Design of Peptides that Fold and Self-Assemble on Graphite.

The graphite-water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a ß-sheet-like conformation at the graphite-water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously, and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite-water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of 6-fold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence.

Thermodynamics of Adsorption on Graphenic Surfaces from Aqueous Solution.

Adsorption of organic molecules from aqueous solution to the surface of carbon nanotubes or graphene is an important process in many applications of these materials. Here we use molecular dynamics simulation, supplemented by analytical chemistry, to explore in detail the adsorption thermodynamics of a diverse set of aromatic compounds on graphenic materials, elucidating the effects of the solvent, surface coverage, surface curvature, defects, and functionalization by hydroxy groups. We decompose the adsorption free energies into entropic and enthalpic components and find that different classes of compounds-such as phenols, benzoates, and alkylbenzenes-can easily be distinguished by the relative contributions of entropy and enthalpy to their adsorption free energies. Overall, entropy dominates for the more hydrophobic compounds, while enthalpy plays the greatest role for more hydrophilic compounds. Experiments and independent simulations using two different force field frameworks (CHARMM and Amber) support the robustness of these conclusions. We determine that concave curvature is generally associated with greater adsorption affinity, more favorable enthalpy, and greater contact area, while convex curvature reduces both adsorption enthalpy and contact area. Defects on the graphene surfaces can create concave curvature, resulting in localized binding sites. As the graphene surface becomes covered with aromatic solutes, the affinity for adsorbing an additional solute increases until a complete monolayer is formed, driven by more favorable enthalpy and partially canceled by less favorable entropy. Similarly, hydroxylation of the surface leads to preferential adsorption of the aromatic solutes to remaining regions of bare graphene, resulting in less favorable adsorption entropy, but compensated by an increase in favorable enthalpic interactions.

1,3-Bis{(E)-[4-(di-methyl-amino)-benzyl-idene]amino}-propan-2-ol: chain structure formation via an O-H⋯N hydrogen bond.

The asymmetric unit of the title compound, C21H28N4O, consists of two unique mol-ecules linked by an O-H⋯N hydrogen bond. The conformation of both C=N bonds is E and the azomethine functional groups lie close to the plane of their associated benzene rings in each of the independent mol-ecules. The dihedral angles between the two benzene rings are 83.14 (4) and 75.45 (4)°. The plane of the one of the N(CH3)2 units is twisted away from the benzene ring by 18.8 (2)°, indicating loss of conjugation between the lone electron pair and the benzene ring. In the crystal structure, O-H⋯N hydrogen bonds together with C-H⋯O hydrogen bonds link neighbouring supra-molecular dimers into a three-dimensional network.

Crystal structure of 1,3-bis-[(E)-benzyl-idene-amino]-propan-2-ol.

In the title compound, C17H18N2O, the central carbon atom with the OH substituent and one of the (E)-benzyl-idene-amino substituents are disordered over two sets of sites with occupancies of 0.851 (4) and 0.149 (4). The relative positions of the two disorder components is equivalent to a rotation of approximately 60° about the C-N single bond. In the crystal, the mol-ecules are held together by O-H⋯N hydrogen bonds, forming simple C(5) chains along the b-axis direction. In addition, pairs of the chains are further aggregated by weak C-H⋯π inter-actions.

Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives.

Understanding the interaction of carbon nanomaterials with proteins is essential for determining the potential effects of these materials on health and in the design of biotechnology based on them. Here we leverage explicit-solvent molecular simulation and multidimensional free-energy calculations to investigate how adsorption to carbon nanomaterial surfaces affects the conformational equilibrium of alanine dipeptide, a widely used model of protein backbone structure. We find that the two most favorable structures of alanine dipeptide on graphene (or large carbon nanotubes) correspond to the two amide linkages lying in the same plane, flat against the surface, rather than the nonplanar α-helix-like and ß-sheet-like conformations that predominate in aqueous solution. On graphenic surfaces, the latter conformations are metastable and most often correspond to amide-π stacking of the N-terminal amide. The calculations highlight the key role of amide-π interactions in determining the conformational equilibrium. Lesser but significant contributions from hydrogen bonding to the high density interfacial water layer or to the hydroxy groups of hydroxylated graphene also define the most favorable conformations. This work should yield insight on the influence of carbon nanotubes, graphene, and their functionalized derivatives on protein structure.

Crystal structure of 1,3-bis-[(E)-4-meth-oxy-benzyl-idene-amino]-propan-2-ol.

The title Schiff base, C19H22N2O3, was synthesized via the condensation reaction of 1,3-di-amino-propan-2-ol with 4-meth-oxy-benzaldehyde using water as solvent. The mol-ecule exists in an E,E conformation with respect to the C=N imine bonds and the dihedral angle between the aromatic rings is 37.25 (15)°. In the crystal, O-H⋯N hydrogen bonds link the mol-ecules into infinite C(5) chains propagating along the a-axis direction. The packing of these chains is consolidated by C-H⋯O inter-actions and C-H⋯π short contacts, forming a three-dimensional network.

Crystal structure of 1,3-bis-(3-tert-butyl-2-hy-droxy-5-methyl-benz-yl)-1,3-diazinan-5-ol monohydrate.

In the title hydrate, C28H42N2O3·H2O, the central 1,3-diazinan-5-ol ring adopts a chair conformation with the two benzyl substituents equatorial and the lone pairs of the N atoms axial. The dihedral angle between the aromatic rings is 19.68 (38)°. There are two intra-molecular O-H⋯N hydrogen bonds, each generating an S(6) ring motif. In the crystal, classical O-H⋯O hydrogen bonds connect the 1,3-diazinane and water mol-ecules into columns extending along the b axis. The crystal structure was refined as a two-component twin with a fractional contribution to the minor domain of 0.0922 (18).

1,3-Bis(3-tert-butyl-2-hy-droxy-5-meth-oxy-benz-yl)hexa-hydro-pyrimidin-5-ol monohydrate.

The asymmetric unit of the title compound, C28H42N2O5·H2O, consists of one half of the organic mol-ecule and one half-mol-ecule of water, both of which are located on a mirror plane which passes through the central C atoms and the hydroxyl group of the heterocyclic system. The hydroxyl group at the central ring is disordered over two equally occupied positions. The six-membered ring adopts a chair conformation, and the 2-hy-droxy-benzyl substituents occupy the sterically preferred equatorial positions. The aromatic rings make dihedral angles of 75.57 (9)° with the mean plane of the heterocyclic ring. The dihedral angle between the two aromatic rings is 19.18 (10)°. The mol-ecular structure features two intra-molecular phenolic O-H⋯N hydrogen bonds with graph-set motif S(6). In the crystal, mol-ecules are connected via O-H⋯O hydrogen bonds into zigzag chains running along the a-axis direction.