Height Of Potential Energy Barrier Research Articles

放射光光電子分光で観た酸素分子によるNi(001)表面酸化膜形成の反応機構

Chemical reaction dynamics on the oxide formation at the Ni(001) surface has been studied via two quantum beams (synchrotron radiation and supersonic molecular beam). It was revealed that NiO layers formation took place at an oxygen coverage less than 0.5 ML depending on translational energy of oxygen molecules. Although dissociative adsorption of oxygen takes place via physical adsorption at lower translational energy than 0.06 eV, direct activated adsorption occurs at higher energy. Potential energy barrier height is 0.3 eV for the first barrier and 1.6 eV for the second one, respectively.

Understanding the Stabilization of Single-Walled Carbon Nanotubes and Graphene in Ionic Surfactant Aqueous Solutions: Large-Scale Coarse-Grained Molecular Dynamics Simulation-Assisted DLVO Theory

Understanding the dispersion of single-walled carbon nanotubes (SWCNTs) and graphene in surfactant aqueous solutions is essential for processing of these materials. Herein, we develop the first theoretical framework, which combines large-scale coarse-grained (CG) molecular dynamics (MD) simulations with the Derjaguin–Landau–Verwey–Overbeek (DLVO) theory and Langmuir isotherm, to inform the mechanisms of surfactant adsorption and induced colloidal stability. By carrying out large-scale CG-MD simulations (∼1 million CPU h), we successfully calculated the surface coverage of the widely used ionic surfactant sodium cholate (SC) on different carbon nanomaterials at experimentally realistic SC concentrations. This was accomplished by simultaneously simulating SC micellization and adsorption in one simulation box. Our theoretical framework further allows us to quantify the surface electric potential and the potential energy barrier height that maintains colloidal stability of dispersed SWCNTs or graphene sheets ...

An Insight into the Regiospecificity of Linoleic Acid Peroxidation Catalyzed by Mammalian 15-Lipoxygenases

15-Lipoxygenases (15-LOs) catalyze the peroxidation reaction of linoleic acid (LA) in mammals producing almost exclusively 13-(S)-hydroperoxyoctadecadienoic acid (13-(S)-HPODE). Although several hypotheses have been formulated, the molecular basis of such enzymatic regiospecificity is unclear. We have here combined quantum mechanics/molecular mechanics (QM/MM) calculations with molecular dynamics simulations to analyze the peroxidation mechanism using a complete rabbit 15-LO-1/LA solvated model. C9 and C13 being equivalent for planarity and spin density, the QM/MM potential energy profiles of the O2 addition to those two atoms were calculated. The difference in the potential energy barrier heights is clear enough to justify that O2 selectively attacks C13 giving 13-(S)-HPODE. Oxygenation at C9 is hindered by two steric-shielding residues (Leu597 and Gln548). The calculated free energy profile at 300 K for the O2 addition to C13 confirms that the peroxidation on C13 is a reversible viable process in agreement with experiments. Thus, the subsequent reduction of the peroxyl radical to give the final hydroperoxidated product is expected to give the irreversibility character to the overall process.

Ions interacting with planar aromatic molecules: Modeling electron transfer reactions

We present theoretical absolute charge exchange cross sections for multiply charged cations interacting with the Polycyclic Aromatic Hydrocarbon (PAH) molecules pyrene C(14)H(10), coronene C(24)H(12), or circumcoronene C(54)H(18). These planar, nearly circular, PAHs are modelled as conducting, infinitely thin, and perfectly circular discs, which are randomly oriented with respect to straight line ion trajectories. We present the analytical solution for the potential energy surface experienced by an electron in the field of such a charged disc and a point-charge at an arbitrary position. The location and height of the corresponding potential energy barrier from this simple model are in close agreement with those from much more computationally demanding Density Functional Theory (DFT) calculations in a number of test cases. The model results compare favourably with available experimental data on single- and multiple electron transfer reactions and we demonstrate that it is important to include the orientation dependent polarizabilities of the molecules (model discs) in particular for the larger PAHs. PAH ionization energy sequences from DFT are tabulated and used as model inputs. Absolute cross sections for the ionization of PAH molecules, and PAH ionization energies such as the ones presented here may be useful when considering the roles of PAHs and their ions in, e.g., interstellar chemistry, stellar atmospheres, and in related photoabsorption and photoemission spectroscopies.

Temperature effects on enzyme-catalyzed reactions within a cell: Monte Carlo simulations for coupled reaction and diffusion

We report Monte Carlo simulations of temperature effects on single-step enzymatic reactions with varied rate constants and diffusion coefficients. For typical systems, where the intrinsic reaction rate is more sensitive to temperature than diffusion, the overall reaction is rate-limited at low temperatures and diffusion-limited at high temperatures. The effective activation energy shifts to a much lower value as temperature is increased. Our results show that the temperature dependence of enzyme-catalyzed reactions within a cell may be only loosely related to a potential energy barrier height. The effective activation energy may be strongly affected by coupling of reaction and diffusion.

Electrical properties of grain boundaries in polycrystalline materials under intrinsic or low doping

An analytical model is developed to study the electrical properties (electric field and potential distributions, potential energy barrier height and polarization phenomenon) of polycrystalline materials at intrinsic or low doping for detector and solar cell applications by considering an arbitrary amount of grain boundary charge and a finite width of grain boundary region. The general grain boundary model is also applicable to highly doped polycrystalline materials. The electric field and potential distributions are obtained by solving Poisson's equation in both depleted grains and grain boundary regions. The electric field and potential distributions across the detector are analysed under various doping, trapping and applied biases. The electric field collapses, i.e. a nearly zero-average electric field region exists in some part of the biased detector at high trapped charge densities at the grain boundaries. The model explains the conditions of existence of a zero-average field region, i.e. the polarization mechanisms in polycrystalline materials. The potential energy barrier at the grain boundary exists if the electric field changes its sign at the opposite side of the grain boundary. The energy barrier does not exist in all grain boundaries in the low-doped polycrystalline detector and it never exists in intrinsic polycrystalline detectors under applied bias condition provided that there is no charge trapping in the grain.

Dipole assisted exciton dissociation at conjugated polymer/fullerene photovoltaic interfaces: A molecular study using density functional theory calculations

Using density functional theory calculations we probe the electronic structure of the P3HT/fullerene supramolecule. Our simulations indicates that the mix of the polymer and fullerene wave functions give rise to a set of intragap charge transfer (CT) states at the polymer/fullerene interface. This overlap of wavefuctions produces a charge transfer in the ground state. The interaction between this effect and the permanent dipole in the polymer creates a dipole across the supramolecule pointing from the fullerene to the polymer. We find that an efficient exciton dissociation is possible because (i) the CT states are energetically favorable intermediary levels for the electron transfer from the polymer to the fullerene; (ii) there is a potential energy barrier height that blocks the hole transfer to the P3HT chain of the complex, keeping the charge carrier confined in the chain next to the P3HT/fullerene system. This barrier is created by the potential energy of the supramolecule’s dipole moment immersed in the electric field of the electron–hole pair. Finally, using a simple analytical model we show that the dipole’s induced barrier height depends critically on the orientation of the dipole vector relative to the polymer backbone. From this analysis we anticipate the main features of a conjugated polymer/fullerene complex with a high efficiency on exciton dissociation.

Electron diffraction and quantum chemical study of the structure and internal rotation in nitroethane

Studies of the molecular structure and spectra of the lower nitroalkanes are complicated due to hindered internal rotation of the nitro group around the C N bond. In the present work, the structure of nitroethane molecule is determined from electron diffraction (ED) data supplemented by results of quantum chemical calculations within the model accounting for the large-amplitude motions and anharmonicity of vibrations in the rigid fragments. Quantum chemical calculations at the MP2, QCISD and B3LYP levels of theory result in contradictory conclusions regarding the location of the minimum of internal rotation potential energy function and potential barrier height. In the ED analysis, parameters of equilibrium geometry were refined simultaneously with scaling of quantum chemical force matrix aimed at fitting experimental vibrational frequencies. The data processing has shown the minimum of the potential energy function of internal rotation of NO 2 group corresponding to the syn-C molecular configuration with torsional angle τ(C C N O) = 0°. Rotation of the nitro group was found to be slightly hindered, with potential energy barrier height in the range of 50–200 cm −1 (with the most probable value near 120 cm −1). The refined parameters of equilibrium molecular configuration are the following: r e(C C) = 1.509(3) Å, r e(C N) = 1.503(3) Å, r e(N O) = 1.213(3) and 1.215(3) Å, ∠ e(C C N) = 112.3(9)°, ∠ e(O N O) = 125.9(5)°.

Origin of soft mode in SbSe xS 1– xI crystals

The behaviour of the potential energy V( z) of the B 1u (A 1) symmetry soft-mode vibrations of atoms in the direction of the z( c ) axis of SbSe x S 1– x I crystals ( x=0, 0.15, 0.45, 1) upon the normal coordinate (relative displacements of atoms) was investigated in the region of the phase transition temperatures. For this B 1u (A 1) symmetry soft mode, the potential energy barrier height Δ V, the potential energy V( z), its harmonic and anharmonic terms were studied as functions of the mixture composition x and temperature T. The dependence of the soft mode frequency ω S upon the composition x and temperature has been established assuming the double-well shape of the potential energy (per atom) V( z).

Synthesis, structure and magnetism of new single molecule magnets composed of MnII2MnIII2 alkoxo-carboxylate bridged clusters capped by triethanolamine ligands.

A family of tetranuclear mixed-valent Mn(II)(2)/Mn(III)(2) complexes of type [Mn(4)(LH(2))(2)(LH)(2)(H(2)O)(x)(RCO(2))(2)](Y)2.nS has been synthesised and structurally characterised, where LH(3) = triethanolamine (N(CH(2)CH(2)OH)(3)), (R=CH(3), x=2, Y = CH(3)CO(2)-, n=2, S = H(2)O; 1), (R=C(6)H(5), x=0, Y=C(6)H(5)CO(2)-, n=1, S = CH(3)CN; 2), (R=C(2)H(5), x=0, Y=ClO(4)(-), n=0; 3). A common structural core was deduced from X-ray crystallography and consists of a rhomboidal (planar-diamond) array with two 7-coordinate Mn(II) "wingtip (w)" centres and two 6-coordinate Mn(III) "body (b)" centres. The Mn(III) ions are bridged to the Mn(II) ions by mu3-oxygen atoms from a deprotonated alcohol "arm" of each tridentate LH(2-) ligand and by mu2-oxygen atoms from each tetradentate LH(2)(-) ligand. The four nitrogen atoms from LH(2-) and LH(2)(-) groups, together with bridging and terminal carboxylates oxygens complete the outer coordination sites around the Mn atoms. A feature of these clusters is that they are linked together in the crystal lattice by hydrogen-bonding interactions involving a non-coordinated hydroxyl arm on each LH(2-) group. Detailed DC and AC magnetic susceptibility measurements and magnetisation isotherms have been made on the three complexes and show that intra-cluster ferromagnetic coupling is occurring between the S = 2 Mn(III) and S = 5/2 Mn(II) ions to yield S = 9 ground states. The g, J(bb) and J(wb) parameters have been deduced. Inter-cluster antiferromagnetic coupling was noted in and this influences the magnetisation versus field behaviour and the temperature and magnitude of the out-of-phase AC chi"M maxima in comparison to those observed for and. An Arrhenius plot of the reciprocal temperature of the maxima in chi"M obtained at different frequencies (10 to 1500 Hz), in the range 1.75 K to 4 K, against the natural logarithm of the magnetization relaxation rate (1/tau) yielded values of the activation energies and pre-exponential factors for two of these new tetranuclear single-molecule magnets (SMMs), and. The activation energies were compared with the potential energy barrier height, U, for magnetisation direction reversal (U = DS(2)) using the axial zero-field splitting parameter, D, deduced from the DC M/H isotherm analysis for these S = 9 species. The very small separation of S = 9 and 8 levels for these clusters highlights the limitations in the determination of D values from M/H data at low temperatures.

Investigation of the Soft Mode of SbSBrxI1−x Crystals

The behaviour of the potential energy V(z) of the B 1u (A 1 ) symmetry soft mode vibrations of atoms in the direction of the z(c) axis of SbSBrxI 1−x crystals (x = 0, 0.2, 0.75, 1) upon the normal coordinate (relative displacements of atoms) was investigated in the region of the phase transition temperatures. For this B 1u (A 1 ) symmetry soft mode, the potential energy barrier height ΔV, the potential energy V(z), its harmonic and anharmonic terms were studied as functions of the mixture composition x and temperature T. The dependence of the soft mode frequency ωS upon the composition x and temperature has been established assuming the double-well shape of the potential energy (per atom) V(z). By employing A 1u (A 2 ) symmetry coordinates, the force constants C of interaction between molecular chains have been obtained. The type of the phase transition has been established by calculating the Rhodes–Wohlfarth factor R. To calculate this factor, the ratio /ΔV depending upon the mixture composition was employed. It has been found that for mixed crystals with x < 0.8, the phase transition is intermediate between order–disorder and displacive types, and for crystals with x > 0.8, the phase transition is of displacive type.

Mode‐selective stereomutation tunneling as compared to parity violation in hydrogen diselenide isotopomers 1,2,3H280Se2

AbstractWe present quantitative calculations of the mode‐selective stereomutation tunneling in the chiral hydrogen diselenide isotopomers X2Se2 with X = H, D, and T. The torsional tunneling stereomutation dynamics were investigated with a quasi‐adiabatic channel quasi‐harmonic reaction path Hamiltonian approach, which treats the torsional motion anharmonically in detail and all remaining coordinates as harmonic (but anharmonically coupled to the reaction coordinate). We also investigated the influence of the excitation of fundamental modes on the stereomutation dynamics and predict which modes should be promoting or inhibiting. Our stereomutation dynamics results and the influence of parity violation on these are discussed in relation to our recent investigations for the analogous molecules H2O2, HSOH, H2S2, and Cl2S2. The electronic potential energy barrier heights for the torsional motion of hydrogen diselenide are similar to those of HSOH, whereas the torsional tunneling splittings are similar to the corresponding values of HSSH. The ground‐state torsional tunneling splittings calculated here for D2Se2 are of the same order as the parity‐violating energy difference reported by Laerdahl and Schwerdtfeger (Phys. Rev. A 1999, 60, 4439), whereas for T2Se2 the corresponding tunneling splitting is about three orders of magnitude smaller.

Competition between C-C and C-H insertion in prototype transition metal-hydrocarbon reactions.

The competition between C-C and C-H insertion in model transition-metal reactions with cyclopropane and propene (C3H6) was studied as a function of total energy. Insertion of neutral transition metal atoms M (= Y, Zr, Nb, and Mo*) into the C-C bonds of cyclopropane led to formation of MCH2 + C2H4, whereas C-H insertion produced MC3H4 + H2. The measured product branching ratios verify the relative potential energy barrier heights for C-C and C-H insertion predicted by ab initio calculations.

Enhanced magnetocrystalline anisotropy indeposited cobalt clusters

The magnetic properties of nanomaterials made by embedding cobaltnanocrystals in a copper matrix have been studied using a SQUIDmagnetometer. The remanent magnetization at temperatures down to1.8 K and the RT (room temperature) field-dependent magnetization of1000- and 8000-atom (average-size) cobalt cluster samples have beenmeasured. In all cases it has been possible to relate themorphology of the material to the magnetic properties. However, itis found that the deposited cluster samples contain a majority ofsintered clusters even at cobalt concentrations as low as 5% byvolume. The remanent magnetization of the 8000-atom samples wasfound to be bimodal, consisting of one contribution from sphericalparticles and one from touching (sintered) clusters. Using a MonteCarlo calculation to simulate the sintering it has been possible tocalculate a size distribution which fits the RT superparamagneticbehaviour of the 1000-atom samples. The remanent magnetization forthis average size of clusters could then be fitted to a simple modelassuming that all the nanoparticles are spherical and have a sizedistribution which fits the superparamagnetic behaviour. This givesa value for the potential energy barrier height (for reversing thespin direction) of 2.0 µeV/atom which is almost four timesthe accepted value for face-centred-cubic bulk cobalt. The remanentmagnetization for the spherical component of the large-clustersample could not be fitted with a single barrier height and it isconjectured that this is because the barriers change as a functionof cluster size. The average value is 1.5 µeV/atom butpresumably this value tends toward the bulk value(0.5 µeV/atom) for the largest clusters in this sample.

Ab initiostudy of hydrogen adsorption to single-walled carbon nanotubes

We perform the density-functional and quantum chemical calculations of adsorption of a hydrogen molecule to various kinds of single-walled carbon nanotubes (SWNT's). The potential energy barrier height (PBH) for the dissociative adsorption of a hydrogen molecule onto the outer wall of a nanotube decreases as the tube diameter decreases. In contrast, the PBH for ${\mathrm{H}}_{2}$ penetration into an open-ended nanotube increases as the tube diameter decreases, independent of the atomic geometry, i.e., zigzag or armchair structures. ${\mathrm{H}}_{2},$ however, cannot adsorb to the inner wall of any type of nanotube. These results on the structure-dependent ${\mathrm{H}}_{2}$ adsorption to SWNT's are reasonably explained by the ${\mathrm{sp}}^{2}\ensuremath{-}{\mathrm{sp}}^{3}$ rehybridization caused by the interaction between the adsorbing hydrogen and carbon atoms of SWNT's.

An ab initio study of the photochemical decomposition of 3, 3-dimethyldiazirine

Photochemical decomposition of 3,3-dimethyldiazirine (DMD) has been computationally investigated by using high-level ab initio calculations in conjunction with the 6-31G and cc-pvdz basis sets. The geometries of minima and transition states, as well as conical intersection points in the seam of crossing of two surfaces, have been optimized with the complete active space self-consistent field (CAS-SCF) method, and their energies, recalculated with second-order multireference perturbation (CAS/MP2) theory. The reaction path starting at the excited n-pi state of DMD is predicted to occur via a nonadiabatic mechanism, giving carbene and molecular dinitrogen (both in their singlet ground states) as the main products; the computed barrier height (1.0 kcal mol(-)(1)) agrees well with the experimental estimate of the activation energy in the singlet excited state (0.0-1.5 kcal mol(-)(1)). Ground state of dimethylcarbene is the only species where a 1,2-hydrogen shift takes place, being the only source of propene. The calculated potential energy barrier height for dimethylcarbene to propene isomerization (2.6 kcal mol(-)(1)) agrees well with the observed activation energy (2.56 kcal mol(-)(1)). No evidence for rearrangement in the first singlet excited state of DMD has been found; such a process would lead to a higher activation energy than the observed one. Consequently, 1,2-hydrogen migration concurrent with N(2) extrusion in the excited state has been ruled out.

An Investigation of the D/H Addition−Elimination and H Atom Abstraction Channels in the Reaction D + H2CO in the Temperature Range 296 K ≤T≤ 780 K

The reactions of H and D atoms with H2CO (H + H2CO → H2 + HCO (1.1), D + H2CO → HD + HCO (2.1), and D + H2CO → H + HDCO (2.2)) have been studied in the temperature range 296 K ≤ T ≤ 780 K in an isothermal discharge flow reactor with EPR detection of D and H atoms and LIF detection of HCO. Simultaneous measurements of the absolute concentration−time profiles of the three species established the occurrence of the D/H isotope exchange reaction (2.2) in addition to the H atom abstraction channel (2.1). The rate constants for the three reactions could be represented by the Arrhenius expressions k1.1(T) = (8.7 ± 1.9) × 1012 exp[−(14.5 ± 0.7) kJ mol-1/RT] cm3 mol-1 s-1, k2.1(T) = (1.2 ± 0.5) × 1013 exp[−(15.8 ± 0.8) kJ mol-1/RT] cm3 mol-1 s-1, and k2.2(T) = (5.9 ± 1.5) × 1012 exp[−(14.7 ± 1.0) kJ mol-1/RT] cm3 mol-1 s-1. A mechanistic analysis of reaction 2.2 using the unimolecular rate theory gave these estimates for the classical potential energy barrier heights in the addition of D and H atoms to H2CO: ΔE0(D + H2CO) = 1360 ± 100 cm-1 and ΔE0(H + H2CO) = 1540 ± 150 cm-1.

Hydrogen transfer in the porphin anion: A quantum dynamical study of vibrational effects

AbstractThe observed temperature‐dependent hydrogen transfer rate constants for the H, D, and T isotopic species of the porphin anion have been reproduced by two different quantum dynamical models. The approach is based on the master equation for the system‐state populations. The models involve adapted localization properties and a simplified interaction with a quantum mechanical heat bath. A one‐dimensional model describes a hindered circular transfer motion of the hydrogen atom between its four stable sites in the plane of the porphin ring framework. With five parameters that are common to the three isotopic species it yields agreement with the observed data. One of the parameters, the height of the fourfold potential energy barrier, predicts an acceptable estimate for the in‐plane N‐H wagging frequency. Interactions of the transfer motion with individual vibrations have been studied for a series of two‐dimensional model systems. There the circular transfer motion is combined with ring framework modes having properties similar to those obtained for porphin by Li and Zgierski [J. Phys. Chem. 95, 4268 (1991)]. For vibrational modes near or above 960 cm−1, strong interactions are found to be unlikely, as they would yield kinetic isotope effects and/or apparent activation energies in disagreement with the experimental data. For low frequency modes of the ring framework, however, sizeable couplings with the transfer cannot be ruled out. An interaction of the type suggested by quantum chemical results reported by Vangberg and Ghosh [J. Phys. Chem. B. 101, 1496 (1997)] has been included in a two‐dimensional model involving a rectangular displacement of the pyrrole rings. With low vibrational frequency, a very large coupling strength, and a barrier close to the predicted one, this model has also been found to be compatible with experiment.

Translational Activation of the SN2 Nucleophilic Displacement Reactions Cl- + CH3Cl (CD3Cl) → ClCH3 (ClCD3) + Cl-: A Guided Ion Beam Study

Guided ion beam tandem mass spectrometry techniques are used to examine promotion of the symmetric bimolecular nucleophilic substitution (SN2) reaction 37Cl- + CH335Cl → 35Cl- + CH337Cl by translational energy. The translational energy threshold for this process is 45 ± 15 kJ/mol, well above the previously reported potential energy barrier height of 10−13 kJ/mol for the SN2 transition state. The collisionally activated process involves conventional SN2 back-side attack at the carbon atom, but passage over the barrier is impeded by nonstatistical dynamical constraints at collision energies just above the barrier. A significant secondary kinetic isotope effect is observed. The cross section for reaction with CH3Cl is about 20% larger than for the reaction with CD3Cl. At high energies, >410 ± 40 kJ/mol, diatomic Cl2- products are observed. The guided ion beam apparatus and data analysis procedures are described in detail.

Ab initio and experimental investigation of the vibrational energy pattern in N 2O 4: the mid and near infrared ranges

Extensive ab initio calculations are performed concerning N 2O 4 in the ground electronic state, at the MP4 and CMRCI levels of theory, using the 6-31G* and cc-pVTZ basis sets. Special care is devoted to internal degrees of freedom characterizing the quasi van der Waals NN bond, namely the torsion and the NN stretch vibrational modes. The role of the methodology is investigated with the help of previous literature results. It is shown that most properties are significantly better described by MP4 than by MP2, but that a variational multireference method, like CMRCI, is however required for all properties linked to the NN bond. The ab initio vibrational analysis is merged with the one of absorption spectra recorded at medium resolution between 700 and 7000 cm −1, using a Fourier transform interferometer. The resulting set of effective vibrational frequencies and anharmonicities is provided. The height of the torsional potential energy barrier is calculated to be 2000 cm −1, at the best level of theory (CMRCI/cc-pVTZ), in agreement with the highest experimental value available.