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Adsorption of water on the Si(100) surface is studied using fully quantum mechanical (QM) calculations and the hybrid QM/MM SIMOMM (surface integrated molecular orbital molecular mechanics) method. When QM and SIMOMM calculations are compared, computationally efficient SIMOMM method gives reasonable result.

Theformation of like-ion pairs, Na–Na橷Cl––Cl–, in aqueoussolution was studied by high-level ab initio methods, classical moleculardynamics (MD), QM/TIP5P, and QM/EFP MD (quantum mechanics/effectivefragment potential molecular dynamics). Ab initio calculations onmodel clusters revealed that the Na(H2O)nNa(n= 2–4)clusters were significantly more stabilized by bridged waters thanthe corresponding Cl–(H2O)nCl–clusters. QM/EFP MD simulationsin solution also predicted a clear local minimum near 3.6 Å onlyfor the Na–Naꖨ, suggesting thatNa–Naꖨ may be more likely to formthan Cl––Cl–pairs in solution.Analysis of the hydration structures further showed that two-waterbridged Na–Naꖨ were dominant atthe local minimum. The preferred formation of Na阩ionpairs in solution appeared to come from significant short-range effects,in particular, charge delocalization (polarization) between the bridgedoxygen p and the vacant valence Naꊶꥬ. [ABSTRACT FROM AUTHOR]

With the help of QM/EFP-MD with modern correlated quantum theories, distinctly different proton transport dynamics for hydronium and hydroxide ions was revealed. The efficiency of proton transfer for hydronium was found to be significantly higher than that for hydroxide, and the difference in efficiency increased as the temperature was lowered. This difference in dynamics suggests that molecular Brownian diffusion may play an important role in hydroxide transport. Our theoretical findings are consistent with recent experimental observations of proton transfer in amorphous solid water.

New theoretical procedures were proposed for the heats of vaporization (ΔHvap) and sublimation (ΔHsub) predictions by adopting effective fragment potential version 2-molecular dynamics (EFP2-MD) simulations. The particular EFP2, as generated by HF/6-31++G(2d,2p), yielded excellent results in the predictions of ΔHvap, where mean absolute deviation (MAD) and root-mean-square deviation (RMSD) for 16 molecules were 0.34 and 0.44 kcal/mol, respectively. By introducing a uniform scaling factor, we further derived a prediction procedure for ΔHsub, where its MAD and RMSD were 0.76 and 0.90 kcal/mol, respectively. Because EFP2-MD does not require any ab initio computations during simulation, computational overhead of our procedures is minimal. We believe that our new procedures for the ΔHvap and ΔHsub predictions could be widely applicable in the areas where accurate chemical information for virtual molecules is critical.

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

The pKa values of HF, HCOOH, CH3COOH, CH3CH2COOH, H2CO3, HOCl, NH4(+), CH3NH3(+), H2O2, and CH3CH2OH in aqueous solution were predicted by QM/MM-MD in combination with umbrella samplings adopting the flexible asymmetric coordinate (FAC). This unique combination yielded remarkably accurate values with the maximum and root-mean-square errors of 0.45 and 0.22 in pKa units, respectively, without any numerical or experimental adjustments. The stability of the initially formed Coulomb pair rather than the proton transfer stage turned out to be the rate-determining step, implying that the stabilizations of the created ions require a large free energy increase. A remarkable correlation between DWR (degree of water rearrangements) and pKa was observed. As such, the large pKa of ethanol can be, in part, attributed to the large water rearrangement, strongly suggesting that proper samplings of water dynamics at dissociated regions are critical for accurate predictions of pKa. Current results exhibit a promising protocol for direct and accurate predictions of pKa. The significant variations in the gas phase deprotonation energies with level of theory appear to be mostly canceled by the similar changes in the averaged solute-solvent interactions, yielding accurate results.

The association process of NaCl in aqueous solution was studied by a combination of quantum mechanical calculations on NaCl(H(2)O)(n) (n = 1-6) clusters and quantum mechanical/effective fragment potential-molecular dynamics (QM/EFP-MD) simulations for NaCl in 292 EFP waters. The interionic hydration structures (IHSs) were topologically classified as "ring" (R), "half-bridge" (H), and "full-bridge" (F) types on the basis of the quantum mechanical calculations. Subsequent IHS analysis on QM/EFP-MD simulations revealed that the NaCl contact ion pair (CIP) mainly involved R type hydration structures while the solvent-separated ion pair (SSIP) was composed of two different groups of F-type hydration structures. Our IHS analysis also discovered H type hydration even at large separation interionic distances (∼7 Å), which is denoted as a dissociating ion pair (DIP). The analysis was able to reveal the most complete interionic structures and their reorganizations of the association process. A strong correlation between the IHSs and interionic distance suggests that not only the solvent reorganization but also the local IHS changes are equally important. Mechanistically, it is suggested that the conversion between ring-type and full-bridge hydration structures is the main rate-determining step of ion-pair association.

The association dynamics of a methanol pair in aqueous solution were theoretically studied with QM/EFP-MD and quantum mechanical methods. Stable contact pairs and solvent separated configurations (SS) were found from simulations with a free energy barrier of 2 kcal/mol, revealing the strong tendency of methanol association. The stable contact pairs were further identified as the hydrophobic (CP(A)) and hydrophilic (CP(B)) species, with the CP(A) having a larger population. Although the free energy difference between the CP(A) and CP(B) is negligible with virtually no associated free energy barrier, the slow isomerization dynamics of intermolecular rotations ensures their individual identity. Further mechanistic analysis revealed that only the CP(A) has a direct path to the SS, showing that hydrophobic attraction initiates the association process. A subsequent intermolecular hydrophilic attraction isomerizes CP(A) and CP(B). Therefore, our results show that both the hydrophobic and hydrophilic attractions between methanol molecules play important roles in the association dynamics. The former operates on the longer intermolecular distance, while the latter is effective in contact pairs.

The surface reaction pathways of dimethylaluminum isopropoxide (DMAI) and water with the H/Si(100)-2 x 1 surface were theoretically investigated with SIMOMM:MP2/6-31G(d). The oxygen atom in DMAI stabilizes an initial complex, facilitating the approach of DMAI to the surface. The methane loss reaction, propane loss reaction, methylation, hydrogen loss reaction, and ring closing reaction channels of the DMAI-surface reactions were identified. Among these, the methane loss reaction depositing -Al(CH3)OCH(CH3)2 was found to be the major channel due to low barrier height and large exothermicity. The ring closing reaction is kinetically the second most accessible channel, even though it is not thermodynamically favorable. On the basis of these theoretical results, recent experimental data were reinterpreted such that the experimentally observed peaks of CH4 and CH(CH3)2OH are in fact the products of these two channels. The propane loss reaction is kinetically the third most probable channel. It produces the surface Si-O bond, which is a reaction unique to DMAI as compared to trimethylaluminum. In summary, the oxygen substitution not only affects the basic nature of the existing potential energy surfaces but also opens new possibilities.

Amorphous Ge nanoparticles with the particle size of approximately 10 nm were prepared by capping butyl groups and were characterized using XAS, TEM, FT-IR reflectance, and electrochemical cycling. The XAS results for the first-cycle Ge nanoparticles exhibited either a little particle aggregation after reformation of the Ge-Ge metallic bond or reformation of Ge-Ge metallic bond followed by a little particle aggregation. More interestingly, butyl groups, being electrochemically stable, remained after cycling, and the quantum mechanical calculation of the thermodynamic energy of the reaction using the GAMESS (General Atomic and Molecular Electronic Structure System) program suggested the formation of a very stable surface Ge-C bond that cannot be easily subjected to the subsequent chemical reactions. Initial charge capacity is 1470 mAh/g with an irreversible capacity ratio of 12%; no capacity fading was observed out to 30 cycles. Even at 5 C rate discharging, capacity retention was 98%, compared to that at 0.2 C rate discharging. In addition, the capacity was fully recovered at 0.2 C rate cycling.

The potential energy surfaces of one, two, and three water molecule sequential adsorptions on the symmetrically chlorinated Si(100)-2 x 1 surface were theoretically explored with SIMOMM:MP2/6-31G(d). The first water molecule adsorption to the surface dimer requires a higher reaction barrier than the subsequent second water molecule adsorption. The lone pair electrons of the incoming water molecule nucleophilically attack the surface Si atom to which the leaving Cl group is bonded, yielding an S(N)2 type transition state. At the same time, the Cl abstracts the H atom of the incoming water molecule, forming a unique four-membered ring conformation. The second water molecule adsorption to the same surface dimer requires a much lower reaction barrier, which is attributed to the surface cooperative effect by the surface hydroxyl group that can form a hydrogen bond with the incoming second water molecule. The third water molecule adsorption exhibits a higher reaction barrier than the first and the second water molecule adsorption channels but yields a thermodynamically more stable product. In general, it is expected that the surface Si-Cl bonds can be subjected to the substitution reactions by water molecules, yielding surface Si-OH bonds, which can be a good initial template for subsequent surface chemical modifications. However, oversaturations can be a competing side reaction under severe conditions, suggesting that the precise control of surface kinetic environments is necessary to tailor the final surface characteristics.

Multireference wave functions were used to study the ethylene and 2-butene surface reactions on Si(100) in their lowest energy singlet states. In addition to the diradical pathway, a pi-complex pathway on the ethylene surface was found. The net barrier for the latter process is 4.5 kcal/mol higher than that for the former, making the pi-complex pathway kinetically less accessible. Therefore, although there is a competition between the two initial channels, the diradical path is slightly favored, and rotational isomerization is possible. However, since the initial potential energy surfaces of the two channels are different, depending on experimental conditions, the branching ratio between the two channels may change. Consequently, the combined effects that would favor one channel over the other may not derive directly from the initial reaction barrier. This provides an explanation of the experimental controversy. As a result, the final distributions of surface products may depend on the experimental kinetic environment, especially when the population change due to the rotational isomerization is expected to be very small. A significantly different reaction channel is found in the 2-butene surface reaction on Si(100), in which a methyl hydrogen easily transfers to the surface yielding a new type of surface product other than the expected [2 + 2] cycloaddition product, with a comparatively small activation barrier. Consequently, the overall surface reactions of ethylene and 2-butene may be quite different. Therefore, direct comparisons between ethylene and 2-butene experimental results would be very useful.