Conformational calculations on odoriferous molecules of sandalwood,I. The search for the odoriferous principle of sandalwood oil

The conformations of two relatively rigid molecules with sandalwood odor have been investigated by molecular mechanics and the semiempirical method AM1. A comparison between both geometries shows that a common structural element exists in the relative rearrangement of a carbinol function and a quarternary carbon atom. The distance of these two centers as well as the electron density agree well in both structures.

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Rechnungen zur Konformation von Molekülen mit Sandelholzgeruch, 1. Mitt.: Die Suche nach dem Geruchsprinzip des Sandelholzöles

Zusammenfassung Die Konformationen zweier relativ starrer Moleküle mit Sandelholzgeruch wurden mit molekularmechanischer und mit einer semiempirischen Methode (AM1) bestimmt. Ein Vergleich der beiden molekularer Geometrien zeigt ein gemeinsames Strukturelement und zwar die relative Anordnung der Carbinolfunktion zu einem quartären Kohlenstoffatom. Sowohl deren Abstand als auch deren Elektronendichte stimmen in beiden Verbindungen überein.

     

Dynamic NMR study on the trans-fused eight-membered ether ring model representing G ring of brevetoxin A

Conformational analysis of the trans-fused eight-membered ether ring model (2) representing G ring of brevetoxin A (1) was carried out by dynamic NMR study in combination with molecular mechanics calculations.     

Improved 3D-QSAR prediction by multiple-conformational alignment: A case study on PTP1B inhibitors

Three-dimension quantitative structure activity relationship (3D-QSAR) was one of the major statistical techniques to investigate the correlation of biological activity with structural properties of candidate molecules, and the accuracy of statistic greatly depended on molecular alignment methodology. Exhaustive conformational search and successful conformational superposition could extremely improve the predictive accuracy of QSAR modeling. In this work, we proposed a solution to optimize QSAR prediction by multiple-conformational alignment methods, with a set of 40 flexible PTP1B inhibitors as case study. Three different molecular alignment methods were used for the development of 3D-QSAR models listed as following: (1) docking-based alignment (DBA); (2) pharmacophore-based alignment (PBA) and (3) co-crystallized conformer-based alignment (CCBA). Among these three alignments, it was indicated that the CCBA was the best and the fastest strategy in 3D-QSAR development, with the square correlation coefficient (r²) and cross-validated squared correlation coefficient (q²) of comparative molecular field analysis (CoMFA) were 0.992 and 0.694; the r² and q² of comparative molecular similarity indices analysis (CoMSIA) were 0.972 and 0.603, respectively. The alignment methodologies used here not only generated a robust QSAR model with useful molecular field contour maps for designing novel PTP1B inhibitors, but also provided a solution for constructing accurate 3D-QSAR model for various disease targets. Undoubtedly, such attempt in QSAR analysis would greatly help us to understand essential structural features of inhibitors required by its target, and so as to discover more promising chemical derivatives.     

AM1 study of conformations of oxocane and 1,3-dioxocane

Summary AM1 semi-empirical SCF MO calculations are reported for important conformations of oxocane (1) and 1,3-dioxocane (2). The boat-chair conformation of1 (BC-1) is found to be the most stable form, whereas the crown family conformation is calculated to be 3.7 kJ·mol^–1 less stable. The boat-boat form of1 is 15.9 kJ·mol^–1 less stable thanBC-1. The boat-chair conformation of2 (BC-1,3) is calculated to be the most stable form of 1,3-Dioxocane. The crown-family conformation and the boat-boat geometry of this compound are 4.2 and 8.3 kJ mol^–1 less stable thanBC-1,3.

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AM1-Rechnungen zu den Konformationen von Oxocane und 1,3-Dioxocan

Zusammenfassung Die wesentlichen Konformationen von Oxocan (1) und 1,3-Dioxocan (2) wurden mittels semiempirischer AM1-Rechnungen (SCF MO) untersucht. Die Wanne-Sessel-Konformation von1 (BC-1) ist am stabilsten; Konformationen aus der Klasse der Kronen sind um 3.7 kJ·mol^–1 energiereicher. Die Wanne-Wanne-Konformation von1 ist um 15.9 kJ·mol^–1 instabiler alsBC-1. Die Wanne-Sessel-Konformation von2 (BC-1,3) ist das stabilste Konformer von 1,3-Dioxocan. Kronenkonformationen und Wanne-Wanne-Geometrien sind um 4.2 und 8.3 kJ·mol^–1 energiereicher alsBC-1,3.

     

The effect of diphenylamine on the electronic, optical, and charge transport properties of BTD-based derivative: Insights from theory

Theoretical investigations have been performed to explore the variation in electronic,optical,and charge transport properties upon the change of the chemical composition along the backbone in 2,1,3-benzothiadiazole(BTD)-based derivative.Narrow difference between hole and electron transportations with the charge hopping model indicates studied BTD-based derivative can be used as good ambipolar transport material in organic light-emitting diodes.     

Polarographic study on the evolution of the diphenylamine as stabiliser of the solid propellants

Differential pulse polarography (DPP) and square wave voltammetry (SWV) were investigated, in order to know the stability of solid propellants which contain diphenylamine. The simultaneous determination of N-nitrousdiphenylamine (NnDPA), 2-nitrodiphenylamine (2nDPA), 4-nitrodiphenylamine (4nDPA) and 2,4-dinitrodiphenylamine (2,4dnDPA) by DPP and SWV was proposed due to these nitro-derivatives appear during the stabilisation process from degradation of diphenylamine (DPA) used as stabiliser in propellant compositions. The proposed methods were successfully applied to the simple base solid propellant (with nitrocellulose as the only active component), with its stabiliser DPA. In all cases and with both the techniques, detection limits ≤0.01 ppm were obtained.When the usual LC procedure was applied to the real sample, no significant differences were found between the obtained results and those given by the electroanalytical techniques. In addition, the detection limits reached by the electrochemical methods were better than those obtained by LC.Moreover, the proposed procedure can be considered an objective test that would avoid the use of the classic stability tests and would allow one to determine the stability of propellants accurately, faster and cheaper than LC methods.     

Assignment of absolute configuration at phosphorus of P-chiral diastereomers of deoxyribonucleoside methanephosphonamidates by means of NMR spectroscopy

Recently, we have prepared a novel class of DNA analogues containing the [3′-NH-P(CH₃)(O)-O-5′] methanephosphonamidate linkage. Synthesis of such analogues requires preparation of the dinucleoside methanephosphonamidates N×N, where N is a 2′-deoxyribonucleoside moiety and × is the methanephosphonamidate linkage. Dimers T×T and C×T were obtained in a non-stereospecific manner giving rise to a pair of P-chiral diastereomers. Such diastereomers were effectively separated into fast and slow migrating ones by means of chromatographic methods (TLC). As described in our previous work (Nawrot et al. Nucleic Acids Res.1998, 26, 2650), the stereochemistry of the phosphorus chiral center of T×T fast migrating diastereomer is R_P and of T×T slow migrating diastereomer is S_P, as established by means of 2D ROESY experiments. Here we describe assignment of the absolute configuration at the phosphorus center of fast and slow migrating diastereomers of C×T dimer. The 2D ROESY sequence with phosphorus decoupling during acquisition used in these measurements allowed observation of the P-Me group as a singlet instead of a ¹H-³¹P-coupled doublet. The apparent advantage of this approach was a much better signal to noise ratio and improved resolution in the F1 dimension. For the fast migrating C×T diastereomer an R_P and for slow migrating C×T diastereomer an S_P configuration was assigned. Conformational analysis of both pairs of diastereomers T×T and C×T indicates significant differences in sugar ring puckering, which strongly depend on the nature of the nucleobase at the 5′-terminus of the dimer. The ribose rings of the 3′-amino-2′,3′-dideoxycytidine moiety of both diastereomers of C×T adopt predominantly a C3′-endo (North) conformation, while thymine-substituted ribofuranoses originating either from C×T or T×T dimers prefer a C2′-endo (South) conformation.     

SCF-MO study of the polyglycine II structure

Summary In order to get insight into the conditions that make polyglycine (PG)II a stable structure, the conformational features of three model molecules closely related to the PGII conformation were investigated. The model molecules selected were glycine dipeptide (AGN), glycine tripeptide (AGGN), and glycine tetrapeptide (AGGGN). Environmental effects were mimicked by means of formaldehyde molecules. The calculations were carried out at the SCF semiempirical level, using the AM1 method. The calculations show that of the three systems considered, only the AGGGN molecule presents a minimum energy conformation which corresponds to a PGII structure. The environmental conditions in which this conformation is found were also analyzed.     

Development of a conformational search strategy for flexible ligands: A study of the potent μ-selective opioid analgesic fentanyl

Summary An extensive conformational search of the potent opioid analgesic, fentanyl, was performed using the semiempirical quantum mechanical method AM1 and the CHARMm potential energy function. A combination of two procedures was used to search the conformational space for fentanyl, which included nested dihedral scans, geometry optimization and molecular dynamics simulation at different temperatures. In addition, the effect of a continuum solvent environment was taken into account by use of appropriate values for the dielectric constant in the CHARMm computations.The results of the conformational search allowed the determination of the probable conformation of fentanyl in polar and nonpolar solvents and of three candidate conformers for its bioactive form.     

<Emphasis Type="Italic">Ab initio</Emphasis> Study of Structural and Conformational Properties of Five- to Nine-Membered Cyclic 1,2,3-Trienes

Summary.  The structures and relative energies of fundamental conformations of cyclopenta-1,2,3-triene, cyclohexa-1,2,3-triene, cylohepta-1,2,3-triene, cycloocta-1,2,3-triene, and cyclonona-1,2,3-triene were calculated by the HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods. Only a C _2v symmetric planar conformation is available to cyclopenta-1,2,3-triene and cyclohexa-1,2,3-triene. The calculated energy barrier for ring inversion of the C _S symmetric puckerd conformation of cyclohepta-1,2,3-triene via the planar geometry is 62.2 kJ·mol⁻¹. The C ₂ symmetric twist conformation of cycloocta-1,2,3-triene was calculated to be the most stable one. Conformational racemization of the twist form takes place via the C _S symmetric half-chair geometry, which is by 60.8 kJ·mol⁻¹ less stable than the twist conformer. The C _S symmetric chair and unsymmetrical twist-boat conformations of cyclonona-1,2,3-triene were calculated to have similar energies; their interconversion takes place via an unsymmetrical low-energy (18.4 kJ·mol⁻¹) transition state. The twist (C ₂) and boat (C _S) geometries of cyclonona-1,2,3-triene are higher in energy by 13.2 and 33.9 kJ·mol⁻¹, respectively. Ring inversion in chair and twist-boat conformations takes place via a twist form as intermediate and requires 33.6 kJ·mol⁻¹. Corresponding author. E-mail: isayavar@yahoo.com Received March 25, 2002; accepted April 4, 2002     

Spatial structure of β-substituted alkoxyvinyl trifluoromethyl ketones

Spatial structure of six β-substituted enones, with common structure R₁O–CR₂CH–COCF₃, were R₁ = C₂H₅, R₂ = H (ETBO); R₁ = R₂ = CH₃ (TMPO); R₁ = C₂H₅, R₂ = C₆H₅ (ETPO); R₁ = C₂H₅, R₂ = 4- O₂NC₆H₄ (ETNO); R₁ = C₂H₅, R₂ = C(CH₃)₃ (ETDO) were investigated by ¹H and ¹⁹F NMR, infrared spectroscopy and AM1 calculations. NMR spectra revealed that enones (MBO), (ETBO) and (TMPO) are exclusively (3E) isomers, whereas in (ETPO), (ETNO) and especially in (ETDO) the percentage of (3Z) isomers is significant and depends on the nature of solvents. Conformational behaviour of studied enones are determined by the rotation around of CC double bond, C–C and C–O single bonds (correspondingly trifluoroacetyl and alkoxy groups), and (EZZ) conformer being the most stable in all cases. IR spectra revealed that with the exception of (ETDO) (EZZ) conformer is most populated in all cases. Bulky substituents like phenyl or tert-butyl group at β-position of enone result in the equilibrium mainly between (EZZ) and (ZZZ) forms, whereas β-hydrogen and β-methyl substituents determine the equilibrium between (EZZ) and (EEZ) or (EZE) conformers.     

A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

Summary The effect of the substitution in position 1 on the low-energy conformations of the oxytocin/vasopressin 20-membered ring was investigated by means of molecular mechanics. Three representative substitutions were considered: -mercapto-,-dimethyl)propionic acid (Dmp), (-mercapto-,-cyclopentamethylene)propionic acid (Cpp), both forming strong antagonists, and (,-dimethyl--mercapto)propionic acid (-Dmp), forming analogs of strongly reduced biological activity, with the -mercaptopropionic (Mpa) residue taken as reference. Both ECEPP/2 (rigid valence geometry) and AMBER (flexible valence geometry) force fields were employed in the calculations. Three basic types of backbone conformations were taken into account which are distinguished by the type of -turn at residues 3 and 4: 1/III, II, and I/III, all types containing one or two intra-annular hydrogen bonds. The allowed (ring-closed) disulfide-bridge conformations were searched by an algorithm formulated in terms of scanning the disulfide-bridge torsional angle C-S-S-C. The ECEPP/2 and AMBER energies of the obtained conformations were found to be in reasonable agreement. Two of the low-energy conformers of the [Mpa¹]-compound agreed very well with the cyclic part of the two conformers found in the crystal structure of [Mpa¹]-oxytocin. An analysis of the effect of -substitution on relative energies showed that the conformations with the N-C-CH₂-CH₂ (₁) and C-CH₂-CH₂-S (₁) angles of the first residue around (–100°, 60°) and (100°, –60°) are not affected; this in most cases implies a left-handed disulfide bridge. In the case of -substitution the allowed values of ₁ are close to ± 60°. This requirement, being in contradiction to the one concerning -substitution, could explain the very low biological activity of the -substituted analogs. The conformational preferences of substituted compounds can largely be explained by the analysis of local interactions within the first residue. Based on the selection of the conformations which are low in energy for both the reference and -substituted compounds, two distinct types of possible binding conformations were proposed, the first one being similar to the crystal conformer with a left-handed disulfide bridge, the second one having a right-handed bridge, but a geometry different from that of the crystal conformer with the right-handed bridge. The first type of disulfide-bridge arrangement is equally favorable for both I/III and II types of backbone structure, while the second one is allowed only for the II type of backbone. No conformation of the I/III type has a low enough energy to be considered as a possible binding conformation for all of the active compounds studied in this work.     

Conformational flexibility of the 1,4-dihydropyridine ring in calcium channel agonists and antagonists molecules

Conformational flexibility of the 1,4-dihydropyridine ring in 4-aryl derivatives of the 2,6-dimethyl-3,5-dicarbmethoxy-1,4-dihydropyridine has been studied using the MM3 molecular mechanics method. Change of the C=C---C---C= endocyclic torsion angle of dihydrocycle in the range of 35° entails an increase of energy less than 1 kcal mol⁻¹. The energy levels below 99% of the molecular population for each molecule were estimated. The interval of the torsion angle change for these regions is about 60°.     

Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics

A molecular dynamics (MD)-based conformational analysis has been performed on a number of cycloalkanes in order to demonstrate the reliability and generality of MD as a tool for conformational analysis. MD simulations on cyclohexane and a series of methyl-substituted cyclohexanes were performed at temperatures between 400 and 1200 K. Depending on the simulation temperature, different types of interconversions (twist-boat–twist-boat, twist- boat–chair and chair–chair) could be observed, and the MD simulations demonstrated the expected correlation between simulation temperature and ring inversion barriers. A series of methyl-substituted 1,3- dioxanes were investigated at 1000 K, and the number of chair–chair interconversions could be quantitatively correlated to the experimentally determined ring inversion barrier. Similarly, the distribution of sampled minimum-energy conformations correlated with the energy-derived Boltzmann distribution. The macrocyclic ring system cyclododecane was subjected to an MD simulation at 1000 K and 71 different conformations could be sampled. These conformations were compared with the results of previously reported conformational analyses using stochastic search methods, and the MD method provided 19 out of the 20 most stable conformations found in the MM2 force field. Finally, the general performance of the MD method for conformational analysis is discussed.     

苯乙烯基吡嗪类化合物的构象研究

有选择地合成了四种结构不同的苯乙烯吡嗪衍生物，测定了它们在不同极性溶剂中的吸收光谱和荧光光谱，根据其在基态条件下可能的分子构象和所得到得到的光谱数据，进一步对该类分子的最佳发光构象做出较为肯定的结论。     

A comparative effect of ring annelation on cation-benzene and anion-benzene

DFT/B3LYP calculations were carried out on several π-complexes formed by cations and anions with annelated benzene, respectively. The binding energies obtained with standard method were corrected by basis set superposition error (BSSE) and zero-point energy (ZPE) during the geometry optimization for all complexes at the same levels of theory, respectively. Some different aspects of the π–cation have been compared to those of π–anion, involving in binding energy changes in effect of ring annelation, the aromaticity of the ring upon complexation, Mulliken and NBO charge-transfer. The effect of BSSE correction during the optimization is very important in some π–anion complexes whether or not using diffuse functions in basis set, and results with at least one set of diffuse functions 6-31+G(d) basis set is a little better than results obtained by 6-31G(d, p) basis set for some π–anion especially for F⁻ complexes.     

A Monte Carlo pharmacophore generation procedure: Application to the human PAF receptor

Summary A novel pharmacophore definition procedure is described, which uses a Monte Carlo method to superimpose molecules. Pharmacophore space is searched by a technique similar to high temperature annealing. Subsequent refinement of candidate pharmacophores by energy minimization produces low-energy conformations that may be involved in receptor binding. The method has been applied to compounds that bind to the human platelet-activating factor (PAF) receptor. Alternative binding site models for the PAF receptor are presented and discussed.A preliminary account of this work has been published elsewhere [1].     

A comparative study by AM1, PM3 and ab initio HF/3-21G methods on the structure and reactivity of monosubstituted carbanion 1,2,4-triazolium ylides

A full conformational analysis of six 1,2,4-monosubstituted carbanion 1,2,4-triazolium ylides 4 a–f was performed using AM1, PM3 and HF/3-21G methods. The C-type conformers were found as the most stable structures by these different methods. This study also includes a qualitative estimation of the chemical behavior of triazolium ylides 4 a–f as nucleophilic agents on the level of ylide carbon atoms. The ab initio 3-21G method seems to be the most suitable in the characterization of these molecular systems.     

Considerations on the recognition of the D1 receptor by agonists

Summary A model of the mechanism for recognition of the D1 receptor has been developed. Conformational analysis for 10 agonists from diverse chemical families was carried out as a first step toward the characterization of the bioactive form. First, maximum structural overlap of the features common to all ligands allowed a simple identification of the candidate bioactive form for each ligand. At a second level of characterization, steric and electronic properties were computed for all accessible structures to analyze those properties that may modulate receptor recognition.     

On the Ground State Energy Hypersurface of Blepharismins and Oxyblepharismins

Summary.  AM1 calculations on blepharismins and oxyblepharismins, which are related photosensory pigments of certain protists, revealed that the accessory substituents of the natural pigments do not lead to a change of the tautomerism and conformational states of the fundamental systems. The valence tautomerism possible in principle for the blepharismins yielding a cycloheptatriene–norcaradiene system was found to reside completely on the side of the cycloheptatriene. With respect to proton tautomerism, the strong predominance of the meso-type 7,15- and 7,14-dioxo tautomers was established in both series. Whereas the conformation of the fundamental condensed aromatic ring system of the oxyblepharismins remains comparable to that of hypericin, the conformational situation of the blepharismins was found to be unique with the phenyl group in an endo-position and dihedral twisting at the unperturbed bay-site only. Received June 29, 2000. Accepted July 12, 2000