Laser control of double proton transfer in porphycenes: towards an ultrafast switch for photonic molecular wires

Electronic excitation energy transfer along a molecular wire depends on the relative orientation of the electronic transition dipole moments of neighboring chromophores. In porphycenes, this orientation is changed upon double proton transfer in the electronic ground state. We explore the possibility to trigger such a double proton transfer reaction by means of an infrared pump-dump laser control scheme. To this end, a quantum chemical characterization of an asymmetrically substituted porphycene is performed using density functional theory. Ground state geometries, the topology of the potential energy surface for double proton transfer, and \(\hbox{S}_0\rightarrow\hbox{S}_1\) transition energies are compared with the parent compound porphycene and a symmetric derivative. Employing a simple two-dimensional model for the double proton transfer, which incorporates sequential and concerted motions, quantum dynamics simulations of the laser-driven dynamics are performed which demonstrate tautomerization control. Based on the orientation of the transition dipole moments, this tautomerization may lead to an estimated change in the Förster transfer coupling of about 60%.     

Proton transfer in a polar solvent from ring polymer reaction rate theory

We have used the ring polymer molecular dynamics method to study the Azzouz-Borgis model for proton transfer between phenol (AH) and trimethylamine (B) in liquid methyl chloride. When the A-H distance is used as the reaction coordinate, the ring polymer trajectories are found to exhibit multiple recrossings of the transition state dividing surface and to give a rate coefficient that is smaller than the quantum transition state theory value by an order of magnitude. This is to be expected on kinematic grounds for a heavy-light-heavy reaction when the light atom transfer coordinate is used as the reaction coordinate, and it clearly precludes the use of transition state theory with this reaction coordinate. As has been shown previously for this problem, a solvent polarization coordinate defined in terms of the expectation value of the proton transfer distance in the ground adiabatic quantum state provides a better reaction coordinate with less recrossing. These results are discussed in light of the wide body of earlier theoretical work on the Azzouz-Borgis model and the considerable range of previously reported values for its proton and deuteron transfer rate coefficients.     

A single transition state serves two mechanisms: an ab initio classical trajectory study of the electron transfer and substitution mechanisms in reactions of ketyl radical anions with alkyl halides

Molecular dynamics has been used to investigate the reaction of a series of ketyl anion radicals and alkyl halides, CH2O(*)(-) + CH3X (X = F, Cl, Br) and NCCHO(*)(-) + CH3Cl. In addition to a floppy outer-sphere transition state which leads directly to ET products, there is a strongly bound transition state that yields both electron transfer (ET) and C-alkylated (SUB(C)) products. This common transition state has significant C-- C bonding and gives ET and SUB(C) products via a bifurcation on a single potential energy surface. Branching ratios have been estimated from ab initio classical trajectory calculations. The SUB(C) products are favored for transition states with short C--C bonds and ET for long C--C bonds. ET reactivity can be observed even at short distances of r(C)(-)(C) = ca. 2.4 A as in the transition state for the reaction NCCHO(*)(-) + CH3Cl. Therefore, the ET/SUB(C) reactivity is entangled over a significant range of the C--C distance. The mechanistic significance of the molecular dynamics study is discussed.     

Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath

A hybrid quantum/classical molecular dynamics approach is applied to a proton transfer reaction represented by a symmetric double well system coupled to a dissipative bath. In this approach, the proton is treated quantum mechanically and all bath modes are treated classically. The transition state theory rate constant is obtained from the potential of mean force, which is generated along a collective reaction coordinate with umbrella sampling techniques. The transmission coefficient, which accounts for dynamical recrossings of the dividing surface, is calculated with a reactive flux approach combined with the molecular dynamics with quantum transitions surface hopping method. The hybrid quantum/classical results agree well with numerically exact results in the spatial-diffusion-controlled regime, which is most relevant for proton transfer in proteins. This hybrid quantum/classical approach has already been shown to be computationally practical for studying proton transfer in large biological systems. These results have important implications for future applications to hydrogen transfer reactions in solution and proteins.     

Water mediated proton transfer in a mesostructured aluminosilicate framework: an ab initio molecular dynamics study

The proton transfer process mediated by water molecules adsorbed in an aluminosilicate framework has been studied using ab initio molecular dynamics simulations. This investigation has been carried out using a quasi-one-dimensional model simulating the mesoporous aluminosilicate channel structures. The effects of both the water loading and temperature of the system have been considered. At low coverage (one water molecule per acid site), the hydroxonium ion (H(3)O)(+) is found to be a transition state, in agreement with earlier studies on zeolites. At a higher water coverage (two water molecules per acid site), the (H(5)O(2))(+) species and the hydrogen bonded "neutral complex" structure are both found to be stable complexes at finite temperatures. The vibrational frequency spectrum is simulated by performing a Fourier transform of the velocity autocorrelation function (VAF), and the peak positions in the VAF are compared with IR measurements and zero-temperature calculations.     

Mass accommodation mechanism of water through monolayer films at water∕vapor interface

The mass transfer dynamics at water∕vapor interface through monolayer films was theoretically investigated by a combination of molecular dynamics and Langevin dynamics simulations. The rare events of mass accommodation are sampled by the Langevin simulation with sufficient statistical accuracy, on the basis of the free energy and friction profiles obtained by the molecular dynamics simulation. The free energy profiles exhibit a barrier in the long-chain monolayers, and the mechanism of the barrier is elucidated in relation to the "water finger" formation. The present Langevin simulation well described the remarkable dependence of the mass accommodation coefficient on the chain length and surface density. The transition state theory for the barrier passage remarkably overestimates the mass accommodation coefficient, and the Kramers or Grote-Hynes theory may not be appropriate, due to large variation of the friction in the entrance channel and∕or broad barrier.     

Theoretical investigation of the "CO in"-"CO out" isomerization in a [2Fe-2S] ferredoxin: free energy profiles and redox states

This paper reports on extensive molecular dynamics simulations (about 40 ns in total) in both the reduced and the oxidized states of Ferredoxin from Cyanobacterium Anabaena PCC7119. These calculations have provided us with the free energy profile of the phi(47) backbone angle which controls the "CO in" to "CO out" transition of Cys46 in the reduced and oxidized Fd7119. Our main motivation has been to identify the time scales involved in the reduction of Fd and single out the amino acid residues crucially affecting the conformational change and, thus, electron transfer. The free energy profiles obtained in this study are relevant to electron transfers in the PSI/Fd7119 and Fd7119/FNR complexes. Our findings based on hydrated ferredoxin simulations are that activated processes are to occur in the protein during electron transfer to and from ferredoxin. The relative stability and the activation barrier of the "CO in" to "CO out" transition can be modulated by the distance between the Ser47 and the Glu94 residues. In our calculations, for short distances, the "CO in" state is favored in the reduced form, whereas for large distances, the "CO out" state becomes increasingly favored. Accordingly, conformational changes in Fd7119 when bound to PSI or FNR can have crucial effects on the kinetics of the electron transfer. Our simulations also show that the hydrogen bond between between Ser47(OG) and Cys46(O) is essential to lock in the "CO out" state. This finding explains why only the Ser47Thr Fd7119 mutant sustains electron transfer activity, as only residues serine and threonine can form a specific hydrogen bond with Cys46(O). Finally, our simulations predict that Phe65 has a large probability of being in close contact with the Cys46(O) at the top of the conformational free energy barrier. This carbonyl/phenyl ring interaction can then facilitate the de-localization of the Fd's electron toward the Pi orbitals of Phe65 aromatic ring which is thought to be crucial to the Fd7119/FNR electron transfer     

化学反应过渡态的结构和动力学

化学反应过渡态决定了包括反应速率和微观反应动力学在内的化学反应的基本特性,而无论是从理论还是实验上研究和观测化学反应过渡态都是极具挑战性的课题.近年来,我国科学家们利用交叉分子束-里德堡氢原子飞行时间谱仪,结合高精度的量子动力学计算,对H＋H2和F＋H2这两个教科书式的典型反应体系进行了全量子态分辨的反应动力学研究,从中得出了关于这两个反应体系的过渡态的结构和动力学性质的结论性的研究成果.     

Ultrafast excited state dynamics of the perylene radical cation generated upon bimolecular photoinduced electron transfer reaction

The ultrafast ground state recovery (GSR) dynamics of the radical cation of perylene, Pe(*+), generated upon bimolecular photoinduced electron transfer in acetonitrile, has been investigated using pump-pump-probe spectroscopy. With 1,4-dicyanobenzene as electron acceptor, the free ion yield is substantial and the GSR dynamics of Pe(*+) was found to depend on the time delay between the first and second pump pulses, Deltat(12), i.e., on the "age" of the ion. At short Deltat(12), the GSR dynamics is biphasic, and at Deltat(12) larger than about 500 ps, it becomes exponential with a time constant around 3 ps. With trans-1,2-dicyanoethylene as acceptor, the free ion yield is essentially zero and the GSR dynamics of Pe(*+) remains biphasic independently of Deltat(12). The change of dynamics observed with 1,4-dicyanobenzene is ascribed to the transition from paired to free solvated ion, because in the pair, the excited ion has an additional decay channel to the ground state, i.e., charge recombination followed by charge separation. The rate constants deduced from the analysis of these GSR dynamics are all fully consistent with this hypothesis.     

The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations

Protein kinases are important enzymes controlling the majority of cellular signaling events via a transfer of the gamma-phosphate of ATP to a target protein. Even after many years of study, the mechanism of this reaction is still poorly understood. Among many factors that may be responsible for the 1011-fold rate enhancement due to this enzyme, the role of the conserved aspartate (Asp166) has been given special consideration. While the essential presence of Asp166 has been established by mutational studies, its function is still debated. The general base catalyst role assigned to Asp166 on the basis of its position in the active site has been brought into question by the pH dependence of the reaction rate, isotope measurements, and pre-steady-state kinetics. Recent semiempirical calculations have added to the controversy surrounding the role of Asp166 in the catalytic mechanism. No major role for Asp166 has been found in these calculations, which have predicted the reaction process consisting of an early transfer of a substrate proton onto the phosphate group. These conclusions were inconsistent with experimental observations. To address these differences between experimental results and theory with a more reliable computational approach and to provide a theoretical platform for understanding catalysis in this important enzyme family, we have carried out first-principles structural and dynamical calculations of the reaction process in cAPK kinase. To preserve the essential features of the reaction, representations of all of the key conserved residues (82 atoms) were included in the calculation. The structural calculations were performed using the local basis density functional (DFT) approach with both hybrid B3LYP and PBE96 generalized gradient approximations. This kind of calculation has been shown to yield highly accurate structural information for a large number of systems. The optimized reactant state structure is in good agreement with X-ray data. In contrast to semiempirical methods, the lowest energy product state places the substrate proton on Asp166. First-principles molecular dynamics simulations provide additional support for the stability of this product state. The latter also demonstrate that the proton transfer to Asp166 occurs at a point in the reaction where bond cleavage at the PO bridging position is already advanced. This mechanism is further supported by the calculated structure of the transition state in which the substrate hydroxyl group is largely intact. A metaphoshate-like structure is present in the transition state, which is consistent with the X-ray structures of transition state mimics. On the basis of the calculated structure of the transition state, it is estimated to be 85% dissociative. Our analysis also indicates an increase in the hydrogen bond strength between Asp166 and substrate hydroxyl and a small decrease in the bond strength of the latter in the transition state. In summary, our calculations demonstrate the importance of Asp166 in the enzymatic mechanism as a proton acceptor. However, the proton abstraction from the substrate occurs late in the reaction process. Thus, in the catalytic mechanism of cAPK protein kinase, Asp166 plays a role of a "proton trap" that locks the transferred phosphoryl group to the substrate. These results resolve prior inconsistencies between theory and experiment and bring new understanding of the role of Asp166 in the protein kinase catalytic mechanism.     

Kinematic effects associated with molecular frames in structural isomerization dynamics of clusters

Kinematic effects associated with movements of molecular frames, which specify instantaneous orientation of molecules, is investigated in structural isomerization dynamics of a triatomic cluster whose total angular momentum is zero. The principal-axis frame is employed to introduce the so-called principal-axis hyperspherical coordinates, with which the mechanism of structural isomerization dynamics of the cluster is systematically analyzed. A force called "democratic centrifugal force" is extracted from the associated kinematics. This force arises from an intrinsic non-Euclidean metric in the internal space and has an effect of distorting the triatomic cluster to a collapsed shape and of trapping the system around collinear transition states. The latter effect is particularly important in that the kinematics effectively makes a basin at the saddle (transition state) on the potential surface. Based on this framework, we study the effect of the gauge field associated with the Eckart frame in internal space, which has not been carefully examined in the conventional reaction rate theories. Numerical comparison between the dynamics with and without the gauge field has revealed that this field has an effect to suppress the rate of isomerization reaction to a considerable amount. Thus a theory neglecting this effect will significantly overestimate the rate of isomerization. We show the physical origin of this suppressing effect.     

Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method

A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic reaction, the classical transmission coefficient kappa(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient kappa(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.     

Modeling crystal growth from solution with molecular dynamics simulations: approaches to transition rate constants

The feasibility of using the molecular dynamics (MD) simulation technique to study crystal growth from solution quantitatively, as well as to obtain transition rate constants, has been studied. The dynamics of an interface between a solution of Lennard-Jones particles and the (100) face of an fcc lattice comprised of solute particles have been studied using MD simulations, showing that MD is, in principle, capable of following growth behavior over large supersaturation and temperature ranges. Using transition state theory, and a nearest-neighbor approximation growth and dissolution rate constants have been extracted from equilibrium MD simulations at a variety of temperatures. The temperature dependence of the rates agrees well with the expected transition state theory behavior.     

Twisted intramolecular charge transfer states: rotationally resolved fluorescence excitation spectra of 4,4'-dimethylaminobenzonitrile in a molecular beam

We report the observation at high resolution of seven vibronic bands that appear within approximately 200 cm(-1) of the electronic origin in the S(1)-S(0) fluorescence excitation spectrum of 4,4'-dimethylaminobenzonitrile (DMABN) in a molecular beam. Surprisingly, each band is found to be split into two or more components by a (coordinated) methyl group tunneling motion which significantly complicates the analysis. Despite this fact, high quality [(Observed-Calculated)< or =30 MHz] fits of each of the bands have been obtained, from which the rotational constants, inertial defects, torsion-rotation interaction constants, methyl group torsional barriers, and transition moment orientations of DMABN in both electronic states have been determined. The data show that DMABN is a slightly pyramidalized (approximately 1 degree) but otherwise (heavy-atom) planar molecule in its ground S(0) state, and that its electronically excited S(1) state has both a more pyramidalized (approximately 3 degrees) and twisted (approximately 25 degrees) dimethylamino group. Large reductions in the methyl group torsional barriers also show that the S(1)<--S(0) electronic transition is accompanied by significant charge transfer from the nitrogen atom to the pi* orbitals of the aromatic ring. Thereby established is the participation of all three vibrational coordinates in the dynamics leading to the "anomalous" emissive behavior of DMABN in the condensed phase.     

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions.     

Classical trajectory simulations of photoionization dynamics of tryptophan: intramolecular energy flow, hydrogen-transfer processes and conformational transitions

One-photon and two-photon ionization dynamics of tryptophan is studied by classical trajectory simulations using the semiempirical parametric method number 3 (PM3) potential surface in "on the fly" calculations. The tryptophan conformer is assumed to be in the vibrational ground state prior to ionization. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for that state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. For the two-photon ionization process the ionization is assumed to go resonantively through the first excited state. Most trajectories are computed, and the analysis is carried out for the first 10 ps. A range of interesting effects are observed. The main findings are as follows: (1) Multiple conformational transitions are observed in most of the trajectories within the ultrafast duration of 10 ps. (2) Hydrogen transfer from the carboxyl group to the amino group and back has been observed. A zwitterion is formed as a transient state. (3) Two new isomers are formed during the dynamics, which have apparently not been previously observed. (4) Fast energy flow between the ring modes and the amino acid backbone is observed for both one- and two-photon ionization. However, the effective vibrational temperatures only approach the same value after 90 ps. The conformation transition dynamics, the proton-transfer processes and the vibrational energy flow are discussed and analyzed.     

Melting of monatomic glass with free surfaces

Melting of monatomic glass with free surfaces has been studied by molecular dynamics simulations in models with Lennard-Jones-Gauss interatomic potential. Models have been heated up from a glassy state toward a normal liquid state. Atomic mechanism of melting has been analyzed via monitoring spatio-temporal arrangements of liquid-like atoms occurred during heating process. Liquid-like atoms are detected via the Lindemann criterion of melting. It is clear that the transition from glass into supercooled liquid of our "ordinary" glass with free surfaces exhibits a non-heterogeneous behavior, i.e., although liquid-like atoms initiate/grow mainly in the surface shell, significant amount of liquid-like atoms also initiates/grows simultaneously in the interior during heating process. We found three characteristic temperatures of melting of glass with a free surface. Temperature dependence of structure and various thermodynamic quantities of the system upon heating is also presented and discussed.     

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Modeling the transition state structure to probe a reaction mechanism on the oxidation of quinoline by quinoline 2-oxidoreductase

Background

Quinoline 2-oxidoreductase (Qor) is a member of molybdenum hydroxylase which catalyzes the oxidation of quinoline (2, 3 benzopyridine) to 1-hydro-2-oxoquinoline. Qor has biological and medicinal significances. Qor is known to metabolize drugs produced from quinoline for the treatment of malaria, arthritis, and lupus for many years. However, the mechanistic action by which Qor oxidizes quinoline has not been investigated either experimentally or theoretically.

Purpose of the study

The present study was intended to determine the interaction site of quinoline, predict the transition state structure, and probe a plausible mechanistic route for the oxidative hydroxylation of quinoline in the reductive half-reaction active site of Qor.

Results

Density functional theory calculations have been carried out in order to understand the events taking place during the oxidative hydroxylation of quinoline in the reductive half-reaction active site of Qor. The most electropositivity and the lowest percentage contribution to the HOMO are shown at C₂ of quinoline compared to the other carbon atoms. The transition state structure of quinoline bound to the active site has been confirmed by one imaginary negative frequency of ?104.500/s and ?1.2365899E+06 transition state energies. The Muliken atomic charges, the bond distances, and the bond order profiles were determined to characterize the transition state structure and the reaction mechanism.

Conclusion

The results have shown that C₂ is the preferred locus of interaction of quinoline to interact with the active site of Qor. The transition state structure of quinoline bound to the active site has been confirmed by one imaginary negative frequency. Moreover, the presence of partial negative charges on hydrogen at the transitions state suggested hydride transfer. Similarly, results obtained from total energy, iconicity and molecular orbital analyses supported a concerted reaction mechanism.