Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD‐based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907‐atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc.     

针对连续变化法测定络合物稳定常数实验中可能出现的设计缺陷的讨论

连续变化法测定络合物组成和稳定常数是大学化学中的经典学生实验。但针对1：2和1：3的络合反应，实验教科书的设计中可能出现数据点过少也就是溶液配制过少的问题。如果按照要求配制溶液，由于没有完全反应的混合溶液，而其他混合溶液给出的数据又都呈良好的线性，就缺少了用来估算曲线的数据点，结果是，将没有足够的数据对稳定常数进行估算。对这种可能出现的数据点过少的实验设计的原因、结果和解决方法进行了探讨。     

Multifunctional triphenylamine polymers synthesized via direct (hetero) arylation polymerization

The design rules for creating multifunctional organic electronic materials are currently limited. By copolymerizing twisted triphenylamine (TPA) and electron rich dioxythiophene (XDOT) monomers via Direct (Hetero) Arylation Polymerization (DHAP), a set of polymers are obtained that perform as yellow to transmissive electrochromic (EC) films with up to 45% contrast, as well as in electroluminescent (EL) applications, achieving a luminance of ∼450 cd/m² in yellow‐green polymer light‐emitting diodes (PLEDs). In addition, polymerizing TPA with a donor‐acceptor‐donor monomer results in a low‐bandgap polymer that achieves power conversion efficiencies up to 2.5% when blended with PC₇₁BM in conventional organic photovoltaic (OPV) devices. Incorporation of TPA units into the polymer backbone largely breaks any aggregation and ordering in the solid‐state, leading to highly soluble materials that form smooth, reproducible thin films. The TPA unit also serves to break conjugation throughout the polymer backbone, providing precise control over optical and electronic properties through choice of comonomer. These results suggest that TPA copolymers can be useful for achieving multi‐functionality without sacrificing facile solution processability, making them promising candidates for multifunctional devices like dual EC/EL displays. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018 , 56, 147–153     

Stuffed Tridymite Structures: Synthesis,Structure, Second Harmonic Generation,Optical, and Multiferroic Properties

The stuffed tridymite structure Ba(Zn/Co)_1−xSi_1−xM_2xO₄ (M=Al³⁺ and Fe³⁺) is explored for the possible multiferroic behavior and to develop new inorganic colored materials. The compounds were synthesized by employing conventional solid-state chemistry methods in the temperature range 1100–1175 °C for 24 h. The powder X-ray diffraction (PXRD) and Rietveld refinement studies indicate that the compounds stabilize in the P63 space group (no. 173). The refinement results were also rationalized by employing Raman spectroscopic studies. The compounds were found to be second harmonic generation (SHG) active and show weak ferroelectric behavior. The co-substitution of Co²⁺ and Fe³⁺ in the structure gives rise to a weak ferromagnetic behavior to the compound, BaCo_0.75Si_0.75Fe_0.5O₄, making it a multiferroic material. The optical studies on the prepared compounds exhibited blue color (Co²⁺ in T_d geometry), purple color (Ni²⁺ in T_d geometry), and simultaneous substitution of Co²⁺ and Fe³⁺ gives rise to blue-green color owing to metal-to-metal charge transfer (MMCT) effect.     

Reaktion von Pyridin-2-Carbonsäure Mit Tetrabutylammonium-Tetrachloro-Nitridotechnetat(VI) Sowie Tetrabutylammonium-Tetrachlorooxotechnetat (V)

Abstract

The reaction of 2-pyridine carboxylic acid (Hpic) with (n-Bu₄N)[TcNCl₄] and (n-Bu₄N)[TcOCl₄] in ethanol and methanol, respectively, yields the dinuclear μ-oxo complex [(pic)₂NTc-O-TcN(pic)(Hpic)Cl] and the monomeric complex [TcO(pic)₂Cl].

Visible and infrared spectroscopy, ESR, ¹H-NMR and ⁹⁹Tc-NMR have been used to characterize the new compounds. The most important field of application for the new compounds synthesized is radiodiagnostics.     

Development and assessment of an intrusive polynomial chaos expansion-based continuous adjoint method for shape optimization under uncertainties

This article contributes to the development of methods for shape optimization under uncertainties, associated with the flow conditions, based on intrusive Polynomial Chaos Expansion (iPCE) and continuous adjoint. The iPCE to the Navier–Stokes equations for laminar flows of incompressible fluids is developed to compute statistical moments of the Quantity of Interest which are, then, compared with those obtained through the Monte Carlo method. The optimization is carried out using a continuous adjoint-enabled, gradient-based loop. Two different formulations for the continuous adjoint to the iPCE PDEs are derived, programmed, and verified. Intrusive PCE methods for the computation of the statistical moments require mathematical development, derivation of a new system of governing equations and their numerical solution. The development is presented for a chaos order of two and two uncertain variables and can be used as a guide to those willing to extend this development to a different set of uncertain variables or chaos order. The developed method and software, programmed in OpenFOAM, is applied to two optimization problems pertaining to the flow around isolated airfoils with uncertain farfield conditions.     

Spectral tuning of InGaAs/GaAs quantum dot infrared photodetectors with bandpass guided‐mode resonance filters

Quantum dot infrared photodetectors can be coupled with micro‐structured filters to create narrowband sensors. Guided‐mode resonance filters based on a high‐index dielectric slab can exhibit bandpass characteristics that are suitable for monolithic integration with focal‐plane arrays. Here, patterned Ge filters were integrated with InGaAs/GaAs quantum dot detectors to linearly tune their 77 K photoresponse peaks from 5.6 µm to 6.2 µm. The dark current was not influenced by these filters but the ability to narrow the photoresponse linewidth was limited by substrate scattering, which is often encountered with front‐side illumination architectures. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

2‐Methoxynaphthylnaphthoquinone and its solvate: synthesis and structure–properties relationship

Because of their unique visual optic and electronic properties, substituted quinones are commonly used as dyes and pigments; nevertheless, a theoretic background of relationship between the structures and optical properties of such compounds seems to be still undeveloped. Two crystalline forms of 2‐methoxynaphth‐1‐yl‐naphthoquinone (MNQ) have been synthesized and characterized by means X‐ray, NMR, UV–VIS, as well as, MS spectroscopy. The interpretation of intriguing optical properties of two crystalline forms of MNQ, based on detailed spectral and structural characterization, as well as, DFT and MP2 computations clearly connects the conformation of the molecules with their optical and electronic properties. Thus, flatter conformation, stabilized by crystal net force, favours the intense electron density transition from auxochrome to chromophore moiety (which corresponds excitation from HOMO to LUMO), as well as, favours the π‐stacking interaction, that eventually results in colour enhancement. At the same time, small molecules of solvents included into the crystal net allow molecules of arylnaphthoquinones to adopt less rigid conformation what has a dramatic optical outcome. Copyright © 2013 John Wiley & Sons, Ltd.     

Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β‐Hairpins

A popular strategy in the de novo design of stable β‐sheet structures for various biomedical applications is the incorporation of aromatic pairs at the non‐hydrogen‐bonding (NHB) position. However, it is important to explicitly understand how aryl pair packing at the NHB region is coordinated with backbone structural rearrangements, and to delineate the benefits and drawbacks associated with stereopositional choice of dissimilar aromatic pairs. Here, we probe the consequences of flipped Trp/Tyr pairs by using engineered permutants at the NHB position of dodecapeptide β‐hairpins, proximal and distal to the turn. Extensive conformational analysis of these peptides using NMR and CD spectroscopy reveal that a classic Edge‐to‐Face and Face‐to‐Edge geometry at the proximal and distal aromatic pairs, respectively, in YW‐WY, is the most stabilizing. Such a preferred packing geometry in YW‐WY results in a highly twisted β‐sheet backbone, with Trp always providing a ‘Face’ orientation to its dissimilar aromatic partner Tyr. Flipping the proximal and/or distal aromatic pair distorts the ideal T‐shaped geometry, and results in alternate aryl arrangements that can adversely affect strand twist and β‐sheet stability. Our study reveals the existence of a strong stereopositional influence on the packing of dissimilar aromatic pairs. Our findings highlight the importance of modeling physical interaction forces while designing protein and peptide structures for functional applications.