Solvent Motions Research Articles

Complete Solvation Response of Coumarin 153 in Ionic Liquids

The dynamic Stokes shift of coumarin 153, measured with a combination of broad-band fluorescence upconversion (80 fs resolution) and time-correlated single photon counting (to 20 ns), is used to determine the complete solvation response of 21 imidazolium, pyrrolidinium, and assorted other ionic liquids. The response functions so obtained show a clearly bimodal character consisting of a subpicosecond component, which accounts for 10-40% of the response, and a much slower component relaxing over a broad range of times. The times associated with the fast component correlate with ion mass, confirming its origins in inertial solvent motions. Consistent with many previous studies, the slower component is correlated to solvent viscosity, indicating that its origins lie in diffusive, structural reorganization of the solvent. Comparisons of observed response functions to the predictions of a simple dielectric continuum model show that, as in dipolar solvents, solvation and dielectric relaxation involve closely related molecular dynamics. However, in contrast to dipolar solvents, dielectric continuum predictions systematically underestimate solvation times by factors of at least 2-4.

A visco-poroelastic theory for polymeric gels

A polymeric gel can imbibe solvent and swell. Besides the dilatational mode of deformation, which involves long-range solvent migration, a gel may also undergo volume-conserved deformation. For a macroscopic gel with covalent cross-links, the volume-conserved deformation is usually much faster. However, these two modes are coupled for deformation at the microscopic level and for gels containing physical cross-links or large solvent molecules. In this paper, we seek to formulate a unified theoretical framework for the transient behaviour of polymeric gels to account for both solvent migration and viscoelastic deformation. Under this framework, we further develop a simple material model, and implement it into a finite-element code for numerical calculations. By simultaneously tracking the solvent migration and motion of polymer network, we evolve the inhomogeneous fields of stress and chemical potential. Several initial-boundary-value problems are solved as illustrative examples. For macroscopic gels with low viscosity, the time scales for viscoelasticity and poroelasticity are separated, and the long-term behaviour is just as that predicted by a poroelastic model. For structures or processes involving sizes comparable to the intrinsic length of a material, the viscoelasticity and poroelasticity must be considered simultaneously, especially when studying impact responses.

Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a β-peptide in solution

Recently, the method of enveloping distribution sampling (EDS) to efficiently obtain free enthalpy differences between different molecular systems from a single simulation has been generalized to compute free enthalpy differences between different conformations of a system [Z. X. Lin, H. Y. Liu, S. Riniker, and W. F. van Gunsteren, J. Chem. Theory Comput. 7, 3884 (2011)]. However, the efficiency of EDS in this case is hampered if the parts of the conformational space relevant to the two end states or conformations are far apart and the conformational diffusion from one state to the other is slow. This leads to slow convergence of the EDS parameter values and free enthalpy differences. In the present work, we apply the EDS methodology to a challenging case, i.e., to calculate the free enthalpy difference between a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix of a hexa-β-peptide in solution from a single simulation. No transition between the two helices was detected in a standard EDS parameter update simulation, thus enhanced sampling techniques had to be applied, which included adiabatic decoupling (AD) of solute and solvent motions in combination with increasing the solute temperature, and lowering the shear viscosity of the solvent. AD was found to be unsuitable to enhance the sampling of the solute conformations in the EDS parameter update simulations. Lowering the solvent shear viscosity turned out to be useful during EDS parameter update simulations, i.e., it did speed up the conformational diffusion of the solute, more transitions between the two helices were observed. This came at the cost of more CPU time spent due to the shorter time step needed for simulations with the lower solvent shear viscosity. Using an improved EDS parameter update scheme, parameter convergence was five-fold enhanced. The resulting free enthalpy difference between the two helices calculated from EDS agrees well with the result obtained through direct counting from a long MD simulation, while the EDS technique significantly enhances the sampling of both helices over non-helical conformations.

Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.

Hydration and temperature interdependence of protein picosecond dynamics

We investigate the nature of the solvent motions giving rise to the rapid temperature dependence of protein picoseconds motions at 220 K, often referred to as the protein dynamical transition. The interdependence of picoseconds dynamics on hydration and temperature is examined using terahertz time domain spectroscopy to measure the complex permittivity in the 0.2-2.0 THz range for myoglobin. Both the real and imaginary parts of the permittivity over the frequency range measured have a strong temperature dependence at >0.27 h (g water per g protein), however the permittivity change is strongest for frequencies <1 THz. The temperature dependence of the real part of the permittivity is not consistent with the relaxational response of the bound water, and may reflect the low frequency protein structural vibrations slaved to the solvent excitations. The hydration necessary to observe the dynamical transition is found to be frequency dependent, with a critical hydration of 0.19 h for frequencies >1 THz, and 0.27 h for frequencies <1 THz. The data are consistent with the dynamical transition solvent fluctuations requiring only clusters of ~5 water molecules, whereas the enhancement of lowest frequency motions requires a fully spanning water network.

Influence of temperature on thymine-to-solvent vibrational energy transfer

At the instant following the non-radiative deactivation of its ππ* electronic state, the vibrational modes of thymine possess a highly non-equilibrium distribution of excitation quanta (i.e., >4 eV in excess energy). Equilibrium is re-established through rapid (5 ps) vibrational energy transfer to the surrounding solvent. The mechanisms behind such vibrational cooling (VC) processes are examined here using femtosecond transient grating and two-dimensional photon echo spectroscopies conducted at 100 K and 300 K in a mixture of methanol and water. Remarkably, we find that this variation in temperature has essentially no impact on the VC kinetics. Together the experiments and a theoretical model suggest three possible mechanisms consistent with this behavior: (i) vibrational energy transfer from the solute to solvent initiates (directly) in intramolecular modes of the solute with frequencies >300 cm(-1); (ii) the relaxation induced increase in the temperature of the environment reduces the sensitivity of VC to the temperature of the equilibrium system; (iii) the time scale of solvent motion approaches 0.1 ps even at 100 K. Mechanism (i) deserves strong consideration because it is consistent with the conclusions drawn in earlier studies of isotope effects on VC in hydrogen bonding solvents. Our model calculations suggest that mechanism (ii) also plays a significant role under the present experimental conditions. Mechanism (iii) is ruled out on the basis of long-lived correlations evident in the photon echo line shapes at 100 K. These insights into photoinduced relaxation processes in thymine are made possible by our recent extension of interferometric transient grating and photon echo spectroscopies to the mid UV spectral region.

Ionic and Free Solvent Motion in Poly(azure A) Studied by ac-Electrogravimetry

This work is focused on the mechanistic aspects of the redox behavior of poly(azure A) taking advantage of the controlled modulation of their oxidation states by ac-electrogravimetry. The originality of this technique is its ability to discriminate between cation and anion involved in the charge compensation process and the accompanying free solvent transfer, directly or indirectly. Two processes were proposed where the faster ionic exchange is considered to be the participation of the anion species acting as counterions whereas the slower one is related to the proton transfer. The proton is implied as reactants for the two electroactive sites identified in the polymer chain, the intermonomeric amino links and the aromatic rings. The ac-electrogravimetry technique was used to study the kinetic aspects of the transfer of proton (H+), anion (NO3– or Cl–), and free solvent in KNO3 and KCl aqueous solutions.

Organization and Dynamics of Membrane Probes and Proteins Utilizing the Red Edge Excitation Shift

Dynamics of confined water has interesting implications in the organization and function of molecular assemblies such as membranes. A direct consequence of this type of organization is the restriction imposed on the mobility of the constituent structural units. Interestingly, this restriction (confinement) of mobility couples the motion of solvent (water) molecules with the slow moving molecules in the assembly. It is in this context that the red edge excitation shift (REES) represents a sensitive approach to monitor the environment and dynamics around a fluorophore in such organized assemblies. A shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of the absorption band, is termed REES. REES relies on slow solvent reorientation in the excited state of a fluorophore that can be used to monitor the environment and dynamics around a fluorophore in a host assembly. In this article, we focus on the application of REES to monitor organization and dynamics of membrane probes and proteins.

Millisecond Time-Scale Protein Dynamics Exists Prior to the Activation of the Bulk Solvent Matrix

Conformational dynamics of proteins is of fundamental importance in their physiological functions. The exact mechanisms and determinants of protein motions, including the regulatory interplay between protein and solvent motions, are not yet fully understood. In the present work, the thermal activation of phosphorescence quenching was measured in oxygen-saturated aqueous protein solutions to explore protein dynamics in the millisecond range. The sample was brought to cryogenic temperatures in a fast cooling process to avoid the bulk crystallization of ice. The phosphorescence quenching effect was followed by the phosphorescence lifetime of either Zn-protoporphyrin substituting the heme in the β-subunits of human hemoglobin (Zn-HbA) or tryptophan residues of Zn-HbA and human myoglobin (Mb), measured in thermal equilibrium at temperatures varied from 8 to 273 K. The quenching effect was attributed primarily to the activation of collisions with O(2) molecules made possible by the activated millisecond time-scale dynamics of the matrix around the chromophores. We find that, in the studied temperature range, the activation of protein global dynamics facilitating oxygen diffusion takes place at clearly separated lower temperatures and independently from bulk solvent dynamics and that the energy and entropy differences between the studied frozen and thermally activated states are specific for the protein.

Evaluation of the Solvent Slaving Concept in Myoglobins Through the Use of Glassy and Sol-Gel Matrices

Functionally important protein dynamics come in a myriad of amplitudes and time scales which makes systematic studies challenging. The Solvent Slaving Model (SSM) orders protein dynamics based on the premise that protein motions are slaved to solvent motions with there being a hierarchy based on which solvent motions the specific protein dynamics are slaved(1, 2). The Protein Dynamic State Model (PDSM) is an extension of the SSM that defines dynamic states based on the temporal window during which specific solvent slaved dynamics are active(3, 4). Both models have yet to be tested systematically. In the present study, the activation energies (Ea's) for several functionally important dynamics are determined for a series of mutants of myoglobin as a function of different solvent matrices chosen to permit manipulation of specific solvent dynamics (e.g α and β relaxations). The matrices used include both trehalose glasses (β relaxations active but no α relaxations) and thin sol-gel films bathed in water/glycerol mixtures (both α and β relaxations active). The results show that for a diverse group of protein dynamics, including conformational averaging and side chain fluctuations and relaxations, the Ea's can be grouped into two broad categories: one with low Ea's (between 5 and 20 kJ/mol) and the other with much higher values (50-70 kJ/mol). The results expose how the time ordering for the onset of the functional influence of different dynamics is the result of the interplay between solvent dependent activation energy and the number of solvent slaved steps required to achieve the specific dynamical process.1. Frauenfelder, H. et al. (2009) ProcNatlAcadSci USA106, 5129-5134.2. Frauenfelder, H. et al. (2002) BiophysChem98, 35-48.3. Samuni, U. et al. (2007) Gene398, 234-248.4. Samuni, U. et al. (2007) JAmChemSoc129, 12756-12764.

Dynamic Mechanisms for Ammonia Borane Thermolysis in Solvent: Deviation from Gas-Phase Minimum-Energy Pathways

The dynamic mechanisms involved in the dehydrogenation of ammonia borane are investigated using quasi-classical trajectory simulations. The effects of solvent and nuclear motion yield qualitatively different results compared to simulations where these considerations are neglected. Not only are rate-limiting barriers substantially different from the gas to solvent phase, trajectories leading from transition states branch to different products depending on the presence or lack of solvent. In addition, the formation of the diammoniate of diborane is shown to be noncompetitive in the gas phase due to the presence of a lower-barrier dehydrogenation pathway. The first comparative analysis of the pathways leading to the thermolysis of ammonia−borane is presented herein.

Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses

When only equilibrium thermodynamics or averages of position-dependent functions in classical molecular dynamics calculations are sought, the choice of the atomic masses in the Hamiltonian becomes irrelevant. Consequently, the masses can be used as free parameters to help improve conformational sampling efficiency in the spirit of Bennett's mass-tensor dynamics (Bennett, C. H. J. Comput. Phys. 1975, 19, 267.). Here we report on the effect of reducing side-chain and solvent masses on the folding behavior of a 9-residue hairpin-forming peptide in solution. A physical motivation for reducing the solvent mass is an effective reduction in solvent viscosity. Side-chain mass scaling is motivated by the idea of solvent potentials of mean force which are employed in select coarse-grained protein models. In the limit of very large mass differences, the mass reduction effectively creates an adiabatic decoupling between solvent, side-chain, and backbone motions, so that both the backbone and side chains move on the instantaneous solvent potential of mean force (PMF) surface, and the backbone additionally moves on the side-chain PMF. Because of the arbitrariness in the choice of masses, this limit only needs to be reached approximately in practice. In particular, we show that a 10-fold reduction in solvent masses and a side-chain mass scale that is intermediate between the scaled solvent and the backbone lead to a quantitative enhancement in conformational sampling.

Dynamical Friction Effects on the Photoisomerization of a Model Protonated Schiff Base in Solution

Photoisomerization involving a conical intersection (CI) for a model protonated Schiff base (PSB) in modeled water and acetonitrile solvents is examined with the inclusion of energy- and momentum-transfer effects described via a generalized Langevin equation (GLE) frictional approach and surface-hopping dynamics. Short-time GLE frictional effects on the model's three coordinates, the intramolecular bond length alternation and torsional PSB coordinates and a solvent coordinate, eliminate several unphysical features associated with a no-friction inertial description and have the general feature of accelerating nonadiabatic transitions to the ground electronic state. The inertial prediction of equal probability formation of ground-state trans and cis isomer products subsequent to the Franck-Condon excitation of the ground cis isomer is replaced by the GLE prediction of a preferential higher proportion of ground-state trans isomer, that is, a successful cis to trans photoreaction. This preference is solvent-dependent and is enhanced in water solvent with its higher friction intensity and short time scales. For the fast water solvent motion, the nonadiabatic transitions to the S(0) ground state are centered around the CI seam (which is due to the solvent coordinate's role as a tuning coordinate), facilitating direct transitions to the ground-state trans isomer. In contrast, for the slower acetonitrile solvent motion, the decay occurs, on average, away from the CI seam in regions with a finite free-energy gap between the excited and ground states, resulting in reduced trans isomer production. Some directions for the extension of the model description are also discussed.

Effects of differential permeability on packed bed supercritical extractors: A theoretical insight

This paper analyses the effects on the extraction kinetics of a solvent flow which is non-uniform in the extraction column bed cross-section. When modeling the extraction kinetics of a solute from a solid matter (for instance of oil from seeds), the solvent motion is normally assumed as consisting in plug flow, eventually corrected by the axial dispersion coefficient. Some experimental evidence put into question this simplified description. We have shown to which extent the effects of a non-uniform extraction bed permeability reflect on the extraction kinetics: in particular conditions, these effects could be even more significant than the effects due to the mass transport resistances governing the extraction of the solute out from the matrix.

Confined Polar Mixtures within Cylindrical Nanocavities

Using molecular dynamics experiments, we have extended our previous analysis of equimolar mixtures of water and acetonitrile confined between silica walls [J. Phys. Chem. B 2009, 113, 12744] to examine similar solutions trapped within carbon nanotubes and cylindrical silica pores. Two different carbon tube sizes were investigated, (8,8) tubes, with radius R(cnt) = 0.55 nm, and (16,16) ones, with R(cnt) = 1.1 nm. In the narrowest tubes, we found that the cylindrical cavity is filled exclusively by acetonitrile; as the radius of the tube reaches approximately 1 nm, water begins to get incorporated within the inner cavities. In (16,16) tubes, the analysis of global and local concentration fluctuations shows a net increment of the global acetonitrile concentration; in addition, the aprotic solvent is also the prevailing species at the vicinity of the tube walls. Mixtures confined within silica nanopores of radius approximately 1.5 nm were also investigated. Three pores, differing in the effective wall/solvent interactions, were analyzed, (i) a first class, in which dispersive forces prevail (hydrophobic cavities), (ii) a second type, where oxygen sites at the pore walls are transformed into polar silanol groups (hydrophilic cavities), and (iii) finally, an intermediate scenario, in which 60% of the OH groups are replaced by mobile trimethylsilyl groups. Within the different pores, we found clear distinctions between the solvent layers that lie in close contact with the silica substrate and those with more central locations. Dynamical modes of the confined liquid phases were investigated in terms of diffusive and rotational time correlation functions. Compared to bulk results, the characteristic time scales describing different solvent motions exhibit significant increments. In carbon nanotubes, the most prominent modifications operate in the narrower tubes, where translations and rotations become severely hindered. In silica nanopores, the manifestations of the overall retardations are more dramatic for solvent species lying at the vicinity of trimethylsilyl groups.

Theoretical Insight into the Photodegradation of a Disulfide Bridged Cyclic Tetrapeptide in Solution and Subsequent Fast Unfolding−Refolding Events

We report the photoinduced peptide bond (C-N) of an amide unit and S-S bond fission mechanisms of the cyclic tetrapeptide [cyclo(Boc-Cys-Pro-Aib-Cys-OMe)] in methanol solvent by using high-level CASSCF/CASPT2/Amber quantum mechanical/molecular mechanical (QM/MM) calculations. The subsequent energy transport and unfolding-refolding events are characterized by using a semiempirical QM/MM molecular dynamics (MD) simulation methodology that is developed in the present work. In the case of high-energy excitation with <193 nm light, the tetrapeptide molecule in the (1)n pi* surface overcomes two barriers with approximately 10.0 kcal/mol, respectively, and uses energy consumption for breaking the hydrogen bond as well as the N-C bond in the amide unit, ultimately leading to the ground state via a conical intersection of CI (S(NP)/S(0)) by structural changes of an increased N-C distance and a O-C-C angle in the amide unit (a two-dimensional model of the reaction coordinates). Following this point, relaxation to a hot molecule with its original structure in the ground state is the predominant decay channel. A large amount of heat (approximately 110.0 kcal/mol) is initially accumulated in the region of the targeted point of the photoexcitation, and more than 60% of the heat is rapidly dissipated into the solvent on the femtosecond time scale. The relatively slower propagation of heat along the peptide backbone reaches a phase of equilibration within 3 ps. A 300 nm photon of light initiates the relaxation along the repulsive S(sigma sigma)((1)sigma sigma*) state and this decays to the CI (S(sigma sigma)/S(0)) in concomitance with the separation of the disulfide bond. Once cysteinyl radicals are generated, the polar solvent of methanol molecules rapidly diffuses around the radicals, forming a solvent cage and reducing the possibility of close contact in a physical sense. The fast unfolding-refolding event is triggered by S-S bond fission and powered by dramatic thermal motion of the methanol solvent that benefits from heat dissipation. The beta-turn opening (unfolding) can be achieved in about 120 ps without the inclusion of the time associated with the photochemical steps and eventually relaxes to a 3(10)-helix structural architecture (refolding) within 200 ps.

Electrochemical and electrogravimetric behaviors of conducting polymer. Theoretical aspects and application to co-polymer films based on juglone

Redox mechanisms of conducting polymers are not yet fully understood. Attractive analytical tools and pertinent models are necessary to achieve this goal. In this paper, numerical simulations based on a theory dealing with ions transfer through electroactive film/electrolyte interface was developed to predict the behavior of a conducting polymer called poly(JUG-co-JUGA). The main advantage of this approach is that it can be applied for any polymer assuming a mixed conducting material and a thin enough film neglecting the transport effect. It is the first time where the same model allows both classical cyclic electrogravimetry (current and mass over a potential scan) and ac-electrogravimetry (electrochemical impedance and mass/potential transfer functions) to be estimated theoretically. Moreover and to our knowledge the electrochemical behavior of poly(JUG-co-JUGA) was examined through these techniques for the first time. It is shown herein that the cation transfer is preponderant but the free solvent motion must be taken into account. This effect is not detected by classical electrochemical measurements but only by combining electrochemical characterization to gravimetric measurements.

On the quenching of MLCT luminescence by amines: The effect of nanoaggregation in the decrease of the reorganization energy

The MLCT luminescence quenching of pyRe(CO) 3bpy + and/or the polymer {[(vpy) 2-vpyRe(CO) 3bpy]CF 3SO 3} n–200 by amines proceeds via an electron transfer reaction which produces amine radical cations and pyRe I(CO) 3(bpy) /–Re I(CO) 3(bpy) , respectively. The quenching follows a typical Stern–Volmer kinetics for both pyRe(CO) 3bpy + and {[(vpy) 2-vpyRe(CO) 3bpy]CF 3SO 3} n–200 . The observed rate constants for the quenching of the Re I-polymer luminescence by amines show “vestiges” of the inverted effect predicted by Marcus while the quenching of pyRe(CO) 3bpy + luminescence follow the Rehm–Weller type of behavior. The lower value obtained for the total reorganization energy of the Re I-polymer than that for pyRe(CO) 3bpy + is rationalized in terms of the retarded solvent motions inside the nanoaggregates formed by the Re I-polymer in acetonitrile solutions.

Tuning Protein Dynamics by Modulating Solvent Motions through Glassy Matrices, Sol-Gels and Reverse Micelles

Many proteins can be viewed as nanodevices whose functions are controlled by a complex array of molecular motions. Functionally important protein dynamics pose a difficult challenge for study in that they span orders of magnitude with respect to amplitudes and time scales. One approach to organizing and systematically studying protein dynamics is based on the degree to which the different protein motions are slaved to different categories of solvent motion. This approach is the basis for the solvent slaving model of Frauenfelder and coworkers and our protein dynamic state model. In the present work, we describe how sol-gels, trehalose-derived glasses and reverse micelles can be used as matrices to systematically tune these different categories of protein dynamics through modulation of solvent dynamics and confinement volume. Through this approach we can dissect out the factors that control the activation energies and onset of activation for dynamics in hemeproteins such as hemoglobin and myoglobin that control substrate/ligand diffusion within the protein as well as escape from or entry into the protein from the solvent.

Searching for solvent cavities via electron photodetachment: The ultrafast charge-transfer-to-solvent dynamics of sodide in a series of ether solvents

It was recently predicted by simulations and confirmed by neutron diffraction experiments that the structure of liquid tetrahydrofuran (THF) contains cavities. The cavities can be quite large and have a net positive electrostatic potential, so they can serve as pre-existing traps for excess electrons created via photodetachment from various solutes. In this paper, we use electron photodetachment via charge-transfer-to-solvent (CTTS) excitation of sodide (Na(-)) to probe for the presence of pre-existing cavities in a series of ether solvents: THF, diethyl ether, 1,2-dimethoxyethane (DME), and diglyme (DG). We find that electrons photodetached from sodide appear after a time delay with their equilibrium spectrum in all of these solvents, suggesting that the entire series of ethers contains pre-existing solvent cavities. We then use the variation in electron recombination dynamics with CTTS excitation wavelength to probe the nature of the cavities in the different ethers. We find that the cavities that form the deepest electron traps turn on at about the same energy in all four ether solvents investigated, but that the density of cavities is lower in DG and DME than in THF. We also examine the dynamics of the neutral sodium species that remains following CTTS photodetachment of an electron from sodide. We find that the reaction of the initially created gas-phase-like Na atom to form a (Na(+),e(-)) tight-contact pair occurs at essentially the same rate in all four ether solvents, indicating that only local solvent motions and not bulk solvent rearrangements are what is responsible for driving the partial ejection of the remaining Na valence electron.