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Copyright of Angewandte Chemie is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD) simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT) potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.

Bimethyl rotor molecules exhibit two kinds of torsion, namely gearing and antigearing. A series of dimethyl ether gearing/antigearing fundamental frequency splitting calculations where separate consideration of exchange repulsion, delocalization interactions, and nonrotational phase space of the torsional coordinate indicate that the splitting is largely due to hyperconjugation between CH bonds of the two-methyl groups.

A study of the analysis and comparison of hindered rotation in disilane to ethane is presented. The results show that even though ethane and disilane exhibit similar central bond expansions, in ethane the effect of C-C bond weakening is overwhelmed by the large, rotationally controlled change in hyperconjugative interactions while in disilane, weakened hyperconjugative interactions leave the nonrotational part of the torisonal coordinate as the paramount contribution to the barrier energetics.

Author(s): Vojislava Pophristic; Lionel Goodman (corresponding author) Many molecules can rotate internally around one or more of their bonds so that during a full 360° rotation, they will change between [...]

The ab initio architecture and torsional barrier for acetone n-radical cation are obtained. The 923 cm-1 MP4/6-311+G(3df,2p) barrier is calculated to be 30% higher than for neutral acetone. This increase is largely attributed to correlation effects and less importantly to increased hyperconjugative stabilization of the equilibrium cation conformer. Ionization is predicted to cause opening of the central CCC angle by 7° and cause the methyl groups to lose the C[sub 3v] symmetry that they possess in neutral acetone. The torsional coordinate for the infrared active b[sub 1] (gearing) rotation is predicted to not lie purely on the torsional potential surface, but to be contaminated by puckering of the CCCO skeleton in both the neutral and cation species, thereby making the b[sub 1] infrared torsional frequencies only partially suitable for sampling the torsional potential surface. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The behavior of the [Zr.sup.4+] tetranuclear polymer, [[[Zr.sub.4][(OH).sub.8][([H.sub.2]O).sub.16].sup.8+] in aqueous solution is studied. The results show that the tetramer is extremely stable and is in the planar form in the aqueous solution.

A study using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, the relationship between molecular conformation and the biomedical function of arylamide polymers is addressed. A common structural feature of the arylamide polymers of interest is a backbone consisting of benzene rings connected by peptide bonds.

The structures of aluminum chlorohydrate monomer, dimer, trimer, and hexamer species are determined by using a combination of Car Parrinello molecular dynamics and ab initio methods. It is found that Cl(super -) ion incorporation in the octahedral structure of aluminum chlorohydrate monomer, dimer, and trimer increases their stability in the gas phase.

Describes the flexing analysis of the ethane barrier energy in terms of structural, steric exchange and hyperconjugative charge-transfer energy contributions using natural bond orbitals. Differences in stereoelectronic dependencies; Effects of the C-C bond expansion on the energy contributions; Importance of the interactions as determinant for the expansion.

Copyright of Angewandte Chemie is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract: Macrocyclization of a stable two‐turn helical aromatic pentamide, that is, an object with diverging ends that are not prone to cyclization, was made possible by the transient introduction of disruptors of helicity in the form of acid‐labile dimethoxybenzyl tertiary amide substituents. After removal of the helicity disruptors, NMR, X‐ray crystallography, and computational studies show that the macrocycle possesses a strained structure that tries to gain as high a helical content as possible despite being cyclic. Two points of disruption of helicity remain, in particular a cis amide bond. This point of disruption of helicity can propagate along the cycle in a fluxional manner according to defined trajectories to produce ten degenerate conformations. [ABSTRACT FROM AUTHOR]

Molecular dynamics was applied to investigate the structural properties and activity of synthesized amphiphilic random copolymers, designed to mimic the antimicrobial activity of natural peptides. It was observed that the structural diversity of the polymers, crucial in controlling their activity and selectivity, could be fine-tuned by controlling their sequential order, molecular weight, chemical nature of side chains and hydrophobicity (ratio of hydrophobic and cationic units).