Molecular Tuning of Reactivity of Zeolite Protons in HZSM-5.

In acidic HZSM-5 zeolite, the reactivity of a methanol molecule interacting with the zeolite proton is amenable to modification via coadsorbing a stochiometric amount of an electron density donor E to form the [(E)(CH3OH)(HZ)] complex. The rate of the methanol in this complex undergoing dehydration to dimethyl ether was determined for a series of E with proton affinity (PA) ranging from 659 kJ mol-1 for C6F6 to 825 kJ mol-1 for C4H8O and was found to follow the expression: Ln(Rate) - Ln(RateN2) = ß(PA - PAN2)γ, where E = N2 is the reference and ß and γ are constants. This trend is probably due to the increased stability of the solvated proton in the [(E)(CH3OH)(HZ)] complex with increasing PA. Importantly, this is also observed in steady-state flow reactions when stoichiometric quantities of E are preadsorbed on the zeolite. As demonstrated with E being D2O, the effect on methanol reactivity diminishes when E is present in excess of the [(E)(CH3OH)(HZ)] complex. It is proposed that the methanol dehydration reaction involves [(E)(CH3OH)(CH3OH)(HZ)] as the transition state, which is supported by the isotopologue distribution of the initial dimethyl ether formed when a flow of CH3OH was passed over ZSM-5 containing one CD3OH per zeolite proton. The implication of this on the mechanism of catalytic methanol dehydration on HZSM-5 is discussed.

Photoisomerization mechanism of iminoguanidinium receptors from spectroscopic methods and quantum chemical calculations.

The hydrazone functional group, when coupled with a pyridyl substituent, offers a unique class of widely tunable photoswitches, whose E-to-Z photoisomerization equilibria can be controlled through intramolecular hydrogen bonding between the N-H hydrazone donor and the pyridyl acceptor. However, little is known about the photoisomerization mechanism in this class of compounds. To address this issue, we report a pyridine-appended iminoguanidinium photoswitch that is functionally related to acylhydrazones and provides insight into the photoisomerization processes between the E and Z configurations. The E-to-Z photoisomerization of the E-2-pyridyl-iminoguanidinium cation (2PyMIG) in DMSO, prepared as the bromide salt, was quantified by 1H NMR, and probed in real time with ultrafast laser spectroscopy. The photoisomerization process occurs on a picosecond timescale, resulting in low fluorescence yields. The multiconfigurational reaction path found with the growing string method features a small barrier (4.3 or 6.5 kcal mol-1) that the E isomer in the π-π* state must overcome to reach the minimum energy conical intersection (MECI) connecting the E and Z isomers of 2PyMIG. While two possible pathways exist depending on the orientation of the pyridine ring, both exhibit the same qualitative features along the path and at their MECIs, involving simultaneous changes in the CCNN and CNNC dihedral angles. Furthermore, the ground state barrier for pyridine ring rotation is readily accessible, thus a low barrier pathway to the experimentally observed Z isomer exists for both MECIs leading to a transition from the E isomer to photoproduct. Combining multiconfigurational reaction path calculations using growing string method with time-resolved fluorescence spectroscopy provided crucial insights into the photoisomerization process of 2PyMIG, resulting in both the computational and experimental results pointing to rapid photoisomerization via a surface crossing between the singlet π-π* and the ground states.

Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport.

The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water-and often the water molecules themselves-to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.

Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites.

A molecular description of the structure and behavior of water confined in aluminosilicate zeolite pores is a crucial component for understanding zeolite acid chemistry under hydrous conditions. In this study, we use a combination of ultrafast two-dimensional infrared (2D IR) spectroscopy and ab initio molecular dynamics (AIMD) to study H2O confined in the pores of highly hydrated zeolite HZSM-5 (∼13 and ∼6 equivalents of H2O per Al atom). The 2D IR spectrum reveals correlations between the vibrations of both terminal and H-bonded O-H groups and the continuum absorption of the excess proton. These data are used to characterize the hydrogen-bonding network within the cluster by quantifying single-, double-, and non-hydrogen-bond donor water molecules. These results are found to be in good agreement with the statistics calculated from an AIMD simulation of an H+(H2O)8 cluster in HZSM-5. Furthermore, IR spectral assignments to local O-H environments are validated with DFT calculations on clusters drawn from AIMD simulations. The simulations reveal that the excess charge is detached from the zeolite and resides near the more highly coordinated water molecules in the cluster. When they are taken together, these results unambiguously assign the complex IR spectrum of highly hydrated HZSM-5, providing quantitative information on the molecular environments and hydrogen-bonding topology of protonated water clusters under extreme confinement.

Differential Condensation of Methane Isotopologues Leading to Isotopic Enrichment under Non-equilibrium Gas-Surface Collision Conditions.

We examine the initial differential sticking probability of CH4 and CD4 on CH4 and CD4 ices under nonequilibrium flow conditions using a combination of experimental methods and numerical simulations. The experimental methods include time-resolved in situ reflection-absorption infrared spectroscopy (RAIRS) for monitoring on-surface gaseous condensation and complementary King and Wells mass spectrometry techniques for monitoring sticking probabilities that provide confirmatory results via a second independent measurement method. Seeded supersonic beams are employed so that the entrained CH4 and CD4 have the same incident velocity but different kinetic energies and momenta. We found that as the incident velocity of CH4 and CD4 increases, the sticking probabilities for both molecules on a CH4 condensed film decrease systematically, but that preferential sticking and condensation occur for CD4. These observations differ when condensed CD4 is used as the target interface, indicating that the film's phonon and rovibrational densities of states, and collisional energy transfer cross sections, have a role in differential energy accommodation between isotopically substituted incident species. Lastly, we employed a mixed incident supersonic beam composed of both CH4 and CD4 in a 3:1 ratio and measured the condensate composition as well as the sticking probability. When doing so, we see the same effect in the condensed mixed film, supporting an isotopic enrichment of the heavier isotope. We propose that enhanced multi-phonon interactions and inelastic cross sections between the incident CD4 projectile and the CH4 film allow for more efficacious gas-surface energy transfer. VENUS code MD simulations show the same sticking probability differences between isotopologues as observed in the gas-surface scattering experiments. Ongoing analyses of these trajectories will provide additional insights into energy and momentum transfer between the incident species and the interface. These results offer a new route for isotope enrichment via preferential condensation of heavier isotopes and isotopologues during gas-surface collisions under specifically selected substrate, gas-mixture, and incident velocity conditions. They also yield valuable insights into gaseous condensation under non-equilibrium conditions such as occur in aircraft flight in low-temperature environments. Moreover, these results can help to explain the increased abundance of deuterium in solar system planets and can be incorporated into astrophysical models of interstellar icy dust grain surface processes.

Time-Dependent Perspective for the Intramolecular Couplings of the N-H Stretches of Protonated Tryptophan.

Quasi-classical direct dynamics simulations, performed with the B3LYP-D3/cc-pVDZ electronic structure theory, are reported for vibrational relaxation of the three NH stretches of the -NH3+ group of protonated tryptophan (TrpH+), excited to the n = 1 local mode states. The intramolecular vibrational energy relaxation (IVR) rates determined for these states, from the simulations, are in good agreement with the experiment. In accordance with the experiment, IVR for the free NH stretch is slowest, with faster IVR for the remaining two NH stretches which have intermolecular couplings with an O atom and a benzenoid ring. For the free NH and the NH coupled to the benzenoid ring, there are beats (i.e., recurrences) in their relaxations versus time. For the free NH stretch, 50% of the population remained in n = 1 when the trajectories were terminated at 0.4 ps. IVR for the free NH stretch is substantially slower than for the CH stretch in benzene. The agreement found in this study between quasi-classical direct dynamics simulations and experiments indicates the possible applicability of this simulation method to larger biological molecules. Because IVR can drive or inhibit reactions, calculations of IVR time scales are of interest, for example, in unimolecular reactions, mode-specific chemistry, and many photochemical processes.

Addressing an instability in unrestricted density functional theory direct dynamics simulations.

In Density Functional Theory (DFT) direct dynamics simulations with Unrestricted Hartree Fock (UHF) theory, triplet instability often emerges when numerically integrating a classical trajectory. A broken symmetry initial guess for the wave function is often used to obtain the unrestricted DFT potential energy surface (PES), but this is found to be often insufficient for direct dynamics simulations. An algorithm is described for obtaining smooth transitions between the open-shell and the closed-shell regions of the unrestricted PES, and thus stable trajectories, for direct dynamics simulations of dioxetane and its •OCH2 -CH2 O• singlet diradical. © 2018 Wiley Periodicals, Inc.

Pronounced changes in atomistic mechanisms for the Cl- + CH3I SN2 reaction with increasing collision energy.

In a previous direct dynamics simulation of the Cl- + CH3I → ClCH3 + I- SN2 reaction, predominantly indirect and direct reaction was found at collision energies Erel of 0.20 and 0.39 eV, respectively. For the work presented here, these simulations were extended by studying the reaction dynamics from Erel of 0.15 to 0.40 eV in 0.05 eV intervals. A transition from a predominantly indirect to direct reaction is found for Erel of 0.27-0.28 eV, a finding consistent with experiment. The simulation results corroborate the understanding that in experiments indirect reaction is characterized by small product translational energies and isotropic scattering, while direct reaction has higher translational energies and anisotropic scattering. The traditional statistical theoretical model for the Cl- + CH3I SN2 reaction assumes the Cl--CH3I pre-reaction complex (A) is formed, followed by barrier crossing, and then formation of the ClCH3-I- post-reaction complex (B). This mechanism is seen in the dynamics, but the complete atomistic dynamics are much more complex. Atomistic SN2 mechanisms contain A and B, but other dynamical events consisting of barrier recrossing (br) and the roundabout (Ra), in which the CH3-moiety rotates around the heavy I-atom, are also observed. The two most important mechanisms are only formation of A and Ra + A. The simulation results are compared with simulations and experiments for Cl- + CH3Cl, Cl- + CH3Br, F- + CH3I, and OH- + CH3I.

Is CH3NC isomerization an intrinsic non-RRKM unimolecular reaction?

Direct dynamics simulations, using B3LYP/6-311++G(2d,2p) theory, were used to study the unimolecular and intramolecular dynamics of vibrationally excited CH3NC. Microcanonical ensembles of CH3NC, excited with 150, 120, and 100 kcal/mol of vibrational energy, isomerized to CH3CN nonexponentially, indicative of intrinsic non-Rice-Ramsperger-Kassel-Marcus (RRKM) dynamics. The distribution of surviving CH3NC molecules vs time, i.e., N(t)/N(0), was described by two separate functions, valid above and below a time limit, a single exponential for the former and a biexponential for the latter. The dynamics for the short-time component are consistent with a separable phase space model. The importance of this component decreases with vibrational energy and may be unimportant for energies relevant to experimental studies of CH3NC isomerization. Classical power spectra calculated for vibrationally excited CH3NC, at the experimental average energy of isomerizing molecules, show that the intramolecular dynamics of CH3NC are not chaotic and the C-N≡C and CH3 units are weakly coupled. The biexponential N(t)/N(0) at 100 kcal/mol is used as a model to study CH3NC → CH3CN isomerization with biexponential dynamics. The Hinshelwood-Lindemann rate constant kuni(ω,E) found from the biexponential N(t)/N(0) agrees with the Hinshelwood-Lindemann-RRKM kuni(ω,E) at the high and low pressure limits, but is lower at intermediate pressures. As found from previous work [S. Malpathak and W. L. Hase, J. Phys. Chem. A 123, 1923 (2019)], the two kuni(ω,E) curves may be brought into agreement by scaling ω in the Hinshelwood-Lindemann-RRKM kuni(ω,E) by a collisional energy transfer efficiency factor ßc. The interplay between the value of ßc, for the actual intermolecular energy transfer, and the ways the treatment of the rotational quantum number K and nonexponential unimolecular dynamics affect ßc suggests that the ability to fit an experimental kuni(ω,T) with Hinshelwood-Lindemann-RRKM theory does not identify a unimolecular reactant as an intrinsic RRKM molecule.

Direct dynamics simulations of the unimolecular dissociation of dioxetane: Probing the non-RRKM dynamics.

In a previous UB3LYP/6-31G* direct dynamics simulation, non-Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular dynamics was found for vibrationally excited 1,2-dioxetane (DO); [R. Sun et al., J. Chem. Phys. 137, 044305 (2012)]. In the work reported here, these dynamics are studied in more detail using the same direct dynamics method. Vibrational modes of DO were divided into 4 groups, based on their characteristic motions, and each group excited with the same energy. To compare with the dynamics of these groups, an additional group of trajectories comprising a microcanonical ensemble was also simulated. The results of these simulations are consistent with the previous study. The dissociation probability, N(t)/N(0), for these excitation groups were all different. Groups A, B, and C, without initial excitation in the O-O stretch reaction coordinate, had a time lag to of 0.25-1.0 ps for the first dissociation to occur. Somewhat surprisingly, the C-H stretch Group A and out-of-plane motion Group C excitations had exponential dissociation probabilities after to, with a rate constant ∼2 times smaller than the anharmonic RRKM value. Groups B and D, with excitation of the H-C-H bend and wag, and ring bend and stretch modes, respectively, had bi-exponential dissociation probabilities. For Group D, with excitation localized in the reaction coordinate, the initial rate constant is ∼7 times larger than the anharmonic RRKM value, substantial apparent non-RRKM dynamics. N(t)/N(0) for the random excitation trajectories was non-exponential, indicating intrinsic non-RRKM dynamics. For the trajectory integration time of 13.5 ps, 9% of these trajectories did not dissociate in comparison to the RRKM prediction of 0.3%. Classical power spectra for these trajectories indicate they have regular intramolecular dynamics. The N(t)/N(0) for the excitation groups are well described by a two-state coupled phase space model. From the intercept of N(t)/N(0) with random excitation, the anharmonic correction to the RRKM rate constant is approximately a factor of 1.5.

A quantum mechanical insight into SN2 reactions: Semiclassical initial value representation calculations of vibrational features of the Cl-⋯CH3Cl pre-reaction complex with the VENUS suite of codes.

The role of vibrational excitation of reactants in driving reactions involving polyatomic species has been often studied by means of classical or quasi-classical trajectory simulations. We propose a different approach based on investigation of vibrational features of the Cl-⋯CH3Cl pre-reaction complex for the Cl- + CH3Cl SN2 reaction. We present vibrational power spectra and frequency estimates for the title pre-reaction complex calculated at the level of classical, semiclassical, and second-order vibrational perturbation theory on a pre-existing analytical potential energy surface. The main goals of the paper are the study of anharmonic effects and understanding of vibrational couplings that permit energy transfer between the collisional kinetic energy and the internal vibrations of the reactants. We provide both classical and quantum pictures of intermode couplings and show that the SN2 mechanism is favored by the coupling of a C-Cl bend involving the Cl- projectile with the CH3 rocking motion of the target molecule. We also illustrate how the routines needed for semiclassical vibrational spectroscopy simulations can be interfaced in a user-friendly way to pre-existing molecular dynamics software. In particular, we present an implementation of semiclassical spectroscopy into the VENUS suite of codes, thus providing a useful computational tool for users who are not experts of semiclassical dynamics.

Direct Chemical Dynamics Simulations.

In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular SN2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.

Potential energy surface stationary points and dynamics of the F- + CH3I double inversion mechanism.

Direct dynamics simulations were performed to study the SN2 double inversion mechanism SN2-DI, with retention of configuration, for the F- + CH3I reaction. Previous simulations identified a transition state (TS) structure, i.e. TS0, for the SN2-DI mechanism, including a reaction path. However, intrinsic reaction coordinate (IRC) calculations from TS0 show it is a proton transfer (PT) TS connected to the F-HCH2I SN2 pre-reaction complex and the FHCH2I- proton transfer post-reaction complex. Inclusion of TS0 in the SN2-DI mechanism would thus involve non-IRC atomistic dynamics. Indeed, trajectories initiated at TS0, with random ensembles of energies as assumed by RRKM theory, preferentially form the SN2-DI products and ∼70% follow the proposed SN2-DI pathway from TS0 to the products. In addition, the Sudden Vector Projection (SVP) method was used to identify which CH3I vibrational mode excitations promote access to TS0 and the SN2-DI mechanism. Results of F- + CH3I simulations, with SVP specified mode excitations, are disappointing. With the CH3 deformations of CH3I excited, the SN2 single inversion mechanism is the dominant pathway. If the CH stretch modes are also excited, proton transfer dominates the reaction. SN2-DI occurs, but with a very small probability of ∼1%. The reasons behind these results are discussed.

Competing E2 and SN2 Mechanisms for the F- + CH3CH2I Reaction.

Anti-E2, syn-E2, inv-, and ret-SN2 reaction channels for the gas-phase reaction of F- + CH3CH2I were characterized with a variety of electronic structure calculations. Geometrical analysis confirmed synchronous E2-type transition states for the elimination of the current reaction, instead of nonconcerted processes through E1cb-like and E1-like mechanisms. Importantly, the controversy concerning the reactant complex for anti-E2 and inv-SN2 paths has been clarified in the present work. A positive barrier of +19.2 kcal/mol for ret-SN2 shows the least feasibility to occur at room temperature. Negative activation energies (-16.9, -16.0, and -4.9 kcal/mol, respectively) for inv-SN2, anti-E2, and syn-E2 indicate that inv-SN2 and anti-E2 mechanisms significantly prevail over the eclipsed elimination. Varying the leaving group for a series of reactions F- + CH3CH2Y (Y = F, Cl, Br, and I) leads to monotonically decreasing barriers, which relates to the gradually looser TS structures following the order F > Cl > Br > I. The reactivity of each channel nearly holds unchanged except for the perturbation between anti-E2 and inv-SN2. RRKM calculation reveals that the reaction of the fluorine ion with ethyl iodide occurs predominately via anti-E2 elimination, and the inv-SN2 pathway is suppressed, although it is energetically favored. This phenomenon indicates that, in evaluating the competition between E2 and SN2 processes, the kinetic or dynamical factors may play a significant role. By comparison with benchmark CCSD(T) energies, MP2, CAM-B3LYP, and M06 methods are recommended to perform dynamics simulations of the title reaction.

Post-transition state dynamics and product energy partitioning following thermal excitation of the F⋯HCH2CN transition state: Disagreement with experiment.

Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH3CN → HF + CH2CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. The experiments were performed at 300 K, and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F⋯HCH2CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation. The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH2CN and then trapping in the CH2CN⋯HF post-reaction potential energy well of ∼10 kcal/mol with respect to the HF + CH2CN products. In contrast to this IRC, five different trajectory types were observed: the majority proceeded by direct H-atom transfer and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH2CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. Simulations with an anharmonic zero-point energy constraint gave product distributions for relative translation, HF rotation, HF vibration, CH2CN rotation, and CH2CN vibration as 5%, 11%, 60%, 7%, and 16%, respectively. In contrast, the experimental energy partitioning percentages to HF rotation and vibration are 6% and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational population for F + CH3CN → HF + CH2CN resemble those for other reactions. A detailed discussion is given of possible origins of the difference between the simulation and experimental energy partitioning dynamics for F + CH3CN → HF + CH2CN. The F + CH3CN reaction also forms the CH3C(F)N intermediate, in which the F-atom adds to the C≡N bond. However, this intermediate and F⋯CH3CN and CH3CN⋯F van der Waals complexes are not expected to affect the F + CH3CN → HF + CH2CN product energy partitioning.

Chemical Dynamics Simulations of Benzene Dimer Dissociation.

Classical chemical dynamics simulations were performed to study the intramolecular and unimolecular dissociation dynamics of the benzene dimer, Bz2 → 2 Bz. The dissociation of microcanonical ensembles of Bz2 vibrational states, at energies E corresponding to temperatures T of 700-1500 K, were simulated. For the large Bz2 energies and large number of Bz2 vibrational degrees of freedom, s, the classical microcanonical (RRKM) and canonical (TST) rate constant expressions become identical. The dissociation rate constant for each T is determined from the initial rate dN(t)/dt of Bz2 dissociation, and the k(T) are well-represented by the Arrhenius eq k(T) = A exp(-E(a)/RT). The E(a) of 2.02 kcal/mol agrees well with the Bz2 dissociation energy of 2.32 kcal/mol, and the A-factor of 2.43 × 10(12) s(-1) is of the expected order-of-magnitude. The form of N(t) is nonexponential, resulting from weak coupling between the Bz2 intramolecular and intermolecular modes. With this weak coupling, large Bz2 vibrational excitation, and low Bz2 dissociation energy, most of the trajectories dissociate directly. Simulations, with only the Bz2 intramolecular modes excited at 1000 K, were also performed to study intramolecular vibrational energy redistribution (IVR) between the intramolecular and intermolecular modes. Because of restricted IVR, the initial dissociation is quite slow, but N(t) ultimately becomes exponential, suggesting an IVR time of 20.7 ps.

Single Solvent Molecules Induce Dual Nucleophiles in Gas-Phase Ion-Molecule Nucleophilic Substitution Reactions.

Direct dynamics simulation of singly hydrated peroxide ion reacting with CH3Cl reveals a new product channel that forms CH3OH + Cl- + HOOH, besides the traditional channel that forms CH3OOH + Cl- + H2O. This finding shows that singly hydrated peroxide ion behaves as a dual nucleophile through proton transfer between HOO-(H2O) and HO-(HOOH). Trajectory analysis attributes the occurrence of the thermodynamically and kinetically unfavored HO--induced pathway to the entrance channel dynamics, where extensive proton transfer occurs within the deep well of the prereaction complex. This study represents the first example of a single solvent molecule altering the nucleophile in a gas-phase ion-molecule nucleophilic substitution reaction, in addition to reducing the reactivity and affecting the dynamics, signifying the importance of dynamical effects of solvent molecules.

Interaction between γC87 and γR242 residues participates in energy coupling between catalysis and proton translocation in Escherichia coli ATP synthase.

Functioning as a nanomotor, ATP synthase plays a vital role in the cellular energy metabolism. Interactions at the rotor and stator interface are critical to the energy transmission in ATP synthase. From mutational studies, we found that the γC87K mutation impairs energy coupling between proton translocation and nucleotide synthesis/hydrolysis. An additional glutamine mutation at γR242 (γR242Q) can restore efficient energy coupling to the γC87K mutant. Arrhenius plots and molecular dynamics simulations suggest that an extra hydrogen bond could form between the side chains of γC87K and ßTPE381 in the γC87K mutant, thus impeding the free rotation of the rotor complex. In the enzyme with γC87K/γR242Q double mutations, the polar moiety of γR242Q side chain can form a hydrogen bond with γC87K, so that the amine group in the side chain of γC87K will not hydrogen-bond with ßE381. As a conclusion, the intra-subunit interaction between positions γC87 and γR242 modulates the energy transmission in ATP synthase. This study should provide more information of residue interactions at the rotor and stator interface in order to further elucidate the energetic mechanism of ATP synthase.

Anharmonic Densities of States for Vibrationally Excited I-(H2O), (H2O)2, and I-(H2O)2.

Monte Carlo sampling calculations were performed to determine the anharmonic sum of states, Nanh( E), for I-(H2O), (H2O)2, and I-(H2O)2 versus internal energy up to their dissociation energies. The anharmonic density of states, ρanh( E), is found from the energy derivative of Nanh( E). Analytic potential energy functions are used for the calculations, consisting of TIP4P for H2O···H2O interactions and an accurate two-body potential for the I-···H2O fit to quantum chemical calculations. The extensive Monte Carlo samplings are computationally demanding, and the use of computationally efficient potentials was essential for the calculations. Particular emphasis is directed toward I-(H2O)2, and distributions of its structures versus internal energy are consistent with experimental studies of the temperature-dependent vibrational spectra. At their dissociation thresholds, the anharmonic to harmonic density of states ratio, ρanh( E)/ρh( E), is ∼2, ∼ 3, and ∼260 for I-(H2O), (H2O)2, and I-(H2O)2, respectively. The large ratio for I-(H2O)2 results from the I-(H2O)2 → I-(H2O) + H2O dissociation energy being more than 2 times larger than the (H2O)2 → 2H2O dissociation energy, giving rise to highly mobile H2O molecules near the I-(H2O)2 dissociation threshold. This work illustrates the importance of treating anharmonicity correctly in unimolecular rate constant calculations.

Perspective: chemical dynamics simulations of non-statistical reaction dynamics.

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.