Experimental solvation free energies are nowadays commonly included as target properties in the validation and sometimes even calibration of condensed-phase force fields. However, this is often done a nonsystematic fashion, by considering available involving an arbitrary collection solutes limited set solvents (e.g., water, octanol, chloroform, cyclohexane, or hexane). Here, approach made more systematic introducing concept cross-solvation ΔsGA:B⊖ for N molecules that all liquid state under...

We recently introduced the CombiFF scheme [Oliveira et al., J. Chem. Theory Comput. 2020, 16, 7525], an approach for automated refinement of force-field parameters against experimental condensed-phase data large compound families. Using this scheme, once time-consuming task target-data selection and curation has been performed, optimization itself is both straightforward fast. As a result, provides ideal framework evaluating influence functional-form decisions on accuracy force field at...

Direct optimization against experimental condensed-phase properties concerning small organic molecules still represents the most reliable way to calibrate empirical parameters of a force field. However, compared corresponding calibration quantum-mechanical (QM) calculations isolated molecules, this approach is typically very tedious and time-consuming. The present article describes an integrated scheme for automated refinement force-field data, considering entire classes constructed using...

The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes organic molecules constructed using fragment library via combinatorial isomer enumeration. One peculiarity this that it relies on an electronegativity-equalization scheme to account induction effects within molecules, with values atomic hardness and electronegativity as electrostatic parameters, rather than partial charges themselves....

This article documents enu, a freely-downloadable, open-source and stand-alone program written in C++ for the enumeration of constitutional isomers stereoisomers molecular formula. The relies on graph theory to enumerate all given formula basis their canonical adjacency matrix. isomer are enumerated as well, automorphism group this list is then reported form SMILES strings within files XML format. specification molecule family interest very flexible code optimized computational efficiency....

Self-assembling of supramolecules composed benzene and cyclohexane tricarboxamide derivatives can form highly organized 1 D fibers exhibiting macrodipoles. The way pack in the condensed phase governs final properties supramolecular material, which macrodipoles be oriented parallel or antiparallel to each other, their magnitude tuned by additional intra-columnar dipole stabilization. X-ray structural elucidation these materials remains a real challenge due difficulty growing single crystals....

The level of accuracy that can be achieved by a force field is influenced choices made in the interaction-function representation and relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example model resolution, charge-derivation procedure, van der Waals combination rules, cutoff distance, treatment long-range interactions. Ideally, assessing effect given FFV on intrinsic force-field requires only specific changed this change...

Abstract The calibration of torsional interaction terms by fitting relative gas‐phase conformational energies against their quantum‐mechanical values is a common procedure in force‐field development. However, much less attention has been paid to the optimization third‐neighbor nonbonded parameters, despite strong coupling with torsions. This article introduces an algorithm termed LLS‐SC, aimed at simultaneously parametrizing and based on energies. It relies self‐consistent (SC) where each...

The CombiFF scheme is a workflow for the automated calibration of force-field parameters against condensed-phase experimental data considering simultaneously entire classes organic molecules. main steps this are: (i) selection molecule family; (ii) enumeration all isomers; (iii) query data; (iv) automatic construction molecular topologies; (v) iterative refinement family. In two recent articles, was applied to design GROMOS-compatible united-atom force fields saturated acyclic haloalkanes...

Abstract Invited for the cover of this issue is group Rodrigo Queiroz Albuquerque at Liverpool John Moores University. The image depicts an antiparallel interaction among macrodipoles inside supramolecular material, each arrow representing macrodipole a 1D column self‐assembled from tricarboxamide derivatives. Read full text article 10.1002/chem.201704548 .

Environmental DNA (eDNA) and invertebrate-derived (iDNA) have been increasingly recognized as a powerful tool for biodiversity assessment conservation management. However, because of uncertainties on the efficiency eDNA/iDNA approach in comparison to conventional methods, its use assess vertebrate diversity is still rare. Here we assessed methods survey across several type samplers, groups, location (tropical vs temperate zones), well be used proxy relative abundance or biomass different...