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1.
A theoretical study of the water-assisted alkaline hydrolysis of 2-azetidinone, 3-formylamino-2-azetidinone and 3-formylamino-2-azetidine-1-sulfonate ion is carried out at the B3LYP/6-31+G* level. The effect of bulk solvent is taken into account using the PCM solvation model while specific solvent effects are represented by the inclusion of an ancillary water molecule along the reaction profile. The calculated free energy barriers in solution are in reasonable agreement with experimental values. The observed substituent effects due to the presence of the 3-formylamino and the SO(3) groups attached to the beta-lactam ring are crucial factors determining the hydrolysis of monobactam antibiotics.  相似文献   

2.
何茂霞  冯大诚  王焕杰  蔡政亭 《中国化学》2005,23(10):1319-1326
The aminolysis and the effect of water on the aminolysis processes of n-methyl β-sultam have been studied using density functional theory (DFF) method at the B3LYP/6-31G* level. The stationary structures and energies have been investigated for both reactions to find two different reaction channels. Specific and general solvent effects have been evaluated and the most favored pathway was found. The presence of solvent disfavors the reaction, whereas the participation of water in the aminolysis reaction plays a positive role and reduces the activation energy greatly. All transition states in the assisted aminolysis are 35-70 kJ/mol lower than those for the non-assisted reaction.  相似文献   

3.
Understanding the mechanisms by which beta-lactamases destroy beta-lactam antibiotics is potentially vital in developing effective therapies to overcome bacterial antibiotic resistance. Class A beta-lactamases are the most important and common type of these enzymes. A key process in the reaction mechanism of class A beta-lactamases is the acylation of the active site serine by the antibiotic. We have modeled the complete mechanism of acylation with benzylpenicillin, using a combined quantum mechanical and molecular mechanical (QM/MM) method (B3LYP/6-31G+(d)//AM1-CHARMM22). All active site residues directly involved in the reaction, and the substrate, were treated at the QM level, with reaction energies calculated at the hybrid density functional (B3LYP/6-31+Gd) level. Structures and interactions with the protein were modeled by the AM1-CHARMM22 QM/MM approach. Alternative reaction coordinates and mechanisms have been tested by calculating a number of potential energy surfaces for each step of the acylation mechanism. The results support a mechanism in which Glu166 acts as the general base. Glu166 deprotonates an intervening conserved water molecule, which in turn activates Ser70 for nucleophilic attack on the antibiotic. This formation of the tetrahedral intermediate is calculated to have the highest barrier of the chemical steps in acylation. Subsequently, the acylenzyme is formed with Ser130 as the proton donor to the antibiotic thiazolidine ring, and Lys73 as a proton shuttle residue. The presented mechanism is both structurally and energetically consistent with experimental data. The QM/MM energy barrier (B3LYP/ 6-31G+(d)//AM1-CHARMM22) for the enzymatic reaction of 9 kcal mol(-1) is consistent with the experimental activation energy of about 12 kcal mol(-1). The effects of essential catalytic residues have been investigated by decomposition analysis. The results demonstrate the importance of the "oxyanion hole" in stabilizing the transition state and the tetrahedral intermediate. In addition, Asn132 and a number of charged residues in the active site have been identified as being central to the stabilizing effect of the enzyme. These results will be potentially useful in the development of stable beta-lactam antibiotics and for the design of new inhibitors.  相似文献   

4.
采用密度泛函理论B3LYP/6-311+G(d,p)方法,计算并考察了喹唑啉酮进行结构互变的质子迁移过程的两种可能途径:(a)分子内质子迁移,(b)水助质子迁移.结果表明,途经b所需要的能垒小,氢键在降低反应能垒方面起重要作用.  相似文献   

5.
The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium-bacteriochlorin, magnesium-chlorin, magnesium-porphin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree-Fock/6-31G* ab initio and density functional B3LYP/6-31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c(1), and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self-consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6-31G* or Hartree-Fock/6-31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree-Fock/6-31G* and B3LYP/6-31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin-like molecules.  相似文献   

6.
O~3+NH→HNO+O~2反应机理的量子化学研究   总被引:1,自引:0,他引:1  
李来才  王欣  田安民 《化学学报》2000,58(9):1099-1102
用密度泛函(DFT)的B3LYP方法(6-31++G^*^*)研究了臭氧与NH自由基反应的微观机理,优化得到反应途径上的反应物,过渡态,中间体和产物的构型,通过振动分析对过渡态和中间体进行了确认。对单点用QCISD(T)/6-31++G^*^*方法计算能量,同时进行零点能校正。研究结果表明:NH与O~3反应有两条不同的反应通道,且均表现为亲电反应特征,两条不同的反应均为强放热反应。  相似文献   

7.
用密度泛函理论(DFT)和从头算(ab initio)方法,在B3LYP/6-31G、 B3LYP/6-31G*、 B3LYP/6-311G*和MP2/6-31G*水平上全优化计算了2,3,7,8-四氯苯并二英(2,3,7,8-TCDD)的几何构型、电子结构和振动频率,并用校正后的频率计算了298~1500 K的标准热力学函数,同时用半经验的PM3 SCF-MO进行了同样的计算,计算结果与实验值及文献值较好地吻合.  相似文献   

8.
The changes in the excited state energies of representative cyclic enones (cyclopentenone and cyclohexenone) induced by lithium ion coordination have been examined using ab initio and DFT methods. Quantitative estimates of the vertical triplet state energies were obtained using configuration interaction calculations at the CIS and CIS(D) levels with the 6‐31+G(d) basis. Inclusion of perturbative doubles corrections has a marked effect on the relative energies of the n–π* and π–π* triplet states. At both CI and CIS(D) levels, lithium complexation is predicted to raise the energy of the n–π* triplet state much more than the π–π* triplet. The trends obtained at the CIS(D) level are reproduced using B3LYP/6‐31+G(d) calculations. Adiabatic excitation energies were also computed by carrying out geometry optimization of the triplet states at the B3LYP level. While the separation between the geometry optimized n–π* and π–π* triplet states is very small for the parent enones, the π–π* triplet is clearly favored in the lithium complexes. These results suggest the possibility of reversing the reactive photoexcited state in enones through cation complexation. The conclusions provide a rationale for interesting variations in product distributions observed for enones in cation exchanged zeolites. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1598–1604, 2001  相似文献   

9.
Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.  相似文献   

10.
A theoretical quantum chemical study of the intramolecular hydrogen bonding interactions in 8-mercaptoquinoline has been carried out. Special attention has been paid to the rotation of S-H bond and intramolecular proton-transfer reactions. Therewith, the B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p), MPW1K/6-311++G(d,p), MPW1K/6-31+G(2d,2p), BH&HLYP/6-311++G(d,p), and G96LYP/6-311++G(d,p) methods have been used. By means of the Onsager and PCM reaction field methods, the effects of solvent on hydrogen-bond energies, conformational equilibria, rotational barriers, and tautomerism in aqueous solution have been studied. These simulations were done at the MPW1K/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels. Natural-bond orbital analysis has been performed to study the intramolecular hydrogen bond (IHB) in the gaseous phase and in aqueous medium. The stability of forms under consideration in solution does not coincide with that in the gaseous phase, underlining a great importance of the electrostatic influence of solvent. Double-proton transfer in the prototropic tautomerization of 8-mercaptoquinoline, one water molecule complex in the gaseous phase and in solution, has been systematically studied. The double-proton transfer occurs concertedly and synchronously. The water-assisted tautomerization is kinetically less, but thermodynamically more favorable, compared to that of the single-proton transfer. As in the case with single-proton transfer, for water-assisted reaction, the tautomerization energies and barrier heights decrease with the increase in dielectric constant, which implies faster and more complete tautomerization of 8-mercaptoquinoline in a polar solvent.  相似文献   

11.
Most quantum mechanical studies of triterpene synthesis have been done on small models. We calculated mPW1PW91/6-311+G(2d,p)//B3LYP/6-31G* energies for many C30H51O+ intermediates to establish the first comprehensive energy profiles for the cationic cyclization of oxidosqualene to lanosterol, lupeol, and hopen-3beta-ol. Differences among these 3 profiles were attributed to ring strain, steric effects, and proton affinity. Modest activation energy barriers and the ample exothermicity of most annulations indicated that the cationic intermediates rarely need enzymatic stabilization. The course of reaction is guided by hyperconjugation of the carbocationic 2p orbital with parallel C-C and C-H bonds. Hyperconjugation for cations with a horizontal 2p orbital (in the plane of the ABCD ring system) leads to annulation and ring expansion. If the 2p orbital becomes vertical, hyperconjugation fosters 1,2-methyl and hydride shifts. Transition states leading to rings D and E were bridged cyclopropane/carbonium ions, which allow ring expansion/annulation to bypass formation of undesirable anti-Markovnikov cations. Similar bridged species are also involved in many cation rearrangements. Our calculations revealed systematic errors in DFT cyclization energies. A spectacular example was the B3LYP/6-311+G(2d,p)//B3LYP/6-31G* prediction of endothermicity for the strongly exothermic cyclization of squalene to hopene. DFT cyclization energies for the 6-311+G(2d,p) basis set ranged from reasonable accuracy (mPW1PW91, TPSSh with 25% HF exchange) to underestimation (B3LYP, HCTH, TPSS, O3LYP) or overestimation (MP2, MPW1K, PBE1PBE). Despite minor inaccuracies, B3LYP/6-31G* geometries usually gave credible mPW1PW91 single-point energies. Nevertheless, DFT energies should be used cautiously until broadly reliable methods are established.  相似文献   

12.
The ammonolysis reaction of 3‐(formylamino)‐4‐methyl‐2‐oxoazetidine‐1‐sulfonate is investigated by quantum‐chemical methods (B3LYP/6‐31+G*) as a model system of the aminolysis reaction of monobactam antibiotics involved in the allergic reaction to these drugs. The influence of the N‐sulfonate group on the β‐lactam ring, reaction intermediates, and transition states is characterized in terms of the geometries and relative energies of the corresponding critical structures located on the B3LYP/6‐31+G* potential‐energy surface. It is shown that the N‐sulfonate group, which has only a moderate impact on the structure and charge distribution of the β‐lactam ring, reduces the rate‐determining ΔG barrier by ca. 20 kcal/mol with respect to a purely uncatalyzed ammonolysis of the unsubstituted system, azetidin‐2‐one. This intramolecular catalytic effect occurs through a −NH−SO↔[−N−SO3H] isomerization process, which is involved in the proton relay from the attacking ammonia molecule to the β‐lactam N‐atom. Our theoretical results predict that, in aqueous solution, monobactams will show an intrinsic reactivity against amine nucleophiles more important than that of penicillins.  相似文献   

13.
The proposed polar nucleophilic mechanism of MAO was investigated using quantum chemical calculations employing the semi-empirical PM3 method. In order to mimic the reaction at the enzyme's active site, the reactions between the flavin and the p-substituted benzylamine substrate analogs were modeled. Activation energies and rate constants of all the reactions were calculated and compared with the published experimental data. The results showed that electron-withdrawing groups at the para position of benzylamine increase the reaction rate. A good correlation between the log of the calculated rate constants and the electronic parameter (sigma) of the substituent was obtained. These results agree with the previous kinetic experiments on the effect of p-substituents on the reduction of MAO-A by benzylamine analogs. In addition, the calculated rate constants showed a correlation with the rate of reduction of the flavin in MAO-A. In order to verify the results obtained from the PM3 method single-point B3LYP/6-31G*//PM3 calculations were performed. These results demonstrated a strong reduction in the activation energy for the reaction of benzylamine derivatives having electron-withdrawing substituents, which is in agreement with the PM3 calculations and the previous experimental QSAR study. PM3 and B3LYP/6-31G* energy surfaces were obtained for the overall reaction of benzylamine with flavin. Results suggest that PM3 is a reasonable method for studying this kind of reaction. These theoretical findings support the proposed polar nucleophilic mechanism for MAO-A.  相似文献   

14.
The radical anion of the highly pyramidalized alkene 1,5-dehydroquadricyclane (1) was generated in the gas phase from the Squires reaction of 1,5-bis(trimethylsilyl)quadricyclane with F-/F2. The electron binding energy and proton affinity of 1*- were determined by bracketing experiments to be 0.6 +/- 0.1 eV and 386 +/- 5 kcal/mol, respectively. These values are in good agreement with values predicted by density functional theory (B3LYP/6-31+G*) and ab initio (CASPT2/6-31+G*) calculations. The experimental heat of hydrogenation of 1, obtained from a thermochemical cycle, was found to be 91 +/- 9 kcal/mol. This value of deltaH(H2) leads to values of 67 +/- 9 kcal/mol for the olefin strain energy (OSE) of 1, 172 +/- 9 kcal/mol for its heat of formation, and 23 +/- 9 kcal/mol for its pi bond dissociation enthalpy. Since the retro-Diels-Alder reaction of neutral 1 is computed to be highly exothermic, the finding that 1*- apparently does not undergo a retro-Diels-Alder reaction is of particular interest. The B3LYP/6-31+G* optimized geometry of 1 suggests that the bonding in this alkene is partially delocalized, presumably because the highly pyramidalized double bond in 1 interacts with the distal cyclopropane bonds in a manner that eventually leads to a retro-Diels-Alder reaction. The good agreement of the B3LYP and (2/2)CASPT2 values for the heat of hydrogenation and OSE of 1 with the experimentally derived values provides indirect evidence for the correctness of the B3LYP prediction that the equilibrium geometry of 1 lies part way along the reaction coordinate to the transition structure for the retro-Diels-Alder reaction.  相似文献   

15.
Several economical methods for geometry optimization, that should be applicable to larger molecules, have been evaluated for 19 phosphorus acid derivatives. MP2/cc-pVDZ geometry optimizations are used as reference points and the geometries obtained from the other methods are evaluated with respect to deviations in bond lengths and angles, from the reference geometries. The geometry optimization methods are also compared to the much used B3LYP/6-31G(d) method. Single point energies obtained by subsequent EDF1/6-31+G(d) or B3LYP/6-31+G(d,p) calculations on the respective equilibrium geometries are also reported relative to the energies obtained from the reference geometries. The geometries from HF/MIDI! optimizations were closer to those of the references than the geometries of the HF/3-21G(d), HF/6-31G(d), and B3LYP/MIDI! optimizations. The EDF1/6-31+G(d) or B3LYP/6-31+G(d,p) single point energies obtained from the HF/3-21G(d), HF/6-31G(d), and B3LYP/MIDI! geometries gave a mean absolute deviation (MAD) from that of the reference geometries of 1.4-3.9 kcal mol m 1 . The HF/MIDI! geometries, however, gave EDF1/6-31+G(d) and B3LYP/6-31+G(d,p) energies with a MAD of only about 0.5 and 0.55 kcal mol m 1 respectively from the energies obtained with the reference geometries. Thus, use of HF/MIDI! for geometry optimization of phosphorus acids is a method that gives geometries of near-MP2 quality, resulting in a fair accuracy of energies in subsequent single point calculations, at a much lower computational cost other methods that give similar accuracies.  相似文献   

16.
The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.  相似文献   

17.
A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA(n)NH(2)) were optimized in the representative helical (3(10)-, 4(13)-, and a "hybrid" kappa-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel beta-sheets with type I turns betaalphaalphaepsilon, n = 6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded beta-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with l-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies DeltaE(GT) were obtained as heats of the isodesmic reactions: AcA(n)NHR + AcOMe --> AcA(x)LacA(y)NHR + AcNHMe (R = H, CH(3)). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Deltae in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C=O group, and O...O repulsion. On the basis of several comparisons of Ala --> Lac DeltaE(GT)'s with heats of the NH --> CH(2) substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol(-1), a figure close to the recent experimental DeltaDeltaG(o) value of 2.6 kcal mol(-1) (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am.Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3(10)-helix D(e) = -1.7 kcal mol(-1), alpha-helix D(e) = -3.8 kcal mol(-1), beta-sheet D(e) = -6.1 kcal mol(-1). The premise of experimental evaluations of the backbone-backbone H-bonding that Ala --> Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and phi(i), psi(i) distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 375; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O...HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3(10)-helix to alpha-helix to beta-sheet.  相似文献   

18.
采用密度泛函B3LYP/6-311G**方法,对3-卤(-F、-Cl、-Br)代吡唑几何构型进行了全自由度优化,获得了它们的几何结构和电子结构。计算结果显示,N1-H型的稳定性大于N2-H型。计算并考察了3-卤代吡唑进行结构互变的质子转移过程的四种可能途径:(a)分子内质子转移;(b)水助质子转移;(c)同种二聚体双质子转移;(d)异种二聚体双质子转移。计算结果表明(以3-氟代吡唑为例),途径d所需要的活化能最小(54.89 kJ/mol),而途径a所需要的活化能最大(198.83kJ/mol),途径b和c的活化能居中间分别为(104.05 kJ/mol和69.05 kJ/mol)。研究还表明氢键在降低活化能方面起着重要的作用,卤素(-F、-Cl、-Br)对活化能的影响不大。  相似文献   

19.
The cyclic chloronium or bromonium carboxylate obtained by addition of Cl+ or Br+ to acrylate anion is shown by PCM/B3LYP/6-31+G* calculations to be not an intermediate but a transition structure for interconversion of equivalent halomethyl oxiranones.  相似文献   

20.
In a previous paper (Hermosilla, L.; Calle, P.; Garcia de la Vega, J. M.; Sieiro, C. J. Phys. Chem. A 2005, 109, 1114), an adequate computational protocol for the calculation of isotropic hyperfine coupling constants (hfcc's) was proposed. The main conclusion concerns the reliability of the scheme B3LYP/TZVP//B3LYP/6-31G* in the predictions of hfcc's with low computational cost. In the present study, we gain insight into the behavior of the above functional/basis set scheme on nuclei of the third row, for which few systematic studies have been carried out up to the present date. The systems studied are neutral, cationic, anionic, localized, and conjugated radicals, containing (29)Si, (31)P, and (33)S nuclei. After carrying out a regression analysis, we conclude that density functional theory (DFT) predictions on the hfcc's of the third-row nuclei are reliable for B3LYP/TZVP by using an optimized geometry with B3LYP/6-31G* combination. By comparison with other much more computationally demanding schemes, namely, B3LYP/cc-pVTZ and B3LYP/cc-pVQZ, we conclude that the B3LYP functional in conjunction with the TZVP basis set is the most useful computational protocol for the assignment of experimental hfcc's, not only for nuclei of first and second rows, but also for those of the third row.  相似文献   

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