A DFT Study of Thiophene Adsorption on the Rh（111） Surfaces

Thiophene adsorption on the Rh(111) surfaces has been investigated by density functional theory.The results show that the adsorption at the hollow and bridge sites is the most stable.The molecular plane of the thiophene ring is distorted,the C=C bond is stretched to 1.448  and the C-C bond is shortened to 1.390.The C-H bonds tilt 22～42oaway from the surface.The calculated adsorption geometries are in reasonable agreement with population analysis and density of states.The thiophene molecule obtains 0.74 electrons,reflecting the interaction between the lone pair of sulfur and the d-orbitals of metal.The reaction paths and transition states for desulfurization of the molecule have been investigated.The bridge adsorption structure of thiophene leads to a thiol via an activated reaction with an energetic barrier of 0.30 eV.This second step is slightly difficult,and dissociation into a C4H4 fragment and a sulfur atom is possible,with an energetic barrier of 0.40 eV.     

Decomposition Mechanism of 5,5′-Bis(tetrazole)-1,1′-dioIate(TKX-50) Anion Initiated by Intramolecular Oxygen Transfer

Density functional theory calculations at the B3LYP/6-31+G^** and B3LYP/6-311++G ^** levels were perfonned on thermal decomposition of 5,5′-bis(tetrazole)-1 ,r-diolate(TKX-50) anion with an intramolecular oxygen transfer being an initial step. Tlie results show that the intramolecular oxygen transfers are the rate-limiting steps for the decomposition of title anion with activation energies being in the range of 287-328 kJ/mol. Judged by the nucleus- independent chemical shift values, the formation of antiaromatic ring in transition state or the decrease of aromaticity of the tetrazole ring of the reactant makes somewhat contribution to the high potential energies of the rate-limiting transition states. However, the activation energies of the following N2 elimination tlirough various pathways are in a low range of 136-166 kJ/mol. The tetrazole ring acts as an electron donor or acceptor in difierent pathways to assist the bond nipture or group elimination. The rate constants in a temperature range of 500-2000 K for all the intramolecular oxygen transferring reactions were obtained. The corresponding linear relationships between InA and 1/T were established.     

Studies on the Oxazaborolidine-catalyzed Enantioselective Reduction of 3-Morpholin-4-yl-1-phenyl-1-propanone with Density Functional Theory

Density functional theory (DFT) has been applied to study the enantioselective reduction of 3-morpholin-4-yl-l-phenyl-l-propanone with borane catalyzed by (S)-4-benzyl-5,5-diphenyl-l,3,2-oxazaborolidine at the B3LYP/6-31G* level. All molecular species involved in the four reaction steps have been fully optimized and the structural parameters are provided, and the micro process of reaction was also investigated. The catalyst-alkoxyborane adduct formed in step Ⅲ exhibits a B-O-B-N tetra-atomic ring. Reaction coordination calculations show that BH3 can react with 3-morpholin-4-yl-l-phenyl-l-propanone spontaneously, resulting in the need of 2 tool BH3 in the reaction.     

Theoretical studies on phosphoraniminato derivatives of Keggin-type polyoxometalates [PW11O39{MVNPPh3}]3− (M = Fe,Ru): Electronic structures and bonding features

Transition metal phosphoraniminato derivatives of Keggin-type polyoxometalates(POMs) are important intermediates in N-transfer reactions.Density functional theory(DFT) has been employed to calculate the electronic structures,bonding features and redox properties of the iron and ruthenium phosphoraniminato derivatives of Keggin-type POMs,[PW11O39{MVNPPh3}] 3-(M = Fe,Ru).Our DFT calculations show that both anions have the same qualitative M-N single bond features.However,the calculations predict that the FeN system possesses a lower energy and more accessible metalnitrogen antibonding orbital than the RuN system.This results in a greater weakening of the Fe-N bond in the reduction process,and thus enhances its N-transfer reactivity.     

COS Activation by Zr~＋ in the Gas Phase：A Case of Two-state Reactivity Process

To elucidate the mechanisms of Zr + reacting with COS,both the quartet and doublet potential energy surfaces (PESs) for reactions of Zr + (4 F,2 D) with COS in the gas phase have been investigated in detail by means of density functional method (B3LYP).To obtain more accurate results,the coupled cluster single-point calculations (CCSD(T)) using B3LYP optimized geometries were performed.For the C-O bond activation,the calculated results indicate that both the quartet and doublet states proceed via an insertion-elimination mechanism.For the C-S bond activation,the quartet reaction has an insertion-elimination mechanism,but the doublet reaction is a direct abstraction of the sulfur atom by Zr +.The C-S bond activation is found to be energetically more favorable than the C-O bond activation.It is found that the reaction of the 4 F gound state of Zr + to yield ZrO + is spin-forbidden (Zr + (4 F) + COS (1 Σ) → ZrO + (2) + CS (1 Σ)) and the crossing points were approximately determined.All the results have been compared with the existing experimental and theoretical data.     

Kinetic calculation for the reaction of H with Si_2H_6 using the variational transition state theory

The reaction of disilane with atomic hydrogen has been studied. This reaction involves both substitution and abstraction. Calculations show that the hydrogen abstraction is the strongest competing channel. The canonical variational transition state theory with a small curvature tunneling correction (SCT) has been used for the kinetic calculation. The theoretical results are in good agreement with the available experimental data. Comparing the reactions of atomic hydrogen with disilane and silane, it can be seen that the reactivity of the Si-H bond is higher in Si2H6than that in SiH4.     

Synthesis, crystal structure and magnetic property of a three-dimensional cagelike polymer [Co(4,4''''-bpy)(NCS)_2(py)_2]_n

A new organic-inorganic hetero-coordination polymer with three different kinds of ligands [Co(4,4'-bpy)(NCS)2(py)2]n is synthesized in the extremely mild condition. The X-ray diffraction reveals that the title polymer has a highly tactic three-dimensional cagelike supramolecular structure. Although the coordination bond makes it a one-dimension chain, the hydrogen bond plays an important role in the formation of 3-D supramolecular frameworks. The determination of magnetic properties has been carried out, and shows that it behaves weak antiferromagnetic property with J(4,4'-bpy) = -3.8 cm-1.     

Exact quantum and TST-CEQ study of the collinear reaction O+HCl

Exact quantum calculations of reaction probabilities have been carried out using hyperspherical coordinates for the collinearr reaction O+HCl(v <1) -OH(v'<1)+Cl . A generalized LEPS potential energy surface with a barrier height of 8.12 kcal/mol has been used in the calculations. According to the calculated results we found that (1) the reaction probability oscillates with energy, (2) the reaction probability shows vibrational adiabaticity, although it is poorer than that for symmetric reaction Cl + HC1. The analysis of resonance has also been done. The reaction rate constants and average cross sections have been calculated by TST-CEQ method. The rate constants are in agreement with that by QCT and smaller than the experimental one. Finally, the threshold has been estimated and is in good agreement with that of the literature.     

Oxygenolysis reaction mechanism of copper-dependent quercetin 2,3-dioxygenase: A density functional theory study

The mechanism of the action of copper-dependent quercetin 2,3-dioxygenase(2,3QD) has been investigated by means of hybrid density functional theory.The 2,3QD enzyme cleaves the O-heterocycle of a quercetin by incorporation of both oxygen atoms into the substrate and releases carbon monoxide.The calculations show that dioxygen attack on the copper complex is energetically favorable.The adduct has a possible near-degeneracy of states between [Cu 2+-(substrate-H +)] and [Cu +-(substrate-H).],and in addition the pyramidalized C 2 atom is ideally suited for forming a dioxygen-bridged structure.In the next step,the C 3-C 4 bond is cleaved and intermediate Int 5 is formed via transition state TS 4.Finally,the O a-O b and C 2-C 3 bonds are cleaved,and CO is released in one concerted transition state(TS 5) with the barrier of 63.25 and 61.91 kJ/mol in the gas phase and protein environments,respectively.On the basis of our proposed reaction mechanism,this is the rate-limiting step of the whole catalytic cycle and is strongly driven by a relatively large exothermicity of 100.86 kJ/mol.Our work provides some valuable fundamental insights into the behavior of this enzyme.     

Theoretical Study on the Hetero-Diels-Alder Reactions between 3-Pyridinedithioesters and 1-Phenylsulfanylbutadiene

The mechanism, catalytic effect and solvent effect of the hetero-Diels-Alder reac- tions between 3-pyridinedithioesters and 1-phenylsulfanylbutadiene have been studied theoretically using density functional theory (DFT) at the B3LYP/6-31G(d) level. The results show that all of these reactions proceed in a concerted but asynchronous way. In some reactions the formation of C-S bond is prior to that of C-C bond and the opposite results are found in other reactions. The BF3 catalyst may lower the activation barriers by changing the energies of LUMO for 3-pyridine- dithioester. THF solvent has trivial influence on the potential energy surface of these reactions. With the BF3-catalyzed reactions, regioselectivity and stereoselectivity observed experimentally were predicted correctly by calculations and these results originate probably from C-H···F interaction in two transition states.     

Density Functional Study on the Mechanism of Amadori Rearrangement Reaction

The reaction mechanism of amadori rearrangement in the initial stage of Maillard reaction has been investigated by means of density functional theory calculations in the gaseous phase and aqueous solution.Cyclic ribose and glycine were taken as the model in the amadori rearrangement.Reaction mechanisms have been proposed,and possibility for the formation of different compounds has been evaluated through calculating the relative energy changes for different steps of the reaction by following the total mass balance.The calculations reveal that the amadori rearrangement initialized via the intramolecular rearrangement,transferring one proton from N(3) to O(4) atom.In the next step,the second proton is also transferred from N(3) to O(4) atom,corresponding to the cleavage of C(4)-O(4) bond and the release of one water molecule.Then another proton is transferred from N(3) to C(5) atom via TS3 with the reaction barrier of 58.3 kcal·mol-1 after tunneling the effect correction calculated at the B3LYP/6-31+G(d) level of theory,and this step is rate limiting for the whole catalytic cycle.Ultimately,the product is generated via keto-enolic tautomerization.Present calculation could provide insights into the reaction mechanism of Maillard reaction since experimental evaluation of the role of intermediates in the Maillard reaction is quite complicated.     

Mn(Ⅲ)-mediated radical reaction of 2-isocyano-6-alkenyl(alkynyl)benzonitriles with arylboronic acids:Synthesis of pyrroloisoquinoline derivatives

A Mn(Ⅲ) mediated radical reaction of new designed multi-functionalized 2-isocyano-6-alkenyl(alkynyl)benzonitriles with arylboronic acids has been developed.This reaction provides a method for the synthesis of pyrroloisoquinoline derivatives through the formation of two C-C bonds and one C-N bond via radical cascade cyclization in one step.     

SYNTHESIS OF 1-SUBSTITUTED-BENZENESULFO-NYL-3-(4'''',6''''-DISUBSTITUTED-s-TRIAZIN.2''''-YL)-1,3,2-DIAZAPHOSPHOLIDINES AND THEIR STRUCTURAL ANALYSES

The reaction of N-substituted-benzenesulfonyl-N'-(4,6-disubstituted-s-triazin-2-yl)-ethylene diamines with tri(dialkylamine)phosphine has been studied and the cyclic products have been obtained by one-pot reaction. It was found from ~1H NMR and ~(13)C NMR analyses that the single bond rotation between the nitrogen atom 3 in the 1,3,2-diazaphospholidines and the carbon atom 2 in the s-triazine was hindered at room temperature, which was further confirmed by X-ray diffraction results. The most stable conformation of the phosphorous heterocycle is envelope-form. From the bond length and the hybridization of the nitrogen atom outside the ring, it was deduced that there was a certain contribution of dπ-pπ bond between P and N atoms.     

DFT Calculations and NBO Analysis of 2-Chloroethylethyldichlorosilane Unimolecular Elimination Kinetics in the Gas Phase

Ab initio molecular orbital calculations have been used to investigate the thermal decomposition kinetics of 2-chloroethylethyldichlorosilane at the B3LYP/6-311+G**,B3PW91/6-311+G**,and MPW1PW91/6-311+G** levels of theory.Among these methods,the results(activation parameters) obtained using the B3LYP/6-311+G** level are in good agreement with the available experimental data.The calculated data imply that in the unimolecular β-elimination reactions of the studied compound in the gas phase,the polarization of C(1)-Cl(3) and C(1)-H(4) bonds in the sense of C(1)δ+-Cl(3)δ-and C(1)δ+-H(4)δ-,respectively,is a determining factor in the gas phase elimination reactions 1,2 and 3.Analysis of bond order,natural bond orbital charges,bond indexes,synchro-nicity parameters,and IRC calculations suggest the elimination of 2-chloroethylethyldichlorosilane via reactions 1～3 can be described as concerted and slightly asynchronous.The transition state structures of these reactions are a four-membered cyclic structure.     

Theoretical insights into the [4 + 2]/retro [4 + 2] cycloaddition approach to the synthesis of biaryls and polycyclic aromatics

A domino [4+2]/retro [4+2] cycloaddition process of cyclohexadienes with arylethynes or benzyne providing access to biaryls and polycyclic aromatics has been studied theoretically using density functional theory calculations. It has been found that the initial Diels-Alder (D-A) reaction acts as the rate-determining step and the consequent [4+2] cycloreversion reaction is feasible under the conditions used. Furthermore, the D-A reaction affects the regioselectivity, the origin of which is essentially derived from the good match of orbital coefficients between dienes and dienophiles as shown by using frontier molecular orbital (FMO) theory. Further investigation of the reactivity reveals that the reactions are predicted to fail to occur if an electron-donor group in the diene or an electron-acceptor group in the dienophile is lacking, as a consequence of the increased FMO energy gap. By further exploring the scope of substrates computationally, benzyne as an active dienophile was predicted to react with a variety of dienes in a cascade reaction under mild conditions with a low energy barrier, with the rate-determining step being the retro [4+2] cycloaddition.     

A Density Functional Study of N-Doped TiO2 Anatase Cluster

A systematic study on geometry, electronic structure and vibrational properties of N-doped TiO2 anatase cluster, within the framework of the density functional theory, has been performed in this work. The calculations confirmed that the most structures in substitutional model consist of a two-coordinate bridge structure and a three-coordinate hollow structure. The calculated results can well explain the red shift in N-doped TiO2 observed in experiments. The study provides an illustration for the N-doped anatase from the viewpoint of chemical bonding theory.     

Effect of Zr and C Co-doping on the Optical Properties and Electronic Structure of TiO_2

The systematic trends and effect introduced by Zr and C co-doping to TiO2 of electronic structure and optical properties of anatase TiO2 have been calculated by the plane-wave ultra-soft pseudopotential density functional theory (DFT) method within the generalized gradient approximation (GGA) for the exchange-correlation potential. Through the current calculations, the density of states (DOS), energy band structure and optical absorption coefficients have been obtained for TiO2 and compared with the doped TiO2, and the influence of electronic structure and optical properties caused by Zr and C co-doping has been presented qualitatively together. The results revealed that the energy band gap has been decreased owing to the doped Zr and C, whereas the optical absorption coefficients have been increased in the region of 400～800 nm and a red shift of absorption band can be found. Accordingly, photo catalytic activity of TiO2 has been enhanced. The current calculations are in good agreement with the experimental data.     

DFT Investigation on the Mechanism of Pd（0） Catalyzed Sonogashira Coupling Reaction

Based on DFT calculations, the catalytic mechanism of palladium(0) atom, commonly considered as the catalytic center for Sonogashira cross-coupling reactions, has been analyzed in this study. In the cross-coupling reaction of iodobenzene with phenylacetylene without co-catalysts and bases involved, mechanistically plausible catalytic cycles have been computationally identified. These catalytic cycles typically occur in three stages: 1) oxidative addition of an iodobenzene to the Pd(0) atom, 2) reaction of the product of oxidative addition with phenylacetylene to generate an intermediate with the Csp bound to palladium, and 3) reductive elimination to couple the phenyl group with the phenylethynyl group and to regenerate the Pd(0) atom. The calculations show that the first stage gives rise to a two-coordinate palladium (Ⅱ) intermediate (ArPdI). Starting from this intermediate, the second oxidative stage, in which the C–H bond of acetylene adds to Pd(Ⅱ) without co-catalyst involved, is called alkynylation instead of transmetalation and proceeds in two steps. Stage 3 of reductive elimination of diphenylacetylene is energetically favorable. The results demonstrate that stage 2 requires the highest activation energy in the whole catalysis cycle and is the most difficult to happen, where co-catalysts help to carry out Sonogashira coupling reaction smoothly.     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

Ab initio VB Studies of the Ground and Low-lying Excited States of BeH and BH

A scheme has been proposed to classify valence bond(VB) wave functions for the calculations of ground and excited states,according to the symmetry properties of one-electron orbitals which are involved in the construction of VB wave functions.This scheme is illustrated by the examples of BeH and BH.Ab initio VB computations of these two test molecules in combination with the present classification scheme give reliable results.For example,calculation results show that the state C2∑ of BeH is stable,with the bonding energy 0.87 eV and bond length 0.238nm,which are in good agreement with those obtained by Gerratt et al.The bonding features of ground and low-lying excited states of BeH and BH are discussed.