Conformational transitions of cyclic D,L-peptides

Conformational transitions of cyclic D,L-hexapeptides have been studied by first-principles calculations. Geometry optimizations for 20 types of homoresidue cyclic D,L-hexapeptide revealed that the cyclic peptides have two types of energetically stable backbone (extended (E) and bound (B) types); and for each type, the amino acid side chains have two orientations (equatorial and axial). Among the four types of isomer [E-type equatorial (E(eq)), B-type equatorial (B(eq)), E-type axial (E(ax)), and B-type axial (B(ax))], B(ax) is the energetically most preferred by most of the 20 encoded amino acid residues, whereas E(ax) is the least preferred. A search for transition states indicated that six types of conformational transition are possible between the isomers of the cyclic peptide, i.e., the backbone-backbone conversions (E(eq)-B(eq) and E(ax)-B(ax) transitions), the side chain-side chain conversions (E(eq)-E(ax) and B(eq)-B(ax) transitions), and the simultaneous conversions of the backbone and the side-chain orientation (E(eq)-B(ax) and E(ax)-B(eq) transitions). All the six transitions proceed with the breaking of the high molecular symmetry (S(6)) and go through the triangular (C(3)) intermediate structure with either equatorial or axial side-chain orientation.     

Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed by two atoms of different chirality and flexibility. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L residues, and their side chains adopt different rotameric states. For short chains, we enumerate exhaustively all possible conformations. For long chains, we sample effectively rare events such as compact conformations and obtain complete pictures of ensemble properties of conformations of these models at all compactness region. This is made possible by using sequential Monte Carlo techniques based on chain growth method. Our results show that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by statistical analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side chain entropy for a given backbone structure. We show that simple rotamer counting underestimates side chain entropy significantly for both extended and near maximally compact conformations. We find that side chain entropy does not always correlate well with main chain packing. With explicit side chains, extended backbones do not have the largest side chain entropy. Among compact backbones with maximum side chain entropy, helical structures emerge as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.     

Efficient and accurate calculations on the electronic structure of B-type poly(dG).poly(dC) DNA by elongation method: first step toward the understanding of the biological properties of aperiodic DNA

Elongation method was applied to determine the electronic structures of B-type poly(dG).poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10(-8) hartreeat. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.     

Theoretical study of the 13C NMR spectroscopy of single-walled carbon nanotubes

The 13C NMR spectroscopy of armchair and zigzag single-walled carbon nanotubes has been investigated theoretically. Spectra for (4,4), (5,5), (6,6), (6,0), (9,0), and (10,0) nanotubes have been simulated based on ab initio calculations of model systems. The calculations predict a dominant band arising from the carbon atoms in the "tube" with smaller peaks at higher chemical shifts arising from the carbon atoms of the caps. The dominant band lies in the range of 128 and 138 ppm. Its position depends weakly on the length, width, and chirality of the tubes. The calculations demonstrate how structural information may be gleaned from relatively low-resolution nanotube 13C NMR spectra.     

Experimental and theoretical investigations of the loss of amino acid side chains in electron capture dissociation of model peptides

Loss of side chains from different amino acid residues in a model peptide framework of RGGGXGGGR under electron capture dissociation conditions were systematically investigated, where X represents one of the twenty common amino acid residues. The alpha-carbon radical cations initially formed by N-Calpha cleavage of peptide ions were shown to undergo secondary dissociation through losses of even-electron and/or odd-electron side-chain moieties. Among the twenty common amino acid residues studied, thirteen of them were found to lose their characteristic side chains in terms of odd-electron neutral fragments, and nine of them were found to lose even-electron neutral side chains. Several generalized dissociation pathways were proposed and were evaluated theoretically with truncated leucine-containing models using ab initio calculations at B3-PMP2/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level. Elimination of odd-electron side chain was associated with the initial abstraction of the hydrogen from the alpha-carbon bearing the side chain by the N-terminal alpha-carbon radical. Subsequent formation of alpha-beta carbon-carbon double bond leads to the elimination of the odd-electron side chain. The energy barrier for this reaction pathway was 89 kJmol-1. This reaction pathway was 111 kJmol-1 more favorable than the previously proposed pathway involving the formation of cyclic lactam. Elimination of even-electron side chain was associated with the initial abstraction of the gamma-hydrogen from the side chain by the N-terminal alpha-carbon radical. Subsequent formation of beta-gamma carbon-carbon double bond leads to the elimination of the even-electron side chain and the migration of the radical center to the alpha-carbon. The energy barrier for this fragmentation reaction was found to be 50 kJmol-1.     

Theoretical study on tertiary structural elements of beta-peptides: nanotubes formed from parallel-sheet-derived assemblies of beta-peptides

Parallel or polar strands of beta-peptides spontaneously form nanotubes of different sizes in a vacuum as determined by ab initio calculations. Stability and conformational features of [CH3CO-(beta-Ala)k-NHCH3]l (1 < or = k < or = 4, 2 < or = l < or = 4) models were computed at different levels of theory (e.g., B3LYP/6-311++G(d,p)// B3LYP/6-31G(d), with consideration of BSSE). For the first time, calculations demonstrate that sheets of beta-peptides display nanotubular characteristics rather than two-dimensional extended beta-layers, as is the case of alpha-peptides. Of the configurations studied, k = l = 4 gave the most stable nanotubular structure, but larger assemblies are expected to produce even more stable nanotubes. As with other nanosystems such as cyclodextrane, these nanotubes can also incorporate small molecules, creating a diverse range of applications for these flexible, biocompatible, and highly stable molecules. The various side chains of beta-peptides can make these nanosystems rather versatile. Energetic and structural features of these tubular model systems are detailed in this paper. It is hoped that the results presented in this paper will stimulate experimental research in the field of nanostructure technology involving beta-peptides.     

The self‐assembled of cyclic D,L‐α‐peptide systems: Insights into the structure and energetics

Cyclic D,L ‐α‐peptides are able to self‐assemble to nanotubes, although the inherent reason of the stability of this kind of nanotube as well as the intrinsic driving force of self‐assembly of the cyclic D ,L ‐α‐peptides still remain elusive. In this work, using several computational approaches, we investigated the structural and energy characteristics of a series of cyclo[(‐L ‐Phe‐D ‐Ala‐)₄] and cyclo[(‐L ‐Ala‐D ‐Ala‐)₄] oligomers. The results reveal that the thermodynamic stability, cooperativity, and self‐assembly patterns of cyclic D ,L ‐α‐peptide nanotubes are mainly determined by the interactions between cross‐strand side chains instead of those between backbones. For cyclo[(‐L ‐Phe‐D ‐Ala‐)₄] oligomers, the steric interaction between cross‐strand side chains, especially the electrostatic repulsion between the phenyls in Phe residues, brings anticooperative effect into parallel stacking mode, which is responsible for the preference of self‐assembling nanotube in antiparallel vs. parallel stacking orientation. Based on our results, a novel self‐assembling mechanism is put forward—it is the L ‐L antiparallel dimer of cyclo[(‐L ‐Phe‐D ‐Ala‐)₄], instead of the commonly presumed monomer, that acts as the basic building block in self assembly. It explains why these cyclic peptides uniquely self‐assemble to form antiparallel nanotubes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Morphological studies of blends of conjugated polymers and acceptor molecules using langevin dynamics simulations

We use coarse‐grained Langevin dynamics simulations of blends of generic conjugated polymers and acceptor molecules to show how architecture (e.g., side chains, backbone flexibility of oligomers) and the pair‐wise interactions between the constituents of the blend affect morphology and phase transition. Alkyl side chains on the conjugated oligomer backbones shift the liquid crystal (LC) transition temperature from that of bare conjugated backbones and the direction of the shift depends on backbone–backbone interactions. Rigid backbones and constrained side chains cause a layer‐by‐layer morphology of conjugated polymers and amorphous acceptors, whereas flexible backbones and unconstrained side chains facilitate highly ordered acceptor arrangement. Strong backbone–backbone attraction shifts LC transition to higher temperatures than weak backbone–backbone attraction, and strong acceptor–acceptor attraction increases acceptor aggregation. Pure macro‐phase separated domains form when all pair‐wise interactions in the blend are strongly attractive, whereas interconnected domains form at intermediate acceptor–acceptor attraction and strong polymer–polymer attractions. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013     

Electronic structures and conductivity in peptide nanotubes

Self-assembling cyclic D,L-peptide nanotubes are electronically insulating and possess wide band gaps (E(g) > 4 eV). Our ab initio electronic structure calculations indicate that the presence of aromatic rings in the side chain of peptide nanotubes significantly reduces the band gap. We investigate the conductivity of the modified peptide nanotubes through calculations of the electron tunneling probability. The electron tunneling probability through a molecule depends on the length of the molecule, L, as e-beta(E)L, where the tunneling beta(E)-factor is strongly energy-dependent. We have calculated beta(E) in three types of peptide nanotubes that have different sequences of amino acid residue, (L-Gln, D-Ala)(4), (L-Gln, D-Leu)(4) and (L-Gln, D-Phe)(4), using the complex band structure approach. We find large beta values near midgap, making these peptide nanotubes a poor tunneling conductor.     

Diketopyrrolopyrrole‐based Conjugated Polymers Bearing Branched Oligo(Ethylene Glycol) Side Chains for Photovoltaic Devices

Conjugated polymers are essential for solution‐processable organic opto‐electronic devices. In contrast to the great efforts on developing new conjugated polymer backbones, research on developing side chains is rare. Herein, we report branched oligo(ethylene glycol) (OEG) as side chains of conjugated polymers. Compared with typical alkyl side chains, branched OEG side chains endowed the resulting conjugated polymers with a smaller π‐π stacking distance, higher hole mobility, smaller optical band gap, higher dielectric constant, and larger surface energy. Moreover, the conjugated polymers with branched OEG side chains exhibited outstanding photovoltaic performance in polymer solar cells. A power conversion efficiency of 5.37 % with near‐infrared photoresponse was demonstrated and the device performance could be insensitive to the active layer thickness.     

A starlike amphiphilic graft copolymer with hydrophilic poly(acrylic acid) backbones and hydrophobic polystyrene side chains

A well‐defined starlike amphiphilic graft copolymer bearing hydrophilic poly(acrylic acid) backbones and hydrophobic polystyrene side chains was synthesized by successive atom transfer radical polymerization followed by the hydrolysis of poly‐(methoxymethyl acrylate) backbone. A grafting‐from strategy was employed for the synthesis of a graft copolymer with narrow molecular weight distribution. Hydrophobic polystyrene side chains were connected to the backbones through stable C? C bonds. The poly(methoxymethyl acrylate) backbones can be easily hydrolyzed with HCl without affecting the hydrophobic polystyrene side chains. This kind of amphiphilic graft copolymer can form stable sphere micelles in water. The sizes of the micelles were dependent on the ionic strength and pH value. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 3687–3697, 2007     

Synthesis and racemization process of chiral carbon nanorings: a step toward the chemical synthesis of chiral carbon nanotubes

A simple and realistic model for the shortest sidewall segments of chiral single-walled carbon nanotubes (SWNTs) has been designed, and one of the chiral carbon nanorings, cyclo[13]paraphenylene-2,6-naphthylene ([13]CPPN, 1) has been successfully synthesized. DFT calculations reveal that the racemization energy of 1 is 8.4 kcal·mol(-1). In addition, some important energetic values, such as racemization barriers and strain energies, of other chiral carbon nanorings have been systematically estimated for future molecular design.     

Comparison of the transfer and green matrix methods for the surface problem in periodic chains

For the first time, ab initio Hartree- Fock calculations for the end states of periodic chains are performed with the transfer matrix formalism. The applicability of the method is tested on semi-infinite Li-, LiH-, HF- and H₂O-chains. It is found that the numerical applications of the transfer matrix method in its applied form on the ab initio level have some drawbacks due to the limited number of perturbed end cells which can be taken into account. The comparison with Green matrix (Koster-Slater) calculations shows that the transfer matrix method in its Hartree-Fock version is not faster; this is contrary to the results reported for tight binding model Hamiltonians.     

Hydrogenation of single-wall carbon nanotubes using polyamine reagents: combined experimental and theoretical study

We combine experimental observations with ab initio calculations to study the reversible hydrogenation of single-wall carbon nanotubes using high boiling polyamines as hydrogenation reagents. Our calculations characterize the nature of the adsorption bond and identify preferential adsorption geometries at different coverages. We find the barrier for sigmatropic rearrangement of chemisorbed hydrogen atoms to be approximately 1 eV, thus facilitating surface diffusion and formation of energetically favored, axially aligned adsorbate chains. Chemisorbed hydrogen modifies the structure and stability of nanotubes significantly and increases the inter-tube distance, thus explaining the improved dispersability in solvents like methanol, ethanol, chloroform, and benzene.     

Modeling of molecular packing and conformation in oligofluorenes

We describe the application of molecular modeling to study problems related to the packing and conformation of oligofluorene molecules in the solid state. First of all, we describe an improved force field for oligofluorenes. The model is based on the MM3 force field for the intramolecular degrees of freedom, but it relies on ab initio calculations for the torsion potential between two monomers and the electrostatic interactions. We also report ab initio calculations of the interaction potentials between fluorene and fluorenone units. The force field has been tested on the crystal structures of a fluorene monomer, a dimer, and a pentamer containing a fluorenone at the center. It has then been employed to study conformational defects of the chains, both in vacuo and in the bulk. We find that certain modes of inversion from right-handed to left-handed helices are also possible within the constraining environment of the crystals. The effect of the presence of two different types of side chains has been also addressed. Finally, the possibility of having two fluorene units parallel and close to each other has been investigated as a model of a ground-state precursor of an excimer. Our simulations show that this configuration is sterically and energetically unfavorable so that formation of an excimer following optical excitation appears to be unlikely.     

Interactions of hydrogen with Pd and Pd/Ni alloy chain-functionalized single walled carbon nanotubes from density functional theory

Density functional theory is employed to study Pd and Pd/Ni alloy monatomic chain-functionalized metallic single walled carbon nanotubes (SWNT(6,6)) and semiconducting SWNT(10,0), and their interactions with hydrogen molecules. The stable geometries and binding energies have been determined for both isolated chains and chains on SWNT surfaces. We found that continuous Pd and Pd/Ni chains form on SWNTs with geometries close to stable geometries in the isolated chains. Ni alloying improves stability of the chains owing to a higher binding energy to both Pd and C atoms. The physical properties of SWNTs are significantly modified by chain functionalization. SWNT(10,0) is transformed to metal by either Pd or alloy chains, or to a smaller band gap semiconductor, depending on the Pd binding site. From calculations for H(2) interactions with the optimized chain-SWNT systems, the adsorption energy per H atom is found to be about 2.6 times larger for Pd/Ni chain-functionalized SWNTs than for pure Pd chain-functionalized SWNTs. Band structure calculations show that the SWNT(10,0) reverts back to semiconductor and SWNT(6,6) has reduced density of states at the Fermi level upon H(2) adsorption. This result is consistent with the experimentally observed increase of electrical resistance when Pd-coated SWNTs are used as H(2) sensing materials. Finally, our results suggest that Pd/Ni-SWNT materials are potentially good H(2)-sensing materials.     

Smart assembly behaviors of hydroxypropylcellulose-graft-poly(4-vinyl pyridine) copolymers in aqueous solution by thermo and pH stimuli

Thermo- and pH-sensitive graft copolymers, hydroxypropylcellulose-graft-poly(4-vinyl pyridine) (HPC-g-P4VP), were synthesized via atom transfer radical polymerization (ATRP) and characterized. The thermo- and pH-induced micellization and stimuli-responsive properties of HPC-g-P4VP graft copolymers in aqueous solution were investigated by transmittance, (1)H NMR, dynamic light scattering (DLS), and so on. For the pH-induced micellization, the P4VP side chains collapse to form the core of the micelles, and the HPC backbones stay in the shell to stabilize the micelles. In the case of thermoinduced micellization, the HPC backbones collapse to form the core of the micelles that was stabilized by the P4VP side chains in the shell upon heating. What's more, the cloud point of the HPC-g-P4VP copolymers in the aqueous solution could be finely tuned by changing the length of P4VP side chains or the pH values. In acidic water, the longer the side chains, the higher the cloud point. For those HPC-g-P4VP copolymers with short side chains, for example, HPC0.05-g-P4VP(3), the lower pH correlates a higher cloud point. The thermo- or pH-induced micelles also have the pH- or thermosensitivity due to their P4VP or HPC shells.     

Structure and stability of Langmuir-Blodgett-Kuhn multilayers containing “hairy-rod” copolymers

The microstructure and thermal stability of Langmuir-Blodgett-Kuhn multilayers containing rod-like polyglutamate copolymers having flexible aliphatic side chains have been studied with x-ray and neutron reflectometry. Upon annealing at 84°C the multilayer structure changes in a manner which is dependent upon the degree of orientation of the rod-like backbones and therefore upon the flow dynamics of the deposition. A sample deposited with a highly convergent flow loses the bilayer structure induced by deposition, whereas samples with less highly aligned backbones may not undergo this relaxation as readily.     

Remote Control of One-Handed Helicity in Polyacetylenes through Flexible Spacers in Water: Impact of the Spacer Length

We report the unprecedented sergeants and soldiers (S&S)-type remote control of one-handed helicity in copolymers of chiral/achiral biphenylylacetylenes bearing amphiphilic oligo(ethylene glycol) (OEG) side chains. A small amount of chiral binaphthyl residues (≤10 mol %) introduced at the terminal of the achiral OEG spacers as many as 80 bonds away from the polymer backbones induced a complete one-handed helix in water through preferential intramolecular encapsulation of the binaphthyl groups within a cavity of the copolymers. A fully one-handed helix can be induced virtually independent of the OEG spacer length and concentrations. At a specific spacer length, however, its helix-sense was inverted. The copolymers also form an excess one-handed helix in organic solvents in an OEG spacer-length dependent manner, yet far from the polymer backbones. We show the superiority of the present covalent-bond driven S&S-type remote helicity control over the corresponding noncovalent helicity induction approach.     

Photoinduced Morphological Transformations of Soft Nanotubes

In water, synthetic amphiphiles composed of a photoresponsive azobenzene moiety and an oligoglycine hydrogen‐bonding moiety selectively self‐assembled into nanotubes with solid bilayer membranes. The nanotubes underwent morphological transformations induced by photoisomerization of the azobenzene moiety within the membranes, and the nature of the transformation depended on the number of glycine residues in the oligoglycine moiety (i.e., on the strength of intermolecular hydrogen bonding). Upon UV‐light irradiation of nanotubes prepared from amphiphiles with the diglycine residue, trans‐to‐cis isomerization induced a transformation from nanotubes (inner diameter (i.d.) 7 nm), several hundreds of nanometers to several tens of micrometers in length, to imperfect nanorings (i.d. 21–38 nm). The cis‐to‐trans isomerization induced by continuous visible‐light irradiation resulted in the stacking of the imperfect nanorings to form nanotubes with an i.d. of 25 nm and an average length of 310 nm, which were never formed by a self‐assembly process. Time‐lapse fluorescence microscopy enabled us to visualize the transformation of nanotubes with an i.d. of 20 nm (self‐assembled from amphiphiles with the monoglycine residue) to cylindrical nanofibers with an i.d. of 1 nm; shrinkage of the hollow cylinders started at the two open ends with simultaneous elongation in the direction of the long axis.