Direct Ab Initio Molecular Dynamics Research Articles

Effects of Residual Water on Proton Transfer-Switching Molecular Device

The excited state proton transfer (ESPT) reaction plays a crucial role in DNA defense and ON-OFF proton-switching molecular devices. o-Hydroxybenzaldehyde (OHBA) is the simplest model-molecule for the ESPT reactions where a proton is transferred from OH to C=O carbonyl groups by photo-excitation. In the present study, the reaction mechanism of ESPT in OHBA was investigated by means of the direct ab initio molecular dynamics (AIMD) method. The triplet (T1) state of OHBA, OHBA(T1), was considered as the excited state of OHBA. The dynamic calculations showed that fast PT occurred from OH to C=O carbonyl groups at the T1 state. The time of PT was calculated to be 34–57 fs in OHBA(T1). The spin density was mainly distributed on the benzene ring (Bz) at time zero. The density was gradually transferred from Bz to C=O as a function of time on the T1 surface. When the spin density on C=O was larger than that on Bz (at time = 35–43 fs), the proton of OH was rapidly transferred to C=O. The localization of spin density on C=O dominated strongly the PT rate. Next, the effects of residual water (H2O) on the PT rate were investigated using OHBA-H2O 1:1-complexes to elucidate the effects of H2O on the PT rate in the ON-OFF proton-switching molecular devices. The PT rates were strongly dependent on the position of H2O around OHBA. The reaction mechanism is discussed based on theoretical results.

Simulation of lithium hydroxide decomposition using deep potential molecular dynamics.

Chemical reactions and vapor-liquid equilibria for molten lithium hydroxide (LiOH) were studied using molecular dynamics simulations and a deep potential (DP) model. The neural network for the model was trained on quantum density functional theory data for a range of conditions. The DP model allows simulations over timescales of hundreds of ns, which provide equilibrium compositions for the systems of interest. Single-phase NPT simulations of the liquid show the decomposition of LiOH into lithium oxide (Li2O) and dissolved water (H2O). These DP results were validated by direct abinitio molecular dynamics simulations that confirmed the accuracy of the model with respect to reaction kinetics and equilibrium properties of the melt. The reactive vapor-liquid behavior of this system was subsequently studied using direct coexistence interfacial DP simulations. Partial pressures of H2O in the vapor are found to be in close agreement with available experimental measurements. By fitting temperature-dependent expressions for the reaction equilibrium and Henry's law constants, the equilibrium composition for any given initial composition and temperature can be quantitatively modeled. For high initial concentrations of Li2O or H2O, mixtures of LiOH + Li2O/H2O are found to undergo phase separation. The present study illustrates how DP-based molecular dynamics simulations can be used for quantitative modeling of multiphase reactive behavior with the accuracy of the underlying abinitio quantum chemical methods.

Intracluster reaction dynamics of NO+(H2O)n.

Nitric oxide (NO) and NO-water clusters play crucial roles in the D-region of the atmosphere because it is postulated that NO+ reacts with H2O to produce nitrous acid (HONO) and H3O+. HONO is the major precursor of the hydroxyl radicals leading to the formation of secondary pollutants. The sources of atmospheric HONO, however, are not fully understood. Previously, the sequential H2O addition reaction, H2O + NO+(H2O)n, and the bi-molecular collision reaction, NO+ + (H2O)n, have been investigated by both experiments and theoretical calculations to determine the formation mechanism of HONO. However, the photo-reactions from NO(H2O)n neutral clusters were not considered for the formation mechanism of HONO. In this study, the intra-cluster reactions of NO+(H2O)n clusters, following ionization of the parent neutral cluster of NO(H2O)n, were investigated using the direct abinitio molecular dynamics method. When n = 4, [NO+(H2O)4]ver [vertical ionization state of NO(H2O)n] yielded HONO and hydrated H3O+ after the intra-cluster reaction, and the reaction time was calculated to be 150fs. The reaction is expressed as [NO+(H2O)n]ver → HONO + H3O+(H2O)n-2 (reactive) (n > 3). Larger clusters of [NO+(H2O)n]ver (n = 5-8) also yield HONO. In contrast, in smaller clusters (n = 1-3), only solvent re-orientation around NO+ occurred after the ionization: [NO+(H2O)n]ver → NO+(H2O)n (solvent re-orientation) (n = 1-3). The hydration energy of H3O+, which depends on the cluster size (n), plays an important role in promoting the formation of HONO. The reaction mechanism is discussed based on theoretical results.

Mechanism of ionic dissociation of HCl in the smallest water clusters.

The dissociation of strong acids into water is a fundamental process in chemistry and biology. Determining the minimum number of water molecules that can result in an ionic dissociation of hydrochloric acid (HCl → H+ + Cl-) remains a challenging subject. In this study, the reactions of H2O with HCl(H2O)n-1 (HCl-H2O cluster), i.e., HCl(H2O)n-1 + H2O (n = 3-7), were investigated by using the direct ab initio molecular dynamics (AIMD) method. Direct AIMD calculations were performed to set the collision energy of H2O to zero for all trajectories. For n = 3, no reaction occurred. In contrast, HCl dissociated to H+ + Cl- at n = 4, forming a contact ion pair (cIP) and solvent-separated ion pair (ssIP) as products. The reactions were expressed as HCl(H2O)3 + H2O → H3O+(H2O)2Cl- (ssIP), and HCl(H2O)3 + H2O → H3O+(Cl-)(H2O)2 (cIP). The ion pair (IP) products were dependent on the collision site of H2O relative to HCl(H2O)3. For n = 5-7, both IPs were formed through the reaction between H2O and HCl(H2O)n-1 (n = 5-7). The reaction between HCl and (H2O)4 (HCl + (H2O)4 → HCl(H2O)4) was non-reactive in IP formation. The reaction mechanism was discussed based on the theoretical results.

Unpolarized laser method for infrared spectrum calculation of amide I C[dbnd]O bonds in proteins using molecular dynamics simulation

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

C-C Bond Formation Reaction Catalyzed by a Lithium Atom: Benzene-to-Biphenyl Coupling.

Transition-metal-catalyzed carbon-carbon (C-C) bond formation is an important reaction in pharmaceutical and organic chemistry. However, the reaction process is composed of multiple steps and is expensive owing to the presence of transition metals. This study proposes a lithium-catalyzed C-C coupling reaction of two benzene molecules (Bz) to form a biphenyl molecule, which is a transition-metal-free reaction, based on ab initio and direct ab initio molecular dynamics (AIMD) calculations. The static ab initio calculations indicate that the reaction of two Bz molecules with Li- ions (reactant state, RC) can form a stable sandwiched complex (precomplex), where the Li- ion is sandwiched by two Bz molecules. The complex formation reaction can be expressed as 2Bz + Li - → Bz(Li -)Bz, where the C-C distance between the Bz rings is 2.449 Å. This complex moves to the transition state (TS) via the structural deformation of Bz(Li-)Bz, where the C-C distance is shortened to 2.118 Å. The barrier height was calculated to be -9.9 kcal/mol (relative to RC) at the MP2/6-311++G(d,p) level. After TS, the C(sp3)-C(sp3) single bond was completely formed between the Bz rings (the C-C bond distance was 1.635 Å) (late complex). After the dissociation of H2 from the late complex, a biphenyl molecule was formed: the C(sp2)-C(sp2) bond. The calculations suggest that the C-C bond coupling of Bz occurred spontaneously from 2Bz + Li-, and biphenyl molecules were directly formed without an activation barrier. Direct AIMD calculations show that the C-C coupling reaction also takes place under electron attachment to Li(Bz)2: Li(Bz)2 + e- → [Li-(Bz)2]ver → precomplex → TS → late complex, where [Li-(Bz)2]ver is the vertical electron capture species of Li(Bz)2. Namely, the C-C coupling reaction spontaneously occurred in Li(Bz)2 owing to electron attachment. Similar C-C coupling reactions were also observed for halogen-substituted benzene molecules (Bz-X, X = F and Cl). Furthermore, this study discusses the mechanism of C-C bond formation in electron capture based on the theoretical results.

Formation Mechanism of Odd- and Even-Numbered Hydrogen Cluster Cations Using the Direct Ab Initio Molecular Dynamics Approach.

The photoreaction of hydrogen clusters caused by cosmic-ray irradiations plays a crucial role in interstellar molecular clouds because the reaction of molecules takes place in these surrounding clusters. Previous gas-phase experiments introduced the reaction products after the ionization of the neutral hydrogen cluster. In the experiments, the odd-numbered hydrogen cluster cation, H+(H2)m, was the main product, while the even-numbered cluster cation, (H2)n+, was the minor product. However, the formation yield of (H2)n+ was significantly low. Despite many theoretical calculations and experiments, the formation mechanism of odd- and even-numbered cluster ions from ionized hydrogen clusters is still unclear. In this study, the direct ab initio molecular dynamics (AIMD) method was applied to the reaction of the hydrogen cluster cation (H2)n+ to understand the abovementioned formation mechanism. The trajectories of (H2)n+ following the vertical ionization of the neutral cluster were calculated. Direct AIMD calculations indicated that odd-numbered cluster cations, H3+(H2)n-2 + H (dissociation), were formed directly as the main product after the ionization of (H2)n. An even-numbered cluster, (H2)n+, was temporally formed when an H-shaped complex composed of three H2 molecules existed within a neutral cluster. However, it was rapidly dissociated to an odd-numbered cluster. Static ab initio calculations suggested that the odd-numbered cluster complex, H3+(H2)n-2-H, could be transferred to even-numbered ions via a transition state with a low energy barrier. The even-numbered cluster cation was formed stepwise from the odd-numbered cluster cation. The formation mechanism of odd- and even-numbered cluster cations is discussed based on these results.

Intracluster Reaction Dynamics of Ionized Micro-Hydrated Hydrogen Peroxide (H2O2): A Direct Ab Initio Molecular Dynamics Study

Hydrogen peroxide (H2O2) is a unique molecule that is applied in various fields, including energy chemistry, astrophysics, and medicine. H2O2 readily forms clusters with water molecules. In the present study, the reactions of ionized H2O2–water clusters, H2O2+(H2O)n, after vertical ionization of the parent neutral cluster were investigated using the direct ab initio molecular dynamics (AIMD) method to elucidate the reaction mechanism. Clusters with one to five water molecules, H2O2–(H2O)n (n = 1–5), were examined, and the reaction of [H2O2+(H2O)n]ver was tracked from the vertical ionization point to the product state, where [H2O2+(H2O)n]ver is the vertical ionization state (hole is localized on H2O2). After ionization, fast proton transfer (PT) from H2O2+ to the water cluster (H2O)n was observed in all clusters. The HOO radical and H3O+(H2O)n−1 were formed as products. The PT reaction proceeds directly without an activation barrier. The PT times for n = 1–5 were calculated to be 36.0, 9.8, 8.3, 7.7, and 7.1 fs, respectively, at the MP2/6-311++G(d,p) level, indicating that PT in these clusters is a very fast process, and the PT time is not dependent on the cluster size (n), except in the case of n = 1, where the PT time was slightly longer because the bond distance and angle of the hydrogen bond in n = 1 were deformed from the standard structure. The reaction mechanism was discussed based on these results.

Understanding Hydrogenation Chemistry at MgB2 Reactive Edges from Ab Initio Molecular Dynamics.

Solid-state hydrogen storage materials often operate via transient, multistep chemical reactions at complex interfaces that are difficult to capture. Here, we use direct ab initio molecular dynamics simulations at accelerated temperatures and hydrogen pressures to probe the hydrogenation chemistry of the candidate material MgB2 without a priori assumption of reaction pathways. Focusing on highly reactive (101̅0) edge planes where initial hydrogen attack is likely to occur, we track mechanistic steps toward the formation of hydrogen-saturated BH4- units and key chemical intermediates, involving H2 dissociation, generation of functionalities and molecular complexes containing BH2 and BH3 motifs, and B-B bond breaking. The genesis of higher-order boron clustering is also observed. Different charge states and chemical environments at the B-rich and Mg-rich edge planes are found to produce different chemical pathways and preferred speciation, with implications for overall hydrogenation kinetics. The reaction processes rely on B-H bond polarization and fluctuations between ionic and covalent character, which are critically enabled by the presence of Mg2+ cations in the nearby interphase region. Our results provide guidance for devising kinetic improvement strategies for MgB2-based hydrogen storage materials, while also providing a template for exploring chemical pathways in other solid-state energy storage reactions.

Reaction mechanism of an intracluster SN2 reaction induced by electron capture.

Bimolecular nucleophilic substitution (SN2) reactions have been widely investigated from both experimental and theoretical points of view because they represent one of the simplest organic reactions. Most studies on SN2 reactions have been focused on bimolecular collision. In contrast, information on intracluster SN2 reactions is limited. In this study, an intracluster SN2 reaction of NF3-CH3Cl triggered by electron attachment was investigated using a direct ab initio molecular dynamics (AIMD) method. In the structure of NF3-CH3Cl, the N-F bond in NF3 is oriented collinearly toward the carbon atom of CH3Cl. After electron capture by NF3-CH3Cl, the F- ion that is generated from the (NF3)- moiety collides with the carbon atom of CH3Cl. The intracluster SN2 reaction occurs as follows: (NF3-CH3Cl)- (electron capture state) → NF2-(F-)-CH3Cl (pre-reaction complex) → transition state (TS) → NF2-CH3F-Cl- (post-reaction complex) → NF2 + CH3F + Cl- (product state). The reaction energy is efficiently transferred to the translational mode of Cl-, and the Cl- ion with a high translational energy is then removed from the system. This energy is significantly larger than that of Cl- formed in the bimolecular SN2 reaction (F- + CH3Cl). The reaction mechanism is discussed based on the theoretical results.

Reaction Dynamics of NO+ with Water Clusters.

The reaction of NO+ with water molecules plays a crucial role in the D-region of the atmosphere because the reaction provides nitrous acid (HONO) and protonated water species (H3O+). In this study, the reaction of NO+ with water clusters, NO+ + (H2O)n (n = 1-7), was investigated by means of the direct ab initio molecular dynamics method to elucidate the reaction mechanism of NO+ in the atmosphere from a theoretical viewpoint. At n = 1 and 2, the reaction of NO+ with (H2O)n led to the formation of a complex: NO+ + (H2O)n → NO+(H2O)n (n = 1 and 2). At n = 3, the formation channel of HONO was open, and HONO was formed according to NO+ + (H2O)n → HONO---H+(H2O)n-1 (n = 3), through which H3O+ was also formed as H+(H2O)2. However, the HONO formation efficiency was significantly low for n = 3. In large clusters with n = 4-7, the HONO formation channel became the main channel, and the dissociation of HONO from the HONO--H+(H2O)n-1 complex occurred in part: NO+ + (H2O)n → HONO---H+(H2O)n-1 → HONO + H+(H2O)n-1. The energetics and reaction mechanism were discussed on the basis of theoretical results.

Direct ab initio molecular dynamics study on the reactions of multi-valence ionized states of water dimer

We investigated the reaction of multi-valence (+2) ionization states of water dimer (H2O)2 using direct ab initio molecular dynamics method. The following multi-valence ionization states were considered. In the direct two-electron ionization state, (H2O)2 was ionized to form (H2O)2 2+ in one step; in the stepwise two-electron ionization state, (H2O)2 was first converted to (H2O)2 + and further ionized after structural relaxation. The (H2O)2 2+ from direct ionization dissociated into two H2O+ ions, while (H2O)2 2+ in stepwise ionization generated H3O+ and OH+ ions from H3O+–OH radical-ion pairs. Additionally, we performed dynamics calculations for the excited state of (H2O)2 2+ generated through direct ionization. The excited (H2O)2 2+ ions also dissociated to form H3O+ and OH+ ions. The reaction mechanism of multi-valence ionization states of (H2O)2 is discussed on the basis of calculation results.

Reactions of Photoionization-Induced CO-H2O Cluster: Direct Ab Initio Molecular Dynamics Study.

The hydrocarboxyl radical (HOCO) is an important species in combustion and astrochemistry because it is easily converted to CO2 after hydrogen reduction. In this study, the formation mechanism of the HOCO radical in a CO–H2O system was investigated by direct ab initio molecular dynamics calculations. Two reactions were examined for HOCO formation. First, the reaction dynamics of the CO–H2O cluster cation, following the ionization of the neutral parent cluster CO(H2O)n (n = 1–4), were investigated. Second, the bimolecular collision reaction between CO and (H2O)n+ was studied. In the ionization of the CO(H2O)n clusters (n = 3 and 4), proton transfer, expressed as CO(H2O)n+ → CO–(OH)H3O+(H2O)n–2, occurred within the (H2O)n+ cluster cation, and the HOCO radical was yielded as a product upon addition of CO and OH. This reaction proceeds under zero-point energy. Also, this radical was effectively formed from the collision reaction of CO with water cluster cation (H2O)n+, expressed as CO + OH(H3O+)(H2O)n–2 → HOCO–H3O+ + (H2O)n–2. If the intermolecular vibrational stretching mode is excited in the CO(H2O)n cluster (vibrational stretching between CO and the water cluster), the HOCO radical was detected after ionization when n = 2. The reaction mechanism was discussed based on the theoretical results.

Formation of Hydrogen Peroxide from O-(H2O)n Clusters.

Hydrogen peroxide (H2O2) has recently received much attention as a safe and clean energy carrier for hydrogen molecules. In this study, based on direct ab initio molecular dynamics (AIMD) calculations, we demonstrated that H2O2 is directly formed via the photoelectron detachment of O-(H2O)n (n = 1-6) (water clusters of an oxygen radical anion). Three electronic states of oxygen atoms were examined in the calculations: O(X)(H2O)n (X = 3P, 1D, and 1S states). After the photoelectron detachment of O-(H2O)n (n = 1) to the 1S state, a complex comprising O(1S) and H2O, O(1S)-OH2, was formed. A hydrogen atom of H2O immediately transferred to O(1S) during an intracluster reaction to form H2O2 as the final product. Simulations were run to obtain a total of 33 trajectories for n = 1 that all led to the formation of H2O2. The average reaction time of H2O2 formation was calculated to be 57.7 fs in the case of n = 1, indicating that the reaction was completed within 100 fs of electron detachment. All the reaction systems O(1S)(H2O)n (n = 1-6) indicated the formation of H2O2 by the same mechanism. The reaction times for n = 2-6 were calculated to range between 80 and 180 fs, indicating that the reaction for n = 1 is faster than that of the larger clusters, that is, the larger the cluster size, the slower the reaction is. The reaction dynamics of the triplet O(3P) and singlet O(1D) potential energy surfaces were calculated for comparison. All calculations yielded the dissociation product O(X)(H2O)n → O(X) + (H2O)n (X = 3P and 1D), indicating that the O(1S) state contributes to the formation of H2O2. The reaction mechanism was discussed based on the theoretical results.

Barrierless HONO and HOS(O)2-NO2 Formation via NH3-Promoted Oxidation of SO2 by NO2.

In the troposphere, the knowledge about nitrous acid (HONO) sources is incomplete. The missing source of sulfate and fine particles cannot be explained during haze events. Air quality models cannot predict high levels of secondary fine-particle pollution. Despite extensive studies, one challenging issue in atmospheric chemistry is identifying the source of HONO. Here, we present direct ab initio molecular dynamics simulation evidence and typical air pollution events of the formation of gaseous HONO, nitrogen dioxide/hydrogen sulfite (HOS(O)2-NO2 or NO2-HSO3) from nitrogen dioxide (NO2), sulfur dioxide (SO2), water (H2O), and ammonia (NH3) molecules in a proportion of 2:1:3:3. The reactions show a new mechanism for the formation of HONO and NO2-HSO3 in the troposphere, especially when the concentration of NO2, SO2, H2O, and NH3 is high (e.g., 2:1:3:3 or higher) in the air. Contrary to the proportion NO2, SO2, H2O, and NH3 equaling to 1:1:3:1 and 1:1:3:2, the proportion (2:1:3:3) enables barrierless reactions and weak interactions between molecules via the formation of HONO, NO2-HSO3, and NH3/H2O. In addition, field observations are carried out, and the measured data are summarized. Correlation analysis supported the conversion of NO2 to HONO during observational studies. The weak interactions promote proton transfer, resulting in the generation of HONO, NO2-HSO3, and NH3/H2O pairs.

Molecular Design of a Reversible Hydrogen Storage Device Composed of the Graphene Nanoflake-Magnesium-H2 System.

Carbon materials such as graphene nanoflakes (GRs), carbon nanotubes, and fullerene can be widely used for hydrogen storage. In general, metal doping of these materials leads to an increase in their H2 storage density. In the present study, the binding energies of H2 to Mg species on GRs, GR–Mgm+ (m = 0–2), were calculated using density functional theory calculations. Mg has a wide range of atomic charges. In the case of GR–Mg (m = 0, Mg atom), the binding energy of one H2 molecule is close to 0, whereas those for m = 1 (Mg+) and 2 (Mg2+) are 0.23 and 13.2 kcal/mol (n = 1), respectively. These features suggest that GR–Mg2+ has a strong binding affinity toward H2, whereas GR–Mg+ has a weak binding energy. In addition, it was found that the first coordination shell is saturated by four H2 molecules, GR–Mg2+–(H2)n (n = 4). Next, direct ab initio molecular dynamics calculations were carried out for the electron-capture process of GR–Mg2+–(H2)n and a hole-capture process of GR–Mg+–(H2)n (n = 4). After electron capture, the H2 molecules left and dissociated from GR–Mg+: GR–Mg2+–(H2)n + e– → GR–Mg+ + (H2)n (H2 is released into the gas phase). In contrast, the H2 molecules were bound again to GR–Mg2+ after the hole capture of GR–Mg+: GR–Mg+ + (H2)n (gas phase) + hole → GR–Mg2+–(H2)n. On the basis of these calculations, a model device with reversible H2 adsorption–desorption properties was designed. These results strongly suggest that the GR–Mg system is capable of H2 adsorption–desorption reversible storage.

Extraordinary negative thermal expansion of two-dimensional nitrides: A comparative ab initio study of quasiharmonic approximation and molecular dynamics simulations

Thermal expansion behavior of two-dimensional (2D) nitrides and graphene were studied by ab initio molecular dynamics (MD) simulations as well as quasiharmonic approximation (QHA). Anharmonicity of the acoustic phonon modes are related to the unusual negative thermal expansion (NTE) behavior of the nitrides. Our results also hint that direct ab initio MD simulations are a more elaborate method to investigate thermal expansion behavior of 2D materials than the QHA. Nevertheless, giant NTE coefficients are found for $h$-GaN and $h$-AlN within the covered temperature range 100--600 K regardless of the chosen computational method. This unusual NTE of 2D nitrides is reasoned with the out-of-plane oscillations related to the rippling behavior of the monolayers.

Hydration effects on proton transfer reactions in the catalytic triad Ser-His-Glu

Abstract An in-depth understanding of irradiation effects on DNA and enzymes is important in elucidating the effect of radiation exposure on humans and animals. The catalytic triad Ser-His-Glu is composed of amino acids serine (Ser), histidine (His), and glutamic acid (Glu). In the present study, the radiation effects on Ser-His-Glu have been investigated theoretically using ab initio and direct ab initio molecular dynamics (AIMD) methods. In addition, the effects of micro-solvation in Ser-His-Glu were studied, because X-ray diffraction experiments revealed that one water molecule is located near Ser-His-Glu. Based on geometry optimizations, it was determined that the presence of the H2O molecule results in two structures: a structure wherein the H2O molecule is added to the Glu position of Ser-His-Glu (H2O(A)), and the one wherein the molecule is bonded to the Ser position (H2O(B)). The reaction dynamics after hole-capture were calculated for three structures including the unhydrated structure of Ser-His-Glu (no-H2O). For these structures, the proton transfer (PT) from His to Glu occurred after hole-capture. The PT rate of the no-H2O and the H2O(B) was within 10 fs, whereas that of the H2O(A) was 15 fs. This is indicative of the effect of micro-solvation on the PT time in Ser-His-Glu. The reaction mechanism was discussed based on the theoretical results.

Hydrogen Dissociation Dynamics from Water Clusters on Triplet-State Energy Surfaces.

The ice surface provides two-dimensional reaction fields for bimolecular collisions in interstellar space. As H2O molecules on the surface are typically exposed to cosmic rays, H2O in the excited state is easily dissociated into H + OH, where a H atom is released from the surface to the gas phase. In the present study, the reaction dynamics of small-sized water clusters on the triplet-state potential energy (T1) surface, following the vertical electronic excitation from the ground state (S0), were investigated using direct ab initio molecular dynamics to provide insights into the generation mechanism of H atoms from an irradiated ice surface. In all clusters, that is, (H2O)n (n = 2-6), the H atom was directly dissociated from one of the H2O molecules in the clusters (direct dissociation), whereas the OH radical remained in the cluster. In the branched form of H2O tetramer (n = 4) and the book form of H2O hexamer (n = 6), the dissociated hydrogen atom (H') collided with the neighboring H2O molecule, and the exchange of H atoms occurred as H' + H2O → H'-H2O (collision) → H'OH + H (hydrogen exchange). The translational energy of the exchanged H atom decreases significantly (by approximately 50%) because the kinetic energy of the H' atom is efficiently transferred to the vibrational modes of the cluster during the H-exchange reaction. The mechanism of H atom dissociation is discussed based on theoretical results.

Proton Transfer Reaction Rates in Phenol-Ammonia Cluster Cation.

Proton transfer (PT) in an interaction system of a hydroxyl-amino group (OH-NH) plays a crucial role in photoinduced DNA and enzyme damage. A phenol-ammonia cluster is a prototype of an OH-NH interaction and is sometimes used as a DNA model. In the present study, the reaction dynamics of phenol-ammonia cluster cations, [PhOH-(NH3)n]+ (n = 1-5), following ionization of the neutral parent clusters, were investigated using a direct ab initio molecular dynamics (AIMD) method. In all clusters, PTs from PhOH+ to (NH3)n were found postionization, the reaction of which is expressed as PhOH+-(NH3)n → PhO-H+(NH3)n. The time of the PT was calculated as 43 (n = 1), 26 (n = 2), and 13 fs (n = 3-5), suggesting that the rate of PT increases with an increase in n and is saturated at n = 3-5. The difference in the PT rate originates strongly from the proton affinity of the (NH3)n cluster. In the case of n = 3-5, a second PT was found, the reaction of which is expressed as PhO-H+(NH3)n → PhO-NH3-H+(NH3)n-1, and a third PT occurred at n = 4 and 5. The time of the PT was calculated as 10-13 (first PT), 80-100 (second PT), and 150-200 fs (third PT) in the case of larger clusters (n = 4 and 5). The reaction mechanism based on the theoretical results is discussed herein.