bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient optimization of large scale MCSCF wave functions with a restricted step algorithm
Authors: Jensen Hans Jo/rgen Aa. , Jo/rgensen Poul , Ågren Hans
Published: July 2002

Auxiliary algorithms for efficient optimization of large scale MCSCF wave functions are devised and implemented in a previously developed direct, second order, restricted step MCSCF program. As demonstrated by the numerical examples, these algorithms drastically reduce the computation time. We also demonstrate efficient optimization of excited states with ‘‘root flipping’’ and of core hole states without variational collapse.
Coupled dipoles in light scattering by randomly oriented chiral particles
Authors: Singham Shermila Brito
Published: July 2002

Light scattering by oriented and randomly oriented chiral particles is compared. It is shown that large magnitude terms in the scattered field products that contribute to the 2×2 off-block-diagonal matrix elements in the oriented particle scattering matrix make no contribution in the orientation averages. A model calculation for a simple chiral particle is described.
Slowing down of relaxation in a complex system by constraint dynamics
Authors: Ngai K. L. , Rajagopal A. K. , Teitler S.
Published: July 2002

In this paper we view a relaxing complex system such as entangled polymer melt to consist of three parts: (1) an individual primary species PS of interest; (2) a heat bath (HB) whose interaction with the PS provides the primary mechanism of relaxation; (3) other relaxing species whose interactions with the PS, the PS-C coupling, are for us the principal characteristic of complexity. The PS-C coupling is represented by time dependent constraints whose effect begins only after the primary relaxation process due to the PS-HB interaction is already underway. The overall process is described both physically and theoretically. The latter is described classically by means of time dependent Dirac constraint theory applied to a Liouville operator formalism. The physical and theoretical discussion leads to a time dependent relaxation rate W(t). The specific form of W(t) is adduced based on the requirement of time-temperature equivalence or thermorheological simplicity. The result is a time independent relaxation rate W0 for times short compared to the onset of the effect of the time dependent constraints at tc=ω−1c, and a time dependent rate W0(ωct)−n for times long compared to tc. The case W0tc<1 is of most interest because the relaxation process then reveals the effect of complexity empirically. The empirically observed result is then just the Kohlrausch form. Furthermore, a second relation between τ0≡W−10 and the effective relaxation time in the Kohlrausch form follows immediately. It is also noted that the present framework can be applied more generally in relaxation phenomena if thermorheological simplicity is viewed as a special case of correlation or constraint scaling in which dW/W=−ndt/t for t>tc.
The equilibrium structure and harmonic vibrational frequencies of ozone: Coupled cluster results including triple excitations
Authors: Magers David H. , Lipscomb William N. , Bartlett Rodney J. , Stanton John F.
Published: July 2002

The highly correlated CCSDT-2 model of electron correlation is applied to computation of the equilibrium geometry and harmonic vibrational frequencies of O3. Comparison of the present results with those of a recent study [J. F. Stanton, W. N. Lipscomb, D. H. Magers, and R. J. Bartlett, J. Chem. Phys. 90, 1077 (1989)] reveal the importance of certain simultaneous three-particle correlation effects (T3) which enter perturbation theory in fifth and higher orders, particularly for asymmetric structures of ozone and, consequently, the B2 stretching frequency. The CCSDT-2 value for ω3 is 1182 cm−1, in reasonable agreement with the experimental value of 1089 cm−1, and considerably better than values obtained with other methods which make more approximations in treating T3. To treat this difficult problem, it appears to be necessary to include terms involving T3 which are nonlinear in the cluster amplitudes into the CC equations.
Mode mixing and chaos induced by potential surface crossings
Authors: Heller Eric J.
Published: July 2002

The effect of Born–Oppenheimer potential energy surface crossings on energy transfer in polyatomic molecules is investigated, classically and quantum mechanically. The hopping from one energy surface to another is enough to cause classical chaos, and strong mixing of the levels quantum mechanically. The rate of classical mixing determines the extent of quantum mixing, even though classical mixing is complete at long times.
Vibrational frequencies for Be3 and Be4
Authors: Rendell Alistair P. , Lee Timothy J. , Taylor Peter R.
Published: July 2002

The harmonic vibrational frequencies of the Be3 and Be4 clusters have been determined using ab initio electronic structure calculations. Large atomic natural orbital (ANO) basis sets have been used in conjunction with high levels of correlation treatment. These include multireference configuration-interaction (MRCI) and single and double coupled-cluster (CCSD) methods, and the CCSD method augmented with a correction for connected triple excitations [CCSD(T)]. In general, all three treatments agree very well. The only substantial disagreement is for the totally symmetric stretching mode in Be3, where the CCSD method yields a harmonic frequency that is 57 cm−1 smaller than the MRCI value. The fundamental vibrational frequencies of Be3 and Be4 have been determined using second-order perturbation theory to obtain anharmonic corrections; Be3 is treated as a symmetric top and Be4 as a spherical top. Full CCSD(T) quartic force fields were used to determine anharmonic constants, vibration–rotation interaction constants, and quartic and sextic centrifugal distortion constants. The anharmonic corrections for the two vibrational modes of Be3 reduce the frequencies by less than 5%, which is typical for bond-stretching vibrations. The a1 and e vibrations of Be4 exhibit somewhat smaller anharmonic corrections that decrease the frequency by about 3%. However, the only IR active mode of Be4 [ω3(t2)] displays a large positive anharmonic correction of +111 cm−1, or almost 20%. Finally, IR intensities have been determined using the double harmonic approximation.
Approximately diabatic states: A relation between effective Hamiltonian techniques and explicit cancellation of the derivative coupling
Authors: Gadéa F. X. , Pélissier M.
Published: July 2002

The identification of specific electronic structures that do not interchange with varying geometry is related to the problem of finding a set of approximately diabatic states. We propose a new transformation to identify such structures from one nuclear configuration to another one. This transformation, used in previously proposed schemes to construct nearly diabatic states, improves the efficiency of these procedures which can be related to the methods minimizing explicitly the nonadiabatic coupling.
Matrix-isolated OCS: The high resolution infrared spectra of a cryogenically solvated linear molecule
Authors: Lang Valerie I. , Winn John S.
Published: July 2002

Spectra of the ν3 vibrational mode of OCS (around 2000 cm−1 ) isolated in solid Ar, Xe, and N2 at cryogenic temperatures and high dilution (1:50 000 typically) have been measured with an interferometric spectrometer at high resolution (0.01 cm−1 ). The spectra have in common a sharp feature (for any one isotopic form) to the red of a much broader feature. They differ in the way these features move and change width with changes in matrix temperature. The environment of the solute, which is deduced in detail in a companion paper, can be assigned to these features, implying that precision line shape measurements can be used to probe the immediate environment of a highly dilute solute. Applications of this technique to the study of photodissociation in cryogenic solids and to the study of diffusion are discussed.
Vibrationally highly excited acetylene as studied by dispersed fluorescence and stimulated emission pumping spectroscopy: Vibrational assignment of the feature states
Authors: Yamanouchi Kaoru , Ikeda Naru , Tsuchiya Soji , Jonas David M. , Lundberg James K. , Adamson George W. , Field Robert W.
Published: July 2002

The dispersed fluorescence (DF) and stimulated emission pumping (SEP) spectra of acetylene originating from single rovibronic levels of the Ã 1Au state were measured with resolutions of 30 and 0.5 cm−1, respectively, in order to examine the vibrational level structure of the electronic ground X̃ 1Σ+g state. The SEP spectra revealed that the number of vibrational levels under each peak in the DF spectra increases with vibrational energy from a single vibrational level below 8000 cm−1 to as many as ten vibrational levels above 16 500 cm−1. Taking account of the fact that a peak in the DF spectrum in the high energy region is composed of more than one level, a DF peak is called a feature state (or a feature). In the DF spectra from two trans-bending levels (v3=2 and 3) of the Ã state a total of 140 DF features between 5 700 and 21 200 cm−1 were detected and long progressions in the trans bend (v″4=6 –18) and CC stretch (v■2=0 –6) were identified.

Below 14 000 cm−1, 26 out of the 50 observed features were unambiguously assigned to these two modes and represented by a second order anharmonic expansion within the ∼20 cm−1 experimental error. At least three additional trans-bend progressions built on excitation in third vibrational mode were identified. Possible assignments of the third mode to the CH stretch (ν″1) and the cis bend (ν■5) are compared. The Darling–Dennison (DD) resonance between the two degenerate bending modes (trans and cis) was proposed as a mechanism to lend Franck–Condon (FC) intensity to the ν″5 mode. The vibrational analysis of the DF features shows that the DF features correspond to the zero-order FC bright basis states. Each feature represents a group of levels which share the character of a zero-order FC bright level. Above 14 000 cm−1, characteristic groups of DF features with a width of around 300 cm−1 appear in the DF spectra originating from both v3=2 and v′3=3. The relative intensity patterns within each group of features in the two DF spectra are nearly identical. Three anharmonic resonances, including the DD resonance, are proposed as a plausible mechanism which splits a single FC bright state into several DF features. The SEP measurement revealed that a single DF feature splits further into several features with widths around 0.5 cm−1. The characteristic nested level structure identified in the DF and SEP spectra are explained in terms of a stepwise energy flow via a series of anharmonic resonances from the initially excited CC stretch/trans-bend vibrations to the remaining vibrational modes.
The vibrational frequencies of difluoroethyne
Authors: Breidung Jürgen , Schneider Winfried , Thiel Walter , Lee Timothy J.
Published: July 2002

Ab initio coupled-cluster calculations with single and double excitations (CCSD) and with a perturbational treatment of connected triple excitations [CCSD(T)] are reported for difluoroethyne using large basis sets. The results for the trans-bending mode ν4 are extremely sensitive to electron correlation and basis set effects. The best theoretical and experimental estimates for the fundamental vibrational frequencies are in excellent agreement.
Structure and melting of a monolayer ethanol film on graphite
Authors: Morishige Kunimitsu
Published: July 2002

The x-ray diffraction measurements of ethanol adsorbed on graphite have been taken over the temperature range 30–215 K and the coverage range 1.75–4.84 molecule/nm2. The analysis of the data by means of the least-squares fitting of the whole pattern shows clearly that zigzag chains of hydrogen bonds are formed in the crystalline monolayer of ethanol where the molecules nearly closely pack together in two dimensions. The diffraction pattern of the liquid monolayer resembles that of the solid monolayer, which suggests the existence of the chain structure of hydrogen bonds retained in the liquid phase. The structure and melting characteristics of the monolayer ethanol film are compared with those of the monolayer methanol.
An extensive ab initio study of the structures, vibrational spectra, quadratic force fields, and relative energetics of three isomers of Cl2O2
Authors: Lee Timothy J. , Rohlfing Celeste McMichael , Rice Julia E.
Published: July 2002

The three lowest-lying isomers of Cl2O2 have been investigated using state-of-the-art ab initio quantum-mechanical methods. Electron correlation methods that have been used include second-order Mo/ller–Plesset perturbation theory, singles and doubles coupled-cluster (CCSD) theory, and the CCSD(T) method, which incorporates a perturbational estimate of the effects of connected triple excitations. Accurate relative energies have been obtained using the CCSD(T) method in conjunction with large atomic natural orbital basis sets that include up to g-type functions. Our best estimate is that the ClClO2 and ClOClO isomers lie 0.9±2.0 and 10.1±4.0 kcal/mol higher in energy (0 K), respectively, than the more stable ClOOCl peroxide form. In order to obtain accurate equilibrium geometries it is necessary to include f-type functions in the one-particle basis set. The vibrational spectra (including IR intensities) of all three isomers are computed and compared with experimental data for ClOOCl and ClClO2. The theoretical and experimental vibrational frequencies agree very well except for the symmetric combination of Cl–O stretches in ClOOCl, where it is concluded that the experimental band is most likely due to the antisymmetric Cl–O stretch. The heat of formation of ClOOCl is computed using an isodesmic reaction involving Cl2O, H2O, and HOOH, and determined to be 34.2 kcal/mol (0 K). The largest uncertainty in this value is due to potential errors in the experimental heat of formation of Cl2O. Using the experimental heat of formation of ClO, the dissociation energy of ClOOCl relative to 2 ClO is computed to be 14.9 kcal/mol at 298 K. The equilibrium structures and vibrational spectra of Cl2O, H2O, and HOOH from our highest-level calculations are found to be in excellent agreement with the available experimental data.
Ab initio multireference study of the BN molecule
Authors: Martin J. M. L. , Lee Timothy J. , Scuseria Gustavo E. , Taylor Peter R.
Published: July 2002

The lowest 1Σ+ and 3Π states of the BN molecule have been studied using multireference configuration interaction (MRCI) and averaged coupled-pair functional (ACPF) methods and large atomic natural orbital (ANO) basis sets, as well as several coupled cluster methods. Our best calculations strongly support a 3Π ground state, but the a 1Σ+ state lies only 381±100 cm−1 higher. The a 1Σ+ state wave function exhibits strong multireference character and, consequently, the predictions of the perturbationally-based single-reference CCSD(T) coupled cluster method are not as reliable in this case as the multireference results. The best theoretical predictions for the spectroscopic constants of BN are in good agreement with experiment for the X 3Π state, but strongly suggest a misassignment of the fundamental vibrational frequency for the a 1Σ+ state.
FONO: A difficult case for theory and experiment
Authors: Lee Timothy J. , Rice Julia E.
Published: July 2002

The equilibrium structures, vibrational spectra, and relative energetics of the FNO2, cis-FONO, and trans-FONO isomers have been investigated using high-levels of ab initio theory. These methods include second-order Mo/ller–Plesset perturbation theory (MP2), singles and doubles coupled-cluster (CCSD) theory, and the CCSD(T) method, which incorporates a perturbational estimate of the effects of connected triple excitations. FNO2 is determined to be 36.9±2.5 kcal/mol (0 K) more stable than cis-FONO, which is more stable than trans-FONO by 2.5±1.0 kcal/mol (0 K). The molecular structure of cis-FONO is shown to have typical F–O and central O–N single bond distances, indicating that cis-FONO has a structure analogous to HONO. The computed vibrational spectrum of cis-FONO is shown to be consistent with infrared matrix isolation experiments, including isotopic shifts. The experimentally deduced structure of FONO (based on a normal coordinate analysis), however, is shown to be incorrect because one of the vibrational bands included in the normal coordinate analysis is either a combination band or an overtone.
Frequency-dependent polarizabilities and first hyperpolarizabilities of H2O
Authors: Luo Yi , Ågren Hans , Vahtras Olav , Jo/rgensen Poul , Spirko Vladimir , Hettema Hinne
Published: July 2002

Static and frequency-dependent dipole polarizabilities α and first hyperpolarizabilities β are calculated for H2O using self-consistent field (SCF) and multiconfigurational self-consistent- field (MCSCF) linear and quadratic response theory. With an active orbital space where one correlating orbital is included for each occupied valence orbital excellent agreement is obtained with the experimental hyperpolarizability. Basis set dependency has been investigated and a detailed vibrational analysis has been carried out.
Instabilities in propagating reaction-diffusion fronts
Authors: Horváth Dezsö , Petrov Valery , Scott Stephen K. , Showalter Kenneth
Published: July 2002

Simple reaction-diffusion fronts are examined in one and two dimensions. In one-dimensional configurations, fronts arising from either quadratic or cubic autocatalysis typically choose the minimum allowable velocity from an infinite spectrum of possible wave speeds. These speeds depend on both the diffusion coefficient of the autocatalytic species and the pseudo-first-order rate constant for the autocatalytic reaction. In the mixed-order case, where both quadratic and cubic channels contribute, the wave speed depends on the rate constants for both channels, provided the cubic channel dominates. Wave propagation is completely determined by the quadratic contribution when it is more heavily weighted. In two-dimensional configurations, with unequal diffusion coefficients, the corresponding two-variable planar fronts may become unstable to perturbations. The instability occurs when the ratio of the diffusion coefficient for the reactant to that for the autocatalyst exceeds some critical value. This critical value, in turn, depends on the relative weights of the quadratic and cubic contributions to the overall kinetics. The spatiotemporal form of the nonplanar wave in such systems depends on the width of the reaction zone, and a sequence showing Hopf, symmetry-breaking, and period-doubling bifurcations leading to chaotic behavior is observed as the width is increased.
A coupled-cluster study of XNO (X=H,F,Cl): An investigation of weak X–N single bonds
Authors: Lee Timothy J.
Published: July 2002

Singles and doubles coupled-cluster (CCSD) theory and the CCSD(T) method, CCSD plus a perturbational estimate of the effects of connected triple excitations, have been used to determine the equilibrium structures, dipole moment, vibrational frequencies, and infrared intensities of the HNO, FNO, and ClNO species. A double polarized triple-zeta (TZ2P) quality basis set was used. The CCSD(T) results are found to be in very good agreement with experiment, indicating that the CCSD(T) method performs well in describing the weak X–NO single bond. The experimental heats of formation of the FNO, and ClNO species are examined for internal consistency with experimental data for FNO2 and ClNO2, by using an isodesmic reaction. It is concluded that the experimental data exhibit a small inconsistency. An approach, involving in addition the use of homodesmic reactions, by which a more consistent set of thermochemical data may be obtained is proposed and discussed.
Intramolecular vibrational redistribution of energy in the stimulated emission pumping spectrum of acetylene
Authors: Jonas David M. , Solina Stephani Ann B. , Rajaram Bhavani , Silbey Robert J. , Field Robert W. , Yamanouchi Kaoru , Tsuchiya Soji
Published: July 2002

Using a combination of low resolution dispersed Ã→X̃ fluorescence spectra and high resolution stimulated emission pumping, we have spectroscopically identified the first stages of vibrational energy flow in the highly vibrationally excited acetylene prepared by Ã→X̃ emission over the energy range 5 000–18 000 cm−1. A detailed study of the stimulated emission pumping (SEP) spectrum of acetylene in the EVIB=7000 cm−1 region, in which we report spectroscopic constants and rovibrational term values for 12 vibrational levels, has conclusively shown that Darling–Dennison resonance between the cis and trans degenerate bending vibrations is the first step in the redistribution of vibrational energy from the initially excited Franck–Condon bright CC stretch and trans-bend vibrational combination levels. This allows an extension of our prior dispersed fluorescence (DF) assignments which suggested the crucial role of Darling–Dennison coupling between the cis and trans bends in IVR [J. Chem. Phys. 95, 6336 (1991)].

We prove that the symmetric CH stretch vibration, previously thought to play a crucial role in the redistribution of vibrational energy, is Franck–Condon inactive. We have also shown that vibrational-l-resonance among the states with excitation of both degenerate bending modes, when combined with a Fermi resonance which couples CC stretch/trans/cis-bend excited states to the antisymmetric CH stretch, determines the subsequent flow of vibrational energy after the Darling–Dennison bending resonance. These resonances all scale with vibrational excitation in nearly the simple manner expected for the lowest order anharmonic terms in the Hamiltonian, which allows the prediction of the fastest processes at high energy from a detailed study of the high resolution spectrum at lower energy. We find some interesting rules for vibrational energy flow in the short time dynamics: (i) CC stretch excitation is necessary for stretch–bend coupling; (ii) if V2″ and V4″ are the quantum numbers of the initially excited bright state, and vb″ = v4″ + v5″ is the total bending quantum number of a state coupled to that bright state, then V4″ ≥ vb″ ≥ (V4″–2V2″); (iii) the total stretch quantum number ns″ = (v1″ + v2″ + v3″) is also conserved by the short time dynamics.

These are severe and well characterized restrictions on the range of quantum numbers accessible to the initial bright state during the first stages of intramolecular vibrational redistribution of energy.
Kinetics of protein folding: The dynamics of globally connected rough energy landscapes with biases
Authors: Saven J. G. , Wang J. , Wolynes P. G.
Published: July 2002

We study relaxation within a biased rough energy landscape as a means of investigating protein folding kinetics. The energies of the conformational states of the protein are taken to be random variables. The degree of similarity of each state with the native is described by an order parameter ρ. The energy is, on average, a decreasing function of ρ, in line with the principle of minimal frustration. The limiting case model described here has global connectivity. There are no restrictions on the change in order parameter in the elementary moves through conformational space. The folding kinetics vary as a function of both the energy gap between the folded and unfolded states and the roughness of the energy landscape. This model yields curved Arrhenius plots that are qualitatively similar to those seen in experiments and in simulations of protein folding. We show that in globally connected models, the Laplace transformed concentrations of species obey a frequency dependent generalization of the law of mass action. We show that when states with intermediate degrees of ordering are included in a globally connected model, one obtains much the same qualitative behavior as some experiments that are often used to justify the existence of specific intermediates along a sequential pathway even though there is no such path in the model. Also we show that for short times, populations of ensembles of configurations are dominated by entropic considerations: an observation in harmony with studies on initial events in folding based on more detailed models. Thus, we believe that this model sheds light on the interpretation of experiments that probe protein folding kinetics.
Analysis of morphology of crystals based on identification of interfacial structure
Authors: Liu X. Y. , Boek E. S. , Briels W. J. , Bennema P.
Published: July 2002

A new theoretical approach for the prediction of the growth habit of crystals is presented. This approach is based on a newly derived relation between the growth rate of crystal surfaces and habit-controlling factors, and includes a key step: a so-called interface structure (IS) analysis. This analysis is to formulate the influence of the fluid phase on the crystal morphology. The essential of the IS analysis is to identify the adsorbed growth units which is in dynamic equilibrium with solid units at the crystal surface, and to calculate their concentration. It follows that a key external habit-controlling factor, the so-called surface scaling factor, can be calculated from the analysis. Based on detailed molecular dynamic (MD) simulation data, our formalism is applied to predict the morphology of urea crystals grown from aqueous solutions. Urea crystals grown from the solutions turn out to possess a needlelike shape, in excellent agreement with experiments. This is one of the first examples of the successful theoretical prediction of morphology of crystals, and will provide a new way of thinking and understanding of the influence of the mother phase on crystal habits.
Ion mobility measurements for O+ and N+ in helium gas at 4.35 K
Authors: Sanderson Joseph , Tanuma Hajime , Kobayashi Nobuo , Kaneko Yozaburo
Published: July 2002

The mobilities of O+ and N+ in He have been measured using a liquid helium cooled, selected ion drift tube, at 4.35 K. Results are compared with previous experimental work at higher temperatures and, in the case of O+, comparison is made with theoretical work, where a good agreement is found. The dependence of mobility on effective temperature is discussed in light of our previous work and our measurements are related to features of the ion–atom potential. In order to facilitate further theoretical analysis, recommended values of mobility are tabulated for O+ and N+ in He and also for O+2, N+2, and CO+ in He.
Theoretical study of conjugation, hyperconjugation, and steric effect in B2D4 (D=H, F, OH, NH2, and CH3)
Authors: Mo Yirong , Lin Zhenyang
Published: July 2002

The rotational barriers of BD2 in B2D4 (D=H, F, OH, NH2, and CH3) are examined in terms of conjugation, hyperconjugation, and steric effect at the level of HF/6-31G*. By deleting or keeping the π orbitals on the boron atoms in the HFSCF calculations, for the first time we are able to analyze the hyperconjugation effect on molecular structures and stabilities quantitatively. In the perpendicular structure of B2H4, hyperconjugation results in the shortening of B–B bond from 1.705 to 1.679 Å and stabilizes the system by 3.1 kcal/mol. For B2D4 systems in which D are π donors, there is a competition between the steric effect and π electronic delocalization. The former prefers a perpendicular conformation while the latter prefers a planar one. For B2F4 and B2(NH2)4, these two factors are comparable and therefore, the rotational barrier is close to zero. For B2(OH)4, the intramolecular hydrogen bonds stabilize the planar structure significantly. For B2(CH3)4, however, steric effect dominates and consequently perpendicular structures are overwhelmingly preferred.
Oscillatory surface forces: A test of the superposition approximation
Authors: Frink Laura J. Douglas , van Swol Frank
Published: July 2002

We report on the density functional theory calculations of electrolyte solutions confined between charged plates. Experiments with the surface forces apparatus have shown that for charged cylinders in simple solvents the surface force is oscillatory at short range. It has been suggested that the total force be considered a superposition of the electrostatic repulsion, the solvation force of a pure solvent, and the van der Waals attraction. In this paper we use the Rosenfeld–Kierlik–Rosinberg (RKR) functional to study a three-component electrolyte solution and explicitly test the superposition approximation. We find that the superposition approximation is a good approximation when the surface charge is low and the salt concentration is high. We also find that a three-component electrolyte can display short-range equilibrium separations in the absence of van der Waals interactions.
‘‘Low-momentum electrons’’ and the electronic structure of small molecules
Authors: Schmider Hartmut
Published: July 2002

The electronic Husimi distribution η(r↘,p↘) is a ‘‘fuzzy’’ density in phase space. Sections through this function with a zero momentum variable (p↘;=0), are shown to be indicative of the spatial locations of chemical bonds and ‘‘free electron pairs’’ in molecules. The distribution η(r↘;0) tends to focus on the inter-nuclear regions in position space. The Laplacian ∇2rη(r↘;0), of the function may be used to enhance its diffuse features. The argument is made that the momentum-space Hessian of the Husimi function at the momentum-origin (p↘=0), includes information about the ‘‘flexibility’’ of the electrons and the anisotropy of the latter. The diagonalization of this tensor supplies a pictorial map of preferred directions of electrons in the low-momentum, i.e., ‘‘valence’’ region of momentum space. Examples studied in this paper include the H2, N2, CH4, H2O, C2H4 and C6H6 systems in their Hartree–Fock approximation.
Associative replica Ornstein–Zernike equations and the structure of chemically reacting fluids in porous media
Authors: Trokhymchuk Andrij , Pizio Orest , Holovko Myroslav , Sokolowski Stefan
Published: July 2002

A model for a chemically associating fluid, adsorbed in a disordered porous media, is proposed. The formation of the associates occurs through the directional bonding between the fluid particles. For simplicity, we restrict our attention to the dimerization of particles. In the absence of association, this model reduces to that of Kaminsky and Monson (KM) for the adsorption of methane in a xerosilica gel. This model is studied by means of the replica Ornstein–Zernike ROZ equations, with the hypernetted chain approximation, extended for associating fluids. It follows from a comparison with the computer simulation data that this theory yields a very good description of the structural properties of the KM model. The influence of the fluid density, the matrix packing fraction, and the association energy on the dimerization in the disordered matrix is studied. The fluid compressibility for the KM model and for the dimerizing fluid in a disordered matrix is obtained via the compressibility equation.
Conformational chain statistics in a model lipid bilayer: Comparison between mean field and Monte Carlo calculations
Authors: Harries Daniel , Ben-Shaul Avinoam
Published: July 2002

A comparison between a mean field theory of chain packing in membranes and micelles and Monte Carlo simulations is presented for model lipid bilayers. In both approaches the “lipids” are modeled as freely jointed (but self-avoiding) chains of spherical segments. The first segment of the chain represents the head group, anchored to the bilayer interface by a harmonic binding potential. The simulations are performed for symmetric bilayers composed of 200 chains, with periodic boundary conditions. Both pure and mixed bilayers (composed of long and short chains) are analyzed. In the simulation nonbonded segments interact via Lennard-Jones potentials, ensuring nearly uniform segment density in the bilayer core, as assumed in the mean field theory. The lateral pressure profiles governing the probability distribution of chain conformations in the mean field theory are related and compared to the tangential pressure profiles calculated from the simulations using Kirkwood–Buff’s molecular theory. The two pressure profiles show very good agreement. We also calculate two conformational chain properties: end-segment distributions and orientational bond order parameters. The end-segment distributions calculated by the two approaches show excellent agreement. The order parameters compare somewhat less satisfactorily, yet we found that the order parameters derived from the simulations depend rather sensitively on the details of the interaction potential. In general, the results of the simulations support the use of the mean field theory as a (simple) tool for studying conformational chain statistics in confined environments and related thermodynamic properties, such as membrane curvature elasticity.
Effects of long-range electrostatic potential truncation on the free energy of ionic hydration
Authors: Ashbaugh Henry S. , Wood Robert H.
Published: July 2002

The free energy of sodium ion hydration calculated from computer simulations employing both the molecular potential truncation and Ewald summation methods for evaluation of long-range electrostatic interactions disagree by 20%. The discrepancy between the free energies determined by both techniques is found to be methodological, resulting from an imbalance in the molecular potential truncation scheme that biases the interaction of the water–oxygen and hydrogens with the ion unequally. A simple physical model is proposed and an analytical expression derived to correct this discrepancy.
Screening of ion–ion correlations in electrolyte solutions adsorbed in electroneutral disordered matrices of charged particles: Application of replica Ornstein–Zernike equations
Authors: Hribar Barbara , Pizio Orest , Trokhymchuk Andrij , Vlachy Vojko
Published: July 2002

The replica Ornstein–Zernike (ROZ) equations for an ionic fluid adsorbed in an electroneutral, disordered matrix of ions were applied to a model where both ionic subsystems were presented as point charges interacting only via Coulomb forces. The effects of fluid (electrolyte) and matrix concentration on the screening of the ion–ion interactions in the fluid phase were investigated. The effects of the prequenching conditions were also examined. It was shown that augmenting the matrix concentration promotes attraction between equally charged ions and repulsion between ions of opposite sign. This peculiar behavior, observed first in the simulation study of Bratko and Chakraborty [J. Chem. Phys. 104, 7700 (1996)], follows straightforwardly from the ROZ equations. Moreover, we generalized the expression for the disorder averaged ion–ion potential for an arbitrary fluid concentration and prequenching conditions. In addition to these results, which are consistent with computer studies, we present some new results that have not been observed in simulations. For example, alternating ionic ordering, generated by the influence of the charged matrix was observed. This contribution can be considered as a first step toward a study of primitive model electrolytes adsorbed in disordered matrices of hard-sphere ions. The solution of this problem will be presented elsewhere.
Molecular dynamics simulations of structural formation of a single polymer chain: Bond-orientational order and conformational defects
Authors: Fujiwara Susumu , Sato Tetsuya
Published: July 2002

The structural formation of a single polymer chain with 500 CH2 groups is studied by the molecular dynamics simulations. Our simulations show that the bond-orientationally ordered structure at low temperatures is formed from a random-coil structure at high temperatures by a gradual stepwise cooling. From the radii of gyration and the bond-orientational order parameters, it is found that the anisotropy of a polymer chain also grows during the growth of the bond-orientational order. In the bond-orientationally ordered structure at low temperatures, 16 stems form a structure with deformed hexagonal symmetry and the stems in the outer layer have a tilted configuration. Furthermore, the gauche states are localized in the fold surface and the conformational states in the fold surface change more readily than those in the orientationally-ordered region.
On lyotropic behavior of molecular bottle-brushes: A Monte Carlo computer simulation study
Authors: Saariaho Mika , Ikkala Olli , Szleifer Igal , Erukhimovich Igor , ten Brinke Gerrit
Published: July 2002

A three dimensional continuous space Monte Carlo computer simulation study is presented to discuss the extension of flexible, linear polymer chains due to the presence of equally flexible side chains. We consider the enhancement of the persistence length of bottle-brush structures in an athermal solution due to steric interactions between the side chains. The largest structure studied consists of a backbone of 100 beads with 50 side chains of 20 beads each. The persistence length λ is evaluated in two different ways using the radius of gyration of the backbone and the bond angle correlation function, respectively. A correct description of the backbone conformations is shown to require at least two characteristic lengths. At a small length scale the backbone behaves flexible; the extension occurs at a larger length scale. There is a strong indication that the ratio between the persistence length and the diameter, which is the determining factor for lyotropic behavior of conventional semiflexible chains, levels off as a function of the side chain length. The value of this ratio is, moreover, too small to induce lyotropic behavior along this line. Recent experimental observations of lyotropic behavior of polymacromonomers are discussed in terms of these findings.
A purely ab initio spectroscopic quality quartic force field for acetylene
Authors: Martin Jan M. L. , Lee Timothy J. , Taylor Peter R.
Published: July 2002

The quartic force field of acetylene was determined using the CCSD(T) method (coupled cluster with all single and double substitutions and quasiperturbative inclusion of connected triple excitations) with a variety of one-particle basis sets of the atomic natural orbital, correlation consistent, and augmented correlation consistent types. The harmonic πg bending frequency ω4 and the corresponding anharmonicity ω4−ν4 are both found to be extremely sensitive to the basis set used, in particular to the presence of a sufficient complement of diffuse functions. (Due to symmetry cancellation, the corresponding effect on the πu mode, i.e., ω5 and ω5−ν5, is much weaker.) Similar phenomena are observed more generally in bending modes for molecules that possess carbon–carbon multiple bonds. Tentative explanations are advanced. Our best computed quartic force field, which combines CCSD(T)/[6s5p4d3f2g/4s3p2d1f] anharmonicities with a geometry and harmonic frequencies that additionally include inner-shell correlation effects, reproduces the observed fundamentals for HCCH, HCCD, DCCD, H13CCH, and H13C13CH with a mean absolute error of 1.3 cm−1, and the equilibrium rotational constant to four decimal places, without any empirical adjustment. Anharmonicity and quartic resonance constants are in excellent agreement with the recent determination of Temsamani and Herman [J. Chem. Phys. 103, 6371 (1995)], except for the vibrational l-doubling constant R45, for which an adjustment to the computed force field is proposed.
Correcting for electrostatic cutoffs in free energy simulations: Toward consistency between simulations with different cutoffs
Authors: Resat Haluk , McCammon J. Andrew
Published: July 2002

The use of electrostatic cutoffs in calculations of free energy differences by molecular simulations introduces errors. Even though both solute–solvent and solvent–solvent cutoffs are known to create discrepancies, past efforts have mostly been directed toward correcting for the solute–solvent cutoffs. In this work, an approach based on the generalized reaction field formalism is developed to correct for the solvent–solvent cutoff errors as well. It is shown using a series of simulations that when the cutoff lengths are significantly smaller than the half unit cell size, and the solute–solvent cutoff is not much larger than the solvent–solvent cutoff, the new algorithm is able to yield better agreement among simulations employing different truncation lengths.
Analytical derivatives for geometry optimization in solvation continuum models. II. Numerical applications
Authors: Cancès E. , Mennucci B. , Tomasi J.
Published: July 2002

We present some numerical applications of a new method addressed to compute analytical derivatives of free energies for continuum solvation models. The examples reported refer to quantum chemical calculations of geometry optimizations at both Hartree–Fock and Density Functional level. When implemented within the solvation method known as Integral Equation 1998 American Institute of Physics.
Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics
Authors: Barth Eric , Schlick Tamar
Published: July 2002

Force splitting or multiple timestep (MTS) methods are effective techniques that accelerate biomolecular dynamics simulations by updating the fast and slow forces at different frequencies. Since simple extrapolation formulas for incorporating the slow forces into the discretization produced notable energy drifts, symplectic MTS variants based on periodic impulses became more popular. However, the efficiency gain possible with these impulse approaches is limited by a timestep barrier due to resonance—a numerical artifact occurring when the timestep is related to the period of the fastest motion present in the dynamics. This limitation is lifted substantially for MTS methods based on extrapolation in combination with stochastic dynamics, as demonstrated for the LN method in the companion paper for protein dynamics. To explain our observations on those complex nonlinear systems, we examine here the stability of extrapolation and impulses to force-splitting in Newtonian and Langevin dynamics. We analyze for a simple linear test system the energy drift of the former and the resonance-related artifacts of the latter technique. We show that two-class impulse methods are generally stable except at integer multiples of half the period of the fastest motion, with the severity of the instability worse at larger timesteps. Extrapolation methods are generally unstable for the Newtonian model problem, but the instability is bounded for increasing timesteps. This boundedness ensures good long-timestep behavior of extrapolation methods for Langevin dynamics with moderate values of the collision parameter. We thus advocate extrapolation methods for efficient integration of the stochastic Langevin equations of motion, as in the LN method described in paper I.
Origin of the complex dynamics in structural isomerization of small clusters: The effects of potential topography
Authors: Seko Chihiro , Takatsuka Kazuo
Published: July 2002

The dependence of lifetime distribution in isomerization dynamics of Ar7-like clusters on the potential topography is reported. Using the scaled Morse potential V=∑i<j(e−2(ρij−ρ0)−2e−(ρij−ρ0)), where ρij is an internuclear distance, and ρ0, the equilibrium distance of the isolated diatomic molecule, is the only independent parameter that uniquely specifies the system Hamiltonian, we have examined the dynamics for two typical values of ρ0. In the high enough energy region, which is called the liquidlike phase, the cluster of a small ρ0 (called a compact cluster) has an exponential form for the lifetime distribution. In contrast, dynamics on the potential with a large ρ0 (a loose cluster) exhibits a large deviation from the exponential form, its mixing dynamics notwithstanding; it displays a large hole in the short lifetime region and a steep clifflike structure in the even shorter lifetime region embedded in the hole. Since the deviation is so clear, the present system offers an excellent example with which to investigate the dependence of phase space structure on the potential topography. We have identified the mechanisms of formation both of the hole and cliff. The hole is particularly important to understand how mixing dynamics can deviate from the statistically simple exponential distribution. By comparing a variety of quantities that characterize the system dynamics, we propose a conceptual picture to understand the basic difference between the dynamics on compact and loose potentials, in which the complexity of the dynamics is ascribed to the bifurcation of the reaction tubes and to the turning-point distributions clinging to the branching places of such bifurcated tubes.
Electron spin resonance studies of 45Sc17O, 89Y17O, and 139La17O in rare gas matrices: Comparison with ab initio electronic structure and nuclear hyperfine calculations
Authors: Knight Lon B. , Kaup John G. , Petzoldt Benjamin , Ayyad Ramzi , Ghanty Tapan K. , Davidson Ernest R.
Published: July 2002

The first nuclear hyperfine measurements of 17O (I=5/2) have been made for Sc17O, Y17O and La17O in their X 2Σ ground electronic states. These metal oxide radicals were generated by the pulsed-laser vaporization of the metals in the presence of 16O2/17O2 and trapped in neon and argon matrices for electron spin resonance investigations. The fully resolved A tensors of the metal and 17O were compared with ab initio theoretical calculations—a comparison previously reported only for the ScO radical. The computational methods employed were unrestricted Hartree–Fock, density functional theory (DFT), and restricted open-shell Hartree–Fock. Having the metal and 17O hyperfine interactions available has permitted a more thorough description of the electronic structure and charge distribution in these metal oxide molecules. An electronic structure comparison with the AlO, GaO, and InO radicals has also been made. Reasonably good agreement between the observed and calculated values of Aiso and Adip were achieved with the DFT method providing the closest agreement.
Vibrational study of a well–barrier–well thiophene–based oligomer in relation to the effective π-conjugation length
Authors: Hernández V. , Casado J. , Kanemitsu Y. , López Navarrete J. T.
Published: July 2002

We have studied the Fourier transform infrared (FTIR) and the Fourier transform Raman (FT-Raman) spectra of a new thiophene-based oligomer in neutral form. The compound has a well–barrier–well structure, where the well parts are two bithienyl end moieties and the barrier part is a vinylene fragment with a larger energy gap. Characteristic features are correlated with vibrational data of unsubstituted α-linked oligothiophenes and α,α′-dimethyl end-capped oligothiophenes to assess information about the effective conjugation length of this oligomer. The FTIR and FT-Raman spectra have also been theoretically calculated at the B3LYP/6-31G** and RHF/6-31G** levels, respectively, to propose a vibrational assignment for the main bands in the whole spectral range.