Journal ArticleDOI
Stacking interactions and intercalative DNA binding.
TLDR
Improved knowledge of stacking interactions may lead to a better understanding of the architecture and inherent flexibility of particular DNA sequences and may provide insight into the principles that dictate the structural changes and specificity patterns observed in the binding of some intercalating ligands to DNA.About:
This article is published in Methods.The article was published on 1998-03-01. It has received 102 citations till now. The article focuses on the topics: Base pair & Stacking.read more
Citations
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Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine.
TL;DR: The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems.
Journal ArticleDOI
Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study
David Reha,Martin Kabeláč,Filip Ryjáček,Jiri Sponer,Judit E. Šponer,Marcus Elstner,Sandor Suhai,Pavel Hobza +7 more
TL;DR: In this paper, isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6‘-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine-thymine (AT) and guanine-cytosine (GC) nucleic acid base pairs were investigated by means of a nonempirical correlated ab initio method.
Journal ArticleDOI
1H NMR investigation of solvent effects in aromatic stacking interactions
TL;DR: From these studies, the association of electron-rich and electron-deficient aedamer monomers was seen to be driven primarily by hydrophobic interactions in polar solvents, but the magnitude of these interactions is modulated to a significant extent by the geometry of the donor--acceptor complex.
Journal ArticleDOI
Anion−π Interactions with Fluoroarenes
Journal ArticleDOI
A Prototype for Graphene Material Simulation : Structures and Interaction Potentials of Coronene Dimers
Yan Zhao,Donald G. Truhlar +1 more
TL;DR: Graphene sheets are the building blocks of carbon nanotubes and a variety of functionalized nanomaterials as mentioned in this paper, and they can be used for computer-aided design of such materials or for the study of aromati...
References
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Journal ArticleDOI
Optimization by Simulated Annealing
TL;DR: There is a deep and useful connection between statistical mechanics and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters), and a detailed analogy with annealing in solids provides a framework for optimization of very large and complex systems.
Journal ArticleDOI
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
Journal ArticleDOI
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell,Piotr Cieplak,Piotr Cieplak,Christopher I. Bayly,Christopher I. Bayly,Ian R. Gould,Ian R. Gould,Kenneth M. Merz,Kenneth M. Merz,David M. Ferguson,David M. Ferguson,David C. Spellmeyer,David C. Spellmeyer,Thomas R. Fox,James W. Caldwell,Peter A. Kollman +15 more
TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
Book
NMR of proteins and nucleic acids
TL;DR: The NMR Assignment Problem in Biopolymers, two-Dimensional NMR With Proteins and Nucleic Acids, and Sequence-Specific Resonance Assignments.