腈水合酶的发酵及酶学性质

红球菌Rhodococceus rhodochrous J1在含有脲和钴的培养基中发酵产生腈水合酶,可以催化丙烯腈水合为丙烯酰胺。调节培养条件使发酵液的酶活力达到6150u／ml。温度30℃,反应体系呈中性酶活性很高并且稳定。底物浓度,酶浓度,反应时间的正交实验表明,底物丙烯腈是显著因子,最佳浓度7％,超过此浓度酶会失活;1min内,水合反应转化率可达80％。浓度超过15％的丙烯酰胺会抑制酶的活性。     

DFT study of HCN and NC?CN reactions with hydrogen species

Energetic feasibility of the formation of aminoacetonitrile (or glycine nitrile) through a sequence of reactions of cyanogen (N?C? C?N) with hydrogen species was evaluated, using density functional theory (DFT) calculations at the B3LYP/ 6‐31++G(d,p) theoretical level. A critical step in the cyanogen hydrogenation is the addition of first H atom. As a result of a positive activation barrier of ～3–6 kcal mol^?1 (depending on the attachment site), this process is hardly feasible under cold gas‐phase interstellar conditions, but might possibly be facilitated in the solid phase by proton tunneling effects. The addition of a third hydrogen atom requires much lower activation energy, especially if H adds on the NH group (0.2–0.8 kcal mol^?1). The second and fourth steps (combination of C₂HN₂ and C₂H₃N₂ radical species with hydrogen atoms) are highly exothermic; the need to get rid of excess energy makes them possible through grain‐surface processes only. As a whole, most of the hydrogenation reactions under study can be expected to take place in the solid phase (icy and silicate grains), and not in the gas phase under cold interstellar conditions. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Photo‐physical Properties of N‐methyl‐3,4‐fulleropyrrolidine and Its Derivatives: A DFT and TD‐DFT Investigation

A series of N‐methyl‐3,4‐fulleropyrrolidine (NMFP) derivatives were designed by selecting different π‐conjugated linkers and electron‐donating groups as D‐π‐A and D‐A systems. The optimised structures and photo‐physical properties of NMFP and its derivatives have been determined using density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods with the B3LYP functional and the 6‐31G basis set. According to the computation analysis, both the π‐conjugated linkers and the electron‐donating groups can influence the electronic and photo‐physical properties of the NMFP derivatives. Our calculated results demonstrated that the electron‐donating groups, with significant electron‐donating ability, had the tendency to increase the highest occupied molecular orbital (HOMO) energy. The π‐conjugated linkers with lower resonance energy decreased the lowest occupied molecular orbital (LUMO) energy and caused a significant decrease in the energy gap (E_g) between the E_HOMO and E_LUMO. A Natural Bond Orbital (NBO) analysis examines the effect of the electron‐donating group, π conjugated linker, and electron‐withdrawing group for these NMFP derivatives. For the NMFP derivatives, a projected density of state (PDOS) analysis demonstrated that the electron density of HOMO and LUMO are concentrated on the electron‐donating group and the π‐conjugated linker, respectively. A TD‐DFT/B3LYP calculation was performed to calculate the electronic absorption spectra of these NMFP derivatives. Both the electron‐donating group and the π‐conjugated linker contribute to the major absorption peaks, which are assigned as HOMO to LUMO transitions and are red‐shifted relative to those of non‐substituted NMFP.     

已烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p),6-31+G(d,p),6-311G(d,p)及6- 311+G(d,p)基组,分别对1-C_6H_(12)~+,2-C_6H_(12)~+和3-C_6H_(12)~+的各种构 象进行了几何构型优化,并在B3LYP/6-311G(d,p)水平上进行了频率分析计算,在 各优化构型上,使用B3LYP和MP2(full)方法进行了超精细结构的计算。计算的3- C_6H_(12)~+的超精细偶合常数比以往的计算结果更好;1-C_6H_(12)~+和2-C_6H_ (12)~+的超精细偶合常数目前尚无实验数据报道,本计算预言了它们的超精细偶合 常数和最稳定构型。     

DFT conformational studies of the HI‐6 molecule

A systematic study of the oxime HI‐6 [1‐(2‐hydroxyiminomethyl‐1‐pyridinium)‐1‐(4‐carboxy‐aminopyridinium)dimethyl ether] hydrochloride, which is one of the most promising antidotes against soman intoxication, was carried out using density functional theory with the B3LYP (Becke, Lee, Yang, and Parr) method and the 6‐31+G*, 6‐31+G*, and 6‐31+G** basis sets. Rotational barriers, equilibrium geometries, and charge distributions were calculated in order to investigate the role of the side chain for the larger oximes used as antidotes in the treatment of neurotoxic organophosphate poisoning. Also reported is the comparison between HI‐6 and pralidoxime (2‐PAM), a smaller oxime previously studied in our research group. It is shown that conformation minima for the protonated E isomer do not depend on the size of the side chain; on the other hand, this effect has a pronounced influence on the protonated Z isomer. For the unprotonated isomers, other effects, such as electrostatic interactions and resonance, should be taken into account in their conformational analysis. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Semi-Empirical and DFT Studies on Structures and Spectra for C78（CH2）2

Eighteen possible isomers of C78（CH2）2 weTe investigated by the INDO method. It was indicated that the most stable isomer was 42,43,62,63-C78（CH2）2, where the -CH2 groups were added to the 6/6 bonds located at the same hexagon passed by the longest axis of C78 （C2v）, to form cyclopropane structures. Based on the most stable four geometries of C78（CH2）2 optimized at B3LYP/3-21G level, the first absorptions in the electronic spectra calculated with the INDO/CIS method and the IR frequencies of the C-C bonds on the carbon cage computed using the AM1 method were blue-shifted compared with those of C78 （C2v） because of the bigger LUMO-HOMO energy gap and the less conjugated carbon cage after the addition. The chemical shifts of ^13C NMR for the carbon atoms on the added bonds calculated at B3LYP/3-21G level were moved upfield thanks to the conversion from sp^2-C to sp^3-C.     

A DFT study for the regioselective 1,3-dipolar cycloadditions of nitrile N-oxides toward alkynylboronates

The mechanism for the 1,3-dipolar cycloaddition of benzonitrile oxide toward ethynyl and propynylboronate has been studied by using density functional theory (DFT) at B3LYP/6-31G* level. These cycloadditions are concerted [3+2] processes. The presence of the two oxygens on the boronic ester precludes the participation of the boron atom on [3+3] processes. The two regioisomeric channels associated to the formation of the isoxazoles bearing the boronic ester unit on the 4- or 5-positions have been characterized. The B3LYP/6-31G* activation parameters are in acceptable agreement with the experiments, allowing to explain the factors controlling these regioselective cycloadditions.     

Calculations of ionization energies and electron affinities for atoms and molecules: A comparative study with different methods

In the present work, we examined the performance of 36 density functionals, including the newly developed doubly hybrid density functional XYG3 (Y. Zhang, X. Xu, and W. A. Goddard III, Proc. Natl. Acad. Sci, USA, 2009, 106, 4963), to calculate ionization energies (IEs) and electron affinities (EAs). We used the well-established G2-1 set as reference, which contains 14 atoms and 24 molecules for IE, along with 7 atoms and 18 molecules for EA. XYG3 leads to mean absolute deviations (MADs) of 0.057 and 0.080 eV for IEs and EAs, respectively, using the basis set of 6-311 + G (3df,2p). In comparison with some other functionals, MADs for IEs are 0.109 (B2PLYP), 0.119 (M06-2X), 0.159 (X3LYP), 0.161 (PBE), 0.162 (B3LYP), 0.165 (PBE0), 0.173 (TPSS), 0.200 (BLYP), and 0.215 eV (LC-BLYP). MADs for EAs are 0.090 (X3LYP), 0.090 (B2PLYP), 0.102 (PBE), 0.103 (M06-2X), 0.104 (TPSS), 0.105 (BLYP), 0.106 (B3LYP), 0.126 (LC-BLYP), and 0.128 eV (PBE0).     

A DFT study of the hydration of monophosphate complexes of iron (III),

A systematic theoretical DFT study of the bonding between the cation Fe³⁺ and the anion was carried out. The role of water ligands is presented. Several isomers with tetrahedral, bipyramidal and octahedral environments around the iron ion were investigated. 5-fold coordination of the Fe³⁺ cation is found when 5 and 6 water molecules are included. Calculated infrared spectra are also presented.     

Synthesis and DFT study of the spectral behavior of new 4‐hydroxycoumarins

4‐Hydroxycoumarins are compounds with a lot of applications as drugs and herbicides. They have very interesting spectral and chemical properties, which are investigated theoretically and experimentally. Some new 4‐hydroxycoumarins with arylydene‐β‐ketoester or arylydene‐2,4‐pentanedione side chain were synthesized by two step synthetic scheme. Their structure was characterized by UV–vis, IR, and ¹H NMR methods. The spectral behavior of the optimized structures of these compounds was reproduced by the hybrid DFT methods B3LYP and B3P86 with 6‐31G** and aug‐cc‐pVDZ basis sets. Electronic excited states and vibrational frequencies were calculated. HF method was also used for comparison, because of the lack of electronic correlation. The theoretical spectra were compared with the experimental ones. A lot of compounds show good agreement between experimental and some of the theoretical data, especially obtained by aug‐cc‐pVDZ basis set. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

A comparative DFT study of tetracyanoquinodimethane and its difluoro and tetrafluoro analogs

The optimized molecular structures, harmonic vibrational wavenumbers and corresponding vibrational assignments, frontier molecular orbitals and UV data of 7,7,8,8-tetracyanoquinodimethane, 2,5-difluoro-7,7,8,8-tetracyanoquinodimethane and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane were computed using quantum mechanical code. Calculations were carried out at Becke-3-Lee-Yang-Parr (B3LYP) functional with density functional theory (DFT) and time-dependent density functional theory (TD-DFT) using the 6–311++G (d,p) basis set. The theoretical results were successfully compared with some of the available experimental data. The influence of fluorine on the structural, vibrational and electronic properties were investigated. The addition of fluorine reduces both the electrical and optical band gaps. The findings of this research can be useful for analogs of the molecules studied which have potential applications in the design of organic semiconductors for electronic devise applications.     

DFT conformational studies of alpha-maltotriose

Recent DFT optimization studies on alpha-maltose improved our understanding of the preferred conformations of alpha-maltose. The present study extends these studies to alpha-maltotriose with three alpha-D-glucopyranose residues linked by two alpha-[1-->4] bridges, denoted herein as DP-3's. Combinations of gg, gt, and tg hydroxymethyl groups are included for both "c" and "r" hydroxyl rotamers. When the hydroxymethyl groups are for example, gg-gg-gg, and the hydroxyl groups are rotated from all clockwise, "c", to all counterclockwise, "r", the minimum energy positions of the bridging dihedral angles (phi(H) and psi(H)) move from the region of conformational space of (-, -), relative to (0 degrees , 0 degrees), to a new position defined by (+, +). Further, it was found previously that the relative energies of alpha-maltose gg-gg-c and "r" conformations were very close to one another; however, the DP-3's relative energies between hydroxyl "c" or "r" rotamers differ by more than one kcal/mol, in favor of the "c" form, even though the lowest energy DP-3 conformations have glycosidic dihedral angles similar to those found in the alpha-maltose study. Preliminary solvation studies using COSMO, a dielectric solvation method, point to important solvent contributions that reverse the energy profiles, showing an energy preference for the "r" forms. Only structures in which the rings are in the chair conformation are presented here.     

Spectroscopic studies of the 1:1 adduct of N-methylmorpholinium-acetate with hydrobromic acid in the crystalline and gaseous state

The 1:1 complex of N-methylmorpholinium-acetate, MMB, with hydrobromic acid (1) has been investigated by single-crystal X-ray analysis, infrared spectroscopy and theoretical calculations. The proton-transfer complex has been observed in the crystalline state, with the COOH⋯Br hydrogen bond with the O⋯Br distance of 3.107(2) Å. In the structure optimized at the B3LYP/6-311++G(d,p) levels of theory the proton is closer to the bromide anion, with the BrH⋯OOC distance of 3.069 Å. The potential energy distributions (PED) have been used for the assignments of IR bands. The experimental and theoretical infrared spectra have been discussed.     

Post-translational modification of Rhodococcus R312 and Comamonas NI1 nitrile hydratases

Nitrile hydratases (NHases) are industrially significant iron- and cobalt-containing enzymes used in the large-scale synthesis of acrylamide. Previous reports have shown that the active site peptides of NHases are post-translationally modified by oxidation of cysteine residues, and that these modifications are essential for catalysis. We report mass spectrometric evidence of the oxidation states of the active site cysteines in the iron coordination spheres of two iron-containing nitrile hydratases, namely R312 NHase from Rhodococcus rhodochrous strain R312 and NI1 NHase from Comamonas testosteroni. At least one of these cysteines is oxidised to a sulfinic acid (SO(2)H) and there is also evidence suggesting an additional oxidation to a sulfenic acid (SOH). This is the first evidence for the presence of these oxidation states for full-length NHases and for Fe-NHases from different microorganisms. The presence of these covalent modifications was confirmed by performing mass spectrometry on the active site peptide of R312 NHase, under native, reduced and carboxymethylated conditions. We also show the nitrosylation of the iron by mass spectrometry, as well as the release of NO by photoirradiation.     

戊烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p)、6-31＋G(d,p)、6-311G(d,p)及6-311＋G(d,p)基组，分别对2-C5H10＋和1-C5H10＋的各种构象进行了几何构型优化，并用B3LYP/6-311G(d,p)进行了频率分析计算.计算预言1-C5H10＋具有非平面构型，与以往报导的从头算计算结论相反.在两个自由基阳离子的各种构象的B3LYP几何构型上，进行了B3LYP和UMP2(full)方法的超精细偶合常数计算，得到了比以往更好的结果.     

Application of the DFT Theory to Study Cobalamin Complexes

The aim of present study is to select the best methodology in the frame of the Density Functional Theory (DFT), which may be employed to study the cobalamin complexes. Our discussion is limited to two approaches, one in which hybrid B3LYP and UB3LYP functionals are used, and the second in which geometry parameters are calculated within LDA-VWN functional, and energies of the investigated systems are computed within RPBE functional. Results of performed calculations show that both methodologies can be successfully applied to study cobalamin derivatives. Probably because of the small ligand binding energies in the studied complexes, the B3LYP and UB3LYP functionals may be used only to predict the pattern of changes in the binding energies. The use of the RPBE functional, originally parameterized to reproduce in a proper way the chemisorption energies of the small molecules on the metallic surfaces, allows to improve their values so as they fit into experimental data. Geometry parameters of the investigated complexes computed within both approaches are in good agreement with the experimental values. Interatomic distances are a little overestimated while calculated within both hybrid functionals, what is in contrast to VWN functional results. The latter, in general, gives shorter distances as observed experimentally.     

A DFT Study for NH3 Adsorption on the GaN （0001） Surface

1 INTRODUCTION Recently, the reaction of NH3 with III-V com- pounds[1～5] has attracted much attention, especially for the wurtzite GaN, since NH3 is the predominant raw stuff for growing crystalline GaN by both of the most important growth techniques[6～9], i.e., organo- metallic chemical vapor deposition (OMCVD) and molecular-beam epitaxy (MBE). Experimentally, Shekhar et al.[2] reported the chemisorption and reaction of hydrogen and ammonia on the single- crystalline GaN (0001…     

DFT study of the IR and Raman spectra of a fluorescent dendron built from cyclotriphosphazene core

Combined experimental and theoretical studies on molecular structure of the zero generation dendron, built from the hexafunctional cyclotriphosphazene core, with five OC₆H₄(CH₂)₂NHSO₂C₁₀H₆N(CH₃)₂ terminal groups and one oxybenzaldehyde group G₀ are reported. The Fourier transform Raman and IR spectra of G₀ have been recorded. Conformations of low energy isomers of G₀ have been studied at quantum-chemical level. The optimized geometry has been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. The theoretical geometrical parameters, harmonic vibrational frequencies, IR intensities and Raman scattering activities are predicted in a good agreement with the experimental data. It was found that dendron molecule G₀ has a concave lens structure with planar OC₆H₄CHO fragments and slightly non-planar cyclotriphosphazene core. Relying on DFT calculations the bands of the core and terminal groups were assigned. The frequencies of ν(NH) bands in the IR spectrum reveal the presence of the H-bonds in the dendron.     

Ab initio and DFT modeling of stereoselective deamination of aziridines by nitrosyl chloride

The stereochemical course of the deamination of cis‐2,3‐dimethylaziridine by nitrosyl chloride was investigated at the QCISD/6‐31G(d) level. Calculations reveal that the reaction takes place in two steps. In the first step, the reactants form a pre‐reactive complex, followed by a spiro‐type bicyclic transition state, which on dissociative cycloelimination gives the N‐nitrosoaziridine intermediate. In the second step, this intermediate undergoes cycloreversion through a slightly asynchronous concerted transition state to form an alkene with the same stereochemistry, which is in total agreement with experiment. In the whole reaction, the denitrosation step is found to be rate‐determining. For comparison, geometry optimizations and energies were also obtained at the B3LYP/6‐31G(d) level. It was found that the B3LYP energy results differed significantly from the QCISD ones. To analyze the reason for this difference, B3LYP calculations were repeated by varying the contribution of exact exchange in the Becke functional. With respect to the QCISD results, it has been shown that the functional with 0% exact exchange yields the best activation barriers, whereas the functional with 30% exact exchange is the most suitable one to carry out the complexation and reaction energy calculations. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005