Abraham's H-bonding parameters alpha and beta have been described in terms of a minimal set of readily obtainable molecular descriptors. These parameters are basically equilibrium constants for complexation of acids with a reference base (alpha) or bases with a reference acid (beta) measured in a non-hydrogen bonding solvent such as tetrachloromethane. The models were developed using partial least squares with a diverse dataset recently compiled by Platts et al., encompassing a wide range of hydrogen bond acids and bases in order to give a robust model. Although less accurate than the model of Platts et al. the descriptors used in this work avoid expensive supermolecule calculations, and allow prediction of hydrogen bonding characteristics from the isolated molecular wave function. These descriptors can then be generated for a large number of compounds, making them ideal for storage in a quantum isostere database (QID), the construction of which we initiated. The QID is a web-based tool developed to predict bioisosteric replacements in lead optimisation projects. The current descriptors provide hydrogen bonding characteristics of molecules of interest.

Download full-text PDF

Source
http://dx.doi.org/10.1039/b816321aDOI Listing

Publication Analysis

Top Keywords

prediction hydrogen
8
hydrogen bond
8
molecular descriptors
8
hydrogen bonding
8
bonding characteristics
8
descriptors
5
refined model
4
model prediction
4
hydrogen
4
bond acidity
4

Similar Publications

Although electrostatic catalysis can enhance the kinetics and selectivity of reactions to produce greener synthetic processes, the highly directional nature of electrostatic interactions has limited widespread application. In this study, the influence of oriented electric fields (OEF) on radical addition and atom abstraction reactions are systematically explored with ion-trap mass spectrometry using structurally diverse distonic radical ions that maintain spatially separated charge and radical moieties. When installed on rigid molecular scaffolds, charged functional groups lock the magnitude and orientation of the internal electric field with respect to the radical site, creating an OEF which tunes the reactivity across the set of gas-phase carbon-centred radical reactions.

View Article and Find Full Text PDF

Combining experiment and theory, the mechanisms of H2 activation by the potassium-bridged aluminyl dimer K2[Al(NON)]2 (NON = 4,5-bis(2,6-diisopropylanilido)-2,7-di-tertbutyl-9,9-dimethylxanthene) and its monomeric K+-sequestered counterpart have been investigated. These systems show diverging reactivity towards the activation of dihydrogen, with the dimeric species undergoing formal oxidative addition of H2 at each Al centre under ambient conditions, and the monomer proving to be inert to dihydrogen addition. Noting that this K+ dependence is inconsistent with classical models of single-centre reactivity for carbene-like Al(I) species, we rationalize these observations instead by a cooperative frustrated Lewis pair (FLP)-type mechanism (for the dimer) in which the aluminium centre acts as the Lewis base and the K+ centres as Lewis acids.

View Article and Find Full Text PDF

Molecular aggregation frequently occurs during material synthesis, cellular processes, and drug delivery systems, often resulting in decreased performance and efficiency. One major reason for such aggregation in an aqueous solution is hydrophobicity. While the basic understanding of the aggregation process of hydrophobic molecules from a thermodynamic standpoint is known, the present literature lacks a connection between the aggregation kinetics and the molecular basis of hydrophobicity.

View Article and Find Full Text PDF

Molecular Strain Accelerates Electron Transfer for Enhanced Oxygen Reduction.

J Am Chem Soc

January 2025

Department of Chemistry, State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, P. R. China.

Fe-N-C materials are emerging catalysts for replacing precious platinum in the oxygen reduction reaction (ORR) for renewable energy conversion. However, their potential is hindered by sluggish ORR kinetics, leading to a high overpotential and impeding efficient energy conversion. Using iron phthalocyanine (FePc) as a model catalyst, we elucidate how the local strain can enhance the ORR performance of Fe-N-Cs.

View Article and Find Full Text PDF

Protein Target Search Diffusion-association/dissociation Free Energy Landscape around DNA Binding Site with Flanking Sequences.

Biophys J

January 2025

Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:

In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!