Volume 117, Issue 24, 22 December 2002
Index of content:
- Special Topic: Single-Molecule Physics and Chemistry
117(2002); http://dx.doi.org/10.1063/1.1521155View Description Hide Description
Statistics and correlations of single-molecule sequences of modulated reactions are explicitly evaluated in the stochastic rate representation. The memory function, introduced through the Gaussian approximation of the stochastic rate expression, characterizes the correlation in single-molecule rate processes in a formalism similar to the stochastic line shape theory. Within this formalism, the on-time correlation is shown to approximate the memory function of the fluctuating rate at discretized effective time separations. A new measurement, the two-event number density, is proposed as a means to map out the memory function over the complete time range. Confirmed by numerical calculations, these relations quantify dynamic disorder caused by conformational fluctuations and hence are useful for analyzingsingle-molecule kinetics.
117(2002); http://dx.doi.org/10.1063/1.1521156View Description Hide Description
A semiflexible Gaussian chain model is used to determine the statistics and correlations of single-molecule fluorescence resonant energy transfer (FRET) experiments on biological polymers. The model incorporates a persistence length in a Rouse chain and describes single-chain dynamics with normal modes. The hydrodynamic interaction is included in the dynamics of the semiflexible Gaussian chain on the preaveraging level. The distribution functions of the fluorescence lifetime and the FRET efficiency provide direct measures of the chain stiffness, and their correlation functions probe the intrachain dynamics at the single-molecule level. When measured with finite time resolution, the instantaneous diffusion coefficient for FRET is much smaller in the collapsed structure than in the coiled structure, and the variation has a quadratic dependence on the donor–acceptor distance. In the fast reaction limit, single-molecule FRET lifetime measurements can be used to map out the equilibrium distribution function of interfluorophore distance. As an example of microrheology, the intrinsic viscoelasticity can be extracted from single-molecule tracking of the Brownian dynamics of polymers in solution.
Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics117(2002); http://dx.doi.org/10.1063/1.1521159View Description Hide Description
This article reviews our efforts in understanding dynamical fluctuations of both conformation and enzymatic reactivity in single biomolecules. The single-molecule approach is shown to be particularly powerful for studies of dispersed kinetics and dynamic disorder. New single-molecule observations have revealed conformational transitions occurring on a broad range of timescales, 100 μs–10 s, offering new clues for understanding energy landscape of proteins, as well as the structural and chemical dynamics therein.
117(2002); http://dx.doi.org/10.1063/1.1521153View Description Hide Description
The ability to probe individual atoms and molecules have made it possible to reveal properties which otherwise would be hidden in the study of an ensemble of atoms and molecules. The scanning tunneling microscope(STM) with its unmatched spatial resolution and versatility literally allows us to touch atoms and molecules one at a time and to carry out experiments which previously were only imagined. One of the great attributes of the STM is that it provides a real space view of the individual molecules and the atomic landscape of their environment, thus removing many of the uncertainties surrounding the nature of the system under study. Combining its imaging, manipulation, spectroscopic characterization, and chemical modification capabilities, the STM has enabled direct visualization of chemistry by revealing the fundamental properties of atoms and molecules and their interactions with each other and the environment. While femtosecond lasers have made it possible to study chemistry at the temporal limit, the STM provides an understanding of chemistry at the spatial limit.
- Theoretical Methods and Algorithms
117(2002); http://dx.doi.org/10.1063/1.1521935View Description Hide Description
The effects of image charges (i.e., induced surface charges of polarization) in spherical geometry and their implication for charged colloidal systems are investigated. We study analytically and exactly a single microion interacting with a dielectric sphere and discuss the similarities and discrepancies with the case of a planar interface. By means of extensive Monte Carlo simulations, we study within the framework of the primitive model the effects of image charges on the structure of the electrical double layer. Salt-free environment as well as salty solutions are considered. A remarkable finding of this study is that the position of the maximum in the counterion density (appearing at moderately surface charge density) remains quasi-identical, regardless of the counterion valence and the salt content, to that obtained within the single-counterion system.
Quantum-classical Liouville approach to molecular dynamics: Surface hopping Gaussian phase-space packets117(2002); http://dx.doi.org/10.1063/1.1522712View Description Hide Description
In mixed quantum-classical molecular dynamics few but important degrees of freedom of a molecular system are modeled quantum mechanically while the remaining degrees of freedom are treated within the classical approximation. Such models can be systematically derived as a first-order approximation to the partial Wigner transform of the quantum Liouville-von Neumann equation. The resulting adiabatic quantum-classical Liouville equation (QCLE) can be decomposed into three individual propagators by means of a Trotter splitting: (1) phase oscillations of the coherences resulting from the time evolution of the quantum-mechanical subsystem, (2) exchange of densities and coherences reflecting non adiabaticeffects in quantum-classical dynamics, and (3) classical Liouvillian transport of densities and coherences along adiabatic potential energy surfaces or arithmetic means thereof. A novel stochastic implementation of the QCLE is proposed in the present work. In order to substantially improve the traditional algorithm based on surface hopping trajectories [J. C. Tully, J. Chem. Phys. 93, 1061 (1990)], we model the evolution of densities and coherences by a set of surface hopping Gaussian phase-space packets (GPPs) with variable width and with adjustable real or complex amplitudes, respectively. The dense sampling of phase space offers two main advantages over other numerical schemes to solve the QCLE. First, it allows us to perform a quantum-classical simulation employing a constant number of particles; i.e., the generation of new trajectories at each surface hop is avoided. Second, the effect of nonlocal operators on the exchange of densities and coherences can be treated beyond the momentum jump approximation. For the example of a single avoided crossing we demonstrate that convergence towards fully quantum-mechanical dynamics is much faster for surface hopping GPPs than for trajectory-based methods. For dual avoided crossings the Gaussian-based dynamics correctly reproduces the quantum-mechanical result even when trajectory-based methods not accounting for the transport of coherences fail qualitatively.
117(2002); http://dx.doi.org/10.1063/1.1518001View Description Hide Description
The third-order optical response of two coupled anharmonic vibrations interacting with a Brownian oscillator bath that induces energy level fluctuations with arbitrary time scales and degree of correlation is calculated. Two-dimensional correlation plots show distinct signatures of these fluctuations in the various possible three pulse, infrared, femtosecond techniques.
Effects of dipole alignment and channel interference on two-photon absorption cross sections of two-dimensional charge-transfer systems117(2002); http://dx.doi.org/10.1063/1.1522408View Description Hide Description
The relationship between two-photon absorption cross sections and the architecture of donor–acceptor substitutions in two-dimensional charge-transfer cumulene-containing aromatic molecules is analyzed. It is shown that a molecular design strategy proposed for one-dimensional charge-transfer molecules must be considerably altered for two-dimensional systems. It is found that the maximal two-photon cross section of such two-dimensional systems can often be well described by a four state model. The importance of the alignment of the transitiondipole moments and of channel interference on the two-photon absorption cross sections is emphasized.
117(2002); http://dx.doi.org/10.1063/1.1523060View Description Hide Description
It is demonstrated that the “corrected Hartree–Fock” (CHF) density matrix functional proposed by Csányi and Arias is identical with the Hartree–Fock–Bogoliubov (HFB) functional of the generalized density matrix up to the sign of the pairing energy term. Using this analogy, variational CHF calculations can be performed much more efficiently by solving the HFB equations for the generalized density matrix than by optimizing separately the natural orbitals and their occupations numbers. A family of CHF-type functionals with a scaled pairing energy is introduced and compared to the closely related antisymmetrized geminal power method.
117(2002); http://dx.doi.org/10.1063/1.1522715View Description Hide Description
The dispersion interaction in the helium dimer is considered from the viewpoint of the force on a nucleus. At large internuclear separations, Brueckner coupled cluster BD(T) forces agree well with near-exact dispersion forces. The atomic density distortion associated with the dispersion force is quantified by comparing the BD(T) dimer density with a superposition of atomic densities. For density functional theory calculations in the Hartree–Fock–Kohn–Sham (HFKS) formalism, the accuracy of the dispersion force is governed by the correlation potential. Calculations using the conventional Lee–Yang–Parr [Phys. Rev. B 37, 785 (1988)] potential only generate a small density distortion, giving forces significantly smaller than BD(T). The BD(T) electron densities are therefore used to determine improved correlation potentials using a modified Zhao–Morrison–Parr (ZMP) approach [Phys. Rev. A 50, 2138 (1994)]. HFKS calculations using these ZMP potentials quantitatively reproduce the distortion, giving dispersion forces in good agreement with BD(T). The dimer ZMP correlation potential is partitioned into two parts, one equal to the sum of two unperturbed spherical atomic correlation potentials and the other representing an interaction potential. HFKS calculations using the former do not generate the distortion; forces are close to Hartree–Fock. Calculations using the latter do generate the distortion, giving forces essentially identical to those from the full dimer potential. The origin of the distortion is traced to the asymmetric structure of the interaction correlation potential in the vicinity of each nucleus.
- Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
The 248 nm photolysis of Time-resolved Fourier transform infrared emission from NO and and quenching of NO117(2002); http://dx.doi.org/10.1063/1.1521724View Description Hide Description
The photolysis of and has been studied at 248 nm by observations of time-resolvedFourier transform infrared emission from the photofragments. The photolysis of produces emission in the and −2 fundamental and overtone bands of and spectralanalysis yields a broad Gaussian-type distribution in the vibrational levels in good agreement with one of two previously reported initial nascent quantum state distributions. Quenching of the higher levels of NO in collisions with produces rate constants which increase with increasing with values between 0.91 and The process is shown to have a larger component of resonance energy transfer from to than previously reported values for the rate constants at lower which are further from resonance. A fast component of IR emission from the nascent excited states of is observed, together with slower decaying emissions near 1450 and 2750 cm−1, assigned as and transitions from high vibrational levels of the ground state formed by quenching of electronically excited produced from the photolysis of A comparison is made of these IR bands with similar features seen in the IR emission from following electronic excitation in the visible region below its dissociation limit. Further emission near 1880 cm−1 accompanies the photolysis of and is tentatively assigned to the direct formation of NO as a photolysis product, with a non-negligible quantum yield in low vibrational levels.
Role of isomerization channel in unimolecular dissociation reaction Ab initio global potential energy surface and classical trajectory analysis117(2002); http://dx.doi.org/10.1063/1.1523058View Description Hide Description
We constructed a full dimensional potential energy function of that can describe both the dissociation and isomerization channels by the modified Shepard interpolation method. Ab initio calculations at the MP2/cc-pVTZ level were carried out to obtain the local potential functions at about 4700 points. The interpolant points were sampled by classical trajectory calculations and by the grid searches in the internal coordinate space. Classical trajectory calculations were performed to examine the intramolecular dynamics associated with the dissociation as well as the product state distributions. The time scale of intramolecular vibrational energy randomization was much faster than that of the dissociationreaction. The dissociation rate was obtained from the classical trajectory results and the effect of the isomerization channel on the dissociation was estimated. The calculated rate constants were compared with those by Rice–Ramsperger–Kassel–Marcus theory.
117(2002); http://dx.doi.org/10.1063/1.1522711View Description Hide Description
The photodissociationdynamics of HOCO in the overtone are studied using a time-dependent wave packet dynamics approach. The dynamics calculations are carried out using a four-dimensional planar model in which the terminal C=O bond (spectator) is fixed at its equilibrium bond distance in the trans-HOCO conformer based on an empirical potential energy surface for HOCO fit to accurate ab initio calculations of the stationary point energies. The branching fraction into the products, and the resonance states associated with are investigated in detail.
117(2002); http://dx.doi.org/10.1063/1.1523059View Description Hide Description
In this work, the vibronic spectroscopy of the p-aminophenol–water 1:1 complex is presented. The vibrational energy levels of the complex were characterized by REMPI spectroscopy up to 2500 cm−1 above the band origin. The dispersed fluorescence spectra were recorded for the B.O., and excitations to characterize the vibrational levels in the state of the complex. Stimulated ion depletion spectroscopy was carried out to determine the higher vibrational levels of the ground state all the way up to ∼3075 cm−1. The structure and the vibrational levels of the complex were calculated ab initio at the HF level and DFT with B3LYP functional for and CIS level for using 6-31G* * basis set. The structure of the complex compared well with the earlier calculations for this case as well as the other ROH–water (R=aromatic group) complexes reported in the literature. However, the redshift in the electronic band origin was almost half of that observed in other cases. A good correlation was shown to exist between the electronic red shifts and the respective values (the in the excited state).
117(2002); http://dx.doi.org/10.1063/1.1522714View Description Hide Description
The kinetic fate of the single rotational states of electronically excited radicals has been studied in the gas phase at room temperature in the presence of CO. Rate constants of the state-to-state relaxation are presented. Further, rate constants were determined for the electronic quenching of single-N states and are compared with the corresponding data for The radiative lifetimes of the rotational levels are given, too. All these processes were found to be more efficient for the B state than those for the A state. Further, collisional mixing of the B with the A state is described quantitatively.
On the theoretical determination of the static dipole polarizability of intermediate size silicon clusters117(2002); http://dx.doi.org/10.1063/1.1521761View Description Hide Description
The B3PW91 method of the density functional theory has been applied to the study of the dipole polarizability of medium size silicon clusters employing pseudopotential on all of them. All electron calculations have been performed for those clusters with less than nine atoms. In addition, we have optimized the structures of the clusters with less than ten atoms. On using the modified genetic algorithm, fourteen conformers of silicon isomers with nine atoms have been determined. The corresponding geometry of these clusters was optimized and their relative stability determined. The calculated polarizabilities are compared with experimental data and previous theoretical results.
117(2002); http://dx.doi.org/10.1063/1.1521726View Description Hide Description
Elastic and rotationally inelastic cross sections have been measured for scattering at two collision energies, 66.3 and 99.0 meV, using the crossed molecular beam technique. The inelastic events are detected by time-of-flight analysis of the scattered He atoms. The data are converted to elastic differential cross sections and inelastic angular-dependent energy loss spectra in the center-of-mass system. They are compared with averaged, full close-coupling calculations of state-to-state cross sections for rotational excitation based on a newly calculated ab initio potential using symmetry-adapted perturbation theory. The agreement with the elastic differential cross sections is excellent. The energy loss spectra are reproduced satisfactorily and among the largest differential cross sections that contributed to the measurements are excitations around all three possible axes for but a preference of the excitation around the in-plane C axis for transitions.
Heats of formation of phosphorus compounds determined by current methods of computational quantum chemistry117(2002); http://dx.doi.org/10.1063/1.1521760View Description Hide Description
The heats of formation of a range of phosphorus containing molecules PH, PO, HPO, HPOH, HOPO, and have been determined by high level quantum chemical calculations. The equilibrium geometries and vibrational frequencies were computed via density functional theory, utilizing the functional and basis set. Atomization energies were obtained by the application of ab initiocoupled clustertheory with single and double excitations from (spin)-restricted Hartree–Fock reference states with perturbative correction for triples [CCSD(T)], in conjunction with basis sets Q, 5) which include an extra function on the phosphorus atoms and diffuse functions on the oxygens, as recommended by Bauschlicher [J. Phys. Chem. A 103, 11126 (1999)]. The valence correlated atomization energies were extrapolated to the complete basis limit and corrected for core–valence (CV) correlation and scalar relativistic effects, as well as for basis set superposition errors (BSSE) in the CV terms. This methodology is effectively the same as the one adopted by Bauschlicher in his study of PO, HPO, HOPO, and Consequently, for these molecules the results of this work closely match Bauschlicher’s computed values. The theoretical heats of formation, whose accuracy is estimated as ranging from to are consistent with the available experimental data. The current set of theoretical data represent a convenient benchmark, against which the results of other computational procedures, such as G3, G3X, and G3X2, can be compared. Despite the fact that G3X2 [which is an approximation to the quadratic CI procedure QCISD(T,Full)/G3Xlarge] is a formally higher level theory than G3X, the heats of formation obtained by these two methods are found to be of comparable accuracy. Both reproduce the benchmark heats of formation on the average to within and, for these molecules at least, they are superior to the basic G3 method. The performance of G3X2 is further improved, however, by the incorporation of BSSE corrections in the CV component of the energies. All the methods have difficulties, however, with molecules which have multiple or highly strained P–P bonds, such as and
Thermal decomposition of iso-propanol: First-principles prediction of total and product-branching rate constants117(2002); http://dx.doi.org/10.1063/1.1522718View Description Hide Description
The unimolecular decomposition of has been studied with a modified GAUSSIAN-2 method. Among the six low-lying product channels identified, the -elimination process (2) via a four-member-ring transition state is dominant below 760 Torr over the temperature range 500–2500 K. At higher pressures and over 1200 K, the cleavage of a C-C bond by reaction (1) producing is predicted to be dominant. The predicted low- and high-pressure limit rate constants for these two major product channels can be given by and respectively. Predicted values compare reasonably with available experimental data; however, values are lower than the experimentally determined apparent rate constant for formation, which may derive in large part from secondary radical reactions. Other minor decomposition products were predicted to have the barriers and The triplet-singlet energy gap for was predicted to be 5.2 kcal/mol, favoring the singlet state.
Ground and excited states of linked and fused zinc porphyrin dimers: Symmetry adapted cluster (SAC)—configuration interaction (CI) study117(2002); http://dx.doi.org/10.1063/1.1521763View Description Hide Description
The symmetry adapted cluster (SAC)/SAC-configuration interaction method was applied to calculate the ground and excited states of zincporphyrinmonomers (without and with phenyl groups, ZnP and ZnPPh, respectively) and meso–meso linked and doubly fused zincporphyrin dimers. Various features of the absorption spectra are studied, clarified, and assigned theoretically. The calculated electronic spectrum of ZnPPh, in comparison with that of ZnP, showed that the phenyl groups affect the spectrum in both the peak positions and intensities. In the dimers, and the interactions of the monomer’s four-orbitals result in an eight-orbital model of the dimers, which plays an important role in the interpretation of the excited states observed in the spectra. In the interaction is smaller and each peak in the split Soret (BI and BII) bands consists of two peaks, in contrast to the prediction based on Kasha’s exciton rule. In the interaction between the two monomer units is so strong that the small highest occupied molecular orbital–lowest unoccupied molecular orbital gap causes the red-shifted Q (1.16 eV) and BI (2.13 eV) bands. In addition, the excitations out of the eight orbitals appear in the low-energy region of the spectrum, which is very different from the case of the monomer. A comprehensive and pictorial analysis is given for the excited states of the dimers in comparison with those of the monomer.