Fast and accurate grid representations for atom‐based docking with partner flexibility

Macromolecular docking methods can broadly be divided into geometric and atom‐based methods. Geometric methods use fast algorithms that operate on simplified, grid‐like molecular representations, while atom‐based methods are more realistic and flexible, but far less efficient. Here, a hybrid approach of grid‐based and atom‐based docking is presented, combining precalculated grid potentials with neighbor lists for fast and accurate calculation of atom‐based intermolecular energies and forces. The grid representation is compatible with simultaneous multibody docking and can tolerate considerable protein flexibility. When implemented in our docking method ATTRACT, grid‐based docking was found to be ∼35x faster. With the OPLSX forcefield instead of the ATTRACT coarse‐grained forcefield, the average speed improvement was >100x. Grid‐based representations may allow atom‐based docking methods to explore large conformational spaces with many degrees of freedom, such as multiple macromolecules including flexibility. This increases the domain of biological problems to which docking methods can be applied. © 2017 Wiley Periodicals, Inc.     

Medium modified fragmentation function: equivalence of the ACSX and QW formalisms in the high-Q2 region

We study the medium modified fragmentation function in high-energy heavy-ion collisions. We show that the ACSX and QW formalisms are equivalent to each other in the high-Q² limit in both theoretical and numerical aspects.     

Heavy-Ion Collisions: Experimental Highlights

Lattice QCD predicts a phase transition between hadronic matter and a system of deconfined quarks and gluons (the Quark Gluon Plasma) at high energy densities. Our current understanding of this new state of matter will be discussed with two key results from the Relativistic Heavy Ion Collider (RHIC).     

First and second coordination spheres in 8-azaxanthinato salts of divalent metal aquacomplexes – Ab initio and DFT study

The hydrogen bonding pattern in complexes of the type [M²⁺(H₂O)₆](dmax)₂ (M = Mn, Ni, Co, Zn, Cd, Hdmax = 1,3-dimethyl-8-azaxanthine), [M²⁺(H₂O)₄(py)₂](dmax)₂ (M = Mn, Co, Zn, Cd, py = pyridine) and [M²⁺(dmax)₂(H₂O)₂(py)₂]·2H₂O (M = Ni, Cu) were studied by ab initio (MP2/LANL2DZ//B3LYP/LANL2DZ) and density functional theory methods (B3LYP/LANL2DZ, B3LYP/6-31G^∗∗ and B3PW91/6-31G^∗∗). The investigation includes a variety of theoretical analyses, which include interaction energy, many body analyses, electron density analysis, topological analysis, Mulliken atomic charges, natural atomic charges and harmonic vibrational analysis. The geometrical parameters and vibrational frequencies of dmax (the mono anion of 1,3-dimethyl-8-azaxanthine), [M²⁺(H₂O)₆] (M = Mn, Ni, Co, Zn, Cd), [M²⁺(H₂O)₄·(py)₂] (M = Mn, Co, Zn, Cd) and the complexes, calculated by the theoretical methods, were compared with the recent X-ray crystallographic results and it was observed that the results are found to agree well with the crystallographic results. The present calculations provide an important physicochemical insight into metal cations with 1,3-dimethyl-8-azaxanthine. The results also reveal the active role of coordinated water molecules in modulating the binding of the cation through a specific network of hydrogen bonds. The topology of the motifs generated by these hydrogen bonds has been characterized, adapting to the second coordination sphere concepts usually applied to the first (monodentate, chelate, and bridge) coordination sphere. The optimized structures of the Cd²⁺, Zn²⁺ and Cu²⁺ complexes further interact among themselves in a less tight fashion to generate three dimensional structures (a tape-like hydrogen bond network). Finally these tape-like hydrogen bond network were optimized using the B3LYP/LANL2DZ basis set.     

Rotating Bose-Einstein condensate in an optical lattice: Formulation of vortex configuration for the ground state

We consider a rotating Bose-Einstein condensate in an optical lattice in the regime in which the system Hamiltonian can be mapped onto a Josephson junction array. In an approximate scheme where the couplings are assumed uniform, the ground state energy is formulated in terms of the vortex configuration. Application of the method for the ladder case presented and the results are compared with Monte-Carlo method.     

Reaction mechanism and rate constants of the CH+CH4 reaction: a theoretical study

Ab initio and density functional calculations have been performed to elucidate the mechanism of CH radical insertion into methane. The results show that the reaction can be viewed to occur via two stages. On the first stage, the CH radical approaches methane without large structural changes to acquire proper positioning for the subsequent stage, where H-migration occurs from CH₄ to CH, along with a C–C bond formation. Where the first stage ends and the second begins, a tight transition state was located using the B3LYP/6-311G(d,p) and MP4(SDQ)/6-311++G(d,p) methods. Using a rigid rotor – harmonic oscillator approach within transition state theory, we show that at the MP5/6-311++G(d,p)//MP4(SDQ)/6-311++G(d,p) level the calculated rate constants are in a reasonably good agreement with experiment in a broad temperature range of 145–581 K. Even at low temperatures, the insertion reaction bottleneck is found about the location of the tight transition state, rather than at long separations between the CH and CH₄ reactants. In addition, high level CCSD(T)-F12/CBS calculations of the remainder of the C₂H₅ potential energy surface predict the CH+CH₄ reaction to proceed via the initial insertion step to the ethyl radical which then can emit a hydrogen atom to form highly exothermic C₂H₄+H products.     

Rotationally resolved state-to-state photoelectron study of zirconium monoxide cation (ZrO+)

Using two-colour visible (Vis)–ultraviolet (UV) photoionisation and pulsed field ionisation–photoelectron (PFI–PE) methods, we have obtained cleanly rotationally resolved photoelectron spectra for ZrO⁺(X ²Δ_3/2,5/2; v⁺ = 0, 1, and 2). The rotation assignment of these state-to-state Vis–UV–PFI–PE spectra has allowed the unambiguous determination of the ground state term symmetry for ZrO⁺(X) to be ²Δ_3/2, and the adiabatic ionisation energy of ⁹⁰Zr¹⁶O, IE(⁹⁰Zr¹⁶O) = 54,948.3(8) cm^?1 [6.81272(10) eV]. The symmetry of the ionic ZrO⁺(X ²Δ_3/2) ground state determined here disagrees with that reported in previous experiments. The rotational and vibrational constants determined in this experiment for the ionic ⁹⁰Zr¹⁶O⁺(X ²Δ_3/2) ground state are: B_e⁺ = 0.4343(8) cm^?1 and α_e⁺ = 0.0019(5) cm^?1, and ω_e⁺ = 991.2(8) cm^?1 and ω_e⁺x_e⁺ = 3.5(8) cm^?1; and those for the ionic ⁹⁰Zr¹⁶O⁺(X ²Δ_5/2) excited spin-orbit state are: B_e⁺ = 0.4357(6) cm^?1 and α_e⁺ = 0.0022(4) cm^?1, and ω_e⁺ = 991.9(8) cm^?1 and ω_e⁺x_e⁺ = 3.6(8) cm^?1, respectively. Based on the latter B_e⁺ value, the equilibrium bond distances are determined to be r_e⁺ = 1.691(2) Å for ⁹⁰Zr¹⁶O⁺(X ²Δ_3/2) and r_e⁺ = 1.688(1) Å for ⁹⁰Zr¹⁶O⁺(X ²Δ_5/2). The IE(ZrO) along with the spectroscopic constants obtained here are valuable for benchmarking the ab initio quantum chemical calculations for energetic and structural predictions of ZrO/ZrO⁺.