ALADDIN is a computer program for the design or recognition of compounds that meet geometric, steric, and substructural criteria. ALADDIN searches a database of three-dimensional structures, marks atoms that meet substructural criteria, evaluates geometric criteria, and prepares a number of files that are input for molecular modification and coordinate generation as well as for molecular graphics. Properties calculated from the three-dimensional structure are described by either properties calculated from the molecule itself or from the molecule as compared to a reference molecule and associated surfaces. ALADDIN was used to design analogues to probe a bioactive conformation of a small molecule and a peptide, to test alternative superposition rules for receptor mapping of the D2 dopamine receptor, to recognize unexpected D2 dopamine agonist activity of existing compounds, and to design compounds to fit a binding site on a protein of known structure. We have found that series designed by ALADDIN show much more subtle variation in shape than do those designed by traditional methods and that compounds can be designed to be very close matches to the objective.
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Alkali cation-π interactions in aqueous systems, modulating supramolecular stereoisomerism of nanoscopic metal-organic capsules.
Nat Commun
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School of Chemistry & SFI AMBER Research Centre, Trinity College Dublin, The University of Dublin, College Green, Dublin, D02 PN40, Ireland.
Contrary to common chemical intuition, cation-π interactions can persist in polar, aqueous reaction solutions, rather than in dry non-coordinative solvent systems. This account highlights how alkali ion-π interactions impart distinctive structure-influencing supramolecular forces that can be exploited in the preparation of nanoscopic metal-organic capsules. The incorporation of alkali ions from polar solutions into molecular pockets promotes the assembly of otherwise inaccessible capsular entities whose structures are distinctive to those of common polyoxovanadate clusters in which {V=O} moieties usually point radially to the outside, shielding the molecular entities.
View Article and Find Full Text PDFIsotropic ↔ anisotropic surface geometry transitions induced by adsorbed surfactants at water/vapor interfaces.
J Chem Phys
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Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
Adsorbates at a water/vapor interface change the surface geometry through altered surface tension, yet detailed theoretical studies are relatively sparse, and many applications focus on ensemble average characteristics. Here, we demonstrate that different interpretations of surface geometry emerge when considering the distributions of surface curvature and orientation as a function of adsorbed surfactant concentration and sterics. At low surface densities, the tributyl phosphate (TBP) sorbed water/vapor surface has an increased presence of ridges that are defined by principal curvatures κ1 and κ2 of opposite signs yet close in magnitude.
View Article and Find Full Text PDFInfluence of Pnictogen and Ligand Framework on the Lewis Acidity and Steric Environment in Pnictogen Pincer Complexes.
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Department of Chemistry, Dalhousie University, 6243 Alumni Crescent, Halifax, B3H 4R2, NS, Canada.
Pnictogen pincer complexes are a fascinating class of compounds due to their dynamic molecular and electronic structures, and valuable stoichiometric or catalytic reactivity. As recognition of their unique chemistry has grown, so too has the library of pincer ligands employed and pnictogen centres engaged to prepare them. Here we computationally study how the choice of pincer ligand framework and pnictogen influence the electronic and steric outcomes within the complexes obtained.
View Article and Find Full Text PDFIntegrated Monomer Synthesis and Framework Assembly: Achieving Isoreticular Modulation of Hydrogen-Bonded Organic Frameworks.
Angew Chem Int Ed Engl
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State Key Laboratory of Chemical Safety, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
Systematic construction of isoreticular hydrogen-bonded organic frameworks (HOFs) promises tailored material properties crucial for diverse applications, yet is challenging due to the weak, flexible, and non-directional nature of hydrogen bonds. Herein, we develop an "integrated monomer synthesis-framework assembly" (ISA) methodology for constructing a series of isoreticular HOFs. Unlike traditional methods where monomers are first synthesized and then assembled into HOFs, the ISA system employs dicyandiamide rigid hydrogen-bonded hexameric clusters as connecting nodes to covalently react with planarized C-symmetric cyano-precursors (C-CPs) to generate diaminotriazine (DAT) monomers, while simultaneously inducing the directional assembly into isoreticular (6,3)-net hcb topological DAT-C-HOFs.
View Article and Find Full Text PDFStructure Prediction of Large RNAs with AlphaFold3 Highlights its Capabilities and Limitations.
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Department of Biochemistry & Molecular Biology, University of Iowa, United States of America. Electronic address:
DeepMind's AlphaFold3 webserver offers exciting new opportunities to make structural predictions of heterogeneous macromolecular systems. Here we attempt to apply AlphaFold3 to large RNA molecules whose 3D atomic structures are unknown but whose physical dimensions have been studied experimentally. One difficulty that we encounter is that models returned by AlphaFold3 often contain severe steric clashes and, less frequently, clear breaks in the phosphodiester backbone, with the probability of both events increasing with the length of the RNA.
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