Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue

All-atom molecular mechanical (MM) force field parameters are developed for a cyclic beta-amino acid, amino-cyclo-pentane-carboxylic acid (ACPC), using a multi-objective evolutionary algorithm. The MM model is benchmarked using several short, ACPC-containing alpha/beta-peptides in water and methanol with SCC-DFTB (self consistent charge-density functional tight binding)/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the tetra-alpha/beta-peptide in water. For the octa-alpha/beta-peptide in methanol, the MM and SCC-DFTB/MM simulations predict the 11- and 14/15-helical form as the more stable conformation, respectively; however, the two helical forms are very close in energy (2-4 kcal/mol) at both theoretical levels, which is also the conclusion from recent NMR experiments. As the first application, the MM model is applied to an alpha/beta-pentadeca-peptide in water with both explicit and implicit solvent models. The stability of the peptide is sensitive to the starting configuration in the explicit solvent simulations due to their limited length ( approximately 10-40 ns). Multiple ( approximately 20 x 20 ns) implicit solvent simulations consistently show that the 14/15-helix is the predominant conformation of this peptide, although substantially different conformations are also accessible. The calculated nuclear Overhauser effect (NOE) values averaged over different trajectories are consistent with experimental data, which emphasizes the importance of considering conformational heterogeneity in such comparisons for highly dynamical peptides.     

Enantioselective organocatalytic Michael addition of aldehydes to nitroethylene: efficient access to gamma2-amino acids

Enantioselective organocatalytic Michael addition of aldehydes to nitroethylene catalyzed by (S)-diphenylprolinol silyl ether provides beta-substituted-delta-nitroalcohols in nearly optically pure form (96-99% ee). The Michael adducts bear a single substituent adjacent to the carbonyl and can be efficiently converted to protected gamma2-amino acids, which are essential for the systematic conformational studies of gamma-peptide foldamers.     

Single-conformation ultraviolet and infrared spectroscopy of model synthetic foldamers: beta-peptides Ac-beta3-hPhe-NHMe and Ac-beta3-hTyr-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-NHMe (1) and Ac-beta3-hTyr-NHMe (2), have been explored under jet-cooled, isolated molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl or phenol ring substituents, respectively. UV-UV hole-burning spectroscopy was used to determine that two conformations of 1 are present, with the transitions due to conformer A, with S0-S1 origin at 34431 cm(-1), being almost 20 times larger than those due to conformer B, with S0-S1 origin at 34404 cm(-1). Only one conformation of 2 was observed. Resonant ion-dip infrared spectroscopy provided single-conformation infrared spectra in the 3300-3700 cm(-1) region. The spectra of conformer A of both molecules have H-bonded and free amide NH stretch infrared transitions at 3400 and 3488 cm(-1), respectively, while conformer B of 1 possesses bands at 3417 and 3454 cm(-1). For comparison with experiment, full optimizations of all low-lying minima of 1 were carried out at the DFT B3LYP/6-31+G* and RIMP2/aug-cc-pVDZ levels of theory, and single point MP2/6-31+G* calculations at the DFT geometries. On the basis of the comparison with previous studies in solution and the calculated results, conformer A of 1 and 2 were assigned to a C6 conformer, while conformer B of 1 was assigned to a unique C8 structure with a weak intramolecular H-bond. The reasons for the preference for C6 over C8 structures and the presence of only two conformations in the jet-cooled spectrum are discussed in light of the predictions from calculations.     

Inherent Conformational Preferences of Ac‐Gln‐Gln‐NHBn: Sidechain Hydrogen Bonding Supports a β‐Turn in the Gas Phase

Gas‐phase single‐conformation spectroscopy is used to study Ac‐Gln‐Gln‐NHBn in order to probe the interplay between sidechain hydrogen bonding and backbone conformational preferences. This small, amide‐rich peptide offers many possibilities for backbone–backbone, sidechain–backbone, and sidechain–sidechain interactions. The major conformer observed experimentally features a type‐I β‐turn with a canonical 10‐membered ring C=O—H?N hydrogen bond between backbone amide groups. In addition, the C=O group of each Gln sidechain participates in a seven‐membered ring hydrogen bond with the backbone NH of the same residue. Thus, sidechain hydrogen‐bonding potential is satisfied in a manner that is consistent with and stabilizes the β‐turn secondary structure. This turn‐forming propensity may be relevant to pathogenic amyloid formation by polyglutamine segments in human proteins.     

Origins of the high 14-helix propensity of cyclohexyl-rigidified residues in beta-peptides

[structure: see text] beta-Peptides containing residues derived from trans-2-aminocyclohexanecarboxylic acid (ACHC) display high population of 14-helical secondary structure in aqueous solution. We show that hydrophobic interactions between cyclohexyl rings are not responsible for this conformation-promoting effect, and that polar groups may be attached to the cyclohexyl ring without diminishing the effect.     

TiIV-mediated reactions between primary amines and secondary carboxamides: amidine formation versus transamidation

Titanium(IV)-mediated reactions between primary amines and secondary carboxamides exhibit different outcomes, amidine formation versus transamidation, depending on the identity of the TiIV complex used and the reaction conditions employed. The present study probes the origin of this divergent behavior. We find that stoichiometric TiIV, either Cp*TiIV complexes or Ti(NMe2)4, promotes formation of amidine and oxotitanium products. Under catalytic conditions, however, the outcome depends on the identity of the TiIV complex. Competitive amidine formation and transamidation are observed with Cp*TiIV complexes, generally favoring amidine formation. In contrast, the use of catalytic Ti(NMe2)4 (< or =20 mol %) results in highly selective transamidation. The ability of TiIV to avoid irreversible formation of oxotitanium products under the latter conditions has important implications for the use of TiIV in catalytic reactions.     

Density functional theory study of beta-hydride elimination of ethyl on flat and stepped Cu surfaces

Plane wave density functional theory calculations have been used to characterize the transition states for beta-hydride elimination of ethyl on Cu(100), Cu(110), Cu(111), and Cu(221). The reaction rates predicted by these calculations have been compared to experiments by including tunneling corrections within harmonic transition state theory. Tunneling corrections are found to be important in describing the peak temperatures observed using temperature programmed desorption experiments on Cu(110), Cu(111), and Cu(221). Once these corrections are included, the effective activation energies obtained from our calculations are in good agreement with previous experimental studies of this reaction on these four Cu surfaces. The transition states determined in our calculations are used to examine two general hypotheses that have been suggested to describe structure sensitivity in metal-catalyzed surface reactions.     

Improved treatment of cyclic β‐amino acids and successful prediction of β‐peptide secondary structure using a modified force field: AMBER*C

We added parameters to the AMBER* force field to model cyclic β‐amino acid derivatives more accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformational preferences, carbon–carbon torsional parameters were modified and incorporated into a force field we call AMBER*C. Simulation of trans‐2‐aminocyclohexanecarboxylic acid (trans‐ACHC) and trans‐2‐aminocyclopentanecarboxylic acid (trans‐ACPC) derivatives using AMBER*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformations than does simulation using AMBER*. AMBER*C molecular dynamics simulations more accurately reproduce the experimental hydrogen‐bonding tendencies of simple diamide derivatives of trans‐ACHC and trans‐ACPC than do simulations using the AMBER* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by β‐amino acid homo‐oligomers. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 763–773, 2000     

The shear modulus of the human vocal fold in a transverse direction

The aim of this study was to measure the shear modulus of the vocal fold in a human hemilarynx, such that the data can be related to direction of applied stress and anatomical context. Dynamic spring rate data were collected using a modified linear skin rheometer using human hemilarynges, and converted to estimated shear modulus via application of a simple shear model. The measurement probe was attached to the epithelial layer of the vocal fold cover using suction. A sinusoidal force of 3g was applied to the epithelium, and the resultant displacement logged at a rate of 1kHz. Force measurement accuracy was 20microg and position measurement accuracy was 4microm. The force was applied in a transverse direction at the midmembranous point between the vocal process and the anterior commissure. The shear modulus of the three female vocal folds ranged from 814 to 1232Pa. The shear modulus of the three male vocal folds ranged from 1021 to 1796Pa. These data demonstrate that it is possible to obtain estimates for the shear modulus of the vocal fold while preserving anatomical context. The modulus values reported here are higher than those reported using parallel plate rheometry. This is to be expected as the tissue is attached to surrounding structures, and is under natural tension.