigated for a minimal model consisting of three coupled degrees of freedom that represent an electron, a proton, and a collective solvent coordinate. Altering the parameters in this model generates a wide range of proton-coupled electron transfer (PCET) dynamics. Four different models are presented in this paper. Three of these models represent sequential mechanisms and one represents a concerted mechanism. The adiabatic potential energy curves as a function of solvent coordinate and the corresponding two-dimensional wave functions, which depend on both the proton and the electron coordinates, are calculated in order to study the possible mechanisms of photoinduced PCET. The surface hopping method “molecular dynamics with quantum transitions” (MDQT), which incorporates nonadiabatic transitions between adiabatic quantum states, is utilized to simulate the dynamics of photoinitiated PCET for two of these model systems. In this application of MDQT the proton and electron coordinates are treated quantum mechanically, and the solvent coordinate is treated classically. A relatively large number (e.g., 11) of mixed proton/electron adiabatic states are included in the MDQT simulations. The reaction is initiated on the electronically excited state, and many different dynamical pathways to lower energy stable states are observed. Nonadiabatic effects are shown to play an essential role in determining the rates and mechanisms of photoinduced PCET reactions. This paper differs from previous studies of PCET reactions in that it presents real-time nonadiabatic molecular dynamics simulations of model PCET reactions initiated on an electronically excited state.
Accurate quantum calculations of thermal rate constants employing MCTDH: H2+OH→H+H2O and D2+OH→D+DOH
Authors: Matzkies Frank , Manthe Uwe
Published: July 2002

An improved approach for the direct calculation of thermal rate constants, employing the multi-configurational time-dependent Hartree (MCTDH) approach and the flux–flux correlation function, is presented. In this approach, the thermal flux operator is diagonalized and its eigenstates are propagated. The cumulative reaction probability is obtained for all energies simultaneously by a simple Fourier transform of the matrix elements between the propagated flux eigenstates. Calculations for the H2+OH→H+H2O reaction, which include all six internal degrees of freedom accurately, demonstrate the accuracy and efficiency of the approach. Previous results for the rate constant are reproduced (for temperatures between 300 K and 600 K) and extended towards lower temperatures (200 K to 300 K). Also, thermal rate constants of the D2+OH→D+DOH reaction have been computed. All six internal degrees of freedom are included accurately in this calculation. The kinetic isotope effect is obtained and compared to experiment.
The NO2 vibronic levels near the X 2A1–A 2B2 conical intersection observed by laser induced dispersed fluorescence
Authors: Kirmse Bernd , Delon Antoine , Jost Remy
Published: July 2002

Following our previous laser induced dispersed fluorescence (LIDFS) study on NO2 [J. Chem. Phys. 95, 5686 (1991)], we observed the vibronic levels up to 13 900 cm−1 by LIDFS. These observations allow one to characterize the effect of the conical intersection between the X 2A1 and A 2B2 electronic potential energy surfaces (PESs). This effect has been investigated by ab initio methods in the same range by Leonardi et al. [J. Chem. Phys. 105, 9051 (1996)]. Globally we observed 420 vibronic levels of A1 or B2 symmetry up to 13 900 cm−1, while 259 were observed previously up to 12 000 cm−1. Most of these levels belong to the X 2A1 state and only 8 to the A 2B2 state. Below 12 000 cm−1, most of the levels belonging to the X 2A1 state have been vibrationally assigned and only a few are significantly mixed with those of the A 2B2 state. In contrast, each vibrational level of the A 2B2 state is mixed with few nearby high vibrational levels of the X 2A1 state via vibronic interactions. The set of the X 2A1 vibrational levels is assigned and completed up to 11 700 cm−1 for the a1 vibrational symmetry (171 levels) and up to 11 000 cm−1 for the b2 symmetry (104 levels). Above these energies the X 2A1–A 2B2 vibronic interactions preclude secure vibrational assignment of most of the levels. The dominant electronic and vibrational characters have been used for the assignments of some levels. The set of zero order vibrational levels of the A 2B2 state can be described by polyads because there is an approximate 2:1:2 ratio between the three vibrational frequencies. The four lowest polyads of B2 vibronic symmetry are analyzed. In addition to the previously observed vibrationless level (0,0,0) of the A 2B2 state (first polyad), the vibrational levels (0,1,0) (second polyad), (0,0,1) or (1,0,0), and (0,2,0) (third polyad) and (0,3,0) (belonging to the fourth polyad) have been observed. Numerous vibronic levels, previously observed by absorption (ICLAS) and/or by LIF, have also been observed by LIDFS. A semiquantitative analysis of these vibronic interactions is presented. The A and B̄ rotational constants of numerous vibrational levels have also been measured. Globally, these results allow a better understanding of the low energy range of X 2A1–A 2B2 vibronic interaction.
An accurate equation of state for the exponential-6 fluid applied to dense supercritical nitrogen
Authors: Fried Laurence E. , Howard W. Michael
Published: July 2002

The exponential-6 potential model is widely used in fluid equation of state studies. We have developed an accurate and efficient complete equation of state for the exponential-6 fluid based on HMSA integral equation theory and Monte Carlo calculations. Our equation of state has average fractional error of 0.2% in pV/NkBT and 0.3% in the excess energy Uex/NkBT. This is a substantial improvement in accuracy over perturbation methods, which are typically used in treatments of dense fluid equations of state. We have applied our equation of state to the problem of dense supercritical N2. We find that we are able to accurately reproduce a wide range of material properties with our model, over a range 0.01⩽P⩽100 GPa and 298⩽T⩽15 000 K.
Femtosecond ultraviolet-visible absorption study of all-trans→13-cis⋅9-cis photoisomerization of retinal
Authors: Yamaguchi Shoichi , Hamaguchi Hiro-o
Published: July 2002

The all-trans→13-cis⋅9-cis photoisomerization reaction of retinal in aerated nonpolar solvents has been studied by femtosecond time-resolved ultraviolet-visible (UV-VIS) absorption spectroscopy. The excited-state absorption spectra in the wavelength region 400–800 nm indicate that there is no all-trans→13-cis⋅9-cis isomerization reaction pathway that is complete in the electronic excited singlet manifold of S1, S2, and S3. The ground-state bleaching recovery of all-trans retinal monitored in the near UV (ultraviolet) wavelength region 310–390 nm shows that a perpendicular excited singlet state (p*) takes part in the all-trans→13-cis⋅9-cis isomerization reaction. The lifetime of p* is about 7 ps, and the precursor of p* is most probably the S2 state. The isomerization quantum yield derived from the femtosecond UV absorption data agrees well with those determined by the HPLC analysis of the photoproduct. The temperature dependence of the isomerization quantum yield indicates the existence of a potential-energy barrier as high as (1.2±0.6)×103 cm−1 on the reaction pathway from the S2 state to the p* state.
Mechanism of platinum-enhanced oxidation of silicon at low temperatures
Authors: Kobayashi Hikaru , Yuasa Toshiro , Yamanaka Kazuhiro , Yoneda Kenji , Todokoro Yoshihiro
Published: July 2002

The mechanism of platinum (Pt)-enhanced oxidation of Si below 300 °C has been investigated by means of high-resolution x-ray photoelectron spectroscopy. When a Pt layer is deposited on the ∼1-nm-thick silicon oxide-covered Si, low-temperature heat treatment grows the silicon oxide layer between the Pt layer and the Si substrate, while silicon oxide is formed mainly on the Pt layer in cases where Pt is directly deposited on the Si substrate. Oxidation is enhanced by the application of a positive bias voltage to the Si substrate with respect to the Pt layer during the heat treatment of the specimens with 〈∼4 nm Pt/silicon oxide/Si(100)〉 structure in oxygen, and in this case, a ∼8-nm-thick oxide layer is formed at 300 °C for 2 h. It demonstrates that oxygen ions are the moving species in the oxide layer. The plots of oxide thickness with respect to oxidation time are linear in the oxide thickness region below 3∼4 nm, indicating that the reaction at the interface is the rate-determining step. The activation energy for the interfacial reaction is estimated to be ∼0.55 eV: much lower than that for oxidation through reaction with oxygen molecules of ∼2 eV. The plots for the subsequent oxidation stage are expressed by logarithmic functions, showing that the migration of oxygen ions in the oxide layer is the rate-limiting process.
Ion binding in tobacco mosaic virus solutions
Authors: Shew Chwen-Yang , Yethiraj Arun
Published: July 2002

The structure of salt-free solutions of tobacco mosaic virus particles is investigated using integral equations with the counterions incorporated explicitly. The results for the structure factor are identical to previous studies which used a Debye–Hückel approximation. The results are explained using a model of the particles as polyacids.
On mean residence and first passage times in finite one-dimensional systems
Authors: Bar-Haim Arie , Klafter Joseph
Published: July 2002

We present a simple derivation of mean residence times (MRTs) and mean first passage times (MFPTs) for random walks in finite one-dimensional systems. The derivation is based on the analysis of the inverse matrix of transition rates which represents the random walk rate equations. The dependence of the MRT and of the MFPT on the initial condition, on the system size, and on the elementary rates is studied and a relationship to stationary solutions is established. Applications to models of light harvesting by supermolecules, and of random barriers, and to relaxation in the Ehrenfest model are discussed in detail. We propose a way to control the MFPT in supermolecules, such as dendrimers, via molecular architecture.
A novel dynamic free-volume theory for molecular diffusion in fluids and interphases
Authors: Xiang Tian-Xiang
Published: July 2002

A novel dynamic free-volume theory is developed to account for the influence of solvent mobility on molecular diffusion in a condensed solvent. In this theory, the diffusion process is viewed as consisting of three sequential steps of opening up a free volume, moving the diffusant into this new free volume, and filling up the position previously occupied by the diffusant. As a fundamental assumption, the time for an elementary diffusive motion is considered to be the summation of the characteristic times for the above three steps. On the basis of this and other assumptions, theoretical formulations for the diffusion coefficients in simple fluids, polymers, and interphases are derived. The model agrees qualitatively with numerous experimental findings with respect to changes of molecular diffusivity with solvent mean free-volume, temperature, and diffusant size. In the mean time, molecular-dynamics simulations of solute diffusion in a monatomic fluid and a lipid membrane are conducted to investigate the influences of solvent relaxation and solute kinetic rates on solute diffusion. The diffusion coefficient is found to depend only weakly on the kinetic velocity of solute as characterized by solute mass but change strongly with solvent mass in the simple fluid and with the chain isomerization time in the lipid bilayer. These findings are in conflict with the previous free-volume theories and the Enskog kinetic theory, but can be described satisfactorily by our present theory.
Time- and frequency-resolved coherent two-dimensional IR spectroscopy: Its complementary relationship with the coherent two-dimensional Raman scattering spectroscopy
Authors: Park Kisam , Cho Minhaeng
Published: July 2002

A theoretical description of the coherent two-dimensional IR spectroscopy is presented. Two consecutive IR pulses can be used to create two consecutive vibrational coherence states. The third off-resonant optical pulse is used to probe the two-dimensional transient grating thus created and then the scattered field is measured. The corresponding nonlinear response functions are obtained in the analytic forms by assuming that the vibrational modes are weakly anharmonic Brownian oscillators. Since one can experimentally control the two delay times as well as the two IR field frequencies, it is possible to extract vital information on the vibrational relaxation in time domain as well as the intra- and intermolecular vibrational mode couplings in frequency domain. Numerical calculations are carried out to clarify the quantitative features of the coherent 2D IR spectroscopic phenomenon.
Magnetic interactions between a [4Fe–4S]1+ cluster and a flavin mononucleotide radical in the enzyme trimethylamine dehydrogenase: A high-field electron paramagnetic resonance study
Authors: Fournel Andre , Gambarelli Serge , Guigliarelli Bruno , More Claude , Asso Marcel , Chouteau Gerard , Hille Russ , Bertrand Patrick
Published: July 2002

Trimethylamine dehydrogenase is a bacterial enzyme which contains two redox centers: a flavin mononucleotide (FMN) group which constitutes the active site and a [4Fe–4S]1+,2+ cluster which transfers the electrons provided by the FMN to an electron-transferring flavoprotein. According to the x-ray crystal structure, the center-to-center distance is equal to 12 Å and the nearest atoms of the two centers are separated by a 4 Å gap. Although this arrangement does not appear especially favorable for mediating strong magnetic interactions, a triplet state electron paramagnetic resonance (EPR) spectrum arising from the intercenter magnetic coupling is observed at X band (9 GHz) when the enzyme is reduced by its substrate. In earlier work, the temperature dependence of this spectrum and its analysis based on a triplet state spin Hamiltonian were used to propose the range (0.8–100 cm−1) for the parameter J0 of the isotropic interaction J0SA.SB, but neither the magnitude of J0 nor its sign could be further specified [R. C. Stevenson, W. R. Dunham, R. H. Sands, T. P. Singer, and H. Beinert, Biochim. Biophys. Acta 869, 81 (1986)]. In the present work, we have studied the interaction EPR spectrum in the range 9–340 GHz. Numerical simulations based on a spin Hamiltonian describing a system of two S=1/2 interacting spins allowed us to determine the full set of parameters describing the magnetic interactions between the FMN radical and the [4Fe–4S]1+ cluster. In particular, our study demonstrates that the coupling is antiferromagnetic with J0=+0.72 cm−1. Although this value corresponds to the lower limit of the range proposed previously, it still appears markedly larger than those measured in biological systems in which a similar arrangement of two paramagnetic centers is found.
Accurate reaction rate calculations including internal and rotational motion: A statistical multi-configurational time-dependent Hartree approach
Authors: Matzkies Frank , Manthe Uwe
Published: July 2002

A statistical approach to the direct calculation of thermal rate constants and cumulative reaction probabilities based on flux correlation functions is presented. It facilitates the accurate treatment of rotational and low frequency vibrational motion in rate constant calculations. Within this approach, a statistical sampling scheme is used to evaluate the trace in the flux correlation function and the multi-configurational time-dependent Hartree (MCTDH) approach is employed to simulate the system dynamics. The OH+Cl→O+HCl reaction is studied to demonstrate the efficiency of the approach. Known results for vanishing total angular, J=0, are reproduced. Moreover, thermal rate constants are calculated including all internal and rotational degrees of freedom explicitly, i.e., without invoking a J-shifting or K-conserving approximation. Based on these results, the accuracy of the J-shifting approximation is discussed.
A direct transform for the nuclear magnetic resonance chemical shift anisotropy
Authors: de Swiet Thomas M.
Published: July 2002

A direct transform of the NMR chemical shift anisotropy, operating on data acquired under magic angle spinning conditions, yielding rotationally invariant quantities, is potentially a source of increased resolution in solid state NMR. The mathematical basis for such a transform is discussed by exploiting an analogy with projection reconstruction. A specific example of the kind of pulse sequence required is given, and optimal sampling of the data is discussed.
Analytical energy gradients of a self-consistent reaction-field solvation model based on CM2 atomic charges
Authors: Zhu Tianhai , Li Jiabo , Liotard Daniel A. , Cramer Christopher J. , Truhlar Donald G.
Published: July 2002

Analytical energy gradients have been derived for an SM5-type solvation model based on Hartree–Fock self-consistent reaction-field theory and CM2 atomic charges. The method is combined with an analytic treatment of the first derivatives of nonelectrostatic first-solvation-shell contributions to the free energy and implemented in the General Atomic and Molecular Electronic Structure System (GAMESS). The resulting equations allow one to use accurate class IV charges to calculate equilibrium geometries of solutes in liquid-phase solutions. The algorithm is illustrated by calculations of optimized geometries and solvation free energies for water, methanol, dimethyl disulfide, and 9-methyladenine in water and 1-octanol.
Glassy dynamics in DNA: Ruled by water of hydration?
Authors: Sokolov A. P. , Grimm H. , Kahn R.
Published: July 2002

Inelastic neutron scattering spectra of DNA-fibers are analyzed using ideas formulated recently in the field of the glass transition. The analysis reveals two temperatures, namely, T∼180–200 K and T∼230 K, at which the dynamics of DNA exhibits qualitative changes. The former is similar to the glass transition temperature, whereas the latter is similar to the crossover temperature recognized now as an important point for the dynamics of the glass transition. Exactly in this temperature range many other hydrated biopolymers show some dynamic transition and strong slowing down of their functions. The crossover temperature appears to be close to the crossover temperature of bulk water. A possible relation of the dynamic transition to functions of biomolecules and also to the dynamic transition in the hydration shell is discussed.
Theory and numerical calculation of pattern formation in shrinking gels
Authors: Maskawa Jun-ichi , Takeuchi Toshiki , Maki Kazuo , Tsujii Kaoru , Tanaka Toyoichi
Published: July 2002

We discuss pattern formation in three-dimensional gels with cylindrical shapes during their shrinking such as volume phase transition. A Ginzburg–Landau theory is given for the pattern formation in shrinking gels. A characteristic feature in shrinking gels is the dense layer formed around the gel surface in the early stage of phase transition. This layer reduce considerably permeation of solvent and the shrinkage practically stops. We introduce the external osmotic pressure and the external elastic stress acting on the gel surface in order to take account of the effect of the layer. Patterns are classified according to the anisotropy and the incompressibility of gels by the linearized stability analysis of the theory. It appears that the external stress term suppresses the growth of the fluctuation with short wavelength. The results obtained by a numerical calculation for the evolution of patterns are also shown.
Electronic states and transitions of bismuth sulfide
Authors: Lingott Rainer M. , Liebermann Heinz-Peter , Alekseyev Aleksey B. , Buenker Robert J.
Published: July 2002

The electronic spectrum of the BiS molecule is described by means of relativistic configuration interaction (CI) calculations employing effective core potentials. Spin-orbit coupling causes the Ω=3/2 components of the X 2Π and A 4Π Λ–S states to undergo an avoided crossing which causes perturbations to occur in the observed X2–X1 band system beginning at v′=5. The present calculations are able to explain these results on a nearly quantitative basis. Spectroscopic constants are computed for nine BiS states up to 20 000 cm−1 and generally good agreement is found between theoretical and available measured values. Four of these states have not yet been observed experimentally and thus the present results should aid in subsequent searches for them. In addition, radiative lifetimes and electric dipole moments have been calculated for each of the BiS states with the relativistic CI wave functions. Finally, these results have been compared in detail with the analogous spectral data for the isovalent BiO molecule.
Femtosecond photoionization of (H2O)n and (D2O)n clusters
Authors: Radi P. P. , Beaud P. , Franzke D. , Frey H.-M. , Gerber T. , Mischler B. , Tzannis A.-P.
Published: July 2002

Cluster ion distributions of water in a molecular beam are investigated by femtosecond ionization at 780 nm and reflectron time-of-flight mass spectrometry. The electric field strength generated by the ultrashort laser pulses is sufficient to efficiently ionize most of the molecules that are present in the molecular beam. In this work ion signals of large water clusters containing up to 60 monomers are reported. Upon ionization rapid proton transfer is observed, leading to the formation of protonated water cluster ions. Unprotonated clusters (H2O)n+(n>2) are not observed in the mass spectra. The configurational energy imparted to the protonated clusters induces unimolecular dissociation on the μs time scale. These metastable reactions are characterized by modeling the ion trajectories in the mass spectrometer. The numerical procedure in conjunction with the integrated parent and daughter intensities results in unimolecular dissociation rates as a function of cluster size. Additional information about proton transfer reactions is obtained by the investigation of deuterium substitutions. Even though these substitutions correspond to large relative changes in the mass of the atom as well as in the zero point energy, unprotonated (D2O)n+ clusters of significant abundance are not produced in supersonic expansions of deuterated water. An additional result of this work is the observation of doubly charged ions above a critical cluster size (n=37).
One-dimensional arrays of oscillators: Energy localization in thermal equilibrium
Authors: Reigada Ramon , Romero Aldo H. , Sarmiento Antonio , Lindenberg Katja
Published: July 2002

All systems in thermal equilibrium exhibit a spatially variable energy landscape due to thermal fluctuations. Thus at any instant there is naturally a thermodynamically driven localization of energy in parts of the system relative to other parts of the system. The specific characteristics of the spatial landscape such as, for example, the energy variance, depend on the thermodynamic properties of the system and vary from one system to another. The temporal persistence of a given energy landscape, that is, the way in which energy fluctuations (high or low) decay toward the thermal mean, depends on the dynamical features of the system. We discuss the spatial and temporal characteristics of spontaneous energy localization in 1D anharmonic chains in thermal equilibrium.
Crossed beam reaction of cyano radicals with hydrocarbon molecules. I. Chemical dynamics of cyanobenzene (C6H5CN; X 1A1) and perdeutero cyanobenzene (C6D5CN; X 1A1) formation from reaction of CN(X 2Σ+) with benzene C6H6(X 1A1g), and d6-benzene C6D6(X 1A1g)
Authors: Balucani N. , Asvany O. , Chang A. H. H. , Lin S. H. , Lee Y. T. , Kaiser R. I. , Bettinger H. F. , Schleyer P. v. R. , Schaefer H. F.
Published: July 2002

The chemical reaction dynamics to form cyanobenzene C6H5CN(X 1A1), and perdeutero cyanobenzene C6D5CN(X 1A1) via the neutral–neutral reaction of the cyano radical CN(X 2Σ+), with benzene C6H6(X 1A1g) and perdeutero benzene C6D6(X 1A1g), were investigated in crossed molecular beam experiments at collision energies between 19.5 and 34.4 kJ mol−1. The laboratory angular distributions and time-of-flight spectra of the products were recorded at mass to charge ratios m/e=103–98 and 108–98, respectively. Forward-convolution fitting of our experimental data together with electronic structure calculations (B3LYP/6−311+G**) indicate that the reaction is without entrance barrier and governed by an initial attack of the CN radical on the carbon side to the aromatic π electron density of the benzene molecule to form a Cs symmetric C6H6CN(C6D6CN) complex. At all collision energies, the center-of-mass angular distributions are forward–backward symmetric and peak at π/2. This shape documents that the decomposing intermediate has a lifetime longer than its rotational period. The H/D atom is emitted almost perpendicular to the C6H5CN plane, giving preferentially sideways scattering. This experimental finding can be rationalized in light of the electronic structure calculations depicting a H–C–C angle of 101.2° in the exit transition state. The latter is found to be tight and located about 32.8 kJ mol−1 above the products. Our experimentally determined reaction exothermicity of 80–95 kJ mol−1 is in good agreement with the theoretically calculated one of 94.6 kJ mol−1. Neither the C6H6CN adduct nor the stable iso cyanobenzene isomer C6H5NC were found to contribute to the scattering signal. The experimental identification of cyanobenzene gives a strong background for the title reaction to be included with more confidence in reaction networks modeling the chemistry in dark, molecular clouds, outflow of dying carbon stars, hot molecular cores, as well as the atmosphere of hydrocarbon rich planets and satellites such as Saturn’s moon Titan. This reaction might further present a barrierless route to the formation of heteropolycyclic aromatic hydrocarbons via cyanobenzene in these extraterrestrial environments as well as hydrocarbon rich flames.
Interactive forces on Aerosol-OT/n-hexane/water/urea reversed micelles by small angle x-ray scattering
Authors: Itri Rosangela , Amaral Carmen Lúcia Costa , Politi Mário José
Published: July 2002

The influence of urea on Aerosol-OT (AOT)/n-hexane/water reversed micelles (RMs) at molar concentration ratio [water]/[AOT]=10 is investigated by means of small angle x-ray scattering. The data are analyzed within the framework of repulsion and attractive interaction potentials through the sticky hard-sphere model. In the absence of urea the simple hard sphere (excluded volume) model applies up to RM volume fraction φ of 0.32. In the presence of 5M urea, the x-ray curves evidence a big influence of the attractive forces in the system for φ=0.06, in good agreement with previous light scattering results, without disturbing the RM structure (shape and size). When φ exceeds this value, a percolation phenomenon is observed by ionic conductance measurements. In addition, the data show an interplay between attractive and repulsive RM interactions at higher φ values, with preservation of the discrete RM structure, without the formation of a “long-lived” bicontinuous phase.
Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling
Authors: Bartels Christian , Schaefer Michael , Karplus Martin
Published: July 2002

Two-dimensional adaptive umbrella sampling with the first umbrella coordinate equal to the potential energy of the system and the second umbrella coordinate equal to a function that discriminates important folded conformations from unfolded conformations is used to determine the equilibrium properties of complex biological systems. Compared to one-dimensional adaptive umbrella sampling with the potential energy as umbrella coordinate (multicanonical sampling), more reliable results can be obtained in certain cases. The method is applied to a helical peptide (RN24) with an analytical continuum solvent potential in combination with the PARAM19 force field of CHARMM. This effective potential energy function has been shown to describe the structural preferences of solvated peptides. With the two-dimensional approach and the deviation from the helical structure as the second umbrella coordinate, a converged description of the structural properties and the thermodynamics of the peptide RN24 is obtained. In particular, we find that the formation of the helix of RN24 occurs as a transition accompanied by a characteristic peak in the heat capacity. A formalism is described that uses the weighting factors obtained from a self-consistent solution of the weighted histogram analysis method equations to combine the results from a series of simulations with different biases and calculate the ensemble average of any dynamical variable as a function of the temperature without the need for extracting the density of states from the simulations. It is shown how the formalism can be used to calculate thermodynamic properties of the system.
A characterization of vibrationally and electronically excited NO2+ by high-resolution threshold photoionization spectroscopy
Authors: Jarvis G. K. , Song Y. , Ng C. Y. , Grant E. R.
Published: July 2002

The pulsed-field ionization zero-electron kinetic-energy (PFI-ZEKE) threshold photoionization spectrum of NO2 from 9.58 to 20 eV is obtained using vacuum ultraviolet synchrotron radiation by means of the Chemical Dynamics Beamline at the Lawrence Berkeley National Laboratory Advanced Light Source. The high resolution afforded by PFI threshold discrimination yields new or refined spectroscopic constants for a number of known excited states of the cation, including the first estimate of the A rotational constant in the a 3B2 state, as well as new fundamental frequencies for the A 1A2 and B 1B2 states, a precise determination of the singlet–triplet splitting in the c 3B1–C 1B1 complex and the first observations of the states, d 3A1 and D 1B2. Most significantly, ZEKE photoelectron detection resolves vibrational structure in the linear X 1Σg+ ground state of NO2+. Vibrational positions in the first electron volt of the spectrum are found to conform with the predictions of a Hamiltonian that includes Fermi resonance and other anharmonic terms derived from earlier multiresonant laser spectroscopic experiments on the lower bending excited states.
A molecular dynamics study of the urea/water mixture
Authors: Idrissi Abdenacer , Sokolić Franjo , Perera Aurélien
Published: July 2002

The short time dynamics of the water–urea mixture is studied herein by molecular dynamics simulations. The local anisotropy of the dynamical properties arising from the highly directional hydrogen bonding interactions and their modification under the influence of increasing the urea concentration is the major focus of the present report. Study of the direction dependant translation and rotation self-diffusion coefficients of both species, as well as that of velocity autocorrelation functions and corresponding power spectra, indicate that the addition of urea leads to an overall isotropy and stiffening of the short time dynamics of both species. It is speculated that some of the well-known properties of the urea/water mixture, such as the denaturation of proteins for example, could find an explanation in these features.
Conserved linking in single- and double-stranded polymers
Authors: Plewa Joseph S. , Witten Thomas A.
Published: July 2002

We demonstrate a variant of the bond fluctuation lattice Monte Carlo model in which moves through cis conformations are forbidden. Ring polymers in this model have a conserved quantity that amounts to a topological linking number. Increased linking number reduces the radius of gyration mildly. A linking number of order 0.2 per bond leads to an 8% reduction of the radius for 128-bond chains. This percentage appears to rise with increasing chain length, contrary to expectation. For ring chains evolving without the conservation of linking number, we demonstrate a substantial anticorrelation between the twist and writhe variables whose sum yields the linking number. We raise the possibility that our observed anticorrelations may have counterparts in the most important practical polymer that conserves linking number, DNA.
Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach
Authors: Kovalenko Andriy , Hirata Fumio
Published: July 2002

We adapt the three-dimensional reference interaction site model (3D-RISM) to calculate the potentials of mean force for ion–molecular solution as a difference between the chemical potential of solvation of a cluster of solutes and of individual ones. The method yields the solvation structure around the cluster of solutes in detail. The solvation chemical potential is obtained for the three-dimensional hypernetted chain (3D-HNC) closure as well as for its partial linearization (3D-PLHNC approximation). The solvation chemical potential is obtained in a closed analytical form for both the 3D-HNC and 3D-PLHNC closures. The 3D-RISM integral equations are solved by using the supercell technique. A straightforward supercell treatment of ionic solute in polar molecular solvent leads to a big error in the potential of mean force as well as the solvation chemical potential, which for simple ions in water amounts to about 35 kcal/mol. We elaborated corrections to the 3D-RISM integral equations, alleviating the artifact of the supercell periodicity with an accuracy of 0.05 kcal/mol or better and restoring the long-range asymptotics of the solute–solvent correlation functions. The dielectrically consistent site–site RISM/HNC theory (DRISM/HNC) is employed for the solvent correlations to provide a proper description of the dielectric properties of solution. This allowed us to extend the description to solution at a finite salt concentration. We converge both the 3D-RISM and site–site DRISM integral equations by using the method of modified direct inversion in the iterative subspace. Owing to the proper initial guess of the correlation functions, iteration begins at once for a given temperature and full molecular charge, avoiding a gradual decrease of the temperature and increase of the site charges, which greatly reduces the computation time. We calculate and discuss the potentials of mean force for sodium chloride in ambient water at infinite dilution as well as at a finite concentration.
Microwave spectrum and molecular structure of the HSC radical
Authors: Habara Hideta , Yamamoto Satoshi
Published: July 2002

The HSC radical, that is a geometrical isomer of the HCS radical, has been identified and characterized by microwave spectroscopy. The HSC radical has been produced in a discharge plasma of a gaseous mixture of H2S and CO, and its rotational spectral lines are observed with a source-modulation spectrometer and a Fourier-transform millimeter-wave spectrometer. The spectrum of the deuterated species, DSC, has also been measured with a source-modulation spectrometer. Rotational constants, centrifugal distortion constants, and spin–rotation interaction constants with their centrifugal distortion corrections for HSC and DSC are determined from the observed transition frequencies by a least-squares method. Furthermore hyperfine interaction constants of the hydrogen nucleus are also determined for HSC. The Fermi contact term of the hydrogen nucleus takes a large positive value, 288.845±0.185 MHz, which indicates that the HSC radical is a σ radical (2A′) in the ground electronic state. The harmonic force field is evaluated from the obtained centrifugal distortion constants and inertial defects. The zero-point vibrational average structure is determined as follows; rz(H–S)=1.390±0.003 Å, rz(S–C)=1.6403±0.0005 Å and αz(HSC)=104.2±0.2°.
An efficient method for calculating molecular excitation energies by time-dependent density-functional theory
Authors: Heinze Habbo H. , Görling Andreas , Rösch Notker
Published: July 2002

We present a new efficient method for determining excitation energies and oscillator strengths of molecules which is based on time-dependent density functional theory (TDDFT). It yields the valence excitation spectrum of a molecule at a fraction of the computational effort necessary for the corresponding ground state calculation. The efficiency of the method originates in the extensive use of auxiliary basis sets. Nevertheless this approach does not lead to significant inaccuracies. The method is applied to benzene, naphtalene, and the higher linearly annelated polycyclic aromatic hydrocarbons anthracene to heptacene. Features and trends in the excitation spectra of these aromatic hydrocarbons are well described by the new TDDFT method. The standard basis sets commonly used in TDDFT based procedures are found to be inadequate for an accurate treatment of excitations into Rydberg-type states.
On information gain by quantum measurements of continuous observables
Authors: Ozawa Masanao
Published: July 2002

A generalization of Shannon’s amount of information into quantum measurements of continuous observables is introduced. A necessary and sufficient condition for measuring processes to have a non-negative amount of information is obtained. This resolves Groenewold’s conjecture completely including the case of measurements of continuous observables. As an application the approximate position measuring process considered by von Neumann and later by Davies is shown to have a non-negative amount of information.