Solvent effects and potential of mean force study of the S_N2 reaction of CH_3F+CN~- in water

We used a combined quantum mechanics and molecular mechanics(QM/MM) method to investigate the solvent effects and potential of mean force of the CH_3F+CN~- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects' contributions to the reaction: 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy.The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol,consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.     

Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase

Chorismate mutase provides an important test of theories of enzyme catalysis, and of modelling methods. The Claisen rearrangement of chorismate to prephenate in the enzyme has been modelled here by a combined quantum mechanics/molecular mechanics (QM/MM) method. Several pathways have been calculated. The sensitivity of the results to details of model preparation and pathway calculation is tested, and the results are compared in detail to previous similar studies and experiments. The potential energy barrier for the enzyme reaction is estimated at 24.5—31.6 kcal mol^?1 (AMl/CHARMM), and 2.7—11.9 kcal mol^?1 with corrections (e.g. B3LYP/6-31 + G(d)). In agreement with previous studies, the present analysis of the calculated paths provides unequivocal evidence of significant transition state stabilization by the enzyme, indicating that this is central to catalysis by the enzyme. The active site is exquisitely complementary to the transition state, stabilizing it more than the substrate, so reducing the barrier to reaction. A number of similar pathways for reaction exist in the protein, as expected. Small structural differences give rise to differences in energetic contributions. Major electrostatic contributions to transition state stabilization come in all cases from Arg90, Arg7, one or two water molecules, and Glu78 (Glu78 destabilizes the transition state less than the substrate), while Arg63 contributes significantly in one model.     

基于参考势的从头算量子力学/分子力学混合方法研究Parvalbumin B蛋白结合钙、镁离子的选择性

蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别. 尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用. 量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述. 但是在分子模拟中采用量子化学方法则太昂贵了. 近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境. 在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的. 随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息. 本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性. 计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性. 并且,量子化学区域的选择对于结果的可靠性也是非常重要的.     

Theoretical study of the [Si,C, P,O] potential energy surface

The structures, energetics, spectroscopies and stability of the doublet [Si, C, P, O] radical are explored at the density functional theory and ab initio levels. Eighteen isomers connected by 22 interconversion transition states are located at the DFT/B3LYP/6-311G(d) level. The structures of the kinetically stable isomers and the relevant transition states are further optimized at the QCISD/6-311G(d) level followed by CCSD(T)/6-311 + G(2df) single-point energy calculations. At the QCISD/6-311G(d) level, the lowest-lying isomer is the cyclic O-cCSiP 8 (0.0 kcal/mol) with considerable kinetic stability of 22.0 kcal/mol. In addition, two bent isomers OSiCP 1 (7.3 kcal/mol) and SiCPO 3 (34.7 kcal/mol) also possess considerable kinetic stability (more than 10.0 kcal/mol). As a result, three isomers 1, 3 and 8 are predicted to be possible candidates for future experimental and astrophysical detection. The bonding nature of the three isomers is analysed. The calculated results are compared with those of the analogous radical [Si, C, N, O]. Implications in the laboratory and interstellar space are also discussed. The predicted structures and spectroscopic properties are expected to be informative for the identification of [Si, C, P, O] in the laboratory and space.     

DFT study on coupling reaction of carbon dioxide with ethylene oxide catalyzed by 1,4,6-triaza-bicyclo[3.3.0]oct-4-enium bromide (TBO.HBr)

ABSTRACT

Chemical fixation of CO₂ with epoxides catalyzed by organic-base salts were found to be efficient among the various catalysts tested due to synergetic effects of HBDs and halide-ions for ring-opening. In this study, 1,4,6-Triaza–bicyclo[3.3.0]oct-4-enium bromide catalyzed conversion of CO₂ and epoxide into cyclic-carbonate has been studied by using DFT method to understand the reaction mechanism and the catalytic performance of TBO.HBr. Two hypothetical reaction mechanisms were proposed for the coupling reaction. Thermodynamic and kinetic parameters were computed for each steps to determine the more favorable route. Mechanism II is more favorable path whereby Br^- ion first interacts with epoxide to form bromo-alcohol, which directed to form carbonate-ion and finally ring-closure step yielded cyclic-carbonate with catalyst-regeneration. Cyclization step is rate-determining step with reaction barrier of 22.696?kcal/mol in gas phase. Ensuing the favorable mechanism, solvent-effects on the reaction barrier has been investigated using water and THF. Mechanism II is still more favorable reaction path in both THF and water. However, the rate-determining step is found to be ring-opening of the epoxide with reaction barrier of 22.658?kcal/mol (wate) and 21.969?kcal/mol (THF). In this study, TBO.HBr exhibited good catalytic activity for the title reaction investigated in both gas phase and solvents.     

Theoretical study on structures and stability of SiC3S isomers

Various levels of calculations are carried out to explore the potential energy surfaces (PES) of singlet and triplet SiC₃S, a molecule of potential interest in interstellar chemistry. At the DFT/B3LYP/6-311G(d) level, a total of 57 minimum isomers and 92 interconversion transition states are located. The structures of the most relevant isomers and transition states are further optimized at the QCISD/6-311G(d) level followed by CCSD(T)/6-311?+?G(2df) single-point energy calculations. At the QCISD level, the lowest-lying isomer is the chain-like SiCCCS ³ 1 (0.0?kcal/mol) with a great kinetic stability of 54.1?kcal/mol. In addition, ring isomers CC-cCSSi ¹ 9 (19.8?kcal/mol), S-cCCCSi ¹ 12 (30.4?kcal/mol), S-cCCSiC ¹ 18 (9.4?kcal/mol), S-cSiCCC ¹ 21 (34.4?kcal/mol) and cage-like isomer cage-SiSCCC ¹ 23 (51.8?kcal/mol) also possess considerable kinetic stability (more than 10.0?kcal/mol). As a result, these six isomers are predicted to be possible candidates for future experimental and astrophysical detection. The bond natures and possible formation pathways in interstellar space of the SiCCCS are discussed. The predicted structure and spectroscopic properties for it are expected to be informative for the identification of SiC₃S and even larger SiC _n S species either in laboratory or in space.     

DFT studies on catalytic dehydrogenation of ammonia borane by Ni(NHC)2

The catalytic dehydrogenation mechanism of ammonia borane (NH₃BH₃, AB) by Ni N‐heterocyclic carbene (NHC) complexes has been investigated by density functional theory. Two possible mechanisms of the dehydrogenation of NH₃BH₃ have been theoretically studied: intramolecular reaction at Ni dicarbene and intermolecular reaction at Ni monocarbene and dicarbene. The facile occurrence of the dehydrogenation of AB was demonstrated by the low activation barriers of the rate‐determining step. It was found that the intramolecular pathway is mostly kinetically favorable with lower activation barrier of 15.51 kcal/mol than the intermolecular pathway. Moreover, for intermolecular dehydrogenation of AB, the activation prefers to take place at monocarbene Ni(NHC) catalyst. Copyright © 2014 John Wiley & Sons, Ltd.     

Theoretical studies on [2 + 2 + 2] reaction mechanisms of three ethynes. More accurate estimation of activation energy

The mechanisms of the [2 + 2 + 2] cycloaddition reaction of three ethyne molecules were studied by ab initio molecular orbital and density functional methods. The transition states range from that of the concerted mechanism with D_3h symmetry to that of the stepwise mechanism with C₂ symmetry. The transition state structure and the activation energy depend on the basis set and computational method employed in the analysis. The activation energy barrier was determined to be in the range of 36–44 kcal/mol. The activation energy determined by various methods corresponds to the interaction energy, which is related to the electron correlation energy. The best estimation of the activation energy barrier is 41.6 kcal/mol, achieved from the relation between the interaction energy and the activation energy. Copyright © 2013 John Wiley & Sons, Ltd.     

Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II

ABSTRACT

Possible mechanisms for water cleavage in oxygen evolving complex (OEC) of photosystem II (PSII) have been investigated based on broken-symmetry (BS) hybrid DFT (HDFT)/def2 TZVP calculations in combination with available XRD, XFEL, EXAFS, XES and EPR results. The BS HDFT and the experimental results have provided basic concepts for understanding of chemical bonds of the CaMn₄O₅ cluster in the catalytic site of OEC of PSII for elucidation of the mechanism of photosynthetic water cleavage. Scope and applicability of the hybrid DFT (HDFT) methods have been examined in relation to relative stabilities of possible nine intermediates such as Mn-hydroxide, Mn-oxo, Mn-peroxo, Mn-superoxo, etc., in order to understand the O–O (O–OH) bond formation in the S₃ and/or S₄ states of OEC of PSII. The relative stabilities among these intermediates are variable, depending on the weight of the Hartree–Fock exchange term of HDFT. The Mn-hydroxide, Mn-oxo and Mn-superoxo intermediates are found to be preferable in the weak, intermediate and strong electron correlation regimes, respectively. Recent different serial femtosecond X-ray (SFX) results in the S₃ state are investigated based on the proposed basic concepts under the assumption of different water-insertion steps for water cleavage in the Kok cycle. The observation of water insertion in the S₃ state is compatible with previous large-scale QM/MM results and previous theoretical proposal for the chemical equilibrium mechanism in the S₃ state . On the other hand, the no detection of water insertion in the S₃ state based on other SFX results is consistent with previous proposal of the O–OH (or O–O) bond formation in the S₄ state . Radical coupling and non-adiabatic one-electron transfer (NA-OET) mechanisms for the OO-bond formation are examined using the energy diagrams by QM calculations and by QM(UB3LYP)/MM calculations . Possible reaction pathways for the O–O and O–OH bond formations are also investigated based on two water-inlet pathways for oxygen evolution in OEC of PSII. Future perspectives are discussed in relation to post HDFT calculations of the energy diagrams for elucidation of the mechanism of water oxidation in OEC of PSII.     

The reaction of carbon and water as catalyzed by a nickel surface

Many of the individual steps which make up the reaction of carbon and water to produce CO and H₂ were studied on a nickel foil surface using temperature-programmed reaction spectroscopy (TPRS), Auger electron spectroscopy (AES), and ultraviolet photoelectron spectroscopy (UPS). Surface graphite and carbide, two metastable surface carbon forms, were prepared by dehydrogeneration of C₂H₂ and served as reactant carbon. UPS of the graphite monolayer in contact with the metal yielded a valence electronic structure that could be interpreted in terms of the bulk band structure of graphite. The fully carbided Ni surface was active for H₂O dissociation with an estimated activation energy ≤ 5 kcal/mol. The reaction of graphitic carbon in contact with the nickel surface and adsorbed oxygen occurs directly without isolated prior breaking of carbon-carbon bonds. The estimated activation energy for the direct reaction was 44 kcal/mol. A different catalytic reaction cycle involving carbon-carbon bond breaking followed by oxidation of the carbide is energetically more demanding. The activation energy for direct carbon-carbon bond breaking was estimated to be between 65 and 70 kcal/mol. Following this demanding step, the reaction between carbidic carbon and oxygen proceeded with estimated activation energy of 31 kcal/mol.     

Combined multi-level quantum mechanics theories and molecular mechanics study of water-induced transition state of OH~- + CO_2 reaction in aqueous solution

The presence of a solvent interacting with a system brings about qualitative changes from the corresponding gasphase reactions. A solvent can not only change the energetics along the reaction pathway, but also radically alter the reaction mechanism. Here, we investigated the water-induced transition state of the OH~- + CO_2→ HCO_3~- reaction using a multi-level quantum mechanics and molecular mechanics method with an explicit water model. The solvent energy contribution along the reaction pathway has a maximum value which induces the highest energy point on the potential of mean force. The charge transfer from OH~- to CO_2 results in the breaking of the OH~- solvation shell and the forming of the CO_2 solvation shell. The loss of hydrogen bonds in the OH~-solvation shell without being compensated by the formation of hydrogen bonds in the CO_2 solvation shell induces the transition state in the aqueous solution. The calculated free energy reaction barrier at the CCSD(T)/MM level of theory, 11.8 kcal/mol, agrees very well with the experimental value, 12.1 kcal/mol.     

Computational study of singlet and triplet sulfonylnitrenes insertion into 1,3‐butadienes: 1,2‐ or 1,4‐cycloaddition?

The formation of N‐trifluoromethylsulfonyl‐2‐vinylaziridine and N‐trifluoromethylsulfonyl‐3‐pyrroline by the reaction of the singlet and triplet trifluoromethanesulfonylnitrenes with s‐cis‐ and s‐trans‐1,3‐butadienes was studied theoretically at the B3LYP/6‐311++G(d,p) and M06‐2X/6‐311++G(d,p) levels of theory. The singlet trifluoromethanesulfonylnitrene adds to s‐cis‐ and s‐trans‐1,3‐butadiene exothermally in one step to give the product of 1,2‐cycloaddition, N‐trifluoromethylsulfonyl‐2‐vinylaziridine, the energy decreasing by 88.5 and 86.2 kcal/mol at the B3LYP level and by 105.2 and 103.0 kcal/mol at the M06‐2X level, respectively. The formed 2‐vinylaziridine can undergo rotation about the C(2)–C_sp2 bond with the barrier not exceeding 3.5 kcal/mol and to rearrange into N‐trifluoromethylsulfonyl‐3‐pyrroline. The triplet trifluoromethanesulfonylnitrene reacts with s‐cis‐ and s‐trans‐1,3‐butadiene in two steps. The first exothermic step is the formation of the triplet diradical adducts. The second step is the spin inversion with the energy raising by 5.8 and 17.8 kcal/mol at the B3LYP level and by 11.0 and 20.8 kcal/mol at the M06‐2X level for the adducts to s‐cis‐ and s‐trans‐1,3‐butadiene, respectively. Recombination of the radical centers occurs selectively to give N‐trifluoromethylsulfonyl‐2‐vinylaziridine that is exothermally rearranged into N‐trifluoromethylsulfonyl‐3‐pyrroline with the energy barrier of 40 kcal/mol at the B3LYP level and of 50 kcal/mol at the M06‐2X level. Copyright © 2014 John Wiley & Sons, Ltd.     

Fe2O3上AsH3催化氧化反应机理的理论研究

本文采用密度泛函理论方法研究了Fe₂O₃上AsH₃的催化氧化反应机理.该反应以Fe₂O₃中的两个Fe原子为不同的活性中心进行研究,每个活性中心均设计了3个步骤. AsH₃分子依次与3个O₂分子在催化剂上相互作用分别形成中间体H₃AsO₂、H₃AsO₄及最终产物H₃AsO₆.研究发现,当氧化反应发生在1号铁原子(Fe1)附近,其速度控制步骤活化自由能垒为49.99 kcal/mol;当氧化反应发生在2号铁原子(Fe2)附近,其活化自由能垒为21.20 kcal/mol,与直接氧化(50.14 kcal/mol)相比大大降低.可见AsH₃在Fe₂O₃上的催化氧化反应更易发生在Fe2附近.     

Mechanistic insights into C‐C cross coupling activities of Pd/Ni‐doped heterofullerenes

Mechanistic insights into Heck and Suzuki‐Miyaura cross coupling reactions with C₅₉M (M = Pd/Ni) catalysts were developed. Density functional theory was used for the analysis of all the intermediates and transition states possible during C‐C cross coupling reactions over the catalysts under study. Oxidative addition, a step common to both Heck and Suzuki‐Miyaura cross coupling reactions, was observed to proceed with smaller activation barriers over C₅₉Pd. Heck coupling of iodobenzene with styrene was observed to proceed via oxidative addition, migratory insertion, and reductive elimination steps. The free energy barriers for oxidative addition, migratory insertion, and reductive elimination steps were 14.8, 11.6, and 4.8 kcal/mol, respectively, over C₅₉Pd, and 17.4, 79.3, and 17.4 kcal/mol, respectively, over C₅₉Ni, indicating oxidative addition and migratory insertion to be the rate‐determining steps over C₅₉Pd and C₅₉Ni, respectively. Similarly for Suzuki‐Miyaura coupling reaction, activation barriers for oxidative addition, transmetalation, and reductive elimination steps were 14.8, 52.4, and 7.9 kcal/mol, respectively, over C₅₉Pd, and 17.4, 64.7, and 60.2 kcal/mol, respectively, over C₅₉Ni, indicating transmetalation step to be the rate‐determining step over both the heterofullerenes.     

Interaction of Ga<Subscript>3</Subscript> cluster with molecular hydrogen: combined DFT and CCSD(T) theoretical study

We have explored the lowest doublet and quartet potential energy surfaces (PES) for the reaction of gallium trimer with H₂. This reaction was studied experimentally by Margrave and co-workers in a noble gas matrix. The detailed reaction paths ending up with the low-energy Ga₃H₂ hydride isomers have been predicted based on the high level ab initio coupled-cluster calculations (CCSD(T)) with large basis set. We have found that the reaction occuring on the lowest doublet PES is described by the activation barrier for H₂ cleavage of about 15 kcal/mol, consistent with experiment. In the most stable Ga₃H₂ hydride structure, whose formation is exothermic by 15 kcal/mol, both H atoms assume three-fold bridged positions. The diterminal planar structure of Ga₃H₂, proposed experimentally from the observed IR spectra, is found to be only 1 kcal/mol less stable than the dibridged form.     

A measurement of surface diffusion across steps on a curved surface (Pd on W)

The surface diffusion of palladium on the curved part of a tungsten crystal is studied by field electron microscopy. The variation of the local coverage distribution is measured by a probe-hole device on the stepped surface region around (001). The measured data allow a determination of the mass transport surface diffusion coefficient D of Pd on W across atomic steps as a function of temperature, coverage and step density. D has been found (1) to be constant for a given step density and for coverages lower than about 5 × 10¹⁴ Pd adatoms/cm², (2) to increase for higher coverages, and (3) to increase with increasing step density for a given coverage. The activation energy of the process is nearly constant (about 24 kcal/mol) for all coverages up to about 6 × 10¹⁴ adatoms/cm², while the pre-exponential factor of D increases with increasing step density. Interpretation of the results gives some information on the diffusion mechanism.     

Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

Magnetic brillouin zone effect on the resistivity of semimetallic-like fermi surface in USb

To probe the effect of the protein environment on the retinal chromophore of rhodopsin, we performed molecular dynamics simulations using combined quantum mechanics/molecular mechanics (QM/MM). The starting geometry of the protein is based on the 2.6Å X-ray structure of bovine rhodopsin of Okada et al. [T. Okada, et al. Proc. Natl. Acad. Sci. USA 99 5982 (2002)]. The wild-type chromophore of rhodopsin according to our calculations shows a highly twisted conformation around the central region, from C10 to C13, due to non-bonded interaction with the protein pocket. The absolute sense of twist of the C11–C12 and C12–C13 bonds is negative (?19 ± 9°) and positive (170 ± 8°), respectively. The 13-demethyl retinal chromophore, in which the methyl group at the C13 position is removed, is less distorted in this region. The C11–C12 bond is less twisted (?15 ± 10°) and the C12–C13 bond is planar (179 ± 9°) . The flattened geometry of this artificial chromophore is supported by spectroscopic evidence.     

Small silver clusters at paramagnetic defects of silica surfaces: A density functional embedded-cluster study

We studied the interaction of small Ag_n clusters (n = 1–4) with paramagnetic defect centers of a dehydroxylated silica surface using an all-electron scalar relativistic density functional method. The surface and adsorption complexes on it were modeled with an accurate quantum mechanics/molecular mechanics (QM/MM) scheme of embedding QM clusters in an elastic polarizable environment, described at the molecular mechanics level (MM). We analyzed two types of frequent point defects as sites for trapping and growing of Ag clusters: a silicon atom with a dangling bond (E′ center), ≡ Si?, and a non-bridging oxygen center (NBO), ≡ Si–O?. The Ag clusters interact with these paramagnetic centers forming strong covalent metal-defect bonds. The high adsorption energy allows one to consider the NBO and E′ sites as traps of single Ag atoms and as centers of cluster growth. We also explored the effect of adsorption on observable electronic properties of the silver clusters and of the defects of the silica surface.