Ab initio molecular orbital study on three feasible mechanisms for substitution of the vinylic carbon in F2C=C(OMs)BMe3−

A substitution on 2,2-difluorovinylic carbon was investigated by using ab initio molecular orbital calculations. Three feasible mechanisms, which are the S_N1-like, the S_N2-type and the addition-elimination mechanisms, were ex- amined for a model borate, 2,2-difluoro-1-mesyloxyvinyl(trimethyl)borate. Four TSs were obtained depending on the position of Li⁺ around the vinylborate although activation energies in the gas phase are rather high (ca. 30–40 kcal mol⁻¹) in comparison with that expected from the experimental conditions. It was confirmed at the SCRF-IPCM calculations that the solvent effect reduces the acti- vation energy of one S_N2-type mechanism very much (4. l kcal mol⁻¹ at the B3LYP/6-31+G^*//RHF/6-31+G^/s* level of theory) while those for the other mechanisms do not change very much. Therefore, the S_N2-type mechanism is applicable to the substitution reaction observed for the vinylborate.     

DFT study on the reaction mechanisms of polyfluorosulfonate ester with F

Gas-phase reaction of C(1)F₃S(2)O₂O(3)C(4)H₂C(5)F₃ and F⁻(16) is investigated using DFT method. The geometries of various stationary points and their relative energies are obtained from 6-31+G*, 6-311G**, and 6-311++G** levels. In the S_N2(C) reaction leading to the cleavage of the C(4)–O(3) bond, the reaction complex results from attacking of F⁻ at a hydrogen atom H11 attached to carbon atom C(4). Afterward, F⁻ is attacking the atom C(4) from the backside of the atom O(3) with the help of the neighboring effect, and meanwhile a multi-membered ring, F(16)–H(11)–C(4)–C(5)–F(16), is being formed. The S_N2(C) reaction is irreversible. On the contrary, the S_N2(S) reaction leading to the cleavage of the S(2)–O(3) bond is reversible, and it is initiated by attacking of F⁻ at the atom S(2) from the backside of the atom O(3). The products of the reaction CF₃SO₃CH₂CF₃ +F⁻ should be, thermodynamically, controlled due to the reversibility of the S_N2(S) reaction, and those result, chemospecifically, from the cleavage of the C–O bond. At last, the SCRF calculations confirm that the solvent effect is preferable to the S_N2(C) reaction.     

醚溶液中烯烃硼氢化反应机理的理论模拟

在B₃LYP/6-31G^*水平上以二甲醚(Me₂O)模拟四氢呋喃(THF)对烯烃在THF溶液中硼氢化反应的机理进行了研究.计算结果发现,烯烃通过类似SN₂的交换过程从醚与BH₃构成的配合物获得BH₃结合成π配合物中间体,这一交换是整个硼氢化反应的决速步骤.     

A theoretical study of the ion pair SN2 reaction between lithium isocyanates with methyl fluoride with inversion and retention mechanism

This paper is devoted to a detailed theoretical study of an ion pair S_N2 reaction LiNCO+CH₃F in the gas phase and in solution at the level of MP2(full)/6-31+G**//HF/6-31+G**. Two possible reaction mechanisms, inversion and retention, are discussed. There are eight possible reaction pathways. The inversion mechanism is more favorable no matter in the gas phase or in solution based on analyses of the transition structures. Methyl isocyanate should form preferentially in the gas phase and more stable methyl cyanate is the main product in solution. The retardation of the reaction in solvents was attributed to the difference in solvation in the separated reactants and in the transition state.     

2-,3-和4-溴甲基吡啶的水解反应的动力学研究

用HPLC测定了2-、3-和4-溴甲基吡啶在60℃、离子强度μ为0.15、pH 0.9～9.9的缓冲溶液中水解成相应的羟甲基吡啶的反应速度.通过数学处理,求得溴甲基吡啶的一级和二级反应速度常数以及溴甲基吡啶共轭酸的一级反应速度常数.水解反应的可能机理是S_N1和S_N2.     

Highly regioselective asymmetric copper-catalyzed allylic alkylation with dialkylzincs using monodentate chiral spiro phosphoramidite and phosphite ligands

The copper complexes of chiral spiro phosphoramidite and phosphite ligands were found to be effective catalysts in the asymmetric allylic alkylations of cinnamyl halides with dialkylzincs. The allylic alkylation products were obtained in high regioselectivities (S_N2′/S_N2 up to 98:2) and enantiomeric excesses of up to 74% for S_N2′ products.     

Using vibrational modes in the search for global minima of atomic and molecular clusters

The reaction between dimethyl sulfide (CH₃SCH₃) and nitrate radical (NO₃) is studied using density functional theory and ab initio methods. The transition state for this reaction is optimized at different levels of theory and basis sets, and then used for kinetics calculations of the rate constant. The CH₃SCH₃ + NO₃ reaction leading to CH₃SCH₂ and HNO₃ is shown to have a negative activation energy and thus negative temperature dependence. The study confirms that the NO₃ radical is a significant contributor to the oxidation of DMS in the troposphere.     

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

We are presenting a theoretical study of the hydrolysis of a β‐lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06‐2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substrate implies the existence of a huge number of possible conformers, some of them implying formation of intramolecular hydrogen bond interaction that can determine the energetics of the conformers defining the different states along the reaction profile. The results show PM3 provides results that are in qualitative agreement with DFT calculations. The free energy profiles show a step‐wise mechanism that is kinetically determined by the nucleophilic attack of a water molecule activated by the proton transfer to the carboxylate group of the substrate (the first step). However, since the main role of the β‐lactamase would be reducing the free energy barrier of the first step, and keeping in mind the barrier obtained from second intermediate to products, population of this second intermediate could be significant and consequently experimentally detected in β‐lactamases, as shown in the literature. © 2012 Wiley Periodicals, Inc.     

Investigation of the properties of some furylpyridine and thienylpyridine derivatives in the gas and aqueous phases using semiempirical methods

The gas and aqueous phase geometries, heats of formation, entropies, dipole moments, proton affinities and methyl cation affinities of some furylpyridines and thienylpyridines have been studied to predict their basicity and pK_a values, using semiempirical AM1, PM3 and MNDO quantum-chemical calculations at SCF level in gas and aqueous phases, with full geometry optimisation.     

Comparison of Photochemical Reactions of m-Cresol in Aqueous Solution and in Ice

We compared the photochemical reaction of m-cresol containing OH precursors such as H₂O₂, NO₂^- and NO₃^- in aqueous solution with those in ice. The results show that the conversion rate of m-cresol in aqueous solution was higher than that in ice. H₂O₂, NO₂^- and NO₃^- all accelerated the photoconversion of m-cresol in both aqueous solution and ice. The photochemical reactions of m-cresol obeys the first order kinetics equation. According to the photoproducts identified by GC-MS, we proposed that hydroxylation and nitration reactions occurred in both aqueous solution and ice. Coupling reaction was common in ice, however, in aqueous solution it was found only in UV system. Our results suggest that the photochemical reactions of m-cresol were different in aqueous solution and in ice.     

Theoretical investigation of isotopic scrambling mechanisms in 2-chloroethyl methyl sulfide

Ab initio and semiempirical molecular orbital calculations have been applied to study the concerted and stepwise isotopic scrambling mechanisms of 2-chloroethyl methyl sulfide in the gas phase and in aqueous solution. The calculations reveal the structural details of the reactants, transition structures, and intermediates involved in this reaction and provide relative energy estimates. The concerted mechanism is found to be competitive with the stepwise mechanism in the gas phase, but the stepwise mechanism is favored in aqueous solution as no true transition structure for the concerted mechanism could be found using the solvation models. A combined approach of evaluating solvation energies with the generalized-Bom-plus-surface-tensions SM _x solvation models of Cramer and Truhlar at ab initio optimized geometries is found to deliver the best agreement with experimentally determined reaction barriers. Together with the recent experimental results of McManus and co-workers, the present study provides insights into the controlling factors involved in the elementary reaction steps of sulfur mustards and a solid foundation for investigations into more complex reactions of related compounds.     

Mechanism of electroreduction of allyl alcohol at platinized platinum electrode in acidic aqueous solution.

The electroreduction of allyl alcohol to form propene at the platinized platinum electrode in acidic aqueous solution has been studied using CV plots, IR, ESR, and MS spectra, and a semiempricial MO method (MOPAC7/AM1, PM3). From the determinations of charge-transfer coefficients, reaction orders and apparent activation energy for the given reaction, the detection of the intermediates such as C(3)H(5)(+), C(3)H(5)(*), and C(3)H(5)(-) species, and PM3 calculations of charge distribution and frontier orbital energies of the reaction species C(3)H(5)OH and C(3)H(5)(+), the authors suggest that in acidic aqueous solution the production of propene via reductive splitting of the C-OH bond situated in the allyl position of allyl alcohol obeys a carbonium ion-carbanion mechanism.     

Hydrolysis of cyano(pyrrolyl-1)borates

The kinetics and mechanism of the hydrolysis of several cyano(pyrrolyl-1)borates in aqueous medium has been investigated. The hydrolysis of cyanophenyl(pyrrolyl-1)-borates, cyano(tripyrrolyl-1)borate and cyanohydro(pyrrolyl-1)borates proceeds via two kinds of reactions; (a) a special H⁺ ion catalyzed reaction (A-1 mechanism) and (b) a H⁺ ion concentration-independent process of S_N1 mechanism. In acidic medium the [BH₂(NC₄H₄)CN]⁻ anion is reversibly protonated at the -carbon of the pyrrolyl group and a product with composition C₄H₅N · BH₂CN, stable towards hydrolysis is also formed.

In the H⁺ ion catalyzed reaction the B---N bond very likely breaks, whereas upon the [H⁺] ion concentration-independent reaction a B---CN cleavage occurs. The presence of the cyano substituent significantly increases the hydrolytic stability of the B---N bond, whereas the pyrrolyl-1-substitution remarkably decreases the stability of the B---CN bonding.     

Calculation of the polymerization process of some 1,1-disubstituted cyclopropanes: the first propagation step

A theoretical study of the first steps of the polymerization propagation process of 1,1 cyano, fluoro and methyl disubstituted cyclopropanes and 1-cyano 1-amino cycloprane is presented. The thermodynamic and kinetic feasibility of the reactions are discussed through 6-31+G(d,p) Hartree–Fock calculations. The anionic initiation and propagation process follows an S_N2 like reaction path mainly governed by the differences in electron affinities between the incoming and outgoing anions, further modulated by the nature of the substituents. Main conclusions are that the π electron-withdrawing groups maintain the barrier heights low, making the process feasible from a kinetic viewpoint. The σ electron-withdrawing groups give more exothermic reactions but their reaction barriers are very high.     

The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each--NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.     

高碳铬铁在氢氧化钠水溶液中电化学氧化过程

铬铁电化学氧化法是一种新的制备铬酸钠的方法,然而高碳铬铁在NaOH水溶液中的电化学氧化过程尚不明确。 采用循环伏安法(CV)、稳态极化法(LSV)等电化学测试方法对金属铬、高碳铬铁在NaOH水溶液中的电化学氧化过程进行研究,通过扫描电子显微镜(SEM)、能量散射谱(EDS)和X射线光电子能谱(XPS)对高碳铬铁电解后固相产物表征,判断固相产物的组成。 结果表明,高碳铬铁不同于金属铬的电氧化过程,它在NaOH溶液中通过Cr(0)→Cr(Ⅵ)的电氧化方式生成铬酸钠,中间产物Cr(OH)₃和Fe(0)发生电化学反应生成稳定的FeCr₂O₄。 随着NaOH浓度的增加,电势较低时,受高碳铬铁中Fe(0)的影响,高碳铬铁容易在NaOH水溶液中发生钝化;当电势足够正时,钝化膜溶解,生成铬酸钠、氢氧化铁和亚铬酸亚铁,同时,阳极表面有氧气析出。 高碳铬铁电化学氧化制备铬酸钠的适宜条件:碱浓度≥2 mol/L,阳极电势≥1.6 V(vs.SCE)。     

Photoluminescence of 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole in aqueous and β-cyclodextrin environments: manifestation of open and closed conformers

Steady-state fluorometric studies have been performed on 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole (HMBDPP) in aqueous and aqueous β-cyclodextrin (β-CD) environments at ambient temperature. The fluorophore mostly shows a single emission in aqueous solution. Addition of β-CD to the aqueous solution of the fluorophore results in the development of another emission band at higher energy. The difference in the fluorometric behaviour is assigned to a remarkable change in the polarity of the microenvironment within the supramolecular structural environment compared to that of the bulk aqueous phase. Semi-empirical calculation (AM1-SCI) rules out the possibility of intramolecular proton transfer reaction in any of the S₀, S₁ and T₁ states of the fluorophore. It is proposed that HMBDPP exists mostly in the intermolecularly hydrogen-bonded form (open conformer) in aqueous solution while within β-CD environment, it is the intramolecularly hydrogen-bonded form (closed conformer) that predominates.     

An unusually acidic methyl group directly bound to acridinium cation

9,10-Dimethylacridinium chloride (1: X = Cl) exhibited strong acidity of pH 3.90 (3.4 x 10(-3) M, 20 degrees C) in an aqueous solution. H-D exchange reaction of 1 in D2O indicated that protons in the 9-methyl group dissociated to generated H+ ions. This is a unique example of a methyl proton functioning as an acid. The acidity derives from the wider pi face in acridinium capable of delocalizing the newly formed negative charge upon proton dissociation. PM3 calculations provided stabilization factors (deltaDeltaH(f)o) between proton dissociated and undissociated forms of several N-heterocycles and also confirmed the acidity observed in acridinium.     

Ab initio GB study of prebiotic synthesis of purine precursors from aqueous hydrogen cyanide: dimerization reaction of HCN in aqueous solution

Ab initio MO GB theory which includes the continuum model of solvent effect using generalized Born formula has been applied to the dimerization reaction of HCN in aqueous solution which is the starting step in prebiotic synthesis of purine precursors from aqueous hydrogen cyanide. Three steps considered were: (i) the reaction of HCN and H₂O to produce the CN⁻ anion, (ii) the reaction of CN⁻ with HCN to give the NC–CH=N⁻ anion, and (iii) the addition of a proton to the anion to give iminoacetonitrile. The formation of CN⁻ ion from HCN in aqueous solution requires 15.1 kcal/mol (the experimental value estimated from the dissociation constant of HCN in water is 14.8 kcal/mol). The reaction of CN⁻ with HCN requires the activation energy of 32.2 kcal/mol (MP2/6-31++G^**//HF/6-31++G^**) to give the dimer. This barrier height is reduced to 26.1 kcal/mol when HCN is associated with H₃O⁺. In the presence of NH₃ in aqueous solution, CN⁻ is produced easily by the reaction of HCN and NH₃ with a low activation energy of 4.3 kcal/mol. It was shown that the formation of CN⁻ becomes easier in ammoniacal solution, and the dimerization occurs efficiently in aqueous solutions which contain NH₃.     

Photosolvolysis of 2-aminobenzl alcohol in aqueous solution

The photosolvolytic behavior of 2-aminobenzyl alcohol (4) was studied in aqueous solution over a range of pH and in moderately concentrated aqueous H₂SO₄ solution. Although reactive at all pH values studied, clean solvolytic reaction was observed only when pHK_a (for ground state dissociation of aryl ammonium ion). A mechanism of reaction in acidic medium is proposed in which the protonated substrate (ArNH₃⁺) is excited to S₁ and then undergoes adiabatic deprotonation to give the electronically excited free base. Subsequent dehydroxylation, which can be assisted by a proton, gives o-quinone methide imine (o-QMI, 5) as the reactive intermediate. Nucleophilic attack by added ROH gives the photosolvolytic product. If pH>pK_a, a significant proportion of 5 reacts with free amine 4, which is sufficiently nucleophilic to compete with H₂O or ROH, eventually giving rise to oligomeric products.