A “quasi‐flexible” automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation

The main purpose of this work is the development and validation of a general scheme based on a systematic and automatic “quasi‐flexible” docking approach for studying stereoselective recognition mechanisms. To achieve our goals we explore the conformational and configurational space for small‐ or medium‐size flexible molecules in a systematic way, seeking a method that is both reasonably accurate and relatively fast from the computational point of view. In particular, we have developed a general computational protocol for the global molecular interaction evaluation (“Glob‐MolInE”) to efficiently explore the orientational and conformational space of flexible selectors and selectands used in modern chiral high‐performance liquid chromatography (HPLC); the enantioselective binding of the selector (S)‐N‐(3,5‐dinitrobenzoyl)‐leucine‐ n‐propylamide (S)‐ 1 towards the selectand N‐(2‐naphthyl)‐alanine methyl ester 2 has been studied; the global minimum obtained for the homochiral associate [S( 1 )/S( 2 )] (Pop. >99%) is very close (RMS≃0.20) to the crystallographically determined structure. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 515–530, 2000     

Structure–property relationship study of the HPLC enantioselective retention of neuroprotective 7‐[(1‐alkylpiperidin‐3‐yl)methoxy]coumarin derivatives on an amylose‐based chiral stationary phase

The enantiomer separation of a number of racemic 7‐[(1‐alkylpiperidin‐3‐yl)methoxy]coumarin derivatives, some of which show outstanding in vitro multitarget neuroprotective activities, was successfully achieved on a polysaccharide‐based chiral stationary phase, bearing amylose tris(3,5‐dimethylphenylcarbamate) as a chiral selector, in normal polar mode (methanol and acetonitrile as the mobile phases). The majority of the screened selectands, especially those bearing 1‐(3‐X‐benzyl)piperidin‐3‐yl moieties, showed baseline enantiomer separations, and compound 8 (X = NO₂) was the best resolved (α = 2.01; R_S = 4.27). Linear free energy relationships, usefully complemented by molecular docking calculations, have the key role in enantioselective retention of aromatic interactions between π‐donor moieties in the chiral selector and π‐acceptor moieties in selectand, strengthened by hydrogen bond interaction between a hydrogen bond donor in the chiral selector and the hydrogen bond acceptor group(s) in the selectand. Statistically, reliable equations highlighted the importance of the substituent's size and substitution pattern (meta better than para) to affect the enantiorecognition of the title compounds. The chromatographic data support the scalability of the optimized experimental conditions for preparative purposes.     

Two new ceramides from the stems of Piper betle L.

<正>Two new ceramides,(2S,3S,4R)-2-N-[(2'R)-2'-hydroxypentacosanoylamino]-nonacosane-1,3,4-triol(1) and(2S,3S,4R,8E)-2- N-[(2'R)-2'-hydroxytetracosanoylamino]-8-eicosylene-1,3,4-triol(2) have been isolated from the stems of Piper betle L.collected from Baoshan city of Yunnan Province in China.Their structures were determined by spectroscopic and chemical methods.     

手性双季铵盐诱导下的硝基甲烷与查尔酮的Michael反应

双季铵盐相转移催化剂具有用量少、催化活性高的特点,比单官能团相转移催化剂的催化性能更为显著。手性季铵盐是进行不对称     

Synthesis and heteronuclear inclusion properties of a novel thiacalix[4]arene-based hard-soft receptor with 1,3-alternate conformation

A novel thiacalix[4]arene ditopic receptor with 1,3-alternate conformation and possessing two complexation sites for hard and soft cations, 5,11,17,23-tetra-tert-butyl-25,27-bis[(N,N-diethylaminocarbonyl)methoxy]-26,28-bis[(pyridylmethyl)oxy]-2,8,14,20-tetrathiacalix[4]arene is prepared. Regioselective synthesis of distal-bis[(N,N-diethylaminocarbonyl)methoxy]thiacalix[4]arene is accomplished by a protection-deprotection method using benzyl groups as a protecting group. The deprotection of benzyl group was succeeded in the presence of solid superacid (Nafion-H) under refluxing benzene. Its complexation behavior is examined by ¹H-NMR titration experiments. The formation of 1:2 homo- and heteronuclear complexes demonstrates that the preorganization, subtle conformational changes and affinity have a pronounced effect on the complexation of the receptor.     

手性双季铵盐诱导下的硝基甲烷与查而酮的Michael反应

为了探讨手性含1,3-亚乙氧基链双季铵盐在立体选择性反应中的不对称诱导效果,研究了硝基甲烷与查而酮的Michael加成反应。     

Bischler-Napieralski Reaction of 2-(3,4-Dimethoxy-2-nitrophenyl)-N-[2-(3,4-dimethoxyphenyl)ethyl]-N-[(S)-1-phenylethyl] acetamide Accompanied by Elimination of Chiral Auxiliary

Chiral 1-benzyltetrahydroisoquinoline alkaloids can be asymmetrically synthesized via Bischler-Napieralski (B-N) cyclization followed by stereoselective NaBH4 reduction (Polniaszek抯 method) of the N- (2-phenylethyl)-2-phenylacetamides bearing chiral auxiliary such as (S)-1-phenylethyl group on the nitrogen atom1-4. Recently Y. Ohishi and co-workers found an unusual B-N reaction on the carbon at 2-position of the A ring, which bears a bromine atom5, 6. They indicated that the steric ef…     

Darstellung und NMR-spektroskopische Charakterisierung von konfigurationsstabilen Diorganozinn(IV)-Komplexen RPhSnL mit Zinn als chiralem Zentrum

Synthesis and Characterization of Configurationally Stable Diorganotin(IV) Complexes with Tin as a Chiral Centre Contrary to the high optical stability of tetraorganotin compounds most heteroleptic organic tin compounds are configurationally instable. We report the synthesis and the characterization of some new enantiomeric and diastereomeric diorganotin(IV) complexes of stable configuration with tin as a chiral centre. The stabilization of the chiral tin atom was realized by complexation with tridentate diacidic esterhydrazone ligands H₂L, which prevent an interconversion at the stereogenic centre. Multinuclear NMR-studies in solution demonstrate, that the configuration of the chiral tin center is configurationally stable up to 160°C. The molecular structure of the complexes Neophyl-phenyl-tin-2[(2-methyl-mercaptothiocarbonyl)-hydrazono]propionate II b and (2-Methyl-butyl-1-yl)-phenyl-tin-[S-methyl-β-N-(2-salicylmethylidene)thiocarbazat] III g have been determined by single crystal X-ray diffraction analysis.     

Chiral recognition of peptide enantiomers by cinchona alkaloid derived chiral selectors: mechanistic investigations by liquid chromatography, NMR spectroscopy, and molecular modeling

The chiral recognition mechanism of a cinchona alkaloid based chiral selector for N-protected peptide enantiomers was investigated. A chiral stationary phase derived from this selector was employed for liquid chromatographic enantiomer separations. It showed exceptionally high enantiomer discrimination for the (all-R)- and (all-S)-enantiomers of dialanine (alpha = 20), while a pronounced loss of chiral recognition occurred upon the insertion of an additional alanine residue into the peptide backbone. This reduction of enantioselectivity was investigated in great detail by NMR spectroscopy of complexes of the chiral selector and the analyte enantiomers accompanied by molecular modeling studies. Investigation of intramolecular NOEs provided the conformational states of the free and complexed forms of the selector. The analysis of complexation-induced shifts yielded information on intermolecular interactions and allowed us to propose binding models, which were further supported by the observation of intermolecular NOEs, indicating the relative arrangements of selector and analytes. Stochastic molecular dynamics simulations were able to reproduce the chromatographic retention orders and energy differences, as well as the intermolecular NOEs. The computational data were used to evaluate the intermolecular forces responsible for analyte binding. In addition, the relative contributions of the fragments of the chiral selector to the enantioselective binding event were assessed. A spatial arrangement of the chiral selector and the analyte allowing the primary ionic interaction as well as hydrogen bonding and pi-pi-stacking to take place simultaneously was found to be essential to obtain very high enantioselectivities.     

A cryosolution infrared and ab initio study of the van der Waals complexes of cyclopentene with hydrogen chloride and boron trifluoride

The formation of weak molecular complexes of cyclopentene with HCl and BF3, dissolved in liquid argon is investigated using infrared spectroscopy. Evidence is found for the formation of 1:1 complexes in which the Lewis acid under study binds to the CC double bond. At higher concentrations of HCl, weak absorption bands due to 1:2 species are also observed. From spectra recorded at different temperatures between 92 and 127 K, the complexation enthalpies for CP.HCl and CP.BF3 are determined to be -9.5(3) and -16.1(9) kJ mol-1, while for CP.(HCl)2 a value of -17.0(6) kJ mol-1 is obtained. For the 1:1 and 1:2 complexes, structural and spectral information is obtained from ab initio calculations at the MP2/6-31+G(d) level. Using free energy perturbation Monte Carlo simulations to calculate the solvation enthalpies and statistical thermodynamics to account for zero-point vibrational and thermal contributions, the complexation energies for CP.HCl and CP.(HCl)2 are estimated from the experimental complexation enthalpies to be -17.4(14) and -34.0(20) kJ mol-1, while the value for CP.BF3 was derived to be -23.4(22) kJ mol-1. The experimental complexation energies are compared with the theoretical values derived from the MP2/6-31+G(d) potential energy surfaces and with single point energies calculated at the MP2/6-311++G(3df,2pd) level.     

Electronic effects of (N2S2)M(NO) complexes (M = Fe, Co) as metallodithiolate ligands

Heterobimetallic complexes comprised of W(CO)4 adducts of (N2S2)M(NO) have been isolated and characterized by nu(CO) and nu(NO)IR spectroscopies and X-ray diffraction. The molecular structures of (N2S2)M(NO) compounds (bme-dach)Co(NO), [(bme-dach)Co(NO)]W(CO)4, and [(bme-dach)Fe(NO)]W(CO)4 [bme-dach = N, N'-bis(2-mercaptoethyl)-1,4-diazacycloheptane)] find the square-pyramidal (bme-dach)M(NO) unit to serve as a bidentate ligand via the cis-dithiolato sulfurs, with a hinge angle of the butterfly bimetallic structures of ca. 130 degrees . The W(CO)4 moiety is used as a probe of the electron-donor ability of the nitrosyl complexes through CO stretching frequencies that display a minor increase as compared to analogous [(N2S2)Ni]W(CO)4 complexes. These findings are consistent with the electron-withdrawing influence of the {Co(NO)}(8) and {Fe(NO)}(7) units on the bridging thiolate sulfurs relative to Ni(2+). Also sensitive to derivatization by W(CO)4 is the NO stretch, which blue shifts by ca. 30 and 50 cm(-1) for the Co and Fe complexes, respectively. Cyclic voltammetry studies find similar reduction potentials (-1.08 V vs NHE in N, N-dimethylformamide solvent) of the (bme-dach)Co(NO) and (bme-dach)Fe(NO) free metalloligands, which are positively shifted by ca. 0.61 and 0.48 V, respectively, upon complexation to W(CO)4.     

Penning ionization of N2O molecules by He*(2(3,1)S) and Ne*(3P2,0) metastable atoms: theoretical considerations about the intermolecular interactions

A theoretical investigation of the intermolecular interaction, operative in collision complexes of He*(2 3S1), He*(2 1S0), and Ne*(3P2,0) with N2O, is carried out to explain the main results of the experimental study reported in the preceding paper. The analysis is carried out by means of a semiempirical method based on the identification, modeling, and combination of the leading interaction components, including the effect of the selective polarization of the more external electronic cloud of the metastable atom in the intermolecular electric field. These and other crucial aspects of our approach have been quantitatively verified by ab initio calculations. The proposed method permits to evaluate the interaction at any configuration of the complexes and provides a useful and inexpensive representation of the intermolecular potential energy for dynamics studies. The main experimental findings can be rationalized taking into account the critical balancing between molecular orientation effects in the intermolecular interaction field and the ionization probability. These orientation effects tend to become less pronounced with increasing collision energy.     

(CH3)2S与HOCl分子间的卤键和氢键相互作用

在DFT-B3LYP/6-311++G**水平上分别求得(CH3)2S…ClOH卤键复合物和(CH3)2S…HOCl氢键复合物势能面上的稳定构型. 频率分析表明, 与单体HOCl相比, 在两种复合物中, 10Cl—11O和12H—11O键伸缩振动频率发生显著的红移. 经MP2/6-311++G**水平计算的含基组重叠误差(BSSE)校正的气相中相互作用能分别为-11.69和-24.16 kJ·mol-1. 自然键轨道理论(NBO)分析表明, 在(CH3)2S…ClOH卤键复合物中, 引起10Cl—11O键变长的因素包括两种电荷转移: (i) 孤对电子LP(1S)1→σ*(10Cl—11O); (ii) 孤对电子LP(1S)2→σ*(10Cl—11O), 其中孤对电子LP(1S)2→σ*(10Cl—11O)转移占主要作用, 总的结果是使σ*(10Cl—11O)的自然布居数增加0.14035e, 同时11O原子的再杂化使其与10Cl成键时s成分增加, 即具有与电荷转移作用同样的“拉长效应”; 在(CH3)2S…HOCl氢键复合物中也存在类似的电荷转移, 但是11O原子的再杂化不同于前者. 自然键共振理论(NRT)进行键序分析表明, 在卤键复合物和氢键复合物中, 10Cl—11O和12H—11O键的键序都减小. 通过分子中原子理论(AIM)分析了复合物中卤键和氢键的电子密度拓扑性质.     

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

BEDAM calculations are described to predict the free energies of binding of a series of anaesthetic drugs to a recently characterized acyclic cucurbituril host. The modeling predictions, conducted as part of the SAMPL3 host-guest affinity blind challenge, are generally in good quantitative agreement with the experimental measurements. The correlation coefficient between computed and measured binding free energies is 70% with high statistical significance. Multiple conformational stereoisomers and protonation states of the guests have been considered. Better agreement is obtained with high statistical confidence under acidic modeling conditions. It is shown that this level of quantitative agreement could have not been reached without taking into account reorganization energy and configurational entropy effects. Extensive conformational variability of the host, the guests and their complexes is observed in the simulations, affecting binding free energy estimates and structural predictions. A conformational reservoir technique is introduced as part of the parallel Hamiltonian replica exchange molecular dynamics BEDAM protocol to fully capture conformational variability. It is shown that these advanced computational strategies lead to converged free energy estimates for these systems, offering the prospect of utilizing host-guest binding free energy data for force field validation and development.     

Free energy perturbation (FEP) simulation on the transition states of cocaine hydrolysis catalyzed by human butyrylcholinesterase and its mutants

A novel computational protocol based on free energy perturbation (FEP) simulations on both the free enzyme and transition state structures has been developed and tested to predict the mutation-caused shift of the free energy change from the free enzyme to the rate-determining transition state for human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The calculated shift, denoted by DeltaDeltaG(1 --> 2), of such kind of free energy change determines the catalytic efficiency (kcat/KM) change caused by the simulated mutation transforming enzyme 1 to enzyme 2. By using the FEP-based computational protocol, the DeltaDeltaG(1 --> 2) values for the mutations A328W/Y332A --> A328W/Y332G and A328W/Y332G --> A328W/Y332G/A199S were calculated to be -0.22 and -1.94 kcal/mol, respectively. The calculated DeltaDeltaG(1 --> 2) values predict that the change from the A328W/Y332A mutant to the A328W/Y332G mutant should slightly improve the catalytic efficiency and that the change from the A328W/Y332G mutant to the A328W/Y332G/A199S mutant should significantly improve the catalytic efficiency of the enzyme for the (-)-cocaine hydrolysis. The predicted catalytic efficiency increases are supported by the experimental data showing that kcat/KM = 8.5 x 10(6), 1.4 x 10(7), and 7.2 x 10(7) min(-1) M(-1) for the A328W/Y332A, A328W/Y332G, and A328W/Y332G/A199S mutants, respectively. The qualitative agreement between the computational and experimental data suggests that the FEP simulations may provide a promising protocol for rational design of high-activity mutants of an enzyme. The general computational strategy of the FEP simulation on a transition state can be used to study the effects of a mutation on the activation free energy for any enzymatic reaction.     

Influence of the chelate ligand structure on the amide methanolysis reactivity of mononuclear zinc complexes

Zinc complexes of three new amide-appended ligands have been prepared and isolated. These complexes, [(dpppa)Zn](ClO4)2 (4(ClO4)2; dpppa = N-((N,N-diethylamino)ethyl)-N-((6-pivaloylamido-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine), [(bdppa)Zn](ClO4)2 (6(ClO4)2; bdppa = N,N-bis((N,N-diethylamino)ethyl)-N-((6-pivaloylamido-2-pyridyl)methyl)amine), and [(epppa)Zn](ClO4)2 (8(ClO4)2; epppa = N-((2-ethylthio)ethyl)-N-((6-pivaloylamido-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine), have been characterized by X-ray crystallography (4(ClO4)2 and 8(ClO4)2), 1H and 13C NMR, IR, and elemental analysis. Treatment of 4(ClO4)2 or 8(ClO4)2 with 1 equiv of Me4NOH.5H2O in methanol-acetonitrile (5:3) results in amide methanolysis, as determined by the recovery of primary amine-appended forms of the chelate ligand following removal of the zinc ion. These reactions proceed via the initial formation of a deprotonated amide intermediate ([(dpppa-)Zn]ClO4 (5) and [(epppa-)Zn]ClO4 (9)) which in each case has been isolated and characterized (1H and 13C NMR, IR, elemental analysis). Treatment of 6(ClO4)2 with Me4NOH.5H2O in methanol-acetonitrile results in the formation of a deprotonated amide complex, [(bdppa-)Zn]ClO4 (7), which was isolated and characterized. This complex does not undergo amide methanolysis after prolonged heating in a methanol-acetonitrile mixture. Kinetic studies and construction of Eyring plots for the amide methanolysis reactions of 4(ClO4)2 and 8(ClO4)2 yielded thermodynamic parameters that provide a rationale for the relative rates of the amide methanolysis reactions. Overall, we propose that the mechanistic pathway for these amide methanolysis reactions involves reaction of the deprotonated amide complex with methanol to produce a zinc methoxide species, the reactivity of which depends, at least in part, on the steric hindrance imparted by the supporting chelate ligand. Amide methanolysis involving a zinc complex supported by a N2S2 donor chelate ligand (3(ClO4)2) is more complicated, as in addition to the formation of a deprotonated amide intermediate free chelate ligand is present in the reaction mixture.     

Recognition by a new chiral dimethyl-substituted phenanthrolino-18-crown-6 diester ligand of the enantiomers of various organic ammonium perchlorates

Two new chiral dimethyl-substituted phenanthrolino-18-crown-6 diester ligands [(S,S)- 3 ] and [(S,S)- 4 ] (see Figure 1) were prepared through the reactions of 1, 10-phenanthroline-2,9-dicarboxylyl dichloride with (S,S)-dimethyl-substituted tricthylene glycol and (S,S)-dimethyl-substituted benzotricthylene glycol, respectively. The complexation of (S,S)- 3 with the enantiomers of various organic ammonium perchlorates in various solvent systems was studied by ¹H nmr spectral techniques and molecular mechanics. The degree of enantiomeric recognition was determined by the difference in the free energy of activation values (ΔΔG^?_C) and the difference in log K values for these interactions. The extensive π system in the ligand plays an important role for the strong interaction and recognition. The ¹H nmr NOESY spectra and molecular mechanics calculations for the interactions of the new ligand with the organic ammonium salts further proved the existence of a π-π interaction.     

Impact of Stable Protein-protein Interaction on Protein Conformational Space

Backbone dihedral angle based clustering approach was applied to investigate the effect of protein complexation on backbone conformational space and the effect on protein dynamics. Three representative enzyme-inhibitor complexes and their comprised proteins were used as models for small-and moderate-sized globular proteins to compare available backbone conformational space before and after complexation. Microsecond time scale molecular dynamic simulations were generated to ensure sufficient statistics. The result suggests that stable protein-protein interactions lead to redistribution of protein backbone mobility and restriction of the protein backbone conformational space, especially for short time scale motions. Surprisingly, these effects are found to be uncorrelated with protein-protein interaction surface. Consistent with many experimental and computational observations, our results indicate that both induced-fit and conformational selection models play roles in stable protein complexation process, with the dominant role being different for different protein complexes.     

Calculation of the crystal-melt interfacial free energy of succinonitrile from molecular simulation

The crystal-metal interfacial free energy for a six-site model of succinonitrile [N triple bond C-(CH(2))(2)-C triple bond N] has been calculated using molecular-dynamics simulation from the power spectrum of capillary fluctuations in interface position. The orientationally averaged magnitude of the interfacial free energy is determined to be (7.0+/-0.4)x10(-3) J m(-2). This value is in agreement (within the error bars) with the experimental value [(7.9+/-0.8)x10(-3) J m(-2)] of Marasli et al. [J. Cryst. Growth 247, 613 (2003)], but is about 20% lower than the earlier experimental value [(8.9+/-0.5)x10(-3) J m(-2)] obtained by Schaefer et al. [Philos. Mag. 32, 725 (1975)]. In agreement with the experiment, the calculated anisotropy of the interfacial free energy of this body-centered-cubic material is small. In addition, the Turnbull coefficient from our simulation is also in agreement with the experiment. This work demonstrates that the capillary fluctuation method of Hoyt et al. [Phys. Rev. Lett. 86, 5530 (2001)] can be successfully applied to determine the crystal-melt interfacial free energy of molecular materials.