Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.     

Phase equilibrium modeling of triglycerides in supercritical fluids

To design a reactor and separator for a supercritical biodiesel process, phase equilibria of multi-component mixtures in supercritical fluids should be determined using group contribution with association equation of state (GCA-EOS) as a thermodynamics method. The model is considered for two systems of reactants and products. System 1 is comprised of methanol and triglycerides from two sources (palm and Jatropha oils); and System 2 is unconverted methanol, FAME (product) and glycerol (by-product). Pressure and temperature diagrams were developed at different mole fraction of methanol (x_MeOH). As x_MeOH increased, the critical temperature (T_c) and pressure (p_c) increased. The increasing temperature causes the immiscibility region and the amount of methanol at the plait point to decrease. The maximum plait point pressure was observed at 19.20 MPa for palm and 19.33 MPa for Jatropha oil systems.     

Ultrafast solvent response upon a change of the solute size in non-polar supercritical fluids

Non-polar solvation dynamics has been investigated using steady-state absorption and emission spectroscopy of the NO A ²Σ⁺(3sσ) Rydberg state in fluid Ar over a wide range of densities spanning the supercritical regime. Equilibrium molecular dynamics simulations were implemented to derive a new isotropic NO A(3sσ)–Ar pair potential which was further used to investigate the role of local density enhancements on the solvation process by non-equilibrium molecular dynamics simulations. These density inhomogeneities were found to have no influence on the solvation dynamics. Furthermore, the latter was shown to take place in a strongly non-linear regime, especially at low temperatures. This process results from the dramatic change of solute–solvent short range interaction associated with the large solute size change upon excitation to the Rydberg state.     

A case against large cluster-induced nonequilibrium solvent effects in supercritical water

Using a partially compressible continuum solvation model, we have shown that solvent compression in just the first two solvation shells (or thereabouts) is all that is required to gain the bulk of the compression-induced enhancement to the solvation energy of ions in supercritical water. This result is found to hold even when the direct, equilibrium solvent-solute cluster involves well over a hundred solvent molecules. We argue that, for charge variation reactions in supercritical water, the observed short-range behavior of the compression-induced solvation free energy precludes the existence of any anomalously large nonequilibrium solvent effects which might be expected on the basis of the very large size of the equilibrium clusters. Received: 8 January 1997 / Accepted: 17 January 1997     

Solvation in supercritical water

Solvation in supercritical water under equilibrium and nonequilibrium conditions is studied via molecular dynamics simulations. The influence of solute charge distributions and solvent density on the solvation structures and dynamics is examined with a diatomic probe solute molecule. It is found that the solvation structure varies dramatically with the solute dipole moment, especially in low-density water, in accord with many previous studies on ion solvation. This electrostrictive effect has important consequences for solvation dynamics. In the case of a nonequilibrium solvent relaxation, if there are sufficiently many water molecules close to the solute at the outset of the relaxation, the solvent response measured as a dynamic Stokes shift is almost completely governed by inertial rotations of these water molecules. By contrast, in the opposite case of a low local solvent density near the solute, not only rotations but also translations of water molecules play an important role in solvent relaxation dynamics. The applicability of a linear response is found to be significantly restricted at low water densities.     

Polar solvation dynamics in supercritical fluids: a mode-coupling treatment

A mode-coupling treatment of polar solvation dynamics in supercritical fluids is presented. The equilibrium solvation time correlation function for the solute fluctuating transition frequency is obtained from the mode-coupling theory method and from molecular-dynamics simulations. The theory is shown to be in good agreement with the simulation. The solvation time correlation function exhibits three distinct time scales, with rapid initial decay, followed by a recurrence at intermediate times, and a slowly decaying long-time tail. Our theoretical analysis shows that the short-time decay arises from the coupling of the solute energy gap to the solvent polarization modes, the recurrence at intermediate times is due to the energy modes, while the slow long-time decay reflects the coupling to the number density modes.     

New topic of supercritical fluids: local activity coefficients of supercritical solvent and cosolvent around solute

The study of inhomogeneity in supercritical fluids (SCFs) is of great importance. In this work, we propose the concept of local activity coefficients in supercritical (SC) solutions, which link thermodynamics and inhomogeneity in SC systems. The local activity coefficients of CO(2)+acetonitrile+phenol blue and CO(2)+acetic acid+phenol blue systems are investigated at 308.15 K in critical region and outside critical region. To do this, the local compositions of CO(2)+acetonitrile and CO(2)+acetic acid mixed solvents around phenol blue are first estimated using UV-visible spectroscopy. Then it is considered that there exist bulk phase and local phase around phenol blue in the systems. The activity coefficients of CO(2) and the cosolvents (acetonitrile or acetic acid) in bulk phase are calculated using Peng-Robinson equation of state. The local activity coefficients of CO(2) and the cosolvents are then calculated on the basis of thermodynamic principles. It is demonstrated that in the critical region the local activity coefficients differ from bulk activity coefficients significantly and are sensitive to pressure. This can explain many unusual phenomena in SC systems in critical region thermodynamically.     

Semi-classical generalized Langevin equation for equilibrium and nonequilibrium molecular dynamics simulation

Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matter in different phases. Normally, the atomic dynamics are described by classical equations of motion and the effect of the environment is taken into account through the fluctuating and frictional forces. Generally, the nuclear quantum effects and their coupling to other degrees of freedom are difficult to include in an efficient way. This could be a serious limitation on its application to the study of dynamical properties of materials made from light elements, in the presence of external driving electrical or thermal fields. One example of such system is single molecule dynamics on metal surface, an important system that has received intense study in surface science. In this review, we summarize recent effort in extending the Langevin MD to include nuclear quantum effect and their coupling to flowing electrical current. We discuss its applications in the study of adsorbate dynamics on metal surface, current-induced dynamics in molecular junctions, and quantum thermal transport between different reservoirs.     

Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models

The physical content of and, in particular, the nonlinear contributions from the Langevin-Debye model are illustrated using two applications. First, we provide an improvement in the Langevin-Debye model currently used in some implicit solvent models for computer simulations of solvation free energies of small organic molecules, as well as of biomolecular folding and binding. The analysis is based on the implementation of a charge-dependent Langevin-Debye (qLD) model that is modified by subsequent corrections due to Onsager and Kirkwood. Second, the physical content of the model is elucidated by discussing the general treatment within the LD model of the self-energy of a charge submerged in a dielectric medium for three different limiting conditions and by considering the nonlinear response of the medium. The modified qLD model is used to refine an implicit solvent model (previously applied to protein dynamics). The predictions of the modified implicit solvent model are compared with those from explicit solvent molecular dynamics simulations for the equilibrium conformational populations of 1,2-dimethoxyethane (DME), which is the shortest ether molecule to reproduce the local conformational properties of polyethylene oxide, a polymer with tremendous technological importance and a wide variety of applications. Because the conformational population preferences of DME change dramatically upon solvation, DME is a good test case to validate our modified qLD model. The present analysis of the modified qLD model provides the motivation and tools for studying a wide variety of other interesting systems with heterogeneous dielectric properties and spatial anisotropy.     

Density dependence of the Stokes shift and solvent reorganization energy in supercritical fluids

The Stokes shifts of coumarin 153 (C153) in CF₃H, CO₂ and C₂H₆ have been measured at several reduced densities (0.3–1.8). For C153 in CF₃H, the shifts increase with a decrease in reduced density and show a maximum value at a reduced density of 0.5. In non-polar solvents, the shifts are not dramatically altered as a function of reduced density but slightly increase with a decrease in the reduced density.     

Solvation structure and dynamics for passivated Au nanoparticle in supercritical CO2: a molecular dynamic simulation

All-atomic molecular dynamics simulations have been performed to study the interfacial structural and dynamical properties of passivated gold nanoparticles in supercritical carbon dioxide (scCO(2)). Simulations were conducted for a 55-atom gold nanocore with thiolated perfluoropolyether as the packing ligands. The effect of solvent density and surface coverage on the structural and dynamical properties of the self-assembly monolayer (SAM) has been discussed. The simulation results demonstrate that the interface between nanoparticle and scCO(2) solvent shows a depletion region due to the preclusion of SAM. The presence of scCO(2) solvent around the passivated Au nanoparticle can lead to an enhanced extension of the surface SAM. Under full coverage, the structure and conformation of SAM are insensitive to the density change of scCO(2) fluid. This simulation results clarify the microscopic solvation mechanism of passivated nanoparticles in supercritical fluid medium and is expected to be helpful in understanding the scCO(2)-based nanoparticle dispersion behavior.     

Solvation of coumarin 153 in supercritical fluoroform

We present a study of local density augmentation around an attractive solute (i.e., giving rise to more attractive interaction with the solvent than solvent-solvent interactions) in supercritical fluoroform. This work is based on molecular dynamics simulations of coumarin 153 in supercritical fluoroform at densities both above and below the critical density, ranging from dilute gas-like to liquid-like, at a reduced temperature (T/T(c)) of 1.03. We focused on studying the structure of the solvation shell and the variation of the solute electronic absorption and emission shifts with density. Quantum calculations at the density functional theory (DFT) level were run on the solute in the ground state, and time-dependent DFT calculations were performed in the solute excited state in order to determine the solute-solvent potential parameters. The results obtained for the Stokes shift are in agreement with the experimental measurements. To evaluate local density augmentation from simulations, we used two different definitions, one based on the solvation number and the other derived from solvatochromic shifts. In the former case, the agreement with experimental results is good, while, in the latter case, better agreement is achieved by perturbatively including the induced-dipole contribution to the solvation energy.     

Solvation shell dynamics studied by molecular dynamics simulation in relation to the translational and rotational dynamics of supercritical water and benzene

The solvation shell dynamics of supercritical water is analyzed by molecular dynamics simulation with emphasis on its relationship to the translational and rotational dynamics. The relaxation times of the solvation number (tau S), the velocity autocorrelation function (tau D), the angular momentum correlation function (tau J), and the second-order reorientational correlation function (tau 2R) are studied at a supercritical temperature of 400 degrees C over a wide density region of 0.01-1.5 g cm(-3). The relaxation times are decomposed into those conditioned by the solvation number n, and the effect of the short-ranged structure is examined in terms of its probability Pn of occurrence. In the low to medium-density range of 0.01-0.4 g cm(-3), the time scales of water dynamics are in the following sequence: tau D>tau S approximately or > tau J approximately or > tau 2R. This means that the rotation in supercritical water is of the "in-shell" type while the translational diffusion is not. The comparison to supercritical benzene is also performed and the effect of hydrogen bonding is examined. The water diffusion is not of the in-shell type up to the ambient density of 1.0 g cm(-3), which corresponds to the absence of the transition from the collision to the Brownian picture, whereas such transition is present in the case of benzene. The absence of the transition in water comes from the fast reorganization of the hydrogen bonds and the enhanced mobility of the solvation shell in supercritical conditions.     

Solvation dynamics in acetonitrile: a study incorporating solute electronic response and nuclear relaxation

The solvent reorganization process after electronic excitation of a polar solute in a polar solvent such as acetonitrile is related mainly to the time evolution of the solute-solvent electrostatic interaction. Modern laser-based techniques have sufficient time resolution to follow this decay in real time, providing information to be confirmed and interpreted by theories and models. We present here a study aimed at the investigation of the different steps involved in the process taking place after a vertical S(0) --> S(1) excitation of a large size chromophore, coumarin 153 (C153), in acetonitrile, from both the solute and the solvent points of view. To do this, we use accurate quantum mechanical calculations for the solute properties within the polarizable continuum model (PCM) and classical molecular dynamics (MD) simulations, both equilibrium and nonequilibrium, for C153 in the presence of the solvent. The geometry of the solute is allowed to change in order to study the role of internal motions in the time-dependent solvation process. The solvent response function has been obtained from the simulation data and compared to experiment, while the comparison between equilibrium and nonequilibrium MD results for the solvation response confirms the validity of the linear response approximation in the C153-acetonitrile system. The MD trajectories have also been used to monitor the structure of the solvation shell and to determine its change in response to the change in the solute partial charges.     

Concerted processes in supercritical fluids

The possibility of obtaining concerted mechanisms of chemical activation in supercritical fluids (SCFs) with the formation of a multicenter general transition state that includes a group of reagent atoms in which the subsequent breaking of chemical bonds and the formation of new chemical bonds start and proceed simultaneously is discussed. Two processes are considered that can occur only in SCF media: the reduction of anthracene in an isopropyl alcohol SCF and the impregnation of the photochromic compound spiroanthrooxazine (SAO) in a polycarbonate matrix in SC CO₂ accompanied by an irreversible conformational rearrangement of the SAO structure. Concepts of the possible dependence of the concerted mechanism of the considered processes on the intertwining or entanglement of electron subsystems in forming multicenter transition states are developed. The decisive role of the electromagnetic component of a physical vacuum in obtaining a high degree of correlation in systems of entangled electrons is discussed.     

Solvation forces between silica bodies in supercritical carbon dioxide

We report Monte Carlo simulations of the solvation pressure between two planar surfaces, which represent the interface of spherical silica nanoparticles in supercritical carbon dioxide. Carbon dioxide (CO2) was modeled as an atomistic dumbbell or a spherical Lennard-Jones particle. The interaction between CO2 molecules and silica surfaces was characterized by the standard Steele potential with energetic heterogeneities representing the hydrogen bonds. The parameters for the solid-fluid interaction potentials were obtained by fitting our simulations to the experimental isotherms of CO2 sorption on mesoporous siliceous materials. We studied the dependence of the solvation force on the distance between planar silica surfaces at T = 318 K, at equilibrium bulk pressures p(bulk) ranging from 69 to 200 atm. At 69 atm, we observed a long-range attraction between the two surfaces, and it vanished when the pressure was increased to 102 and then 200 atm. The results obtained with different fluid models were consistent with each other. According to our observations, energetic heterogeneities of the surface have negligible influence on the solvation pressure. Using the Derjaguin approximation, we calculated the solvation forces between spherical silica nanoparticles in supercritical CO2 from the solvation pressures between the planar surfaces.     

Rotational viscosity of fluids composed of linear molecules: an equilibrium molecular dynamics study

In this paper, we investigate the rotational viscosity for a chlorine fluid and for a fluid composed of small linear molecules by using equilibrium molecular dynamics simulations. The rotational viscosity is calculated over a large range of state points. It is found that the rotational viscosity is almost independent of temperature in the range studied here but exhibits a power-law dependency on density. The rotational viscosity also shows a power-law relationship with the molecular length, and the ratio between the shear and rotational viscosities approaches 0.5 for the longest molecule studied here. By changing the number of atoms or united atomic units per molecule and by keeping the molecule length fixed, we show that fluids composed of molecules which have a rodlike shape have a lower rotational viscosity. We argue that this phenomenon is due to the reduction in intermolecular connectivity, which leads to larger fluctuations around the values possessed by the fluid on average. The conclusions here can be extended to fluids composed of uniaxial molecules of arbitrary length.     

Temporal asymmetry of fluctuations in nonequilibrium steady states: links with correlation functions and nonlinear response

The presence of temporal asymmetries in fluctuation paths of nonequilibrium systems has recently been confirmed numerically in nonequilibrium molecular dynamics simulations of particular deterministic systems. Here we show that this is a common feature of homogeneously driven and thermostatted, reversible, deterministic, chaotic, nonequilibrium systems of interacting particles. This is done by expressing fluctuation paths as correlation functions. The theoretical arguments look rather general, and we expect them to easily extend to other forms of driving and thermostats. The emergence of asymmetry is also justified using the transient time correlation function expression of nonlinear response theory. Numerical simulations are used to verify our arguments.     

Degradation of polycaprolactone in supercritical fluids

The degradation of polycaprolactone (PCL) was studied in subcritical and supercritical toluene from 250 to 375 °C at 50 bar. The degradation was also investigated in various solvents like ethylbenzene, o-xylene and benzene at 325 °C and 50 bar. The effect of pressure on degradation was also evaluated at 325 °C at various pressures (35, 50 and 80 bar). The variation of molecular weight with time was analyzed using gel permeation chromatography and modeled using continuous distribution kinetics to evaluate the degradation rate coefficients. PCL degrades by random chain scission in subcritical conditions (250-300 °C) and by chain end scission (325-375 °C) in supercritical conditions in toluene. The degradation of PCL in other solvents at 325 °C was by chain end scission under both subcritical and supercritical conditions indicating that the mode of scission depends on the temperature and not on the supercriticality of the solvent. The thermogravimetric analysis of PCL was investigated at various heating rates (2-24 °C/min) and the activation energy was determined using Friedman, Ozawa and Kissinger methods. It was shown that PCL degrades by random scission at lower temperatures and by chain end scission at higher temperatures again indicating that the mode of scission is dependent on the temperature.