Theoretical investigations are carried out on reaction mechanism of the reactions of CF3CH2NH2 (TFEA) with the OH radical by means of ab initio and DFT methods. The electronic structure information on the potential energy surface for each reaction is obtained at MPWB1K/6-31+G(d,p) level and energetic information is further refined by calculating the energy of the species with a Gaussian-2 method, G2(MP2). The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation. Our calculation indicates that the H abstraction from –NH2 group is the dominant reaction channel because of lower energy barrier. The rate constants of the reaction calculated using canonical transition state theory (CTST) utilizing the ab initio data. The agreement between the theoretical and experimental rate constants is good at the measured temperature. From the comparison with CH3CH2NH2, it is shown that the fluorine substution decreases the reactivity of the C-H bond. 相似文献
The intermolecular potential energy surface (IPS) in the mixtures of CH4–Kr gases from ab initio calculations has been explored. The ab initio calculation was performed at the second-order Møller–Plesset perturbation theory (MP2), with the 6-311+G(2df,2pd) basis set, for three relative orientations of two CH4–Kr molecules as a function of CH4–Kr separation distance. In this work, the IPS, U(r), of the CH4–Kr complex has been investigated, where the vertex (V), edge (E) and face (F) of CH4 approaches to Kr have been considered. Then, adjustable parameters of the Lennard-Jones and Buckingham potential energy function are fitted to the ab initio MP2/6-311+G(2df,2pd) interaction energies for three different orientations. Assuming a given set of parameters, we theoretically obtained second virial coefficients for the CH4–Kr system, and compared with the experimental data at different temperatures. Trivial differences can be observed between the experimental and computational results. 相似文献
Adenovirus virus-associated RNA (VAI) provides protection against the host antiviral response in part by inhibiting the interferon-induced double stranded RNA-activated protein kinase (PKR). VAI consists of three base-paired regions; the apical stem responsible for the interaction with double-stranded RNA binding motifs (dsRBMs) of PKR, the central stem required for inhibition, and the terminal stem. The solution conformation of VAI and VAI lacking the terminal stem were determined using SAXS that suggested extended conformations that are in agreement with their secondary structures. Solution conformations of VAI lacking the terminal stem in complex with the dsRBMs of PKR indicated that the apical stem interacts with both dsRNA-binding motifs whereas the central stem does not. Hydrodynamic properties calculated from ab initio models were compared to experimentally determined parameters for model validation. Furthermore, SAXS envelopes were used as a constraint for the in silico modeling of tertiary structure for RNA and RNA–protein complex. Finally, full-length PKR was also studied, but concentration-dependent changes in hydrodynamic parameters prevented ab initio shape determination. Taken together, results provide an improved structural framework that further our understanding of the role VAI plays in evading host innate immune responses. 相似文献
Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (Pced) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of Pced using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of Pced. Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (Pcore), that is surrounded by flexible regions with α-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales Pced structures suggests that Pced evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes. 相似文献
All the equilibrium conformations of 34 analogues of acetylcholine (ACh) with the general formula R-C(O)O-Alk-N+(CH3)3 are calculated by the method of molecular mechanics. In the series R-C(O)O-(CH2)2-N+(CH3)3, a reliable correlation is found between the molecular volume of the substrate and the rate of its hydrolysis by acetylcholinesterase (AChE); the absence of such a correlation is demonstrated for butyryl-cholinesterase (BChE). Theoretical conformational analysis confirms that the completely extended tt conformation of ACh is productive for the hydrolysis by AChE, which agrees with the results of X-ray analysis of AChE. AChE is shown to hydrolyze only those substrates that form equilibrium conformers compatible in the mutual arrangement of trimethylammonium group, carbonyl carbon, and carbonyl oxygen with the tt conformation of ACh; in this case, the rate of substrate hydrolysis depends on the total population of these conformers. A reliable correlation was found between the population of the semifolded (tg?) conformation of the choline moiety of substrate molecules and rate of their BChE hydrolysis. In a series of CH3-C(O)O-Alk-N+(CH3)3, the rate of BChE hydrolysis is demonstrated to depend on the total population of conformations compatible in the mutual arrangement of functionally important atoms with the tg? conformation of ACh. The tg? conformation of ACh is concluded to be productive for BChE hydrolysis. Similar orientations of the substrate molecules relative to the catalytic triads of both AChE and BChE are proven to coincide upon the substrate productive sorption in their active sites. It is hypothesized that the sorption stage is rate-limiting in cholinesterase hydrolysis and the enzyme hydrolyzes the ACh molecule in its energetically favorable conformation. 相似文献
An improved synthesis of VO(CysOCH3)2, (CysOCH3 the anion of cysteine methyl ester), is reported, as is an analogous preparation of VO(CysOCH2CH3)2, (CysOCH2CH3 the anion of cysteine ethyl ester). These are the first two examples of isolated vanadium-cysteine compounds. The oxidation of VO(CysOCH3)2 in DMSO is a reversible one electron change at 0.24 V versus SCE followed by a rapid chemical reaction which produces a stable vanadium(V) species. This species is reduced back to the vanadium(IV) complex at −1.30 V. The electrochemistry of VO(Cys-OCH2CH3)2 is nearly identical to that of the methyl ester compound. 相似文献
Abstract Conformational flexibility of the methyl methoxymethyl phosphonate anion (CH3-O-PO2- CH2-O-CH3)?, a nuclease resistant alternative to the phosphodiester linkage in DNA, have been investigated by ab initio quantum mechanical calculations. The potential of backbone torsional degrees of freedom of methyl methoxymethyl phosphonate anion (MMP) was determined at the Hartree-Fock (HF) 3–21G* level using the adiabatic mapping technique. Energies, geometries, and effective atomic charges of different conformers were calculated at HF/6–31G* and MP2/6–31G* levels of theory. These were compared to the results obtained for dimethyl phosphate calculated at the same level. The impact on DNA structure from inserting a methylene group between phosphorus and oxygen of the nucleoside sugar moiety was examined via distance- and angle-constrained geometry optimizations. Due to its high flexibility, MMP has been shown to be compatible with both A and B forms of DNA. 相似文献
The synthesis of tetrapeptide-based β-turn mimetics containing spirocyclic glucose-templated 3-hydroxyproline hybrids Glc3′(S)-5′(R)(CH2OH)HypH and Glc3′(S)-5′(S)(CH2OH)HypH as proline mimetics is presented. NMR-based conformational analysis of Ac-Leu-d-Phe-[Glc3′(S)-5′(R)(CH2OH)HypH]-Val-NMe2 and Ac-Leu-d-Phe-[Glc3′(S)-5′(S)(CH2OH)HypH]-Val-NMe2 demonstrates the presence of β-turn conformations. Different turn structures were observed by changing the stereochemistry at 5′-position of Glc3′(S)-5′(R)(CH2OH)HypH. The major prolyl amide cis isomer of glucose-protected tetrapeptide Ac-Leu-d-Phe-[Glc(MOM)43′(S)-5′(R)(CH2OMOM)HypH]-Val-NMe211 and glucose unprotected Ac-Leu-d-Phe-[Glc3′(S)-5′(R)(CH2OH)HypH]-Val-NMe213 forms a type VI β-turn conformation. In contrast, the major prolyl amide trans rotamer of tetrapeptide Ac-Leu-d-Phe-[Glc(MOM)43′(S)-5′(S)(CH2OMOM)HypH]-Val-NMe212 conserves a similar β-turn conformation as the Gramicidin S-based peptide fragment Ac-Leu-d-Phe-Pro-Val-NMe216. 相似文献
Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. 相似文献
To assign the observed vibrationsl modes in the resonance Raman spectrum of the retinylidene chromophore of rhodopsin, we have studied chemically modified retinals. The series of analogs investigated are the n-butyl retinals substituted at C9 and C13. The results obtained for the 11-cis isomer have clearly assigned the CCH3 vibrational frequencies observed in the spectrum of the retinylidene chromophore. The data show that the C(9)CH3 stretching vibration can be assigned to the vibrational mode observed in the 1017 cm?1 region, and the vibration detected at 997 cm?1 can be assigned to the C(13CH3 vibration. The C(5)CH3 stretching mode does not contribute to the vibrations observed in this region. The splitting in the C(n)CH3 (n = 9, 13) vibration is characteristic of the 11-cis conformation. The results on the modified retinals do not support the hypothesis that the splitting arises from equilibrium mixtures of 11-cis, 12-s-cis and 11-cis, 12-s-trans in solution. Thus, this splitting cannot be used to determine whether the chromophore in rhodopsin is in a 12-s-cis or 12-s-trans conformation. However, our results demonstrate that there are other vibrational modes in the spectra which are sensitive to this conformational equilibrium and we use the presence of a strong ~ 1271 cm?1 mode in bovine and squid rhodopsin spectra as an indication that the chromophore in these pigments is 11-cis, 12-s-trans. 相似文献
The conformational energy surfaces of analogues of the dipeptide unit of polypeptides and proteins are calculated by ab initio methods using extended basis sets.The calculations are not particularly sensitive to the choice of (extended) basis set.The calculations are shown to support a particular empirical method parameterized with respect to crystal data. Non-hydrogen bonded conformations agree to within 3 kcal mol?1, even for conformations in which quite considerable degrees of atomic overlap occur.Hydrogen bonded conformations, are, however, in less satisfactory agreement and it is the ab initio calculations which appear to be at fault.A simple correction is applied to the ab initio energy for hydrogen bonded conformations, and with the use of the empirical energy surface a full quantum mechanical conformational energy map is interpolated for the alanyl dipeptide.The effect of flexibility in the peptide backbone is taken into account, and supports recent empirical findings that distortions in valence angles must be considered in calculations of the conformational behaviour of peptides. 相似文献
CH3Hg(II)OH forms complexes at pH 8 with tyrosine and with tyrosine ethyl ester (TEE) that are detected by ultraviolet difference absorption spectra. With Kf defined by CH3HgOH + HB CH3HgB + H2O, we find log Kf = 3.61 (tyrosine) and 3.36 (TEE). A heavy-atom effect is observed in frozen glasses of the complexes; this indicates a close interaction between Hg and the chromophore. No UV difference spectrum or heavy-atom effect is observed with N-acetyl tyrosine ethyl ester, indicating that complexing at the phenol O does not occur, and suggesting that binding occurs at the amine N. Zero field optically detected magnetic resonance (ODMR) measurements of the CH3Hg(II)-tyrosine triplet state give (D, E) = (0.129, 0.047) or (0.134, 0.041) cm?1 depending upon assignment of transitions. D of tyrosine is relatively unaffected, but E is reduced by CH3Hg(II) complexing. Low-temperature kinetic measurements show that the shortest lived sublevel of the complex is Tz, where z lies along the phenol long axis in tyrosine. A dominant 11.6-msec component in the 77 K decay of the phosphorescence is consistent with the individual sublevel lifetimes obtained by ODMR. 相似文献
The incorporation of Me14COONa into aloesaponol I, laccaic acid D methyl ester and aloesaponarin I was demonstrated. The biosynthetic relation between aloesaponol I and aloesaponarin I was established, but incorporation of aloesaponol I into laccaic acid D methyl ester, or vice versa was not demonstrated and this result was confirmed by an investigation using labelled laccaic acid D methyl (14CH3) ester. It was possible to show that aloesaponol I and laccaic acid D methyl ester were biosynthesized in parallel in Aloe saponaria. 相似文献
We present a systematic investigation of the nature and strength of the hydrogen bonding in HX···HX and CH3X…HX (X = Br, Cl and F) dimers using ab initio MP2/aug-cc-pVTZ calculations in the framework of the quantum theory of atoms in molecules (QTAIM) and electron localisation functions (ELFs) methods. The electron density of the complexes has been characterised, and the hydrogen bonding energy, as well as the QTAIM and ELF parameters, is consistent, providing deep insight into the origin of the hydrogen bonding in these complexes. It was found that in both linear and angular HX…HX and CH3X…HX dimers, F atoms form stronger HB than Br and Cl, but they need short (~2 Å) X…HX contacts. 相似文献
Conformation in aqueous solution at pH 6.95 of tripeptides having cyclic dipeptide backbones, cyclo[l-Glu(l-Leu-OBzl)-l-His] and cyclo[l-Glu(l-Leu-OH)-l-His], was investigated by u.v., c.d. and n.m.r. spectroscopy and by the lanthanide probe method. In the major conformation of cyclo[l-Glu(l-Leu-OBzl)-l-His], the cyclic dipeptide backbone takes a flagpole-boat conformation in which the sidechain of the l-His residue is nearly parallel with the backbone plane and the sidechain of the l-Glu residue protrudes outside the backbone plane. In the major conformation of cyclo[l-Glu(l-Leu-OH)-l-His], the cyclic dipeptide backbone takes a flagpole-boat conformation in which the sidechains of the l-His and l-Glu residues are accommodated in the same side of the backbone plane so that the imidazolyl sidechain of l-His residue is twisted slightly. Tripeptides were not found to change the conformation when metal salts or ammonium salts such as Cl?H3N?(CH2)11 COOEt, Gly-OEt-HCl, dl-Val-OEt-HCl and l-Leu-OEt-HCl were added, but a significant conformation change occurred upon adding d-Leu-OEt·HCl. If the same situation holds with the addition of α-amino acid p-nitrophenyl ester hydrochlorides, the previously reported enantiomer-selective catalysis by the tripeptides which hydrolysed d-Leu-OPh(NO2·HCl faster than l-Leu-OPh(NO2)·HCl can be explained; that is, the tripeptides change the conformation only when d-Leu-OPh(NO2)·HCl is bound and consequently the intramolecular reaction is facilitated. This phenomenon may be compared with that of ‘induced fit’ in enzyme catalysis. 相似文献