Journal ArticleDOI
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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In this paper, the authors present an approach to generate electrostatic potential (ESP) derived charges for molecules, which optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule.Abstract:
We present a new approach to generating electrostatic potential (ESP) derived charges for molecules. The major strength of electrostatic potential derived charges is that they optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided, of course, that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule. Previously, the major weaknesses of these charges have been that they were not easily transferable between common functional groups in related molecules, they have often been conformationally dependent, and the large charges that frequently occur can be problematic for simulating intramolecular interactionsread more
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High-resolution X-ray structure of an acyl-enzyme species for the class D OXA-10, β-lactamase
Laurent Maveyraud,Dasantila Golemi-Kotra,Akihiro Ishiwata,Oussama Meroueh,Shahriar Mobashery,Jean-Pierre Samama +5 more
TL;DR: β-Lactamases are resistance enzymes for β-lactam antibiotics that hydrolyze the β- lactam moieties of these antibiotics, rendering them inactive.
Journal ArticleDOI
Structure, conformation and biological activity of a novel lipodepsipeptide from Pseudomonas corrugata: cormycin A.
Andrea Scaloni,Mauro Dalla Serra,Pietro Amodeo,Luisa Mannina,Rosa Maria Vitale,Anna Laura Segre,Oscar Cruciani,Francesca Lodovichetti,Maria Luigia Greco,Alberto Fiore,Monica Gallo,Chiara D'Ambrosio,M. Coraiola,Gianfranco Menestrina,Antonio Graniti,Vincenzo Fogliano +15 more
TL;DR: The structure of a novel lipodepsipeptide, cormycin A, produced in culture by the tomato pathogen Pseudomonas corrugata was elucidated by combined protein chemistry, mass spectrometry and two-dimensional NMR procedures, suggesting that c Cormycin derivatives could find promising applications, either as antifungal compounds for topical use or as post-harvest biocontrol agents.
Journal ArticleDOI
United-atom acyl chains for CHARMM phospholipids.
TL;DR: An implicit-hydrogen model for saturated and monounsaturated acyl chains, aimed at complementing the all-atom CHARMM27 model for phospholipid headgroups is proposed, which accelerates a typical bilayer simulation by about 50% while sacrificing a minimal amount of detail with respect to the fully atomistic description.
Journal ArticleDOI
Coordination-Directed Self-Assembly of M12L24 Nanocage: Effects of Kinetic Trapping on the Assembly Process
TL;DR: The spontaneous formation of spherical complex M12L24, which is composed of 12 palladium ions and 24 bidentate ligands, is demonstrated by molecular dynamics simulations by demonstrating the kinetic trapping behaviors sensitively depend on the bend angle of ligands and the metal-ligand binding strength.
Journal ArticleDOI
Removal of Azo Dyes: Intercalation into Sonochemically Synthesized NiAl Layered Double Hydroxide
Madhavi N. Pahalagedara,Milinda Samaraweera,Saminda Dharmarathna,Chung-Hao Kuo,Lakshitha Pahalagedara,José A. Gascón,Steven L. Suib +6 more
TL;DR: In this paper, a sonochemical method was employed in the synthesis of nickel aluminum layered double hydroxides (NiAl-LDH) and the materials were used as adsorbents for the removal of the reactive azo dye, Remazol Brilliant Violet (RBV-5r).
References
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Journal ArticleDOI
The MIDAS display system
TL;DR: At the core of MIDAS is a hierarchical database system, designed specifically for macromolecules, that is both compact in its storage requirements and fast in its data access.