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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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Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
Karl T. Debiec,David S. Cerutti,Lewis R. Baker,Angela M. Gronenborn,David A. Case,Lillian T. Chong +5 more
TL;DR: The AMBER ff15ipq force field for proteins is the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent, and reproduces penta-alanine J-coupling constants exceptionally well.
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Making sense of enthalpy of vaporization trends for ionic liquids: new experimental and simulation data show a simple linear relationship and help reconcile previous data
Sergey P. Verevkin,Dzmitry H. Zaitsau,Vladimir N. Emel’yanenko,Andrei V. Yermalayeu,Christoph Schick,Hongjun Liu,Edward J. Maginn,Safak Bulut,Ingo Krossing,Roland S. Kalb +9 more
TL;DR: New experimental data, based on the concurring results from quartz crystal microbalance, thermogravimetric analyses, and molecular dynamics simulation have revealed a clear linear dependence of IL vaporization enthalpies on the chain length of the alkyl group on the cation.
Journal ArticleDOI
Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.
TL;DR: The absolute hydration free energy for a set of 239 neutral ligands spanning diverse chemical functional groups commonly found in drugs and drug-like candidates is calculated using the molecular dynamics free energy perturbation method with explicit water molecules, and compared to experimental data as well as its counterparts obtained using implicit solvent models.
Journal ArticleDOI
Single-molecule detection with a millimetre-sized transistor.
Eleonora Macchia,Kyriaki Manoli,Brigitte Holzer,Cinzia Di Franco,Matteo Ghittorelli,Fabrizio Torricelli,Domenico Alberga,Giuseppe Felice Mangiatordi,Gerardo Palazzo,Gaetano Scamarcio,Luisa Torsi,Luisa Torsi +11 more
TL;DR: A millimetre-sized field effect transistor capable of selective single-molecule Immunoglobulin-G detection is demonstrated and can revolutionize the current approach to protein detection.
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Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies
TL;DR: A method for optimizing solute-water van der Waals interactions to reproduce experimental solvation free energy data is introduced and applied to the optimization of a fixed charge force field and advanced water model (TIP4P-Ew).
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.