Nonadiabatic molecular dynamics simulations of correlated electrons in solution. 2. A prediction for the observation of hydrated dielectrons with pump-probe spectroscopy

The hydrated dielectron is a highly correlated, two-electron, solvent-supported state consisting of two spin-paired electrons confined to a single cavity in liquid water. Although dielectrons have been predicted to exist theoretically and have been used to explain the lack of ionic strength effect in the bimolecular reaction kinetics of hydrated electrons, they have not yet been observed directly. In this paper, we use the extensive nonadiabatic mixed quantum/classical excited-state molecular dynamics simulations from the previous paper to calculate the transient spectroscopy of hydrated dielectrons. Because our simulations use full configuration interaction (CI) to determine the ground and excited state two-electron wave functions at every instant, our nonequilibrium simulations allow us to compute the absorption, stimulated emission (SE), and bleach spectroscopic signals of both singlet and triplet dielectrons following excitation by ultraviolet light. Excited singlet dielectrons are predicted to display strong SE in the mid infrared and a transient absorption in the near-infrared. The near-infrared transient absorption of the singlet dielectron, which occurs near the peak of the (single) hydrated electron's equilibrium absorption, arises because the two electrons tend to separate in the excited state. In contrast, excitation of the hydrated electron gives a bleach signal in this wavelength region. Thus, our calculations suggest a clear pump-probe spectroscopic signature that may be used in the laboratory to distinguish hydrated singlet dielectrons from hydrated electrons: By choosing an excitation energy that is to the blue of the peak of the hydrated electron's absorption spectrum and probing near the maximum of the single electron's absorption, the single electron's transient bleach signal should shrink or even turn into a net absorption as sample conditions are varied to produce more dielectrons.     

Full configuration interaction computer simulation study of the thermodynamic and kinetic stability of hydrated dielectrons

The hydrated electron is a unique solvent-supported state comprised of an excess electron that is confined to a cavity by the surrounding water. Theoretical studies have suggested that two-electron solvent-supported states also can be formed; in particular, simulations indicate that two excess electrons could pair up and occupy a single cavity, forming a so-called hydrated dielectron. Although hydrated dielectrons have not been observed directly by experiment, their existence has been posited to explain the lack of an ionic strength effect in hydrated electron bimolecular annihilation [Schmidt, K. H.; Bartels, D. M. Chem. Phys. 1995, 190, 145]. To determine whether dielectrons may be created in the laboratory, we use thermodynamic integration (TI), combined with mixed quantum/classical molecular dynamics simulation, to examine the thermodynamic stability of hydrated electrons and dielectrons. For the dielectron calculations, we solve the two-electron quantum problem using full configuration interaction. Our results suggest that hydrated dielectrons are thermodynamically unstable relative to separated (single) hydrated electrons, although we also show that increasing the pressure could drive the equilibrium toward the formation of dielectrons. Because the simulations suggest that hydrated dielectrons are kinetically stable, we also examine a scenario for creating metstable, nonequilibrium populations of dielectrons, which involves the capture of a newly injected electron by a preexisting, equilibrated hydrated electron. These calculations, which allow for the full nonadiabatic relaxation of the injected electron, show that hydrated electrons may indeed act as trapping sites for unequilibrated electrons, so that capture may be a viable mechanism for creating dielectrons. We suggest possible experimental procedures to create such nonequilibrium hydrated dielectrons using either pulse radiolysis or ultrafast spectroscopic techniques.     

Polarizable interaction potential for molecular dynamics simulations of actinoids(III) in liquid water

In this work, we have developed a polarizable classical interaction potential to study actinoids(III) in liquid water. This potential has the same analytical form as was recently used for lanthanoid(III) hydration [M. Duvail, P. Vitorge, and R. Spezia, J. Chem. Phys. 130, 104501 (2009)]. The hydration structure obtained with this potential is in good agreement with the experimentally measured ion-water distances and coordination numbers for the first half of the actinoid series. In particular, the almost linearly decreasing water-ion distance found experimentally is replicated within the calculations, in agreement with the actinoid contraction behavior. We also studied the hydration of the last part of the series, for which no structural experimental data are available, which allows us to provide some predictive insights on these ions. In particular we found that the ion-water distance decreases almost linearly across the series with a smooth decrease of coordination number from nine to eight at the end.     

Charge-transfer-to-solvent-driven dissolution dynamics of I- (H2O)2-5 upon excitation: excited-state ab initio molecular dynamics simulations

In contrast to the extensive theoretical investigation of the solvation phenomena, the dissolution phenomena have hardly been investigated theoretically. Upon the excitation of hydrated halides, which are important substances in atmospheric chemistry, an excess electron transfers from the anionic precursor (halide anion) to the solvent and is stabilized by the water cluster. This results in the dissociation of hydrated halides into halide radicals and electron-water clusters. Here we demonstrate the charge-transfer-to-solvent (CTTS)-driven femtosecond-scale dissolution dynamics for I-(H2O)n=2-5 clusters using excited state (ES) ab initio molecular dynamics (AIMD) simulations employing the complete-active-space self-consistent-field (CASSCF) method. This study shows that after the iodine radical is released from I-(H2O)n=2-5, a simple population decay is observed for small clusters (2 相似文献   

Nonadiabatic molecular dynamics of photoexcited Li2(+) Ne(n) clusters

We investigate the relaxation of photoexcited Li(2)(+) chromophores solvated in Ne(n) clusters (n = 2-22) by means of molecular dynamics with surface hopping. The simplicity of the electronic structure of these ideal systems is exploited to design an accurate and computationally efficient model. These systems present two series of conical intersections between the states correlated with the Li+Li(2s) and Li+Li(2p) dissociation limits of the Li(2)(+) molecule. Frank-Condon transition from the ground state to one of the three lowest excited states, hereafter indexed by ascending energy from 1 to 3, quickly drives the system toward the first series of conical intersections, which have a tremendous influence on the issue of the dynamics. The states 1 and 2, which originate in the Frank-Condon area from the degenerated nondissociative 1(2)Π(u) states of the bare Li(2)(+) molecule, relax mainly to Li+Li(2s) with a complete atomization of the clusters in the whole range of size n investigated here. The third state, which originates in the Frank-Condon area from the dissociative 1(2)Σ(u)(+) state of the bare Li(2)(+) molecule, exhibits a richer relaxation dynamics. Contrary to intuition, excitation into state 3 leads to less molecular dissociation, though the amount of energy deposited in the cluster by the excitation process is larger than for excitation into state 1 and 2. This extra amount of energy allows the system to reach the second series of conical intersections so that approximately 20% of the clusters are stabilized in the 2(2)Σ(g)(+) state potential well for cluster sizes n larger than 6.     

Femtosecond relaxation dynamics of solvated electrons in liquid ammonia.

The ultrafast relaxation dynamics of the well-known solvated electron in liquid ammonia solutions are investigated with femtosecond near-infrared pump-probe absorption spectroscopy. Immediately after photoexcitation, the dynamic absorption spectrum of the electron is substantially red-shifted with respect to its stationary spectrum. A subsequent dynamic blue shift of the pump-probe spectrum occurs on a timescale of 150 fs. The data are understood in terms of ground-state "cooling" and can be quantitatively simulated by an intuitive temperature-jump model employing a dynamically evolving Kubo line shape for the electronic resonance. A simple estimate implies that, on average, the electron in the liquid is coordinated to six nearest-neighbor ammonia molecules. An equivalent analysis of the data based on a bubble-formation/cavity-contraction mechanism is briefly outlined.     

Moving solvated electrons with light: nonadiabatic mixed quantum/classical molecular dynamics simulations of the relocalization of photoexcited solvated electrons in tetrahydrofuran (THF)

Motivated by recent ultrafast spectroscopic experiments [Martini et al., Science 293, 462 (2001)], which suggest that photoexcited solvated electrons in tetrahydrofuran (THF) can relocalize (that is, return to equilibrium in solvent cavities far from where they started), we performed a series of nonequilibrium, nonadiabatic, mixed quantum/classical molecular dynamics simulations that mimic one-photon excitation of the THF-solvated electron. We find that as photoexcited THF-solvated electrons relax to their ground states either by continuous mixing from the excited state or via nonadiabatic transitions, approximately 30% of them relocalize into cavities that can be over 1 nm away from where they originated, in close agreement with the experiments. A detailed investigation shows that the ability of excited THF-solvated electrons to undergo photoinduced relocalization stems from the existence of preexisting cavity traps that are an intrinsic part of the structure of liquid THF. This explains why solvated electrons can undergo photoinduced relocalization in solvents like THF but not in solvents like water, which lack the preexisting traps necessary to stabilize the excited electron in other places in the fluid. We also find that even when they do not ultimately relocalize, photoexcited solvated electrons in THF temporarily visit other sites in the fluid, explaining why the photoexcitation of THF-solvated electrons is so efficient at promoting recombination with nearby scavengers. Overall, our study shows that the defining characteristic of a liquid that permits the photoassisted relocalization of solvated electrons is the existence of nascent cavities that are attractive to an excess electron; we propose that other such liquids can be found from classical computer simulations or neutron diffraction experiments.     

The structure of the hydrated electron. Part 2. A mixed quantum/classical molecular dynamics embedded cluster density functional theory: single-excitation configuration interaction study

Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess electron density with the frontier orbitals of the first-shell solvent molecules cannot explain the observed magnetic, vibrational, and electronic properties of this species. Despite the need for multielectron effects to explain these important properties, the ensemble-averaged radial wavefunctions and energetics of the highest occupied and three lowest unoccupied orbitals of the hydrated electrons in our hybrid model are close to the s- and p-like states obtained in one-electron models. Thus, one-electron models can provide a remarkably good approximation to the multielectron picture of the hydrated electron for many applications; indeed, the two approaches appear to be complementary.     

Atomistic molecular dynamics simulations of model C(36) fullerite

We report atomistic molecular dynamics investigations of a model C(36) fullerite in which the fullerene molecules are modeled as rigid cages over which the carbon atoms occupy fixed interaction sites, distributed in space according to the experimentally known atomic positions in the molecule. Carbon sites belonging to different molecules are assumed to interact via a 12-6 Lennard-Jones-type potential; the parameters of the latter are employed in the framework of a molecular dynamics fitting procedure, through which the ambient condition physical quantities characterizing the hcp structure of solid C(36) are eventually reproduced. We discuss applications of the adopted modelization to the C(36) phases in a temperature range spanning from 300 to 1500 K, and compare the obtained results to the available data for C(36) and other fullerenes, and to the predictions of the well known Girifalco central potential modelization of interactions in fullerenes, as applied to the C(36) case.     

Precision of free energies calculated by molecular dynamics simulations of peptides in solution

Errors in free energies for molecular replacement and for conformation change of a small model peptide have been determined empirically by repeated simulations from different starting points. All calculations have been done using thermodynamic integration, in which the system's potential energy is coupled to a parameter λ, that is increased or decreased by a small amount at each step of the simulation. The effects of several factors that may alter the precision are evaluated. These factors include: the length of the simulation, the dependence of the potential energy on λ, the use of conformational restraints, and their magnitude and form. The methods used for restraint and conformational forcing are described in detail. The free energy change, calculated as the mean from several successive simulations with alternately increasing and decreasing λ, is found to be independent of the length of the simulations. As expected, longer simulations produce more precise results. The variation of the calculated free energies is found to consist of two parts, a random error and a systematic hysteresis, i.e., a dependence on the direction in which λ changes. The hysteresis varies as the inverse of the length of the simulation and the random error as the inverse square root The advantage of the use of a different (nonlinear) dependence of the attractive and repulsive parts of the nonbonded potential energy on the coupling parameter when “creating” particles in solution is found to be very large. This nonlinear coupling was found to be superior to the use of linear coupling and a nonlinear change of the coupling parameter with the simulation time. The hysteresis in conformational free energy calculations is found to increase markedly if too weak a forcing restraint is chosen. It is shown how to deconvolute the contribution of a torsional restraint from the dependence of the free energy on a torsion angle.     

Molecular simulations of aqueous electrolyte solubility: 1. The expanded-ensemble osmotic molecular dynamics method for the solution phase

We have developed a molecular-level simulation technique called the expanded-ensemble osmotic molecular dynamics (EEOMD) method, for studying electrolyte solution systems. The EEOMD method performs simulations at a fixed number of solvent molecules, pressure, temperature, and overall electrolyte chemical potential. The method combines elements of constant pressure-constant temperature molecular dynamics and expanded-ensemble grand canonical Monte Carlo. The simulated electrolyte solution systems contain, in addition to solvent molecules, full and fractional ions and undissociated electrolyte molecular units. The fractional particles are coupled to the system via a coupling parameter that varies between 0 (no interaction between the fractional particle and the other particles in the system) and 1 (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the constant pressure-constant temperature equations of motion and accompanied by random changes in the coupling parameter. The coupling-parameter changes are accepted with a probability derived from the expanded-ensemble osmotic partition function corresponding to the prescribed electrolyte chemical potential. The coupling-parameter changes mimic insertion/deletion of particles as in a crude grand canonical Monte Carlo simulation; if the coupling parameter becomes 0, the fractional particles disappear from the system, and as the coupling parameter reaches unity, the fractional particles become full particles. The method is demonstrated for a model of NaCl in water at ambient conditions. To test our approach, we first determine the chemical potential of NaCl in water by the thermodynamic integration technique and by the expanded-ensemble method. Then, we carry out EEOMD simulations for different specified values of the overall NaCl chemical potential and measure the concentration of ions resulting from the simulations. Both computations give consistent results, validating the EEOMD methodology.     

Atomistic molecular dynamics simulations on the interaction of TEMPO-oxidized cellulose nanofibrils in water

Atomistic molecular dynamics simulations were carried out to obtain information on the rheological, aggregation and disintegration properties of carboxylated (TEMPO-oxidized) cellulose nanofibrils with different functionalization levels. The magnitude of the inter-fibril interaction was quantified for parallel nanofibrils using the umbrella sampling method. The obtained potential of mean force was found highly sensitive to the charge configuration for intermediate functionalization levels. This feature was further studied with an electrostatic model for similar charge configurations and system periodicity as in the case of the molecular dynamics simulations. The electrostatic contribution of the charged surfaces varied from repulsive to attractive depending on the distribution of the carboxylate groups and nearby counter-ions, as well as the distance between the fibrils. The simulated deviations from average behavior for single fibrils in both models suggest heterogeneity in their aggregation and disintegration behavior. This was seen in disintegration experiments, where the differences in disintegration energy and in the structural variation qualitatively agreed with the model predictions. As to aggregation behavior, the studied case with parallel fibrils reflects the upper boundary of the repulsive interaction.     

A combined QM/MM molecular dynamics simulations study of nitrate anion (NO3-) in aqueous solution

The structural and dynamical properties of NO3- in dilute aqueous solution have been investigated by means of two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set. On the basis of both HF and B3LYP methods, a well-defined first hydration shell of NO3- is obtainable, but the shell is quite flexible and the hydrogen-bond interactions between NO3- and water are rather weak. With respect to the detailed analysis of the geometrical arrangement and vibrations of NO3-, the experimentally observed solvent-induced symmetry breaking of the ion is well reflected. In addition, the dynamical information, i.e., the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence time of water molecules surrounding the NO3- ion, clearly indicates the "structure-breaking" ability of this ion in aqueous solution. From a methodical point of view it seems that both the HF and B3LYP methods are not too different in describing this hydrated ion by means of a QM/MM simulation. However, the detailed analysis of the dynamics properties indicates a better suitability of the HF method compared to the B3LYP-DFT approach.     

Characterization of supramolecular polyphenol-chromium(III) clusters by molecular dynamics simulations

The binding of Cr(III) with (2R,3S,4R)-(+)-3,3',4,4',7-flavanpentol in aqueous solution is investigated by atomistic molecular dynamics simulations concentrating the analysis of the sampled data on the polyphenol ability to chelate metal ions and to form large noncovalently bonded molecular and supramolecular architectures.     

A multireference configuration interaction investigation of the excited-state energy surfaces of fluoroethylene (C2H3F)

Multireference configuration interaction with singles and doubles (MR-CISD) calculations has been performed for the optimization of conical intersections and stationary points on the fluoroethylene excited-state energy surfaces. For the planar ground state geometry, the vertical spectrum including 3s and 3p Rydberg states was calculated. From this geometry, a rigid torsion around the CC bond strongly reduces the energy gap between S0 and S1 states. Furthermore, a search for the minimum of the crossing seam shows that there exists a conical intersection close to the twisted structure and two additional ones for cis and trans pyramidalized structures. These three intersections are connected by the same seam. We have shown that the Hula-Twist process is an alternative way to the direct CC twisting in order to reach this part of the seam. Other conical intersections were also located in the CH3CF and CH2FCH, H-migration, and C(3v) structures. The photodynamics of the system is discussed based on topological features of these intersections.     

Polymerization molecular dynamics simulations. I. Cross-linked atomistic models for poly(methacrylate) networks

A methodology to build cross-linked atomistic structures for poly(methacrylates) is presented. The methodology is based on a polymerization molecular dynamics (MD) scheme in which monomers are allowed to react with each other during an MD simulation. The criteria for forming chemical bonds is based on distances between prespecified reactive centres on the monomers and growing polymer chains. The simulated rate of monomer diffusion is increased through the use of scaled charges and approximations in non-bond energy calculations. Local energetic stresses caused by bond formation are relaxed through the use of an explicit velocity rescaling molecular dynamics algorithm. An example network consisting of a typical dental resin is constructed and presented.     

Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model.

Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transfer reactions. Its complexity makes experimental characterization difficult, and so, theoretical approaches are valuable. The comparison of molecular dynamics free energy simulations with simpler models such as a dielectric continuum model is especially useful for obtaining qualitative insights. We have analyzed a charge insertion process that models deprotonation or mutation of an important side chain in the active site of the enzyme aspartyl-tRNA synthetase. Complexes with the substrate aspartate and the analogue asparagine were studied. The resulting dielectric relaxation was found to involve both ligand and side chain rearrangements in the active site and to account for a large part of the overall charging free energy. With the continuum model, charge insertion is performed along a two-step pathway: insertion into a static environment, followed by relaxation of the environment. These correspond to different physical processes and require different protein dielectric constants. A low value of approximately 1 is needed for the static step, consistent with the parametrization of the molecular mechanics charge set used. A value of 3-6 (depending on the exact insertion site and the nature of the ligand) is needed to describe the dielectric relaxation step. This moderate value indicates that, for this system, the local protein polarizability in the active site is within at most a factor of 2 of that expected at nonspecific positions in a protein interior.     

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.