Ligand-to-metal charge-transfer dynamics in a blue copper protein plastocyanin: a molecular dynamics study

Equilibrium and nonequilibrium dynamics of a blue copper protein plastocyanin in an oxidized state are studied by molecular dynamics (MD) simulation. Potential energy functions of the lowest seven electronic states, including ligand-to-metal charge-transfer (LMCT) and copper d --> d excited states, were taken from our previous work (Ando, K. J. Phys. Chem. B 2004, 108, 3940), which employed ab initio molecular orbital and density functional calculations on the active-site model. The equilibrium MD simulations in the ground state indicate that ligand motions coupled to transition from the ground state to the LMCT state are mostly represented by stretching and bending vibrations of the Cu-S(Cys) distance, Ndelta(His)-Cu-Ndelta(His) angle, and S(Cys)-Cu-[Ndelta(His)]2 trigonal pyramid structure. The nonequilibrium dynamics on the LMCT potential exhibit rapid decays in which surface crossings to the d --> d and the first excited states occur in 70-80 fs. The crossing dynamics mostly correlate with cleavage of the Cu-S(Cys) bond and the associated response in the Ndelta(His)-Cu-Ndelta(His) moiety. The average dynamics of the vertical energy gap coordinates exhibit an overdamped decay with a recurrence oscillation in 500 fs, which shows clear coherence surviving after the ensemble averaging. This oscillation stems mostly from the recoiling motion of the Ndelta(His)-Cu-Ndelta(His) part. The dynamics of the energy gaps after this coherent oscillation are randomized such that the ensemble average yields flat profiles along time, although each single trajectory exhibits fluctuations with amplitudes large enough to reach surface crossings. These indicate that the relaxation from the LMCT state first occurs via ballistic and coherent potential crossings in 70-80 and 500 fs, followed by thermally activated random transitions.     

Ab initio nonadiabatic dynamics study of ultrafast radiationless decay over conical intersections illustrated on the Na3F cluster

We present a theoretical approach for the ultrafast nonadiabatic dynamics based on the ab initio molecular dynamics carried out "on the fly" in the framework of the configuration interaction method combined with Tully's surface hopping algorithm for nonadiabatic transitions. This approach combined with our Wigner distribution approach allows us to perform accurate simulations of femtosecond pump-probe spectra in the systems where radiationless transitions among electronic states take place. In this paper we illustrate this by theoretical simulation of ultrafast processes and nonradiative relaxation in the Na(3)F cluster, involving three excited states and the ground electronic state. Furthermore, we show that our accurate simulation of the photoionization pump-probe spectrum is in full agreement with the experimental signal. Based on the nonadiabatic dynamics at high level of accuracy and taking into account all degrees of freedom, the nonradiative lifetime for the 1 (1)B(1) excited state of Na(3)F has been determined to be approximately 900 fs.     

Energetics and dynamics in MbCN: CN--vibrational relaxation from molecular dynamics simulations

The dynamics of the cyanide anion bound to sperm-whale myoglobin is investigated using atomistic simulations. With density-functional theory, a 2D potential energy surface for the cyanide-heme complex is calculated. Two deep minima with a stabilization energy of approximately 50 kcal/mol corresponding to two different binding orientations (Fe-CN and Fe-NC) of the ligand are found. The Fe-CN conformation is favored over Fe-NC by several kcal/mol. Mixed quantum mechanics/molecular mechanics calculations show that the binding orientation affects the bond strength of the ligand, with a significantly different bond length and a 25 cm-1 shift in the fundamental CN-frequency. For the molecular dynamics (MD) simulations, a 3-center fluctuating charge model for the Fe-CN unit is developed that captures polarization and ligand-metal charge transfer. Stability arguments based on the energetics around the active site and the CN- frequency shifts suggest that the Fe-CN conformation with epsilon-protonation of His epsilon 64 are most likely, which is in agreement with experiment. Both equilibrium and nonequilibrium MD simulations are carried out to investigate the relaxation time scale and possible relaxation pathways in bound MbCN. The nonequilibrium MD simulations with a vibrationally excited ligand reveal that vibrational relaxation takes place on a time scale of hundreds of picoseconds within the active site. This finding supports the hypothesis that the experimentally observed relaxation rate (3.6 ps) reflects the repopulation of the electronic ground state.     

Solvent effects on isomerization and spectral properties of photochromic-switching diarythene derivatives in polar and apolar solutions

The photocyclization behavior and dynamic conformational transition of photochromic switches of diarythene derivatives in solutions are investigated by using the density functional theory (DFT) and molecular dynamics (MD) simulations. Three possible conformations, antiparallel (anti), parallel (para), and twist, for the open-ring isomers of 1,2-bis(2-methylbenzothiophene-3-yl)maleic anhydride are located. Both PCM-B3LYP/6-31G* calculations and MD simulations demonstrate that anti and twist open-ring isomers can interconvert freely in n-hexane and acetonitrile solutions at room temperature. The statistical ratio of twist to anti isomers from MD simulations is 2.09 in n-hexane and 1.07 in CH(3)CN, in qualitative agreement with those (1.18 in n-hexane and 1.05 in CH(3)CN) estimated from Arrhenius analysis of DFT activation energies. The solvent polarity has little influence on the isomerization of open-ring isomers in the ground state. Due to the evident charge transfer upon excitations, the solvent effects on the electronic structures and absorption spectra of low-lying excited states (S(1) and S(2)) are more significant. For such charge-transfer excited states, the long-range corrected functional CAM-B3LYP gives better agreement with the experimental spectra than B3LYP. The solvent polarity and polarization of the charge-transfer excited states are crucial for fabricating the novel functionalized photochromic molecular switches.     

A model electronic Hamiltonian to study low-lying electronic states of [Fe(bpy)3]2+ in aqueous solution

A simple model electronic Hamiltonian to describe the potential energy surfaces of several low-lying d-d states of the [Fe(bpy)(3)](2+) complex is developed for use in molecular dynamics (MD) simulation studies. On the basis of a method proposed previously for first-row transition metal ions in aqueous solution, the model Hamiltonian is constructed using density functional theory calculations for the lowest singlet and quintet states. MD simulations are then carried out for the two spin states in aqueous solution in order to examine the performance of the model Hamiltonian. The simulation results indicate that the present model electronic Hamiltonian reasonably describes the potential energy surfaces of the two spin states of the aqueous [Fe(bpy)(3)](2+) system, while retaining sufficient simplicity for application in simulation studies on excited state dynamics.     

Vibrational energy relaxation of the ND-stretching vibration of NH(2)D in liquid NH(3)

The vibrational energy relaxation from the first excited ND-stretching mode of NH(2)D dissolved in liquid NH(3) is studied using molecular dynamics simulations. The rate constants for inter- and intramolecular energy transfer are calculated in the framework of the quantum-classical Landau-Teller theory. At 273 K and an ammonia density of 0.642 g cm(-3) the calculated ND-stretch lifetime of τ = 9.1 ps is in good agreement with the experimental value of 8.6 ps. The main relaxation channel accounting for 52% of the energy transfer involves an intramolecular transition to the first excited state of the umbrella mode. The energy difference between both states is taken up by the near-resonant bending vibrations of the solvent. Less important for the ND-stretch lifetime are both the direct transition to the ground state and intramolecular relaxation via the NH(2)D bending modes contributing 23% each. Our calculations imply that the experimentally observed weak density dependence of τ is caused by detuning the resonance between the ND-stretch-umbrella energy gap and the solvent accepting modes which counteracts the expected linear increase of the relaxation rate with density.     

Ab initio description of photoabsorption and electron transfer in a doubly-linked porphyrin-fullerene dyad

Structure, photoabsorption and excited states of two representative conformations obtained from molecular dynamics (MD) simulations of a doubly-linked porphyrin-fullerene dyad DHD6ee are studied by using both DFT and wavefunction based methods. Charge transfer from the donor (porphyrin) to the acceptor (fullerene) and the relaxation of the excited state are of special interest. The results obtained with LDA, GGA, and hybrid functionals (SVWN, PBE, and B3LYP, respectively) are analyzed with emphasis on the performance of used functionals as well as from the point of view of their comparison with wavefunction based methods (CCS, CIS(D), and CC2). Characteristics of the MD structures are retained in DFT optimization. The relative orientation of porphyrin and fullerene is significantly influencing the MO energies, the charge transfer (CT) in the ground state of the dyad and the excitation of ground state CT complex (g-CTC). At the same time, the excitation to the locally excited state of porphyrin is only little influenced by the orientation or cc distance. TD-DFT underestimates the excitation energy of the CT state, however for some cases (with relatively short donor-acceptor separations), the use of a hybrid functional like B3LYP alleviates the problem. Wavefunction based methods and CC2 in particular appear to overestimate the CT excitation energies but the inclusion of proper solvation models can significantly improve the results.     

Electronic coherence dynamics in trans-polyacetylene oligomers

Electronic coherence dynamics in trans-polyacetylene oligomers are considered by explicitly computing the time dependent molecular polarization from the coupled dynamics of electronic and vibrational degrees of freedom in a mean-field mixed quantum-classical approximation. The oligomers are described by the Su-Schrieffer-Heeger Hamiltonian and the effect of decoherence is incorporated by propagating an ensemble of quantum-classical trajectories with initial conditions obtained by sampling the Wigner distribution of the nuclear degrees of freedom. The electronic coherence of superpositions between the ground and excited and between pairs of excited states is examined for chains of different length, and the dynamics is discussed in terms of the nuclear overlap function that appears in the off-diagonal elements of the electronic reduced density matrix. For long oligomers the loss of coherence occurs in tens of femtoseconds. This time scale is determined by the decay of population into other electronic states through vibronic interactions, and is relatively insensitive to the type and class of superposition considered. By contrast, for smaller oligomers the decoherence time scale depends strongly on the initially selected superposition, with superpositions that can decay as fast as 50 fs and as slow as 250 fs. The long-lived superpositions are such that little population is transferred to other electronic states and for which the vibronic dynamics is relatively harmonic.     

Shielding of ionic interactions by sulfur dioxide in an ionic liquid

The effect of adding SO2 on the structure and dynamics of 1-butyl-3-methylimidazolium bromide (BMIBr) was investigated by low-frequency Raman spectroscopy and molecular dynamics (MD) simulations. The MD simulations indicate that the long-range structure of neat BMIBr is disrupted resulting in a liquid with relatively low viscosity and high conductivity, but strong correlation of ionic motion persists in the BMIBr-SO2 mixture due to ionic pairing. Raman spectra within the 5相似文献   

Nuclear quantum effects on the nonadiabatic decay mechanism of an excited hydrated electron

We present a kinetic analysis of the nonadiabatic decay mechanism of an excited state hydrated electron to the ground state. The theoretical treatment is based on a quantized, gap dependent golden rule rate constant formula which describes the nonadiabatic transition rate between two quantum states. The rate formula is expressed in terms of quantum time correlation functions of the energy gap and of the nonadiabatic coupling. These gap dependent quantities are evaluated from three different sets of mixed quantum-classical molecular dynamics simulations of a hydrated electron equilibrated (a) in its ground state, (b) in its first excited state, and (c) on a hypothetical mixed potential energy surface which is the average of the ground and the first excited electronic states. The quantized, gap dependent rate results are applied in a phenomenological kinetic equation which provides the survival probability function of the excited state electron. Although the lifetime of the equilibrated excited state electron is computed to be very short (well under 100 fs), the survival probability function for the nonequilibrium process in pump-probe experiments yields an effective excited state lifetime of around 300 fs, a value that is consistent with the findings of several experimental groups and previous theoretical estimates.     

Fluorescence spectra of organic dyes in solution: a time dependent multilevel approach

Classical all-atom molecular dynamics (MD) simulations and quantum mechanical (QM) time-dependent density functional theory (TD-DFT) calculations are employed to study the conformational and photophysical properties of the first emitter excited state of tetramethyl-rhodamine iso-thiocyanate fluorophore in aqueous solution. For this purpose, a specific and accurate force field has been parameterised from QM data to model the fluorophore's first bright excited state. During the MD simulations, the consequences of the π→π* electronic transition on the structure and microsolvation sphere of the dye has been analysed in some detail and compared to the ground state behaviour. Thereafter, fluorescence has been calculated at the TD-DFT level on configurations sampled from the simulated MD trajectories, allowing us to include time dependent solvent effects in the computed emission spectrum. The latter, when compared with the absorption spectrum, reproduces well the experimental Stokes shift, further validating the proposed multilevel computational procedure.     

Ultrafast dynamics of metal complexes of tetrasulphonated phthalocyanines

A promising material in medicine, electronics, optoelectronics, electrochemistry, catalysis, and photophysics, tetrasulphonated aluminum phthalocyanine (AlPcS(4)), is investigated by means of steady-state and time-resolved pump-probe spectroscopies. Absorption and steady-state fluorescence spectroscopy indicate that AlPcS(4) is essentially monomeric. Spectrally resolved pump-probe data are recorded on time scales ranging from femtoseconds to nanoseconds. The nature of these fast processes and pathways of the competing relaxation processes from the initially excited electronic states in aqueous and organic (dimethyl sulfoxide) solutions are discussed. The decays and bleaching recovery have been fitted in the ultrafast window (0-10 ps) and later time window extending to nanoseconds (0-1 ns). While the excited-state dynamics have been found to be sensitive to the solvent environment, we were able to show that the fast dynamics is described by three time constants in the ranges of 115-500 fs, 2-25 ps, and 150-500 ps. We were able to ascribe these three time constants to different processes. The shortest time constants have been assigned to vibrational wavepacket dynamics. The few picosecond components have been assigned to vibrational relaxation in the excited electronic states. Finally, the 150-500 ps components represent the decay from S(1) to the ground state. The experimental and theoretical treatment proposed in this paper provides a basis for a substantial revision of the commonly accepted interpretation of the Soret transition (B transition) that exists in the literature.     

Solvent effects on internal conversions and intersystem crossings: the radiationless de-excitation of acrolein in water

An extended version of the averaged solvent electrostatic potential from molecular dynamics data (ASEP/MD) method oriented to the study of the solvent effects on internal conversion and intersystem crossing processes is presented. The method allows for the location of crossing points between free energy surfaces both in equilibrium and in frozen solvent conditions. The ground and excited states of the solute molecule are described at the complete active space self-consistent field (CASSCF) level while the solvent structure is obtained from molecular dynamics simulations. As an application, we studied the nonradiative de-excitation of s-trans-acrolein 1(n --> pi*) in aqueous solution. We found that the solvent modifies the relative stability of the different crossing points but not enough as to alter the relative order of stability with respect to the in vacuo situation. The relaxation through an equilibrium path involves a strong solvent reorganization. On the contrary, the nonequilibrium path does not involve solvent motion and the de-excitation could proceed with the same speed as in vacuo.     

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations

The conformational dynamics in the flaps of HIV-1 protease plays a crucial role in the mechanism of substrate binding. We develop a kinetic network model, constructed from detailed atomistic simulations, to determine the kinetic mechanisms of the conformational transitions in HIV-1 PR. To overcome the time scale limitation of conventional molecular dynamics (MD) simulations, our method combines replica exchange MD with transition path theory (TPT) to study the diversity and temperature dependence of the pathways connecting functionally important states of the protease. At low temperatures the large-scale flap opening is dominated by a small number of paths; at elevated temperatures the transition occurs through many structurally heterogeneous routes. The expanded conformation in the crystal structure 1TW7 is found to closely mimic a key intermediate in the flap-opening pathways at low temperature. We investigated the different transition mechanisms between the semi-open and closed forms. The calculated relaxation times reveal fast semi-open ? closed transitions, and infrequently the flaps fully open. The ligand binding rate predicted from this kinetic model increases by 38-fold from 285 to 309 K, which is in general agreement with experiments. To our knowledge, this is the first application of a network model constructed from atomistic simulations together with TPT to analyze conformational changes between different functional states of a natively folded protein.     

Time-dependent configuration-interaction calculations of laser-pulse-driven many-electron dynamics: controlled dipole switching in lithium cyanide

We report simulations of laser-driven many-electron dynamics by means of the time-dependent configuration interaction singles (doubles) approach. The method accounts for the correlation of ground and excited states, is capable of describing explicitly time-dependent, nonlinear phenomena, and is systematically improvable. Lithium cyanide serves as a molecular test system in which the charge distribution and hence the dipole moment are shown to be switchable, in a controlled fashion, by (a series of) laser pulses which induce selective, state-to-state electronic transitions. One focus of our time-dependent calculations is the question of how fast the transition from the ionic ground state to a specific excited state that is embedded in a multitude of other states can be made, without creating an electronic wave packet.     

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system.