Following the streambed reaction on potential-energy surfaces: a new robust method

A simple procedure with low computational efforts is proposed to follow the reaction path of the potential-energy hypersurface (PES) starting from minima or saddle points. The method uses a modification of the so-called “following the reduced gradient” [Quapp W, Hirsch M, Imig O, Heidrich D (1998) J Comput Chem 19:1087]. The original method connects points where the gradient has a constant direction. In the present article the procedure is replaced by taking iterative varying directions of the gradient controlled by the last tangent of the searched curve. The resulting minimum energy path is that valley floor gradient extremal (GE) which belongs to the smallest (absolute) eigenvalue of the Hessian and, hence, that GE which usually leads along the streambed of a chemical reaction. The new method avoids third derivatives of the PES and obtains the GE of least ascent by second-order calculations only. Nevertheless, we are able to follow the streambed GE uphill or downhill. We can connect a minimum with its saddles if the streambed leads up to a saddle, or we find a turning point or a bifurcation point. The effectiveness and the characteristic properties of the new algorithm are demonstrated by using polynomial test surfaces, an ab initio PES of H₂O, and the analytic potentials of Lennard-Jones (LJ) clusters. By tracing the streambeds we located previously identified saddle points for LJ _N with N=3, 7, 8, and 55. Saddles for LJ _N with N=15, 20, and 30 as presented here are new results. Received: 8 March 2000 / Accepted: 17 July 2000 / Published online: 24 October 2000     

Theoretical study on the mechanism of reaction between 3-hydroxy-3-methyl-2-butanone and malononitrile catalyzed by lithium ethoxide

The The mechanism of reaction between 3-hydroxy-3-methyl-2-butanone and malononitrile for the synthesis of 2-dicyanomethylene-4, 5, 5-trimethyl-2,5-dihydrofuran-3-carbonitrile catalyzed by lithium ethoxide was investigated by density functional theory (DFT). The geometries and the frequencies of reactants, intermediates, transition states and products were calculated at the B3LYP/6-31G(d) level. The vibration analysis and the IRC analysis verified the authenticity of transition states. The reaction processes were confirmed by the changes of charge density at the bond-forming critical point. The results indicated that lithium ethoxide is an effective catalyst in the synthesis of 2-dicyanomethylene-4, 5, 5-trimethyl-2, 5-dihydrofuran-3-carbonitrile from malononi-trile and 3-hydroxy-3-methyl-2-butanone. The activation energy of the reaction with lithium ethoxide was 115.86 kJ·mol⁻¹ less than the uncatalyzed reaction. The mechanism of the lithium ethoxide catalyzed reaction differed from the mechanism of the uncatalyzed reaction.     

Theoretical investigation on the reaction of adhesion unit dopa in mussel with electrolyzing seawater

Adhesive proteins secreted by the marine mussel could bind strongly to all kinds of surfaces, for instance, ship hulls and petroleum pipelines. Studies indicated that there was an unusual amino acid 3,4-dihydroxy-l-phenylanine (dopa), which was the crucial super adhesive unit in the proteins. The technology of electrolyzing seawater was employed to generate HOCl solution to hinder the adhesion. However, the detailed anti-fouling mechanism of HOCl solution remained unknown to be fully explained. Herein, we theoretically reported a study of single molecular (dopa) reaction under the HOCl solution environment, which would be helpful to reveal the anti-fouling mechanism through electrolyzing seawater. By using the density functional theory (DFT) quantum mechanics procedure, we theoretically studied the reaction mechanism of the adhesive unit dopa in mussel with electrolyzing seawater. Two possible pathways (1 and 2) were obtained (Fig. 6). The transition state for each pathway was determined, the intrinsic reaction coordinate (IRC) was analyzed and the mechanism had been confirmed. The calculations indicated dopa tended to have electrophonic attacking substitution reaction to generate 3-chlorine-4,5-dihydroxyphenylalanine (dopa-Cl) with different pathways, which hindered the formulation of conjuncted dopa–dopa and thus the stickiness among mussel adhesive proteins reduced. The transition states computation showed that pathway (1) had one transition state (TS1-1) with an activation energy of 102.22 kJ mol⁻¹, while pathway (2) had two transition states (TS2-1, TS2-2) with activation energies of 191.98 kJ mol⁻¹ and 42.00 kJ mol⁻¹ respectively and one intermediate (IM2-1). Rate constant value of pathway (1) was much bigger than that of pathway (2) regardless of high or low temperature, which meant that in the reaction process, pathway (1) was the favorable reaction step; but as the temperature rose, the competitiveness of pathway (2) gradually increased. After the theoretical calculation, we found that it was Cl⁺ played an important and direct role in the dopa's modification.     

Theoretical study of the reaction of Cu with OCS

The reactivity of Cu⁺ with OCS on both singlet and triplet potential energy surfaces (PES) has been investigated at the UB3LYP/6-311+G(d) level. The object of this investigation was the elucidation of the reaction mechanism. The calculated results indicated that both the C–S and C–O bond activations proceed via an insertion–elimination mechanism. Intersystem crossing between the singlet and triplet surfaces may occur along both the C–S and C–O bond activation branches. The ground states of CuS⁺ and CuO⁺ were found to be triplets, whereas CuCO⁺ and CuCS⁺ have singlet ground states. The C–S bond activation is energetically much more favorable than the C–O bond activation. All theoretical results are in line with early experiments.     

Theoretical study of the reaction of Ni with OCS

The reactivity of Ni⁺ with OCS on both doublet and quartet potential energy surfaces (PES) has been investigated at the B3LYP/6-311+G(d) level. The object of this investigation was the elucidation of the reaction mechanism. The calculated results indicated that both the CS and CO bond activations proceed via an insertion–elimination mechanism. Intersystem crossing between the doublet and quartet surfaces may occur along both the CS and CO bond activation branches. The ground states of NiS⁺ and NiO⁺ were found to be quartets, whereas NiCO⁺ and NiCS⁺ have doublet ground states. The CS bond activation is energetically much more favorable than the CO bond activation. All theoretical results are in line with early experiments.     

苯基及取代苯基四唑异构反应的量子化学研究

与四唑相同，对位取代苯基四唑有两种异构体（见图1）.几十年来，实验工作者对这类化合物在医药和农业等方面的应用研究表现出浓厚兴趣［‘-‘1.最近，我们用从头计算和PM3等方法研究了四唑两种异构体间异构化反应的机理问.为了探明这类反应的取代基效应，本文报导用PM3方法[6]     

Theoretical study on the mechanism of OH + HCNO reaction

A detailed mechanistic study of the OH + HCNO reaction, in which the products P _i with i=1, 2, . . . ,7 are involved, is carried out by means of CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p)+ZPVE computatio-nal method to determine a set of reasonable pathways. It is shown that P ₆ (CO + H₂NO) and P ₃ (HNO +HCO) are the major product channels with a minor contribution from P ₅ (NO + H₂CO), whereas the other channels for P ₁ (H₂O + NCO), P ₂ (NH₂ + CO₂), P ₄ (HCN + HO₂) and P ₇(CO + H₂ + NO) are less favorable. All these theoretical results are in harmony with experimental facts.     

DFT study on mechanism of the classical Biginelli reaction

The condensation of benzaldehyde, urea, and ethyl acetoacetate according to the procedure described by Biginelli was investigated at the B3LYP/6-31G（d）, B3LYP/6-31 ＋G（d,p）, and B3LYP/6-311＋G（3df,2p）//B3LYP/6-31＋G（d,p） levels to explore the reaction mechanism. According to the mechanism proposed by Kappe, structures of five intermediates were optimized and four transition states were found. The calculation results proved that the mechanism proposed by Kappe is right.     

SCRCR′CO重排反应的量子化学研究

用MINDO／3方法研究SCRCR′CO的热重排反应的机理，给出了活化能和IRC途径，讨论了活化能与取代基R′和迁移基R的性质之间的内在联系．     

Theoretical investigation on the reaction of N2O and CO catalyzed by Fe(C6H6)

The reaction of N₂O with CO, catalyzed by Fe⁺(C₆H₆) and producing N₂ and CO₂, has been investigated at the UB3LYP/6-311+G(d) level. The computation results revealed that the reaction of Fe⁺(C₆H₆), N₂O and CO, is an O-atom abstraction mechanism. For the reaction channels, the geometries and the vibrational frequencies of all species have been calculated and the frequency modes analysis also have been given to elucidate the reaction mechanism. On the basis for geometry optimizations, the thermodynamic data of these reactions channels have been calculated using the statistical theory at 295.15 K and pressure of 0.35 Torr. Using Eyring transition state theory with Wigner correction, the activation thermodynamic data, rate constant and frequency factors for the these reaction channels also have been given. The results showed that CO and N₂O do not react without catalyst and Fe⁺(C₆H₆) can excellently mediate the reaction of N₂O and CO.     

SCRCR'CO重排反应的量子化学研究

用ＭＩＮＤＯ／３方法研究ＳＣＲＣＲ’ＣＯ的热重排反应的机理，给出了活化能和ＩＲＣ途径，讨论了活化能与取代基Ｒ’和迁移基Ｒ的性质之间的内在联系。     

CH3(2A′)自由基与臭氧反应机理的量子化学研究

用量子化学UMP2方法，在6-311++G**基组水平上研究了CH3(2A′)自由基与臭氧反应机理，全参数优化了反应过程中反应物、中间体、过渡态和产物的几何构型，在UQCISD(T)/6-311++G**水平上计算了它们的能量；并对它们进行了振动分析，以确定中间体和过渡态的真实性；同时应用经典过渡态理论计算了反应的速率常数，并与实验值进行了比较, CH3自由基与臭氧反应速率常数的理论计算结果为: 4.73×10－14 cm3•molecule－1•s－1，与实验报导的结果(k=2.52×10－14 cm3•molecule－1•s－1)很接近，同时发现CH3(2A′)自由基与O3的反应是强放热反应.     

On the determination of dynamic surface tensions by means of a modified bubble pressure method

A method for the determination of the dynamic surface tension of surfactant solutions is presented which allows to cover adsorption times down to 10 seconds. This method is based on the determination of the pressure inside two communicating bubbles. There is no deformation of the solution/air interface during the experimental procedure. Hence, in evaluating the kinetic data no surface area enlargement has to be taken into account. An automatically operating procedure should allow to cover adsorption times down to approximately one second and should improve the measuring accuracy substantially. Experimental investigations with aqueous n-decanoic acid solutions using the method proposed provided evidence that decanoic acid is adsorbed by a diffusioncontrolled mechanism.     

Reactive domains of energy hypersurfaces and the stability of minimum energy reaction paths

Special properties of the Riemannian metric for energy hypersurfaces, defined within the framework of the Born-Oppenheimer approximation, are utilized in devising a partitioning scheme for domains of nuclear coordinates. The chemically important coordinate domains are distinguished from domains of lesser importance by their curvature properties. Conditions are derived for the stability of minimum energy reaction paths, and the effects of instability regions are investigated. Instability domains along minimum energy paths may allow small vibrational perturbations to alter the outcome of the chemical reaction.     

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

In this work three-dimensional potential energy surfaces of the first five singlet states of OHF are developed based on fits of more than 10,000 highly accurate ab initio points. An approximate treatment is presented for the calculation of the anisotropy parameter describing the electron angular distribution photodetached from a molecular anion. This method is used to calculate the angle-resolved photoelectron spectra in the photodetachment of OHF⁻. The wave packet formed in the neutral OHF system is placed at the transition state region, and yields the formation of OH + F and HF + O products. The results are compared with the recent experimental measurements published by Neumark [D.M. Neumark, Phys. Chem. Chem. Phys. 7 (2005) 433]. The intensity found at low electron kinetic energy including these five states and the three lower triplet states is found to be low. To analyze the effect of higher electronic states more excited ¹Σ⁻, ³Σ⁺ and ³Δ states are calculated at collinear geometry. The agreement with the experimental data improves, thus demonstrating that the correct simulation of the photodetachment spectrum at 213 nm involves at least 12 electronic states. All the structures of the experimental spectra are semiquantitatively reproduced finding an overall good agreement. It is concluded that the main problem of the simulation is in the intensity and anisotropy parameters. An alternative to their calculation would be to fit their values to reproduce the experimental results, but this would require to separate the contribution arising from different final electronic states.     

Theoretical study on the reaction mechanism of bis-addition of methyl azide to C60

The selectivity of attacking sites and the reaction mechanisms of the bis-addition of methyl azide with its corresponding azafulleroid (C₆₀NCH₃) have been investigated using AM1 semi-empirical and density functional methods. The whole reaction processes can be divided into two stages. The first stage is the 1,3-dipolar cycloaddition (1,3-DC) reaction of methyl azide with C₆₀NCH₃ giving rise to a triazoline intermediate and the second is the N₂ elimination. Based on the charge distributions, four patterns of the addition sites have been discussed. In view of the energy barriers, two kinds of 6–6 double bonds, which are in the most and the second vicinities of the –NCH₃ addend group of the C₆₀NCH₃, are the two most possible attack sites in the reaction of 1,3-DC. The analyses of the π-orbital axis vector (POAV) and the deformation and interaction energies indicate that it is the favorable interaction energy rather than the strain release that dominates the two preferential attacking patterns. The subsequent thermal elimination of N₂ takes place via two steps in which the breaking of N–N single bond precedes the cleavage of the C–N bonds of the unsubstituted N atom. The N₂ elimination occurs simultaneously with the formation of the new C–N bonds (corresponding to the substituted N atom), giving rise to two isomers of the bisadducts. One is a double azafulleroid with two N atoms bonding to two consecutive 5-6 junctions of the same pentagon, and the other with two N atoms bonding to two alternate 5-6 junctions of the same pentagon. The analysis of the energy results shows that although the former reaction is preferred to some extent, both of the two reactions can take place and both of the two bisadducts are in principle obtainable.     

Resistance transitions detected by analysis of the voltammetry of tetrathiafulvalene microparticles adhered to electrode surfaces under conditions of dynamic resistance compensation

Dynamic resistance compensated cyclic voltammograms have been obtained when solid tetrathiafulvalene (TTF) is converted to a highly conducting TTF⁺ salt. Two resistance transitions were detected, one being related to bulk transformation of solid by nucleation-growth TTF^+/0 processes and the other occurring with negligible detectable current and mass changes in the reversible potential region. The general usefulness of obtaining resistance–potential data and maintaining a linear potential–time (scan rate) relationship by employing dynamic IR_u (I=current, R_u=uncompensatedcellresistance) in mechanistic studies of the voltammetry of solids adhered to electrode surfaces is emphasized.     

Mechanism(s) of thermal decomposition of N-Nitrosoamides: A density functional theory study

The thermal decomposition of N-nitrosoamides has experimentally been demonstrated to depend on several factors, such as temperature, solvent and the substituents on the substrate. Consequently, a number of reaction mechanisms have been proposed for this process in the literature. In this work, we present a comprehensive computational investigation in which we examine the detailed reaction mechanisms for two N-nitrosoamides (with aliphatic and aromatic substituents) in two different solvents (mesitylene and methanol). It is shown that the reaction mechanism can change dramatically with the nature of the substrate and the choice of solvent. Importantly, it is found that the polar solvent stabilizes ion-pairs that are unstable in the non-polar solvent, which can play a key role in the mechanism.     

Kinetic study of the formation reaction of colloidal silica spheres in microgravity using aircraft

Polymerization reactions of colloidal silica spheres via the hydrolysis and dehydration processes of tetraethyl orthosilicate with ammonia and a tiny amount of water in ethyl alcohol have been studied in microgravity by the parabolic flights of a MU-300 rear-jet aircraft. Induction periods and polymerization rates are determined by fast-scanning transmitted-light-intensity measurements and the fast-scanning dynamic light-scattering method. Direct observation of the reaction mixtures is also made with a charge-coupled device video camera. Reproducible and reliable data are obtained in microgravity compared with those in gravity. Increases in the induction times and decreases in the polymerization rates are observed in microgravity compared with those in gravity. One of the main reasons for these observations is the fact that the translational Brownian movement of the reactants and/or product spheres is free from downward translational movement in microgravity. Very weak convection of the reaction suspensions in microgravity is another important factor. Received: 10 November 1998 Accepted in revised form: 12 January 1999     

Ab initio and DFT calculations on the initial step in thiamin catalysis

The diphosphate ester (ThDP) of thiamin (vitamin B₁) is an important cofactor of enzymes within the carbohydrate metabolism. The initial reaction step shared by all ThDP-dependent enzymes is the deprotonation of the C2–H of the thiazolium ring. The replacement of the 4′-amino group by a hydroxyl one in the pyrimidine ring leads to the oxy-ThDP analogue which is known as an antagonist in thiamin catalysis.

Ab initio and DFT calculations on the MP2/6-31G* and B3LYP/6-31G* level were performed to study the proton relay function in thiamin and oxythiamin systems. Both MP2 and B3LYP calculations show significant differences of the reaction coordinate of the ylide formation in the systems. Tautomers, protonated and deprotonated species of both systems show different trends regarding their stability. The influence of correlation effects on the results is discussed by comparison with the HF-SCF/6-31G* data. Frequency calculations on the B3LYP/6-31G* level were performed to characterize the minima and transition state structures, respectively.