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Competition between adiabatic and nonadiabatic fragmentation pathways in the unimolecular decay of the ArI2(B) van der Waals complex.

The competition between vibrational and electronic predissociations of the ArI2(B) van der Waals complex has been studied using several dynamical computational methods: exact quantum wave-packet propagation, time-dependent golden rule, and quasiclassical trajectory with quantum jumps model. Five electronic states are considered using recent three-dimensional coupled surfaces obtained with a perturbative diatoms-in-molecules method. Final vibrational and electronic populations, predissociation rates, and absorption spectra have been computed for I2(B,v=18-24)<--I2(X,v=0) excitations within the complex. The contribution of vibrational predissociation into the total decay oscillates as a function of vibrational excitation due to intramolecular vibrational relaxation in a sparse-intermediate regime, which induces irregular variations of the total decay rate. Franck-Condon oscillations control the branching ratios of the individual electronic predissociation channels. However, since these oscillations are out of phase as a function of vibrational excitation, they have limited effect on the oscillatory behavior of the total predissociation rate. Comparison between exact quantum and perturbative golden rule calculations shows that vibrational predissociation has some impact on the electronic predissociation process and affects the final electronic distributions. On the contrary, vibrational product distributions are not significantly affected by the electronic predissociation. A classical description of the ArI2 dynamics provides an averaged picture of the competing predissociation processes, being better adapted for treating intermolecular vibrational relaxation in the statistical limit.

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Theory of time-resolved photoelectron imaging. Comparison of a density functional with a time-dependent density functional approach.

Time-resolved photoelectron differential cross sections are computed within a quantum dynamical theory that combines a formally exact solution of the nuclear dynamics with density functional theory (DFT)-based approximations of the electronic dynamics. Various observables of time-resolved photoelectron imaging techniques are computed at the Kohn-Sham and at the time-dependent DFT levels. Comparison of the results serves to assess the reliability of the former method and hence its usefulness as an economic approach for time-domain photoelectron cross section calculations, that is applicable to complex polyatomic systems. Analysis of the matrix elements that contain the electronic dynamics provides insight into a previously unexplored aspect of femtosecond-resolved photoelectron imaging.

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Decoherence-free quantum information processing with four-photon entangled states.

Decoherence-free states protect quantum information from collective noise, the predominant cause of decoherence in current implementations of quantum communication and computation. Here we demonstrate that spontaneous parametric down conversion can be used to generate four-photon states which enable the encoding of one qubit in a decoherence-free subspace. The immunity against noise is verified by quantum state tomography of the encoded qubit. We show that particular states of the encoded qubit can be distinguished by local measurements on the four photons only.

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Computational studies on class I ribonucleotide reductase: understanding the mechanisms of action and inhibition of a cornerstone enzyme for the treatment of cancer.

This review provides a synthesis of recent work, using computational methods, on the action and inhibition mechanisms of class I ribonucleotide reductase (RNR). This enzyme catalyzes the rate-limiting step of the pathway for the synthesis of DNA monomers and, therefore, has long been regarded as an important target for therapies aiming to control pathologies that depend strongly on DNA replication. In fact, over the last years, several molecules, which are able to impair RNR activity by different mechanisms, have been applied effectively in anti-cancer, anti-viral and anti-parasite therapies. A better understanding of the chemical mechanisms involved in normal catalysis and in inhibition of the enzyme is important for the rational design of more specific and effective inhibitor compounds. To achieve this goal, computational methods, particularly quantum chemical calculations, have been used more and more frequently. The ever-growing capabilities of these methods together with undeniable advantages make it a stimulating area for research purposes.

Animals↗

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

Biophysics↗

Aromaticity in stable tiara nickel thiolates: computational and structural analysis.

Quantum chemical calculations as well as crystallographic analyses show that the Ni(n) rings in the tiara Ni thiolates, [NiS2]n and [Ni(SR)2]n (n = 3-6), have highly symmetric polygonal structures. We find that such structural features primarily arise from the effective delocalization of the d-orbital electrons across the Ni(n) rings leading to bond length equalization and thereby aromaticity. We introduce the d-orbital aromaticity for the first time to explain the experimentally observed polygonal structures of these cyclic metal rings bridged by thiol linkages.

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Room temperature magnetic quantum cellular automata

All computers process information electronically. A processing method based on magnetism is reported here, in which networks of interacting submicrometer magnetic dots are used to perform logic operations and propagate information at room temperature. The logic states are signaled by the magnetization direction of the single-domain magnetic dots; the dots couple to their nearest neighbors through magnetostatic interactions. Magnetic solitons carry information through the networks, and an applied oscillating magnetic field feeds energy into the system and serves as a clock. These networks offer a several thousandfold increase in integration density and a hundredfold reduction in power dissipation over current microelectronic technology.

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Fast quantum algorithm for numerical gradient estimation.

Given a black box for f, a smooth real scalar function of d real variables, one wants to estimate [symbol: see text]f at a given point with n bits of precision. On a classical computer this requires a minimum of d + 1 black box queries, whereas on a quantum computer it requires only one query regardless of d. The number of bits of precision to which f must be evaluated matches the classical requirement in the limit of large n.

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Quantitative cavities and reactivity in stages of crystal lattices: mechanistic and exploratory organic photochemistry.

In continuing our research on solid-state organic photochemistry, we have been investigating the phenomenon of reactivity in stages. In this study we present new examples where the photochemical reactivity changes discontinuously at some point in the conversion. In these instances, the reaction course of the solid differs from that in solution. One example is the reaction of 2-methyl-4,4-diphenylcyclohexenone, where an unusual reaction course was encountered in the solid state; and, of two possible mechanisms, one was established by isotopic labeling. A second case is that of 4,5,5-triphenylcyclohexenone. The solid-state reaction of this enone was found to give a new photochemical transformation, the Type C rearrangement, a process that involves a delta to alpha aryl migration. In the case of 3-tert-butyl-5,5-diphenylcyclohexenone the Type C rearrangement occurred even in solution. The stage behavior was investigated using X-ray analysis and Quantum Mechanics/Molecular Mechanics computations. This permitted us to determine the sources and details of the stage phenomenon. The analysis revealed how a product molecule as a neighbor affects reactivity. The computations were employed to follow the course of a solid-state reaction from reactant through the succeeding stages. Additionally, the Delta-Density Analysis was utilized to ascertain the electronic nature of molecular changes. Besides product composition changing with extent of conversion, the reaction quantum yield was found to change as one stage gave way to a succeeding one.

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Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra.

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG(n):dC(n) and dA(n):dT(n) double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG(5)C(5) and dA(5)T(5) double helices in D(2)O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP6-31G(*) calculations for the nine basis modes. The simulated 2D IR spectra of dG(n):dC(n) double helix in D(2)O solution are directly compared with closely related experimental results. The 2D IR spectra of dG(n):dC(n) and dA(n):dT(n) are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

Base Pairing↗

Objective performance characteristics of a new asymmetric screen-film system.

A study of the objective imaging characteristics of a new asymmetric screen-film system is presented herein. The system is characterized by high x-ray absorption asymmetric screens, and a low-noise, high-contrast asymmetric film having near-zero crossover. Comparisons are made with the imaging characteristics of two widely used conventional screen-film systems. Sensitometry, modulation transfer function, and noise power spectra were measured using standard methods. Granularity, noise equivalent quanta, and detective quantum efficiency were computed from these. The new screen-film system has an average gradient at lung-field densities between the two conventional systems studied, while the mediastinum contrast exceeds both conventional systems. The lung-field modulation transfer function half bandwidth of the new asymmetric system exceeds that of both conventional systems by 60%. At mid exposures the detective quantum efficiency of the new asymmetric system is comparable to those of the conventional systems studied. However, the exposure range over which detective quantum efficiency remains high is substantially wider.

Humans↗

Forbidden Electronic Transitions between the Singlet Ground State and the Triplet Excited State of Pt(II) Complexes.

Direct access to the triplet emitting state from the ground state is observed for Pt(II) complexes containing heterocyclic (CwedgeC', CwedgeN, NwedgeN') and bis(diphenylphosphino)alkane (PwedgeP') ligands. Extinction coefficients for such transitions are in the range 4-25 M(-)(1) cm(-)(1). Emission quantum yields resulting from singlet-to-triplet excitation are as high as 61-77 times the emission quantum yields resulting from singlet-to-singlet excitation at 296 K. The intersystem crossing quantum yield from the singlet excited state to triplet emitting state is lower than 2% at 296 K but is greatly enhanced at 77 K. The forbidden electronic transition observed for Pt(II) complexes is attributed to result from spin-orbit coupling due to the presence of Pt(II) in the skeleton structure. The importance of excitation spectra on the computation of emission quantum yields is discussed.

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A model for the organization of chlorophyll-protein complex of photosystem II and analysis of its photochemical efficiency and excitation migration.

A model is proposed for the organization of chlorophyll-protein complex in photosystem II (PS II) of higher plants. The rates of exciton migration and exciton trapping have been computed using stochastic method to find out the photochemical efficiency of the dimeric PS II. Three dimeric PS II units are assumed to form a group, as transfer of the exciton to the light harvesting bed of the nearest neighbour on either side may only be effective. A relationship has been deduced between the fractions of the reaction centre traps closed and the number of jumps (J) required by the exciton for trapping. The photochemical efficiency and fluorescence quantum yield are computed using J as the parameter in an empirical equation.

Chlorophyll↗

Equilibrium structures for butadiene and ethylene: compelling evidence for pi-electron delocalization in butadiene.

Equilibrium structures have been determined for s-trans-1,3-butadiene and ethylene after adjusting the rotational constants obtained from rotational spectroscopy by vibration-rotation constants calculated from the results of quantum chemical calculations. For butadiene, the formal C=C bond length is 1.338 A, and the formal C-C bond length is 1.454 A. For ethylene, the C=C bond length is 1.3305 A. These values appear to be good to 0.001 A. It is shown for the first time that pi-electron delocalization has the structural consequences of increasing the length of the formal double bond by 0.007 A and decreasing the length of the formal single bond by 0.016 A. Comparisons are made with structures computed with several quantum chemical models. The MP2/cc-pVTZ results agree best with the new re structure.

Butadienes↗

Multidimensional quantum trajectories: applications of the derivative propagation method.

In a previous publication [J. Chem. Phys. 118, 9911 (2003)], the derivative propagation method (DPM) was introduced as a novel numerical scheme for solving the quantum hydrodynamic equations of motion (QHEM) and computing the time evolution of quantum mechanical wave packets. These equations are a set of coupled, nonlinear partial differential equations governing the time evolution of the real-valued functions C and S in the complex action, S=C(r,t) + iS(r,t)/Planck's over 2pi, where Psi(r,t)=exp(S). Past numerical solutions to the QHEM were obtained via ensemble trajectory propagation, where the required first- and second-order spatial derivatives were evaluated using fitting techniques such as moving least squares. In the DPM, however, equations of motion are developed for the derivatives themselves, and a truncated set of these are integrated along quantum trajectories concurrently with the original QHEM equations for C and S. Using the DPM quantum effects can be included at various orders of approximation; no spatial fitting is involved; there is no basis set expansion; and single, uncoupled quantum trajectories can be propagated (in parallel) rather than in correlated ensembles. In this study, the DPM is extended from previous one-dimensional (1D) results to calculate transmission probabilities for 2D and 3D wave packet evolution on coupled Eckart barrier/harmonic oscillator surfaces. In the 2D problem, the DPM results are compared to standard numerical integration of the time-dependent Schrodinger equation. Also in this study, the practicality of implementing the DPM for systems with many more degrees of freedom is discussed.

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Spectroscopic and computational studies of Co1+cobalamin: spectral and electronic properties of the "superreduced" B12 cofactor.

The 4-coordinate, low-spin cob(I)alamin (Co1+Cbl) species, which can be obtained by heterolytic cleavage of the Co-C bond in methylcobalamin or the two-electron reduction of vitamin B12, is one of the most powerful nucleophiles known to date. The supernucleophilicity of Co1+Cbl has been harnessed by a number of cobalamin-dependent enzymes, such as the B12-dependent methionine synthase, and by enzymes involved in the biosynthesis of B12, including the human adenosyltransferase. The nontoxic nature of the Co1+Cbl supernucleophile also makes it an attractive target for the in situ bioremediation of halogenated waste. To gain insight into the geometric, electronic, and vibrational properties of this highly reactive species, electronic absorption, circular dichroism (CD), magnetic CD, and resonance Raman (rR) spectroscopies have been employed in conjunction with density functional theory (DFT), time-dependent DFT, and combined quantum mechanics/molecular mechanics computations. Collectively, our results indicate that the supernucleophilicity of Co1+Cbl can be attributed to the large destabilization of the Co 3dz2-based HOMO and its favorable orientation with respect to the corrin macrocycle, which minimizes steric repulsion during nucleophilic attack. An intense feature in the CD spectrum and a prominent peak in the rR spectra of Co1+Cbl have been identified that may serve as excellent probes of the nucleophilic character, and thus the reactivity, of Co1+Cbl in altered environments, including enzyme active sites. The implications of our results with respect to the enzymatic formation and reactivity of Co1+Cbl are discussed, and spectroscopic trends along the series from Co3+Cbls to Co2+Cbl and Co1+Cbl are explored.

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Topological protection and quantum noiseless subsystems.

Encoding and manipulation of quantum information by means of topological degrees of freedom provides a promising way to achieve natural fault tolerance that is built in at the physical level. We show that this topological approach to quantum information processing is a particular instance of the notion of computation in a noiseless quantum subsystem. The latter then provides the most general conceptual framework for stabilizing quantum information and for preserving quantum coherence in topological and geometric systems.

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A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO).

A two-level hierarchical scheme, generalized distributed data interface (GDDI), implemented into GAMESS is presented. Parallelization is accomplished first at the upper level by assigning computational tasks to groups. Then each group does parallelization at the lower level, by dividing its task into smaller work loads. The types of computations that can be used with this scheme are limited to those for which nearly independent tasks and subtasks can be assigned. Typical examples implemented, tested, and analyzed in this work are numeric derivatives and the fragment molecular orbital method (FMO) that is used to compute large molecules quantum mechanically by dividing them into fragments. Numeric derivatives can be used for algorithms based on them, such as geometry optimizations, saddle-point searches, frequency analyses, etc. This new hierarchical scheme is found to be a flexible tool easily utilizing network topology and delivering excellent performance even on slow networks. In one of the typical tests, on 16 nodes the scalability of GDDI is 1.7 times better than that of the standard parallelization scheme DDI and on 128 nodes GDDI is 93 times faster than DDI (on a multihub Fast Ethernet network). FMO delivered scalability of 80-90% on 128 nodes, depending on the molecular system (water clusters and a protein). A numerical gradient calculation for a water cluster achieved a scalability of 70% on 128 nodes. It is expected that GDDI will become a preferred tool on massively parallel computers for appropriate computational tasks.

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