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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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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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Force fields and molecular dynamics simulations
TL;DR: The basic concepts needed to understand the Molecular Dynamics technique are reviewed, including a general overview of the main algorithms employed to integrate the equations of motion, compute the long-range forces, work on different thermodynamic ensembles, or reduce the computational time.
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Novel Donepezil-Based Inhibitors of Acetyl- and Butyrylcholinesterase and Acetylcholinesterase-Induced β-Amyloid Aggregation
Pelayo Camps,Xavier Formosa,Carles Galdeano,Tània Gómez,Diego Muñoz-Torrero,Michele Scarpellini,Elisabet Viayna,Albert Badia,M. Victòria Clos,Antoni Camins,Mercè Pallàs,Manuela Bartolini,Francesca Mancini,Vincenza Andrisano,Joan Estelrich,Mònica Lizondo,Axel Bidon-Chanal,F. Javier Luque +17 more
TL;DR: A novel series of donepezil-tacrine hybrids designed to simultaneously interact with the active, peripheral and midgorge binding sites of acetylcholinesterase have been synthesized and tested, exhibiting IC50 values in the subnanomolar or low nanomolar range in most cases.
Journal ArticleDOI
New tacrine-huperzine A hybrids (huprines): highly potent tight-binding acetylcholinesterase inhibitors of interest for the treatment of Alzheimer's disease.
Pelayo Camps,El Achab R,Jordi Morral,Diego Muñoz-Torrero,Albert Badia,Josep-Eladi Baños,Nuria M. Vivas,Xavier Barril,Modesto Orozco,Francisco J. Luque +9 more
TL;DR: Molecular modeling simulations of the AChE-inhibitor complex provided a basis to explain the differences in inhibitory activity of these compounds and supported the tight-binding character of compounds (-)-20 and (-)-30 and showed their ability to cross the blood-brain barrier.
Journal ArticleDOI
Terminal π–π stacking determines three-dimensional molecular packing and isotropic charge transport in an A–π–A electron acceptor for non-fullerene organic solar cells
TL;DR: In this paper, the intermolecular arrangements in the ITIC film via atomistic molecular dynamics simulations were studied and it was shown that three-dimensional molecular packing is formed in the ItIC film through local intermolescular π-π stacking between the terminal acceptor units.
Journal ArticleDOI
Biomolecular electrostatics and solvation: a computational perspective.
Pengyu Ren,Jaehun Chun,Dennis G. Thomas,Michael J. Schnieders,Marcelo Marucho,Jiajing Zhang,Nathan A. Baker +6 more
TL;DR: The solvation of biomolecules with a computational biophysics view toward describing the phenomenon is discussed, and the main focus lies on the computational aspect of the models.
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.