Very fast tunneling in the early stage of reaction dynamics

The difference between quantum and classical survival probabilities for molecular dissociation dynamics in the time domain, which arises mainly from quantum mechanical tunneling, has interesting characteristics that are not noticed through the counterpart in energy domain. It is shown that the early stage undergoes a fast tunneling, while the later stage is characterized with a long-lasting slow tunneling. The mechanism of this behavior is analyzed in terms of a quasi-semiclassical theory featuring the geometrical distribution of the so-called tunneling points. In particular, the role of dynamical tunneling is discussed as a phenomenon that typifies the time dependence of tunneling dynamics. It is predicted that these tunneling characteristics will be reflected in the isotope effect and should be experimentally observable.     

Reaction path dynamics and theoretical rate constants for the SiH3Cl+H→SiH2Cl+H2 reaction by ab initio direct dynamics method

Ab initio direct dynamics method has been used to study the title reaction. Electronic structure information including geometries, gradients and force constants (Hessians) are calculated at the UQCISD/6-311+G^** level. Energies along the minimum energy path are improved by a series of single-point G2//QCISD calculations. The changes of the geometries, vibratioanal frequencies, potential energies and total curvature along the reaction path are discussed. The rate constants in the temperature range 200–3000 K are calculated by canonical variational transition state theory with small-curvature tunneling correction (CVT/SCT) method. The results show that the variational effect is small and in the lower temperature range, the small curvature tunneling effect is important for the reaction.     

STM数据采集分析计算机系统

扫描隧道显微镜(STM)是1982年问世的研究物质表面结构的新型仪器,近几年来得到了很大的发展。与其它各种类型的显微镜相比,它的最大优点是具有较高的分辨率(平行和垂直于样品表面方向的分辨率分别可达1和0.1),共弱点是数据的处理和显示功能不强。发展STM的自动控制、数据采集、实时显示和数据分析的计算机系统,对于改进仪器的性能至关重要。本文介绍我们研制的一套STM数据采集、存储、实时显示和数据分析系统,并以用该系统采集的高取向石墨数据为例,介绍系统的软件功能。     

Potential energy surface for the CCl4 + H --> CCl3 + ClH reaction: kinetics and dynamics study

An analytical potential energy surface for the gas-phase CCl4 + H --> CCl3 + ClH reaction was constructed with suitable functional forms to represent vibrational modes. This surface is completely symmetric with respect to the permutation of the four chlorine atoms and is calibrated with respect to experimental thermal rate constants available over the temperature range 297-904 K. On this surface, the thermal rate constants were calculated using variational transition-state theory with semiclassical transmission coefficients over a wider temperature range 300-2500 K, therefore obtaining kinetics information at higher temperatures than are experimentally available. This surface was also used to analyze dynamical features, such as tunneling and reaction-path curvature. In the first case, the influence of the tunneling factor is very small since a heavy chlorine atom has to pass through the barrier. In the second, it was found that vibrational excitation of the Cl-H stretching mode can be expected in the exit channel.     

Theoretical Studies on CH3SiH3+H→CH3SiH2+H2 Reaction with the Variational Transitional State Theory

The abstract reaction of CH3SiH3 with H has been studied by using the“direct dynamics”method of variational transition-state theory,which is based on the information on geometries,frequencies and energies calculated by ab initio along the minimum energy path.The rate constants and transmission coefficients were calculated for the temperature range 298～1700K.The result indicates that the variational effect on this reaction is great and the tunneling effect is very obvious at room temperature.The rate constants calculated match well with the experimental value.     

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

The role of tunneling for two proton-transfer steps in the reactions catalyzed by triosephosphate isomerase (TIM) has been studied. One step is the rate-limiting proton transfer from Calpha in the substrate to Glu 165, and the other is an intrasubstrate proton transfer proposed for the isomerization of the enediolate intermediate. The latter, which is not important in the wild-type enzyme but is a useful model system because of its simplicity, has also been examined in the gas phase and in solution. Variational transition-state theory with semiclassical ground-state tunneling was used for the calculation with potential energy surface determined by an AM1 method specifically parametrized for the TIM system. The effect of tunneling on the reaction rate was found to be less than a factor of 10 at room temperature; the tunneling becomes more important at lower temperature, as expected. The imaginary frequency (barrier) mode and modes that have large contributions to the reaction path curvature are localized on the atoms in the active site, within 4 A of the substrate. This suggests that only a small number of atoms that are close to the substrate and their motions (e.g., donor-acceptor vibration) directly determine the magnitude of tunneling. Atoms that are farther away influence the effect of tunneling indirectly by modulating the energetics of the proton transfer. For the intramolecular proton transfer, tunneling was found to be most important in the gas phase, to be similar in the enzyme, and to be the smallest in water. The major reason for this trend is that the barrier frequency is substantially lower in solution than in the gas phase and enzyme; the broader solution barrier is caused by the strong electrostatic interaction between the highly charged solute and the polar solvent molecules. Analysis of isotope effects showed that the conventional Arrenhius parameters are more useful as experimental criteria for determining the magnitude of tunneling than the widely used Swain-Schaad exponent (SSE). For the primary SSE, although values larger than the transition-state theory limit (3.3) occur when tunneling is included, there is no clear relationship between the calculated magnitudes of tunneling and the SSE. Also, the temperature dependence of the primary SSE is rather complex; the value of SSE tends to decrease as the temperature is lowered (i.e., when tunneling becomes more significant). For the secondary SSE, the results suggest that it is more relevant for evaluating the "coupled motion" between the secondary hydrogen and the reaction coordinate than the magnitude of tunneling. Although tunneling makes a significant contribution to the rate of proton transfer, it appears not to be a major aspect of the catalysis by TIM at room temperature; i.e., the tunneling factor of 10 is "small" relative to the overall rate acceleration by 10(9). For the intramolecular proton transfer, the tunneling in the enzyme is larger by a factor of 5 than in solution.     

H原子和(CH3)2SiH2抽提反应的理论研究

采用UMP2/6-31G(d)理论水平优化了H原子和(CH3)2SiH2抽提反应势能面上的所有驻点,并在此水平基础上进行了内禀反应坐标(IRC)的计算,得到该反应的反应途径(MEP)。应用变分过渡态理论及最小能量途径半经典绝热基态隧道效应校正(MEPSAG)、小曲率半经典绝热基态隧道效应校正(SCSAG)等方法对上述反应进行了动力学研究,期望从理论上提供一套温度范围较宽、精度较高的动力学数据,为阐明反应机理和解释实验结果提供理论依据。     

Tunneling Electron Induced Fluorescence from Single Porphyrin Molecules Decoupled by Striped-Phase Octanethiol Self-assembled Monolayer

We investigate tunneling electron induced luminescence from isolated single porphyrin molecules that are decoupled by striped-phase self-assembled monolayer of octanethiol from the underneath Au(111) substrate. Intrinsic single-molecule electroluminescence has been realized by such decoupling at both bias polarities. The photon emission intensity acquired from the molecular lobe is found stronger than that from the molecular center. These re-sults provide useful information on the understanding of electroluminescent behavior and mechanism in molecular tunnel junctions.     

Importance of anharmonicity, recrossing effects, and quantum mechanical tunneling in transition state theory with semiclassical tunneling. A test case: the H2 + Cl hydrogen abstraction reaction

The hydrogen abstraction reaction from H2 by the Cl atom is studied by means of the variational transition state theory with semiclassical tunneling coefficients on the BW2 potential energy surface. Vibrational anharmonicity and coupling between the bending modes are taken into account. The occurrence of trajectories that recross the transition state is estimated by means of the canonical unified statistical method and by classical trajectories calculations. Different semiclassical methods for tunneling calculations are tested. Our results show that anharmonicity has a small but nonnegligible effect on the thermal rate constants, recrossing can be neglected, and tunneling is adequately described by the least-action approximation, and less successfully by the large-curvature version 3 approximation. However, the large-curvature version 4 and small-curvature approximations lead to a severe underestimation of tunneling. Thermal rate constants calculated using transition state theory including anharmonicity and tunneling agree very well with accurate quantal thermal rate constants over a wide temperature range, although the improvement over the harmonic transition state theory with the microcanonically optimized semiclassical tunneling approximation (based on version 3 of the large-curvature tunneling method) used in a previous study of this reaction is only marginal.     

Long-distance electron tunneling in proteins

Long-distance tunneling is the major mechanism of electron transfer (ET) in proteins. For a number of years, a major question has been whether specific electron tunneling pathways exist. This question is still debated in the literature, because the pathways are not observed directly, and interpretation of experimental results on ET rates involves ambiguities. The extremely small tunneling interactions are difficult to calculate accurately. Recently, there has been remarkable progress in the area; however, some problems still remain unresolved. The accurate prediction of the absolute rates of long-distance ET reactions and other biological charge-transfer reactions is a particularly pressing issue. The current theoretical calculations indicate that the specific paths do exist in static protein structures. However, the protein motions can result in significant averaging of the spatial tunneling patterns, and it is not clear how accurately subtle quantum interference effects are described by the present theories. The key to resolving these issues is to perform accurate, first-principles calculations of electron tunneling that include the dynamics of the protein. This paper reviews some of theoretical issues of electron tunneling dynamics in inhomogeneous organic media.     

Ambient Bistable Single Dipole Switching in a Molecular Monolayer

Reported here is a molecular dipole that self‐assembles into highly ordered patterns at the liquid‐solid interface, and it can be switched at room temperature between a bright and a dark state at the single‐molecule level. Using a scanning tunneling microscope (STM) under suitable bias conditions, binary information can be written at a density of up to 41 Tb cm^?2 (256 Tb/in²). The written information is stable during reading at room temperature, but it can also be erased at will, instantly, by proper choice of tunneling conditions. DFT calculations indicate that the contrast and switching mechanism originate from the stacking sequence of the molecular dipole, which is reoriented by the electric field between the tip and substrate.     

Tunneling time in driven double-well system using entangled molecular dynamics method

We calculate quantum tunneling time in the double-well system without perturbation and with symmetry-breaking driven force using the entangled trajectory molecular dynamics method in the present article. Without perturbation, quantum tunneling time decreased with the increase of the energy, and the different contributions of the barrier traversal time and the intrinsic decay time have been shown. The tunneling time dependence on the amplitude and frequency of the symmetry-breaking driven force are present. In the case of weak driven force, tunneling time has a minimum value in the resonant frequency. For strong driven force, chaos brings a huge change to quantum dynamics, tunneling time significantly becomes short. Finally, we directly show the enhancement of quantum tunneling process by chaotic behavior of entangled trajectories and indicate that it was caused by quantum effect.     

Formation of a Tunneling Product in the Photorearrangement of o‐Nitrobenzaldehyde

The photochemical rearrangement of o ‐nitrobenzaldehyde to o ‐nitrosobenzoic acid, first reported in 1901, has been shown to proceed via a distinct ketene intermediate. In the course of matrix isolation experiments in various host materials at temperatures as low as 3 K, the ketene was re‐investigated in its electronic and vibrational ground states. It was shown that hitherto unreported H‐tunneling dominates its reactivity, with half‐lives of a few minutes. Unexpectedly, the tunneling product is different from o ‐nitrosobenzoic acid formed in the photoprocess: Once prepared by irradiation, the ketene spontaneously rearranges to an isoxazolone via an intriguing mechanism initiated by H‐tunneling. CCSD(T)/cc‐pVTZ computations reveal that this isoxazolone is neither thermodynamically nor kinetically favored under the experimental conditions, and that formation of this unique tunneling product constitutes a remarkable and new example of tunneling control.     

Methyl rotational tunneling dynamics of p-xylene confined in a crystalline zeolite host

The methyl rotational tunneling spectrum of p-xylene confined in nanoporous zeolite crystals has been measured by inelastic neutron scattering (INS) and proton nuclear magnetic resonance (NMR), and analyzed to extract the rotational potential energy surfaces characteristic of the methyl groups in the host-guest complex. The number and relative intensities of the tunneling peaks observed by INS indicate the presence of methyl-methyl coupling interactions in addition to the methyl-zeolite interactions. The INS tunneling spectra from the crystals (space group P2(1)2(1)2(1) with four crystallographically inequivalent methyl rotors) are quantitatively interpreted as a combination of transitions involving two coupled methyl rotors as well as a transition involving single-particle tunneling of a third inequivalent rotor, in a manner consistent with the observed tunneling energies and relative intensities. Together, the crystal structure and the absence of additional peaks in the INS spectra suggest that the tunneling of the fourth inequivalent rotor is strongly hindered and inaccessible to INS measurements. This is verified by proton NMR measurements of the spin-lattice relaxation time which reveal the tunneling characteristics of the fourth inequivalent rotor.     

Scanning tunneling microscopy, orbital-mediated tunneling spectroscopy, and ultraviolet photoelectron spectroscopy of metal(II) tetraphenylporphyrins deposited from vapor.

Thin films of vapor-deposited Ni(II) and Co(II) complexes of tetraphenylporphyrin (NiTPP and CoTPP) were studied supported on gold and embedded in Al-Al(2)O(3)-MTPP-Pb tunnel diodes, where M = Ni or Co. Thin films deposited onto polycrystalline gold were analyzed by ultraviolet photoelectron spectroscopy (UPS) using He I radiation. Scanning tunneling microscopy (STM) and orbital-mediated tunneling spectroscopy (STM-OMTS) were performed on submonolayer films of CoTPP and NiTPP supported on Au(111). Inelastic electron tunneling spectroscopy (IETS) and OMTS were measured in conventional tunnel diode structures. The highest occupied pi molecular orbital of the porphyrin ring was seen in both STM-OMTS and UPS at about 6.4 eV below the vacuum level. The lowest unoccupied pi molecular orbital of the porphyrin ring was observed by STM-OMTS and by IETS-OMTS to be located near 3.4 eV below the vacuum level. The OMTS spectra of CoTPP had a band near 5.2 eV (below the vacuum level) that was attributed to transient oxidation of the central Co(II) ion. That is, it is due to electron OMT via the half-filled d(z)(2) orbital present in Co(II) of CoTPP. The NiTPP OMTS spectra show no such band, consistent with the known difficulty of oxidation of the Ni(II) ion. The STM-based OMTS allowed these two porphyrin complexes to be easily distinguished. The present work is the first report of the observation of STM-OMTS, tunnel junction OMTS, and UPS of the same compounds. Scanning tunneling microscope-based orbital-mediated tunneling provides more information than UPS or tunnel junction-based OMTS and does so with molecular-scale resolution.     

Dissociation dynamics of propargyl chloride molecular ion near the reaction threshold: manifestation of quantum mechanical tunneling

The Cl loss from the propargyl chloride molecular ion has been investigated using mass-analyzed ion kinetic energy spectrometry (MIKES). The kinetic energy release distribution in the unimolecular dissociation has been determined. The potential energy surface for the mechanistic pathway has been calculated at the B3LYP/6-311G** density functional theory level. The calculated potential energy surface suggested that the threshold dissociation of the propargyl chloride molecular ion produces the C(3)H(3)(+) ion, only with the cyclopropenium structure, and with the release of a large amount of kinetic energy. This is in agreement with experimental results. Also, calculation of the rate constants with statistical rate models predicted that the reaction observed on a microsecond time scale occurs via tunneling through the rate-determining isomerization barrier for H-atom transfer. It has been found that a broad lifetime distribution is a manifestation of quantum mechanical tunneling of a precursor prepared under thermal conditions. Reinterpretation of previous photoelectron-photoion coincidence results taking into account the tunneling effect necessitated raising the critical energy to 0.64 eV from the energy of 0.34 eV reported previously. Copyright 2000 John Wiley & Sons, Ltd.     

Tunneling splitting and decay of metastable states in polyatomic molecules: invariant instanton theory

This paper gives an overview of recently developed instanton theory of multidimensional tunneling and demonstrates its applicability to real polyatomic systems. One of the key features of the present formulation is rigorous solution of the multidimensional Hamilton-Jacoby and transport equations which constitutes the basis of the semiclassical theory accurate up to the first order in the Planck constant variant Planck's over 2pi. Apart from this fundamental assumption of the semiclassical dynamics the present instanton theory is exact, i.e. it neither involves any further approximation, nor relies on any models. For practical application, the theory is supplemented by numerical methods to construct a multi-dimensional tunneling path (instanton) and to combine the semiclassical theory with high-quality quantum chemical calculations. Emphasis is put on the instanton theory of tunneling splitting in polyatomic molecules. Importance of accurate potential energy surface (PES) information and multidimensional effects is demonstrated by applications to real molecules. The theory of life time of metastable states is also briefly explained.     

Theory of electron tunneling through a bridge molecule with two electronic levels at low temperatures

A theory of electron tunneling through a single-center bridge redox group that has two electronic levels participating in the electron transfer process is presented. The temperature is presumed to be low enough to ignore activation redox conversions of the bridge group. Salient features of this system are due both to the presence of two electroactive states of the bridge group and to relaxation processes along the reaction coordinate. The processes in question make the tunneling current time-dependent at fixed potentials and can bring about hysteresis in current-voltage curves when cycling the bias potential. Effects of inelastic tunneling with excitation of vibrations of a local quantum degree of freedom are considered.     

Including anharmonicity in the calculation of rate constants. II. The OH+H2-->H2O+H reaction

A recently developed method for calculating anharmonic vibrational energy levels at nonstationary points along a reaction path that is based on second-order perturbation theory in curvilinear coordinates is combined with variational transition state theory with semiclassical multidimensional tunneling approximations to calculate thermal rate constants for the title reaction. Two different potential energy surfaces were employed for these calculations, an improved version of the author's surface 5 and the WSLFH surface of Wu et al. [J. Chem. Phys. 113, 3150 (2000)]. We present detailed comparisons of rate constants computed for the two surfaces with and without anharmonicity and with various approximations for incorporating tunneling along the reaction path. The results for this system are quite sensitive to the surface employed, the choice of coordinates (curvilinear versus rectilinear), and the inclusion of anharmonicity. A comparison with experiment provides information on the accuracy of these surfaces.     

The widespread occurrence of enzymatic hydrogen tunneling,andits unique properties,lead to a new physical model for the origins of enzyme catalysis

The investigation of C-H bond activation by enzymes over the past several decades has revealed a plethora of deviations from semi-classical kinetic models. Although the early enzymatic results were interpreted in the context of a tunneling correction, the emergent properties are now seen to be largely incompatible with this type of analysis as well. This chapter introduces some of the experimental data that form the basis for our present understanding. A vibronically nonadiabatic model, that has a number of features in common with the Marcus treatment for electron transfer, offers a robust physical picture for the hydrogen tunneling behavior seen in both native enzymes and in enzymes that have been perturbed either by site-specific mutagenesis or by perturbation of the reaction conditions. Native enzymes under optimal conditions most commonly show behavior that requires a heavy atom donor-acceptor distance that is in the range of 2.7 Å. This compression beyond van der Waals distances is proposed to arise from the process of enzymatic conformational sampling. The absence of any evolutionary driving force to optimize tunneling for deuterium transfer (natural abundance < 0.02%), together with the frequent observation that the enthalpic barrier for deuterium transfer is the same or very similar to that for protium transfer, leads to the proposal that tunneling is a consequence of a generic property of enzyme function in which overall protein flexibility enables the generation of active sites that can be quite compressed.