Mechanisms of photoisomerization of the prenylated flavin mononucleotide cofactor: a theoretical study.

The enzymatic decarboxylation of α,ß-unsaturated acids using the ferulic acid decarboxylase (Fdc1) enzyme and prenylated flavin mononucleotide (prFMN) cofactor is a potential, environmentally friendly reaction for the biosynthesis of styrene and its derivatives. However, experiments showed that the enzyme activity of Fdc1 depends on the ring structure of prFMN, namely, the iminium and ketimine forms, and the loss of enzyme activity results from prFMNim → prFMNket photoisomerization. To obtain insight into this photochemical process and to improve the enzyme efficiency of Fdc1, two proposed photoisomerization mechanisms with different proton sources for the acid-base reaction were studied herein using theoretical methods. The potential energy surfaces calculated using the density functional theory method with the Becke, 3-parameter, and Lee-Yang-Parr hybrid functionals and DZP basis set (DFT/B3LYP/DZP) and TD-DFT/B3LYP/DZP methods confirmed that the light-dependent reaction occurs in the rate-determining proton transfer process and that the mechanism involving intermolecular proton transfer between prFMNim and Glu282 (external base) is energetically more favorable than that involving intramolecular proton transfer in prFMNim (internal base). The thermodynamic results obtained from the transition state theory method suggested that the exothermic relaxation energy in the photo-to-thermal process can promote the spontaneous formation of a high-energy-barrier transition state, and an effective enzymatic decarboxylation could be achieved by slowing down the formation of the undesirable thermodynamically favorable product (prFMNket). Because the rate constant for formation of the high-energy-barrier transition state varies exponentially over the temperature range of 273-298 K, and experimental results have shown that incubating Fdc1 on ice results in a complete loss of enzyme activity, it is recommended to perform the decarboxylation reaction at 285 K to strike a balance between minimizing enzyme stability loss at 273 K and mitigating the effects of UV irradiation. The computational strategy and fundamental insights obtained in this study could serve as guidelines for future theoretical and experimental investigations on the same and similar photochemical systems.

Photoluminescence mechanisms of BF2-formazanate dye sensitizers: a theoretical study.

Photodynamic therapy (PDT) is an alternative, minimally invasive treatment for human diseases such as cancer. PDT uses a photosensitizer to transfer photon energy directly to cellular 3O2 to generate 1O2 (Type II), the toxicity of which leads to cancer cell death. In this work, the photoluminescence mechanisms of a BF2-formazanate dye sensitizer (BF2-FORM) and its iodinated derivative (BF2-FORM-D) were studied using complementary theoretical approaches; the photoluminescence pathways in the S1 and T1 states were studied using density functional theory (DFT) and time-dependent (TD)-DFT methods, the kinetic and thermodynamic properties of the pathways using the transition state theory (TST), and the time evolution and dynamics of key processes using non-adiabatic microcanonical molecular dynamics simulations with surface-hopping dynamics (NVE-MDSH). Evaluation of the potential energy surfaces (PESs) in terms of the rotations of the phenyl rings suggested a pathway for the S1 → S0 transition for the perpendicular structure, whereas two pathways were anticipated for the T1 → S0 transition, namely, [T1 → S0]1 occurring immediately after the S1/T1 intersystem crossing (ISC) and [T1 → S0]2 occurring after the S1/T1 ISC and T1 equilibrium structure relaxation, with the T1 → S0 energy gap being comparable to the energy required for 3O2 → 1O2. The PESs also showed that because of the heavy-atom effect, BF2-FORM-D possessed a significantly smaller S1/T1 energy gap than BF2-FORM. The TST results revealed that at room temperature, BF2-FORM-D was thermodynamically more favorable than the parent molecule. Analysis of the NVE-MDSH results suggested that the librational motions of the phenyl rings play an important role in the internal conversion (IC) and ISC, and the S1/T1 ISC and T1 → S0 transitions could be enhanced by varying the irradiation wavelength and controlling the temperature. These findings can be used as guidelines to improve and/or design photosensitizers for PDT.

Heavy Atom Effect on the Intersystem Crossing of a Boron Difluoride Formazanate Complex-Based Photosensitizer: Experimental and Theoretical Studies.

Photodynamic therapy (PDT) is a photochemical-based treatment approach that involves using light to activate photosensitizers (PSs). Attractively, PDT is one of the alternative cancer treatments due to its noninvasive technique. By utilizing the heavy atom effect, this work modified a class of formazan dyes to improve intersystem crossing (ISC) to improve reactive oxygen species (ROS) generation for PDT treatment. Two methods were used to observe the ROS generation enhanced by ISC of the synthesized complexes including, (1) recording DPBF decomposition caused by the ROS, and (2) calculating the potential energy curves for photophysical mechanisms of BF2 -formazanate dyes using the DFT and nudged elastic band (NEB) methods. The photophysical properties of the dyes were studied using spectroscopic techniques and X-ray crystallography, as well as DFT calculations. The experimental and theoretical results and in vitro cellular assays confirmed the potential use of the newly synthesized iodinated BF2 -formazanate dyes in PDT.

Kinetics and thermodynamics of enzymatic decarboxylation of α,ß-unsaturated acid: a theoretical study.

Enzymatic decarboxylation of α,ß-unsaturated acid through ferulic acid decarboxylase (FDC1) has been of interest because this reaction has been anticipated to be a promising, environmentally friendly industrial process for producing styrene and its derivatives from natural resources. Because the local dielectric constant at the active site is not exactly known, enzymatic decarboxylation to generate ß-methylstyrene (ß-MeSt) was studied under two extreme conditions (ε = 1 and 78 in the gas phase and aqueous solution, respectively) using the B3LYP/DZP method and transition state theory (TST). The model molecular clusters consisted of an α-methylcinnamate (Cin) substrate, a prenylated flavin mononucleotide (PrFMN) cofactor and all relevant residues of FDC1. Analysis of the equilibrium structures showed that the FDC1 backbone does not play the most important role in the decarboxylation process. The potential energy profiles confirmed that the increase in the polarity of the solvent could lead to significant changes in the energy barriers, especially for the transition states that involve proton transfer. Analysis of the rate constants confirmed the low/no quantum mechanical tunneling effect in the studied temperature range and that inclusion of the fluctuation of the local dielectric environment in the mechanistic model was essential. Because the computed rate constants are not compatible with the time resolution of the stopped-flow spectrophotometric experiment, the direct route for generating ß-MeSt after CO2 elimination (acid catalyst (2)) is unlikely to be utilized, thereby confirming that indirect cycloelimination in a low local dielectric environment is the rate determining step. The thermodynamic results showed that the elementary reactions that involve charge (proton) transfer are affected by solvent polarity, thereby leading to the conclusion that overall, the enzymatic decarboxylation of α,ß-unsaturated acid is thermodynamically controlled at high ε. The entropy changes due to the generation of molecules in the active site appeared more pronounced than that due to only covalent bond breaking/formation or structural reorientation. This work examined in detail for the first time the scenarios in each elementary reaction and provided insight into the effect of the fluctuations in the local dielectric environment on the enzymatic decarboxylation of α,ß-unsaturated acids. These results could be used as guidelines for further theoretical and experimental studies on the same and similar systems.

The Grotthuss mechanism for bifunctional proton transfer in poly(benzimidazole).

Poly(benzimidazole) (PBI) has received considerable attention as an effective high-temperature polymer electrolyte membrane for fuel cells. In this work, the Grotthuss mechanism for bifunctional proton transfer in PBI membranes was studied using density functional theory and transition state theory. This study focused on the reaction paths and kinetics for bifunctional proton transfer scenarios in neutral ([PBI]2), single (H+[PBI]2) and double-protonated (H2+[PBI]2) dimers. The theoretical results showed that the energy barriers and strength for H-bonds are sensitive to the local dielectric environment. For [PBI]2 with ε = 1, the uphill potential energy curve is attributed to extraordinarily strong ion-pair H-bonds in the transition structure, regarded as a 'dipolar energy trap'. For ε = 23, the ion-pair charges are partially neutralized, leading to a reduction in the electrostatic attraction in the transition structure. The dipolar energy trap appears to prohibit interconversion between the precursor, transition and proton-transferred structures, which rules out the possibility for [PBI]2 to be involved in the Grotthuss mechanism. For H+[PBI]2 and H2+[PBI]2 with ε = 1, the interconversion involves a low energy barrier, and the increase in the energy barrier for ε = 23 can be attributed to an increase in the strength of the protonated H-bonds in the transition structure: the local dielectric environment enhances the donor-acceptor interaction of the protonated H-bonds. Analysis of the rate constants confirmed that the quantum effect is not negligible for the N-H+ … N H-bond especially at low temperatures. Agreement between the theoretical and experimental data leads to the conclusion that the concerted bifunctional proton transfer in H2+[PBI]2 in a high local dielectric environment is 'the rate-determining scenario'. Therefore, a low local dielectric environment can be one of the required conditions for effective proton conduction in acid-doped PBI membranes. These theoretical results provide insights into the Grotthuss mechanism, which can be used as guidelines for understanding the fundamentals of proton transfers in other bifunctional H-bond systems.

Unimolecular photolysis mechanisms of formamide: the effect of thermal energy.

The photochemistry of molecules with peptide bonds is of both theoretical and experimental interest. Among these molecules, formamide (HCONH2) has been frequently selected as a representative in the study of proteins. Because several fundamental questions remained unanswered, particularly the role of thermal energy, the unimolecular photodissociations of HCONH2 were studied using the CASPT2(6,9)/aug-cc-pVDZ method and transition state theory (TST). The theoretical results verify that C-N dissociation is both kinetically and thermodynamically favorable in the S1 state. In addition, the dissociated radical products (HCO and NH2) could be precursors in the other dissociation channels owing to their high reactivities. The NH3-CO and NH3-OC H-bond complexes were reportedly observed to display the highest quantum yield in a UV experiment because the processes for determining the rates of isomerization dissociations of HCO and NH2 (which involve formyl hydrogen transfer) are spontaneous and kinetically favorable. Similarly, the van der Waals complex between HNCO and H2 represents the common end product with HCO and NH2 as the precursors. This is because the S1 and T1 relax-scan potential energy curves for the dehydrogenation straightforwardly intersect the S0 state with approximately similar structures at the intersection points. Therefore, the promotion of the intersystem crossing by a noble-gas cryogenic matrix appears inessential as previously reported. In contrast, we conjectured that the xenon matrix used in the UV experiment helps promote the van der Waals complex by reducing the energy barriers for dehydrogenation rather than by enhancing the rate of intersystem crossing from the singlet to triplet state. It was concluded that HCN, HNC, and H2O (dehydration) were formed via a two-step process, wherein, the cleavage of the C-O bond in formamidic acid first occurs in the S1 state. This is followed by the hydrogen/proton transfer from HCNH to OH on barrierless potentials. Overall, the mechanisms proposed in this work reveal the role of thermal energy and effects of variations in the multiconfigurational characteristics along the potential energy curves in detail. The available information on these aspects is limited, and the present results could provide insights into unimolecular photodissociations; these could be beneficial in future theoretical and experimental studies on this and other similar systems.

Near-Infrared Fluorescent pH Responsive Probe for Targeted Photodynamic Cancer Therapy.

We developed a pH dependent amino heptamethine cyanine based theranostic probe (I2-IR783-Mpip) that can be activated by near infrared light. I2-IR783-Mpip, in acidic condition, exhibited an intense, broad NIR absorption band (820-950 nm) with high singlet oxygen generation upon exposure to NIR light (~850 nm). Theoretical calculations showed that the protonation of the probe in an acidic environment decreased the molecular orbital energy gaps and increased the intramolecular charge transfer efficiency. I2-IR783-Mpip exhibited good photodynamic efficiency towards liver hepatocellular carcinoma cells under physiological and slightly acidic conditions while normal human embryonic kidney cells remained alive under the same conditions. Detection of intracellular reactive oxygen species (ROS) in cells treated with I2-IR783-Mpip after NIR light exposure confirmed PDT efficiency of the probe in acidic environment. Moreover, I2-IR783-Mpip also demonstrated efficient phototoxicity under deep-seated tumour cell system. We believed this is the first PDT agent that possesses intrinsic tumour binding and selectively eradicate tumour in acidic environment under 850 nm NIR lamp.

Photolytic mechanisms of hydroxylamine.

The photodissociation of small molecules has been extensively studied because of the increase in environmental problems related to the atmosphere of the Earth. In this work, the photodissociation mechanisms of hydroxylamine (NH2OH) as a model molecule in its lowest singlet-excited (S1) state were systematically studied using the complete active space second-order perturbation theory (CASPT2) and transition state theory (TST). In particular, this study focused on nonradiative relaxation processes that convert the S0 → S1 excited-state molecule to its products in their respective electronic ground states. The potential energy curves obtained from relaxed scans suggest that O-H dissociation is the preferred process in the S1 state. For the N-O and N-H dissociation pathways, thermally excited precursors were hypothesized to form in the S0 state to circumvent O-H dissociation. Thus, S0 → S1 vertical excitations lead to transition structures in the S1 state, which fragment to their respective electronic-ground-state products. The thermodynamic and kinetic results confirmed the precursor hypothesis, showing that the exothermic energy caused by the formation of HNO and H2 is sufficient to generate such precursors in the S0 state. Additionally, the TST confirmed that unimolecular isomerization-dissociation is a two-step process that generates products effectively by direct photolysis of the corresponding covalent bonds. In particular, the process consists of O-H bond dissociation, followed by spontaneous isomerization and formation of H2 in its electronic ground state, resulting in the high quantum yield observed in the UV absorption experiments in the preferential formation of HNO and H2. The configuration interaction coefficients of the characteristic structures on the potential energy curves revealed considerable changes in the multiconfigurational character of the wavefunctions, especially for the transition structures. These are characterized by the development of Rydberg orbitals, being produced at the intersection of the S0 and S1 states. The present study highlights the effects of thermal selectivity and the multiconfigurational character of the wavefunctions on photodissociation. Because detailed information on the photolytic mechanisms of isolated NH2OH is limited both theoretically and experimentally, these results provide fundamental insight into unimolecular photodissociation, posing ground for future studies on related systems.

Mechanisms of photoexcitation and photoionization in small water clusters.

The mechanisms of photoexcitation and photoionization in small water clusters in gas phase, (H2O) n ; n = 2-3, are studied using the complete active-space second-order perturbation theory (CASPT2) with the aug-cc-pVDZ basis set. The present study characterizes for the first time the structures and energetics of common transition and intermediate complexes in the photoexcitation and photoionization mechanisms in the lowest singlet-excited state. The ab initio results showed that the photoexcitation of the water monomer by a single photon can directly generate [OH]˙ and [H]˙ in their respective electronic-ground states, and a single photon with approximately the same energy can similarly lead to the photoexcitation and also to the photoionization in the water clusters. The S0 → S1 excitation leads to strong polarization of the O-H⋯O H-bond and to the formation of the water dimer radical cation transition state complex [(H2O)2]+˙, from which [OH]˙, [H]˙, and [H3O]+˙ can be generated. These products are obtained from [(H2O)2]+˙ by the direct dissociation of the O-H bond upon photoexcitation and by proton transfer and the formation of a metastable charge-separated Rydberg-like H-bond complex ([H3O]+˙⋯[OH]˙) upon photoionization. The proposed mechanisms suggest that in the gas phase, the photoexcitation and photoionization processes are most likely bimolecular reactions, in which all the transition and intermediate charged species are more stabilized than in a unimolecular reaction. The theoretical results provide insights into the photoexcitation and photoionization mechanisms of molecular clusters and can be used as guidelines for further theoretical and experimental studies.

The mechanism of excited state proton dissociation in microhydrated hydroxylamine clusters.

The dynamics and mechanism of excited-state proton dissociation and transfer in microhydrated hydroxylamine clusters are studied using NH2OH(H2O)n (n = 1-4) as model systems and the DFT/B3LYP/aug-cc-pVDZ and TD-DFT/B3LYP/aug-cc-pVDZ methods as model calculations. This investigation is based on the Förster acidity scheme and emphasizes the photoacid dissociation in the ground (S0) and lowest singlet-excited states (S1) and the interplay between the photo and thermal excitations. The quantum chemical results suggest that the intermediate complexes are formed only in the S1 state in a low local-dielectric environment (e.g., ε = 1) and that upon the S0→ S1 transition, the photon energy excites mostly NH2OH, which leads to a homolytic cleavage of the O-H bond and to dynamically stable charge-separated Rydberg-like H-bond complexes (e.g., NH2O˙-H3O(+)˙). The potential energy surfaces for proton displacement in the smallest Rydberg-like H-bond complex support the intersection of the S0 and S1 states in low local-dielectric environments, whereas in a high local-dielectric environment (e.g., ε = 78), these two states are completely separated. Based on the static results, a photoacid-dissociation mechanism that involves Rydberg-like H-bond complex formation, an H-bond chain extension and fluctuations in the local-dielectric environment is proposed. NVT-BOMD simulations confirm the static results and show that the dynamic behavior of the dissociating proton in the S1 state is not different from that of the protonated H-bond systems in the ground state, which consists of the oscillatory shuttling and structural diffusion motions. These findings allow our theoretical methods, which have been used successfully in protonated H-bond systems in the ground state, to be applied in the study of the photoacid-dissociation processes. The current theoretical study suggests effective steps as well as guidelines for the investigation of the dynamics of the photoacid-dissociation and transfer processes in the Förster acidity scheme, provided that the exciting photon does not lead to a significant change in the structure of the intermediate complex in the excited state.

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 CH(3)OH(2)(+)(CH(3)OH)(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 H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(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 CH(3)OH(2)(+)(CH(3)OH)(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 CH(3)OH 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 transfer reactions and dynamics of sulfonic acid group in Nafion®.

Proton transfer reactions and dynamics of the hydrophilic group (-SO(3)H) in Nafion® were studied at low hydration levels using the complexes formed from CF(3)SO(3)H, H(3)O(+) and nH(2)O, 1 ≤n≤ 3, as model systems. The equilibrium structures obtained from DFT calculations suggested at least two structural diffusion pathways at the -SO(3)H group namely, the "pass-through" and "pass-by" mechanisms. The former involves the protonation and deprotonation at the -SO(3)H group, whereas the latter the proton transfer in the adjacent Zundel complex. Analyses of the asymmetric O-H stretching frequencies (ν(OH)) of the hydrogen bond (H-bond) protons showed the threshold frequencies (ν(OH*)) of proton transfer in the range of 1700 to 2200 cm(-1). Born-Oppenheimer Molecular Dynamics (BOMD) simulations at 350 K anticipated slightly lower threshold frequencies (ν(A)(OH*,MD)), with two characteristic asymmetric O-H stretching frequencies being the spectral signatures of proton transfer in the H-bond complexes. The lower frequency (ν(A)(OH,MD))) is associated with the oscillatory shuttling motion and the higher frequency (ν(B)(OH,MD))) the structural diffusion motion. Comparison of the present results with BOMD simulations on protonated water clusters indicated that the -SO(3)H group facilitates proton transfer by reducing the vibrational energy for the interconversion between the two dynamic states (Δν), resulting in a higher population of the H-bonds with the structural diffusion motion. One could therefore conclude that the -SO(3)H groups in Nafion® act as active binding sites which provide appropriate structural, energetic and dynamic conditions for effective structural diffusion processes in a proton exchange membrane fuel cell (PEMFC). The present results suggested for the first time a possibility to discuss the tendency of proton transfer in H-bond using Δν(BA)(OH,MD)) and provided theoretical bases and guidelines for the investigations of proton transfer reactions in theory and experiment.

Proton transfer reactions and dynamics in protonated water clusters.

Proton transfer reactions and dynamics were theoretically studied using the hydrogen-bond (H-bond) complexes formed from H(3)O(+) and nH(2)O, n = 1-4, as model systems. The investigations began with searching for characteristics of transferring protons in the gas phase and continuum aqueous solution using DFT method at the B3LYP/TZVP level, followed by Born-Oppenheimer molecular dynamics (BOMD) simulations at 350 K. B3LYP/TZVP calculations revealed the threshold asymmetric O-H stretching frequencies (ν(OH)*) for the proton transfers in the Zundel complex (H(5)O) in the gas phase and continuum aqueous solution at 1984 and 1881 cm(-1), respectively. BOMD simulations suggested lower threshold frequencies (ν(OH,MD)* = 1917 and 1736 cm(-1), respectively), with two characteristic ν(OH,MD) being the IR spectral signatures of the transferring protons. The low-frequency band could be associated with the "oscillatory shuttling motion" and the high-frequency band with the "structural diffusion motion". These can be regarded as the spectroscopic evidences of the formations of the shared-proton structure (O···H(+)···O) and the H(3)O(+)-H(2)O contact structure (O-H(+)···O), respectively. Since the quasi-dynamic equilibrium between the Zundel and Eigen complexes was suggested to be the rate-determining step, in order to achieve an "ideal" maximum efficiency of proton transfer, a concerted reaction pathway should be taken. The most effective interconversion between the two proton states, the shared-proton structure and the H(3)O(+)-H(2)O contact structure, can be reflected from comparable intensities of the oscillatory shuttling and structural diffusion bands. The present results iterated the previous conclusions that static proton transfer potentials cannot provide complete description of the structural diffusion process and it is essential to incorporate thermal energy fluctuations and dynamics in the model calculations.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

Effects of metal ion and solute conformation change on hydration of small amino acid.

The effects of metal ion and solute conformation change on the structures, energetic and dynamics of water molecules in the first hydration shell of amino acid were studied, using three forms of alanine (Ala) and Li(+)/Ala as model molecules. The theoretical investigations were started with construction of the test-particle model (T-model) potentials for all molecules involved and followed by molecular dynamics (MD) simulations of [Ala](aq) and [Li(+)/Ala](aq) at 298 K. The MD results showed that the hydrogen bond (H-bond) networks of water at the functional groups of Ala are strengthened by the metal ion binding, whereas the rotation of the N-C(alpha) bond from the angle phi=0 degrees to 180 degrees brings about smaller effects which cannot be generalized. It was also shown that the dynamics of water molecule in the first hydration shell of amino acid could be estimated from the total-average potential energy landscapes and the water exchange diagrams. The MD results suggested inclusion of an additional dynamic step in the water exchange process, in which water molecule moves inside a channel within the first hydration shell of solute, before leaving the channel at some point. The theoretical results reported in the present work iterated the necessity to include explicit water molecules in the model calculations.

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 (H9O4+) 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 (H5O2+) 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 ion's 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.

Structures and stability of salt-bridge in aqueous solution.

Structures and stability of salt-bridges in aqueous solutions were investigated using a complex formed from the guanidinium (Gdm+) and formate (FmO-) ions as a model system. The Test-particle model (T-model) potentials to describe the interactions in the Gdm+-H2O, FmO(-)-H2O and Gdm+-FmO- complexes were constructed, tested and applied in molecular dynamics (MD) simulations of the aqueous solutions at 298 K. The three-dimensional structures and energetic of the hydrogen bond (H-bond) networks of water in the first hydration shells of the Gdm+ and FmO- ions, as well as the Gdm+-FmO- complex, were visualized and analyzed using various probability distribution (PD) maps. The structures of the average potential energy landscapes at the H-bond networks were employed to characterize the stability and dynamic behavior of water molecules in the first hydration shells of the solutes. It was observed that water molecules in the first hydration shell of the close-contact Gdm+-FmO- complex form associated H-bond networks, which introduce a net stabilization effect to the ion-pair, whereas those in the interstitial H-bond network destabilize and break the solvent-separated Gdm+-FmO- complex. The present results showed that, in order to provide complete insights into the structures and stability of ion-pairs in aqueous solutions, explicit water molecules have to be included in the model calculations.