Quantum Dynamic Effects at Insertion Minimum Reaction: H+LiF Reaction

The quantum transition state concept provides an intuitive and numerically efficient framework for the description of quantum state-resolved reactive scattering and thermal reaction processes. Combining multiconfigurational time-dependent Hartree wave packet dynamics calculations with a flux correlation function based analysis, rigorous full-dimensional calculations of initial state-selected and state-to-state reaction probabilities for six atom reactions are feasible. In these calculations, a set of wave packets is generated in the transition state region, propagated into the asymptotic area, and analyzed. In the present work, an alternative approach which employs counter-propagating sets of wave packets is introduced. Outgoing wave packets started in the transition state region are matched with incoming wave packets generated in the reactant (or product) asymptotic area. Studying the H + CH4 → H2 + CH3 reaction as a prototypical example, one finds that the incoming wave packets can be propagated closely up to the transition state region with minor numerical effort. Employing cross correlation functions of incoming and outgoing wavefunctions, the propagation times required for the outgoing wave packet and thus the numerical costs of the entire calculation can be reduced significantly. Detailed full-dimensional calculations studying initial state-selected reaction probabilities for the H + CH4 → H2 + CH3 reaction are presented to illustrate the new approach. It is found that converged results can be obtained using shorter propagation times of the outgoing wave packets and less single-particle functions.

We investigate the transition-state (TS) region of the potential energy surface (PES) of the reaction tBu3P + H2 + B(C6F5)3 → tBu3P-H(+) + (-)H-B(C6F5)3 and the dynamics of the TS passage at room temperature. Owing to the conformational inertia of the phosphane⋅⋅⋅borane pocket involving heavy tBu3P and B(C6F5)3 species and features of the PES E(P⋅⋅⋅H, B⋅⋅⋅H | B⋅⋅⋅P) as a function of P⋅⋅⋅H, B⋅⋅⋅H, and B⋅⋅⋅P distances, a typical reactive scenario for this reaction is a trajectory that is trapped in the TS region for a period of time (about 350 fs on average across all calculated trajectories) in a quasi-bound state (scattering resonance). The relationship between the timescale of the TS passage and the effective conformational inertia of the phosphane⋅⋅⋅borane pocket leads to a prediction that isotopically heavier Lewis base/Lewis acid pairs and normal counterparts could give measurably different reaction rates. Herein, the predicted quasi-bound state could be verified in molecular collision experiments involving femtosecond spectroscopy.

Initial state-selected reaction probabilities for the H+CH(4)→H(2)+CH(3) reaction are computed for vanishing total angular momentum by full-dimensional calculations employing the multiconfigurational time-dependent Hartree approach. An ensemble of wave packets completely describing reactivity for total energies up to 0.58 eV is constructed in the transition state region by diagonalization of the thermal flux operator. These wave packets are then propagated into the reactant asymptotic region to obtain the initial state-selected reaction probabilities. Reaction probabilities for reactants in all rotational states of the vibrational 1A(1), 1F(2), and 1E levels of methane are presented. Vibrational excitation is found to decrease reactivity when reaction probabilities at equivalent total energies are compared but to increase reaction probabilities when the comparison is done at the basis of equivalent collision energies. Only a fraction of the initial vibrational energy can be utilized to promote the reaction. The effect of rotational excitation on the reactivity differs depending on the initial vibrational state of methane. For the 1A(1) and 1F(2) vibrational states of methane, rotational excitation decreases the reaction probability even when comparing reaction probabilities at equivalent collision energies. In contrast, rotational energy is even more efficient than translational energy in increasing the reaction probability when the reaction starts from the 1E vibrational state of methane. All findings can be explained employing a transition state based interpretation of the reaction process.

The elementary vapor-phase reaction between Cl atoms and HCHO has been studied by ab initio methods. Calculations at the MP2, MP3, MP4(SDTQ), CCSD, CCSD(T), and MRD-CI levels of theory show that the reaction is characterized by a low electronic barrier; excluding the effects of spin-orbit splitting in Cl, our best estimate at the MRD-CI/aug-cc-pVTZ//RHF-RCCSD(T)/aug-cc-pVTZ level of theory predicts a Born-Oppenheimer barrier height of 0.7 kJ mol-1. The energies of the lowest six electronic states as resulting from MRD-CI calculations are presented at discrete points along the reaction path, and two avoided crossings are found in the transition state region. The spin-orbit splitting in Cl is also calculated along the reaction path; it is not negligible in the transition state region and is found to increase the barrier by only 1.4 kJ mol-1 at the RCCSD(T)/aug-cc-pVTZ transition state geometry. The minimum energy path of the reaction connects an energetically weakly stabilized adduct on the flat potential surface on the reactant side and an energetically strongly stabilized postreaction adduct. The reaction rate coefficient and the kinetic isotope effects were calculated using improved canonical variational theory with small curvature tunneling (ICVT/SCT), and the results were compared to experimental data. The experimental reaction rate coefficient is reproduced within its uncertainty limits by variational transition state theory with interpolated single-point energy corrections (ISPE) at the MP4(SDTQ) level of theory and by conventional transition state theory with interpolated optimized energies (IOE) at the MRD-CI//RCCSD(T) level of theory and interpolated optimized geometries at the RCCSD(T) level of theory on an MP2/aug-cc-pVTZ potential energy surface when employing scaled vibrational frequencies.

Probing the Energy Landscape of Protein Folding/Unfolding Transition States

Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the SN2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).

The work presented in this thesis explores two distinct fields of organometallic chemistry with a common goal of selectively transforming cheap and abundant feedstocks to value-added chemicals using homogeneous catalysts. Chapter 1 presents the synthesis and characterization of a series of bis(diphenylphosphino)amine ligands and their corresponding chromium(III) trichloride complexes. The isolated chromium complexes are precursors to highly active catalysts for the selective oligomerization of ethylene to 1-hexene and 1-octene. The unique feature of the ligands presented herein is the presence of coordinating functionalities tethered to the nitrogen backbone. These act as hemilabile donors, which stabilize the active species and/or transition states during catalysis. This increased stability leads to more productive catalysts. Furthermore, important solvent and additive effects have been investigated. While reactions in non-polar solvents exhibit poor activity at lower ethylene pressures, those in more polar solvents are highly active and generate very little undesired polymer. Varying the solvent has a significant impact on 1-hexene/1-octene selectivity as well. Experiments with potentially coordinating additives result in a higher tendency for 1-octene formation. An investigation of catalyst decomposition is also discussed. Chapter 2 presents synthetic, structural and reactivity studies on a series of Group 7 carbonyl derivatives relevant to synthesis gas conversion. Reduction of the carbonyl precursors with a hydride source generates the corresponding formyl species. This reaction is facilitated when more electrophilic carbonyl complexes are employed. Neutral and cationic Fischer carbene complexes were prepared by the reaction of the formyl species with boranes and alkyltriflates, respectively. Further reduction of Group 7 methoxycarbenes with a hydride leads to the formation of a reactive methoxymethyl species. Dimethyl ether release is obtained from treatment of a manganese methoxymethyl species with a hydride. Moreover, subjecting manganese methoxymethyl complexes to an atmosphere of CO generates acyl complexes via migratory insertion. Preliminary mechanistic details are presented.

Streffer, Friedrich Theoretical Investigation of Cooperative Effects of H-Bonds in Biomolecular Systems The present work investigates signatures of cooperative effects of H-bonds especially in DNA with statistical and quantum chemical methods. Part I investigates results of information-theoretical analyses of DNA sequences of living organisms, which are tested qualitatively and quantitatively with respect to their biological aspects and/or implications. The results concern ’long-range correlations’ and ’fractals’ in intron-containing DNA sequences, their possible ’linguistic’ structure, and other related aspects. The investigations demonstrate that the findings a ’fractal’ structure in DNA are trivially equivalent to variations of the base pair composition, or patchiness, of different regions in a natural DNA sequence. It is explicitly shown that neither a well-defined ’scaling’ or ’fractal’ exponent, nor a well-defined Zipf exponent of the ’linguistic’ test does exist. The biological origins of such variations are discussed. Quantitative comparisons of natural DNAs with computer-generated, artificial sequences are made. But the present work shows that certain natural DNA sequences (especially those with compact genomes) do have certain stochastic characteristics (say, pseudo-fractal exponents, averaged Zipf slopes, etc.) which are intrinsically different from artificial sequences. To shed more light on this point, investigations concerning the short range correlation of base pair, which may be caused by short-lived quantum entanglement of protons, are presented. The most striking finding is that quantum entanglement appears preferably between the third base of a codon and the first base of the following one. Results on a large number of DNA sequences of various types and from widely different taxa are reported. Additionally, results of current investigations concerning the so-called ’detrended fluctuation analysis’ and the ’Kullback information measure’ of DNA sequences are reported. Part II deals with quantum chemical investigations of the AT, GC and the artificial κχ base pair. Different levels of theory have been applied with full geometry optimization and the ’frozen-core’ approximation; among them are B3LYP/6-31G** and MP2/6-31G**. The calculations in the ’frozen-core’ approximation confirm the double well character of all investigated potential energy surfaces, with a decreased energy of the transition states on the inclusion of the electron correlation effects. Couplings of the different proton transfer reactions are discussed, testing quantitavely the assumptions of a quantum mechanical Jordan-Block structure found in the GC pase pair. The geometry optimization of the relevant stationary points of the double proton transfer reactions in the AT and GC base pair has been performed at the B3LYP/6-31G** level of theory. The most striking finding is found during the normal mode analysis of the vibrations. A vibrational mode involving the relevant protons for the double proton transfer does exist in the GC base pair and all tautomers, whereas the AT base pair does not have such a vibrational mode. Implications are discussed. Finally, two experiments are proposed to test the findings.

Transition state spectroscopy of open shell systems: Angle-resolved photodetachment spectra for the adiabatic singlet states of OHF

BACKGROUND A hidden Markov model (HMM) is used for exon prediction on DNA of genes Plasmodium falciparum that has a model structure based on exon region structure in coding sequence (CDS). The objective research was to develop a new structure model to predict exon on DNA-genes of Plasmodium falciparum based on CDS structure using the HMM system. METHODS Model design in CDS, between two exon regions can be found one intron region and the model state number is used for its region. Its state number is used by separating start codon from first exon region and stop codon from the last exon region up to 9. The Viterbi algorithm and the backward-forward method for transition as well as emission states are used for training process. Furthermore, Viterbi and Baum-Welch algorithms are used for the testing process. The correlation coefficient (CC) was used as performance indicator, as the ratio of the estimated state in the output and the original state in the input of the model. RESULTS The simulation results has shown that the CC values depend on the given of the backward-forward transition state values randomly. The model with state number 9 showed the highest average of CC values of 0.7289 for Viterbi algorithm, and is 0.7166 for Baum-Welch algorithm. However, the lowest average of CC values has been found for the model with state number five. Its values are 0.6735 by using Viterbi algorithm and 0.6661 by using Baum-Welch algorithm. CONCLUSION The new structure model based on HMM system was valid to predict exon on DNA-genes of Plasmodium falciparum.

In the present work, the reaction mechanisms for thermal decomposition of cyclohexane in the gas phase have been investigated using quantum chemical calculations and transition-state theory. Three series of reaction schemes containing 38 elementary reactions are proposed. The geometry optimization and vibrational frequencies of reactants, transition states, and products are determined at the BH&HLYP/cc-pVDZ level, while energies are calculated at the CCSD(T)/cc-pVDZ level. The rate constants for the reactions without transition states, including the initial steps of cyclohexane decomposition (C–C bond scission or C–H bond scission), are obtained by the canonical variational transition-state theory (CVT), while the rate constants for the other reactions with saddle-point transition states are obtained by the conventional transition-state theory (TST) in the temperature range of 300–3000 K. The rate constants are in good agreement with data available from the literature. The kinetic parameters in the modifi...

We report real wave packet (WP) calculations of reaction probabilities, cross sections, rate constants, and product distributions of the reaction N(4S)+O2(X 3∑g−)→NO(X 2∏)+O(3P). We propagate initial WPs corresponding to several O2 levels, and employ reactant coordinates and a flux method for calculating initial-state-resolved observables, or product coordinates and an asymptotic analysis for calculating state-to-state quantities. Exact or J-shifting calculations are carried out at total angular momentum J=0 or J&amp;gt;0, respectively. We employ the recent X 2A′ S3 potential energy surface (PES) by Sayós et al. and the earlier a 4A′ PES by Duff et al. In comparing S3 results with the WP ones of a previous X 2A′ S2 PES, we find lower S3 energy thresholds and larger S3 probabilities, despite the higher S3 barrier. This finding is due to the different features of the doublet PESs in the reactant and product channels, at the transition state, and in the NO2 equilibrium region. We analyze the effects of the O2 initial level and show that tunneling through the S3 barrier enhance the room-temperature rate constant by ∼3.7 times with respect to the previous S2 WP rate. The agreement with the room-temperature experimental result is thus notably improved. The NO vibrational distribution is inverted and the rotational ones are strongly oscillating. We explain these nonstatistical results showing that the reaction partners approach each other with a large impact parameter. The WP vibrational distribution is however different from that observed, which is oscillating. WP calculations show that the new S3 PES describes accurately several features of the X 2A′ state, although a lowering of its barrier height by ∼0.56 kcal/mol should bring calculated and observed rate constants in full agreement.

Variational transition state theory is reformulated in terms of compound state resonances associated with the transition state region. The use of the formalism is illustrated for two-dimensional model problems, which are treated by the adiabatic theory of reactions and by perturbation theory. The limitations of the latter are delineated for the case of a biquadratic (quartic) coupling of the reaction coordinate to a transverse vibration. 51 refs.

We present measured and calculated photodetachment spectra of OHCl−, and we interpret the results in terms of the vibrational structure of the transition state of the O+HCl→OH+Cl reaction. The measured spectra exhibit two distinct features—an intense broad peak at high electron kinetic energies and a less intense shoulder at lower energies. Superimposed on these broad features are several sharper structures, but they are barely discernible from noise in the spectrum. To interpret these spectra, we have used a recently developed global 3A″ potential surface for the O+HCl reaction to calculate Franck–Condon factors, using an L2 method (i.e., expansion in terms of square integrable basis functions) to approximate the scattering wave functions on the reactive surface. Assignment of the spectrum has been assisted using the results of quantum coupled channel calculations for the same surface. The resulting calculated spectrum shows the same broad features as the measured spectrum. There is also fine structure with spacings and energies that are similar to the experiment, but specific features do not match. To interpret both the broad and fine features in the theoretical spectrum, a hierarchical analysis is applied wherein this spectrum is decomposed by a tree construction into components of increasingly higher resolution. The physical meaning of each of these components is then determined by plotting ‘‘smoothed states’’ that are obtained from the tree coefficients. This leads to the conclusion that the two broad features in the spectrum are made up of progressions in hindered rotor states of the Cl–OH complex, with the most intense feature corresponding to OH(v=0) and the weaker shoulder corresponding to OH(v=1). There is evidence for Feshbach resonance features in the v=1 feature, but it appears that most of the fine structure is due to hindered rotor states.

Multi-alkali photocathode in super generation image intensifier is different from previous multi-alkali photocathode between the production processes,so the photoelectric emission characteristics are different from previous multi-alkali photocathode.In this paper,through the measurement of multi-alkali photocathode spectral reflectivity and transmissivity,according to the law of conservation of energy,cathode spectral absorption rate was obtained.Spectral absorption rate indicates that,only when the photon greater than 1.333 eV,cathode absorption rates began to increase quickly.The cathode spectral absorption shows that cathode will not absorb any photons if light incident photon is less than the absorption limit,i.e.933 nm wave absorption limit.In the cathode surface electron affinity further reduced circumstances,cathode photoemission long wave theory threshold is determined by long-wave absorption limit.In the electronic transition process after absorption of a photon,transition energies increase less than the absorption of the incident photon energy,i.e.the presence of an energy loss.The higher of a photon is,the higher electronic transition level is,the more loss is.At the same time,the higher of a photon is;the higher-energy level transition electron,the lower electronic transition probability is.Photocathode quantum efficiency is determined by the absorption rate,the transition probability and transition level,energy loss of diffusion process and other factors,thus photocathode quantum efficiency is in the presence of long wave threshold and shortwave threshold also.Photocathode quantum efficiency in 587 nm reaches the maximum value,after that decreases with the photon increases,when 3.6 eV,the quantum efficiency is reduced to zero.Cathode in photon of 3.6 eV the absorption coefficient is still high,but due to the electronic transition probability is low,while the electron diffusion process of loss is big,thus in spite of cathode on lower wavelength has high absorption coefficient,but the quantum efficiency is still low.Therefore on shortwave,cathode absorbed shortwave photon is converted into a photoconductive,lattice vibration and other forms of energy;the photoelectric emission utilization rate is very low.