Energetic analyses of chair and boat conformations of maleimide substituted cyclohexane derivatives

An analysis of the conformational preferences of two maleimide substituted cyclohexane derivatives proposed as scaffolds for HIV-1 fusion inhibitors is presented. Hybrid Low Mode-Monte Carlo (1:1) conformational searches using seven different force fields were performed in combination with the GBSA(water) solvent model. Low energy structures identified in this way were subjected to geometry optimization on the B3LYP/6-31G** surface. Solvent effects were included in the quantum calculation using the self-consistent reaction field model for water. Quantum results indicate that the 1,3,5-maleimide functionalized 1,3,5-methyl cyclohexane is more stable in the boat conformation, whereas 1,3,5-maleimide functionalized cyclohexane adopts the expected chair conformation with equatorial arms. None of the force fields studied was able to predict the unexpected preference for the boat conformation of 1,3,5-maleimide functionalized 1,3,5-methyl cyclohexane. Comparison of low energy and experimental structures was also performed.     

The NMR spectra and conformations of cyclic compounds–III: The conformations of some pinane derivatives

The 220 MHz ¹H spectra of isoverbanone, nopinone and verbanone are reported. The spectra of the first two are completely assigned but that of verbanone only partially. The coupling constants obtained provide information about the conformation of these molecules. The isoverbanone molecule is almost Y shaped, but that of nopinone is between a Y shape and a half-chair conformation with the six membered ring bent away form the gem dimethyl groups. These conformations are consistent with the known steric interactions in these molecules.     

用于环己烷氧化混合产物的分析方法

针对环己烷空气液相氧化混合产物的不同特性，采用了不同的测定方法：环己基过氧化氢采用间接碘量法定量；酸和酯采用酸碱滴定法定量；环己醇和环己酮等有机物采用气相色谱法，但进样前先加入三苯基膦以避免环己基过氧化氢的干扰。该方法回收率为96．62％～101．69％，相对标准偏差为1．12％～5．09％。     

Performance of efficient minimization algorithms as applied to models of peptides and proteins

We test the efficiency of three minimization algorithms as applied to models of peptides and proteins. These include: the limited memory quasi-Newton (L-BFGS) of Liu and Nocedal; the truncated Newton (TN) with automatic preconditioner of Nash; and the nonlinear conjugate gradients (CG) of Shanno and Phua. The molecules are modeled by two energy functions, one is the Gromos 87 united atoms force field (defining the energy E_GRO), which takes into account the intramolecular interactions only; the second is defined by the energy E_tot=E_GRO+E_solv, where E_solv is an implicit solvation free every term based on the solvent-accessible surface area of the atoms. The molecules studied are cyclo-(d -Pro¹–Ala²–Ala³–Ala⁴–Ala⁵) (31 atoms), axinastatin 2 [cyclo-(Asn¹–Pro²–Phe³–Val⁴–Leu⁵–Pro⁶–Val⁷), 62 atoms], and the protein bovine pancreatic trypsin inhibitor (58 residues, 568 atoms). With E_GRO, the performance of TN with respect to the CPU time is found to be ∼1.2 to 2 times better than that of both L-BFGS and CG, whereas, with E_tot, L-BFGS outperforms TN by a factor of 1.5 to 2.5, and CG by a larger factor. Still, the quality of the solution in terms of the value of the minimized energy and the gradient norm, obtained with TN, is always equivalent to, or better than, those obtained with L-BFGS and CG. The performance is analyzed in terms of criteria outlined by Nash and Nocedal. We find the distribution of the Hessian eigenvalues to be a reliable predictor of efficiency. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 354–364, 1999     

High pressure phase studies of some liquid crystalline cyclohexane derivatives by differential thermal analysis

T(p) phase diagrams for the mesomorphic compounds trans-4-n-butylcyclohexane-1-carboxylic acid 4-cyanophenyl ester (D4N), trans4-n-pentylcyclohexane-1-carboxylic acid 4-n-pentylphenyl ester (D55), trans-4,4'-di-n-propyl-1,1-bicyclohexyl-cis-4-carbonitrile (33CCN), trans-4-methoxy-4'-propyl-1,1'-bicyclohexane (3O1CCH) and trans-4-methoxy-4'-n-butyl-1,1'-bicyclohexane (4O1CCH) are presented. The experiments were performed using high pressure microcomputer-assisted differential thermal analysis equipment in the temperature range 300 to 500 K up to a maximum pressure of 8 kbar. Some special high pressure effects for liquid crystals, such as pressure-induced or pressure-limited phases and changes from monotropic to enantiotropic polymorphism were observed. For the correlation of the experimental results, an extension of the Simon equation was used; one of the regression parameters of the clearing curve equation was found to be correlated with the molecular structure of the liquid crystal substances under test.     

Applications of some bounds to density functionals for atoms

In this article, some applications of lower bounds to density-dependent functionals in terms of radial expectation values are performed. These diverse applications include accurate upper bounds to the exact kinetic energy and to conjecture a wide set of relationships among radial and momentum expectation values. Some open questions for the improvement of these results are remarked upon. © 1995 John Wiley & Sons, Inc.     

The stereochemistry of the SRN1 reaction in some cyclohexane derivatives

The substitution reactions of nitrocyclohexanes 8, 9, 12 and 23 with various nucleophiles were studied and were found to proceed by the electron-transfer initiated S_RN1 mechanism. Epimeric products were formed and the proportion of epimers under both thermodynamic and kinetic control normally reflected the bulk of the incoming nucleophile relative to the substituent which was present at the reaction site. In the reaction of 23 with relatively high concentrations of PhS^? in HMPA the reaction proceeded with high stereoretention. The results of these reactions are discussed in terms of the stability of radical configuration and the rate and mode of radical anion dissociations and associations.     

Preparation and some properties of maleimido acids and maleoyl derivatives of peptides.

N-Alkoxycarbonylmaleimides 3 have been prepared and used to convert amino acids to maleimido acids (6–8) in aqueous solution. The carboxyl group of maleimido acids can be activated for amide or peptide synthesis (e.g., in the N-succinimidyl esters 10); t-butyl-based protecting groups can be cleaved without damage to the maleimide moiety. Peptides carrying maleimide groups are accessible either from the maleimido acids (e.g., 11b, 15) or by direct maleoylation (e.g., 16b). The maleoyl group can be cleaved off by successive mild alkaline and acid hydrolysis or by hydrazinolysis. The reactivity of maleimides toward thiol groups suggests the use of maleimido acids and maleoylpeptides for preparing a wide range of conjugates of biochemical interest.     

Sequence and structural duality: designing peptides to adopt two stable conformations

To improve our understanding of conformational transitions in proteins, we are attempting the de novo design of peptides that switch structural state. Here, we describe coiled-coil peptides with sequence and structural duality; that is, features compatible with two different coiled-coil motifs superimposed within the same sequence. Specifically, we promoted a parallel leucine-zipper dimer under reducing conditions, and a monomeric helical hairpin in an intramolecularly disulfide bridged state. Using an iterative process, we engineered peptides that formed stable structures consistent with both targets under the different conditions. Finally, for one of the designs, we demonstrated a one-way switch from the helical hairpin to the coiled-coil dimer upon addition of disulfide-reducing agents.     

Free radical addition of cyclopentane and cyclohexane to halogeno derivatives of 1,2-difluoroethene

Free radical addition reactions between cyclopentane and cyclohexane and a range of difluoroalkenes, CF₂CXY (X, Y = H, F, Cl, Br) gave a series of adducts bearing difluoromethylene substituents, R-CF₂-CXYH (R = c-C₅H₉ or c-C₆H₁₁), in reasonable yield even though telomerisation and halogen transfer (when X, Y = Cl, Br) can compete. Dehydrofluorination of the adducts gave several new polyhalogenated alkenes.     

Mass-spectrometric analysis of some derivatives of α,β-didehydrotryptophan and peptides including it

Summary It has been established that the mass spectra of N-Bz, and N-Ac derivatives of peptides containing ,-didehydrotryptophan residues have characteristic peaks of ions with m/e 130, 156 (157), and 183; these permit the identification in peptides of the ,-didehydrotryptophan residue, which is unstable on hydrolysis. In the course of the fragmentation of dehydropeptides by the amino acid route, the formation of the intense peak of the ion of an azlactone of aN-acyl-,-didehydrotryptophan is characteristic. The mass-spectrometric method can be used for determining the amino acid sequences of peptides containing ,-didehydrotryptophan residues.M. V. Lomonosov Moscow State University. M. M. Shemyakin Institute of Bioorganic Chemistry, Academy of Sciences of the USSR, Moscow. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 187–181, March–April, 1979.     

Preferred conformations of some 2-pyridyl substituted thiourea derivatives. A reinvestigation of NMR spectral data

A previous report involving ¹H nmr spectra of some 1-phenyl and 1-benzoyl 3-(2-pyridyl)thioureas was reinvestigated and found to be incorrect. Analysis of the data permits the designation of preferred conformations for these systems.     

Dipole moments and molecular conformations of some thioanhydrides

Electric dipole moments of methyl thiobenzoate (1.70 D), thiophthalic anhydride (3.92 D) and dibenzoyl sulphide (3.88 D) have been measured in benzene at 25° C. The predicted moments of these compounds were calculated and the results interpreted in terms of their conformations.     

New 6,6'-disubstituted-binaphthol derivatives as chiral dopants: Synthesis and temperature dependence of molecular conformations

A number of new chiral binaphthol (BN) derivatives with different substituents R,R' in the 6,6'-positions in open (BN-diethylethers) and bridged forms (BN-acetals) have been synthesized. The syntheses of the chiral 6,6'-disubstituted-2,2'-diethoxy-1,1'-binaphthyls (R,R' = -CH'CHCHO, -CH'CH-(p-BrPh), -CH'CH-(p-CHOPh)) and the chiral 9,14-disubstituted-dinaphtho [2,1-d:1',2'-f][1,3] dioxepins with R,R' = -CH'CH-(p-BrPh), -CH'CH-(p-CHOPh) are reported for the first time. The possible liquid crystalline properties and molar twisting powers (β_M) in three different nematic liquid crystals (LCs) of the BN derivatives were investigated. Derivatives with spatially extended substituents in the 6,6'-positions (e.g. styryl or vinyl) show unusually high molar twisting power (up to 124.5μm^-1). A direct correlation between the magnitude of β_M and the length of the substituents was found. Bridged forms, in which the dihedral angle θ between the naphthyl moieties is ≊ 54°, show higher twisting power than the corresponding open forms, where θ is allowed to vary around 90° resulting in an equilibrium between transoid and cisoid forms. From the different temperature dependencies of β_M of the open and bridged BN_s, a molecular model was developed relating the molecular conformation and twisting power. Although no mesophase was found in any of the compounds synthesized, they can be considered as important precursors for the synthesis of potential chiral BN-containing LCs.     

A critical comparison of search algorithms applied to the optimization of protein side-chain conformations

Three different optimization algorithms are applied to solving the problem of finding the best side-chain conformations with a test set of 14 globular proteins having known crystallographic conformations. It is shown that simulated annealing, simple and modified genetic algorithms, and a heuristic combinatorial approach achieve similar optimal solutions, with the exception of simulated annealing applied to the largest proteins. The efficiency of the different algorithms, however, shows wide variations. General conclusions are drawn concerning the optimal approach to such problems. © 1993 John Wiley & Sons, Inc.