On the theory of organic catalysis "on water"

A molecular origin of the striking rate increase observed in a reaction on water is studied theoretically. A key aspect of the on-water rate phenomenon is the chemistry between water and reactants that occurs at an oil−water phase boundary. In particular, the structure of water at the oil−water interface of an oil emulsion, in which approximately one in every four interfacial water molecules has a free (“dangling”) OH group that protrudes into the organic phase, plays a key role in catalyzing reactions via the formation of hydrogen bonds. Catalysis is expected when these OH's form stronger hydrogen bonds with the transition state than with the reactants. In experiments more than a 5 orders of magnitude enhancement in rate constant was found in a chosen reaction. The structural arrangement at the “oil−water” interface is in contrast to the structure of water molecules around a small hydrophobic solute in homogeneous solution, where the water molecules are tangentially oriented. The latter implies that a breaking of an existing hydrogen-bond network in homogeneous solution is needed in order to permit a catalytic effect of hydrogen bonds, but not for the on-water reaction. Thereby, the reaction in homogeneous aqueous solution is intrinsically slower than the surface reaction, as observed experimentally. The proposed mechanism of rate acceleration is discussed in light of other on-water reactions that showed smaller accelerations in rates. To interpret the results in different media, a method is given for comparing the rate constants of different rate processes, homogeneous, neat and on-water, all of which have different units, by introducing models that reduce them to the same units. The observed deuterium kinetic isotope effect is discussed briefly, and some experiments are suggested that can test the present interpretation and increase our understanding of the on-water catalysis

Microscopic structure and dynamics of air/water interface by computer simulations-comparison with sum-frequency generation experiments

The air/water interface was simulated and the mode amplitudes and their ratios of the effective nonlinear sum-frequency generation (SFG) susceptibilities (A_(eff)'s) were calculated for the ssp, ppp, and sps polarization combinations and compared with experiments. By designating “surface-sensitive” free OH bonds on the water surface, many aspects of the SFG measurements were calculated and compared with those inferred from experiment. We calculate an average tilt angle close to the SFG observed value of 35, an average surface density of free OH bonds close to the experimental value of about 2.8 × 10^(18) m^(−2), computed ratios of A_(eff)'s that are very similar to those from the SFG experiment, and their absolute values that are in reasonable agreement with experiment. A one-parameter model was used to calculate these properties. The method utilizes results available from independent IR and Raman experiments to obtain some of the needed quantities, rather than calculating them ab initio. The present results provide microscopic information on water structure useful to applications such as in our recent theory of on-water heterogeneous catalysis

The silicon (100) surface and its organic modifications

Two- and three-dimer cluster models, in chapter 2, were used to elucidate the structures of small models of the Si(100) surface. CASSCF (complete active space SCF) geometry optimizations find symmetric structures to be the global minima, with no local minima at buckled structures. The effect of the dynamic part of electron correlation on surface structure was assessed by performing single point multi-reference perturbation theory (MRMP) calculations along the three buckling normal modes. The MRMP results are in qualitative agreement with the CASSCF predictions. In chapter 3, the adsorption of water on the Si(100) surface is presented. Calculations show that, except for the reactant, a single configurational wave function is sufficient for a correct description of the reaction. The adsorbed OH group in an isolated product can nearly freely rotate between the trans and gauche minima. Interactions between the OH groups and the dangling bonds are small and do not appear to change the OH orientation. However, the interdimer hydrogen bonding is stronger and forces the OH orientation to be perpendicular to the dimer bond. The free rotation of the OH group in an isolated dimer model and the hydrogen bonding picture in an extended cluster model are consistent with the experimental finding for the OH orientation in the product. In chapter 4, the structures and energetics of benzene adsorption on Si(100) are presented. Both CASSCF(10,10) and MCQDPT2//CASSCF(10,10) results consistently predict the [4+2] structure to be the global minimum. While the [4+2] addition of benzene on the Si(100) surface is a barrier less cycloaddition reaction as is the regular [4+2] reaction, the [2+2] reaction occurs with a barrier of 16.0 kcal/mol at the MCQDPT2//CASSCF(10,10) level of theory. The modification of the Hessian part of SIMOMM (surface integrated molecular orbital molecular mechanics) appears in chapter 5. The influence of including MM displacements in the original SIMOMM method of numerical Hessian routine is considered, and the results are discussed

Flow-Induced Voltage Generation Over Monolayer Graphene in the Presence of Herringbone Grooves

While flow-induced voltage over a graphene layer has been reported, its origin remains unclear. In our previous study, we suggested different mechanisms for different experimental configurations: phonon dragging effect for the parallel alignment and an enhanced out-of-plane phonon mode for the perpendicular alignment (Appl. Phys. Lett. 102:063116, 2011). In order to further examine the origin of flow-induced voltage, we introduced a transverse flow component by integrating staggered herringbone grooves in the microchannel. We found that the flow-induced voltage decreased significantly in the presence of herringbone grooves in both parallel and perpendicular alignments. These results support our previous interpretation

Analytic Derivatives of Quartic-Scaling Doubly Hybrid XYGJ-OS Functional: Theory, Implementation, and Benchmark Comparison with M06-2X and MP2 Geometries for Nonbonded Complexes

Analytic first derivative expression of opposite-spin (OS) ansatz-adapted quartic scaling doubly hybrid XYGJ-OS functional is derived and implemented into Q-Chem. The resulting algorithm scales quartically with system size as in OS-MP2 gradient, by utilizing the combination of Laplace transformation and density fitting technique. The performance of XYGJ-OS geometry optimization is assessed by comparing the bond lengths and the intermolecular properties in reference coupled cluster methods. For the selected nonbonded complexes in the S22 and S66 data sets used in the present benchmark test, it is shown that XYGJOS geometries are more accurate than M06-2X and RI-MP2, the two quantum chemical methods widely used to obtain accurate geometries for practical systems, and comparable to CCSD(T) geometries

On the absolute thermodynamics of water from computer simulations: A comparison of first-principles molecular dynamics, reactive and empirical force fields

We present the absolute enthalpy, entropy, heat capacity, and free energy of liquid water at ambient conditions calculated by the two-phase thermodynamic method applied to ab initio, reactive and classical molecular dynamics simulations. We find that the absolute entropy and heat capacity of liquid water from ab initio molecular dynamics (AIMD) is underestimated, but falls within the range of the flexible empirical as well as the reactive force fields. The origin of the low absolute entropy of liquid water from AIMD simulations is due to an underestimation of the translational entropy by 20% and the rotational entropy by 40% compared to the TIP3P classical water model, consistent with previous studies that reports low diffusivity and increased ordering of liquid water from AIMD simulations. Classical MD simulations with rigid water models tend to be in better agreement with experiment (in particular TIP3P yielding the best agreement), although the TIP4P-ice water model, the only empirical force field that reproduces the experimental melting temperature, has the lowest entropy, perhaps expectedly. This reiterates the limitations of existing empirical water models in simultaneously capturing the thermodynamics of solid and liquid phases. We find that the quantum corrections to heat capacity of water can be as large as 60%. Although certain water models are computed to yield good absolute free energies of water compared to experiments, they are often due to the fortuitous enthalpy-entropy cancellation, but not necessarily due to the correct descriptions of enthalpy and entropy separately