Pressure distributions and shock shapes for 12.84 deg/7 deg on-axis and bent-nose biconics in air at Mach 6

Pressure distributions and shock shapes on a spherically blunted, 12.84 deg /7 deg on axis biconic and a spherically blunted, 12.84 deg/7 deg bent nose biconic at Mach 6 in air were measured. The angle of attack, referenced to the axis of aft cone, was varied from 0 deg to 25 deg in nominal 5 deg increments. Two values of free stream Reynolds number based on model length were tested. Predictions from simple, theories and from a supersonic, three dimensional, external invsicid code (STEIN) are compared with measured values. Predicted STEIN shock shapes and windward pressures are in agreement with measured values for both biconics over the present range of angle of attack

Embedded density functional theory for covalently bonded and strongly interacting subsystems

Embedded density functional theory (e-DFT) is used to describe the electronic structure of strongly interacting molecular subsystems. We present a general implementation of the Exact Embedding (EE) method [J. Chem. Phys. 133, 084103 (2010)] to calculate the large contributions of the nonadditive kinetic potential (NAKP) in such applications. Potential energy curves are computed for the dissociation of Li^+–Be, CH_3–CF_3, and hydrogen-bonded water clusters, and e-DFT results obtained using the EE method are compared with those obtained using approximate kinetic energy functionals. In all cases, the EE method preserves excellent agreement with reference Kohn–Sham calculations, whereas the approximate functionals lead to qualitative failures in the calculated energies and equilibrium structures. We also demonstrate an accurate pairwise approximation to the NAKP that allows for efficient parallelization of the EE method in large systems; benchmark calculations on molecular crystals reveal ideal, size-independent scaling of wall-clock time with increasing system size

Tables and charts of equilibrium thermodynamic properties of ammonia for temperatures from 500 to 50,000 K.

Equilibrium thermodynamic properties for pure ammonia were generated for a range of temperature from 500 to 50,000 K and pressure from 0.01 to 40 MN/sq m and are presented in tabulated and graphical form. Properties include pressure, temperature, density, enthalpy, speed of sound, entropy, molecular-weight ratio, specific heat at constant pressure, specific heat at constant volume, isentropic exponent, and species mole fractions. These properties were calculated by the method which is based on minimization of the Gibbs free energy. The data presented herein are for an 18-species ammonia model. Heats of formation and spectroscopic constants used as input data are presented. Comparison of several thermodynamic properties calculated with the present program and a second computer code is performed for a range of pressure and for temperatures up to 30,000 K

Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)]

We show that the two phase points considered in the recent simulations of liquid para hydrogen by Hone and Voth lie in the liquid-vapor coexistence region of a purely classical molecular dynamics simulation. By contrast, their phase point for ortho deuterium was in the one-phase liquid region for both classical and quantum simulations. These observations are used to account for their report that quantum mechanical effects enhance the diffusion in liquid para hydrogen and decrease it in ortho deuterium

Symplectic quaternion scheme for biophysical molecular dynamics

Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit condition for an integrator to possess a conserved quantity, an explicit expression for the conserved quantity of a symplectic integrator, the latter following and in accord with Calvo and Sanz-Sarna, Numerical Hamiltonian Problems (1994), and extension of the explicit expression to general systems with a flat phase space

An Unusual Hydrogen Migration/C−H Activation Reaction with Group 3 Metals

A novel hydrogen migration from the phenyl ring to the pyridine ring of an yttrium pyridyl complex supported by a 1,1′-ferrocene diamide ligand is reported. Density functional theory calculations were instrumental in probing the mechanism for this transformation

Reaction of Group III Biheterocyclic Complexes

Group III alkyl complexes supported by a ferrocene diamide ligand (1,1′-fc(NSitBuMe_2)_2) have been found to be reactive toward aromatic N-heterocycles such as 1-methylimidazole and pyridines. These reactions were investigated experimentally and computationally. An initial C−H activation event is followed by a coupling reaction to form biheterocyclic complexes, in which one of the rings is dearomatized. In the case of 1-methylimidazole, the biheterocyclic compound could not be isolated and further led to an imidazole ring-opened product; in the case of pyridines, it transformed into an isomer with extended conjugation of double bonds. Mechanisms for both reactions are proposed on the basis of experimental and computational results. DFT calculations were also used to show that an energetically accessible pathway for the ring-opening of pyridines exists

Enhancing Cation Diffusion and Suppressing Anion Diffusion via Lewis-Acidic Polymer Electrolytes

Solid polymer electrolytes (SPEs) have the potential to increase both the energy density and stability of lithium-based batteries, but low Li^+ conductivity remains a barrier to technological viability. SPEs are designed to maximize Li^+ diffusivity relative to the anion while maintaining sufficient salt solubility. It is thus remarkable that poly(ethylene oxide) (PEO), the most widely used SPE, exhibits Li^+ diffusivity that is an order of magnitude smaller than that of typical counterions at moderate salt concentrations. We show that Lewis-basic polymers like PEO favor slow cation and rapid anion diffusion, while this relationship can be reversed in Lewis-acidic polymers. Using molecular dynamics, polyboranes are identified that achieve up to 10-fold increases in Li^+ diffusivities and significant decreases in anion diffusivities, relative to PEO in the dilute-ion regime. These results illustrate a general principle for increasing Li^+ diffusivity and transference number with chemistries that exhibit weaker cation and stronger anion coordination

Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

During DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates. The dynamics of this process are crucial to the overall effectiveness of catalysis. Although Xray crystal structures of DNA polymerase I with substrate dNTPs have revealed key structural states along the catalytic pathway, solution fluorescence studies indicate that those key states are populated in the absence of substrate. Herein, we report the first atomistic simulations showing the conformational changes between the closed, open, and ajar conformations of DNA polymerase I in the binary (enzyme:DNA) state to better understand its dynamics. We have applied long time-scale, unbiased molecular dynamics to investigate the opening process of the fingers domain in the absence of substrate for B. stearothermophilis DNA polymerase in silico. These simulations are biologically and/or physiologically relevant as they shed light on the transitions between states in this important enzyme. All closed and ajar simulations successfully transitioned into the fully open conformation, which is known to be the dominant binary enzyme-DNA conformation from solution and crystallographic studies. Furthermore, we have detailed the key stages in the opening process starting from the open and ajar crystal structures, including the observation of a previously unknown key intermediate structure. Four backbone dihedrals were identified as important during the opening process, and their movements provide insight into the recognition of dNTP substrate molecules by the polymerase binary state. In addition to revealing the opening mechanism, this study also demonstrates our ability to study biological events of DNA polymerase using current computational methods without biasing the dynamics