Computational analysis of local membrane properties

In the field of biomolecular simulations, dynamics of phospholipid membranes is of special interest. A number of proteins, including channels, transporters, receptors and short peptides are embedded in lipid bilayers and tightly interact with phospholipids. While the experimental measurements report on the spatial and/or temporal average membrane properties, simulation results are not restricted to the average properties. In the current study, we present a collection of methods for an efficient local membrane property calculation, comprising bilayer thickness, area per lipid, deuterium order parameters, Gaussian and mean curvature. The local membrane property calculation allows for a direct mapping of the membrane features, which subsequently can be used for further analysis and visualization of the processes of interest. The main features of the described methods are highlighted in a number of membrane systems, namely: a pure dimyristoyl-phosphatidyl-choline (DMPC) bilayer, a fusion peptide interacting with a membrane, voltage-dependent anion channel protein embedded in a DMPC bilayer, cholesterol enriched bilayer and a coarse grained simulation of a curved palmitoyl-oleoyl-phosphatidyl-choline lipid membrane. The local membrane property analysis proves to provide an intuitive and detailed view on the observables that are otherwise interpreted as averaged bilayer properties.     

Synthesis and Investigation of the V‐shaped Tröger′s Base Derivatives as Hole‐transporting Materials

V‐shaped Tröger′s base core has been investigated as a central linking unit in the synthesis of new charge‐transporting materials for optoelectronic applications. The studied molecules have been synthesized in two steps from relatively inexpensive starting materials, and demonstrate high glass transition temperatures, good stability of the amorphous state, and comparatively high hole drift mobility (up to 0.011 cm² V^?1 s^?1).     

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large‐Scale Mutation Scan

The prediction of mutation‐induced free‐energy changes in protein thermostability or protein–protein binding is of particular interest in the fields of protein design, biotechnology, and bioengineering. Herein, we achieve remarkable accuracy in a scan of 762 mutations estimating changes in protein thermostability based on the first principles of statistical mechanics. The remaining error in the free‐energy estimates appears to be due to three sources in approximately equal parts, namely sampling, force‐field inaccuracies, and experimental uncertainty. We propose a consensus force‐field approach, which, together with an increased sampling time, leads to a free‐energy prediction accuracy that matches those reached in experiments. This versatile approach enables accurate free‐energy estimates for diverse proteins, including the prediction of changes in the melting temperature of the membrane protein neurotensin receptor 1.     

Hole-transporting hydrazones

This tutorial review covers recent contributions in the area of hole-transporting hydrazones, which are widely used in optoelectronic devices. It is addressed to students and researchers interested in the synthesis and properties of organic electroactive materials. The thermal, charge transport and other properties of electroactive hydrazones are compared and the relationships between the molecular structures and properties are emphasized. The first part discusses the low-molar-mass hydrazones and presents examples of their synthetic routes and chemical structures. In the second part, polymeric arylaldehyde hydrazones containing hydrazone moieties as the side substituents and in the main-chain are described.     

Synthesis and cyclizations of N-(2,3-, 3,4- and 3,5-dimethylphenyl)-beta-alanines

A series of 1-aryl substituted dihydro-, 5-methyl-dihydro- and 6-methyl-dihydro-2,4(1H,3H)pyrimidinediones and their 2-thio analogues were obtained by reaction of the corresponding beta-alanines or alpha-methyl- and beta-methyl-beta-alanines with urea or potassium thiocyanate. The reaction of N-(2,3- and 3,5-dimethylphenyl)-alpha-methyl-beta-alanines with ethyl acetoacetate gave 1-(2,3- or 3,5-dimethylphenyl)-2,5-dimethyl-1,4,5,6-tetrahydro-4(1H)pyridones. The combined spectral data obtained by (1)H-, (13)C-,(1)H/(13)C (HETCOR) NMR and IR provided useful information about the structure of the products synthesized in this work.     

Synthesis and Functionalization of 8‐Methyl‐2h‐pyrimido [2,1‐c][1,2,4]triazine‐3,6(1h,4h)‐dione

6‐Methyl‐2‐methylthio‐4‐oxopyrimidin‐3(4H)‐yl)acetohydrazide on heating in benzylamine undergo cyclization to 8‐methyl‐2H‐pyrimido[2,1‐c][1,2,4]triazine‐3,6(1H, 4H)‐dione, which under treatment with bromine in glacial acetic acid was converted to 7‐bromo substituted derivative and at reflux with Lawesson's reagent yielded 3‐thioxo compound. The latter reacted with primary and secondary amines to give 3‐amino substituted pyrimidotriazines and on alkylation—the corresponding S‐alkyl derivatives.     

Molecular vibrations-induced quantum beats in two-dimensional electronic spectroscopy

Quantum beats in nonlinear spectroscopy of molecular aggregates are often attributed to electronic phenomena of excitonic systems, while nuclear degrees of freedom are commonly included into models as overdamped oscillations of bath constituents responsible for dephasing. However, molecular systems are coupled to various high-frequency molecular vibrations, which can cause the spectral beats hardly distinguishable from those created by purely electronic coherences. Models containing damped, undamped, and overdamped vibrational modes coupled to an electronic molecular transition are discussed in this paper in context of linear absorption and two-dimensional electronic spectroscopy. Analysis of different types of bath models demonstrates how do vibrations map onto two-dimensional spectra and how the damping strength of the coherent vibrational modes can be resolved from spectroscopic signals.     

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design. However, their broad uptake and impact is held back by the notoriously complex setup of the calculations. Only a few tools other than the free energy perturbation approach by Schrödinger Inc. (referred to as FEP+) currently enable end-to-end application. Here, we present for the first time an approach based on the open-source software pmx that allows to easily set up and run alchemical calculations for diverse sets of small molecules using the GROMACS MD engine. The method relies on theoretically rigorous non-equilibrium thermodynamic integration (TI) foundations, and its flexibility allows calculations with multiple force fields. In this study, results from the Amber and Charmm force fields were combined to yield a consensus outcome performing on par with the commercial FEP+ approach. A large dataset of 482 perturbations from 13 different protein–ligand datasets led to an average unsigned error (AUE) of 3.64 ± 0.14 kJ mol⁻¹, equivalent to Schrödinger''s FEP+ AUE of 3.66 ± 0.14 kJ mol⁻¹. For the first time, a setup is presented for overall high precision and high accuracy relative protein–ligand alchemical free energy calculations based on open-source software.

Relative ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design.