Watching Na atoms solvate into (Na+,e-) contact pairs: untangling the ultrafast charge-transfer-to-solvent dynamics of Na- in tetrahydrofuran (THF)

With the large dye molecules employed in typical studies of solvation dynamics, it is often difficult to separate the intramolecular relaxation of the dye from the relaxation associated with dynamic solvation. One way to avoid this difficulty is to study solvation dynamics using an atom as the solvation probe; because atoms have only electronic degrees of freedom, all of the observed spectroscopic dynamics must result from motions of the solvent. In this paper, we use ultrafast transient absorption spectroscopy to investigate the solvation dynamics of newly created sodium atoms that are formed following the charge transfer to solvent (CTTS) ejection of an electron from sodium anions (sodide) in liquid tetrahydrofuran (THF). Because the absorption spectra of the sodide reactant, the sodium atom, and the solvated electron products overlap, we first examined the dynamics of the ejected CTTS electron in the infrared to build a detailed model of the CTTS process that allowed us to subtract the spectroscopic contributions of the sodide bleach and the solvated electron and cleanly reveal the spectroscopy of the solvated atom. We find that the neutral sodium species created following CTTS excitation of sodide initially absorbs near 590 nm, the position of the gas-phase sodium D-line, suggesting that it only weakly interacts with the surrounding solvent. We then see a fast solvation process that causes a red-shift of the sodium atom's spectrum in approximately 230 fs, a time scale that matches well with the results of MD simulations of solvation dynamics in liquid THF. After the fast solvation is complete, the neutral sodium atoms undergo a chemical reaction that takes place in approximately 740 fs, as indicated by the observation of an isosbestic point and the creation of a species with a new spectrum. The spectrum of the species created after the reaction then red-shifts on a approximately 10-ps time scale to become the equilibrium spectrum of the THF-solvated sodium atom, which is known from radiation chemistry experiments to absorb near approximately 900 nm. There has been considerable debate as to whether this 900-nm absorbing species is better thought of as a solvated atom or a sodium cation:solvated electron contact pair, (Na+,e-). The fact that we observe the initially created neutral Na atom undergoing a chemical reaction to ultimately become the 900-nm absorbing species suggests that it is better assigned as (Na+,e-). The approximately 10-ps solvation time we observe for this species is an order of magnitude slower than any other solvation process previously observed in liquid THF, suggesting that this species interacts differently with the solvent than the large molecules that are typically used as solvation probes. Together, all of the results allow us to build the most detailed picture to date of the CTTS process of Na- in THF as well as to directly observe the solvation dynamics associated with single sodium atoms in solution.     

Microsolvation of the sodium and iodide ions and their ion pair in acetonitrile clusters: a theoretical study

The structural and thermodynamic properties of Na+(CH3CN)n, I-(CH3CN)n, and NaI(CH3CN)n clusters have been investigated by means of room-temperature Monte Carlo simulations with model potentials developed to reproduce the properties of small clusters predicted by quantum chemistry. Ions are found to adopt an interior solvation shell structure, with a first solvation shell containing approximately 6 and approximately 8 acetonitrile molecules for large Na+(CH3CN)n and I-(CH3CN)n clusters, respectively. Structural features of Na+(CH3CN)n are found to be similar to those of Na+(H2O)n clusters, but those of I-(CH3CN)n contrast with those of I-(H2O)n, for which "surface" solvation structures were observed. The potential of mean force calculations demonstrates that the NaI ion pair is thermodynamically stable with respect to ground-state ionic dissociation in acetonitrile clusters. The properties of NaI(CH3CN)n clusters exhibit some similarities with NaI(H2O)n clusters, with the existence of contact ion pair and solvent-separated ion pair structures, but, in contrast to water clusters, both types of ion pairs adopt a well-defined interior ionic solvation shell structure in acetonitrile clusters. Whereas contact ion pair species are thermodynamically favored in small clusters, solvent-separated ion pairs tend to become thermodynamically more stable above a cluster size of approximately 26. Hence, ground-state charge separation appears to occur at larger cluster sizes for acetonitrile clusters than for water clusters. We propose that the lack of a large Na+(CH3CN)n product signal in NaI(CH3CN)n multiphoton ionization experiments could arise from extensive stabilization of the ground ionic state by the solvent and possible inhibition of the photoexcitation mechanism, which may be less pronounced for NaI(H2O)n clusters because of surface solvation structures. Alternatively, increased solvent evaporation resulting from larger excess energies upon photoexcitation or major solvent reorganization on the ionized state could account for the observed solvent-selectivity in NaI cluster multiphoton ionization.     

Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane nafion

Solvation properties of the hydrated excess proton are studied in a hydrophilic pocket of Nafion 117 through a series of molecular dynamics simulations. The multistate empirical valence bond (MS-EVB) methodology, which enables the delocalization of the excess proton through the Grotthuss hopping mechanism, was employed for one of the excess protons in the simulation cell. Simulations were performed such that "classical" nondissociable hydronium cations and a single excess proton treated with the MS-EVB methodology were at a concentration ratio of 39:1. Two degrees of hydration of the Nafion polymer electrolyte membrane were simulated, each displaying the same marked difference between the solvation structures of the classical versus MS-EVB treated (Grotthuss shuttling) excess proton species. These differences are attributed to the solvent dynamics needed to transfer the cation between the solvent separated and contact pair positions about the sulfonic acid counterion. The results demonstrate that it is generally impossible to describe the low pH conditions in the hydrophilic domains of Nafion without the explicit treatment of Grotthuss delocalization in the underlying molecular dynamics model for the excess protons.     

Microscopic hydration of the sodium chloride ion pair

Hydration of ion pairs is an essential process in various physicochemical phenomena occurring in solutions. Isolated clusters of an ion pair solvated with finite number of waters have been considered as a model system for the critical evaluation of microscopic interactions involved in the process, and theoretical studies have contributed exclusively to the subject up to now. Here we report the first experimental characterization of structure and internal dynamics of hydrated ion pairs, NaCl-(H2O)n (n = 1-3). The measurements of their rotational spectra have proven that the clusters have cyclic forms, in which Na+ and Cl- ions are strongly interacted with the O and H atoms of the solvent molecules, respectively. The Na-Cl distance shows a pronounced increase with the successive addition of water molecules. The separation for n = 3 approaches the value predicted for the contact ion-pair state in aqueous solution by recent molecular dynamics simulations.     

Understanding solvent effects in the selective conversion of fructose to 5-hydroxymethyl-furfural: a molecular dynamics investigation

Selective conversion of fructose to 5-hydroxymethyl-furfural (HMF) involves the participation of high-boiling solvents like dimethyl sulfoxide (DMSO). In order to replace DMSO with low-boiling solvents, it is imperative that we understand the effect of DMSO solvation in protecting (i) HMF from rehydration and humins formation reactions and (ii) fructose from side reactions, other than its dehydration to HMF. In the present work, molecular dynamics simulations of HMF and fructose in water and in water-DMSO mixtures are carried out using the OPLS-AA force field. Radial pair distribution functions, coordination numbers and the hydrogen-bond network between the HMF/fructose molecule and the solvent molecules are analysed. The local 3-dimensional picture of the arrangement of solvent molecules around the solute, which cannot be accessed from pair distribution functions, is also computed. We show preferential coordination of DMSO around HMF and explain how this could provide a shielding effect to the HMF molecule, thus protecting it from further rehydration to levulinic acid and formic acid and from humins formation. In the case of fructose, the presence of DMSO also reduces the number of water molecules in the immediate vicinity of fructose. Though fewer water molecules coordinate around fructose, they are bound strongly to it. Analysis of the local 3-dimensional arrangement of DMSO molecules suggests that it protects the fructose molecule from side reactions that would lead to condensation or reversion products. However, the presence of DMSO molecules does not hamper the water molecules coming into contact with the oxygen atom of the hydroxyl groups of fructose, which is required for a proton transfer from water to fructose, to initiate the dehydration reaction to HMF.     

Elucidating the initial dynamics of electron photodetachment from atoms in liquids using variably-time-delayed resonant multiphoton ionization

We study the photodetachment of electrons from sodium anions in room temperature liquid tetrahydrofuran (THF) using a new type of three-pulse pump-probe spectroscopy. Our experiments use two variably-time-delayed pulses for excitation in what is essentially a resonant 1+1 two-photon ionization: By varying the arrival time of the second excitation pulse, we can directly observe how solvent motions stabilize and trap the excited electron prior to electron detachment. Moreover, by varying the arrival times of the ionization (excitation) and probe pulses, we also can determine the fate of the photoionized electrons and the distance they are ejected from their parent Na atoms. We find that as solvent reorganization proceeds, the second excitation pulse becomes less effective at achieving photoionization, and that the solvent motions that stabilize the excited electron following the first excitation pulse occur over a time of approximately 450 fs. We also find that there is no spectroscopic evidence for significant solvent relaxation after detachment of the electron is complete. In combination with the results of previous experiments and molecular dynamics simulations, the data provide new insight into the role of the solvent in solution-phase electron detachment and charge-transfer-to-solvent reactions.     

Preferential solvation dynamics in liquids: how geodesic pathways through the potential energy landscape reveal mechanistic details about solute relaxation in liquids

It is not obvious that many-body phenomena as collective as solute energy relaxation in liquid solution should ever have identifiable molecular mechanisms, at least not in the sense of the well-defined sequence of molecular events one often attributes to chemical reactions. What can define such mechanisms, though, are the most efficient relaxation paths that solutions take through their potential energy landscapes. When liquid dynamics is dominated by slow diffusive processes, there are mathematically precise and computationally accessible routes to searching for such paths. We apply this observation to the dynamics of preferential solvation, the relaxation around a newly excited solute by a solvent composed of different components with different solvating abilities. The slow solvation seen experimentally in these mixtures stems from the dual needs to compress the solvent and to do solvent-solvent exchanges near the solute. By studying the geodesic (most efficient) paths for this combined process in a simple atomic liquid mixture, we show that the mechanism for preferential solvation features a reasonably sharp onset for slow diffusion, and that this diffusion involves a sequential, rather than concerted, series of solvent exchanges.     

Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation

We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.     

Ion pairing as a possible clue for discriminating between sodium and potassium in biological and other complex environments

For a series of biologically relevant anions, we present free energy changes upon replacing potassium with sodium in a contact ion pair. Calculations performed using a combination of molecular dynamics simulations and ab initio methods demonstrate the ordering of anions in a Hofmeister series. Small anionic groups such as carboxylates preferentially pair with sodium, while intermediate cases such as chloride or monovalent phosphate exhibit almost no specificity, and large anions (e.g., methylsulfonate) prefer potassium over sodium. These results can rationalize different behavior of Na+ versus K+ at the surface of hydrated proteins, DNA, and reversed micelles.     

Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36

Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.     

FACTS: Fast analytical continuum treatment of solvation

An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume and spatial symmetry of the solvent that is displaced from around a solute atom by its neighboring atoms. The two measures of solvent displacement are combined in empirical equations to approximate the atomic (or self) electrostatic solvation energy and the solvent accessible surface area. The former directly yields the effective Born radius, which is used in the generalized Born (GB) formula to calculate the solvent-screened electrostatic interaction energy. A comparison with finite-difference Poisson data shows that atomic solvation energies, pair interaction energies, and their sums are evaluated with a precision comparable to the most accurate GB implementations. Furthermore, solvation energies of a large set of protein conformations have an error of only 1.5%. The solvent accessible surface area is used to approximate the nonpolar contribution to solvation. The empirical approach, called FACTS (Fast Analytical Continuum Treatment of Solvation), is only four times slower than using the vacuum energy in molecular dynamics simulations of proteins. Notably, the folded state of structured peptides and proteins is stable at room temperature in 100-ns molecular dynamics simulations using FACTS and the CHARMM force field.     

Hydration of alkali ions from first principles molecular dynamics revisited

Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.     

Quantum Chemical Microsolvation by Automated Water Placement

We developed a quantitative approach to quantum chemical microsolvation. Key in our methodology is the automatic placement of individual solvent molecules based on the free energy solvation thermodynamics derived from molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). This protocol enabled us to rigorously define the number, position, and orientation of individual solvent molecules and to determine their interaction with the solute based on physical quantities. The generated solute–solvent clusters served as an input for subsequent quantum chemical investigations. We showcased the applicability, scope, and limitations of this computational approach for a number of small molecules, including urea, 2-aminobenzothiazole, (+)-syn-benzotriborneol, benzoic acid, and helicene. Our results show excellent agreement with the available ab initio molecular dynamics data and experimental results.     

Is ammonia a better solvent than water for contact ion pairs?

The existence of a charge-transfer-to-solvent process when a KI contact ion pair (CIP) dissolved in supercritical water (SCW) is excited by UV light was confirmed by use of electronic structure calculations applied to molecular dynamics trajectories. We observed similar behavior with fluid density as that found for the KI-CIP in supercritical ammonia (SCA); nevertheless, there are some distinct features in the two supercritical solvents. First, the effect of the solvent field due to the molecules lying beyond the first solvation shell is very different in SCW compared with that observed in SCA; in SCW it actually has a destabilizing effect over the ground and excited states. Second, our results for the thermodynamic behavior of the CIP indicate that SCA is better solvent than SCW for this species. The differences found can be attributed to the solvent molecules surrounding the CIP and bridging the two ions; they shield more efficiently the ion pair from long-range solvent effects in SCA. The different behavior is partially attributed to a stronger solvent-solvent interaction in SCW than in SCA.     

Solvation of excess electrons in LiF ionic pair matrix: evidence for a solvated dielectron from ab initio molecular dynamics simulations and calculations

Ab initio molecular dynamics simulations and first-principles calculations reveal the existence of a solvated dielectron species, (2e)s, in an LiF ionic matrix. The nature of the solvation mechanism and the stability of the species was explored. In addition to electrostatic interactions, a hole-orbital coupling among solvent molecules may significantly enhance the stability of the solvated electrons and govern the extent of electron solvation. This hole-orbital coupling is different from either an electrostatic coupling or conventional chemical bonding, and it may be described as a transition between them.     

Many-body potentials for aqueous Li(+), Na(+), Mg(2+), and Al(3+): comparison of effective three-body potentials and polarizable models

Many-body potentials for the aqueous Li(+), Na(+), Mg(2+), and Al(3+) ions have been constructed from ab initio cluster calculations. Pure pair, effective pair, effective three-body, and effective polarizable models were created and used in subsequent molecular dynamics simulations. The structures of the first and second solvation shells were studied using radial distribution functions and angular-radial distribution functions. The effective three-body and polarizable potentials yield similar first-shell structures, while the contraction of the O-O distances between the first and second solvation shells is more pronounced with the polarizable potentials. The definition of the tilt angle of the water molecules around the ions is discussed. When a proper definition is used, it is found that for Li(+), Mg(2+), and Al(3+) the water molecules prefer a trigonal orientation, but for Na(+) a tetrahedral orientation (ion in lone-pair direction) is preferred. The self-diffusion coefficients for the water molecules and the ions were calculated; the ionic values follow the order obtained from experiment, although the simulated absolute values are smaller than experiment for Mg(2+) and Al(3+).     

基于分子动力学模拟和连续介质模型的自由能计算方法*

近些年,基于分子动力学模拟和连续介质模型的自由能计算方法受到了越来越多的关注,其中MM/PBSA就是最具代表性的方法.在MM/PBSA中,体系的焓变采用分子力学(MM)的方法计算得到;溶剂效应中极性部分对自由能的贡献通过解Poisson-Boltzmann(PB)方程的方法计算得到;溶液效应中非极性部分对自由能的贡献则通过分子表面积(SA)计算得到.本文结合我们科研组的工作,就近几年MM/PBSA方法的最新进展做了较为详细的阐述,同时对MM/PBSA的发展前景进行了展望.     

Probing the transition from hydrophilic to hydrophobic solvation with atomic scale resolution

Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L(1,3) edge EXAFS at 50 ps time delay points to the formation of an expanded water cavity around the iodine atom, in good agreement with classical and quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. These also show that while the hydrogen atoms pointed toward iodide, they predominantly point toward the bulk solvent in the case of iodine, suggesting a hydrophobic behavior. This is further confirmed by quantum chemical (QC) calculations of I(-)/I(0)(H(2)O)(n=1-4) clusters. The L(1) edge sub-picosecond spectra point to the existence of a transient species that is not present at 50 ps. The QC calculations and the QM/MM MD simulations identify this transient species as an I(0)(OH(2)) complex inside the cavity. The simulations show that upon electron abstraction most of the water molecules move away from iodine, while one comes closer to form the complex that lives for 3-4 ps. This time is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform an H-bond network. Only then is the interaction with the solvation shell strong enough to pull the water molecule of the complex toward the bulk solvent. Overall, much of the behavior at early times is determined by the reorientational dynamics of water molecules and the formation of a complete network of hydrogen bonded molecules in the first solvation shell.