The self-assembly of the C38H14-buckybowl, a fragment bowl of the C70 fullerene, has been studied with scanning tunneling microscopy on the Cu(111) surface. Isolated molecules adsorb bowl opening-up with the center C6 ring parallel to the surface. In extended 2D islands, however, 1/3 of the molecules are oriented such that the bowl opening points down. From a detailed analysis of relative orientation of the molecules, the nature of intermolecular lateral interactions is identified. In densely packed islands, π-π bonding between convex sides of the bowls dominate, while π-H bonding between rim and convex sides plays the important role in small molecular 2D clusters.
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http://dx.doi.org/10.1021/jacs.6b02412 | DOI Listing |
J Chem Inf Model
September 2021
Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, United States.
The spike protein of SARS-CoV-2 binds to the ACE2 receptor its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analyses at molecular, amino acid (AA), and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex for SARS-CoV and SARS-CoV-2 with its Alpha and Beta variants. Our study uses the molecular dynamics (MD) simulations with the molecular mechanics generalized Born surface area (MM-GBSA) method to predict the binding free energy (BFE) and to determine the actual interacting AAs, as well as two quantum chemical protocols based on the density functional theory (DFT) implementation.
View Article and Find Full Text PDFTalanta
August 2018
Collaborative Innovation Center of Chemistry for Energy Materials(iChEM), Shanghai Key Laboratory of Molecular Catalysis and Functional Material, Department of Chemistry and Laser Chemistry Institute, Fudan University, Shanghai 200433, China. Electronic address:
Cyclodextrins (CDs) are a class of macrocyclic molecules that have exhibited many promising applications in various fields. The knowledge of the complexation modes and recognition mechanisms of CDs with their guests are of paramount importance for rational design of more variants with controlled properties. Herein we investigated the binding conformations and the structural characteristics of α-/β-CD with three amino acids (AA, AA=Gly, L-Leu, L-Phe) in the gas phase by a combined experimental and computational approach.
View Article and Find Full Text PDFChemistry
March 2017
Departament de Ciència de Materials i Química Física, Universitat de Barcelona and IQTCUB, Av. Diagonal 645, 08028, Barcelona, Spain), E-mail.
Dithiazolyl (DTA)-based radicals have furnished many examples of organic spin-transition materials, some of them occurring with hysteresis and some others without. Herein, we present a combined computational and experimental study aimed at deciphering the factors controlling the existence or absence of hysteresis by comparing the phase transitions of 4-cyanobenzo-1,3,2-dithiazolyl and 1,3,5-trithia-2,4,6-triazapentalenyl radicals, which are prototypical examples of non-bistable and bistable spin transitions, respectively. Both materials present low-temperature diamagnetic and high-temperature paramagnetic structures, characterized by dimerized (⋅⋅⋅A-A⋅⋅⋅A-A⋅⋅⋅) and regular (⋅⋅⋅A⋅⋅⋅A⋅⋅⋅A⋅⋅⋅A⋅⋅⋅) π-stacks of radicals, respectively.
View Article and Find Full Text PDFChemistry
March 2017
Department of Chemistry, Indian Institute of Technology Madras, Chennai-, 600036, Tamil Nadu, India.
A design approach that incorporates structural requirements for the formation of a 1D assembly, fibril stability, and fibril-fibril interactions for gelation was attempted by using amino acid-based sulfamides with the general structure Aa-NH-SO -NH-Aa (Aa=amino acid). A preference for 1D assembly alone was not a sufficient condition for gelation, which became evident from studies involving sulfamide esters 1-5. Reducing the crystallization tendency without hindering unidirectional growth was executed through diacids of the sulfamide precursors with various amines that form an envelope around the sulfamide core through salt bridges.
View Article and Find Full Text PDFJ Phys Chem A
August 2015
Department of Chemistry, Savitribai Phule Pune University, Pune 411 007, India.
Amino acid ionic liquids (AAILs) have attracted significant attention in the recent literature owing to their ubiquitous applications in diversifying areas of modern chemistry, materials science, and biosciences. The present work focuses on unraveling the molecular interactions underlying AAILs. Electronic structures of ion pairs consisting of amino acid cations ([AA(+)], AA = Gly, Ala, Val, Leu, Ile, Pro, Ser, Thr) and their ester substituted derivatives [AAE(+)] interacting with nitrate anion [NO3(-)] have been obtained from the dispersion corrected M06-2x density functional theory.
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