Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test

We report here a test of the Semi-Explicit Assembly (SEA) model in the solvation free energy category of the SAMPL3 blind prediction event (summer 2011). We tested how dependent the SEA results are on the chosen force field by performing calculations with both the General Amber and OPLS force fields. We compared our SEA results with full molecular dynamics simulations in explicit solvent. Of the 20 submissions, our SEA/OPLS results gave the second smallest RMS errors in free energies compared to experiments. SEA gives results that are very similar to those of its underlying force field and explicit solvent model. Hence, while the SEA water modeling approach is much faster than explicit solvent simulations, its predictions appear to be just as accurate.     

Solvent density effects on the solvation behavior and configurational structure of bare and passivated 38-atom gold nanoparticle in supercritical ethane

In exploring the effects of solvent density on the mode and the degree of solvation of the bare and passivated 38-atom gold particle in supercritical ethane, we have extended the molecular dynamics simulations of the system, reported previously,(34) to cover a range of isotherms in the T > T(c) regime, where T(c) is the critical temperature of the solvent. Consonant with our previous observations, the modes of solvation of the bare and the passivated particle, deduced from the radial distribution of the solvent about the metal core center of mass, are found to be vastly different from each other at all solvent densities: while the molecules solvating the bare particle form a well-defined, two-region layer around it, those solvating the passivated particle are loosely dispersed in the passivating layer. For the bare particle, the degree of solvation (vartheta) as a function of solvent density passes through a maximum occurring in the close vicinity of the critical point, consistent with our previous results and in agreement with Debenedetti's theoretical analysis,(22,23) which predicts a solvation enhancement effect in the critical region for systems where the unlike solvent/solute interaction is much stronger than the solvent/solvent interaction. Taking the degree of solvation (vartheta) as a measure of solvent quality, we have investigated how the solvent quality would vary along the solvent-density isotherms. In the solvent-density regime rho > rho(c), the solvent quality is found to be a decreasing function of the density as a result of progressive dominance of the excluded volume effect over the attractive particle/solvent interactions. The particle/solvent affinity is greatly reduced in the presence of the passivating layer, resulting in considerable shrinkage of the good-solvent-quality domain in the supercritical regime. The solvent environment and the presence of the passivating chains produce significant disorder in the equilibrium structure assumed by the nanoparticle core.     

Two-dimensional measurements of the solvent structural relaxation dynamics in dipolar solvation

Resonant-pump polarizability response spectroscopy (RP-PORS) is based on an optical heterodyne detected transient grating (OHD-TG) method with an additional resonant pump pulse. In RP-PORS, the resonant pump pulse excites the solute-solvent system and the subsequent relaxation of the solute-solvent system is monitored by the OHD-TG spectroscopy. RP-PORS is shown to be an excellent experimental tool to directly measure the solvent responses in solvation. In the present work, we extended our previous RP-PORS (Park et al., Phys. Chem. Chem. Phys., 2011, 13, 214-223) to measure time-dependent transient solvation polarizability (TSP) spectra with Coumarin153 (C153) in acetonitrile. The time-dependent TSP spectra showed how the different solvent intermolecular modes were involved in different stages of the solvation process. Most importantly, the inertial and diffusive components of the solvent intermolecular modes in solvation were found to be spectrally and temporally well-separated. In a dipolar solvation of C153, high-frequency inertial solvent modes were found to be driven instantaneously and decay on a subpicosecond timescale while low-frequency diffusive solvent modes were induced slowly and decayed on a picosecond timescale. Our present result is the first experimental manifestation of frequency-dependent solvent intermolecular response in a dipolar solvation.     

Elution mechanism of polypeptides in reversed-phase liquid chromatography based on the critical threshold of organic solvent to induce abrupt change in adsorption capacity to the column packing

Adsorption capacity of polypeptides to the column packing in a solution containing multiple organic solvents was found to be expressed by means of an fn value, which is the sum of the ratios of the content of each organic solvent in the solution to the critical content of each organic solvent to cause abrupt change in the adsorption capacity, and to change abruptly at the point where the fn value becomes 1. Additionally, our results indicate that each polypeptide is eluted by the eluent containing a specific organic solvent content regardless of gradient elution rate in reversed-phase liquid chromatography, and that total organic solvent content in the eluent containing polypeptides is equal to the critical content. Considering the power law relationship between the retention times and the gradient elution rates, our results suggest that the elution of each polypeptide in reversed-phase liquid chromatography is mainly controlled by abrupt change in the adsorption capacity induced by change in the organic solvent content of the eluent during a gradient elution process, and that the abrupt change repeats across the critical threshold while a polypeptide moves through the column, and as a result, each polypeptide is concentrated in the eluent with the critical threshold.     

Simulating the formation of sodium:electron tight-contact pairs: watching the solvation of atoms in liquids one molecule at a time

The motions of solvent molecules during a chemical transformation often dictate both the dynamics and the outcome of solution-phase reactions. However, a microscopic picture of solvation dynamics is often obscured by the concerted motions of numerous solvent molecules that make up a condensed-phase environment. In this study, we use mixed quantum/classical molecular dynamics simulations to furnish the molecular details of the solvation dynamics that leads to the formation of a sodium cation-solvated electron contact pair, (Na(+), e(-)), in liquid tetrahydrofuran following electron photodetachment from sodide (Na(-)). Our simulations reveal that the dominant solvent response is comprised of a series of discrete solvent molecular events that work sequentially to build up a shell of coordinating THF oxygen sites around the sodium cation end of the contact pair. With the solvent response described in terms of the sequential motion of single molecules, we are then able to compare the calculated transient absorption spectroscopy of the sodium species to experiment, providing a clear microscopic interpretation of ultrafast pump-probe experiments on this system. Our findings suggest that for solute-solvent interactions similar to the ones present in our study, the solvation dynamics is best understood as a series of kinetic events consisting of reactions between chemically distinct local structures in which key solvent molecules must be considered to be part of the identity of the reacting species.     

Solvent mediated interactions close to fluid-fluid phase separation: microscopic treatment of bridging in a soft-core fluid

Using density functional theory we calculate the density profiles of a binary solvent adsorbed around a pair of big solute particles. All species interact via repulsive Gaussian potentials. The solvent exhibits fluid-fluid phase separation, and for thermodynamic states near to coexistence the big particles can be surrounded by a thick adsorbed "wetting" film of the coexisting solvent phase. On reducing the separation between the two big particles we find there can be a "bridging" transition as the wetting films join to form a fluid bridge. The effective (solvent mediated) potential between the two big particles becomes long ranged and strongly attractive in the bridged configuration. Within our mean-field treatment the bridging transition results in a discontinuity in the solvent mediated force. We demonstrate that accounting for the phenomenon of bridging requires the presence of a nonzero bridge function in the correlations between the solute particles when our model fluid is described within a full mixture theory based upon the Ornstein-Zernike equations.     

Temperature dependence of the conformational relaxation time of polymer molecules in elongational flow: Invariance of the molecular weight exponent

Using an elongational flow technique, we have investigated the relationship between the molecular conformational relaxation time and the molecular weight for a solvent whose quality was altered thermally from near θ to a good solvent state. The materials used were closely monodisperse samples of atactic polystyrene. The results show that the relaxation time τ varies with the molecular weight M as τ ∝ M^1.5, independent of the solvent quality, a result which apparently is at variance with the observed molecular weight dependence of intrinsic viscosity. Despite this invariance of the molecular weight exponent with solvent quality, our results also show that the coils do expand when the solvent quality was increased in agreement with the mean-field theory of Flory.     

Local hydrodynamics of solvent near diffusing dendrimers: A test of the new Stokes–Einstein relation

We have reported a new Stokes–Einstein relation (SER) for size determination and tested it by different nanoparticles. We assumed that the breakdown for SER results from local increases in viscosity. Here we investigate hydrodynamics of solvent near dendrimers to further test generality of our new theory. We discuss simulations of dendrimers in comparison to nanoparticles, experimental data on dendrimers from literature, and our theory. Local viscosity and local diffusivity of solvent near dendrimers are estimated by persistence times and exchange times, respectively. We find that the local dynamics of solvent near dendrimers of low density stay almost the same as that of bulk solvent. While the motions of solvent particles slow down near dendrimers of high density. This is similar with changes in local dynamics of solvent near nanoparticles. According to the causes we proposed for the deviation of SER, this is consistent with our findings that the SER works for the dendrimers of low density, while it fails for the dendrimers of high density. The new SER is then tested to predict size of the dendrimers accurately. Taking this together with the results for the nanoparticles, we believe that the new theory is general. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1380–1392     

Hydrogen bonding and solvatochromatic shift of the lowest 1(n, pi*) excitation of s-tetrazine in its hydrated clusters and dilute solutions

Hydrogen bonding involving azine and its derivatives such as nucleic bases is very important for understanding the structure and function of biological systems. In this work, we have investigated the hydrogen bonding structures of the hydrated cluster and dilute aqueous solution of s-tetrazine using computer simulation techniques, and evaluated the absorption and fluorescence shifts of the lowest 1(n, pi*) excitation of s-tetrazine solution using our solvent shift method. For the s-tetrazine-water cluster, a linear orthodox hydrogen bond arrangement is predicted in both ground and excited states with small structural and energetic differences, and a bifurcated hydrogen bond isomerization is anticipated. Further, ab initio calculations have verified these conformations. For the s-tetrazine-water solution, a mixture of two hydrogen bonding arrangements is found to be in both ground and excited states, resulting in small magnitudes of absorption and fluorescence solvent shifts. This finalizes our series investigation of hydrogen bonding and solvent shifts of dilute azines in water.     

Studies on the changes in the composition of solvent during photochemical generation of uranous ions in uranium loaded 30 % TBP-n-dodecane-HNO3 system

Present investigation describes our study on photochemical generation of uranous ions and consequent degradation of solvent in the uranium loaded 30 % Tributyl phosphate-n-dodecane-nitric acid system. Samples of 30 % TBP-n-dodecane loaded with uranium were subjected to UV photolysis at 254, 300 and 350 nm respectively. Wavelength dependent formation of U(IV) has been determined spectrophotometrically by measuring absorbance at 656 nm. Additionally, photochemical yield of U(IV) has also been estimated semi quantitatively as a function of time of photolysis. The changes in the solvent composition under different photochemical conditions have been studied by examination of comparative gas chromatographic profiles of the solvent before and after photolysis. Among the wavelength of photo irradiation studied, the yield of U(IV) was found to be optimum at 300 nm with least degradation of PUREX solvent.     

溶剂-导体界面电子转移溶剂重组能的球-界面模型

在连续介质理论基础上, 根据热力学基本原理, 用一个外加电场Eex将非平衡态2[Enon2, Dnon2]变成约束平衡态[E*2, D*2], 推导出了正确普适的溶剂重组能公式. 基于球-界面近似, 推导出了正确的溶剂-导体界面电子转移溶剂重组能公式. 和Marcus的公式相比, 本文的结果多了(εs-εop)/(εop(εs-1))因子. 对极性溶剂, 预测的溶剂重组能约为Marcus模型所得结果的一半. 以C343(Coumarin 343)-TiO2体系为算例, 计算了溶剂重组能并与实验值进行了比较.     

Calculation of the (29)si NMR chemical shifts of aqueous silicate species

A DFT methodology for calculating (29)Si NMR chemical shifts of silicate species typically present prior to nucleation in zeolite synthesis solutions, incorporating solvent effects through an implicit representation is presented. We demonstrate how our methodology can reproduce the experimentally observed spectra and, by comparison to well characterized peaks in two different experimental studies, demonstrate the transferability and robustness of the methodology. We discuss certain cases in which caution must be exercised when implicit solvent representations are used for calculating silicate cluster geometries: those cases in which intramolecular hydrogen bonding can play a significant role in the geometry. A number of reassignments of previous tentative experimental assignments are proposed, and we also make assignments for the challenging substituted four-ring species. We present all of our computed chemical shift for previously observed species together with a number of other viable silicate clusters to serve as a reference point for future experimental studies.     

Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory

The polarizable continuum model (PCM) for describing the solvent effect was combined with the fragment molecular orbital-based time-dependent density functional theory (TDDFT). Several levels of the many-body expansion were implemented, and the importance of the many-body contributions to the singlet-excited states was discussed. To calibrate the accuracy, we performed a number of the model calculations using our method and the regular TDDFT in solution, applying them to phenol and polypeptides at the long-range corrected BLYP/6-31G* level. It was found that for systems up to 192 atoms the largest error in the excitation energy was 0.006 eV (vs. the regular TDDFT/PCM of the full system). The solvent shifts and the conformer effects were discussed, and the scaling was found to be nearly linear. Finally, we applied our method to the lowest singlet excitation of the photoactive yellow protein (PYP) in aqueous solution and determined the excitation energy to be in reasonable agreement with experiment. The excitation energy analysis provided the contributions of individual residues, and the main factors as well as their solvent shifts were determined.     

Theoretical study of the role of solvent Stark effect in electron transitions

The possible influence of the solvent Stark effect (SSE) on the solvatochromic shift in electron transitions has been analyzed by using the ASEP/MD (averaged solvent electrostatic potential from molecular dynamics) method. With this purpose, four molecules, two polar (acrolein and formaldehyde) and two non-polar (p-difluorobenzene and trans-difluoroethene) have been studied in solvents of diverse polarity. Independently of the nature of the system we found that the contribution of SSE on the average value of the solvent shift or on the multipole moment values is negligible. In the case of centro-symmetric molecules, our results permit to discard the SSE as cause of the solvent shift found, which must be assigned to the electrostatic interaction of the solute quadrupole and higher multipoles with the solvent. As the SSE values provide also a measure of the errors introduced by the mean field approximation (MFA), these results indicate that MFA permits a very accurate determination of the solvent shift at the same time that it reduces drastically the computational cost. Finally, a new procedure suited to the ASEP/MD method has been presented that permits to estimate the inhomogeneous broadening of spectral bands, complementing the information provided by mean field theories. This procedure does not need additional quantum calculations and its computational cost is minimal.     

Influence of temperature on peak shape and solvent compatibility: implications for two-dimensional liquid chromatography

Solvent compatibility is a limiting factor for the success of two-dimensional liquid chromatography (2-D LC). In the second dimension, solvent effects can result in overpressures as well as in peak broadening or even distortion. A peak shape study was performed on a one-dimensional high-performance liquid chromatography (HPLC) system to simulate the impact of peak distorting solvent effects on a reversed-phase second dimension separation operated at high temperatures. This study includes changes in injection volume, solute concentration, column inner diameter, eluent composition and oven temperature. Special attention was given to the influence of high temperatures on the solvent effects. High-temperature HPLC (HT-HPLC) is known to enhance second dimension separations in terms of speed, selectivity and solvent compatibility. The ability to minimise the viscosity contrast between the mobile phases of both dimensions makes HT-HPLC a promising tool to avoid viscosity mismatch effects like (pre-)viscous fingering. In case of our study, viscosity mismatch effects could not be observed. However, our results clearly show that the enhancement in solvent compatibility provided by the application of high temperatures does not include the elimination of solvent strength effects. The additional peak broadening and distortion caused by this effect is a potential error source for data processing in 2-D LC.     

Prediction of the 1H and 13C NMR spectra of alpha-D-glucose in water by DFT methods and MD simulations

We have applied computational protocols based on DFT and molecular dynamics simulations to the prediction of the alkyl 1H and 13C chemical shifts of alpha-d-glucose in water. Computed data have been compared with accurate experimental chemical shifts obtained in our laboratory. 13C chemical shifts do not show a marked solvent effect. In contrast, the results for 1H chemical shifts provided by structures optimized in the gas phase are only fair and point out that it is necessary to take into account both the flexibility of the glucose structure and the strong effect exerted by solvent water thereupon. Thus, molecular dynamics simulations were carried out to model both the internal geometry as well as the influence of solvent molecules on the conformational distribution of the solute. Snapshots from the simulation were used as input to DFT NMR calculations with varying degrees of sophistication. The most important factor that affects the accuracy of computed 1H chemical shifts is the solute geometry; the effect of the solvent on the shielding constants can be reasonably accounted for by self-consistent reaction field models without the need of explicitly including solvent molecules in the NMR property calculation.     

Solvent size effect on the depletion layer of a polymer solution near an interface

By varying polymer concentration phi0p and Flory-Huggins parameter chi, the effect of solvent size on the depletion interaction between polymer coils and a hard wall was investigated by the real-space version of self-consistent field theory (SCFT). The depletion profiles and depletion thickness indicated that the depletion effect is strong in less good solvent with large molecular volume. Through the analysis of the respective free energies of polymer coils and solvent molecules, we found that the increment in the translation entropy of the solvent is the key to strengthening the depletion interaction. On the basis of the SCFT results, we define a solvent with volume about one to six times that of the polymer segment as a "middle-sized solvent". The density oscillations previously studied by Van der Gucht et al. and Maassen et al. were also observed in our simulation, and the addition of middle-sized solvent will magnify the amplitude of the oscillations. The solvent-size-dependent depletion interaction may be an explanation for the reduced entanglement and promoted crystallization behavior of polymer coils prepared from the solution with middle-sized solvent.     

Synthesis of urea picket porphyrins and their use in the elucidation of the role buried solvent plays in the selectivity and stoichiometry of anion binding receptors

The synthesis of alpha,alpha-5,10-diurea and alpha,alpha,alpha-5,10,15-triurea picket porphyrins are detailed in this report. In previous reports, these porphyrins, along with alpha,alpha,alpha,alpha-5,10,15,20-tetraurea picket porphyrin, were used to demonstrate the important role one buried solvent molecule plays in the selectivity and stoichiometry of binding inorganic anions. Building on prior work, this report discusses the results of acetate anion binding studies between tetra- and diurea picket porphyrins (the latter does not contain a buried solvent molecule in the anion-receptor complex), compares differences in thermodynamic data obtained from van't Hoff plots of a porphyrin anion receptor able to utilize buried solvent in its binding motif with one that does not, and compares the crystal structure of a tetraurea porphyrin 1-chloride anion complex that contains buried solvent with new X-ray crystal structures of tetraurea porphyrin 1-dichloride or bisdihydrogenphosphate anion complexes that contain no buried solvent. Data from our previous work, and the work described herein, demonstrates that one buried solvent molecule provides stability to the receptor-anion complex that is similar in energy to a moderately strong hydrogen bond.     

An ab initio investigation of the Buckingham birefringence of furan, thiophene, and selenophene in cyclohexane solution

Using a recently developed quadratic response methodology for the calculation of frequency-dependent third-order properties of molecules in solution, we investigate the Buckingham birefringence of furan, thiophene, and selenophene in cyclohexane solution. These systems are chosen since accurate experimental data are available, allowing for a direct comparison of experimental observations with our theoretical estimates. Our model for describing the solvent effects is based on a dielectric continuum approach for the solvent, and uses a molecule-shaped cavity. Our results show qualitatively different Buckingham constants and effective quadrupole centers calculated with and without the solvent, and only when the solvent is included are the qualitative trends observed experimentally reproduced. It is demonstrated that a significant part of this effect arises from the geometry relaxation of the molecules in the solvent.