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Publications (90)
Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics simulations with string-method determination of complex reaction coordinates to elucidate the molecular mechani...
The dynamics of water at interfaces between an electrode and an electrolyte are essential for the transport of redox species and for the kinetics of charge transfer reactions next to...
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we u...
The effects of ions on liquid water’s structural, dynamical, and thermodynamical properties have key implications for a wide range of biological and technological processes. Based on simulations and analytic modeling, we have recently developed a framework that allows to rationalize the effects of solutes and interfaces on water reorientation dynam...
Whether the air-water interface decreases or increases the acidity of simple organic and inorganic acids compared to the bulk is critically important in a broad range of environmental and biochemical processes. However, a consensus has not yet been achieved on this key question. Here we use machine learning-based reactive molecular dynamics simulat...
The self-diffusion of water molecules plays a key part in a broad range of essential processes in biochemistry, medical imaging, material science, and engineering. However, its molecular mechanism and the role played by the water hydrogen-bond network rearrangements are not known. Here we combine molecular dynamics simulations and analytic modeling...
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motions. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein sidechains. Here, we u...
Liquid water confined within nanometer‐sized channels exhibits a strongly reduced local dielectric constant perpendicularly to the wall, especially at the interface, and this has been suggested to induce faster electron transfer kinetics at the interface than in the bulk. We study a model electron transfer reaction in aqueous solution confined betw...
Liquid water confined within nanometer-sized channels exhibits a surprisingly low dielectric constant along the direction orthogonal to the channel walls. This is typically assumed to result from a pronounced heterogeneity across the sample: the dielectric constant would be bulk-like everywhere except at the interface, where it would be dramaticall...
The dynamics of a vibrational frequency in a condensed phase environment, i.e., the spectral diffusion, has attracted considerable interest over the last two decades. A significant impetus has been the development of two-dimensional infrared (2D-IR) photon-echo spectroscopy that represents a direct experimental probe of spectral diffusion, as measu...
Hydrogen-bond exchanges drive many dynamical processes in water and aqueous solutions. The extended jump model (EJM) provides a quantitative description of OH reorientation in water based on contributions from hydrogen-bond exchanges, or jumps, and the “frame” reorientation of intact hydrogen-bond pairs. Here, we show that the activation energies o...
The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.
Evolution has led to conserved enzyme families that efficiently catalyze the same chemical reaction but in radically different thermal environments. In particular, some enzymes need to be stable and to work in very hot conditions that usually lead to protein melting. Using atomistic simulations and analytic modeling, it is shown that the temperatur...
Thermal adaptation of enzymes is essential for both living organism development in extreme conditions and efficient biocatalytic applications. However, the molecular mechanisms leading to a shift in catalytic activity optimum temperatures remain unclear, and there is increasing experimental evidence that thermal adaptation involves complex changes...
A key aspect of life's evolution on Earth is the adaptation of proteins to be stable and work in a very wide range of temperature conditions. A detailed understanding of the associated molecular mechanisms would also help to design enzymes optimized for biotechnological processes. Despite important advances, a comprehensive picture of how thermophi...
The reorientation dynamics of water at electrified graphene interfaces was recently shown to exhibit a surprising and strongly asymmetric behavior: positive electrode potentials slow down interfacial water reorientation, while for increasingly negative potentials water dynamics first accelerates before reaching an extremum and then being retarded f...
For proteins in solvent mixtures, the relative abundances of each solvent in their solvation shell have a critical impact on their properties. Preferential solvation of a series of proteins in water-glycerol mixtures is studied here over a broad range of solvent compositions via classical molecular dynamics simulations. Our simulation results revea...
The properties of water at an electrified graphene electrode are studied via classical molecular dynamics simulations with a constant potential approach. We show that the value of the applied electrode potential has dramatic effects on the structure and dynamics of interfacial water molecules. While a positive potential slows down the reorientation...
For proteins in solvent mixtures, the relative abundances of each solvent in their solvation shell have a critical impact on their properties. Preferential solvation of a series of proteins in water-glycerol mixtures is studied here over a broad range of solvent compositions via classical molecular dynamics simulations. Our simulation results revea...
Aqueous ionic solutions are ubiquitous in chemistry and in biology. Experiments show that ions affect water dynamics, but a full understanding of several questions remains needed: why some salts accelerate water dynamics while others slow it down, why the effect of a given salt can be concentration-dependent, whether the effect of ions is rather lo...
We study the librational absorption spectra of water nanodroplets in reverse micelles by time-domain THz spectroscopy: an additional feature at 830 cm−1 is assigned by molecular dynamics simulations to water molecules bonded to phosphate heads.
We use ab initio molecular dynamics simulation to study the effect of hydrophobic groups on the dynamics of water molecules in aqueous solutions of trimethylamine N-oxide (TMAO). We show that hydrophobic groups induce a moderate (<2-fold) slowdown of water reorientation and hydrogen-bond dynamics in dilute solutions, but that this slowdown rapidly...
The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm⁻¹ reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopoo...
Enzymes are widely used in non-aqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in non-aqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyz...
The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Re...
We combine classical and ring polymer molecular dynamics simulations with the molecular jump model to provide a molecular description of the nuclear quantum effects (NQEs) on water reorientation and hydrogen-bond dynamics in liquid H2O and D2O. We show that while the net NQEs is negligible in D2O, it leads to a ∼13% acceleration in H2O dynamics com...
Long-range ordering of water around solutes has been invoked repeatedly in the literature as the key to understanding its biological function. Recently, it has been shown that in a dilute 8 mM aqueous NaCl solution the orientational correlation between water molecules extends beyond 8 nanometers. This was interpreted as arising from a long-range ef...
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular d...
In this chapter we present the basic principles of transition state theory (TST) and a number of its applications to the study of enzymatic reactions. The assumptions of TST are discussed, as are the refinements to account for the failure of those assumptions, in particular that of no recrossing of the transition state surface. The selection of a r...
In this chapter, we review the available experimental data and molecular models describing the effect of different solvents, including water, on the catalytic activity of enzymes. While a popular picture suggests that water acts as a lubricant of the protein conformational motions required for catalysis, we show that this dynamical picture is not s...
The structure and dynamics of phospholipid reverse micelles are studied by molecular dy-namics. We report all-atom unconstrained simulations of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC) reverse micelles in benzene of increasing sizes, with water to surfactant number ratios ranging from Wo = 1 to 16. The aggregation number, i.e., the number of DOPC...
The reorientation and hydrogen-bond dynamics of water molecules within the hydration shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are investigated via molecular dynamics simulations and an analytic jump model, which provide valuable new molecular level insights into these dynamics. Different sources of he...
Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question...
We report on the orientational dynamics of water at an extended hydrophobic interface with an octadecylsilane self-assembled monolayer on fused silica. The interfacial dangling OH stretch mode is excited with a resonant pump and its evolution followed in time by a surface-specific, vibrationally resonant, infrared-visible sum-frequency probe. High...
Traditional descriptions of vibrational energy transfer consider a quantum oscillator interacting with a classical environment. However, a major limitation of this simplified description is the neglect of quantum decoherence induced by the different interactions between two distinct quantum states and their environment, which can strongly affect th...
Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation i...
We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term 'dynamics' has been used with different meanings, we first return to the Transition State Theory rate constant, its assumptions and the choices it involves,...
A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water respectively in the bulk and in the hydratio...
The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. He...
The dynamics of water are dramatically modified upon confinement in nanoscale hydrophilic silica pores. In particular, the OH reorientation dynamics of the interfacial water are non-exponential and dramatically slowed relative to the bulk liquid. A detailed analysis of molecular dynamics simulations is carried out to elucidate the microscopic origi...
We present a detailed molecular-dynamics study of water reorientation and hydrogen-bond dynamics in a strong confinement situation, within the narrow pores of an all-silica Linde type A (LTA) zeolite. Two water loadings of the zeolite are compared with the bulk case. Water dynamics are retarded in this extreme hydrophobic confinement and the slowdo...
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysoz...
The perturbation induced by a hydrophobic solute on water dynamics is essential in many biochemical processes, but its mechanism and magnitude are still debated. A stringent test of the different proposed pictures is provided by recent NMR measurements by Qvist and Halle (J. Am. Chem. Soc. 2008, 130, 10345-10353) which showed that unexpectedly, the...
There are fundamental and not yet fully resolved questions concerning the impact of solutes, ions in particular, on the structure and dynamics of water, which can be formulated as follows: Are the effects of ions local or long-ranged? Is the action of cations and anions on water cooperative or not? Here, we investigate how the reorientation and hyd...
In this paper we present a theoretical investigation of proton conduction in a 2-tethered poly-vinyl-imidazole system, an N-heterocyclic-based membrane used as electrolyte in proton exchange membrane fuel cells (PEMFCs). In particular a detailed analysis, combining Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations, shows the u...
The dynamics of water molecules within the hydration shell surrounding a biomolecule can have a crucial influence on its biochemical function. Characterizing their properties and the extent to which they differ from those of bulk water have thus been long-standing questions. Following a tutorial approach, we review the recent advances in this field...
Water dynamics at the surface of two homologous proteins with different thermal resistances is found to be unaffected by the different underlying amino-acid compositions, and when proteins are folded it responds similarly to temperature variations. Upon unfolding the water dynamics slowdown with respect to bulk decreases by a factor of two. Our fin...
We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water's reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the aspherici...
A detailed theoretical investigation of the charge transport mechanism in poly(4-vinyl-imidazole) (P4VI), the parent polymer of a series of N-heterocyclic-based membranes used as an electrolyte in proton exchange membrane fuel cells, is presented. In particular, Density Functional Theory (DFT) results obtained for small model systems (protonated im...
The reorganization of water's hydrogen-bond (HB) network by breaking and making HBs lies at the heart of many of the pure liquid's special features and many aqueous media phenomena, including chemical reactions, ion transport and protein activity. An essential role in this reorganization is played by water molecule reorientation, long described by...
Hydration shell dynamics plays a critical role in protein folding and biochemical activity and has thus been actively studied through a broad range of techniques. While all observations concur with a slowdown of water dynamics relative to the bulk, the magnitude and molecular origin of this retardation remain unclear. Via numerical simulations and...
The reorientation dynamics of water confined within nanoscale, hydrophilic silica pores are investigated using molecular dynamics simulations. The effect of surface hydrogen-bonding and electrostatic interactions are examined by comparing with both a silica pore with no charges (representing hydrophobic confinement) and bulk water. The OH reorienta...
The mechanism of the OH bond reorientation in liquid methanol and ethanol is examined. It is found that the extended jump model, recently developed for water, describes the OH reorientation in these liquids. The slower reorientational dynamics in these alcohols compared to water can be explained by two key factors. The alkyl groups on the alcohol m...
Molecular dynamics and analytic theory results are presented for the reorientation dynamics of first hydration shell water molecules around fluoride and iodide anions. These ions represent the extremes of the (normal) halide series in terms of their size and conventional structure-making and -breaking categorizations. The simulated reorientation ti...
The reorientation dynamics of interfacial water molecules was recently shown to change non-monotonically next to surfaces of increasing hydrophilicity, with slower dynamics next to strongly hydrophobic (apolar) and very hydrophilic surfaces, and faster dynamics next to surfaces of intermediate hydrophilicities. Through a combination of molecular dy...
Liquid water is remarkably labile in reorganizing its hydrogen-bond (HB) network through the breaking and forming of HBs. This rapid restructuring, which occurs on the picosecond time scale, is critical not only for many of the pure liquid’s special features but also for a range of aqueous media phenomena, including chemical reactions and protein a...
Water translational and reorientational dynamics in concentrated solutions of amphiphiles are investigated through molecular dynamics simulations and analytic modeling. We evidence the critical importance of the solute concentration in determining the magnitude of the slowdown in water dynamics compared to the bulk situation. The comparison of conc...
The dynamics of water next to hydrophobic groups is critical for several fundamental biochemical processes such as protein folding and amyloid fiber aggregation. Some biomolecular systems, like melittin or other membrane-associated proteins, exhibit extended hydrophobic surfaces. Due to the strain these surfaces impose on the hydrogen (H)-bond netw...
Water reorientation was recently suggested via simulations to proceed through large angular jumps, but direct experimental evidence has so far remained elusive. Here we show that both infrared pump−probe and photon echo spectroscopies can provide such evidence through the measurement of the two-dimensional anisotropy decay. We calculate these two-d...
We discuss some key aspects of our recent theoretical work on water reorientation dynamics, which is important in a wide range
of phenomena, including aqueous phase chemical reactions, protein folding, and drug binding to proteins and DNA. It is shown
that, contrary to the standard conception that these dynamics are diffusional, the reorientation o...
The reorientation of a water molecule is important for a host of phenomena, ranging over--in an only partial listing--the key dynamic hydrogen-bond network restructuring of water itself, aqueous solution chemical reaction mechanisms and rates, ion transport in aqueous solution and membranes, protein folding, and enzymatic activity. This review focu...
Water hydrogen-bond (HB) dynamics around amino acids in dilute aqueous solution is investigated through molecular dynamics simulations and analytic modeling. We especially highlight the critical role played by hydrophilic HB acceptors: the strength of the HB formed with water has a pronounced effect on the HB dynamics, in accord with several experi...
The hydrogen bond dynamics of water in a series of amphiphilic solute solutions are investigated through simulations and analytic modeling with an emphasis on the interpretation of experimentally accessible two-dimensional infrared (2D IR) photon echo spectra. We evidence that for most solutes the major effect in the hydration dynamics comes from t...
The water and hydrogen-bond dynamics is investigated in aqueous solutions. Based on numerical simulations and analytic models, we offer an interpretation for the recent time-resolved vibrational spectroscopy experiments.
We show that previous interpretations of the liquid water quasielastic neutron scattering spectra have largely underestimated the water reorientation time. Through molecular dynamics simulations and an extended jump model, we reconcile these results with the times obtained via other techniques such as NMR and ultrafast infrared spectroscopies. This...
The dynamics of water molecules next to hydrophobic solutes is investigated, specifically addressing the recent controversy raised by the first time-resolved observations, which concluded that some water molecules are immobilized by hydrophobic groups, in strong contrast to previous NMR conclusions. Through molecular dynamics simulations and an ana...
In aqueous solution, the water molecules in the layer surrounding an ion rearrange through exchange reactions, in which the attractive hydrogen (H) bond between a water molecule and this ion switches to a new H bond between that water and another water molecule. This exchange and its time scale are critical in a wide range of chemical and biochemic...
We detail and considerably extend the analysis recently presented in Science 2006, 311, 832- 835 of the molecular mechanism of water reorientation based on molecular dynamics simulations and the analytic framework of the extended jump model (EJM). The water reorientation is shown to occur through large-amplitude angular jumps due to the exchange of...
We investigate several different methods to determine the water residence time next to a solute from molecular dynamics simulations. The popular computational prescription due to Impey et al. ( J. Phys. Chem. 1983, 87, 5071-5083) is shown to be extremely sensitive to the t* tolerance time value (designed to account for barrier recrossing effects),...
Subpicosecond absorption spectroscopy is used to characterize the primary photoinduced processes in a class of push-pull polyenes bearing a julolidine end group as the electron donor and a diethylthiobarbituric acid end group as the electron acceptor. The excited-state decay time and relaxation pathway have been studied for four polyenes of increas...
Water molecule rotational dynamics within a chloride anion's first hydration shell are investigated through simulations. In contrast to recent suggestions that the ion's hydration shell is rigid during a water's reorientation, we find a labile hydration sphere, consistent with previous assessments of chloride as a weak structure breaker. The nondif...
We study how water OH reorientation dynamics’ short and long-time contributions depend on the hydrogen(H)-bond strength. The initial librational reorientation occurs within a cone. We show quantitatively that the stronger the H-bond, the smaller the cone angle and librational reorientation amplitude. The long-time decay is independent of the initia...
Molecular Dynamics simulations are used to examine the title issue for the I-/HOD/D2O solution system in connection with recent ultrafast infrared spectroscopic experiments. It is argued that the long "modulation time" associated with the spectral diffusion of the OH frequency, extracted in these experiments, should be interpreted as reflecting the...
Despite long study, a molecular picture of the mechanism of water reorientation is still lacking. Using numerical simulations,
we find support for a pathway in which the rotating water molecule breaks a hydrogen bond (H-bond) with an overcoordinated
first-shell neighbor to form an H-bond with an undercoordinated second-shell neighbor. The H-bond cl...
An explicit formulation for intermolecular vibration–vibration (VV) energy transfer is applied to the energy transfer between a hydrogen fluoride (HF) molecule and the symmetric, antisymmetric and bend overtone vibrations of its hydrogen-bonded neighboring water molecule in aqueous solution. The results are analyzed in terms of coupling factor stre...
A theoretical formulation is presented for the dissociation of aromatic radical anions in solution, [Ar−X]•- → Ar• + X-, and applied to the dissociation of the p-cyanochlorobenzene radical anion [CN−Φ−Cl]•- in several solvents. Key ingredients of the description are (i) the inclusion of the conical intersection (CI) aspects of the problem and (ii)...
The theoretical formulation presented for the solution reaction path and rate constant for the radical anion [CN−Φ−Cl]•- dissociation in solution, described in the preceding paper of this series of work, hereafter referenced as I. The reaction paths that lead to the bent geometry transition state, which is required for the avoidance of the conical...
The linear and nonlinear optical properties of charged push−pull polyenes (CPPP) are, respectively, of interest in connection with unusual linear spectroscopic solvatochromic behavior in solution and other polar media and applications ranging from second harmonic generation to imaging and probing of biological systems. The CPPP are charged conjugat...
A new theoretical formulation is given for the reaction rate and path for the important reaction class of aromatic radical anion dissociation in solution [Ar-X]-.-->Ar. + X-, and is illustrated for the case of the cyanochlorobenzene radical anion [CN-phi-CI]-. in dimethylformamide. Among the theory's novel features is the inclusion of the conical i...
Subpicosecond absorption and gain spectroscopy are used to investigate the excited-state behavior of push-pull polyenes made of a diethylthiobarbituric acid electron-acceptor group and a dibutylaniline electron-donor group linked by a pi-conjugated chain. Four polyenes of increasing length, ranging from n = 2 to 5 double bonds, are compared. The re...
In this paper, we report on intramolecular electron transfer, distorsional relaxation or isomerization reactions in a few classes of commercial or recently engineered organic compounds in solution. We also show the role of the solvent polarity as well as solvent dynamics in the deactivation pathway and in the reaction kinetics. The reactions are pr...
Subpicosecond spectroscopy of push−pull polyenes, previously designed to achieve large optical nonlinearities, reveals an isosbestic point in the time-resolved gain band in polar solvents. The compounds possess a diethylthiobarbituric acid electron-withdrawing group and a dibutylaniline electron-releasing group coupled by a π-conjugated chain. The...
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