首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 15 毫秒
1.
Computation of accurate intramolecular hydrogen-bonding energies for peptides is of great importance in understanding the conformational stabilities of peptides and developing a more accurate force field for proteins. We have proposed a method to determine the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies in glycine and alanine peptides. In this article, the method is further applied to evaluate the intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies in peptides. The optimal structures of the intramolecular 10-membered ring N-H...O=C hydrogen bonds in glycine and alanine tripetide molecules are obtained at the MP2 level with 6-31G(d), 6-31G(d,p), and 6-31+G(d,p) basis sets. The intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies are then evaluated based on our method at the MP2/6-311++G(3df,2p) level with basis set superposition error correction. The intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies are calculated to be in the range of -6.84 to -7.66, -4.44 to -4.98, and -6.95 to -7.88 kcal/mol. The method is also applied to estimate the individual intermolecular hydrogen-bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, formamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen-bonding energies in the four dimers are calculated to be -1.77, -1.67, -6.35, and -4.82 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -6.23, and -4.93 kcal/mol predicted by the supermolecular method.  相似文献   

2.
A manganese(Ⅱ) complex (tataH)2[Mn(pydc)2]·4H2O (C20H28MBN14O12, Mr = 711.50, tata = 2,4,6-triamino-1,3,5-triazine, pydcH2 = pyridine-2,6-dicarboxylic acid) has been synthesized and its crystal structure was determined by single-crystal X-ray diffraction. The crystal belongs to the triclinic system, space group P1^-, with a = 9.9847(3), b = 10.9813(3), c = 15.2616(5)A, a = 101.5310(10), β = 90.2610(10), γ = 116.4600( 10)% V = 1459.44(8)A^3, Z = 2, Dc = 1.619 g/cm^3,μ = 0.539 mm^-1, F(000) = 734, the final R = 0.0292 and wR = 0.0745. In the crystal the Mnn atom is six-coordinated by four carbonyl oxygen atoms and two pyridine nitrogen atoms from two tridentate pydc ligands to furnish a distorted octahedral geometry. The complex shows the A…D…D'…A' H-bonded tetramer. The molecules are packed in a three-dimensional framework structure by the combination of O-H…O, N-H…O and N-H…N hydrogen bonds between (tataH)^+, [Mn(pydc)2]^2- and crystal water.  相似文献   

3.
The hydrogen-bonding ability of five-membered heteroaromatic molecules containing one chalcogen and two heteroatoms with nitrogen in addition to chalcogen, respectively, have been analyzed using density functional and molecular orbital methods through adduct formation with water. The stabilization energies for all the adducts are established at B3LYP/6-31+G* and MP2/6-31+G* levels after correcting for the basis set superposition error by using the counterpoise method and also corrected for zero-point vibrational energies. A natural bond orbital analysis at B3LYP/6-31+G* level and natural energy decomposition analysis at HF/6-31+G* using MP2/6-31+G* geometries have been carried out to understand the nature of hydrogen-bonding interaction in monohydrated heterocyclic adducts. Nucleus-independent chemical shift have been evaluated to understand the correlation between hydrogen bond formation and aromaticity.  相似文献   

4.
The reactions of Co(C1O4)2·6H2O and Co(NO3)2.6H2O with the di-Schiff base ligand N,N'-bis-(1-benzimidazo-2-yl-ethylidene)-ethane-1,2-diamine (LA) in ethanol have been investigated. The reactions of LA with excess amount of cobalt salts yield the six-coordinate complexes [CoL2](ClO4)E·H2O 1 and [CoL2](NO3)E·H2O 2 as isolatable products (L= N-(1- benzimidazo-2-yl-ethylidene)-ethane-1,2-diamine), where L is a tri-dentate mono-Schiff base ligand, resulting from the hydrolysis of the precursor di-Schiff base LA. Both complexes were characterized by X-ray crystallography. Crystal data for complex 1: monoclinic, space group P21/c, a = 11.9214(10), b = 23.5828(17), c = 14.0387(12)A, β = 135.219(4)°, C22H30Cl2CoN8O9, Mr = 680.37, V = 2780.1(4) A^3 ,Z = 4, Dc = 1.625 g/cm^3,μ(MoKa) = 0.876 mm^-1, F(000) = 1404, the final R = 0.0725 and wR = 0.1530 for 5726 observed reflections (I 〉 2σ(I)). Crystal data for complex 2: monoclinic, space group P21/c, a = 18.2162(16), b = 10.0610(6), c = 18.593(2)A, β = 130.099(3)°, C22H30CoN10O7, Mr = 605.49, V = 2606.5(4) A3 Z = 4, Dc = 1.543 g/cm^3,μ(MoKa) = 0.722 mm^-1, F(000) = 1260, the final R = 0.0619 and wR = 0.1429 for 5194 observed reflections (I 〉 2σ(I)). X-ray diffraction analysis reveals that each cobalt atom in the two complexes is chelated by six nitrogen atoms from two tridentate iigands L, exhibiting a slightly distorted octahedral coordination sphere. In both complexes, the strong hydrogen-bonding interactions between the lattice waters and N-H groups of the ligands result in 1D chains which are further connected by ClO4^- (or NO3^-) groups to form a 3D framework. In complex 2, the strong π-π interactions increase the stability of the structure.  相似文献   

5.
In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.  相似文献   

6.
The structures of the complexes formed between N-methylol ethanone(model molecule of ceramide) and azacyclopentane-2-one(the model molecule of azone) have been fully optimized at the B3LYP/6-311++G** level.The intermolecular hydrogen bonding interaction energies have been calculated by using the B3LYP/6-311++G**,B3LYP/6-311++G(2df,2p),MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p) methods,respectively.The results show that strong O–H···O=C,N–H···O=C and C–H···O=C hydrogen bonds could exist between azacyclopentane-2-one and N-methylol ethanone.The formation of the complexes might change the conformation of ceramide molecule and thus cause better percutaneous permeation for the drugs.This is perhaps the origin of the permeation enhances the activity of azone for medicament,as is in accordance with the experimental results.The hydrogen-bonding interactions follow the order of(a) (c) (b) (d) (g) ≈(e) ≈(i) (h) (f).The analyses of frequency,NBO,AIM and electron density shift are used to further reveal the nature of the complex formation.In the range of 263.0~328.0 K,the complex is formed via an exothermic reaction,and the solvent with lower temperature and dielectric constant is favorable to this process.  相似文献   

7.
Hydrogen bonding was studied in 24 pairs of isopropyl alcohol and phenol as one partner, and water and amino-acid mimics (methanol, acetamide, neutral and protonated imidazole, protonated methylalamine, methyl-guanidium cation, and acetate anion) as the other partner. MP2/6-31+G* and MP2/aug-cc-pvtz calculations were conducted in the gas phase and in a model continuum dielectric environment with dielectric constant of 15.0. Structures were optimized in the gas phase with both basis sets, and zero-point energies were calculated at the MP2/6-31+G* level. At the MP2/aug-cc-pvtz level, the BSSE values from the Boys-Bernardi counterpoise calculations amount to 10-20 and 5-10% of the uncorrected binding energies of the neutral and ionic complexes, respectively. The geometry distortion energy upon hydrogen-bond formation is up to 2 kcal/mol, with the exception of the most strongly bound complexes. The BSSE-corrected MP2/aug-cc-pvtz binding energy of -27.56 kcal/mol for the gas-phase acetate...phenol system has been classified as a short and strong hydrogen bond (SSHB). The CH3NH3+...isopropyl alcohol complex with binding energy of -22.54 kcal/mol approaches this classification. The complete basis set limit (CBS) for the binding energy was calculated for twelve and six complexes on the basis of standard and counterpoise-corrected geometry optimizations, respectively. The X...Y distances of the X-H...Y bridges differ by up to 0.03 A as calculated by the two methods, whereas the corresponding CBS energy values differ by up to 0.03 kcal/mol. Uncorrected MP2/aug-cc-pvtz hydrogen-bonding energies are more negative by up to 0.35 kcal/mol than the MP2/CBS values, and overestimate the CCSD(T)/CBS binding energies generally by up to 5% for the eight studied complexes in the gas phase. The uncorrected MP2/aug-cc-pvtz binding energies decreased (in absolute value) by 11-18 kcal/mol for the ionic species and by up to 5 kcal/mol for the neutral complexes when the electrostatic effect of a polarizable model environment was considered. The DeltaECCSD(T) - DeltaEMP2 corrections still remained close to their gas-phase values for four complexes with 0, +/-1 net charges. Good correlations (R2 = 0.918-0.958) for the in-environment MP2/aug-cc-pvtz and MP2/6-31+G* hydrogen-bonding energies facilitate the high-level prediction of these energies on the basis of relatively simple MP2/6-31+G* calculations.  相似文献   

8.
Binding energies for hydrogen-bonded complexes of six cyclic ethers with five hydrogen-bond donor molecules that mimic selected amino acid side chains have been calculated at the MP2/6-31G*, MP2/6-31+G*, MP2/6-311++G**(single point), and MP2/aug-cc-pvtz levels, using geometries obtained with or without counterpoise corrections throughout the geometry optimization. The calculated basis set superposition error (BSSE) amounts to 10-20% and 5-10% of the uncorrected binding energies for the neutral and ionic species, respectively, at the MP2/aug-cc-pvtz level. The authors conclude that the O...H distances in the hydrogen bonds and binding energies for the studied systems may be determined with uncertainties of up to 0.08 A and 1-2 kcal/mol, respectively, in comparison with the MP2/aug-cc-pvtz values at a reasonable computational cost by performing standard geometry optimization at the MP2/6-31+G* level. Hydrogen-bond formation energies are more negative for cyclic ethers compared to their counterparts with a C=C double bond in the ring next to the oxygen atom. The less negative hydrogen-bonding energy and the increased O...H separation have been attributed to the reduced basicity of the ether oxygen when the lone pairs can enter conjugation with the pi-electrons of the Calpha=Cbeta double bond. The present study is the first step toward the development of an affordable computational level for estimating the binding energies of natural product, fused ring ether systems to the human estrogen receptor.  相似文献   

9.
A new method is proposed to quick predict the strength of intermolecular hydrogen bonds. The method is employed to produce the hydrogen-bonding potential energy curves of twenty-nine hydrogen-bonded dimers. The calculation results show that the hydrogen-bonding potential energy curves obtained from this method are in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction, which demonstrate that the method proposed in this work can be used to calculate the hydrogen-bonding interactions in peptides. Supported by the National Natural Science Foundation of China (Grants Nos. 20573049 and 20633050) and the research fund of the Educational Department of Liaoning Province (2004C019, 20060469)  相似文献   

10.
A conformational search was performed for the 12-crown-4 (12c4)-alkali metal cation complexes using two different methods, one of them is the CONFLEX method, whereby eight conformations were predicted. Computations were performed for the eight predicted conformations at the HF/6-31+G*, MP2/6-31+G*//HF/6-31+G*, B3LYP/6-31+G*, MP2/6-31+G*//B3LYP/6-31+G*, and MP2/6-31+G* levels. The calculated energies predict a C4 conformation for the 12c4-Na+, -K+, -Rb+, and -Cs+ complexes and a C(s) conformation for the 12c4-Li+ complex to be the lowest energy conformations. For most of the conformations considered, the relative energies, with respect to the C4 conformation, at the MP2/6-31+G*//B3LYP/6-31+G* are overestimated, compared to those at the MP2/6-31+G* level, the highest level of theory considerd in this report, by 0.2 kcal/mol. Larger relative energy differences are attributed to larger differences between the B3LYP and MP2 optimized geomtries. Binding enthalpies (BEs) were calculated at the above-mentioned levels for the eight conformations. The agreement between the calculated and experimental BEs is discussed.  相似文献   

11.
Ab initio (MP2/6-311+G and MP4(SDTQ)/6-311+G//MP2/6-311+G) and density functional (B3LYP/6-311+G) calculations on the ring closure reactions of conjugated nitrile ylides 1a-e, 3, and 6 to the corresponding oxazoles 2a, 5, 7, and 8; thiazoles 2b and 4; imidazole 2c; and pyrroles 2d and 2e, respectively, are reported. Vinyl nitrile ylides 1d and 1e cyclize with a substantially higher barrier than nitrile ylides containing a heteroatom. Geometric features as well as electronic structures as obtained by NBO analysis are indicative of a pericyclic, monorotatory 1, 5-electrocyclization of 1d and 1e. For nitrile ylides where X = heteroatom, a pseudopericyclic heteroelectrocyclization pathway, characterized by in-plane attack of the heteroatom's lone pair at the nitrile ylide group, is found. For 3 and 6, where two different cyclization products are possible, the calculated barriers and reaction energies are in line with the experimentally observed direction of reaction. Vinyl nitrile ylides 1d and 1e are characterized by an allene, acyl substituted derivatives 1a, 1b, 3, and 6 by a propargyl type structure. The nitrogen derivative 1c represents an intermediate case.  相似文献   

12.
Structure, stability, and hydrogen-bonding interaction in phenol, water, and phenol-water clusters have been investigated using ab initio and density functional theoretical (DFT) methods and using various topological features of electron density. Calculated interaction energies at MP2/6-31G level for clusters with similar hydrogen-bonding pattern reveal that intermolecular interaction in phenol clusters is slightly stronger than in water clusters. However, fusion of phenol and water clusters leads to stability that is akin to that of H(2)O clusters. The presence of hydrogen bond critical points (HBCP) and the values of rho(r(c)) and nabla(2)rho(r(c)) at the HBCPs provide an insight into the nature of closed shell interaction in hydrogen-bonded clusters. It is shown that the calculated values of total rho(r(c)) and nabla(2)rho(r(c)) of all the clusters vary linearly with the interaction energy.  相似文献   

13.
The complexes formed by calcium ion and 12 common amino acids were investigated systematically in the gas phase at the level of MP2/6-311++G(d,p)//MP2/6-3 1G(d,p).The results show that the salt-bridge structure is the most preferred motif for Ca2+ binding aliphatic amino acids without heteroatom in the side chain,while charge-solvated(CS) structure is the most preferred motif for Ca2+ binding other amino acids except for glutamine and lysine.IR spectra of Gln-Ca2+ and Asn-Ca2+ complexes were calculated and compared well with the available experiments.From the study in aqueous solution,the bidentate salt-bridge structure was determined to be the most favorable for all the twenty kinds of amino acids to chelate Ca2+ to both the oxygen atoms of the negatively carboxylate group in the backbone.  相似文献   

14.
1-Methylpiperazine was employed to crystallize with 2,4-dihydroxybenzoic acid and 1,8-naphthalene acid, affording two multi-component hydrogen-bonding salts [(C5H14N2)2+·(C7H5O4)2-·H2O](1) and [(C5H14N2)2+(C12H6O4)2ˉ·2H2O](2). These two forms of salts are both monoclinic systems with space group P21/c(14). The lattice parameters of salts 1 and 2 are a=1.32666(10) nm, b=0.90527(7) nm, c=1.67107(13) nm, β=103.125(1)° and a=1.4950(2) nm, b=0.75242(15) nm, c=1.6563(3) nm, β=92.834(2)°, respectively. Expected classical hydrogen bonds N―H…O and O―H…O appear in the chargetransfer salts, and asymmetric units of these two forms both contain water molecules which play a significant role in building novel supramolecular architectures. Robust hydrogen-bond interactions between 1-methylpiperazine and aromatic acid provide sufficient driving force to direct the two crystals to three-dimensional structures. Weak interactions C―H…O emerging in salts 1 and 2 further enhance their crystal structures. As a consequence, hydrogen-bonding interactions in these compounds afford diverse 3D net supramolecular architectures. Thermal stability of these compounds was investigated by thermogravimetric analysis(TGA).  相似文献   

15.
Pharmacokinetic (PK) evaluation of polyphenolic metabolites over 24 h was conducted in human subjects (n = 13, BMI = 22.7 ± 0.4 kg/m2) after acute mango pulp (MP), vitamin C (VC) or MP + VC test beverage intake and after 14 days of MP beverage intake. Plasma and urine samples were collected at different time intervals and analyzed using targeted and non-targeted mass spectrometry. The maximum concentrations (Cmax) of gallotannin metabolites were significantly increased (p < 0.05) after acute MP beverage intake compared to VC beverage alone. MP + VC beverage non-significantly enhanced the Cmax of gallic acid metabolites compared to MP beverage alone. Pyrogallol (microbial-derived metabolite) derivatives increased (3.6%) after the 14 days of MP beverage intake compared to 24 h acute MP beverage intake (p < 0.05). These results indicate extensive absorption and breakdown of gallotannins to galloyl and other (poly)phenolic metabolites after MP consumption, suggesting modulation and/or acclimation of gut microbiota to daily MP intake.  相似文献   

16.
The reaction of N(4S)+CH3X(X=Cl、Br) was studied by the ab initio method. The geometries of the reactants, transition states and products were optimized at the MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single-point calculations for all the stationary points were carried out at the MP2/6-311++G(3df,2p) and the QCISD(T)/6-311+G(d,p) levels using the MP2/6-311+G(d,p) optimized geometries. The energies of all the stationary points were calculated by the G2MP2 method. The results of this theoretical study indicate that the reaction has three reaction channels: H abstraction reaction channel a, Cl or Br abstraction reaction channel b and substitution reaction channel c. For the N(4S)+CH3Cl reaction, reaction channel a is the main reaction channel. Reaction channels b and c may have a slight contribution in the reaction. For the N(4S)+CH3Br reaction, reaction channel a is the main reaction channel. Reaction channels b and c may have some contribution in the reaction.  相似文献   

17.
分别在MP2/3-21G**、CCSD(T)/3-21G**//MP2/3-21G**和B3LYP/3-21G**3种水平上, 计算研究了气相反应Cl2+2HI=2HCl+I2的机理, 求得一系列四中心和三中心的过渡态. 通过比较六种反应通道的活化能大小, 得到了相同的结论:双分子基元反应Cl2+HIHCl+ICl和ICl+HII2+HCl的最小活化能小于Cl2、HI和ICl的解离能, 从理论上证明了反应Cl2+2HI=2HCl+I2将优先以分子与分子作用形式分两步完成. 用内禀反应坐标(IRC)验证了MP2/3-21G**方法计算得到的过渡态.  相似文献   

18.
A conformational search was performed for 18-crown-6 using the CONLEX method at the MM3 level. To have a more accurate energy order of the predicted conformations, the predicted conformations were geometry optimized at the HF/STO-3G level and the 198 lowest energy conformations, according to the HF/STO-3G energy order, were geometry optimized at the HF/6-31+G level. In addition, the 47 nonredundant lowest energy conformations, according to the MP2/6-31+G energy order at the HF/6-31+G optimized geometry, hereafter the MP2/6-31+G//HF/6-31+G energy order, were geometry optimized at the B3LYP/6-31+G level. According to the MP2/6-31+G//B3LYP/6-31+G energy order, three conformations had energies lower than the experimentally known Ci conformation of 18c6. At the MP2/6-31+G//B3LYP/6-31+G level, the S6 lowest energy conformation is more stable by 1.96 kcal/mol than this Ci conformation. This was confirmed by results at the MP2/6-31+G level with an energy difference of 1.84 kcal/mol. Comparison between the structure of the S6 conformation of 18c6 and the S4 lowest energy conformation of 12-crown-4, as well as other important conformations of both molecules, is made. It is concluded that the correlation energy is necessary to have an accurate energy order of the predicted conformations. A rationalization of the conformational energy order in terms of the hydrogen bonding and conformational dihedral angles is given. It is also suggested that to have a better energy order of the predicted conformations at the MM3 level, better empirical force fields corresponding to the hydrogen bond interactions are needed.  相似文献   

19.
在RHF/6-31G(d)水平下,对C5H10NH(NH3)n(n=1~3)氢键团簇的平衡构型进行了从头算研究,优化得到各种可能的平衡构型.C5H10NH(NH3)为线型氢键结构,而C5H10NH(NH3)2为三元环结构,C5H10NH(NH3)3为四元环结构.在MP2/6-31G(d)//B3LYP/6-31G(d)水平下,对最稳定构型C5H10NH(NH3)n(Ⅰ)(n=1~3)的分子轨道进行布居分析,并且对相应的占据轨道进行指认.C5H10NH(NH3)n(Ⅰ)(n=1~3)垂直电离势的计算结果表明,形成氢键团簇后,分子的垂直电离势降低.  相似文献   

20.
A series of substituted 2-nitrosiminobenzothiazolines (2) were synthesized by the nitrosation of the corresponding 2-iminobenzothiazolines (6). Thermal decomposition of 2a--f and of the seleno analogue 7 in methanol and of 3-methyl-2-nitrosobenzothiazoline (2a) in acetonitrile, 1,4-dioxane, and cyclohexane followed first-order kinetics. The activation parameters for thermal deazetization of 2a were measured in cyclohexane (Delta H(++) = 25.3 +/- 0.5 kcal/mol, Delta S(++) = 1.3 +/- 1.5 eu) and in methanol (Delta H(++) = 22.5 +/- 0.7 kcal/mol, Delta S(++) = -12.9 +/- 2.1 eu). These results indicate a unimolecular decomposition and are consistent with a proposed stepwise mechanism involving cyclization of the nitrosimine followed by loss of N(2). The ground-state conformations of the parent nitrosiminothiazoline (9a) and transition states for rotation around the exocyclic C==N bond, electrocyclic ring closure, and loss of N(2) were calculated using ab initio molecular orbital theory at the MP2/6-31G* level. The calculated gas-phase barrier height for the loss of N(2) from 9a (25.2 kcal/mol, MP4(SDQ, FC)/6-31G*//MP2/6-31G* + ZPE) compares favorably with the experimental barrier for 2a of 25.3 kcal/mol in cyclohexane. The potential energy surface is unusual; the rotational transition state 9a-rot-ts connects directly to the orthogonal transition state for ring-closure 9aTS. The decoupling of rotational and pseudopericyclic bond-forming transition states is contrasted with the single pericyclic transition state (15TS) for the electrocyclic ring-opening of oxetene (15) to acrolein (16). For comparison, the calculated homolytic strength of the N--NO bond is 40.0 kcal/mol (MP4(SDQ, FC)/6-31G*//MP2/6-31G* + ZPE).  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号