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A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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TLDR
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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Biological and molecular docking studies on coagulin-H: Human IL-2 novel natural inhibitor.
M. Ahmed Mesaik,Zaheer-ul-Haq,Shahnaz Murad,Zakiah Ismail,Noor Rain Abdullah,H Kauar Gill,Atta-ur-Rahman,Muhammad Yousaf,R Ali Siddiqui,Aqeel Ahmad,M. Iqbal Choudhary +10 more
TL;DR: Docking studies predicted that coagulin-H (1) binds to receptor binding site of IL-2 more effectively than prednisolone (2), a commonly used immune modulating drug and was identified as a potential immunosuppressive candidate.
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Solubility of glucose in tetrabutylammonium bromide based deep eutectic solvents: Experimental and molecular dynamic simulations
TL;DR: In this paper, the authors measured the solid-liquid equilibrium (SLE) of glucose in three novel low cost deep eutectic solvents (DES) namely tetrabutylammonium bromide [TBAB]-Imidazole, TTEB]-ethylene glycol, and [TTAB]-glycerol over the temperature ranging from 29915-35315 K. The experimental solubility data was correlated with the Apelblat empirical equation along with regression using local composition models.
Journal ArticleDOI
Structure and Thermodynamics of α-, β-, and γ-Cyclodextrin Dimers. Molecular Dynamics Studies of the Solvent Effect and Free Binding Energies†
TL;DR: In this paper, the α-, β-, and γ-cyclodextrin (CyDs) dimers were studied by molecular dynamics simulations in water as an explicit solvent.
Journal ArticleDOI
Computer Simulation for Adsorption of CO 2, N 2 and Flue Gas in a Mimetic MCM-41
TL;DR: In this paper, the full-atom MCM-41 model is constructed by caving cylindrical pores from an amorphous silica matrix and energetically optimized.
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Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands
S.G. Krimmer,Jonathan Cramer,Michael Betz,Veronica Fridh,Robert Karlsson,Andreas Heine,Gerhard Klebe +6 more
TL;DR: One of the designed inhibitors established the most pronounced water network of all inhibitors tested so far, composed of several fused water polygons, and showed 50-fold affinity enhancement with respect to the original methylated parent ligand.
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.