Analysis of the reaction force for a gas phase S(N)2 process: CH3Cl + H2O --> CH3OH + HCl

The "reaction force" F(R(c)) is the negative derivative of a system's potential energy V(R(c)) along the intrinsic reaction coordinate of a process. If V(R(c)) goes through a maximum, as is commonly the case, then F(R(c)) has a characteristic profile: a negative minimum followed by zero at the transition state and then a positive maximum. These features reflect four phases of the reaction: an initial one of reactant preparation, followed by two of transition to products, and then relaxation of the latter. In this study, we have analyzed, in these terms, a gas-phase S(N)2 substitution, selected to be CH3Cl + H2O --> CH3OH + HCl. We examine, at the B3LYP/6-31G level, the geometries, energetics, and molecular surface electrostatic potentials, local ionization energies, and internal charge separation.     

Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics

The dissociation of a weak acid - a histidine residue - in water was investigated by means of constrained Car-Parrinello ab initio molecular dynamics. Both linear and coordination constraints were employed, and the structural, electronic, and dynamical transformations along the respective reaction coordinates were analyzed. The calculated potentials of mean force for the dissociation of a hydrogen atom from the Nepsilon and Ndelta positions of the imidazole ring reveal that protonated forms are approximately 9.0-9.5 kcal/mol more stable than the deprotonated. This result seems to agree well with the experimental estimate based on pKa. A possible transition state for the deprotonation has also been identified. Analysis of the electron localization function indicates that the proton transfer along the selected reaction path is not a fully concerted process.     

Reaction force decomposition of activation barriers to elucidate solvent effects

The reaction force F(Rc) of a chemical or physical process is given by the negative derivative of the potential energy V(Rc) along the intrinsic reaction coordinate Rc. F(Rc) unambiguously and naturally divides the activation barrier in each direction into two contributions, one of which has been found to reflect preparative structural factors, Eact,prep, and the other corresponds to the first part of the transition to products, Eact,trans. We have analyzed F(Rc) for an SN2 substitution reaction in both the gas and aqueous phases. Although the overall forward and reverse activation barriers are significantly lowered by the solvent, the Eact,trans are very little affected. Thus the increased rates that are predicted for this process in aqueous solution can be attributed to the solvent facilitating the structural effects in the preparative stages, decreasing the Eact,prep. This example shows how the reaction force decomposition of activation barriers can help to elucidate the roles played by external factors, e.g., solvents.     

Theoretical study of CH…O hydrogen bond in proton transfer reaction of glycine

Density functional theory (DFT) calculations are used to study the strength of the CH…O H‐bond in the proton transfer reaction of glycine. Comparison has been made between four proton transfer reactions (ZW1, ZW2, ZW3, SCRFZW) in glycine. The structural parameters of the zwitterionic, transition, and neutral states of glycine are strongly perturbed when the proton transfer takes place. It has been found that the interaction of water molecule at the side chain of glycine is high in the transition state, whereas it is low in the zwitterionic and neutral states. This strongest multiple hydrogen bond interaction in the transition state reduces the barrier for the proton transfer reaction. The natural bond orbital analysis have also been carried out for the ZW2 reaction path, it has been concluded that the amount of charge transfer between the neighboring atoms will decide the strength of H‐bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Photoswitchable electrochemical behaviour of a [FeFe] hydrogenase model with a dithienylethene derivative

A diiron dithiolate complex 1o with a dithienylethene (DTE) phosphine ligand has been elaborately designed and fully investigated by spectroscopic and DFT computational studies. Upon irradiation with UV light, the DTE moiety in complex 1o undergoes an excellent photocyclization reaction to attain ring-closed state 1c in high yield (>95%), accompanied by a colour change from orange to deep blue. On the other hand, upon irradiation with visible light (>460 nm), ring-closed form 1c in CH(3)CN solution reverts perfectly into ring-open form 1o. Both 1o and 1c were characterised by IR, (1)H, (31)P, (19)F NMR and electrochemical spectroscopy. The electrochemical behaviours of both the open and closed forms were investigated by cyclic voltammetry. Upon photocyclization reaction, a 290 mV (from -2.29 V to -2.00 V) positive shift is induced in the potential of electrochemical catalytic proton reduction, due to the electron-withdrawing effect of the ring-closed DTE moiety. Consequently, complex 1 can reversibly photoswitch the potential of proton reduction on the [FeFe] moiety.     

Effect of thermal history on kappa-carrageenan hydrogelation by differential scanning calorimetry

The effect of thermal history on gel-sol transition was investigated by highly sensitive differential scanning calorimetry (DSC) in order to clarify the non-equilibrium state of κ-carrageenan hydrogels. κ-Carrageenan with a concentration from 0.5% to 5.0% was used. When concentration of solution was lower than 2.0%, homogeneous κ-carrageenan gel was formed when aqueous solution was fully equilibrated. When concentration exceeded 3.0%, a sub-peak could be observed at the low temperature side of the main peak. It was indicated that helices having various sizes and different kinds of defects are present in the junction zone. Thermal histories, such as cooling rate from the sol state or annealing at around gel-sol transition temperature, markedly affect the junction zone formation. A large junction zone is formed at a slow gelation rate, and also that many small junction zones form at a fast gelation speed.     

Effect of absolute laser phase on reaction paths in laser-induced chemical reactions

Potential surfaces, dipole moments, and polarizabilities are calculated by ab initio methods [unrestricted MP2(full)/6-311++G(2d,2p)] along the reaction paths of the F+CH4 and Cl+CH4 reaction systems. It is found that in general dipole moments and polarizabilities exhibit peaks near the transition state. In the case of X=F these peaks are on the products side and in the case of X=Cl they are on the reactants side indicating an early transition state in the case of fluorine and a late transition state in the case of chlorine. An analysis of the geometric changes along the reaction paths reveals a one-to-one correspondence between the peaks in the electric properties and peaks in the rate of change of certain internal geometric coordinates along the reaction path. Interaction with short infrared intense laser fields pulses leads to the possibility of interferences between the dipole and polarizability laser-molecule interactions as a function of laser phase. The larger dipole moment in the Cl+CH4 reaction can lead to the creation of deep wells (instead of energy barriers) and new strongly bound states in the transition state region. This suggests possible coherent control of the reaction path as a function of the absolute phase of the incident field, by significant modification of the potential surfaces along the reaction path and, in particular, in the transition state region.     

Mechanistic information from pressure acceleration of hydride formation via proton binding to a cobalt(I) macrocycle

The effect of pressure on proton binding to the racemic isomer of the cobalt(I) macrocycle, CoL(+) (L = 5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene), has been studied for a series of proton donors using pulse radiolysis techniques. The second-order rate constants for the reaction of CoL(+) with proton donors decrease with increasing pK(a) of the donor acid, consistent with a reaction occurring via proton transfer. Whereas the corresponding volumes of activation (DeltaV) are rather small and negative for all acids (proton donors) with pK(a) values below 8.5, significantly larger negative activation volumes are found for weaker acids (pK(a) > 9.5) containing OH groups as proton donors. In the latter case, the observed DeltaV for these protonation reactions show a correlation with the reaction volumes (DeltaV degrees (ion)) for the ionization of the weak acids with a slope of 0.44, indicating that bond dissociation of the weak acid molecule bound to the metal center proceeds approximately halfway at the transition state along the reaction coordinate in terms of volume changes.     

Double proton transfer reactions with plateau-like transition state regions: pyrazole-trifluoroacetic acid clusters

The double proton transfer reactions between carboxylic acids and pyrazole were studied by computational methods up to the coupled-cluster level. Introduction of substituents allowed for a systematic modulation of the reaction profile, resulting in imaginary frequencies of the associated transition states between -1180 and -45 cm(-1). In the latter case, a local transition state is replaced by an extremely flat (plateaulike) transition region, which constitutes the transition from a concerted toward a stepwise mechanism. Vertical excitation energies along the reaction path reveal that the feature of a plateau in the ground state is mirrored in the excited states.     

Hydration effects on the reaction with an open-shell transition state: QM/MM-ER study for the dehydration reaction of alcohol in hot water

The reaction mechanism for the dehydration of 1,4-butanediol in hot water has been investigated by means of the hybrid quantum mechanical/molecular mechanical approach combined with the theory of energy representation (QM/MM-ER). We have assumed that the proton transfers along the hydrogen bonds of the water molecules catalyze the reaction, where the transition state (TS) forms a singlet biradical electronic structure. It has been revealed by the simulation that the biradical electronic state at the TS changes to zwitterionic structure in solution due to the hydration of the polar solvent. Such the electronic structure change gives rise to the substantial stabilization of the TS in hot water. As a result, the water-catalytic path becomes more favorable in aqueous solution than another possible path that proceeds without proton transfers as opposed to the reaction mechanism in the gas phase. Furthermore, the activation free energy computed by the present method is in excellent agreement with the experimental result.     

Proton transfer in a polar solvent from ring polymer reaction rate theory

We have used the ring polymer molecular dynamics method to study the Azzouz-Borgis model for proton transfer between phenol (AH) and trimethylamine (B) in liquid methyl chloride. When the A-H distance is used as the reaction coordinate, the ring polymer trajectories are found to exhibit multiple recrossings of the transition state dividing surface and to give a rate coefficient that is smaller than the quantum transition state theory value by an order of magnitude. This is to be expected on kinematic grounds for a heavy-light-heavy reaction when the light atom transfer coordinate is used as the reaction coordinate, and it clearly precludes the use of transition state theory with this reaction coordinate. As has been shown previously for this problem, a solvent polarization coordinate defined in terms of the expectation value of the proton transfer distance in the ground adiabatic quantum state provides a better reaction coordinate with less recrossing. These results are discussed in light of the wide body of earlier theoretical work on the Azzouz-Borgis model and the considerable range of previously reported values for its proton and deuteron transfer rate coefficients.     

Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath

A hybrid quantum/classical molecular dynamics approach is applied to a proton transfer reaction represented by a symmetric double well system coupled to a dissipative bath. In this approach, the proton is treated quantum mechanically and all bath modes are treated classically. The transition state theory rate constant is obtained from the potential of mean force, which is generated along a collective reaction coordinate with umbrella sampling techniques. The transmission coefficient, which accounts for dynamical recrossings of the dividing surface, is calculated with a reactive flux approach combined with the molecular dynamics with quantum transitions surface hopping method. The hybrid quantum/classical results agree well with numerically exact results in the spatial-diffusion-controlled regime, which is most relevant for proton transfer in proteins. This hybrid quantum/classical approach has already been shown to be computationally practical for studying proton transfer in large biological systems. These results have important implications for future applications to hydrogen transfer reactions in solution and proteins.     

Mechanistic insights on how hydroquinone disarms OH and OOH radicals

Phenol derivatives are distinguished as successful free radical scavengers. We present a detailed analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radical with emphasis on changes that take place in the vicinity of the transition state. Quantum theory of atoms in molecules is employed to elucidate the sequence of positive and negative charge transfer by studying selected properties of the three key atoms (the transferring hydrogen, the donor atom, and the acceptor atom) along intrinsic reaction path. The presented results imply that in both reactions, which are examples of proton coupled electron transfer, proton, and electron get simultaneously transferred to the radical oxygen atom. The fact that the hydrogen's charge and volume do not monotonously change in the vicinity of the transition state in the product valley results from the adjacency of the proton and the electron to the donor and the acceptor oxygen atoms. Obtaining a detailed understanding of mechanisms by which free radicals are disarmed is of paramount importance given the effects of those highly reactive species on biological systems. A comprehensive analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radicals, based on changes of selected electronic properties of the three most relevant atoms (hydrogen donor, hydrogen acceptor, and the hydrogen itself), along the reaction coordinate, can be obtained by first‐principles calculations.     

生色团连接的苯骈三氮唑衍生物的激发态分子内质子转移

用从头算和密度泛函理论研究了对硝基二苯乙烯作为生色团连接的2-(2-羟基-苯基)-苯骈三氮唑的衍生物2-羟基-5-[对硝基-二苯乙烯基-氧亚甲基]-苯基-(2H-苯骈三氮唑)(C1)和4′-硝基-3,4-二[2-羟基-(2H-苯骈三氮唑)-苄氧基]-二苯乙烯(C2)发生激发态分子内质子转移(ESIPT)的可能性.系统研究了C1和C2发生ESIPT的互变异构体的基态与激发态的性质变化,包括相关的键长、键角等结构参数,Mulliken电荷和偶极矩,前线轨道以及势能曲线.计算结果表明,对于C1来讲,酮式(keto)的基态(K)不存在稳定结构,因此发生基态分子内质子转移(GSIPT)可能性很小.酮式的激发态(K*)的氢键强度要远强于烯醇式(enol)的激发态(E*)的氢键强度.分子在光致激发后,质子供体所带负电荷减小而质子受体所带负电荷增加.在K*,HOMO→LUMO的电子跃迁导致电子密度从"酚环"向质子化杂环转移.E*→K*跃迁只需要克服较小的能垒(约41 kJ.mol-1).计算结果表明C1发生ESIPT的可能性很大.C2由于具有高能量,其具有基态的单质子转移特征的异构体EK(同时含烯醇E与酮K结构)、具有基态的双质子转移特征的异构体2K(含有双酮结构),以及具有双酮结构特征的激发态2K*均无法获得它们的稳定结构,因此,基态分子内单或双质子转移和激发态分子内双重质子转移发生的可能性极小.然而,由于双烯醇式的激发态(2E*)和EK的激发态(EK*)存在稳定结构,且2E*→EK*跃迁具有低能垒,因此C2有可能发生激发态分子内单重质子转移.本文进一步计算了两个分子的紫外-可见吸收光谱与荧光发射光谱,获得了具有较大斯托克位移的ESIPT的荧光发射峰.     

A multilayered representation,quantum mechanical and molecular mechanics study of the CH3F + OH− reaction in water

The bimolecular nucleophilic substitution (S_N2) reaction of CH₃F + OH^? in aqueous solution was investigated using a combined quantum mechanical and molecular mechanics approach. Reactant complex, transition state, and product complex along the reaction pathway were analyzed in water. The potentials of mean force were calculated using a multilayered representation with the DFT and CCSD(T) level of theory for the reactive region. The obtained free energy activation barrier for this reaction at the CCSD(T)/MM representation is 18.3 kcal/mol which agrees well with the experimental value at ～21.6 kcal/mol. Both the solvation effect and solute polarization effect play key roles on raising the activation barrier height in aqueous solution, with the former raising the barrier height by 3.1 kcal/mol, the latter 1.5 kcal/mol. © 2013 Wiley Periodicals, Inc.     

Direct dynamics study on the reaction of N2H4 with F atom: a hydrogen abstraction reaction?

We present a systematic direct ab initio dynamics investigation of the reaction between N2H4 and F atom, which is predicted to have three possible reaction channels. The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of all reaction channels were calculated at the UB3LYP/6-31+G(d,p) level of theory. Energetic information of stationary points and the points along the MEPs was further refined by means of the CCSD(T)/aug-cc-pVTZ method. The calculated results revealed that the first two primary channels (N2H4+F-->N2H3+HF) are equivalent and occur synchronously via the formation of a pre-reaction complex with Cs symmetry rather than via the direct H abstraction. The pre-reaction complex then evolves into a hydrogen-bonding intermediate through a transition state with nearly no barrier and a high exothermicity, which finally makes the intermediate further decompose into N2H3 and HF. Another reaction channel of minor role (N2H4+F-->NH2F+NH2) was also found during the calculations, which has the same Cs pre-reaction complex but forms NH2F and NH2 via another transition state with high-energy barrier and low exothermicity. The rate constants of these channels were calculated using the improved canonical variational transition state theory with the small-curvature tunneling correction (ICVT/SCT) method. The three-parameter ICVT/SCT rate constant expressions of k(ICVT/SCT) at the CCSD(T)/aug-cc-pVTZ//UB3LYP/6-31+G(d,p) level of theory within 220-3000 K were fitted as (7.64x10(-9))T (-0.87) exp(1180/T) cm3 mole-1 s-1 for N2H4+F-->N2H3+HF and 1.45x10(-12)(T/298)(2.17) exp(-1710/T) cm3 mole-1 s-1 for N2H4+F-->NH2F+NH2.