Linear free energy relationship and kinetic isotope effects as measures for the transition state variation. A computational study

Linear free energy relationship (LFER) and kinetic isotope effects (KIEs) are frequently used experimental means to study reaction mechanisms, in particular the nature of transition states (TSs). Density functional theory (B3LYP/6-311+G**) calculations were carried out on a model reaction, acid-catalyzed ionization of phenylethyl alcohol, to analyze how experimentally observable properties, such as nonlinearity in the Hammett and Br?nsted relations and variation in KIE, are related to a variation of the transition state structure and the mechanism. Several conclusions and insights were obtained: (1) Linear Hammett plots with a dual parameter treatment may not be evidence for an invariable TS structure for a series of reactions. (2) Variations of KIEs indeed reflect the variations of TS structures. (3) Nonlinear Br?nsted plots cannot always be taken as evidence for a stepwise mechanism. (4) A TS structure in the gas phase may change much more easily than a TS structure in solution.     

Is the CH2OH + O2 → CH2 = O + HO2 Reaction Barrierless? An Ab Initio Study on the Reaction Mechanism

The reaction mechanism of the CH₂OH + O₂ gas-phase reaction was investigated by means of ab initio calculations. MP2 and QCISD methodologies were used to obtain the stationary points on the potential energy surface. Single-point high-level QCISD(T) calculations were performed over the QCISD results in order to refine the energy of the transition states and the minima found. A new transition state concerning the initial O₂ addition to the CH₂OH radical was found, not reported so far for this reaction. Extra CCSD optimisation and single-point high-level CCSD(T) calculations upon the QCISD results confirm this TS. Additional RASSCF calculations show that its wave function has no significant multireferential character.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

硝酰氯和顺/反亚硝酸氯及其互变异构反应的理论研究

用密度泛函理论（DFT）的B3LYP方法和6－311＋G（3df）基组，计算了气态下硝酰氯和顺／反应硝酸氯的几何构型、电子结构、红外光谱以及热力学性质，并讨论了它们的互变异构反应，分析了过渡态的结构。结果表明，B3LYP／6－311＋G（3df）计算得到的结果与实验值及CCSD（T）方法计算结果吻合，且更适应于研究反应机理，ClNO2转变为cis-ClONO的过渡态（TS1）偏离平面构型；cis-ClONO和trans-ClONO互变反应的过渡态（TS2）属于内旋转位垒；高水平计算表明不存在由ClNO2直接转变为trans-ClONO的过渡态，而是得到了一个十分接近异裂产物的二级马鞍点（2SP）。根据得到的热力学函数计算了气态时各温度下互变异构反应的平衡常数。     

Connection between the upper and lower energy regions of the potential energy surface of the ground electronic state of the HSO2 system

The importance of the HSO(2) system in atmospheric and combustion chemistry has motivated several works dedicated to the study of associated structures and chemical reactions. Nevertheless, controversy still exists about a possible connection between the upper and lower energy regions of the potential energy surface (PES) for the ground electronic state of the system. Very recently, a path to connect these regions was proposed based on studies at the CASPT2/aug-cc-pV(T+d)Z level of calculation but the small energy difference between some of the transitions states along that path suggested the necessity of calculations at a higher level of theory. In the present work, we report a CCSD(T)/aug-cc-pV(T+d)Z study of the stationary states associated to the proposed connection path, including assessment of the most reliable complete basis set (CBS) extrapolation scheme for the system. Among the new features, the present calculations show that there are no structures corresponding to the HSO(2)(b) minimum and the TS3 saddle point obtained at the CASPT2 level and that the connection path between the upper and lower energy regions of the PES for the ground electronic state involves only one transition state and most probably more than one electronic state.     

Roles of C-H...O=S and pi-stacking interactions in the 2-bromoacrolein complex with N-tosyl-(S)-tryptophan-derived oxazaborolidinone catalyst

[structures: see text] Ab initio and density functional calculations were employed to examine the structures and binding energies of various complexes between 2-bromolacrolein and N-tosyl-(S)-tryptophan-derived B-butyl-1,3,2-oxazaborolidin-5-one (NTOB), a catalyst commonly used for Diels-Alder reactions. Our calculations show that the chiral oxazaborolidinone catalyst serves as a tridentate complexation agent via B...O donor-acceptor, C-H...O hydrogen-bonded, and pi-stacking interactions. The most stable complex (1TS) is predicted to have a binding energy of -93 kJ mol(-1) (deltaG(298) = -29 kJ mol(-1)). The formyl C-H...O hydrogen bond and pi-stacking interaction are the key factors governing the relative stabilities of the four acrolein-NTOB complexes examined. The calculated structure and binding properties of 1TS are consistent with the experimental results on the absorption spectrum of the acrolein-NTOB complex and the effects of substituents on the reactivity of Diels-Alder reactions. 1TS differs from Corey's proposed model of transition-state assembly in two aspects: (1) it involves the s-trans-acrolein and (2) it favors a C-H...O interaction via the sulfonyl oxygen (C-H...O=S), rather than the ring oxygen (C-H...O-B). This calculated structure of the acrolein-catalyst complex provides an alternate explanation of the origin of stereoselectivity in the NTOB-catalyzed Diels-Alder reactions.     

Single-molecule force spectroscopy measurements of bond elongation during a bimolecular reaction

It is experimentally challenging to directly obtain structural information of the transition state (TS), the high-energy bottleneck en route from reactants to products, for solution-phase reactions. Here, we use single-molecule experiments as well as high-level quantum chemical calculations to probe the TS of disulfide bond reduction, a bimolecular nucleophilic substitution (S N2) reaction. We use an atomic force microscope in force-clamp mode to apply mechanical forces to a protein disulfide bond and obtain force-dependent rate constants of the disulfide bond reduction initiated by a variety of nucleophiles. We measure distances to the TS or bond elongation (Delta x), along a 1-D reaction coordinate imposed by mechanical force, of 0.31 +/- 0.05 and 0.44 +/- 0.03 A for thiol-initiated and phosphine-initiated disulfide bond reductions, respectively. These results are in agreement with quantum chemical calculations, which show that the disulfide bond at the TS is longer in phosphine-initiated reduction than in thiol-initiated reduction. We also investigate the effect of solvent environment on the TS geometry by incorporating glycerol into the aqueous solution. In this case, the Delta x value for the phosphine-initiated reduction is decreased to 0.28 +/- 0.04 A whereas it remains unchanged for thiol-initiated reduction, providing a direct test of theoretical calculations of the role of solvent molecules in the reduction TS of an S N2 reaction. These results demonstrate that single-molecule force spectroscopy represents a novel experimental tool to study mechanochemistry and directly probe the sub-?ngstr?m changes in TS structure of solution-phase reactions. Furthermore, this single-molecule method opens new doors to gain molecular level understanding of chemical reactivity when combined with quantum chemical calculations.     

Photodissociation of acetic acid in the gas phase: an ab initio study

Photodissociation of acetic acid in the gas phase was investigated using ab initio molecular orbital methods. The stationary structures on the ground-state potential energy surfaces were mainly optimized at the MP2 level of theory, while those on the excited-state surfaces were determined by complete active space SCF calculations with a correlation-consistent basis set of cc-pVDZ. The reaction pathways leading to different photoproducts are characterized on the basis of the computed potential energy surfaces and surface crossing points. The calculations reproduce the experimental results well and provide additional insight into the mechanism of the ultraviolet photodissociation of acetic acid and related compounds.     

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

The nature of the hydrolysis of phosphate monoester dianions in solutions and in proteins is a problem of significant current interest. The present work explores this problem by systematic calculations of the potential surfaces of the reactions of a series of phosphate monoesters with different leaving groups. These calculations involve computational studies ranging from ab initio calculations with implicit solvent models to ab initio QM/MM free energy calculations. The calculations reproduce the observed linear free energy relationship (LFER) for the solution reaction and thus are consistent with the overall experimental trend and can be used to explore the nature of the transition state (TS) region, which is not accessible to direct experimental studies. It is found that the potential surface for the associative and dissociative paths is very flat and that the relative height of the associative and dissociative TS is different in different systems. In general, the character of the TS changes from associative to dissociative upon decrease in the pKa of the leaving group. It is also demonstrated that traditional experimental markers such as isotope effects and the LFER slope cannot be used in a conclusive way to distinguish between the two classes of transition states. In addition it is found that the effective charges of the TS do not follow the previously assumed simple rule. Armed with that experience we explore the free energy surface for the GTPase reaction of the RasGap system. In this case it is found that the surface is flat but that the lowest TS is associative. The present study indicates that the nature of the potential surfaces for the phosphoryl transfer reactions in solution and proteins is quite complicated and cannot be determined in a conclusive way without the use of careful theoretical studies that should, of course, reproduce the available experimental information.     

CH3CH2+O(3P)反应机理的理论研究

The reaction for CH3CH2+O(3P) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single-point calculations for all the stationary points were carried out at the QCISD(T)/6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major products are the CH2O＋CH3, CH3CHO+H and CH2CH2+OH in the reaction. For the products CH2O＋CH3 and CH3CHO+H, the major production channels are A1: (R)→IM1→TS3→(A) and B1: (R)→IM1→TS4→(B), respectively. The majority of the products CH2CH2+OH are formed via the direct abstraction channels C1 and C2: (R)→TS1(TS2)→(C). In addition, the results suggest that the barrier heights to form the CO reaction channels are very high, so the CO is not a major product in the reaction.     

Reactivity and selectivity in the Wittig reaction: a computational study

The salt-free Wittig reaction of non-, semi-, and stabilized ylides has been investigated on realistic systems using density functional theory (DFT) calculations, including continuum solvation. Our results provide unequivocal support for the generally accepted mechanism and are in very good agreement with experimental selectivities. This study shows that E/Z selectivity of non- and semi-stabilized ylides cannot be fully understood without considering the energy of the elimination TS. The influence of ylide stabilization and the nature of phosphorus substituents on reversibility of oxaphosphetane formation is clarified. Unexpectedly, the puckering ability of addition TSs is shown not to depend on ylide stabilization, but the geometry of the TS is decided by an interplay of 1,2; 1,3; and C-H...O interactions in the case of non- and semi-stabilized ylides, whereas a dipole-dipole interaction governs the addition TS structures for stabilized ylides. The well-known influence of ylide stabilization on selectivity of PPh(3) derivatives is explained as follows: in non- and semi-stabilized ylides reactions, cis and trans addition TSs have, respectively, puckered and planar geometries, and selectivity is governed by an interplay of 1,2 and 1,3 interactions. For stabilized ylides, the high E selectivity is due to a strong dipole-dipole interaction at the addition TS. The influence of the nature of phosphorus substituents on selectivity is also detailed, the different behavior of (MeO)(3)PCHCO(2)Me ylides being explained by their lower dipole. This novel picture of the factors determining TS structures and selectivity provides a sound basis for the design of new ylides.     

Hydrolysis theory for cisplatin and its analogues based on density functional studies

Hydrolysis of cisplatin, the most widely used anticancer drug in the world, is believed to be the key activation step before the drug reaching its intracellular target DNA.To obtain an accurate hydrolysis theory for this important class of square-planar Pt(II) complexes, three typical reactions, i.e., the first and second hydrolyses of cisplatin and the hydrolysis of [Pt(dien)Cl](+) (dien = diethylenetriamine), were studied at the experimental temperature with the solvent effect using mPW1PW91/SDD from a comprehensive methodological study on the Hartree-Fock (HF) ab initio method, electron correlation methods, pure density functional theory (DFT) methods, and hybrid HF-DFT methods with several basis sets. The true five stationary states in the second-order nucleophilic substitution (S(N)2) pathway for the hydrolysis process, namely, reactant (R) --> intermediate 1 (I1) --> TS --> intermediate 2 (I2) --> product (P) were obtained and characterized theoretically for the first time. The most remarkable structural variations and the associated atomic charge variations in the hydrolysis process were found to occur in the equatorial plane of the five-coordinate trigonal-bipyramidal (TBP)-like structures of I1, TS, and I2. The reaction with the TS structure of smaller L-M-E angle and more lengthened M-L and M-E bonds was found to have a smaller Gibbs free energy change and accordingly the better hydrolysis yield. It is found that the sum of the three concentric angles in the TBP's equator is near 360 degrees in I1 and I2 and is almost 360 degrees in TS in each reaction. The associated energy profiles again demonstrated a typical S(N)2 reaction curve. The computed forward and backward reaction enthalpy (Delta H(++)) and reaction entropy (Delta S(++)) in the rate-determining step I1 --> TS --> I2 are in good agreement with the experiments. Natural bonding orbital population analysis shows that the charge-separating extent follows the same order of Delta G in studied reactions. Comparing with the computational results of gas-phase reactions, it can be concluded that the solvent effect should be considered to obtain an accurate hydrolysis picture. The most affected structural parameters after solvation are related to the equatorial plane of the TBP-like geometry. The results provide theoretical guidance on detailed understanding on the mechanism of the hydrolysis of cisplatin, which could be useful in the design of novel Pt-based anticancer agents.     

Enantiomerization study of some alpha-nitroketones by dynamic high-resolution gas chromatography

The kinetics of the reversible enantiomer interconversion of 3-nitrobutan-2-one (1), 3-nitropentan-2-one (2), and 2-nitropentan-3-one (3) have been studied by dynamic high-resolution gas chromatography (DHRGC) by using a beta-cyclodextrin derivative chiral stationary phase; the process occurs via enolization of the keto forms. The DHRGC experiments involving the studied nitroketones and the chiral stationary phase show chromatographic profiles with a typical interconversion plateau in the temperature range between 130 and 160 degrees C. Computer simulation of the experimental chromatographic elution profiles was employed for the determination of rate constants and the corresponding enantiomerization barriers (k, DeltaG#(T), DeltaH#, and DeltaS#). The highly negative entropy of activation (DeltaS# values from -19 to -37 cal mol(-1) K(-1)) points to a transition state (TS) with large charge separation. The obtained results for 1-3 show the dramatic effect of an alpha-nitro-substituent on the rate of enolization of simple ketones, when compared with those for 3-chloro-2-butanone and 3-methyl-2-pentanone. To get some information on the separate contributions of the stationary liquid phase and the mobile gas phase on the studied process, some DFT ab initio calculations have been performed for the same compounds.     

Theoretical study of initiated reaction mechanism of polymerization of maleic anhydride catalyzed by OH−1 anion

A theoretical study of the polymerization reaction mechanism of maleic anhydride (MA) initiated by hydrate is presented. The reaction pathway has been studied with the density functional theory (DFT) method at the B3LYP/6‐311G** level. The geometrical parameters of transition states (TS) are optimized; intrinsic reaction coordinate (IRC) calculations have also been performed to obtain further credible features. Frequency analyses of all the stationary points are calculated at the same basis sets. The total energies of all geometries are corrected at second‐order Møller–Plesset (MP2)/6‐311G**. Calculation results reveal that the reaction mechanism is attributable to anion polymerization. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

SiH3+O(3P)反应机理的理论研究

The reaction for SiH3+O(3P) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The single point calculations for all the stationary points were carried out at the QCISD(T) /6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major pathway is the SiH3+O(3P)→IM1→TS3→IM2→TS8→HOSi+H2. The other minor products include the HSiOH+H, H2SiO+H and HSiO+H2. Furthermore, the products HOSi, HSiO and HSiOH(cis) can undergo dissociation into the product SiO. In addition, the calculations provide a possible interpretation for disagreement about the mechanism of the reaction SiH4+O(3P). It suggests that the products HSiOH, H2SiO and SiO observed by Withnall and Andrews are produced from the secondary reaction SiH3+O(3P) and not from the reaction SiH4+O(3P).     

烷基咪唑型卤盐类离子液体的合成机理研究

用密度泛函理论考察了甲基咪唑和一系列的卤代烷烃(氯乙烷,氯丁烷,溴乙烷,溴丁烷)反应合成咪唑类离子液体的反应机理. 在B3LYP/6-31++G**//B3LYP/6-31G*基组水平上找到了两条反应路径：路径A(反应物→TS1→P1)和路径B(反应物→TS2→P2). 在路径A中, 卤素离子和咪唑环C2上的氢质子形成氢键；在路径B中, 卤素离子和咪唑环C5上的氢质子形成氢键. 计算发现, 氢键的形成在反应中起到了非常重要的作用, 特别是咪唑环C2上的氢质子在和卤素离子成氢键后形成了一个五员环结构的过渡态, 该过渡态能量较低. 经过渡态TS1的反应途径其活化能要低于经过渡态TS2的反应途径, 反应路径A为主要的反应通道. 计算结果表明, 经过渡态TS1的反应途径是一放热过程, 这和实验观察现象一致.     

Theoretical study of the mechanism of CH2CO + CN reaction

The potential energy surface information of the CH₂CO + CN reaction is obtained at the B3LYP/6‐311+G(d,p) level. To gain further mechanistic knowledge, higher‐level single‐point calculations for the stationary points are performed at the QCISD(T)/6‐311++G(d,p) level. The CH₂CO + CN reaction proceeds through four possible mechanisms: direct hydrogen abstraction, olefinic carbon addition–elimination, carbonyl carbon addition–elimination, and side oxygen addition–elimination. Our calculations demonstrate that R→IM1→TS3→P3: CH₂CN + CO is the energetically favorable channel; however, channel R→IM2→TS4→P4: CH₂NC + CO is considerably competitive, especially as the temperature increases (R, IM, TS, and P represent reactant, intermediate, transition state, and product, respectively). The present study may be helpful in probing the mechanism of the CH₂CO + CN reaction. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Can we predict the structure and stability of molecular crystals under increased pressure? First‐principles study of glycine phase transitions

The aim of this study was to determine whether the periodic density functional theory (DFT) calculations can be used for accurate prediction of the influence of the increased pressure on crystal structure and stability of molecular solids. To achieve this goal a series of geometry optimization and thermodynamic parameters calculations were performed for γ‐glycine and δ‐glycine structures at different pressure values using CASTEP program. In order to perform most accurate geometry optimization various exchange‐correlation functionals defined within generalized gradient approximation (GGA): PBE, PW91, RPBE, WC, PBESOL as well as defined within local density approximation (LDA), i.e. CAPZ, were tested. Geometry optimization was carried out using different dispersion correction methods (i.e. Grimme, TS, OBS) or without them. The linear response density functional perturbation theory (DFPT) was used to obtain the phonon dispersion curves and phonon density of states from which thermodynamic parameters, such as: free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) were evaluated. The results of the geometry optimization depend strongly on the choice of the DFT functional. Calculated differences between the free energy of the studied polymorphic forms at the studied pressure values were consistent with experimental observations on their stability. The computations of thermodynamic properties not only confirmed the order of stability of two studied forms, but also enabled to predict the pressure at which this order is reversed. The results obtained in this study have proven that the plane‐wave basis set first principles calculations under periodic conditions is suitable for accurate prediction of crystal structure and stability. © 2018 Wiley Periodicals, Inc.     

Ensemble-averaged QM/MM kinetic isotope effects for the S(N)2 reaction of cyanide anions with chloroethane in DMSO solution

The existence of solvent fluctuations leads to populations of reactant-state (RS) and transition-state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of values for individual configurations. Average kinetic isotope effects 〈KIE〉 for NC(-) + EtCl → NCEt + Cl(-) in DMSO solution at 30?°C are best obtained as the ratio 〈f(RS)〉/〈f(TS)〉 of isotopic partition function ratios separately averaged over all RS and TS configurations. In this way the hybrid AM1/OPLS-AA potential yields 〈KIE〉 values for all six isotopic substitutions (2° α-(2)H(2), 2° β-(2)H(3), α-(11)C/(14)C, leaving group (37)Cl, and nucleophile (13)C and (15)N) for this reaction in the correct direction as measured experimentally. These thermally-averaged calculated KIEs may be compared meaningfully with experiment, and only one of them differs in magnitude from the experimental value by more than one standard deviation from the mean. This success contrasts with previous KIE calculations based upon traditional methods without averaging. The isotopic partition function ratios are best evaluated using all (internal) vibrational and (external) librational frequencies obtained from Hessians determined for subsets of atoms, relaxed to local minima or saddle points, within frozen solvent environments of structures sampled along molecular dynamics trajectories for RS and TS. The current method may perfectly well be implemented with other QM or QM/MM methods, and thus provides a useful tool for investigating KIEs in relation to studies of chemical reaction mechanisms in solution or catalyzed by enzymes.     

手性噁唑磷烷-硼烷催化还原苯乙酮对映选择性的理论研究

应用密度泛函理论BHandH/6-31G**计算方法研究新型手性非金属催化剂1,3,2-噁唑磷烷-硼烷催化还原苯乙酮的对映选择性反应机理, 确定了在反应途径上的反应物、络合物、过渡态, 中间体和对映体中间产物. 计算结果表明, 该对映选择性还原反应是两个平行的分步反应, 对映体产物主要是(R)构型. 采用同样的方法研究了对映选择性还原反应在甲苯中的溶剂化效应. SCRF计算显示, 甲苯溶剂不改变反应的机理, 但能降低各驻点的能量和(R)反应的位垒, 有利于催化还原反应朝生成(R)构型中间产物的方向进行.     

CASSCF and CASPT2 calculations on the cleavage and ring inversion of bicyclo[2.2.0]hexane find that these reactions involve formation of a common twist-boat diradical intermediate.

(6/6)CASSCF and CASPT2/6-31G calculations have been performed to understand the experimental finding of Goldstein and Benzon (J. Am. Chem. Soc. 1972, 94, 5119) that exo-bicyclo[2.2.0]hexane-d(4) (1b) undergoes ring inversion to form endo-bicyclo[2.2.0]hexane-d(4) (4b) faster than it undergoes cleavage to form cis,trans-1,5-hexadiene-d(4) (3b). Goldstein and Benzon also found that the latter reaction, which must occur via a chairlike transition structure (TS), is much faster than cleavage of 1b to trans,trans-1,5-hexadiene-d(4) (2b) via a boatlike TS. Our calculations reveal that all three of these reactions involve ring opening of 1, through a boat diradical TS (BDTS), to form a twist-boat diradical intermediate (TBDI). TBDI can reclose to 4 via a stereoisomeric boat diradical TS (BDTS'), or TBDI can cleave, either via a half-chair diradical TS (HCDTS) to form 3 or via a boat TS (BTS) to form 2. The calculated values of DeltaH(++) = 34.6 kcal/mol, DeltaS(++) = -1.6 eu, and DeltaH(++) = 35.2 kcal/mol, DeltaS(++) = 2.0 eu for ring inversion of 1 to 4 and cleavage of 1 to 3, respectively, are in excellent agreement with the values measured by Goldstein and Benzon. The higher value of DeltaH(++) = 37.6 kcal/mol, computed for cleavage of TBDI to 2, is consistent with the experimental finding that very little 2b is formed when 1b is pyrolyzed. The relationships between BDTS, HCDTS, and BTS and the chair and boat Cope rearrangement TSs (CCTS and BCTS) are discussed.