Search results for "Non-covalent interaction"
showing 10 items of 74 documents
Quantum-Chemical Insights into the Self-Assembly of Carbon-Based Supramolecular Complexes
2018
Understanding how molecular systems self-assemble to form well-organized superstructures governed by noncovalent interactions is essential in the field of supramolecular chemistry. In the nanoscience context, the self-assembly of different carbon-based nanoforms (fullerenes, carbon nanotubes and graphene) with, in general, electron-donor molecular systems, has received increasing attention as a means of generating potential candidates for technological applications. In these carbon-based systems, a deep characterization of the supramolecular organization is crucial to establish an intimate relation between supramolecular structure and functionality. Detailed structural information on the se…
Mapping the fluorophilicity of a hydrophobic pocket: synthesis and biological evaluation of tricyclic thrombin inhibitors directing fluorinated alkyl…
2006
In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics f…
A Fluorine Scan at the Catalytic Center of Thrombin: CF, COH, and COMe Bioisosterism and Fluorine Effects on pKa and logD Values
2006
A series of 16 tricyclic thrombin inhibitors was prepared by using the 1,3-dipolar cycloaddition of azomethine ylides derived from 3- or 4-hydroxyproline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide as the key step. The terminal pyrrolidine ring of the inhibitors was systematically substituted to explore the potential bioisosteric behavior of C-F, C-OH, and C-OMe residues pointing into the environment of the catalytic center of a serine protease. X-ray crystal structure analyses revealed a distinct puckering preference of this ring. Substitution by F, HO, and MeO has a strong effect on the basicity of the adjacent pyrrolidine nitrogen center which originates from two sigma-indu…
Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections.
2015
In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the bas…
Magneto-structural and theoretical study of the weak interactions in a Mn(II) complex with a very unusual N,O-chelating coordination mode of 2-aminot…
2017
International audience; The Mn(II) complex {[Mn(atpa)(H2O)2]·H2O}n (1),with the dicarboxylate ligand 2-aminoterephthalic acid (H2atpa), has been synthesized and crystallographically, spectroscopically and magnetically characterized. Complex 1 shows a very unusual 1κ2N,O coordination mode of the aminoterephthalate dianion with the Mn(II) ion. One of the carboxylate groups shows a syn-anti-μ2-η1:η1 binding mode to form a 2D square grid. The magnetic properties of this compound can be very well reproduced with a regular S = 5/2 chain model with a very weak antiferromagnetic coupling constant of J = −0.2 cm−1 through the single syn-anti carboxylate bridges. EPR measurement also supports the exp…
A Discrete P⋅⋅⋅II⋅⋅⋅P Assembly: The Large Influence of Weak Interactions on the31P NMR Spectra of Phosphane–Diiodine Complexes
2006
Thioethers, except derivatives of [7-R-7,8-C2B9H11] , are more weakly coordinating ligands than phosphanes. This difference is evidenced by the I I distances in the spokeshaped charge-transfer (CT) complexes R2S·I2 and R3P·I2 (Figure 1). The I I distance is sensitive to the strength of the interaction between the s* LUMO orbital on I2 and the HOMO orbital of the donor atom: the stronger the donor, the longer the I I distance. In these spoke CT complexes, the I I distance varies from 3.2 0.2 7 in R3P·I2 adducts [5] to 2.80 0.05 7 in R2S·I2 adducts, [6] indicating the weaker donor character of the thioether group. Whereas extended I2 arrays, spoke adducts of I2, polyiodides, and other structu…
Association of 2-acylaminopyridines and benzoic acids. Steric and electronic substituent effect studied by XRD, solution and solid-state NMR and calc…
2013
Abstract Eight single crystal X-ray structures, solid-state NMR spectroscopic, and theoretical studies utilizing QTAIM methodology were used to characterize the 2-acyl (alkyl in acyl = methyl, ethyl, t-butyl, and 1-adamantyl) amino-6-R-pyridine/4-R′-benzoic acid (R,R′ = H or Me) cocrystals. As expected among alkyl groups 1-adamantyl due to its bulkiness has the most significant effect on the relative positions of molecules in cocrystals. In addition, the subtle electronic and steric effects by the methyl substituents were observed. The theoretical calculations with full geometry optimizations are in agreement with the experimental findings (geometry, energy of hydrogen bonds). Based on the …
ChemInform Abstract: Mukaiyama-Michael Reactions with trans-2,5-Diarylpyrrolidine Catalysts: Enantioselectivity Arises from Attractive Noncovalent In…
2014
The 2,5-diphenylpyrrolidine-catalyzed enantioselective Mukaiyama—Michael reaction between substituted furans and enals is studied.
Energy interactions in amyloid-like fibrils from NNQQNY.
2014
We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of t…
2-Acylamino-6-pyridones: breaking of an intramolecular hydrogen bond by self-association and complexation with double and triple hydrogenbonding coun…
2012
2-Acylamino-6-pyridones (acyl = RCO, where R = Me, Et, i-Pr, t-Bu, and 1-adamantyl) were previously characterized by X-ray diffractometry and solid-state NMR techniques by us. One of these compounds was used recently in organocatalysis. The series is now studied in solution and by computational methods recommended for noncovalent interactions (DFT/M05). These compounds showed interesting behavior during dilution and titration experiments monitored by (1)H NMR. 2-Acylamino-6-pyridones change their conformation at higher concentrations, forming double hydrogen-bonded dimers and trimers in which an uncommon steric effect is observed. To the best of our knowledge, this is the first example of s…