Conformational behavior of peptides containing residues of 3-azetidinesulfonic (3AzeS) and 4-piperidinemethanesulfonic (4PiMS) acids

The conformational behavior of four model peptides containing residues of 3-azetidinesulfonic (3AzeS) and 4-piperidinemethane sulfonic (4PiMS) acids was studied in both a crystalline state and in solution using X-ray, NMR, and IR experiments. It was found that in the crystalline state, both of the models di- and tripeptides studied adopted extended conformations and demonstrated considerable conformational flexibility. In solution, it is likely that a flexible ensemble of conformations is adopted, including extended structures and more compact ones without persistent hydrogen bonds. One of the most interesting features of the peptides was the axial chirality observed due to the slow rotation around the amide bond formed by the endocyclic nitrogen atoms of the non-chiral 3AzeS and 4PiMS residues. It was shown for one of the derivatives that the configuration of the chiral axis had an impact on the conformation of the neighboring amino acid residue.     

Relationship between Molecular Properties and Conformation of Chiral Alkanes

Mixtures of the diastereomers of 2,2,3,5,6-pentamethylheptane were prepared in two ways, either starting with compounds of (3R)-configuration, or from compounds of (5R)-configuration. Comparison of the GC. and optical rotatory power of the fractions of these two mixtures permitted the unambiguous assignment of the absolute configuration and molar rotatory power to the various diastereomers ([M] = + 119.1° for the (3R, 5R)- and [M] = + 79.8° for the (3R, 5S)-diastereomer). The very high molar rotatory power which was expected on the basis of the conformational analysis carried out with a rotational-isomeric-3-states model is interpreted as arising from the molecular ‘conformational rigidity’, i.e. from the presence of only few conformers. Conformational properties of these compounds were computed using a new approach, which scans the whole space of each bond (2 π) in 5° steps and calculates the conformational energy based upon semiempirical potential functions. The conformational flexibility of each bond of the two diastereomers is evaluated in terms of the a priori probability density function of that bond. This allows us to analyze in detail how configurational differences affect conformational properties. The molar rotatory power of the two diastereomers as calculated with a new method recently developed in our group is in excellent agreement with experimental data. The molar rotatory power is analyzed in terms of the contribution of the single bonds.     

Toward a synthetically useful stereoselective C-H amination of hydrocarbons

Reaction between a sulfur(VI) compound and an iodine(III) oxidant in the presence of a catalytic quantity (<=3 mol %) of a rhodium(II) catalyst leads to the formation of a chiral metallanitrene of unprecedented reactivity. The latter allows intermolecular C-H amination to proceed in very high yields up to 92% and excellent diastereoselectivities up to 99% with C-H bond containing starting materials as the limiting component. The scope of this C-H functionalization includes benzylic and allylic substrates as well as alkanes. Secondary positions react preferentially, but insertion into activated primary C-H bonds or sterically accessible tertiary sites is also possible. Cooperative effects between the nitrene precursor and the chiral catalyst at the origin of these good results have also been applied to kinetic resolution of racemic sulfonimidamide. This methodology paves the way to the use of Csp3-H bonds as synthetic precursors for the introduction of a nitrogen functionality into selected positions.     

The role of intra- and intermolecular interactions in determining the conformation and mode of packing of crystalline polymers—I. Poly(cis-1,4-butadiene)

Conformational energy calculations on an isolated chain of poly(cis-1,4-butadiene) have been performed, allowing for the variation of all bond angles and torsion angles. Various minimum energy and high symmetry conformations are accessible to the chain. Packing energy calculations have been performed for chains having tci symmetry, allowing for the variation of symmetry, unit cell constants and internal rotation angles. Unlike the behaviour observed for other polymers, the chain conformation which minimizes the total (conformational plus packing) energy is sensibly different from that of minimum energy for the isolated chain. The agreement between experimental and calculated data of the crystal structure analysis may be considered as very good.     

diSBPred: A machine learning based approach for disulfide bond prediction

The protein disulfide bond is a covalent bond that forms during post-translational modification by the oxidation of a pair of cysteines. In protein, the disulfide bond is the most frequent covalent link between amino acids after the peptide bond. It plays a significant role in three-dimensional (3D) ab initio protein structure prediction (aiPSP), stabilizing protein conformation, post-translational modification, and protein folding. In aiPSP, the location of disulfide bonds can strongly reduce the conformational space searching by imposing geometrical constraints. Existing experimental techniques for the determination of disulfide bonds are time-consuming and expensive. Thus, developing sequence-based computational methods for disulfide bond prediction becomes indispensable. This study proposed a stacking-based machine learning approach for disulfide bond prediction (diSBPred). Various useful sequence and structure-based features are extracted for effective training, including conservation profile, residue solvent accessibility, torsion angle flexibility, disorder probability, a sequential distance between cysteines, and more. The prediction of disulfide bonds is carried out in two stages: first, individual cysteines are predicted as either bonding or non-bonding; second, the cysteine-pairs are predicted as either bonding or non-bonding by including the results from cysteine bonding prediction as a feature.The examination of the relevance of the features employed in this study and the features utilized in the existing nearest neighbor algorithm (NNA) method shows that the features used in this study improve about 7.39 % in jackknife validation balanced accuracy. Moreover, for individual cysteine bonding prediction and cysteine-pair bonding prediction, diSBPred provides a 10-fold cross-validation balanced accuracy of 82.29 % and 94.20 %, respectively. Altogether, our predictor achieves an improvement of 43.25 % based on balanced accuracy compared to the existing NNA based approach. Thus, diSBPred can be utilized to annotate the cysteine bonding residues of protein sequences whose structures are unknown as well as improve the accuracy of the aiPSP method, which can further aid in experimental studies of the disulfide bond and structure determination.     

Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space

A new stochastic (Monte Carlo) procedure, termed torsional flexing, has been devised for searching the conformational space of cyclic molecules. Torsional flexing causes a local, torsion angle-biased, distortion of a ring bond in a cyclic molecule. Because torsional flexing does not cause large atomic movements, even when it is applied to several bonds simultaneously, subsequent energy minimization generally proceeds rapidly. Nevertheless, the torsional flexing method is prone to generate structures that cross energy barriers so that the structure resulting after energy minimization is frequently a different conformer of the cyclic molecule. Conformational searches on cycloheptadecane, oxobrefeldin A, cyclopenta-L -alanine, and rifamycin SV based upon torsional flexing indicated that torsional flexing is among the best methods yet devised for searching the conformational space of flexible cyclic molecules. © 1993 John Wiley & Sons, Inc.     

Peptoid atropisomers

We report the isolation of N-aryl peptoid oligomers that adopt chiral folds, despite the absence of chiral centers. Peptoid monomers incorporating ortho-substituted N-aryl side chains are identified that exhibit axial chirality. We observe significant energy barriers to rotation about the stereogenic carbon-nitrogen bond, allowing chromatographic purification of stable atropisomeric forms. We study the atropisomerism of N-aryl peptoid oligomers by computational modeling, NMR, X-ray crystallography, dynamic HPLC, and circular dichroism. The results demonstrate a new approach to promote the conformational ordering of this important class of foldamer compounds.     

Net directed 180° aryl-aryl bond rotation in a prototypical achiral biaryl lactone synthetic molecular motor

Net directed 180° bond rotation was achieved through diastereoselective ring-opening reactions in an achiral biaryl lactone using a chiral nucleophile followed by re-lactonization. The efficiency of the directed bond rotation has been determined by HPLC-MS to be 50% and 20% with two different chiral nucleophiles. These results demonstrate the potential for a prototype of a chemically driven synthetic molecular motor which has the advantages of both simplicity and flexibility in operation and is the first example of the use of a chiral auxiliary to induce transient axial chirality resulting in net directed bond rotation.     

ORD and CD studies of poly[(S)(−)-N-α-methylbenzylethylenimine]

The advantages of chiral N-substituted polyethylenimines for the chiroptical study of macromolecular conformations in solution have been considered. Poly[(S)(?)-N-α-methylbenzylethylenimine] (poly-3) and five model compounds have been obtained and their chiroptical properties studied. The cyclic dimer and tetramer of imine 3 are suitable models for the chiroptical study of configurational and conformational behaviour of randomly coiled and helical poly-3 in solution. Unlike the disordered poly-3 in acidified solvents and the configurational models in various solvents, helical poly-3 in hydrocarbon solvents has positive optical rotation and positive CD-band of the tertiary amine chromophore at 223 nm. The appearance of this inherently chiral chromophore of the helix explains the observed changes of the sign and values of the optical rotation of poly-3 in various solvents which are mainly caused by conformational transformations of the main chain. The presence of helical conformations of poly-3 in solution are also confirmed by optical rotation data of stereocopolymers and the concentration dependence data of ORD curves of poly-3. This conclusion agrees with NMR and i.r.-data.     

Structure, thermochemistry, and conformational analysis of peroxides ROOR and hydroperoxides ROOH (R = Me, But, CF3)

The equilibrium structures, total energies, and harmonic frequencies of peroxides ROOR and ROOH (R = Me, Bu^t, CF₃) were calculated using the perturbation theory (MP4//MP2 method) and density functional approach (B3LYP) in the 6-31G(d,p) basis set. The conformational flexibility of peroxides under rotation about the O-O bond was investigated. It was found that the stable conformation of a peroxide molecule is determined by superposition of the destabilizing effects (repulsion between the lone electron pairs, steric hindrances) and the interaction of the nonbonding orbitals of oxygen atoms with the antibonding orbitals of the adjacent polar bonds. The latter effect stabilizes the nonplanar structure of the peroxide molecule. The role of orbital interactions in manifestation of the d-effect (distortion of the tetrahedral configuration of the X₃CO fragment of peroxide molecule) was revealed. The vibrational spectra of peroxides were calculated and compared with the experimental data. The potential energy distribution over normal vibrations was analyzed. The enthalpies of formation and the bond strengths in the molecules of compounds examined were calculated in the framework of the isodesmic reaction approach.     

Theoretical conformational analysis of a simple sulphilimine model

The topomerization (bond rotation andS-pyramidal inversion) of a simple sulphilimine model, H₂SNH has been studied with the aid ofab initio SCF MO calculations. The highest rotation barrier occurs when the H₂SN moiety is planar, < HSN = 120 °. The maxima of the inversion crossections occur at the planar conformation for all rotation angles α as expected, however, the minima belong to different values when α is varied. The minimum energy path between the two lowest minima of the conformational energy surface consists of a pure inversion section and a section which is mostly rotation. The optimum values of the < HSN bond angles are significantly smaller than the corresponding < RSN bond angles of sulphilimines of bulkierR substituents.     

Chiroptical spectroscopy of surfactants

Three different chiroptical spectroscopic methods, namely, optical rotation, electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) have been evaluated for studying the aggregation of sodium dodecylsulfate (SDS), an achiral surfactant, using garcinia acid disodium salt (GADNa) as a chiral probe. The specific rotation and ECD of GADNa are found to be altered by the aggregation of SDS, suggesting for the first time that achiral surfactants can be characterized with chiroptical spectroscopy using appropriate chiral probes. In addition, a chiral compound, fluorenyl methyloxy carbonyl l-leucine sodium salt (FLNa) is found for the first time to behave as a surfactant in water, with 205 ?(2) surface area per molecule at the air-water interface, critical micelle concentration (CMC) of 0.18 M, and Gibbs energy of micellization of -14 kJ/mol. The specific rotation of FLNa in water is found to increase with concentration beyond CMC, suggesting the formation of chiral aggregates. Different conformations of FLNa amenable to micellization have been identified using quantum chemical conformational analysis and their specific rotations calculated. The formation of lamellar aggregates of FLNa in water is suggested to be the cause for increase in specific rotation with concentration beyond CMC.     

Origin of threefold methyl torsional potential in methylindoles

In this article, we present a systematic study on mono-methylindoles to investigate the electronic origin of the threefold symmetric component (V ₃) of the methyl torsional potential barrier in the ground electronic state (S ₀). The structures and the torsional potential parameters of these molecules were evaluated from ab initio calculation using Hartree-Fock (HF), second order Mollar Plesset perturbation (MP2) and B3LYP density functional level of theories and Gaussian type basis set 6-31G(d, p). Natural bond orbital (NBO) analysis of these molecules were carried out using B3LYP/6-31G(d, p) level of calculation to understand the formation of the threefold V ₃ term arising from the changes of various non-covalent interactions during methyl rotation. Our analysis reveals that the contributions from π orbitals play a dominant role in the barrier height determination in this class of molecules. The threefold term in the barrier arises purely from the interactions non-local to the methyl group in case when the methyl group has two single bonds vicinal to it. On the other hand, it is the local interaction that determines the potential energy barrier when the methyl group has one single bond and one double bond vicinal to it. However, in all these cases, the magnitude of the energy barrier depends on the resonance structure formation in the benzene ring frame upon rotation of the methyl group and, therefore, the energetics of the barrier cannot be understood without considering the molecular flexing during methyl rotation.     

Conformational preferences of the axial ligands in some metalloporphyrins. A theoretical study

The conformational preferences of the axial ligands have been determined for several metalloporphyrins MPL and MPLL′ (M = Mo, Fe; P = porphine dianion; L and L′ being the axial ligands). For MoP(C₂H₂) a qualitative analysis indicates that the conformation with the acetylenic bond eclipsing two Mo-N bonds will be favored. Ab initio SCF calculations indicate that:

1. iron porphyrins with an axial imidazole ligand show a flat potential energy curve for the rotation of the imidazole ligand;
2. iron porphyrins with a dioxygen ligand prefer the staggered conformation with the O-O bond projecting along the bisectors of the Fe-N bonds;
3. in the cis-dinitrosyl molybdenum porphyrin, the nitrosyl ligands should be eclipsed with respect to the Mo-N_pyr bonds.

These theoretical predictions are compared with the experimental structures from the literature.     

Steric effects in the aerobic oxidation of pi-allylnickel(II) complexes with N-heterocyclic carbenes

Pi-allylchloro(NHC)nickel(II) complexes were synthesized and their reactions with O2 were studied. Ligand steric effects were found to determine the difference between rapid oxidation of the allyl group to produce bis-mu-hydroxonickel complexes and no observable reaction. The ability of the metal-NHC bond to rotate correlates with the ability of the complex to react with O2. In the limiting cases, conformationally restricted complexes are stable to O2 and complexes with rapid Ni-NHC bond rotation react rapidly with O2. Complexes with intermediate conformational flexibility were found to exhibit lesser reactivity with O2. On the basis of the observed inertness of complexes with saddle-shaped ligands to O2, we propose the adoption of a nonplanar geometry upon reaction with O2 to be required. The issue of conformational flexibility versus rigidity is expected to directly impact the catalytic behavior of metal-NHC complexes.     

Toward the development of a general chiral auxiliary. Part 6: Structural effects on diastereoselection using camphor derived lactams: evaluation of (1R,4S)-1,7,7-trimethyl-3-azabicyclo[2.2.1]hept-5-en-3-one as a chiral controller

A new camphor-derived chiral lactam was designed, prepared and evaluated as a chiral controller in asymmetric Diels–Alder and aldol reactions. The new lactam, bearing a C(5)C(6) double bond, was anticipated to afford higher diastereofacial selection resulting from the removal of additional steric hindrance to reagent approach distal to the geminal dimethyl bridge by comparison with the previously studied saturated analogue (the favored mode approach in the saturated analogue). Surprisingly, a deterioration in the extent of diastereofacial selectivity was observed for both reaction types. These results are interpreted in terms of the geometric changes imposed upon the ring system as a whole by introduction of the unsaturation.     

Bispidine Platform as a Tool for Studying Amide Configuration Stability

In this work, the solution conformations of seventeen 3,7-diacyl bispidines were studied by means of NMR spectroscopy including VT NMR experiments. The acyl groups included alkyl, alkenyl, aryl, hetaryl, and ferrocene moieties. The presence of syn/anti-isomers and their ratios were estimated, and some reasons explaining experimental facts were formulated. In particular, all aliphatic and heterocyclic units in the acylic R(CO) fragments led to an increased content of the syn-form in DMSO-d₆ solutions. In contrast, only the anti-form was detected in DMSO-d₆ and CDCl₃ in the case when R = Ph, ferrocenyl, (R)-myrtenyl. In the case of a chiral compound derived from the natural terpene myrtene, a new dynamic process was found in addition to the expected inversion around the amide N-C(O) bond. Here, rotation around the CO-C=C bond in the acylic R fragment was detected, and its energy was estimated. For this compound, ΔG for amide N-C(O) inversion was found to be equal to 15.0 ± 0.2 kcal/mol, and for the rotation around the N(CO)–C^2′ bond, it was equal to 15.6 ± 0.3 kcal/mol. NMR analysis of the chiral bispidine-based bis-amide was conducted for the first time. Two X-ray structures are reported. For the first time, the unique syn-form was found in the crystal of an acyclic bispidine-based bis-amide. Quantum chemical calculations revealed the unexpected mechanism for amide bond inversion. It was found that the reaction does not proceed as direct N-C(O) bond inversion in the double-chair (CC) conformation but rather requires the conformational transformation into the chair–boat (CB) form first. The amide bond inversion in the latter requires less energy than in the CC form.     

The conformational behaviour of some p-tolylsulphlnamides

Eight sulphinamides of the type p-CH₃C₆H₄-S(O)-NHR, where R represents an aliphatic group, were investigated by means of IR spectroscopy. The doubling of the SO stretching frequency of the free molecules is discussed in terms of conformational isomerism, originated by the rotation around the S-aryl axis. The two conformers participate differently in the H bond, NH-OS. The doublets of the NH bands in the spectra of the free molecules occur because of the existence of two conformations and are due to the rotation about the SN axis. The H bonds influence the conformational behaviour of the molecules. The H bond enthalpies are estimated by calorimetric measurements to lie between about 6 and 20 kJ for the complete association of one mol monomer. The NMR spectra show that the NH proton is part of the spin-spin coupling system.     

Conformational aspects of glutathione tripeptide: electron density topological & natural bond orbital analyses

Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density $ \nabla^{2} $ ρ(r) from Bader’s atom in molecules theory. Charge transfer energies based on natural bond orbital analysis are also considered to interpret these intramolecular hydrogen bonds. Our results show that these hydrogen bonds are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the stabilization energy of hydrogen bond increases. Furthermore, the back bone and side chain (Ramachandran map) orientations of various ionic forms of glutathione have been studied and conformation of each constitution of glutathione tripeptide (i.e., Glu, Cys, and Gly moieties) was determined. In most species side chain conformation were found to be hindered gauche–gauche orientation by intramolecular hydrogen bonds.