The Journal of Chemical Physics

Published by American Institute of Physics
Online ISSN: 1089-7690
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Article
We compare three different simple models for water. They all show a phase behavior and anomalies that are characteristic of water. We compare these models and their features and evaluate the phase diagram, the density anomaly, and the liquid-liquid transition line. Additionally, we show that the characteristic behavior present in all three models can be deduced from the fact that all three models include three microscopic states for nearest neighbor configurations. We therefore propose an even simpler three-state model for water that still captures the phase transitions and the density anomaly. Finally, we show that this simple three-state model shows in fact all four possible scenarios discussed in the literature for the phase behavior of liquid water, if the parameters are adjusted accordingly.
 
Article
We present a linear-response approach for time-dependent density-functional theories using time-adiabatic functionals. The resulting theory can be performed both in the time and in the frequency domain. The derivation considers an impulsive perturbation after which the Kohn-Sham orbitals develop in time autonomously. The equation describing the evolution is not strictly linear in the wave function representation. Only after going into a symplectic real-spinor representation does the linearity make itself explicit. For performing the numerical integration of the resulting equations, yielding the linear response in time, we develop a modified Chebyshev expansion approach. The frequency domain is easily accessible as well by changing the coefficients of the Chebyshev polynomial, yielding the expansion of a formal symplectic Green's operator.
 
Article
The determination of state population probability within the framework of time-dependent density functional theory (TDDFT) has remained a widely open question. The aim of this study is to find out whether and how this probability can be extracted from time-dependent density, which has been used as the basic variable within TDDFT. We propose an effective method to calculate state population probabilities, which has been well validated in benchmark case studies on nonresonant (detuned) Rabi oscillations of a Na atom, Na2 dimer, and Na4 cluster irradiated by a monochromatic laser.
 
Article
The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.
 
Article
Free-volume theory for understanding depletion phenomena in mixtures of two species is generally derived using scaled-particle theory for those specific entities. Here we first give a general scaled-particle method for convex bodies in terms of the characteristic geometrical measures of the depletion agent, i.e., its volume, surface area, and integrated mean curvature, in mixtures with hard spheres. Second, we show that similar results can be derived from fundamental-measure theory. This different approach allows us to get a deep insight into the meaning of the various contributions to the theory from a geometrical point of view. From these two methods we arrive at a generalized "recipe" to free-volume theory. This recipe can be based on a desired equation of state for any convex shape of the depletion agents and is also valid for (polydisperse) mixtures of those. This is illustrated by mixtures of spheres with ellipsoids, spheres with several geometries as models for disklike mesogens, e.g., gibbsite, as well as depletion of spheres due to bar-shaped colloids, e.g., goethite.
 
The ratio I  NET /I  NC  on a logarithmic scale versus 1000/T. The dashed line through the data represents the linear least-squares fit. Error bars are comparable to the data symbol size.
The measured FTIR spectra in the water lysozyme system with the hydration level h = 0.3, at three different temperatures; respectively, in the native state below (T = 190 K (a)) and above (T = 300 K (b)) the protein dynamical crossover and finally in the irreversible denatured state (T = 350 K (c)). The figure shows the water and the peptide (amide I, II, and III) components.
The temperature behaviors of the extracted FWHM of the water bending (top panel) and of the amide II components (bottom panel) for hydrated lysozyme samples (h = 0.3 and 0.37). Data measured in bulk and water confined in nanotubes are also reported. Circles regard the contribution of fully bonded molecules belonging to the HB tetrahedral network (or LDL at ∼1560 cm−1) whereas triangles represent the remaining part (HDL). For the amide II component the contributions of the N–H bending and C–N stretching are reported. These latter data give evidence of a dramatic change just at T  C . Error bars are comparable to the data symbol size.
The bending spectrum of pure bulk water at 303 K (top) in the range 1300 < ν < 1800 cm−1. The peptide groups (amide I, amide II, and amide III) falling in the same spectral range (bottom panel).
Evidence for the protein dynamic transition. (Top panel) The mean-squared atomic displacement MSD averaged over all the hydrogen atoms, ⟨X 2⟩, as a function of temperature for the H2O and D2O hydrated lysozyme samples at the hydration level h = 0.30.  20  The arrow indicates the crossover temperature T  C . In the inset is reported the behavior of the protein water self-diffusion coefficient D(T), at the same hydration, that shows the strong-fragile crossover at T  L  ≃ T  C .  49  (Bottom panel) The spectral area, relative to the total FTIR measured area, of the water bending components for h = 0.3 and 0.37.
Article
The "dynamic" or "glass" transition in biomolecules is as important to their functioning as the folding process. This transition occurs in the low temperature regime and has been related to the onset of biochemical activity that is dependent on the hydration level. This protein transition is believed to be triggered by the strong hydrogen bond coupling in the hydration water. We study the vibrational bending mode and measure it using Fourier Transform Infrared spectroscopy. We demonstrate that at the molecular level the hydration water bending mode bonds the C=O and N-H peptide groups, and find that the temperature of the "dynamic" protein transition is the same as the fragile-to-strong dynamic transition in confined water. The fragile-to-strong dynamic transition in water governs the nature of the H bonds between water and peptides and appears to be universal in supercooled glass-forming liquids.
 
Article
We have studied the potentially ionospherically significant reaction between N(2)2+ with O2 using position-sensitive coincidence spectroscopy. We observe both nondissociative and dissociative electron transfer reactions as well as two channels involving the formation of NO+. The NO+ product is formed together with either N+ and O in one bond-forming channel or O+ and N in the other bond-forming channel. Using the scattering diagrams derived from the coincidence data, it seems clear that both bond-forming reactions proceed via a collision complex [N2O2]2+. This collision complex then decays by loss of a neutral atom to form a daughter dication (NO2(2+) or N2O2+), which then decays by charge separation to yield the observed products.
 
Article
The infrared spectrum of the complex between o-H2 and H2O, D2O, or HDO, isolated in a matrix of solid p-H2, has been studied between 20 and 4500 cm(-1). In addition the infrared spectrum of the complex between p-D2 and H2O in solid o-D2 has been studied. The spectral shifts are interpreted as the result of the quadrupole-dipole interaction between hydrogen and water.
 
The slope of the free energy dF /dλ as a function of λ for a changing the charge of a Lennard-Jones particle in a box of explicit water from-e/2 to +e/2. Results for both TI and AIM methods are shown for 10 6 dynamics steps. The data show the averages (data points) and standard deviations (error bars) from 16 independent simulations for each method. The errorbars are too small to resolve on the plot shown, however, it should be noted that the average uncertainty in the the slope for AIM is 0.38 kcal/mol and for TI is 1.05 kcal/mol, suggesting that AIM has the ability to produce a more precise profile compared to TI. Thus, AIM is preferred over TI for computing the potential of mean force for this system. The smoothness of the profile also suggests that the switching function U λ of Eq. (24) used in this report is adequate.
The slope of the free energy    d F ∕ d λ    as a function of   λ   for changing the Lennard-Jones size of a neutral particle in a box of explicit water. Results for both TI and AIM methods are shown for    10 6    dynamics steps. The data show the averages (data points) and standard deviations (error bars) from 16 independent simulations for each method. The figure demonstrates that AIM has the ability to sample the   λ   path more efficiently, thus producing a much smoother and more precise profile compared to TI. Thus, AIM is preferred over TI for computing the potential of mean force for this system. In addition, the smoothness of the profile suggests that the switching function    U λ    of Eq. (25) used in this report is adequate.
Article
We present a detailed comparison of computational efficiency and precision for several free energy difference (DeltaF) methods. The analysis includes both equilibrium and nonequilibrium approaches, and distinguishes between unidirectional and bidirectional methodologies. We are primarily interested in comparing two recently proposed approaches, adaptive integration, and single-ensemble path sampling to more established methodologies. As test cases, we study relative solvation free energies of large changes to the size or charge of a Lennard-Jones particle in explicit water. The results show that, for the systems used in this study, both adaptive integration and path sampling offer unique advantages over the more traditional approaches. Specifically, adaptive integration is found to provide very precise long-simulation DeltaF estimates as compared to other methods used in this report, while also offering rapid estimation of DeltaF. The results demonstrate that the adaptive integration approach is the best overall method for the systems studied here. The single-ensemble path sampling approach is found to be superior to ordinary Jarzynski averaging for the unidirectional, "fast-growth" nonequilibrium case. Closer examination of the path sampling approach on a two-dimensional system suggests it may be the overall method of choice when conformational sampling barriers are high. However, it appears that the free energy landscapes for the systems used in this study have rather modest configurational sampling barriers.
 
Article
The SR11(0) and SR11(1) branch features of the [15.8] and [16.0]2Pi1/2-X 4Sigma- (0,0) subband systems of rhodium monoxide, RhO, have been studied at near the natural linewidth limit of resolution by optical Stark spectroscopy using laser induced fluorescence detection. The Stark shifts and splittings were analyzed to produce the magnitude of the permanent electric dipole moment, |mu|, of 3.81(2) D for the X 4Sigma3/2- (v=0) state. The results are compared to density functional theory calculations. Trends in observed values of |mu| across the 4d series of transition metal monoxides are interpreted in terms of simple single configuration molecular orbital correlation diagrams.
 
Article
The Zeeman effect in the (0,0) bands of the B(4)Γ(5/2)-X(4)Φ(3/2) system of titanium monohydride, TiH, and titanium monodeuteride, TiD, has been recorded and analyzed. Magnetic tuning of the spectral features recorded at high resolution (full width at half maximum ≅ 35 MHz) and at a field strength of 4.5 kG is accurately modeled using an effective Zeeman Hamiltonian. The determined magnetic g-factors for the X(4)Φ(3/2) (v = 0) state deviate only slightly from those expected for an isolated (4)Φ(3/2) state whereas those for the B(4)Γ(5/2)(v = 0) deviate significantly from those of an isolated (4)Γ(5/2) state. The rotational dependence of the magnetic tuning in the B(4)Γ(5/2)(v = 0) state is attributed to perturbations from a nearby (4)Φ state.
 
Article
The rotational line-integrated photoabsorption cross sections corresponding to the delta(0,0) band of the nitric oxide (NO) molecule at 295 K, calculated with the molecular quantum-defect orbital methodology, are in rather good accord with the experimental measurements available in the literature. The achieved results are of straightforward use in atmospheric chemistry, such as in the assessment of the NO photodissociation rate constant, which is of great relevance for atmospheric modeling. (c) 2005 American Institute of Physics.
 
Article
The low-rotational levels of the b (3)Pi-X (1)Sigma(+)(0,0) band of copper monofluoride, CuF, were recorded field free and in the presence of a static electric field. The field-free spectrum was analyzed to produce a refined set of fine and hyperfine parameters for the b (3)Pi(v=0) state. The permanent electric dipole moment, mu, for the b (3)Pi(v=0) and X (1) summation operator(+)(v=0) states were determined to be 2.36(2) and 5.26(2) D, respectively, from the analysis of the observed Stark shifts. The experimental mu values are compared to theoretical predictions. The change in mu upon excitation and the hyperfine parameters are discussed in terms of the proposed electronic configuration for the b (3)Pi and X (1)Sigma(+) states. The optical Stark spectroscopy of the A (2)Pi(3/2)-X (2)Sigma(+)(0,0) subband of YO was also recorded and analyzed to precisely calibrate the electric field strength. The determined mu values are 3.714(5) and 4.542(40) D for the A (2)Pi(3/2)(v=0) and X (2)Sigma(+)(v=0) states, respectively.
 
Article
The fine and hyperfine interaction parameters in the [18.8] (3)Phi (upsilon=0) and X (3)Phi (upsilon=0) states of cobalt monofluoride, CoF, have been determined from an analysis of high-resolution laser induced fluorescence spectra of the [18.8] (3)Phi(3)-X (3)Phi(3) and [18.8] (3)Phi(4)-X (3)Phi(4) band systems. The previously reported pure rotational transitions of the X (3)Phi(4)(upsilon=0) state [T. Okabayashi and M. Tanimoto, J. Mol. Spectrosc. 221, 149 (2003)] were included in the data set. The hyperfine parameters for (59)Co (I=72) and (19)F (I=12) have been interpreted using atomic data together with a proposed molecular orbital description for the [18.8](3)Phi(i) and X (3)Phi(i) states. A comparison of the hyperfine parameters in the X (3)Phi state of cobalt monohydride, CoH, with those of the X (3)Phi state of CoF reveals that the bonding in the two molecules is significantly different. It is shown that, in a situation where the Omega substates of a multiplet degenerate electronic state are analyzed separately, the Fermi contact parameter b can be determined with fair accuracy from the apparent centrifugal distortion of the hyperfine structure.
 
Article
The Zeeman tuning of the P(1)(0) line (nu=17 568.35 cm(-1)) of the A (7)Pi-X (7)Sigma(+) (0,0) band of manganese monohydride, MnH, has been investigated. The laser induced fluorescence spectrum of a supersonic molecular beam sample was recorded at a resolution of approximately 40 MHz and with field strengths of up to 362.0 mT. The observed spectrum was successfully fitted using a traditional effective Zeeman Hamiltonian to determine an effective magnetic g-factor for the J=2 level of the F(1)-spin component of the A (7)Pi(v=0) state. Spectral predictions of the P(1)(0) line at field strengths used in magnetic trapping experiments are presented.
 
Article
Restricted-spin coupled-cluster single-double plus perturbative triple excitation {RCCSD(T)} calculations were carried out on the X (2)B(1) and A (2)A(1) states of AsH(2) employing the fully relativistic small-core effective core potential (ECP10MDF) for As and basis sets of up to the augmented correlation-consistent polarized valence quintuple-zeta (aug-cc-pV5Z) quality. Minimum-energy geometrical parameters and relative electronic energies were evaluated, including contributions from extrapolation to the complete basis set limit and from outer core correlation of the As 3d(10) electrons employing additional tight 4d3f2g2h functions designed for As. In addition, simplified, explicitly correlated CCSD(T)-F12 calculations were also performed employing different atomic orbital basis sets of up to aug-cc-pVQZ quality, and associated complementary auxiliary and density-fitting basis sets. The best theoretical estimate of the relative electronic energy of the A (2)A(1) state of AsH(2) relative to the X (2)B(1) state including zero-point energy correction (T(0)) is 19,954(32) cm(-1), which agrees very well with available experimental T(0) values of 19,909.4531(18) and 19,909.4910(17) cm(-1) obtained from recent laser induced fluorescence and cavity ringdown absorption spectroscopic studies. In addition, potential energy functions (PEFs) of the X (2)B(1) and A (2)A(1) states of AsH(2) were computed at different RCCSD(T) and CCSD(T)-F12 levels. These PEFs were used in variational calculations of anharmonic vibrational wave functions, which were then utilized to calculate Franck-Condon factors (FCFs) between these two states, using a method which includes allowance for anharmonicity and Duschinsky rotation. The A(0,0,0)-X single vibronic level (SVL) emission spectrum of AsH(2) was simulated using these computed FCFs. Comparison between simulated and available experimental vibrationally resolved spectra of the A(0,0,0)-X SVL emission of AsH(2), which consist essentially of the bending (2(n)) series, suggests that there is a significant loss in intensity in the low emission energy region of the experimental spectrum.
 
Article
We report quasiclassical trajectory (QCT) calculations of the correlated product distributions and branching ratios of the reactions F+CHD(3)(v(1)=0,1)-->HF(v)+CD(3)(v) and DF(v)+CHD(2)(v) using a recently published ab initio-based full-dimensional global potential energy surface [G. Czako et al., J. Chem. Phys. 130, 084301 (2009)]. Harmonic normal mode analysis is done for the methyl products to determine the classical actions of each normal mode and then standard histogram binning and Gaussian binning (GB) methods are employed to obtain quantum state-resolved probabilities of the products. QCT calculations have been performed for both the vibrationally ground state and the CH stretching excited F+CHD(3)(v(1)=0,1) reactions at eight different collision energies in the 0.5-7.0 kcal/mol range. HF and DF vibrationally state-resolved rotational and angular distributions, CD(3) and CHD(2) mode-specific vibrational distributions, and correlated vibrationally state-specific distributions for the product pairs have been obtained and the correlated results were compared to the experiment. We find that the use of GB can be advantageous especially in the threshold regions. The CH stretching excitation in the reactant does not change the CD(3) vibrational distributions significantly, whereas the HF molecules become vibrationally and rotationally hotter. On the other hand in the case of the DF+CHD(2) channel the initially excited CH stretch appears mainly "intact" in the CHD(2) product and the DF distributions are virtually the same as formed from the ground state CHD(3) reaction. The computed results qualitatively agree with recent crossed molecular beam experiment [W. Zhang et al., Science 325, 303 (2009)] that (a) CHD(2)(v(1)=1) is the most populated product state of the F+CHD(3)(v(1)=1) reaction and this reaction produces much less CHD(2)(v=0) compared to the reaction F+CHD(3)(v=0); (b) the cross section ratio of CHD(2)(v(1)=1):CHD(2)(v=0) formed from the reactions F+CHD(3)(v(1)=1):F+CHD(3)(v=0) is less than 1 and shows little collision energy dependency; (c) the reactant CH stretch excitation increases the DF:HF ratio at low collision energies; (d) the correlated vibrational and angular distributions for DF(v)+CHD(2)(v(1)=0,1) from the ground state and stretch-excited reactions, respectively, are almost identical.
 
Article
Detailed quasiclassical trajectory calculations of the reaction H+CH4(nu3 = 0,1)-->CH3 + H2 using a slightly updated version of a recent ab initio-based CH5 potential energy surface [X. Zhang et al., J. Chem. Phys. 124, 021104 (2006)] are reported. The reaction cross sections are calculated at initial relative translational energies of 1.52, 1.85, and 2.20 eV in order to make direct comparison with experiment. The relative reaction cross section enhancement ratio due to the excitation of the C-H antisymmetric stretch varies from 2.2 to 3.0 over this energy range, in good agreement with the experimental result of 3.0 +/- 1.5 [J. P. Camden et al., J. Chem. Phys. 123, 134301 (2005)]. The laboratory-frame speed and center-of-mass angular distributions of CH3 are calculated as are the vibrational and rotational distributions of H2 and CH3. We confirm that this reaction occurs with a combination of stripping and rebound mechanisms by presenting the impact parameter dependence of these distributions and also by direct examination of trajectories.
 
Article
D3h and C2v geometries and energies, vertical excitation energies, as well as minimal energy paths as function of the O(1)(z)-X-O(2) angle α were obtained for XO3 ((0,1,-1)) (X = B, Al, Ga; C, Si, Ge; N, P, As; S, Se) molecules and ions with 22 and 23 valence electrons (VE), using density functional theory (DFT), coupled cluster with single and double substitutions with noniterative triple excitations (CCSD(T)), equation of motion (EOM)-CCSD, time-dependent DFT, and multi-reference configuration interaction methods. It is shown that pseudo Jahn-Teller (PJT) coupling increases as the central atom X becomes heavier, due to decreases in excitation energies. As is well known for CO3, the excited (1)E' states of the 22 VE systems SiO3, GeO3; NO3 (+), PO3 (+), AsO3 (+); BO3 (-), AlO3 (-), GaO3 (-) have strong vibronic coupling with the (1)A1' ground state via the e' vibrational modes, leading to a C2v minimum around α = 145°. For first and second row X atoms, there is an additional D3h minimum (α = 120°). Interacting excited states have minima around 135°. In the 23 VE systems CO3 (-), SiO3 (-); NO3, PO3; SO3 (+), coupling of the excited (2)E' with the (2)A2' ground state via the e' mode does not generate a C2v state. Minima of interacting excited states are close to 120°. However, due to very strong PJT coupling, a double-well potential is predicted for GeO3 (-), AsO3, and SeO3 (+), with a saddle point at D3h symmetry. Interaction of the b2 highest occupied molecular orbital with the b2 lowest unoccupied molecular orbital, both oxygen lone pair molecular orbitals, is seen as the reason for the C2v stabilization of 22 VE molecules.
 
Article
The hydrated nucleoside anions, uridine(-)(H(2)O)(n=0-2), cytidine(-)(H(2)O)(n=0-2), and thymidine(-)(H(2)O)(n=0,1), have been prepared in beams and studied by anion photoelectron spectroscopy in order to investigate the effects of a microhydrated environment on parent nucleoside anions. Vertical detachment energies (VDEs) were measured for all eight anions, and from these, estimates were made for five sequential anion hydration energies. Excellent agreement was found between our measured VDE value for thymidine(-)(H(2)O)(1) and its calculated value in the companion article by S. Kim and H. F. Schaefer III.
 
Article
Neutral superexcited states in molecular oxygen converging to the O(2)(+) c (4)Σ(u)(-) ion state are excited and probed with femtosecond time-resolved photoelectron spectroscopy to investigate predissociation and autoionization relaxation channels as the superexcited states decay. The c (4)Σ(u)(-) 4sσ(g) v=0, c (4)Σ(u)(-) 4sσ(g) v=1, and c (4)Σ(u)(-) 3dσ(g) v=1 superexcited states are prepared with pulsed high-harmonic radiation centered at 23.10 eV. A time-delayed 805 nm laser pulse is used to probe the excited molecular states and neutral atomic fragments by ionization; the ejected photoelectrons from these states are spectrally resolved with a velocity map imaging spectrometer. Three excited neutral O* atom products are identified in the photoelectron spectrum as 4d(1) (3)D(J)°, 4p(1) (5)P(J)° and 3d(1) (3)D(J)° fragments. Additionally, several features in the photoelectron spectrum are assigned to photoionization of the transiently populated superexcited states. Using principles of the ion core dissociation model, the atomic fragments measured are correlated with the molecular superexcited states from which they originate. The 4d(1) (3)D(J)° fragment is observed to be formed on a timescale of 65 ± 5 fs and is likely a photoproduct of the 4sσ(g) v = 1 state. The 4p(1) (5)P(J)° fragment is formed on a timescale of 427 ± 75 fs and correlated with the neutral predissociation of the 4sσ(g) v = 0 state. The timescales represent the sum of predissociation and autoionization decay rates for the respective superexcited state. The production of the 3d(1) (3)D(J)° fragment is not unambiguously resolved in time due to an overlapping decay of a v = 1 superexcited state photoelectron signal. The observed 65 fs timescale is in good agreement with previous experiments and theory on the predissociation lifetimes of the v = 1 ion state, suggesting that predissociation may dominate the decay dynamics from the v = 1 superexcited states. An unidentified molecular state is inferred by the detection of a long-lived depletion signal (reduction in autoionization) associated with the B (2)Σ(g)(-) ion state that persists up to time delays of 105 ps.
 
Article
Photodissociation studies using ion imaging are reported, measuring the coherence of the polarization of the S((1)D(2)) fragment from the photolysis of single-quantum state-selected carbonyl sulfide (OCS) at 223 and 230 nm. A hexapole state-selector focuses a molecular beam of OCS parent molecules in the ground state (nu2=0mid R:JM=10) or in the first excited bending state (nu2=1mid R:JlM=111). At 230 nm photolysis the Im[a1 (1)(parallel, perpendicular)] moment for the fast S(1D2) channel increases by about 50% when the initial OCS parent state changes from the vibrationless ground state to the first excited bending state. No dependence on the initial bending state is found for photolysis at 223 nm. We observe separate rings in the slow channel of the velocity distribution of S(1D2) correlating to single CO(J) rotational states. The additional available energy for photolysis at 223 nm is found to be channeled mostly into the CO(J) rotational motion. An improved value for the OC-S bond energy D0=4.292 eV is reported.
 
Article
The electronic structure of the phospho-olivine Li(x)FePO4 was studied using soft-x-ray-absorption (XAS) and emission spectroscopies. Characteristic changes in the valence and conduction bands are observed upon delithation of LiFePO4 into FePO4. In LiFePO4, the Fe-3d states are localized with little overlap with the O-2p states. Delithiation of LiFePO4 gives stronger hybridization between Fe-3d states and O-2p states leading to delocalization of the O-2p states. The Fe L-edge absorption spectra yield "fingerprints" of the different valence states of Fe in LiFePO4 and FePO4. Resonant soft-x-ray-emission spectroscopy at the Fe L edge shows strong contributions from resonant inelastic soft x-ray scattering (RIXS), which is described using an ionic picture of the Fe-3d states. Together the Fe L-edge XAS and RIXS study reveals a bonding character of the Fe 3d-O2p orbitals in FePO4 in contrast to a nonbonding character in LiFePO4.
 
Article
We investigated spin-orbit-induced intersystem crossing effects in the title reaction by the time-dependent wave-packet method combined with an extended split operator scheme. We performed non-adiabatic calculations of the fine-structure-resolved cross section and adiabatic calculations of integral cross section. The calculations are based on the potential energy surfaces of (3)A(') and the two degenerate (3)A('') states [S. Rogers, D. Wang, A. Kuppermann, and S. Walch, J. Phys. Chem. A 104, 2308 (2000)], together with the spin-orbit coupling matrix [B. Maiti and G. C. Schatz, J. Chem. Phys. 119, 12360 (2003)] and singlet (1)A(') potential energy surface [J. Dobbyn and P. J. Knowles, Faraday Discuss. 110, 247 (1998)]. The results of the O((3)P) + D2 are similar to those of the O((3)P) + H2 reaction. The product spin state-resolved reaction cross section and the total reaction cross section both show that the adiabatic channel is dominant in all cases, and the non-adiabatic channels have cross sections of several orders of magnitude smaller than the adiabatic channels at high collision energy. Although the cross sections caused by the intersystem crossing effects in the O((3)P) + D2 reaction are larger than those in the O((3)P) + H2 reaction, the differences in non-adiabaticity between these two reaction systems are quite modest. Based on the results of the O((3)P) + H2 reaction, we can predict that the influence of spin-orbit on the total reaction cross sections of the O((3)P) + D2 reaction is also insignificant. However, these non-adiabatic effects can be reflected in the presence of some forward-scattering in the angular distribution for the OD product.
 
Article
The dynamics of the IR emission induced by excitation of the acetylene molecule at the 3(2) Ka2, A1Au<--4(1) la1, X1Sigmag+ transition was investigated. Vibrationally resolved IR emission spectra were recorded at different delay times after the laser excitation pulse. The observed IR emission was assigned to transitions between vibrational levels of the acetylene molecule in the ground state. Values of the relaxation parameters of different vibrational levels of the ground state were obtained. The Ti-->Tj transition was detected by cavity ring-down spectroscopy in the 455 nm spectral range after excitation of the acetylene molecule at the same transition. Rotationally resolved spectra of the respective transition were obtained and analyzed at different delay times after the laser excitation pulse. The dynamics of the S1-->Tx-->T1-->S0 transitions was investigated, and the relaxation parameter values were estimated for the T1 state.
 
Article
Glassy dynamics of rigid molecules is still a matter of controversy: the physics behind the relaxation process at time scales faster than that ruled by the viscosity, the so called Johari-Goldstein process, is not known. In this work we unravel the mechanism of such a process by using a simple molecular model in which the centers of mass of the molecules are forming an ordered lattice, and molecular reorientation is performed by jumps between equilibrium orientations. We have studied the dynamics of simple quasi-tetrahedral molecules CBr(n)Cl(4-n), n = 0, 1, 2, in their monoclinic phases by means of dielectric spectroscopy and nuclear quadrupole resonance: the first technique allows to measure in a broad time scale but it is insensitive to molecular particularities, while the second has a restricted time window but senses the movement of each chlorine atom separately. The dynamic picture emerging from these techniques is that the secondary relaxation process is related to the different molecular surroundings around each nonequivalent atom of the molecule. Dynamical heterogeneities thus seem to be the cause of the secondary relaxation in this simple model of glass.
 
Article
By the counterpoise-correlated potential energy surface method (interaction energy optimization), five structures of the C(2)H(4-n)F(n)-HF (n = 0,1,2) dimers with all real frequencies have been obtained at MP2/aug-cc-pVDZ level. The influence of F substituent effect on the structure and pi-hydrogen bond of dimer has been discussed. For C(2)H(4-n)F(n)-HF (n = 1,2), the pi-hydrogen bonds are elongated comparing with that for C(2)H(4)-HF. For C(2)H(3)F-HF, g-C(2)H(2)F(2)-HF, cis-C(2)H(2)F(2)-HF, the pi-hydrogen bonds are further deformed. These changes (elongate, shift, and deformation) of pi-hydrogen bond mainly come from deformation of pi-electron cloud of C=C bond. The pi-electron cloud is pushed towards the one C atom, the pi H-bond shift also to the C direction. Since the two lobes of pi-electron cloud have deviated slightly from the molecular vertical plane passing through C=C bond, the pi-hydrogen bond is sloped. Intermolecular interaction energies of the dimers are calculated to be -3.9 for C(2)H(4)-HF, -2.8 for C(2)H(3)F-HF, -2.1 for g-C(2)H(2)F(2)-HF, -1.6 for cis-C(2)H(2)F(2)-HF, -1.3 kcal/mol for trans-C(2)H(2)F(2)-HF, at CCSD(T)/aug-cc-pVDZ level.
 
Article
We have carried out parallel tempering Monte Carlo calculations on the binary six-atom mixed Lennard-Jones clusters, Ar(n)Xe(6-n) (n=0,1,2). We have looked at the classical configurational heat capacity C(V)(T) as a probe of phase behavior. All three clusters show a feature in the heat capacity in the region of 15-20 K. The Ar(2)Xe(4) cluster exhibits a further peak in the heat capacity near 7 K. We have also investigated dynamical properties of the Ar(2)Xe(4) cluster as a function of temperature using molecular dynamics. We report the interbasin isomerization rate and the bond fluctuation parameter obtained from these calculations. At 7 K, the isomerization rate is on the order of 0.01 ns(-1); at 20 K, the isomerization rate is greater than 10 ns(-1). Furthermore, at 7 K, the bond fluctuation parameter is less than 3%; at 20 K, it is in the range of 10-15% (depending on the sampling time used). Using this information, together with Monte Carlo quenching data, we assign the 15-20 K feature in the heat capacity to a solid-liquid phase change and the 7-K peak to a solid-solid phase change. We believe this is the smallest Lennard-Jones cluster system yet shown to exhibit solid-solid phase change behavior.
 
Color online Simulated and measured hexapole focusing spectra of OCSv 2 =0,1. Upper panel: the measured hexapole spectrum open circles for ground state OCSv 2 =0 shows two peaks which can be assigned to the focusing, by second order Stark effect, of OCSv 2 =0 JlM = 100 around 7.8 kV and OCSv 2 =0 JlM =200 around 13.5 kV. Individual rotational states of the OCS molecule are simulated: JlM = 100 dashed line and 200 dot-dashed line. The solid line gives the sum of the two rotational states with a relative weight of the population of n100 : n200 = 1 : 0.92. Lower panel: the measured hexapole spectrum open circle and the simulated spectrum solid line for OCSv 2 =1 JlM molecules with one quantum of vibrational excitation. The focusing curves of individual JlM rotational states are shown by the colored curves and are labeled by the quantum numbers JlM. The simulations were run for a molecular beam with a central translational velocity of 540 m / s and a translational temperature of 17 K.
Hexapole focusing spectra of OCS (20% in Ar) detected by parent molecule ionization through     Δ   3  ← ←  X ̃    Σ  +   1       0 0 0    (solid circle),    2 1 1    (open square), and    2 2 2    (open triangle) vibronic transitions. Each peak in all three spectra corresponds to an individual rotational state of the OCS parent molecule or to a convolution of several rotational states (see Fig. 3). The intensity of the spectrum detected through the    2 2 2    transition of OCS was multiplied by a factor of 3 for better viewing. The hexapole voltage is the voltage difference between the positive and the negative rods.
Molecular beam profile. We measured the intensity of the OCS ions as we varied the time delay between the molecular beam and the laser beam. From the width of the gas pulse we determine the translational temperature of the molecular beam.
Slice images of    CO  ( J )     measured in one laser experiment with the laser frequency tuned to three different    CO  ( J )     levels, (a)    J = 60   , (b)    J = 63   , and (c)    J = 67   . The images shown are a cut of 1050 by 1050 real pixels of the 2048 by 2048 CCD pixels. The total number of ion events in these images are (a) 8411, (b) 35310, and (c) 3268. Clearly visible are three rings in each image and the diameter of the rings decrease with increasing rotational state.
Article
Using hexapole quantum state-selection of OCS (v(2)=0,1,2/JlM) and high-resolution slice imaging of quantum state-selected CO(J), the state-to-state cross section OCS (v(2)=0,1,2/JlM)+hnu-->CO(J)+S((1)D(2)) was measured for bending states up to v(2)=2. The population density of the state-selected OCS (v(2)=0,1,2 /JlM) in the molecular beam was obtained by resonantly enhanced multiphoton ionization of OCS and comparison with room temperature bulk gas. A strong increase of the cross section with increasing bending state is observed for CO(J) in the high J region, J=60-67. Integrating over all J states the authors find sigma(v(2)=0):sigma(v(2)=1):sigma(v(2)=2)=1.0:7.0:15.0. A quantitative comparison is made with the dependence of the transition dipole moment function on the bending angle.
 
Article
Inelastic collision processes between neutral Mg atoms and Rb(+) ions, both in their ground states, have been studied by means of a crossed molecular beam technique measuring the decay fluorescence of the excited species formed. Emissions corresponding to Mg(3 (1)P(1)), Mg(3 (3)D(3,2,1)), and Mg(4 (3)S(1)), formed by direct target excitation, Rb(5 (2)P(3/2,1/2)), Rb(6 (2)P(3/2,1/2)) produced by electron capture and also the phosphorescent emission due to decay of Mg(3 (3)P(1)), have been detected and the corresponding absolute cross-section values measured both as total values and resolved into their J states. No polarization measurements could be made. Ab initio calculations using pseudopotentials have been performed and from these a manifold of adiabatic energy curves correlating with the different entry and exit channels have been obtained, allowing to propose a qualitative interpretation of the results, such as the shape of the cross section vs energy for different transitions and the oscillating nature of the branching ratios due to interference effects.
 
Article
We report measurements of the incidence translational energy dependence of steric effects in collisions of NO(v = 3) molecules with a Au(111) surface using a recently developed technique to orient beams of vibrationally excited NO molecules at incidence energies of translation between 0.08 and 0.89 eV. Incidence orientation dependent vibrational state distributions of scattered molecules are detected by means of resonance enhanced multiphoton ionization spectroscopy. Molecules oriented with the N-end towards the surface exhibit a higher vibrational relaxation probability than those oriented with the O-end towards the surface. This strong orientation dependence arises from the orientation dependence of the underlying electron transfer reaction responsible for the vibrational relaxation. At reduced incidence translational energy, we observe a reduced steric effect. This reflects dynamical steering and re-orientation of the NO molecule upon its approach to the surface.
 
N 2 O eigenphase sums for a 28-state CC calculation. 
N 2 O electronic excitation cross section for a 28-state CC calculation from initial state 1 A 1 . 
Total cross sections for N 2 O with theoretical comparison; solid line: present results (Q-mol with the Born correction); short dashed line: present (Q-mol without the Born correction); dashed line: Winstead and Mckoy; 14 dashed-dotted line: Sarpal et al.; 8 dotted line: Michelin et al.; 7 dashed-dotteddotted line: Tennyson and Morgan. 2 
Article
We report electron impact total cross sections, Q(T), for e-N(2)O scattering over an extensive range of impact energies approximately from 0.1 eV to 2000 eV. We employ an ab initio calculation using R-matrix formalism below the ionization threshold of the target and above it we use the well established spherical complex optical potential to compute the cross sections. Total cross section is obtained as a sum of total elastic and total electronic excitation cross sections below the ionization threshold and above the ionization threshold as a sum of total elastic and total inelastic cross sections. Ample cross section data for e-N(2)O scattering are available at low impact energies and hence meaningful comparisons are made. Good agreement is observed with the available theoretical as well as experimental results over the entire energy range studied here.
 
Elastic cross sections integrated from 20 • to 130 •. ePOLYSCAT (O), SCAR (∇), Srivastava et al. 10 experimental data ( * ).
Elastic cross sections plus rotational excitation cross sections. POLYDCS (solid red line), SCAR (dashed blue line), Faure et al. 12 (dotted-dashed black line), Srivastava et al. 10 experimental data (*).
Integral elastic cross sections. ePOLYSCAT (solid red line), SCAR (dotted blue line), SCAR without the absorption potential term (dashed green line).
Article
We report theoretical integral and differential cross sections for electron scattering from hydrogen cyanide derived from two ab initio scattering potential methods. For low energies (0.1-100 eV), we have used the symmetry adapted-single centre expansion method using a multichannel scattering formulation of the problem. For intermediate and high energies (10-10 000 eV), we have applied an optical potential method based on a screening corrected independent atom representation. Since HCN is a strong polar molecule, further dipole-induced excitations have been calculated in the framework of the first Born approximation and employing a transformation to a space-fixed reference frame of the calculated K-matrix elements. Results are compared with experimental data available in the literature and a complete set of recommended integral elastic, inelastic, and total scattering cross sections is provided from 0.1 to 10 000 eV.
 
Article
Inelastic and charge-transfer excitation processes in collisions between ground-state neutral Mg atoms and K+ ions have been studied by means of a crossed molecular-beam technique. Decay fluorescent emissions from Mg(3 1P1),Mg(4 3S1), and Mg(3s(1)3d(1), 3(3)D3,2,1) as well as the phosphorescent emission due to Mg(3 3P1) have been observed from excited Mg atoms and the charge-transfer emission decays from K(4 2P 3/2,1/2), K(5 2P 3/2, 1/2), K(6 2S 1/2), and K(4 2D 5/2, 3/2) for excited K atoms. The corresponding absolute cross-sections values versus collision energy functions were determined in the 0.10-3.80 keV laboratory energy range. In order to interpret the experimental results, accurate ab initio full configuration-interaction calculations using pseudopotentials have been performed for the (Mg-K)+ system, giving a manifold of adiabatic singlet and triplet potential-energy curves correlating with the different collision channels, which allow a qualitative interpretation of the emission excitation functions measured for the different processes studied. A comparative study with other Mg-alkali ion systems previously studied is also included.
 
Article
Electron attachment rates for SF(6) and C(7)F(14) were measured in a magnetized Q machine plasma at an electron temperature of 0.2+/-0.02 eV and with neutral gas pressures of P approximately 10(-4) Torr. The rate constants for attachment to SF(6) and C(7)F(14) were (7.6+/-2.0)x10(-8) and (2.2+/-0.9)x10(-7) cm(3) s(-1), respectively.
 
Article
The dynamic properties of plastic crystalline mixed adamantane's derivatives namely cyanoadamantane (75%) and chloroadamantane (25%) were investigated by dielectric and nuclear magnetic resonance (NMR) spectroscopy, covering a spectral range of 12 decades in the temperature range 110-420 K. Phase transformations were studied and dynamical parameters of the plastic (I), glassy (Ig), and ordered (III) phases were determined and compared with those of pure compounds. The dynamics of the supercooled plastic phase is characterized by an alpha-process exhibiting an Arrhenius behavior which classified the mixed compound as a strong glass former. In the plastic phase, NMR relaxation times were interpreted by using a Frenkel model, which takes into account structural equilibrium positions. This model explains adequately the experimental results by considering two molecular motions. In both the glassy state and plastic phase the motional parameters agree with those of 1-cyanoadamantane. On the contrary, in the ordered phase, the motional parameters related to the uniaxial rotation of chloroadamantane molecules indicate an accelerated motion.
 
Article
Based on several force fields (COMPASS, modified TIP3P and SPC/E) high-density amorphous ice is simulated by use of isothermal-isobaric molecular dynamics at a pressure of p approximately 0.3 GPa in the temperature range from 70 to 300 K. Starting at low temperature a large number of heating/cooling cycles are performed and several characteristic properties (density, total energy, and mobility) are traced as functions of temperature. While the first cycles are showing irreversible structural relaxation effects data points from further cycles are reproducible and give clear evidence for the existence of a glass-to-liquid transition. Although, the observed transition temperatures T(g) are dependent on the actual force field used and slightly dependent on the method adopted the results indicate that high-density amorphous ices may indeed be low-temperature structural proxies of ultraviscous high-density liquids.
 
Article
The study of strongly absorbing liquids such as water and aqueous buffers using terahertz absorption spectrometer was presented. water samples were prepared at 22°C using distilled de-ionized water, and distilled de-ionized water buffered at 3 and 8 with mM potassium phosphate. The absorption spectra of distilled de-ionized water and aqueous 50mM phosphate buffers were measured over the frequency range of 0.3-3.72 THz. The measurements below ∼ 1.5 THz were found to be converging with the FIR laser transmission spectroscopy and FIR grating measurements.
 
Article
The van der Waals complexes consisting of single tetracene chromophore molecules with an attached H(2), HD, or a D(2) molecule have been assembled inside cold (0.37 K), large ( approximately 1.5 x 10(4) atoms) helium droplets. Their laser-induced fluorescence spectra exhibit typically three well isolated fairly sharp [deltanu(full width at half maximum) approximately 0.5 cm(-1)] bands in the spectral region 22220-22300 cm(-1). Their positions differ for each isotopomer and also are different for each of the ortho- and para-spin modifications. The common feature (except for D(2)) with the largest redshift at about 30 cm(-1), found also in other related free complexes, is attributed to a strongly bound site above one of the two central benzene rings. The other major features come in pairs spaced 3 cm(-1) apart and are not found in similar gas phase studies. This doublet is assigned to a less tightly bound peripheral site with either slightly different configurations or states of the aduct or possibly the He atoms which are stabilized by the surrounding helium bath. The common feature and one branch of the doublet exhibit a pronounced narrow fine structure with spacings of only 0.1 cm(-1), which is nearly the same for all complexes as well as for the bare chromophore, and maybe be due to partially resolved rotational structure of the bands.
 
Article
The formation of Ar and H2 clusters, having up to 900 particles in helium droplets, has been studied via laser induced fluorescence of attached Mg-phthalocyanine (Mg-Pc) molecules. In the experiments, one Mg-Pc molecule in average was added to each He droplet either before or after the cluster species, and the shift of the spectrum of the Mg-Pc molecules was studied as a function of the cluster size. For Ar clusters, about a factor of 2 smaller matrix shift was observed for the late pickup of the Mg-Pc molecules as compared with the prior pickup, indicating that in the former case, the Mg-Pc molecules reside on the surface of the preformed Ar clusters. On the other hand, the spectra of the Mg-Pc molecules attached to H2 clusters are independent of the pickup order, which is consistent with Mg-Pc molecules residing near the center of the H2 clusters in both cases. Therefore H2 clusters remain fluxional in helium droplets at T=0.38 K. No significant differences in the spectra were observed between the para-H2 and ortho-H2 clusters.
 
Article
Extensive experimental work has been carried out to characterize the stable Na-vacancy ordering patterns at various compositions of layered Na(x)CoO(2). However, contradictions and debates prevail in the literature, particularly at high Na concentrations x>0.5. Understanding of the exotic electronic properties in this system requires a thorough understanding of the Na-vacancy structural orderings. Using density functional theory in the generalized gradient approximation (GGA), combined with a cluster expansion structure prediction algorithm we have found an intricate set of Na-vacancy ordered ground states in Na(x)CoO(2) (0.5< or =x< or =1). We demonstrate a newly predicted ordering pattern between 0.67< or =x< or =0.71. By comparing the first principles electronic structure methods within the GGA and GGA+U (Hubbard U correction) approximations, we demonstrate that at certain Na concentration the stable ordering is affected by charge localization on the Co layer through coupling between the Na and Co lattices.
 
Article
Jet cooled NO molecules are scattered at 45° with respect to the surface normal from a liquid gallium surface at E(inc) from 1.0(3) to 20(6) kcal/mol to probe rotationally and electronically inelastic scattering from a gas-molten metal interface (numbers in parenthesis represent 1σ uncertainty in the corresponding final digits). Scattered populations are detected at 45° by confocal laser induced fluorescence (LIF) on the γ(0-0) and γ(1-1) A(2)Σ ← X(2)Π(Ω) bands, yielding rotational, spin-orbit, and λ-doublet population distributions. Scattering of low speed NO molecules results in Boltzmann distributions with effective temperatures considerably lower than that of the surface, in respectable agreement with the Bowman-Gossage rotational cooling model [J. M. Bowman and J. L. Gossage, Chem. Phys. Lett. 96, 481 (1983)] for desorption from a restricted surface rotor state. Increasing collision energy results in a stronger increase in scattered NO rotational energy than spin-orbit excitation, with an opposite trend noted for changes in surface temperature. The difference between electronic and rotational dynamics is discussed in terms of the possible influence of electron hole pair excitations in the conducting metal. While such electronically non-adiabatic processes can also influence vibrational dynamics, the γ(1-1) band indicates <2.6 × 10(-4) probability for collisional formation of NO(v = 1) at surface temperatures up to 580 K. Average translational to rotational energy transfer is compared from a hard cube model perspective with previous studies of NO scattering from single crystal solid surfaces. Despite a lighter atomic mass (70 amu), the liquid Ga surface is found to promote translational to rotational excitation more efficiently than Ag(111) (108 amu) and nearly as effectively as Au(111) (197 amu). The enhanced propensity for Ga(l) to transform incident translational energy into rotation is discussed in terms of temperature-dependent capillary wave excitation of the gas-liquid metal interface.
 
Article
We investigate the thermodynamic behavior of the thirteen center uniform Lennard-Jones dipole-dipole cluster [(LJDD)(13)] for a wide range of dipole moment strengths. We find a relatively wide range of potential parameters where solid-solid coexistence manifests itself. Using structural characterization methods we determine the shape of the few isomers that contribute to the solid-solid coexistence region. The thermal distributions of the size of the net dipole moment are broad even at the coldest temperatures of the simulation where the (LJDD)(13) cluster is solid.
 
Article
A deuterated sample of CO2 structure I (sI) clathrate hydrate (CO2·8.3 D2O) has been formed and neutron diffraction experiments up to 1.0 GPa at 240 K were performed. The sI CO2 hydrate transformed at 0.7 GPa into the high pressure phase that had been observed previously by Hirai et al. [J. Phys. Chem. 133, 124511 (2010)] and Bollengier et al. [Geochim. Cosmochim. Acta 119, 322 (2013)], but which had not been structurally identified. The current neutron diffraction data were successfully fitted to a filled ice structure with CO2 molecules filling the water channels. This CO2+water system has also been investigated using classical molecular dynamics and density functional ab initio methods to provide additional characterization of the high pressure structure. Both models indicate the water network adapts a MH-III "like" filled ice structure with considerable disorder of the orientations of the CO2 molecule. Furthermore, the disorder appears to be a direct result of the level of proton disorder in the water network. In contrast to the conclusions of Bollengier et al., our neutron diffraction data show that the filled ice phase can be recovered to ambient pressure (0.1 MPa) at 96 K, and recrystallization to sI hydrate occurs upon subsequent heating to 150 K, possibly by first forming low density amorphous ice. Unlike other clathrate hydrate systems, which transform from the sI or sII structure to the hexagonal structure (sH) then to the filled ice structure, CO2 hydrate transforms directly from the sI form to the filled ice structure.
 
Article
We describe a new grid-based (or localized orbital-based) method for treating the effects of exchange and correlation on electronic transmission through a molecular target where there are initially other bound electrons. Our algorithm combines the approaches of (i) solid-state grid-based algorithms using self-energies and (ii) the complex Kohn method from electron-molecule scattering. For the general problem of a molecular target with n-electrons, our algorithm should ideally solve for electronic transmission with a computational cost scaling as n(2), although the present implementation is limited to one-dimensional problems. In this paper, we implement our algorithm to solve three one-dimensional model problems involving two electrons: (i) Single-channel resonant transmission through a double-barrier well (DBW), where the target already contains one bound-state electron [Rejec et al., Phys. Rev. B 67, 075311 (2003)]; (ii) multichannel resonant transmission through a DBW, where the incoming electron can exchange energy with the bound electron; (iii) transmission through a triple-barrier well (TBW), where the incoming electron can knock forward the bound electron, yielding a physical model of electron-assisted electron transfer. This article offers some insight about the role and size of exchange and correlation effects in molecular conduction, where few such rigorous calculations have yet been made. Such multibody effects have already been experimentally identified in mesoscopic electron transport, giving rise to the "0.7 anomaly," whereby electrons traveling through a narrow channel pair up as singlets and triplets. We expect the effect of electronic correlation to be even more visible for conduction through molecules, where electrons should partially localize into bonding and antibonding orbitals.
 
Article
Thermal conductivity measurements show that ice continues to amorphize for several days when kept at a fixed pressure p in the 0.79-0.88 GPa range, and fixed temperature T in the 127-130 K range. Thermal conductivity kappa decreases according to a stretched exponential in time, and its limiting long time value kappa( infinity ) varies with p and T. At 0.8 GPa and 128 K, kappa( infinity ) remains 2.5 times the value observed for high-density amorph. Consequences of these findings for our understanding of amorphization are discussed.
 
Article
A laser-based, pulsed, narrow-band source of submillimeter-wave radiation has been developed that is continuously tunable from 0.1 THz to 14.3 THz. The source is based on difference-frequency mixing in the nonlinear crystal trans-4(')-(dimethylamino)-N-methyl-4-stilbazolium tosylate. By varying the pulse length, the bandwidth of the submillimeter-wave radiation can be adjusted between 85 MHz and 2.8 MHz. This new radiation source has been integrated in a vacuum-ultraviolet-submillimeter-ware double-resonance spectrometer, with which low-frequency transitions of atoms and molecules in supersonic beams can be detected mass-selectively by photoionization and time-of-flight mass spectrometry. The properties of the radiation source and spectrometer are demonstrated in a study of 33f ← nd Rydberg-Rydberg transitions in Xe with n in the range 16-31. The frequency calibration of the submillimeter-wave radiation was performed with an accuracy of 2.8 MHz. The narrowest lines observed experimentally have a full-width at half-maximum of ∼3 MHz, which is sufficient to fully resolve the hyperfine structure of the Rydberg-Rydberg transitions of (129)Xe and (131)Xe. A total of 72 transitions were measured in the range between 0.937 THz and 14.245 THz and their frequencies are compared with frequencies calculated by multichannel quantum defect theory.
 
Article
The spectrum of methylene in the 1.3-1.4 and 0.89-0.94 microm wavelength regions has been recorded in absorption using frequency-modulated cw diode and Ti:sapphire laser sources. The spectral lines have Doppler-limited resolution and have been assigned to bands in the b(1)B1 <-- a(1)A1 electronic spectrum of the radical. In three of the four bands studied, the lower state is the bend excited, v2" = 1, level of the a state and two of the upper levels lie below the energy of the degenerate linear configuration of the b/a pair. Together with previously measured data pertaining to v2" = 1, the data have been used to refine the precision of the experimentally determined rotational structure in this level. Although several K" = 1 levels do show shifts of more than 0.1-0.2 cm(-1), multiple strong perturbations due to near-resonant background X(3)B1 rovibrational levels, such as are known to occur in the a(1)A1, v2" = 0 level have not been found in v2" = 1. Absorption lines due to the predominantly triplet X(040) 4(14) level, responsible for most of the perturbation of a(010) 5(15), have been identified in the spectra. The data also fix the energies of the b(0,0,0)2, a(0,7,0)1, b(0,2,0)3, and a(0,10,0)2 upper vibronic levels, where the numbers in parentheses are the vibrational quantum numbers with superscript K, the projection of the total angular momentum on the a-inertial axis.
 
Article
Using both a difference frequency spectrometer and a Fourier transform spectrometer, we have measured transitions in the 12 (2)0<--01 (1)0 band of carbon dioxide at room temperature and pressures up to 19 atm. The low-pressure spectra were analyzed using a variety of standard spectral profiles, all with an asymmetric component to account for weak line mixing. For this band, we have been able to retrieve experimental line strengths and the broadening and weak mixing parameters. In this paper we also compare the suitability of the energy-corrected sudden model to predict mixing in the two previously measured Q branches 20 (0)0<--01 (1)0, the 11 (1)0<--00 (0)0, and the present Q branch of pure CO(2), all at room temperature.
 
Distributions of single point energies for a selection of amino acids and the chlorophyll and-carotene cofactors. Energies are calculated at PW91/ 6-31Gd level for isolated, terminated residues at their in situ geometry. = fully optimized geometry and = heavy atoms at original x-ray coordinates. Superimposed are normal distribution curves obtained from the average energies and their standard deviations for the optimized data. Note that for the chlorophyll and-carotene cofactors there are no overlaps of the distributions between the x-ray and optimized QR sets.
(Color) Detail of the H-bonding interactions for the possible redox active residues TYR7-C and TYR67-C. H-bond lengths in Å, non-H-bonding hydrogens omitted for clarity.
(Color) Simultaneously optimized residues (in situ) associated with the central cluster about the    C 3    axis showing the central    Na +    ion and the triplicate GLN119-L and SER42-L residues: (a) all residues and (b) detail of the coordination and H bonding about the central    Na +    ion, with coordinative bonds to the    Na +    ion in orange and H bonds in green.
(Color) Calculation constructed for the DFT optimization of ASN192-A (shown in red). Residues or part thereof included in the DFT level of the calculation but fixed in space are shown in blue. Residues or part thereof contained in the PM3 level of the calculation are shown in orange. H bonds involving ASN192-A are shown in green and determine the DFT/PM3 partitioning.
(Color)     CL 2  1101    at x-ray and stereochemically corrected, optimized geometry. Phytyl chain and all hydrogens except epimeric hydrogen omitted for clarity.
Article
We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150,000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW916-31G(d) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal "active site." To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53 kcal mol(-1) and eliminates the enormous 115 kcal mol(-1) energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the "special pair" of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered.
 
Top-cited authors
Stefan Grimme
  • University of Bonn
Stephan Ehrlich
  • Schrödinger Inc.
Thom H Dunning
  • University of Washington Seattle
Martin Head-Gordon
  • University of California, Berkeley
Hans-Joachim Werner
  • Universität Stuttgart