Taba: A Tool to Analyze the Binding Affinity

Evaluation of ligand-binding affinity using the atomic coordinates of a protein-ligand complex is a challenge from the computational point of view. The availability of crystallographic structures of complexes with binding affinity data opens the possibility to create machine-learning models targeted to a specific protein system. Here, we describe a new methodology that combines a mass-spring system approach with supervised machine-learning techniques to predict the binding affinity of protein-ligand complexes. The combination of these techniques allows exploring the scoring function space, generating a model targeted to a protein system of interest. The new model shows superior predictive performance when compared with classical scoring functions implemented in the programs Molegro Virtual Docker, AutoDock4, and AutoDock Vina. We implemented this methodology in a new program named Taba. Taba is implemented in Python and available to download under the GNU license at https://github.com/azevedolab/taba . © 2019 Wiley Periodicals, Inc.     

Competition between Liquid-liquid De-mixing,Crystallization, and Glass Transition in Solutions of PLA of Different Stereochemistry and DEET

Liquid-liquid(L-L)de-mixing and vitrification of solutions of either crystallizable poly(L-lactic acid)(PLLA)or non-crystallizable poly(D/L-lactic acid)(PDLLA)with 50 m%N,N-diethyl-3-methylbenzamide(DEET)were analyzed by calorimetry and cloud-point measurements,which allows drawing conclusions about the effect of polymer stereochemistry on the phase behavior.Regardless of the PLA stereochemistry,vitrification of the solutions on fast cooling,hindering crystallization of PLLA,occurred below-20℃ and suppressed prior L-L de-mixing.The experimental results prove that crystallization in samples containing crystallizable PLLA,observed at around 55℃ on slow cooling,is not preceded by L-L de-mixing.     

pH Tuning of Water-Soluble Arylazopyrazole Photoswitches

Arylazopyrazoles are an emerging class of photoswitches with redshifted switching wavelength, high photostationary states, long thermal half-lives and facile synthetic access. Understanding pathways for a simple modulation of the thermal half-lives, while keeping other parameters of interest constant, is an important aspect for out-of-equilibrium systems design and applications. Here, it is demonstrated that the thermal half-life of a water-soluble PEG-tethered arylazo-bis(o-methylated)pyrazole (AAP) can be tuned by more than five orders of magnitude using simple pH adjustment, which is beyond the tunability of azobenzenes. The mechanism of thermal relaxation is investigated by thorough spectroscopic analyses and density functional theory (DFT) calculations. Finally, the concepts of a tunable half-life are transferred from the molecular scale to the material scale. Based on the photochromic characteristics of E- and Z-AAP, transient information storage is showcased in form of light-written patterns inside films cast from different pH, which in turn leads to different times of storage. With respect to prospective precisely tunable materials and time-programmed out-of-equilibrium systems, an externally tunable half-life is likely advantageous over changing the entire system by the replacement of the photoswitch.     

Aqueous Diels–Alder reactions for thermochemical storage and heat transfer fluids identified using density functional theory

Thermal storage and transfer fluids have important applications in industrial, transportation, and domestic settings. Current thermal fluids have relatively low specific heats, often significantly below that of water. However, by introducing a thermochemical reaction to a base fluid, it is possible to enhance the fluid's thermal properties. In this work, density functional theory (DFT) is used to screen Diels–Alder reactions for use in aqueous thermal fluids. From an initial set of 52 reactions, four are identified with moderate aqueous solubility and predicted turning temperature near the liquid region of water. These reactions are selectively modified through 60 total functional group substitutions to produce novel reactions with improved solubility and thermal properties. Among the reactions generated by functional group substitution, seven have promising predicted thermal properties, significantly improving specific heat (by as much as 30.5%) and energy storage density (by as much as 4.9%) compared to pure water.     

Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems

The most classic approach to the dynamics of an n-dimensional mechanical system constrained by d independent holonomic constraints is to pick explicitly a new set of (n − d) curvilinear coordinatesparametrizingthe manifold of configurations satisfying the constraints, and to compute the Lagrangian generating the unconstrained dynamics in these (n − d) configuration coordinates. Starting from this Lagrangian an unconstrained Hamiltonian H(q,p) on 2(n−d) dimensional phase space can then typically be defined in the standard way via a Legendre transform. Furthermore, if the system is in contact with a heat bath, the associated Langevin and Fokker-Planck equations can be introduced. Provided that an appropriate fluctuation-dissipation condition is satisfied, there will be a canonical equilibrium distribution of the Gibbs form exp(−βH) with respect to the flat measure dqdp in these 2(n − d) dimensional curvilinear phase space coordinates. The existence of (n − d) coordinates satisfying the constraints is often guaranteed locally by an implicit function theorem. Nevertheless in many examples these coordinates cannot be constructed in any tractable form, even locally, so that other approaches are of interest. In ambient space formulations the dynamics are defined in the full original n-dimensional configuration space, and associated 2n-dimensional phase space, with some version of Lagrange multipliers introduced so that the 2(n − d) dimensional sub-manifold of phase space implied by the holonomic constraints and their time derivative, is invariant under the dynamics. In this article we review ambient space formulations, and explain that for constrained dynamics there is in fact considerable freedom in how a Hamiltonian form of the dynamics can be constructed. We then discuss and contrast the Langevin and Fokker-Planck equations and their equilibrium distributions for the different forms of ambient space dynamics.     

Ultra‐Small Plutonium Oxide Nanocrystals: An Innovative Material in Plutonium Science

Apart from its technological importance, plutonium (Pu) is also one of the most intriguing elements because of its non‐conventional physical properties and fascinating chemistry. Those fundamental aspects are particularly interesting when dealing with the challenging study of plutonium‐based nanomaterials. Here we show that ultra‐small (3.2±0.9 nm) and highly crystalline plutonium oxide (PuO₂) nanocrystals (NCs) can be synthesized by the thermal decomposition of plutonyl nitrate ([PuO₂(NO₃)₂] ? 3 H₂O) in a highly coordinating organic medium. This is the first example reporting on the preparation of significant quantities (several tens of milligrams) of PuO₂ NCs, in a controllable and reproducible manner. The structure and magnetic properties of PuO₂ NCs have been characterized by a wide variety of techniques (powder X‐ray diffraction (PXRD), X‐ray absorption fine structure (XAFS), X‐ray absorption near edge structure (XANES), TEM, IR, Raman, UV/Vis spectroscopies, and superconducting quantum interference device (SQUID) magnetometry). The current PuO₂ NCs constitute an innovative material for the study of challenging problems as diverse as the transport behavior of plutonium in the environment or size and shape effects on the physics of transuranium elements.     

Fused Perylene–Phthalocyanine Macrocycles: A New Family of NIR‐Dyes with Pronounced Basicity

The synthesis and characterization of a new type of chromophore, namely PePc consisting of a central phthalocyanine core and four fused perylene–bisimide (PBI) units is described for the first time. The entire architecture represents a highly extended conjugated heterocyclic π‐system with C_4h symmetry. In order to guarantee pronounced solubility in organic solvents the corresponding PBI units were bay‐functionalized with tert‐butylphenoxy substituents. Next to the metal‐free macrocycle, PePcH₂, also metallated macrocycles PePcM (M=Zn, Ni, Pb, Ru, Fe) were synthesized. The extensive fusion of the corresponding aromatic building blocks to the very large extended π‐system leads to a very narrow HOMO–LUMO gap and as a consequence to transparency in the visible but light absorption in the NIR region. Significantly, the azomethine N‐atoms N1?N4 of PePcM and PePcH₂ are highly basic. The corresponding tetraprotonated systems can only be deprotonated with very strong non‐nucleophilic bases such as phosphazene bases. In the protonated forms PePcMH₄⁴⁺ and PePcMH₆⁴⁺ the absorption maximum is shifted back to the visible region due to the loss of conjugation. The experimental findings were corroborated with quantum mechanical calculations.     

Free-radical selective functionalization of 1,4-naphthoquinones by perfluorodiacyl peroxides

Perfluoroalkyl radicals, generated by thermal decomposition of perfluorodiacyl peroxides, react selectively with quinone rings of 1,4-naphthoquinones. In the presence of a non-conjugated alkene such as 1-hexene, perfluoroalkyl radicals add to the double bonds of the olefin forming a radical adduct, which selectively adds to the naphthoquinone ring. Several perfluorodiacyl peroxides have been synthesized and used for the direct and alkene-mediated functionalization of naphthoquinones. Geometrical parameters and electron density topology of all perfluorodiacyl peroxides have been calculated by the density functional formalism and quantum theory of atoms in molecules to attempt a rationalization of the experimental reactivity.     

The Influence of Exocyclic Stereochemistry on the Tethered Aminohydroxylation Reaction

A new strategy that employs an exocyclic stereocenter to effect diastereocontrol in the tethered aminohydroxylation (TA) reaction is applied to the stereoselective synthesis of a range of amino alcohols in good to excellent yields, and with anti selectivities of up to 20:1. The influence of the reaction conditions and substrate parameters on the level of diastereocontrol is described. Furthermore, an “inside alkoxy” model is employed to rationalize the sense and degree of stereoselectivity observed in these systems.