CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations, in a fashion consistent with the CHARMM27 all-atom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg(2+) and di-metal bridge complexes. Target data was generated via density-functional calculations at the B3LYP/6-311++G(3df,2p)// B3LYP/6-31++G(d,p) level. Partial atomic charges were initially derived from CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges. Lennard-Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle, and torsion parameters were derived from the density-functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the nonstandard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze-trapped catalytic intermediates, metal ion binding and occupation, and thio effects.     

Controlled stacking of charged block copolymer micelles

Using poly(acrylic acid)-b-poly(methyl acrylate)-b-polystyrene (PAA-b-PMA-b-PS) triblock copolymers or a mixture of different molecular weight PAA-b-PS diblock copolymers, stacks of polymeric micellar assemblies, such as disks and Y-shaped cylinders, were formed through intermicellar interactions. Whereas micelles hierarchically stacked together, micellar interactions within the stack defined a uniform micelle geometry and size for up to micrometers in length. The kinetic pathway dependence and stability of the stacked assemblies were studied, and possible intermicellar interactions between micelles within the stacks are proposed.     

Morphologies of microphase-separated conformationally asymmetric diblock copolymers

The equilibrium morphological behavior of a series of conformationally asymmetric linear diblock copolymers is characterized via small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). The linear diblock molecules of polyisoprene and poly(t-butylmethacrylate) (PtBMA) are prepared anionically over a range of PtBMA volume fractions 0.17 to 0.85. Solution light-scattering experiments are performed on PtBMA homopolymer at theta conditions, and the results were compared with PI data in the literature in order to characterize the degree of conformational asymmetry between the respective blocks. This conformational asymmetry is quantified by an ε of 0.75. The experimental results are compared with morphological behavior calculated utilizing self-consistent mean field theory for a diblock system with ε = 0.75. At middle to high PtBMA volume fractions, ϕ_PtBMA > 0.30, the experimental morphological behavior agrees well with the calculated behavior; the microphase boundaries are slightly shifted to higher volume fractions of the PtBMA block due to its larger Kuhn length. At ϕ_PtBMA < 0.30, however, discrepancies are found in the volume fraction dependence of experimentally determined morphological behavior and that calculated theoretically. Interestingly, extremely well-ordered cylindrical microstructures were observed for PI cylinder domains embedded in PtBMA matrices; these samples were prepared by solvent casting with no treatment, such as shearing, to enhance long-range order. These well-ordered cylinder structures contrast with PtBMA cylinders in a PI matrix on the opposite side of the phase diagram that have very poor long-range order. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2629–2643, 1997     

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

Benchmark calculations of proton affinities and gas-phase basicities of molecules most relevant to biological phosphoryl transfer reactions are presented and compared with available experimental results. The accuracy of proton affinity and gas-phase basicity results obtained from several multi-level model chemistries (CBS-QB3, G3B3, and G3MP2B3) and density-functional quantum models (PBE0, B1B95, and B3LYP) are assessed and compared. From these data, a set of empirical bond enthalpy, entropy, and free energy corrections are introduced that considerably improve the accuracy and predictive capability of the methods. These corrections are applied to the prediction of proton affinity and gas-phase basicity values of important biological phosphates and phosphoranes for which experimental data does not currently exist. Comparison is made with results from semiempirical quantum models that are commonly employed in hybrid quantum mechanical/molecular mechanical simulations. Data suggest that the design of improved semiempirical quantum models with increased accuracy for relative proton affinity values is necessary to obtain quantitative accuracy for phosphoryl transfer reactions in solution, enzymes, and ribozymes.     

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

Pseudorotation reactions of biologically relevant oxyphosphoranes were studied by using density functional and continuum solvation methods. A series of 16 pseudorotation reactions involving acyclic and cyclic oxyphosphoranes in neutral and monoanionic (singly deprotonated) forms were studied, in addition to pseudorotation of PF5. The effect of solvent was treated by using three different solvation models for comparison. The barriers to pseudorotation ranged from 1.5 to 8.1 kcal mol(-1) and were influenced systematically by charge state, apicophilicity of ligands, intramolecular hydrogen bonding, cyclic structure and solvation. Barriers to pseudorotation for monoanionic phosphoranes occur with the anionic oxo ligand as the pivotal atom, and are generally lower than for neutral phosphoranes. The OCH3 groups were observed to be more apicophilic than OH groups, and hence pseudorotations that involve axial OCH3/equatorial OH exchange had higher reaction and activation free energy values. Solvent generally lowered barriers relative to the gas-phase reactions. These results, together with isotope 18O exchange experiments, support the assertion that dianionic phosphoranes are not sufficiently long-lived to undergo pseudorotation. Comparison of the density functional results with those from several semiempirical quantum models highlight a challenge for new-generation hybrid quantum mechanical/molecular mechanical potentials for non-enzymatic and enzymatic phosphoryl transfer reactions: the reliable modeling of pseudorotation processes.     

Unique toroidal morphology from composition and sequence control of triblock copolymers

The mechanism by which the unique toroidal supramolecular assemblies were formed for triblock copolymers of acrylic acid (AA), methyl acrylate (MA), and styrene (S), PAA99-b-PMA73-b-PS66, was probed in this study by investigating the influences of the block copolymer compositions and sequences. Two triblock copolymers, PAA99-b-PMA73-b-PS66 and PAA99-b-PS76-b-PMA62, and two diblock copolymers, PAA99-b-PMA155 and PAA99-b-PS133, were studied under experimental solution-state conditions that involved a range of solvent/nonsolvent (tetrahydrofuran/water) compositions, each in the presence of 2,2'-(ethylenedioxy)bis(ethylamine). The resulting morphologies were determined by transmission electron microscopy. The failures to afford toroidal supramolecular assemblies from both diblock copolymers having comparable lengths of the total hydrophobic chain segment, either entirely PMA or entirely PS, and from the triblock copolymer having a reversed connection sequence for the hydrophobic (PMA and PS) segments demonstrate the unique self-assembly behaviors of triblock copolymers and the importance of the block copolymer sequence.     

Injectable solid peptide hydrogel as a cell carrier: effects of shear flow on hydrogels and cell payload

β-hairpin peptide-based hydrogels are a class of injectable solid hydrogels that can deliver encapsulated cells or molecular therapies to a target site via syringe or catheter injection as a carrier material. These physical hydrogels can shear-thin and consequently flow as a low-viscosity material under a sufficient shear stress but immediately recover back into a solid upon removal of the stress, allowing them to be injected as preformed gel solids. Hydrogel behavior during flow was studied in a cylindrical capillary geometry that mimicked the actual situation of injection through a syringe needle in order to quantify effects of shear-thin injection delivery on hydrogel flow behavior and encapsulated cell payloads. It was observed that all β-hairpin peptide hydrogels investigated displayed a promising flow profile for injectable cell delivery: a central wide plug flow region where gel material and cell payloads experienced little or no shear rate, and a narrow shear zone close to the capillary wall where gel and cells were subject to shear deformation. The width of the plug flow region was found to be weakly dependent on hydrogel rigidity and flow rate. Live-dead assays were performed on encapsulated MG63 cells 3 h after injection flow and revealed that shear-thin delivery through the capillary had little impact on cell viability and the spatial distribution of encapsulated cell payloads. These observations help us to fundamentally understand how the gels flow during injection through a thin catheter and how they immediately restore mechanically and morphologically relative to preflow, static gels.     

The interplay of metal and supporting ligand in labile coordination to pincer complexes of Ag(I)

The bis(imino)pyridine scaffold provides support for the synthesis and characterization of unique Ag(I) pincer complexes [{ArN=CPh}(2)(NPh)]Ag(+)(OTf)(-) (Ar = 2,5-(t)Bu(2)C(6)H(3)3; 2,6-(i)Pr(2)C(6)H(3) 4). The bonding interactions between the cation-anion and between the bis(imino)pyridine ligand and the Ag centre are presented. Coordination of pyridine, toluene, 2-butyne and cyclooctene to the Ag centre led to the isolation and crystallographic characterization of labile transient adduct species. Bonding analysis of the adducts revealed conventional ligand-Ag coordination and important unconventional electron donation from the ligand to a π*-orbital of the bis(imino)pyridine group.     

Synthesis of 7,7'-dihydroxy-8,8'-biquinolyl (azaBINOL) via Pd-catalyzed directed double C-H functionalization of 8,8'-biquinolyl: emergence of an atropos from a tropos state

7,7'-Dihydroxy-8,8'-biquinolyl (azaBINOL) was prepared from 2-chloroaniline in four steps: (1) the Skraup reaction, (2) Ni-catalyzed reductive coupling of 8-chloroquinoline, (3) Pd(II)-catalyzed double C-H functionalization of 8,8'-biquinolyl mediated by PhI(OAc)(2), and (4) saponification. During the third step, an axially chiral (atropos type) biaryl molecule was directly generated from an essentially achiral (tropos type) biaryl starting material.     

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

The structure and dynamics of the hepatitis delta virus ribozyme (HDVr) are studies using molecular dynamics simulations at several stages along its catalytic reaction path, including reactant, activated precursor, transition state mimic and product states, departing from an initial structure based on the C75U mutant crystal structure (PDB: 1VC7). Results of five 350 ns molecular dynamics simulations reveal a spontaneous rotation of U-1 that leads to an in-line conformation and support the role of protonated C75 as the general acid in the transition state. Our results provide rationale for the interpretation of several important experimental results, and make experimentally testable predictions regarding the roles of key active site residues that are not obvious from any available crystal structures.