We report on the development and validation of the OPLS4 force field. OPLS4 builds upon our previous work with OPLS3e to improve model accuracy on challenging regimes of drug-like chemical space that includes molecular ions and sulfurcontaining moieties. A novel parametrization strategy for charged species, which can be extended to other systems, is introduced. OPLS4 leads to improved accuracy on benchmarks that assess small-molecule solvation and protein−ligand binding.

AutoQSAR demonstrates similar or better predictive performance as compared with published results for four of the six endpoints while requiring minimal human time and expertise.

We establish the requisite design for aryleneethynylene polymers that give rise to single-handed helical wrapping of single-walled carbon nanotubes (SWNTs). Highly charged semiconducting polymers that utilize either an (R)- or (S)-1,1'-bi-2-naphthol component in their respective conjugated backbones manifest HRTEM and AFM images of single-chain-wrapped SWNTs that reveal significant preferences for the anticipated helical wrapping handedness; statistical analysis of these images, however, indicates that ∼20% of the helical structures are formed with the "unexpected" handedness. CD spectroscopic data, coupled with TDDFT-based computational studies that correlate the spectral signatures of semiconducting polymer-wrapped SWNT assemblies with the structural properties of the chiral 1,1'-binaphthyl unit, suggest strongly that two distinct binaphthalene SWNT binding modes, cisoid-facial and cisoid-side, are possible for these polymers, with the latter mode responsible for inversion of helical chirality and the population of polymer-SWNT superstructures that feature the unexpected polymer helical wrapping chirality at the nanotube surface. Analogous aryleneethynylene polymers were synthesized that feature a 2,2'-(1,3-benzyloxy)-bridged (b)-1,1'-bi-2-naphthol unit: this 1,1'-bi-2-naphthol derivative is characterized by a bridging 2,2'-1,3 benzyloxy tether that restricts the torsional angle between the two naphthalene subunits along its C1-C1' chirality axis to larger, oblique angles that facilitate more extensive van der Waals contact of the naphthyl subunits with the nanotube. Similar microscopic, spectroscopic, and computational studies determine that chiral polymers based on conformationally restricted transoid binaphthyl units direct preferential facial binding of the polymer with the SWNT and thereby guarantee helically wrapped polymer-nanotube superstructures of fixed helical chirality. Molecular dynamics simulations provide an integrated picture tying together the global helical superstructure and conformational properties of the binaphthyl units: a robust, persistent helical handedness is preferred for the conformationally restricted transoid binaphthalene polymer. Further examples of similar semiconducting polymer-SWNT superstructures are reported that demonstrate that the combination of single-handed helical wrapping and electronic structural modification of the conjugated polymer motif opens up new opportunities for engineering the electro-optic functionality of nanoscale objects.

The MAX1 β-hairpin peptide (VKVKVKVK-V(D)PPT-KVKVKVKV-NH2) has been shown to form nanofibrils having a cross-section of two folded peptides forming a hydrophobic, valine-rich core, and the polymerized fibril exhibits primarily β-sheet hydrogen bonding.1-7 These nanofibrils form hydrogel networks through fibril entanglements as well as fibril branching.8 Fibrillar branching in MAX1 hydrogel networks provide the ability to flow under applied shear stress and immediately reform a hydrogel solid on cessation of shear. New β-hairpins were designed to limit branching during nanofibril growth because of steric specificity in the assembled fibril hydrophobic core. The nonturn valines of MAX1 were substituted by 2-naphthylalanine (Nal) and alanine (A) residues, with much larger and smaller side chain volumes, respectively, to obtain LNK1 (Nal)K(Nal)KAKAK-V(D)PPT-KAKAK(Nal)K(Nal)-NH2. LNK1 was targeted to self-associate with a specific "lock and key" complementary packing in the hydrophobic core in order to accommodate the Nal and Ala residue side chains. The experimentally observable manifestation of reduced fibrillar branching in the LNK1 peptide is the lack of solid hydrogel formation after shear in stark contrast to the MAX1 branched fibril system. Molecular dynamics simulations provide a molecular picture of interpeptide interactions within the assembly that is consistent with the branching propensity of MAX1 vs LNK1 and in agreement with experimental observations.

The highly charged, conjugated polymer poly[p-{2,5-bis(3-propoxysulfonicacidsodiumsalt)}phenylene]ethynylene (PPES) has been shown to wrap single-wall carbon nanotubes (SWNTs), adopting a robust helical superstructure. Surprisingly, PPES adopts a helical rather than a linear conformation when adhered to SWNTs. The complexes formed by PPES and related polymers upon helical wrapping of a SWNT are investigated using atomistic molecular dynamics (MD) simulations in the presence and absence of aqueous solvent. In simulations of the PPES/SWNT system in an aqueous environment, PPES spontaneously takes on a helical conformation. A potential of mean force, ΔA(ξ), is calculated as a function of ξ, the component of the end-to-end vector of the polymer chain projected on the SWNT axis; ξ is a monotonic function of the polymer's helical pitch. ΔA(ξ) provides a means to quantify the relative free energies of helical conformations of the polymer when wrapped about the SWNT. The aqueous system possesses a global minimum in ΔA(ξ) at the experimentally observed value of the helical pitch. The presence of this minimum is associated with preferred side chain conformations, where the side chains adopt conformations that provide van der Waals contact between the tubes and the aliphatic components of the side chains, while exposing the anionic sulfonates for aqueous solvation. The simulations provide a free energy estimate of a 0.2 kcal/mol/monomer preference for the helical over the linear conformation of the PPES/SWNT system in an aqueous environment.