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1.
Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,  相似文献   

2.
An ab initio molecular dynamics simulations have been carried out for the dissociative recombination reaction of the deuterium-substituted hydronium cation, HD2O+ + e , at the state-averaged multiconfigurational self-consistent field level. In the present simulations, five electronic states of HD2O were included explicitly, and nonadiabatic transitions among adiabatic electronic states were taken into account by the Tully’s fewest switches algorithm. It is shown that the dominant products, OD + D + H, were generated in 63% of trajectories, while the products, OH + 2D, were generated in only 11% of trajectories, indicating that the release of a light fragment H is favored over the release of a heavy fragment D. This result is in conformity with the observation that there is a larger amount of deuterium substituted species than the non-substituted species in the interstellar space. Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue.  相似文献   

3.
A β-hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α-H atom with ab initio calculation at the B3LYB/6-31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre- and post-reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method. The reaction profile of these α-H abstraction reactions was constructed. The effects of the aqueous solution were estimated by the conductor-like polarizable continuum model (CPCM) model. Rate constants were calculated with transition state theory. The reaction rate of the OH α-H abstraction varies among these three different sites. The differences among these three sites were rationalized in terms of the molecular and electronic structures of the reactive complexes along the reaction pathway. The explicit solvation effect was estimated through the similar abstraction of a zwitterionic glycine with the combination of microsolvation and a CPCM model. Our results indicate that the α-H abstraction at certain sites requires explicit salvation to obtain accurate results. A replica exchange molecular dynamics simulation was performed to demonstrate the structural change due to this type of abstraction.  相似文献   

4.
When driven far from equilibrium,nonlinear chemical reactions often show a variety of self-organization behavior,including chemical oscillations,waves,chaos and patterns[1].Recently,the study of such nonlinear phenomena in‘complex’systems,such as the li…  相似文献   

5.
6.
The interaction of naproxen with β-cyclodextrin and its derivatives (hosts) as well as polymer has been studied using UV Visible (UV–Vis), Fourier Transform Infrared (FTIR), Nuclear Magnetic Resonance (NMR) spectroscopy and Scanning electron microscopy (SEM). In this paper, the solid inclusion complexes were prepared by freeze drying method. The formation constants of the complexes were determined by UV–Vis method. The adsorption properties of naproxen with β-Cyclodextrin bonded silica stationary phase (CDS) were studied for an in-depth understanding of the host–guest interaction. The inclusion process involving naproxen and hosts was investigated by using the PM3 quantum–mechanical semiempirical method. The stabilization energy values obtained from the semiempirical calculation showed the same relation with the formation constant values determined by UV–Vis spectroscopy.  相似文献   

7.
We study by molecular dynamics simulations the hydration of -cyclodextrin. Our simulations show that within these barrel-shaped molecules hydrophobicity dominates, while at the top and bottom sides of the barrel interactions with water are mostly hydrophilic in nature. These results agree with crystallographic data at 120 K and, in particular, with the spontaneous hydration process of a cyclodextrin crystal in wet atmosphere. The predicted structure of the hydration shells is discussed and compared with previous molecular mechanics calculations which report an overall hydrophobic behavior. Moreover, the temperature dependence of the hydration process is discussed.  相似文献   

8.
The dependence of N–H stretching-mode frequencies in representative di- and trialkyl ureas on the conformational state of the ureido group has been studied by ab initio MO calculations using HF/3-21G and HF/6-31G** basis sets. The molecules studied were 1,3-dimethylurea, 1-methyl-3,3-dimethylurea and 1-methyl-3,3-di-iso-propylurea. The principal conclusions from the ab initio results are:
  • 1.the transtrans conformer (N–H bonds trans to the CO bond) has N–H stretching bands with about 20–30 cm−1 higher frequency than the respective ciscis structure, in accord with earlier literature assignments based on experimental data;
  • 2.the N–H stretching frequency interval in tri-substituted ureas is 15–20 cm−1 higher than the N–H band position in the 1,3-disubstituted molecule studied, the effect being determined mostly by the higher N–H stretching force constant;
  • 3.in the absence of the steric hindrance the stable rotameric forms of the ureido grouping are almost planar at HF/3-21G level of calculations, while HF/6-31G** calculations predict a slightly pyramidal structure at the nitrogen atoms in the transtrans conformer;
  • 4.in 1-methyl-3,3-di-iso-propylurea the steric influence of the two bulky iso-propyl groups cause a deviation from planarity of the N–H bond. The non-planar conformation is accompanied by a shift of the N–H stretching mode frequency towards higher values; and
  • 5.the variations of the theoretically estimated N–H stretching-mode frequencies appear to be principally determined by changes in the N–H stretching force constants in the different molecules.
© 1997 Elsevier Science B.V.  相似文献   

9.
For a single, intense 7 μm linearly polarized laser pulse, we found that the branching ratio for the fragmentation of ClCHO+ → Cl + HCO+, H + ClCO+, HCl++CO depended strongly on the orientation of the molecule (J. Phys. Chem. Lett. 2012 , 3 2541). The present study explores the possibility of controlling the branching ratio for fragmentation by using two independent pulses with different frequencies, alignment and delay. Born-Oppenheimer molecular dynamics simulations in the laser field were carried out with the B3LYP/6-311G(d,p) level of theory using combinations of 3.5, 7 and 10.5 μm sine squared pulses with field strengths of 0.03 au (peak intensity of 3.15×1013 W/cm2) and lengths of 560 fs. A 3.5 μm pulse aligned with the C-H bond and a 10.5 μm pulse perpendicular to the C-H bond produced a larger branching ratio for HCl++CO than a comparable single 7 μm pulse. When the 10.5 μm pulse was delayed by one quarter of the pulse envelope, the branching ratio for the high energy product, (HCl++CO 73%) was a factor of three larger than the low energy product (Cl + HCO+, 25%). By contrast, when the 3.5 μm pulse was delayed by one quarter of the pulse envelope, the branching ratio was reversed (HCl++CO 38%; Cl + HCO+, 60%). Continuous wavelet analysis was used to follow the interaction of the laser with the various vibrational modes as a function of time. © 2018 Wiley Periodicals, Inc.  相似文献   

10.
The search for the possible binding site of manzamine A to glycogen synthase kinase 3β(GSK-3β) was performed by molecular docking followed by molecular dynamics simulation and calculations of the Gibbs free energy of inhibitor—kinase binding. The cavity between the glycine-rich loop, the loop C, and the activation loop is the most likely site of interaction.  相似文献   

11.
The reaction mechanism and kinetics for the abstraction of hydrogen and addition of hydroxyl radical (OH) to 2′-deoxycytidine have been studied using density functional theory at MX06-2X/6-311+G(d,p) level in aqueous solution. The optimized geometries, energies, and thermodynamic properties of all stationary points along the hydrogen abstraction reaction and the addition reaction pathways are calculated. The single-point energy calculations of the main pathways at CCSD(T)/6-31+G(d,p)//MX06-2X/6-311+G(d,p) level are performed. The rate constants and the branching ratios of different channels are evaluated using the canonical variational transition (CVT) state theory with small-curvature tunneling (SCT) correction in aqueous solution to simulate the biological system. The branching ratios of hydrogen abstraction from the C1′ site and the C5′ site and OH radical addition to the C5 site and the C6 site are 57.27% and 12.26% and 23.85% and 5.69%, respectively. The overall calculated rate constant is 4.47?×?109 dm3 mol?1 s?1 at 298 K which is in good agreement with experiments. The study could help better understand reactive oxygen species causing DNA oxidative damage.  相似文献   

12.
The effect of intermolecular O-H O hydrogen bonding on the molecular structure of phenol has been studied by SCF ab initio MO calculations at the HF/6-31G * level. The systems investigated are eight phenol-water complexes and the dimer and trimer of phenol. Optimized geometries show that hydrogen bond formation causes a consistent pattern of changes in the structure of the molecule. When phenol acts as a proton donor, the expected increase ofr (O-H) is accompanied by a slight decrease ofr(C-O) and of the internal ring angles at theipso andpara positions, and by an increase ofr(C ipso © ortho ). These changes suggest that the relative contribution of polar canonical forms to the electronic structure of the molecule increases upon hydrogen bond formation, since this enhances the strength of the interaction. The opposite changes occur when phenol acts as a proton acceptor, except forr(O-H), which is the same as in the free molecule. If phenol acts as a proton donorand as a proton acceptor, the two hydrogen bonds become stronger due to a synergic effect. In this case, however, the structural deformation of the molecule is less pronounced than in the previous cases, due to the opposite effect of the two hydrogen bonds. The available experimental evidence on gas-crystal structural differences for phenol is critically reviewed, also in the light of the present results on gas-phase complexes.  相似文献   

13.
The base form of the local anaesthetic kazcaine (BFK, [1-(2-ethoxyethyl)-4-ethynyl-4-benzoyloxypiperidine, C18H23NO3]) and β-cyclodextrin (β-CD) co-crystallized as BFK:β-CD inclusion complex in 1:2 M ratio from a mixture of water and ethanol while the filtered mother liquor yielded crystals of free BFK. X-ray diffraction showed that the crystals of BFK and its inclusion complex with β-CD belong to monoclinic (P21/c) and triclinic (P1) space groups, respectively. The crystals of free BFK are stabilized by pairs of C–H?O, C–H?π and ≡C–H?O type interactions and van der Waals contacts. In the 1:2 BFK:β-CD complex the two β-CD molecules are in hydrogen-bonding contact with their primary hydroxyl groups, the 1-(2-ethoxyethyl)-4-ethynyl-piperidine moiety being located in one and the benzoyloxy group of BFK in the other β-CD. This crystal structure is of the channel-type, the β-CD molecules of the 1:2 BFK:β-CD complex interacting with their secondary hydroxyl groups. The pharmacological activities of the 1:2 BFK/β-CD inclusion complex have been determined in mice, rats, porpoises and rabbits and compare favourably with those of kazcaine, procaine, dicaine, lidocaine and trimecaine. The methods used include terminal (superficial), infiltration, conduction anaesthesia, and acute toxicity.  相似文献   

14.
Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, first principles MD or Car-Parrinello method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics/chemistry (liquid phosphorus). Dynamical, finite temperature, simulations deriving interatomic forces from state-of-the-art density functional calculations represent a substantial advance over both (i) traditional pointwise total energy and electronic band structure calculations and (ii) classical MD simulations with empirical or semi-empirical forces, and have already yielded qualitatively new insights in several fields.  相似文献   

15.
16.
Ab initio study of the adsorption of dimethyl methylphosphonate (DMMP) and trimethyl phosphate (TMP) on three types of models simulating the calcium oxide surface (non-hydroxylated Ca4O4, completely hydroxylated Ca4O4(OH)2H2, and partially hydroxylated Ca4O4(OH)H) was performed. The target molecule and the surface hydroxyl groups were optimized while the CaO fragment was kept frozen. The intermolecular interactions were investigated applying Bader’s Atoms in Molecules theory. The maps of electrostatic potential of the studied adsorption systems were also produced. The interaction energies of studied adsorption systems corrected by the basis set superposition error were obtained. The most energetically favorable adsorption of DMMP and TMP was found at the configuration where the oxygen atoms of the P=O and methoxy groups point toward the Ca cation of the surface. The P atom points toward the O atom of the surface and forms a P–O chemical bond. This configuration was revealed for the non-hydroxylated and partially hydroxylated CaO-DMMP and CaO-TMP systems. The presence and number of surface hydroxyl groups on the CaO models play a key role in the adsorption of the studied compounds. DMMP and TMP were found to be much less stable on the completely hydroxylated CaO surface where they are adsorbed only via weak electrostatic interactions and H-bonding to the surface oxygen atoms and hydroxyl groups. TMP was found to be slightly more stable on this type of surface than DMMP. The difference in stability is even larger if one compares this TMP system with the complex of tabun adsorbed on completely hydroxylated CaO surface model (Michalkova et al. Chem Phys Lett 438:72, 2007).
J. LeszczynskiEmail:
  相似文献   

17.
Qualitative molecular orbital theory is central to our understanding of the bonding and reactivity of molecules and materials across chemistry. Advances in computational technology and methodology, however, have made ab initio or density functional theory calculations a simpler alternative, offering reliable results on increasingly large systems in a reasonable time-scale without the need for concerns about the approximations and parameterization of semi-empirical one-electron based methods. In this perspective, we illustrate how the availability of higher-level computational results can augment, rather than supplant, the insights provided by approaches such as the simple and extended Hückel methods. We begin by describing a way to parameterize Hückel-type Hamiltonians against DFT results for intermetallic systems. The potential for chemical understanding embodied by such orbital-based models is then demonstrated with two schemes of bonding analysis that originated in them (but can be extended to DFT results): the μ(3)-acid/base model and the μ(2)-Hückel chemical pressure analysis, which translate the molecular concepts of acidity and electronic/steric competition, respectively, into the context of intermetallic chemistry.  相似文献   

18.
The infrared spectra of α- and β-d-galactose were recorded, both in the mid-IR range (4000-500 cm−1) and in the far-IR (500-50 cm−1). The Raman spectra were also obtained. These spectra constitute the basis of a crystalline-state force field established for these two molecules through a normal coordinate analysis. A modified Urey—Bradley—Shimanouchi force field was combined with an intermolecular potential energy function which includes van der Waals interactions, electrostatic terms and an explicit hydrogen bond function. The force constants were varied, so as to obtain an agreement between the observed vibrational frequencies and the calculated ones of α-d-galactose. The force field obtained was then applied to α-d-galactose O-d5 and β-d-galactose, in order to test its transferability. The computed potential energy distribution was found to be compatible with previous assignments for d-glucose, particularly for the modes involving C6 and COH groups. For β-d-galactose the same force field was used with changing the force constants due to the C1 and C6 groups.  相似文献   

19.
In the field of enzymatic catalysis, creating activity from a non catalytic scaffold is a daunting task. Introduction of a catalytically active moiety within a protein scaffold offers an attractive means for the creation of artificial metalloenzymes. With this goal in mind, introduction of a biotinylated d6-piano-stool complex within streptavidin (SAV) affords enantioselective artificial transfer-hydrogenases for the reduction of prochiral ketones. Based on an X-ray crystal structure of a highly selective hybrid catalyst, displaying significant disorder around the biotinylated catalyst [η6-(p-cymene)Ru(Biot-p-L)Cl], we report on molecular dynamics simulations to shed light on the protein–cofactor interactions and contacts. The results of these simulations with classical force field indicate that the SAV-biotin and SAV-catalyst complexes are more stable than ligand-free SAV. The point mutations introduced did not affect significantly the overall behavior of SAV and, unexpectedly, the P64G substitution did not provide additional flexibility to the protein scaffold. The metal-cofactor proved to be conformationally flexible, and the S112K or P64G mutants proved to enhance this effect in the most pronounced way. The network of intermolecular hydrogen bonds is efficient at stabilizing the position of biotin, but much less at fixing the conformation of an extended biotinylated ligand. This leads to a relative conformational freedom of the metal-cofactor, and a poorly localized catalytic metal moiety. MD calculations with ab initio potential function suggest that the hydrogen bonds alone are not sufficient factors for full stabilization of the biotin. The hydrophobic biotin-binding pocket (and generally protein scaffold) maintains the hydrogen bonds between biotin and protein.  相似文献   

20.
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