Solvation Of Molecules In Water Research Articles

Excited State Proton Transfer of Quinone Cyanine 9: Implications on the Origin of Super‐Photoacidity

AbstractThe front cover artwork is provided by the Ultrafast Dynamics Laboratory at Pohang University of Science and Technology (Republic of Korea). The image shows the initial snapshot of quinone cyanine 9 that is undergoing excited‐state proton transfer on a very fast time scale aided by the solvation of water molecules. Read the full text of the Article at 10.1002/cptc.202000254.

Influence of Cations on the Fluorescence Quenching of an Ionic, Sterically Congested Pyrenyl Moiety by Iodide in Water.

Quenching of the excited singlet states of a water-soluble, sterically congested tetraarylpyrene, 1,3,6,8-tetrakis(2,6-dimethyl-4-(α-carboxy)methoxyphenyl)pyrene (Py4C), by a series of iodide salts has been investigated by steady-state and time-resolved fluorescence measurements. Access to the pyrenyl group of Py4C is restricted sterically as a result of the four flanking (2,6-dimethylphenoxy)acetic acid groups and the energy costs associated with their rotation. Deprotonation of the carboxylic acid groups of Py4C permits examination of ion-ion electrostatic interactions on the rates of quenching by iodide salts in which different steric and electrostatic factors are introduced by varying the cationic portions. At the same concentrations and with the same cations, chloride anions are ineffective quenchers. The quenching rate constants of Py4C by iodide are found to correlate linearly with the ionic radii of the cations and their enthalpies of hydration. These correlations are discussed in terms of the Hofmeister series. Furthermore, the results indicate that the cations that flank Py4C decrease the quenching efficiency of iodide through polarization and shielding effects (i.e., lowering the effective charge), which isolate to varying degrees the π-system. The effects of the different cations on quenching the fluorescence of a simpler and sterically unencumbered pyrenyl derivative, 1-pyrenylbutyric acid (PyBu), by iodide are much smaller. Overall, the results with Py4C indicate that the fluorescence quenching efficiency by iodide is influenced by direct interactions with the cations associated with the carboxylate groups of Py4C and not the solvation of water molecules. This observation is germane to a topic of current debate: Are the effects of the cations more closely related to bulk water properties or to direct ion-ion interactions? The conclusions obtained from these studies are applicable clearly to a wide variety of other systems in which ion pairing influences cooperative or inhibitory interactions.

SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors

This special issue of the Journal of Computer-Aided Molecular Design is the culmination of the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) challenge and workshop. SAMPL3 had three datasets: blinded small-molecule hydration energies, provided by Peter Guthrie [1]; two novel host–guest systems, including eleven unpublished binding energies, provided by Adam Urbach and Lyle Issacs [2], and a monumental dataset including structural and affinity data for 500 fragments against Trypsin, provided by Tom Peat [3]. The SAMPL3 workshop saw over 40 attendees while the SAMPL3 challenge received 103 submissions from 23 participating groups using a variety of methods including: discrete and dynamic conformational sampling; implicit, semi-implicit and explicit water models; and myriad of force-fields and charge models. Gilson [2] and Geballe [1] have provided summaries of the host–guest challenge and solvation-energy challenge respectively. As with prior SAMPL challenges, many different approaches generated high-quality predictions yet no single technique distinguished itself significantly. Nevertheless, many important insights into the strengths and limitations of computational and experimental methods were developed through SAMPL. SAMPL3 was the first blinded challenge to include prediction of host–guest binding affinities. Host–guest binding affinities provided an outstanding blind challenge, as they are simple enough to encourage participants to recognize, explore and address assumptions and errors. Most participants had great difficulty modeling the aspartyl-protease-like formal charges found in the host molecules. This is concerning, for while ionization sites occur commonly in protein–ligand systems, rarely are they addressed at the level of detail participants found necessary for this host–guest system. More host–guest examples should be included in future SAMPL challenges as their streamlined nature highlights assumptions that can be too easily overlooked. SAMPL is one of several projects that provide blinded or prospective experimental challenges to the computational community [4–6]. These projects are intended to serve as both a guidepost for computational progress and a meeting ground for experimental and computational scientist. However, it has been a struggle to generate mutual interest between computational and experimental scientists. This year, SAMPL had a breakthrough in the form of Lyle Issacs (host–guest affinities) and Tom Peat (trypsin structures and affinities). Lyle and Tom are experimentalists who provided data to SAMPL3, attended the SAMPL workshop, and provided insights and challenges to the computational scientists. We hope they are the first of many experimentalists to join SAMPL and challenge theorists with their data. Unfortunately, no experimental collaborator has emerged to provide prospective hydration free energies, which have been part of each of the four SAMPL evaluations. Hydration energies are the most basic measure of the solvation of molecules in water. Aqueous solvation plays a critical role in most biophysical and biochemical phenomenon, and our ability to accurately predict biophysical processes is limited by our ability to accurately calculate solvation interactions. Hydration energies represent one of the simplest experiments that allow us to evaluate these predictions. As a consequence, comparison to hydration energies is a fundamental tool for evaluating force fields and electrostatic models (for example see [7]). A. G. Skillman (&) OpenEye Scientific Software, Santa Fe, NM, USA e-mail: skillman@eyesopen.com

Collision Dynamics and Solvation of Water Molecules in a Liquid Methanol Film

Environmental molecular beam experiments are used to examine water interactions with liquid methanol films at temperatures from 170 K to 190 K. We find that water molecules with 0.32 eV incident kinetic energy are efficiently trapped by the liquid methanol. The scattering process is characterized by an efficient loss of energy to surface modes with a minor component of the incident beam that is inelastically scattered. Thermal desorption of water molecules has a well characterized Arrhenius form with an activation energy of 0.47{\pm}0.11 eV and pre-exponential factor of 4.6 {\times} 10^(15{\pm}3) s^(-1). We also observe a temperature dependent incorporation of incident water into the methanol layer. The implication for fundamental studies and environmental applications is that even an alcohol as simple as methanol can exhibit complex and temperature dependent surfactant behavior.

Dissecting the THz spectrum of liquid water from first principles via correlations in time and space

Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at approximately 200 cm(-1) is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm(-1) approximately 2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules--even in the absence of well-defined resonances.

Computer simulation of cellulose solvation in polar solvents

The solvation of cellulose molecules in water and N-methylmorpholine N-oxide has been investigated by the molecular-dynamics method. An analysis of simulation results yields the conformational characteristics of cellulose molecules in these solvents: the mean-square distance between polymer chain ends and the radial distribution function of monomer units. The radial distribution functions of oxygen atoms of solvents relative to protons of carbohydrate molecules are estimated. This step makes it possible to draw conclusions about the number and character of hydrogen bonds and the local structure of solvate shells.

Molecular dynamics simulation study of water near critical conditions. I. Structure and solvation free energetics

The structure and solvation free energetics of water under ambient and near critical conditions are studied with the Molecular Dynamics (MD) computer simulation method. By employing the truncated adiabatic basis-set description with 10 basis functions (TAB/10D), the water electronic structure variation both in and out of its molecular plane and associated polarizability effects are accounted for. It is found that the average dipole moment μ̄s of a water molecule varies considerably with the thermodynamic conditions; while the TAB/10D model yields μ̄s=2.65 D under an ambient condition, it reduces to 2.24 D in supercritical water at temperature 673 K and density 0.66 g cm−3. The MD results on the radial distribution functions and static and optical dielectric constants are in reasonable agreement with experiments. The fluctuations of the local electric field are found to be significant, so that at elevated temperatures, it can sometimes be in the opposite direction of the local water dipole vector. Also, the free energy curves associated with solvation of water molecules become tighter and more asymmetric with increasing temperature and decreasing density. The dynamic and spectroscopic properties of supercritical water are studied in the following paper [B. D. Bursulaya and H. J. Kim, J. Chem. Phys. 110, 9656 (1999)].