bluuebunny/crossref_metadata_2025 huggingface dataset:
An intermolecular potential function model applied to acetylene dimer, carbon dioxide dimer, and carbon dioxide acetylene
Authors: Muenter J. S.
Published: July 2002

A general model to describe intermolecular potential functions for weakly bound molecular complexes is described. The model is designed to be complex enough to reproduce many observed details of van der Waals molecules, yet be simple enough that the required input data are readily available. The distributed multipole picture of monomer charge distributions is used to calculate electrostatic energies and atom–atom Lennard-Jones terms describe repulsion and dispersion. The individual atom C6 coefficients are derived from long-range molecular C6 values and the C12 coefficients are based on conventional van der Waals atomic radii. This model is applied to (HCCH)2, (CO2)2, and HCCH–CO2. The resulting potential functions are compared in detail, with particular emphasis placed on understanding why (HCCH)2 and (CO2)2 have such different structures.
The energetics and structure of nickel clusters: Size dependence
Authors: Cleveland Charles L. , Landman Uzi
Published: July 2002

The energetics of nickel clusters over a broad size range are explored within the context of the many-body potentials obtained via the embedded atom method. Unconstrained local minimum energy configurations are found for single crystal clusters consisting of various truncations of the cube or octahedron, with and without (110) faces, as well as some monotwinnings of these. We also examine multitwinned structures such as icosahedra and various truncations of the decahedron, such as those of Ino and Marks. These clusters range in size from 142 to over 5000 atoms. As in most such previous studies, such as those on Lennard-Jones systems, we find that icosahedral clusters are favored for the smallest cluster sizes and that Marks’ decahedra are favored for intermediate sizes (all our atomic systems larger than about 2300 atoms). Of course very large clusters will be single crystal face-centered-cubic (fcc) polyhedra: the onset of optimally stable single-crystal nickel clusters is estimated to occur at 17 000 atoms. We find, via comparisons to results obtained via atomistic calculations, that simple macroscopic expressions using accurate surface, strain, and twinning energies can usefully predict energy differences between different structures even for clusters of much smaller size than expected. These expressions can be used to assess the relative energetic merits of various structural motifs and their dependence on cluster size.
Solvation dynamics for an ion pair in a polar solvent: Time-dependent fluorescence and photochemical charge transfer
Authors: Carter Emily A. , Hynes James T.
Published: July 2002

The results of a molecular dynamics (MD) computer simulation are presented for the solvation dynamics of an ion pair instanteously produced from a neutral pair, in a model polar aprotic solvent. These time-dependent fluorescence dynamics are analyzed theoretically to examine the validity of several linear response theory approaches, as well as of various theoretical descriptions (e.g., Langevin equation) for the solvent dynamics per se. It is found that these dynamics are dominated for short times by a simple inertial Gaussian behavior, a feature which is absent in many current theoretical treatments, and which is related to the approximate validity of linear response theory. Nonlinear aspects, such as an overall spectral narrowing, but a transient initial spectral broadening, are also discussed. A model photochemical charge transfer process is also briefly considered to elucidate aspects of the connection between solvation dynamics and chemical kinetic population evolution.
Structure and dynamics of grafted polymer layers: A Monte Carlo simulation
Authors: Lai Pik-Yin , Binder Kurt
Published: July 2002

The bond fluctuation model of polymer chains on lattices is used to study layers of polymers anchored with one end at a hard wall, assuming good solvent conditions and repulsive interactions between the monomers and the wall. Chain lengths from N=10 to N=80 and grafting densities σ from 0.025 to 0.20 are considered, both for the ‘‘quenched’’ case, where the anchor points are kept fixed at randomly chosen surface sites, and the ‘‘annealed’’ case, where lateral diffusion of the anchored ends at the wall is considered. Profiles of monomer density and free end density, chain linear dimensions parallel and perpendicular to the wall, as well as corresponding mean square displacements of inner and end monomers are studied and discussed in the light of current theoretical predictions, and it is shown that most of these properties can be understood in terms of appropriate scaling concepts. Both the relaxation of the total chain configurations and the time dependence of monomer mean square displacements are studied. In the annealed case the lateral diffusion constant D is found to behave as D∼σ−qN−p, where q=2/3 and p crosses over from p≊1 at small σ to p≊2 at large σ. The results for the relaxation time τ are consistent with the recent scaling prediction τ∼σbNa with a=3 and b=2/3.
Detection and spectroscopy of single pentacene molecules in a p-terphenyl crystal by means of fluorescence excitation
Authors: Ambrose W. P. , Basché Th. , Moerner W. E.
Published: July 2002

Recent advances in fluorescence excitation spectroscopy with high efficiency have produced greatly improved optical spectra for the first electronic transition of individual single molecules of pentacene in p-terphenyl crystals at low temperatures (1.5 to 10 K). Two classes of single molecule behavior are observed: class I molecules have time-independent resonance frequencies, and class II molecules show a diffusive motion among several resonant frequencies with time which we term ‘‘spectral diffusion’’ by analogy with a similar effect which is common in amorphous materials. The temperature dependence of the linewidth and the power dependence of the fluorescence emission rate and of the linewidth are reported and analyzed. Various forms of the surprising class II behavior are described, including jumping among several discrete frequencies, creeping toward the center of the inhomogeneous line in many small steps, and a wandering among many possible resonance frequencies. The occurrence of class II behavior is restricted to the wings of the inhomogeneous line suggesting that the effect is correlated with some form of local disorder. The spectral diffusion rate increases with increasing temperature, suggesting that the effect may be due to phonon-assisted transitions of local degrees of freedom around the pentacene defect whose source remains to be identified conclusively.
Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard-sphere liquid
Authors: Zhou Huan-Xiang , Szabo Attila
Published: July 2002

Molecular dynamics simulations of the kinetics of a model of the reaction A+B→B in a dense hard-sphere liquid are compared with the predictions of the Smoluchowski approach to diffusion-influenced reactions. The theory employs the radiation boundary condition at contact with an intrinsic rate constant determined by the low-density collision frequency and the potential of mean force determined by the pair distribution function. Hydrodynamic interactions are ignored and the relative diffusion coefficient is taken as twice the self-diffusion constant. Considering the lack of free parameters and the many-body nature of the problem, the agreement between theory and simulations is surprisingly good over a wide range of B concentrations. Of particular interest is that the above theory provides an exact description of the kinetics at short times.
Femtosecond solvation dynamics in acetonitrile: Observation of the inertial contribution to the solvent response
Authors: Rosenthal Sandra J. , Xie Xiaoliang , Du Mei , Fleming Graham R.
Published: July 2002

The solvation dynamics of acetonitrile were characterized by a time resolved fluorescence shift measurement determined via the fluorescence upconversion technique. The solvation response is clearly two part in character. The fast initial relaxation accounts for ∼80% of the amplitude and is well fit by a Gaussian of 120 fs FWHM, giving a decay time of 70 fs. The slower tail is exponential with a decay time of ∼200 fs. Comparison of the results to molecular dynamics simulations performed by Maroncelli [J. Chem. Phys. 94, 2085 (1991)] reveal the fast initial part of the solvent response arises from small amplitude inertial rotational motion of molecules in the first solvation shell. The implications of a large amplitude, rapid inertial Gaussian component in the solvent response for theoretical descriptions of chemical reaction dynamics in solution are discussed.
Microscopic simulations of macroscopic dielectric constants of solvated proteins
Authors: King Gregory , Lee Frederick S. , Warshel Arieh
Published: July 2002

Microscopic simulation of solvated proteins are used to evaluate the relationship between the macroscopic field and macroscopic polarization, thus providing the corresponding dielectric constant, ε̄. This parameter is evaluated by two different methods which are first examined and calibrated by calculating the dielectric constant of bulk water. These calculations indicate that the reaction field, which represents the effect of the missing solvent around the given explicit region, must be included in the simulations in order to obtain a reasonable value for ε̄. The corresponding effect is not related to the reduction of the effective interactions between charges in the reference region but to the intrinsic value of ε̄ in that region. This means that vacuum calculations of ε̄ in proteins might underestimate its actual value. Or in other words, calculations of ε̄ in proteins must include the effect of the reaction field or a sufficiently large number of surrounding solvent molecules. Having included the surrounding solvent in simulations of trypsin, we find that ε̄ depends on the actual protein site. In particular, we find that ε̄ can be as large as 10 in sites of catalytic importance. It is pointed out that the dielectric constant that should be used in calculations of protein properties depends on the part of the system which is not treated explicitly and is not necessarily the macroscopic ε̄. For example, using ε̄ in electrostatic calculations that consider the protein polar groups explicitly accounts twice for some aspects of the protein polarity. Finally, possible ways to use microscopically determined dielectric constants for electrostatic calculations in protein are considered.
Brownian motion, hydrodynamics, and the osmotic pressure
Authors: Brady John F.
Published: July 2002

It is shown that the osmotic pressure of a colloidal dispersion can be interpreted as the isotropic part of the macroscopic particle stress in the suspension. The particle stress is in turn expressible in terms of hydrodynamic interactions among the suspended particles. Thus, there is a completely mechanical definition of the osmotic pressure, just as there is for the pressure in a molecular fluid. For an equilibrium suspension of colloidal particles subjected to thermal Brownian forces, this mechanical definition is shown to be exactly equal to the usual ‘‘thermodynamic’’ one. The derivation given here places the equilibrium and nonequilibrium properties of macroparticle fluids on the same mechanical foundation that underlies the statistical mechanics of simple liquids. Furthermore, through this development the relationship between hydrodynamics and kinetic-theory-like descriptions of colloids is explained.
Collision-induced absorption in mixtures of symmetrical linear and tetrahedral molecules: Methane–nitrogen
Authors: Birnbaum G. , Borysow A. , Buechele A.
Published: July 2002

The far infrared absorption of a CH4–N2 mixture was measured at 297, 195, and 162 K from 30 to 650 cm−1. The spectral invariants γ1 and α1, proportional, respectively, to the zeroth and first spectral moments, due to bimolecular collisions between CH4 and N2 were obtained from these data and compared with theoretical values. The theory for collision-induced dipoles between a tetrahedral and a diatomic or symmetrical linear molecule includes contributions not previously considered. Whereas the theoretical values of γ1 are only somewhat greater than experiment at all temperatures, including those obtained from the data of Dagg et al., the theoretical values of α1 are significantly lower than the experimental values. From the theoretical spectral moments for the various induced dipole components, the parameters of the BC shape were computed and theoretical spectra were constructed. Good agreement was obtained at the lower frequencies, but with increasing frequencies the theoretical spectra were increasingly less intense than the experimental spectra. Although the accuracy of the theoretical results may suffer from the lack of a reliable potential function, it does not appear that this high frequency discrepancy (also reflected in α1) can be removed by any conceivable modification in the potential.
Benchmark calculations with correlated molecular wave functions. II. Configuration interaction calculations on first row diatomic hydrides
Authors: Peterson Kirk A. , Kendall Rick A. , Dunning Thom H.
Published: July 2002

Potential energy functions have been calculated for the electronic ground states of the first row diatomic hydrides BH, CH, NH, OH, and HF using single- (HF+1+2) and multi- (GVB+1+2 and CAS+1+2) reference internally contracted single and double excitation configuration interaction (CI) wave functions. The convergence of the derived spectroscopic constants and dissociation energies with respect to systematic increases in the size of the one-particle basis set has been investigated for each method using the correlation consistent basis sets of Dunning and co-workers. The effect of augmenting the basis sets with extra diffuse functions has also been addressed. Using sets of double (cc-pVDZ) through quintuple (cc-pV5Z) zeta quality, the complete basis set (CBS) limits for Ee, De, re, and ωe have been estimated for each theoretical method by taking advantage of the regular convergence behavior. The estimated CBS limits are compared to the available experimental results, and the intrinsic errors associated with each theoretical method are discussed. The potential energy functions obtained from GVB+1+2 and CAS+1+2 calculations are observed to yield very comparable spectroscopic constants, with errors in De ranging from 0.4 kcal/mol for BH to 2.9 kcal/mol for HF. The contraction errors associated with the internally contracted multireference CI have also been calculated for each species; while found to increase from BH to HF, they are, in general, small for all calculated spectroscopic constants. For the cc-pVDZ basis sets, spectroscopic constants have also been determined from full CI calculations.
The limiting behavior of water hydrating a phospholipid monolayer: A computer simulation study
Authors: Alper Howard E. , Bassolino-Klimas Donna , Stouch Terry R.
Published: July 2002

We report molecular dynamics simulations of water hydrating a lipid (dimyristoylphosphatidylcholine) monolayer under conditions chosen to eliminate simulation artifacts. These simulations provide a description of the behavior of the membrane–water interface that agrees with recent experimental studies. In particular, we find that the hydrating water orients to contribute the positive end of its dipole to the substantially positive electrostatic potential of the membrane interior, consistent with interpretations of recent experiments. In addition, recent experiments show that this water reorients rapidly on the NMR time scale. Our results concur, however the relatively rapid water motion does not preclude the preferential ordering that we observe. The limiting behavior of the system shows three hydration shells about the lipid PC headgroups and significant hydrogen bonding of water to the phosphate groups. The choline group experiences different environments, and the structure of the first hydration shell clearly corresponds to a clathrate. The motion of the hydrating water was found to be slower than that of bulk water, and the computed residence times for water about the lipids (20 ps about choline, 10 ps about phosphate) were in excellent agreement with results of NMR experiments. This further shows that water resides in a clathrate shell longer than in a shell about ions. In addition, we show that the structure and dynamics of water hydrating the lipids are very sensitive to the treatment of the long-range interactions. In particular, the radial structure sharpens considerably, a third hydration shell about the phosphate was observed only with large cutoffs, and hydrogen bonding of water to the lipids increased by 25%. The water moved more slowly than bulk when large cutoffs were employed but moved faster than bulk water when small cutoffs were used and the residence times for water about the lipids were twofold–fivefold larger using large cutoffs. In general it was found that the lipids significantly influence water out to several hydration shells, and that water hydrating the lipids behaves differently than bulk water.
Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties
Authors: Woon David E. , Dunning Thom H.
Published: July 2002

An accurate description of the electrical properties of atoms and molecules is critical for quantitative predictions of the nonlinear properties of molecules and of long-range atomic and molecular interactions between both neutral and charged species. We report a systematic study of the basis sets required to obtain accurate correlated values for the static dipole (α1), quadrupole (α2), and octopole (α3) polarizabilities and the hyperpolarizability (γ) of the rare gas atoms He, Ne, and Ar. Several methods of correlation treatment were examined, including various orders of Moller–Plesset perturbation theory (MP2, MP3, MP4), coupled-cluster theory with and without perturbative treatment of triple excitations [CCSD, CCSD(T)], and singles and doubles configuration interaction (CISD). All of the basis sets considered here were constructed by adding even-tempered sets of diffuse functions to the correlation consistent basis sets of Dunning and co-workers. With multiply-augmented sets we find that the electrical properties of the rare gas atoms converge smoothly to values that are in excellent agreement with the available experimental data and/or previously computed results. As a further test of the basis sets presented here, the dipole polarizabilities of the F− and Cl− anions and of the HCl and N2 molecules are also reported.
Integrating the Car–Parrinello equations. II. Multiple time scale techniques
Authors: Tuckerman Mark E. , Parrinello Michele
Published: July 2002

In this paper, new techniques for integrating the Car–Parrinello equations based on multiple time scale methodology are presented. The formalism of multiple time scale methodology based on operator factorizations of the classical Liouville propagator is reviewed. It is shown how the techniques are applied to Car–Parrinello for use with the velocity Verlet and Gaussian dynamics schemes presented in the preceding paper [M. E. Tuckerman and M. Parrinello, J. Chem. Phys. 101, 1302 (1994)], and a detailed discussion is presented of how a reference system for Car–Parrinello simulations may be chosen. It is shown that the use of such techniques can save up to a factor of 5–10 in cpu time over the standard methods.
Density functional calculations on first-row transition metals
Authors: Russo Thomas V. , Martin Richard L. , Hay P. Jeffrey
Published: July 2002

The excitation energies and ionization potentials of the atoms in the first transition series are notoriously difficult to compute accurately. Errors in calculated excitation energies can range from 1 to 4 eV at the Hartree–Fock level, and errors as high as 1.5 eV are encountered for ionization energies. In the current work we present and discuss the results of a systematic study of the first transition series using a spin-restricted Kohn–Sham density-functional method with the gradient-corrected functionals of Becke and Lee, Yang and Parr. Ionization energies are observed to be in good agreement with experiment, with a mean absolute error of approximately 0.15 eV; these results are comparable to the most accurate calculations to date, the quadratic configuration interaction single, double (triple) [QCISD(T)] calculations of Raghavachari and Trucks. Excitation energies are calculated with a mean error of approximately 0.5 eV, compared with ∼1 eV for the local density approximation and 0.1 eV for QCISD(T). These gradient-corrected functionals appear to offer an attractive compromise between accuracy and computational effort.
Conformational behavior of gaseous glycine by a density functional approach
Authors: Barone Vincenzo , Adamo Carlo , Lelj Francesco
Published: July 2002

Density functional calculations with large basis sets have been performed for nine conformers of neutral glycine. The results obtained by standard, even gradient corrected functionals are significantly different from the best post-Hartree–Fock computations and the available experimental data. Inclusion of some Hartree–Fock exchange significantly improves matters, thus providing a promising protocol for the study of noncovalent interactions in biomolecules.
Theory of the structure of adsorbed block copolymers: Detailed comparison with experiment
Authors: Baranowski R. , Whitmore M. D.
Published: July 2002

We present a numerical, self-consistent field study of adsorbed diblock copolymers in thermal solvents, with a detailed and quantitative comparison with recent experiments performed on poly(dimethylsiloxane-block-styrene) copolymer spread as a monolayer at the free surface of ethyl benzoate [M. S. Kent, L. T. Lee, B. Farnoux, and F. Rondelez, Macromolecules 25, 6240 (1992); M. S. Kent, L. T. Lee, B. J. Factor, F. Rondelez, and G. S. Smith, J. Chem. Phys. 103, 2320 (1995)]. These neutron reflectivity experiments, for the first time, independently varied both the molecular weight and surface density, and probed the size and nature of the depletion layer at the surface. In the calculations, the polymer and solvent are characterized by realistic values of the pure component densities, the Kuhn length and the Flory interaction parameter. We examine the properties of the dangling block, specifically the depletion layer, the thickness of the brush, the maximum polymer concentration and its location, and the dependence of these properties on surface density and molecular weight. We obtain very good agreement with the experiments, especially for the functional dependences, which indicate that these systems are not in the asymptotic brush limit. We also argue that this conclusion applies to many experiments, some of which were previously thought to be in the asymptotic limit.
Logic gates in excitable media
Authors: Tóth Ágota , Showalter Kenneth
Published: July 2002

The interaction of chemical waves propagating through capillary tubes is studied experimentally and numerically. Certain combinations of two or more tubes give rise to logic gates based on input and output signals in the form of chemical waves and wave initiations. The geometrical configuration, the temporal synchronization of the waves, and the ratio of the tube radius to the critical radius of the excitable medium determine the features of the logic gates.
Experiments on the kinetics of field evaporation of small ions from droplets
Authors: Loscertales I. G. , Fernández de la Mora J.
Published: July 2002

The phenomenon of ion evaporation from charged liquid surfaces is at the basis of electrospray ionization, a source of a stunning variety of gas phase ions. It is studied here by producing a monodisperse cloud of charged droplets and measuring the charge q and diameter dr of the residue particles left after complete evaporation of the solvent. When the droplets contain small monovalent dissolved ions, the electric field E on the surface of their solid residues is found to be independent of dr. One can thus argue that the source of small ions in electrospray ionization is field-emission, and not other proposed mechanisms such as Dole’s charged residue model. A consequence of the observed independence of E on dr is that the rate of ion ejection is simply related to the rate of solvent evaporation, estimated here as that for a clean surface of pure solvent.

The reduction G(E) brought about by the electric field E in the activation energy for ion evaporation has thus been inferred as a function of the measured field E in the range 1.5<E(V/nm)<3.25. It agrees surprisingly well with the so-called Schottky hump from the image potential model (IPM), GIPM=(e3E/4πε0)1/2. This remarkably simple result is paradoxical in view of two major objections raised earlier against the use of the IPM for ion evaporation from liquids. However, the correct mechanism (first introduced by Iribarne and Thomson) leading to an attractive interaction between the liquid surface and the escaping ion is not the creation of an image charge, but the polarization of the dielectric liquid by the ion. In the limit of a large dielectric constant ε≫1, the image force and the polarization force coincide numerically, though the later sets in much faster and is apparently free from the paradox raised by Röllgen. Also, the dielectric nature of the liquid and its strong screening of the net charges near its surface resolves another paradox raised by Fenn regarding the discrete distribution of charges. This screening also introduces a correction in the model proposed by Iribarne and Thomson for G(E), making its predictions virtually indistinguishable from those of GIPM(E). In conclusion, small ions observed in electrospray ionization are produced by field-emission. Measured ionization rates are well represented by results from a ‘‘polarization potential model’’ which appears to be physically sound. These predictions coincide with those from the IPM in the limit ε≫1, the only case studied so far.
A general method for constructing multidimensional molecular potential energy surfaces from ab initio calculations
Authors: Ho Tak-San , Rabitz Herschel
Published: July 2002

A general interpolation method for constructing smooth molecular potential energy surfaces (PES’s) from ab initio data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an a posteriori error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easily extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He–He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson et al. [J. Chem. Phys. 99, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent ab initio calculations by Tao et al. [J. Chem. Phys. 101, 8680 (1994)], and a three-dimensional potential energy surface of the H+3 molecular ion using highly accurate ab initio calculations of Röhse et al. [J. Chem. Phys. 101, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by Röhse et al. using a low order polynomial fitting procedure.
Block Lanczos and many-body theory: Application to the one-particle Green’s function
Authors: Weikert H.-G. , Meyer H.-D. , Cederbaum L. S. , Tarantelli F.
Published: July 2002

The importance of the block or band Lanczos method for many-body Green’s function calculations of atomic and molecular systems is discussed. The usual computation schemes for determining the Green’s function involve the diagonalization of Hermitian secular matrices. Considerable numerical difficulties arise, on the one hand, from the size of these matrices and, on the other hand, from the large number of eigenvalues and eigenvectors which often need to be computed in practice. In the case of the one-particle Green’s function it is shown how the computational effort of the diagonalization process can be substantially reduced using block Lanczos. The proposed procedure which consists of a block Lanczos ‘‘prediagonalization’’ and a subsequent diagonalization of the resulting smaller secular matrices quite naturally exploits the specific structure of the secular problems encountered. Its computational performance is demonstrated in a model application to the benzene molecule. The calculation of the complete valence-shell ionization spectra of the systems BeF2−4, BeF−3, and BeF2 is devised as a further application of the method in the particular case where the treatment of the full secular problem is computationally prohibitively expensive.
Dipole bound, nucleic acid base anions studied via negative ion photoelectron spectroscopy
Authors: Hendricks J. H. , Lyapustina S. A. , de Clercq H. L. , Snodgrass J. T. , Bowen K. H.
Published: July 2002

The anions of the nucleic acid bases, uracil and thymine, were studied by negative ion photoelectron spectroscopy. Both monomer anions exhibit spectroscopic signatures that are indicative of dipole bound excess electrons. The adiabatic electron affinities of these molecules were found to be 93±7 meV for uracil and 69±7 meV for thymine. No conventional (valence) anions of these molecules were observed.
Micellization of strongly segregated block copolymers
Authors: Förster Stephan , Zisenis Mathias , Wenz Eckhard , Antonietti Markus
Published: July 2002

Series of diblock copolymers of the type poly(styrene-b-4-vinylpyridine) (PS-P4VP) are synthesized via anionic polymerization. In toluene, a selective solvent for the PS block, well-defined micelles with narrow molecular weight distribution are formed. Size and shape of the micelles are characterized by static (SLS) and dynamic light scattering (DLS), and electron microscopy (EM). The aggregation number Z exhibits a scaling relation Z∝N1.93P4VPN−0.79PS, where N is the degree of polymerization of each block. We find this behavior close to a Z∼N2AN−0.8B limiting scaling law which appears to be a characteristic of strongly segregated diblock and triblock copolymer systems as well as low molecular weight cationic, anionic, and nonionic surfactants. A simple micellization model is developed that predicts aggregation numbers of surfactants, diblock, triblock, and graft copolymers. The corona dimension Dh as measured by DLS scales as Dh∝Z0.21N0.63PS in agreement with the theoretical prediction D∼Z1/5N3/5B for starlike molecules in good solvents. Neither unimers nor a critical micelle concentration are observed. Instead at very low concentrations the excess scattering intensity increases due to the formation of large particles.
Calculation of classical trajectories with a very large time step: Formalism and numerical examples
Authors: Olender Roberto , Elber Ron
Published: July 2002

A new algorithm to compute long time molecular dynamics trajectories is presented. The technique is based on the stochastic path integral of Onsager and Machlup. Trajectories of fixed length of time are computed by path optimization between two end points. Modes of motion with periods shorter than the discrete time step are automatically filtered out, making the trajectories stable for almost an arbitrary time step. Several numerical examples are provided, including motions on the Mueller potential and a conformational transition in alanine dipeptide. Paths similar to the usual molecular dynamics trajectories are obtained, employing time steps 100 times larger than those used in straightforward molecular dynamics.
On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters
Authors: Andricioaei Ioan , Straub John E.
Published: July 2002

Generalized Monte Carlo and molecular dynamics algorithms which provide enhanced sampling of the phase space in the calculation of equilibrium thermodynamic properties is presented. The algorithm samples trial moves from a generalized statistical distribution derived from a modification of the Gibbs–Shannon entropy proposed by Tsallis. Results for a one-dimensional model potential demonstrate that the algorithm leads to a greatly enhanced rate of barrier crossing and convergence in the calculation of equilibrium averages. Comparison is made with standard Metropolis Monte Carlo and the J-walking algorithm of Franz, Freeman and Doll. Application to a 13-atom Lennard-Jones cluster demonstrates the ease with which the algorithm may be applied to complex molecular systems.
Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water
Authors: Hünenberger Philippe H. , van Gunsteren Wilfred F.
Published: July 2002

Different schemes for treating the electrostatic interactions in molecular dynamics simulations are investigated: charge-group truncation with or without reaction-field correction, atomic truncation with or without reaction-field correction, and Ewald summation. When a reaction-field correction is applied, the influence of the size of the radius selected for the spherical boundary to the continuum is also considered. The different schemes are applied to simple point charge water simulations, and simulated energetic, transport, structural, and dielectric properties are compared. It is concluded that (i) the inclusion of a reaction-field correction in a charge-group truncation scheme induces significant changes in different types of properties, and that a number of properties are not identical to those observed using the Ewald scheme, (ii) when the reaction-field correction is included in an atomic truncation scheme instead, the agreement with the Ewald results is in general improved, and (iii) the increase (decrease) of the radius of the boundary to the continuum by 0.1 (nm) with respect to the cutoff radius induces in both cases a degradation of the simulated properties. Special attention is paid to the calculation of the dielectric permittivity from the simulations. Due to the finite size of the statistical ensembles considered, this property is not assumed to be isotropic, and the degree of anisotropy is used instead as a test for convergence. Since the incorporation of the reaction-field correction into an atomic truncation scheme leads, when systems of high dielectric permittivity are considered, to electrostatic interactions which implicitly contain a (physically reasonable) shifting function and properties which are comparable to those obtained using the Ewald method, this scheme is a clear improvement over a charge-group-based truncation when a reaction-field correction is used in molecular dynamics simulations of noncharged systems.
Solvent dependence of the first hyperpolarizability of p-nitroanilines: Differences between nonspecific dipole–dipole interactions and solute–solvent H-bonds
Authors: Huyskens François L. , Huyskens Pierre L. , Persoons André P.
Published: July 2002

In this paper, the influence of solvents on the first hyperpolarizability β of nonlinear optical (NLO) molecules is studied at 25 °C for solutions of p-nitroaniline and N,N-dimethyl paranitroaniline in some 50 solvents belonging to different classes. The hyperpolarizabilities deduced from measured hyper-Rayleigh scattering are the relative ones with as reference that of paranitroaniline in 1,4-dioxane. Taking for the latter the literature value of 16.9 10−30 esu, the β values vary from 14.4 to 29.9 10−30 esu for paranitroaniline and from 28.7 to 46.2 10−30 esu for N,N-dimethyl paranitroaniline. A selection of the solvents is made on the basis of the fraction of the time γ0 during which the NLO molecule is not involved in H-bonding with the solvent molecules. γ0 can be determined from the solubility in the given solvent. The formation of specific solute–solvent interactions as H-bonds always increases the hyperpolarizability β. In the absence of such interactions, the hyperpolarizability increases with the square root of the gaseous dipole moment of the solvent molecule and decreases when the mean interdistance between the center of the NLO molecule and the closest solvent dipole increases. A statistical study of a large number of solvents leads indeed to the correlation β=βgas+aμS/VS where a is a constant for a given NLO molecule. When H-bonds are formed the correlation becomes: β=βgas+γ0aμS/VS+(1−γ0)bμS, where b is a constant for a given NLO molecule. H-bond formation enhances the hyperpolarizability because it reduces the distance between the neighboring solvent dipole and the center of the NLO molecule to a constant value, independent of VS.
Molecular orbital study of H2 and CH4 activation on small metal clusters. I. Pt, Pd, Pt2, and Pd2
Authors: Cui Qiang , Musaev Djamaladdin G. , Morokuma Keiji
Published: July 2002

The electronic structure of Pd/Pt dimer and the detailed reaction mechanism of H2 and CH4 activation on these clusters have been studied with density functional (B3LYP) and complete active space second-order perturbation (CASPT2) theories. It was found that B3LYP calculations gave reliable results on the electronic structures of the Pd/Pt dimers, in comparison with our CASPT2 calculations and data from previous theoretical investigations. Full geometry optimization has been carried out in the current study in contrast to previous work where only limited potential energy scans have been carried out, which led to dramatically different reaction mechanisms. In the case of Pt2+H2/CH4, H–H/C–H activation preferentially takes place at first on one metal atom via structures far from planar, then one of the H atoms migrates to the other Pt atom with negligible barrier. On both the singlet and the triplet state, H–H activation is barrierless, while C–H activation has a distinct barrier on the singlet state for reaction starting from the ground triplet state Pt2. In contrast, Pd2 is found to activate the H–H bond without barrier on the singlet state, while the triplet states are very high in energy. In the CH4 activation, two paths, referred as symmetric and asymmetric paths, respectively, have been found. The characters of the metal dimers and the differences between Pd2 and Pt2 systems have been analyzed based on MO diagrams. Results from the current study are consistent with the recent experimental observations of Cox et al. on the reactivities of unsupported Pdn and Ptn.
Analytical second derivatives of the free energy in solution by polarizable continuum models
Authors: Cossi Maurizio , Barone Vincenzo
Published: July 2002

We present an algorithm for the analytical evaluation of free energy second derivatives with respect to nuclear displacements in the framework of the polarizable continuum model (PCM). The algorithm has been obtained for two recently proposed PCM versions, namely the conductor-like and the isotropic integral equation formalism models, and it can be applied to Hartree–Fock and to density functional SCF calculations on closed- and open-shell systems. The formal derivation is shown in detail and a number of numerical tests are presented: the applications show that analytical results are in excellent agreement with those obtained numerically and, as in vacuo, the analytical procedure is far more efficient. The presented algorithm can be routinely used with an upcoming release of the Gaussian program.
Random heteropolymer adsorption on disordered multifunctional surfaces: Effect of specific intersegment interactions
Authors: Srebnik Simcha , Chakraborty Arup K. , Bratko Dusan
Published: July 2002

Biopolymers adsorb on cell and virus surfaces with great specificity. Recently, theoretical and computational studies have inquired as to whether there are any universal design strategies that nature employs in order to affect such recognition. Specifically, the efficacy of multifunctionality and quenched disorder as essential design strategies has been explored. It has been found that when random heteropolymers interact with disordered multifunctional surfaces, a sharp transition from weak to strong adsorption occurs when the statistics characterizing the sequence and surface site distributions are related in a special way. The aforementioned studies consider the intersegment interactions to be much weaker than the surface site interactions. In this work we use nondynamic ensemble growth Monte Carlo simulations to study the effect of the competition between frustrating intersegment and segment–surface interactions. We find that as the intersegment interactions become stronger, the transition from weak to strong adsorption occurs at higher surface disorder strengths. This trend is reversed beyond a threshold strength of the intersegment interactions because interactions with the surface are no longer able to “unravel” the dominant conformations favored by the intersegment interactions.
Reaction field effects on nitrogen shielding
Authors: Zhan Chang-Guo , Chipman Daniel M.
Published: July 2002

Solvation effects on nuclear magnetic shielding at nitrogen in the CH3CN, CH3NO2, CH3NCS, and CH3ONO2 molecules are studied using electronic structure calculations. Reaction field theory together with a dielectric continuum is invoked to describe solute-solvent electrostatic interactions, using a solute electronic isodensity contour to define the cavity surface. With the common approach that treats only surface polarization effects, it is found that the nitrogen shielding is very sensitive to the cavity size and usually provides results in reasonable agreement with experiment only for rather large cavity sizes corresponding to contour values of ∼0.000 25–0.0005 a.u. With a more complete treatment that also includes volume polarization effects arising from penetration of the solute charge density outside the cavity, the nitrogen shielding becomes much less sensitive to the cavity size and reasonable agreement with experiment can be obtained with contour values ∼0.001–0.003 a.u., which is more consistent with previous findings on the optimum cavity size for determination of free energies of solvation.
Evolution of lowest singlet and triplet excited states with number of thienyl rings in platinum poly-ynes
Authors: Chawdhury N. , Köhler A. , Friend R. H. , Wong W.-Y. , Lewis J. , Younus M. , Raithby P. R. , Corcoran T. C. , Al-Mandhary M. R. A. , Khan M. S.
Published: July 2002

Soluble, rigid-rod organometallic polymers trans-[-Pt(PBu3n)2–C≡C–R–C≡C–]∞ (R=bithienyl 2, terthienyl 3) have been synthesized in good yields by the CuI-catalyzed dehydrohalogenation reaction of trans-[Pt(PBu3n)2Cl2] with one equivalent of the diterminal alkynyl oligothiophenes H–C≡C–R–C≡C–H in CH2Cl2/iPr2NH at room temperature. We report the thermal properties, and the optical absorption, photoluminescence, and photocurrent action spectra of 1 (trans-[–Pt(PBu3n)2–C≡C–R–C≡C–]∞, R=thienyl), 2 and 3 as a function of the number of thiophene rings within the bridging ligand. With increasing thiophene content, the optical gap is reduced and the vibronic structure of the singlet emission changes toward that typical for oligothiophenes. We also find the intersystem crossing from the singlet excited state to the triplet excited state to become reduced, while the singlet–triplet energy gap remains unaltered. The latter implies that, in these systems, the T1 triplet excited state is extended over several thiophene rings. The photoconducting properties do not depend on the size of the thiophene fragment. We discuss and compare our results with studies on oligothiophenes and related organometallic polymers.
High resolution photoelectron spectroscopy of C60−
Authors: Wang Xue-Bin , Ding Chuan-Fan , Wang Lai-Sheng
Published: July 2002

Vibrationally resolved photoelectron spectra of C60− are reported at three photon energies: 355, 266, and 193 nm. Complicated vibrational structures were observed for the transition to the C60 ground state with both the Ag and Hg modes being active. An extra feature was observed in the energy gap region between the highest occupied and lowest unoccupied orbitals of C60 in the 266 nm spectra only and it was attributed to an autodetachment process. We also report the most accurate measurement of the electron affinity of C60 (2.689±0.008 eV).
Effects of basis set and electron correlation on the calculated interaction energies of hydrogen bonding complexes: MP2/cc-pV5Z calculations of H2O–MeOH, H2O–Me2O, H2O–H2CO, MeOH–MeOH, and HCOOH–HCOOH complexes
Authors: Tsuzuki Seiji , Uchimaru Tadafumi , Matsumura Kazunari , Mikami Masuhiro , Tanabe Kazutoshi
Published: July 2002

The MP2 intermolecular interaction energies of the title complexes were calculated with the Dunning’s correlation consistent basis sets (cc-pVXZ, X=D, T, Q, and 5) and the interaction energies at the basis set limit were estimated. The second-order Mo/ller–Plesset (MP2) interaction energies greatly depend on the basis sets used, while the Hartree–Fock (HF) energies do not. Small basis sets considerably underestimate the attractive interaction. The coupled cluster single double triple [CCSD(T)] interaction energies are close to the MP2 ones. The expected CCSD(T) interaction energies of the H2O–MeOH, H2O–Me2O, H2O–H2CO, MeOH–MeOH, and HCOOH–HCOOH complexes at the basis set limit are −4.90, −5.51, −5.17, −5.45, and −13.93 kcal/mol, respectively, while the HF/cc-pV5Z energies are −3.15, −2.58, −3.60, −2.69, and −11.29 kcal/mol, respectively. The HF calculations greatly underestimate the attractive energies and fail to predict the order of the bonding energies in these complexes. These results show that a large basis set and the consideration of an appropriate electron correlation correction are essential to study interactions of hydrogen bonding complexes by ab initio molecular orbital calculation.
Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion
Authors: Mazur Alexey K.
Published: July 2002

Internal coordinate molecular dynamics (ICMD) is a recent efficient method for modeling polymer molecules which treats them as chains of rigid bodies rather than ensembles of point particles as in Cartesian MD. Unfortunately, it is readily applicable only to linear or tree topologies without closed flexible loops. Important examples violating this condition are sugar rings of nucleic acids, proline residues in proteins, and also disulfide bridges. This paper presents the first complete numerical solution of the chain closure problem within the context of ICMD. The method combines natural implicit fixation of bond lengths and bond angles by the choice of internal coordinates with explicit constraints similar to Cartesian dynamics used to maintain the chain closure. It is affordable for large molecules and makes possible 3–5 times faster dynamics simulations of molecular systems with flexible rings, including important biological objects like nucleic acids and disulfide-bonded proteins.