The Hydrated Excess Proton in the Zundel Cation H5O2+: The Role of Ultrafast Solvent Fluctuations

The nature of the excess proton in liquid water has remained elusive after decades of extensive research. In view of ultrafast structural fluctuations of bulk water scrambling the structural motifs of excess protons in water, we selectively probe prototypical protonated water solvates in acetonitrile on the femtosecond time scale. Focusing on the Zundel cation H₅O₂⁺ prepared in room‐temperature acetonitrile, we unravel the distinct character of its vibrational absorption continuum and separate it from OH stretching and bending excitations in transient pump‐probe spectra. The infrared absorption continuum originates from a strong ultrafast frequency modulation of the H⁺ transfer vibration and its combination and overtones. Vibrational lifetimes of H₅O₂⁺ are found to be in the sub‐100 fs range, much shorter than those of unprotonated water. Theoretical results support a picture of proton hydration where fluctuating electrical interactions with the solvent and stochastic thermal excitations of low‐frequency modes continuously modify the proton binding site while affecting its motions.     

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid‐based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high‐resolution, three‐dimensional grid. The CPPTRAJ implementation, called GIST‐cpptraj, has a simple, easy‐to‐use command line interface, and is open source and freely distributed. We have also developed a set of open‐source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST‐cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.     

FTIR Spectroscopy of Ion Solvation of LiClO4 and LiSCN in Acetonitrile, Benzonitrile, and Propylene Carbonate

FTIR spectra of lithium perchlorate and lithium thiocyanate in acetonitrile,benzonitrile, and propylene carbonate were recorded in the temperature range from 5to 45°C. New bands due to solvent molecules in the primary solvation shell ofthe lithium ions were detected in the region of the CN stretching mode of thenitriles and of the CO stretching mode of propylene carbonate. The band structureswere studied in detail by deconvolution with band-fitting procedures and meancation solvation numbers were deduced from the band area of the bulk solvent.For the systems acetonitrile—lithium perchlorate, benzonitrile—lithiumperchlorate, and benzonitrile—lithium thiocyanate, solvation numbers of free andbound lithium ions were calculated with the help of the degree of associationobtained from suitable anion vibrations.     

Slow coarsening in a class of driven systems

The coarsening process in a class of driven systems is studied. These systems have previously been shown to exhibit phase separation and slow coarsening in one dimension. We consider generalizations of this class of models to higher dimensions. In particular we study a system of three types of particles that diffuse under local conserving dynamics in two dimensions. Arguments and numerical studies are presented indicating that the coarsening process in any number of dimensions is logarithmically slow in time. A key feature of this behavior is that the interfaces separating the various growing domains are macroscopically smooth (well approximated by a Fermi function). This implies that the coarsening mechanism in one dimension is readily extendible to higher dimensions. Received 3 April 2000     

Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study

The conformational preferences of oligopeptides of an ϵ-amino acid (2-((1R,3S)-3-(aminomethyl)cyclopentyl)acetic acid, Amc₅a) with a cyclopentane substituent in the C^β−C^γ−C^δ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc₅a oligomers (dimer to hexamer) was the H₁₆ helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H₁₆ helix population in solution. The Amc₅a hexamer adopted a stable left-handed (M)-2.3₁₆ helical conformation with a rise of 4.8 Å per turn. The hexamer of Ampa (an analogue of Amc₅a with replacing cyclopentane by pyrrolidine) adopted the right-handed mixed (P)-2.9_18/16 helical conformation in chloroform and the (M)-2.4₁₆ helical conformation in water. Therefore, hexamers of ϵ-amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.     

Insight into molecular interactions and solvation properties of methylammonium perchlorate in acetonitrile-dimethylsulfoxide binary mixtures: Compressibility,viscometric and dissolution thermodynamic studies

Densities (ρ), ultrasonic velocities (u) and viscosities (ƞ) of Methylammonium perchlorate (CH₃NH₃ClO₄) in binary solvent mixtures of Acetonitrile (AN) and Dimethylsulfoxide (DMSO) containing 0.0, 0.20, 0.40, 0.60, 0.80 and 1.0 ​mol fraction of DMSO at various temperatures ranging from 298K–328K at atmospheric pressure, have been measured. From the experimental data important parameters, namely, apparent molal volume (V_Φ), isentropic compressibility (K_s), limiting apparent molal isentropic compressibility (K^o_s,ɸ), A and B-viscosity coefficients from Jones-Dole equation, B/V_ɸ^o values and viscous flow related thermodynamic properties have been derived. Interpretation of the obtained thermodynamic parameters was done with regards to solute-solvent and solute-solute interactions and structure breaking and making potential of the solutes in solution. To evaluate the extent of preferential solvation, K^o_s,ɸ values and B-coefficients for the electrolytes have been further split up into the contribution of individual ion (K^o_s,ɸ± and B_± values) by reference electrolyte method.     

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at a low concentration in the water. We find that the OD vibration of HDO relaxes via an intermediate level, that is characterized by a hydrogen-bond that is stronger than in the ground state. With increasing concentration the lifetime of the excited state increases from 1.8 ps to 2.4 ps and the lifetime of the intermediate level from 0.6 ps to 1.0 ps. Regarding the orientational dynamics we observe biexponential behavior, which finds its origin in the presence of two classes of water molecules. There is a fraction of water molecules that has bulk-like orientational dynamics (τ_rot = 2.5 ps) and a fraction of immobilized water molecules (τ_rot > 10 ps). The relative abundance of the two fractions is determined by the nature and concentration of the solute. We find that the hydrophobic solute groups are responsible for the immobilization of water molecules. Every methyl group causes the immobilization of approximately 4 water OH groups. The hydrophilic solute groups, on the other hand, do not hinder the reorientation and the water molecules solvating them reorient with the same rate as in the bulk liquid.     

Thermodynamic parameters of solvation of nonelectrolytes in aqueous solutions of amides of carboxylic acids

Interaction and reorganization contributions to solvation enthalpies of nonelectrolytes in aqueous solutions of amides of carboxylic acids with different degree of N-substitution and N-methylpyrrolidone are calculated. The data are discussed using structurally thermodynamic characteristics of water-amide systems obtained by us previously. It is found that the type of concentration dependence of the solvation enthalpy of nonelectrolytes in all solutions investigated is determined by the type of reorganization component. It is shown that the highest solvation exothermicity of nonelectrolytes in water is due to the lowest value of the reorganization contribution in spite of that nonelectrolytes interact weaker with water than with non aqueous components.     

Effect of intramolecular cyclization on the enthalpies of solvation of tetramethylurea in water and alkanols at 298.15 K

The enthalpies of solution of N,N′-dimethylethyleneurea (1,3-dimethyl-2-imidazolidinone) in water, methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, and t-butanol (2-methyl-2-propanol) were measured calorimetrically at 298.15 K. For comparison purposes, the previous data on enthalpic effects of 1,1,3,3-tetramethylurea dissolution (solvation) in the same solvents were analyzed. It has been concluded that the intramolecular cyclization of tetramethylurea, to form dimethylethyleneurea, results in strengthening of the solute solvation and this tendency is more pronounced in a non-aqueous (alcoholic) medium.