Kritsana Sagarik

Statistical mechanical simulations on properties of liquid pyridine

Abstract An intermolecular potential describing the interaction between pyridine molecules was constructed using the test-particle model (T-model). The computed T-model potential was used in the investigation of the equilibrium structures and binding energies of pyridine dimers. It was found that a herringbone structure is the most stable dimer in the gas phase. The results of the statistical mechanical simulations revealed that this dimer structure may not be present in an appreciable amount in the liquid phase. The molecular dynamics (MD) simulations confirmed that the molecular motions of pyridine in the liquid phase are rather anisotropic, as can be seen from the computed rotational diffusion constants. This finding is in good agreement with the experimental investigation on reorientational motions of pyridine reported by Kintzinger and Lehn.

INTERMOLECULAR POTENTIAL FOR PHENOL BASED ON THE TEST PARTICLE MODEL

Abstract An intermolecular potential to describe the interaction between phenol molecules was constructed using the test particle model (T-model). The T-model potential was used in the calculation of the equilibrium structures and energies of phenol dimers and trimers. The absolute and local energy minima on the T-model potential energy surface were examined by ab initio calculations with the second-order Moller-Plesset perturbation (MP2) theories. The equilibrium structures of phenol dimers computed from the T-model potential agree well with the MP2 results, and are compatible with those deduced from rotational coherence spectroscopy. The hydrogen bonds (H-bonds) in phenol-water 1:1 complexes were also investigated using the T-model potentialsand MP2 calculations. The results are in good agreement with the previous ab initio calculations with a larger basis set and experiment in the gas phase. Structures and energies of liquid phenol, as well as phenol in aqueous solution, were studied using Molecular Dynamics (MD) and Monte Carlo (MC) simulations, respectively. The results are discussed in comparison with available theoretical and experimental results on the same and similar systems.

Preferential solvation of Ca2+ in aqueous ammonia solution: Classical and combined ab initio quantum mechanical/molecular mechanical molecular dynamics simulations

Classical and combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations have been performed to investigate the solvation structure of Ca2+ in 18.4% aqueous ammonia solution. The classical molecular dynamics simulation has been carried out based on pairwise additive potentials. For the QM/MM scheme, the first solvation sphere of Ca2+ is treated by Born–Oppenheimer ab initio quantum mechanics using LANL2DZ basis sets, while the rest of the system is described based on classical pairwise additivity. The results indicate the importance of the QM treatment in obtaining a reliable geometrical arrangement as well as the correct coordination number of the solvated ion. Within the first solvation sphere of Ca2+, the QM/MM simulation reveals a polyhedral structure with an average coordination number of 7.2, consisting of 5.2 water and 2 ammonia molecules, compared to the corresponding value of 9.7 composed of 6.7 water and 3 ammonia molecules obtained by classical pair potential simulation. The preference for ligands is discussed on the basis of detailed simulation results.

Ab initio QM/MM dynamics of H3O+ in water.

A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6–8 water molecules. It is treated at the Hartree‐Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O  4+ ) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O  2+ ) structure. Besides the three nearest‐neighbor water molecules directly hydrogen‐bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ions hydration shell indicate that such next‐nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton.

Structure and dynamics of hydrated NH 4+: An ab initio QM/MM molecular dynamics simulation

A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate solvation structure and dynamics of NH  4+ in water. The most interesting region, the sphere includes an ammonium ion and its first hydration shell, was treated at the Hartree–Fock level using DZV basis set, while the rest of the system was described by classical pair potentials. On the basis of detailed QM/MM simulation results, the solvation structure of NH  4+ is rather flexible, in which many water molecules are cooperatively involved in the solvation shell of the ion. Of particular interest, the QM/MM results show fast translation and rotation of NH  4+ in water. This phenomenon has resulted from multiple coordination, which drives the NH  4+ to translate and rotate quite freely within its surrounding water molecules. In addition, a “structure‐breaking” behavior of the NH  4+ is well reflected by the detailed analysis on the water exchange process and the mean residence times of water molecules surrounding the ion.

The influence of small monovalent cations on neighbouring N…HO hydrogen bonds

Abstract The influence of small monovalent metal ions on hydrogen bonds of the OH…N type is studied with the example Li + /H 2 ONH 3 . The net stabilization effect is discussed and compared with the OH…O system. The applicability of the semi-empirical CNDO/2 method and ab initio calculations with extended and minimal basis sets is investigated.

Intermolecular potential for benzoic acid-water based on the test-particle model and statistical mechanical simulations of benzoic acid in aqueous solutions

Structures and interaction energies of benzoic acid‐water (BA‐H2O) 1:1, 1:2, 2:1 and 2:2 complexes were investigated using intermolecular potentials derived from the test-particle model (T-model). The absolute and some lowestlying minimum energy geometries of the 1:1 and 1:2 complexes were examined using ab initio calculations with the Hartree‐Fock (HF) and the second order Moller‐Plesset (MP2) perturbation theories. The T-model, HF and MP2 calculations revealed that cyclic arrangements of hydrogen bonds (H-bonds) between the COOH group and H2O represent the absolute minimum energy geometries of the 1:1 and 1:2 complexes. The results on the 2:1 and 2:2 complexes showed that the cyclic H-bonds in the dimers could be opened to allow insertion of water molecules. Based on the T-model potentials, aqueous solutions of BA and (BA)2 were investigated by conducting a series of molecular dynamic (MD) simulations. It was found that, except at the solute‐solute H-bonds, the hydration structures of the cyclic H-bond planar (CHP) and side-on type (SOT) dimers are not substantially diAerent from a single BA. The atom‐ atom pair correlation functionsOgORUU derived from MD simulations suggested that, in very dilute aqueous solution, the cyclic H-bonds in the CHP and SOT dimers are not stable and can be disrupted by the solute‐solvent H-bond interaction and thermal energy fluctuation. ” 2000 Elsevier Science B.V. All rights reserved.

Dynamics and mechanism of structural diffusion in linear hydrogen bond

Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H‐bond) chain were studied, using the CH3OH2+(CH3OH)n complexes, n = 1–4, as model systems. The present investigations used B3LYP/TZVP calculations and Born‐Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H‐bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H3O+(H2O)n and CH3OH2+(H2O)n complexes, n = 1–4. It was found that the H‐bond chains with n = 1 and 3 represent the most active intermediate states and the CH3OH2+(CH3OH)n complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared‐proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared‐proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH3OH molecules in the H‐bond chain, and the quasi‐dynamic equilibriums between the shared‐proton structure (n = 3) and the close‐contact structures (n ≥ 4). The latter prohibits proton transfer reaction in the H‐bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared‐proton intermediate state.

Proton dissociation and transfer in a phosphoric acid doped imidazole system

The dynamics and mechanisms of proton exchange in a phosphoric acid (H3PO4) doped imidazole (Im) system were studied using a quantum chemical method at the B3LYP/TZVP level and Born–Oppenheimer molecular dynamics (BOMD) simulations. The theoretical studies began with selecting the appropriate presolvation models for proton dissociation and transfer, which were represented by embedded and terminal hydrogen bond (H-bond) structures of H+(H3PO4)(Im)n(n = 1–4), respectively. B3LYP/TZVP calculations confirmed that excess proton conditions are required to promote proton exchange, and the intermediate complexes are preferentially formed in a low local-dielectric environment. In contrast, a high local-dielectric environment is required to stabilize the positive charge and prevent the proton from returning to the original Im molecule. The static results also revealed that the embedded structure with n = 2 represents the smallest, most active intermediate complex for proton dissociation, whereas the terminal structure with n = 3 favors proton transfer in the Im H-bond chain. BOMD simulations confirmed the static results and further suggested that the fluctuations of the H-bond chain lengths and the local-dielectric environment must be included in the proton dissociation and transfer mechanisms. Analyses of the time evolutions of torsional angles in the Im H-bond chain showed characteristic solvent structure reorganization, regarded as helical-rotational motion, which drives the proton away from the H3PO4 dopant. The current theoretical results showed in detail for the first time the interplay among the “key molecular motions” that fundamentally underlie the dynamics and mechanisms of proton exchange in the H3PO4 doped Im H-bond system.

Dynamics of proton transfer in imidazole hydrogen-bond chains

The dynamics and mechanism of proton transfer in the imidazole (Im) hydrogen-bond (H-bond) chain were studied using a unit cell of the Im crystal structure (H+(Im)n, n = 2–4) as a model system and B3LYP/TZVP calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations as model calculations. The B3LYP/TZVP results suggested that only linear H-bond structures are involved in proton transfer and H+(Im)2 is the smallest, most active Zundel-like intermediate complex, which is preferentially formed in a low local dielectric environment. The potential energy curves for proton displacement confirmed the Eigen–Zundel–Eigen scenario that consists of breaking and forming H-bonds in the Im H-bond chain, and because the energy barrier for the reorientation of Im molecule is high, the ring-flip process is ruled out from the proton-transfer mechanism. The BOMD results over the temperature range of 298 to 500 K confirmed that proton transfer in the Im H-bond chain is a local (short-range) process by showing that the activation energies for proton displacement in H+(Im)2 and H+(Im)4 are nearly the same and comparable to experimental and theoretical values. The proton transfer profiles and vibrational spectra suggested that at low temperatures, the N–N vibration, transferring proton and librational motion in the protonated H-bond are synchronized (coherent), resulting in effective structural diffusion process. The 1H NMR results confirmed these findings and further revealed that the dynamics of proton transfer at low and high temperatures are different due to the interferences of vibrational and librational motions and increases in the oscillatory shuttling motion at elevated temperatures. These theoretical results lead to the conclusion that the rate-determining process of proton transfer in the Im system is the oscillatory shuttling motion in the Zundel-like intermediate complex and does not necessarily involve reorientation of Im molecule as a key process.