Car-Parrinello-based ab initio molecular dynamics simulations (CPMD) combined with metadynamics (MTD) simulations were used to determine the reaction energetics for the beta-D-xylose condensation reaction to form beta-1,4-linked xylobiose in a dilute acid solution. Protonation of the hydroxyl group on the xylose molecule and the subsequent breaking of the C-O bond were found to be the rate-limiting step during the xylose condensation reaction. Water and water structure was found to play a critical role in these reactions due to the proton's high affinity for water molecules. The reaction free energy and reaction barrier were determined using CPMD-MTD. We found that solvent reorganization due to proton partial desolvation must be taken into account in order to obtain the correct reaction activation energy. Our calculated reaction free energy and reaction activation energy compare well with available experimental results.

The acidity constant pKa for polymeric organic acid is expected to be different from its corresponding monomer value due to the change of chemical environment upon polymerization. Thermodynamic cycles were used to determine the free-energy changes for the proton dissociation processes in aqueous solution and the corresponding pKa values for monomer methacrylic acid and several similar carboxylic acids. First-principles calculations and continuum solvation model were used to determine the gas-phase and solvation free energies, respectively. A protocol was developed to use the efficient density functional calculations with B3LYP functional instead of the demanding CBS-QB3 method to determine the gas-phase free energies with relative high accuracy, thus enabling the determination of pKa values for the short oligomers of methacrylic acid. The predicted pKa values for the dimer and trimer of methacrylic acid are higher by about 0.8 pKa units than the predicted monomer value.

Systems of poly(ethylene oxide) with dissolved inorganic salts are used as solid polymer electrolytes in high energy density batteries. Amorphous tetraglyme [CH 3 O(CH 2 CH 2 O) 4 CH 3 ], a model for amorphous PEO, and tetraglyme:LiCF 3 SO 3 (lithium triflate) with an ether oxygen:Li + ratio of 10:1 were studied by molecular dynamics (MD) simulations at 300 and 400 K. Conformational and structural analyses of Li + interactions with tetraglyme and triflate ion oxygens are consistent with decreased Li + coordination by tetraglyme and increased ionic aggregation at the higher temperature. Dihedral angle population density distributions for tetraglyme chains show that the trans conformation is favored for C-O bonds while the more compact gauche conformation is favored for C-C bonds and is enforced by coordination of adjacent oxygens to Li + . Calculated populations of tetraglyme conformational triads indicate that the most stable conformation around Li + -tetraglyme oxygens is tgt. Mean-square radius of gyration and end-to-end distance of pure tetraglyme chains decrease with increasing temperature and upon Li + -tetraglyme oxygen complexation, but increase at 400 vs 300 K for tetraglyme:LiCF 3 SO 3 . The calculated Li + coordination number remains the same with increasing temperature, but triflate ions contribute more oxygens to Li + coordination at 400 K (4.8) than at 300 K (4.6). The MDderived populations of Li + -CF 3 SO 3associated species are compared with vibrational spectral data. The increase in populations of [Li 2 CF 3 SO 3 ] + and [Li 3 CF 3 SO 3 ] 2+ from both MD simulations and IR data implies that Li + -CF 3 SO 3association is increased at higher temperature. Monodentate and bidentate coordination geometries of Li + by CF 3 SO 3were found. The increase in monodentate coordination of Li + by CF 3 SO 3at the higher temperature frees Li + to bridge between different CF 3 SO 3ions.

An oligomeric model for poly(ethylene oxide), tetraglyme, with NaCF 3 SO 3 at an ether oxygen:Na + ratio of 10:1 was used to represent the amorphous phase of PEO:salt systems in molecular dynamics simulations at 300 K and 400 K. Na + -tetraglyme interactions were examined by calculating chain dimensions, dihedral angle population distribution, and conformational triad populations of coordinating tetraglyme chains. All results consistently show that the Na + -ether oxygen coordination induces more compact chains by enforcing a gauche conformation for C-C bonds and introducing a strong preference for tgt conformations in the C-O-C-C-O-C bond sequence. Na + -O(tetraglyme) and Na + -O(triflate) radial distribution functions reveal that triflate ions contribute more oxygens (4.9 at 300 K and 5.3 at 400 K) than tetraglyme (2.2 at 300 K and 2.0 at 400 K) to the first coordination shell of Na + . Populations of aggregates consisting of a triflate ion coordinated to 0-3 Na + were available from vibrational spectra and were also calculated from equilibrated trajectories. Both results agree well, and the computational results indicate that Na + -CF 3 SO 3 -association increases with increasing temperature. The results are compared with results from a previously studied tetraglyme:LiCF 3 SO 3 system. Unlike Li + in the tetraglyme:LiCF 3 SO 3 system, bidentate coordination of Na + by CF 3 SO 3 -becomes more favorable at the higher temperature, at the expense of monodentate and tridentate coordination.

The effects of ring substitution on the pK(a) value of benzenesulfonic acid (BSA) were investigated using a combined quantum mechanical and classical approach. Ring substitution with strong electron-withdrawing elements such as F, Cl, and Br is found to enhance the acidity of the BSA. More importantly, ring substitution with -NO(2) groups which form an extended conjugated pi-system with the benzene ring exhibits the strongest enhancement of the acidity. The effects of polymerization on the styrenesulfonic acid (SSA) were also investigated by solving the classical Poisson-Boltzmann equation. It is found that polymerization significantly decreases the acidity of SSA due to the alteration of the electrostatic environment surrounding the acid group upon polymerization. The average pK(a) value converges to 2.9 from the corresponding monomer value of -0.53 at a degree of polymerization of 8-12. These results shed significant light on how to design sulfonic-acid-based solid acid catalysts to achieve desired catalytic properties.

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KEYWORDS:ab initio calculations ¥ density functional calculations ¥ molecular dynamics ¥ water ¥ vibrational spectroscopy Dramatic experimental advances allow measurements of vibrational frequencies for molecules in condensed phases to determine polymer conformations, protein folds and folding pathways, and enzyme mechanisms, [1, 2] but computational approaches to assist in mode assignments for condensed-phase vibrations have not kept pace. Traditional methods for calculating molecular vibrations are based on solving an eigenvalue problem formulated from Wilson FG matrices. [3] Solvent effects on molecular vibrations may be incorporated by using a continuum solvent model [4] or adapting classical molecular dynamics (MD), [5] quantum MD, [6] or QM/MM [7] programs to construct a Hessian matrix and solve the eigenvalue problem at a series of time steps. These methods are all limited by the harmonic approximation. Continuum solvent models are incapable of replicating specific solute-solvent interactions, and dynamics methods require considerable computer time to construct and diagonalize the Hessian matrix at each time step. Fourier transform-based methods [8, 9] cannot be used with Monte Carlo simulations, give vibrational frequencies but not the associated modes, and/or require longer trajectories to resolve closely spaced vibrational frequencies. [10,11] This contribution demonstrates the capabilities of multivariate statistical analysis [12,13] of quantum MD or QM/MM trajectories to calculate vibrational frequencies for an isolated water molecule, water dimer, and liquid water. Tests were chosen to determine the accuracy of principal mode analysis (PMA) for calculating intramolecular vibrations of small molecules, intermolecular vibrations involving noncovalent contacts, and vibrations of small molecules in a condensed phase. Unlike conventional matrix diagonalization methods, PMA incorporates some anharmonicity and performs a time average before solving a single eigenvalue equation. Compared to transform-based methods, PMA requires shorter trajectories, typically gives lower frequencies, and gives vibrational modes in addition to frequencies.tional hydrate formed as the solution was cooled, but the composition reflected the lower concentration of THF. So, first of all, we observed the small cages being filled with methane, as the occupancy of the large cages by THF decreased. Eventually, the methane also replaced some THF in the large cages. When the THF concentration was sufficiently low, pure sI methane hydrate was formed when the appropriate phase boundary was crossed, thus giving a complex mixture of solid phases.The present study can be considered to be a first attempt to explore the microscopically complex behavior of mixed hydrates in heterogeneous states through hydrate phase equilibrium determination, NMR spectroscopic analysis of cage occupancy, and microimaging observation to follow water consumption.

Stiffness plays an important role in diagnosing renal fibrosis. However, kidney stiffness is altered by perfusion changes in many kidney diseases. Therefore, the aim of the current study is to determine the correlation of kidney stiffness with water intake. We hypothesize that kidney stiffness will increase with 1 L of water intake due to increased water perfusion to the kidneys. Additionally, stiffness of the kidneys will correlate with apparent diffusion coefficient (ADC) and fractional anisotropy (FA) values before and after water intake. A 3 T MRI scanner was used to perform magnetic resonance elastography and diffusion tensor imaging of the kidneys on 24 healthy subjects (age range: 22‐66 years) before and after water intake of 1 L. A 3D T1‐weighted bladder scan was also performed to measure bladder volume before and after water intake. A paired t‐test was performed to evaluate the effect of water intake on the stiffness of kidneys, in addition to bladder volume. A Spearman correlation test was performed to determine the association between stiffness, bladder volume, ADC and FA values of both kidneys before and after water intake. The results show a significant increase in stiffness in different regions of the kidney (ie, percentage increase ranged from 3.6% to 7.5%) and bladder volume after water intake (all P < 0.05). A moderate significant negative correlation was observed between change in kidney stiffness and bladder volume (concordance correlation coefficient = ‐0.468, P < 0.05). No significant correlation was observed between stiffness and ADC or FA values before and after water intake in both kidneys (P > 0.05). Water intake caused a significant increase in the stiffness of the kidneys. The negative correlation between the change in kidney stiffness and bladder volume, before and after water intake, indicates higher perfusion pressure in the kidneys, leading to increased stiffness.