Cooperativity in noncovalent interactions

AS Mahadevi, GN Sastry - Chemical reviews, 2016 - ACS Publications
After conquering the atomic structure about a century ago, chemists have been largely
interested in understanding the concept of chemical bond and the formation of a molecule …

Molecular clusters of π-systems: theoretical studies of structures, spectra, and origin of interaction energies

KS Kim, P Tarakeshwar, JY Lee - Chemical reviews, 2000 - ACS Publications
Much interest has been evinced on the properties of weakly bound van der Waals
complexes of π-systems because of their utility in diverse fields (Figure 1). 1-14 Theoretical …

Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes

S Paul, SK Bag, S Das, ET Harvill, C Dutta - Genome biology, 2008 - Springer
Background Halophilic prokaryotes are adapted to thrive in extreme conditions of salinity.
Identification and analysis of distinct macromolecular characteristics of halophiles provide …

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

J Šponer, J Leszczynski… - … : Original Research on …, 2001 - Wiley Online Library
This review summarizes results concerning molecular interactions of nucleic acid bases as
revealed by advanced ab initio quantum chemical (QM) calculations published in last few …

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs

J Šponer, P Jurecka, P Hobza - Journal of the American Chemical …, 2004 - ACS Publications
Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and
stability of nucleic acids. The study presents reference ab initio structures and interaction …

Thermodynamic parameters for DNA sequences with dangling ends

S Bommarito, N Peyret, JSL Jr - Nucleic acids research, 2000 - academic.oup.com
The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide
dangling ends on a Watson–Crick pair are reported. In most instances, dangling ends are …

Nature and magnitude of aromatic stacking of nucleic acid bases

J Šponer, KE Riley, P Hobza - Physical Chemistry Chemical Physics, 2008 - pubs.rsc.org
This review summarises recent advances in quantum chemical calculations of base-stacking
forces in nucleic acids. We explain in detail the very complex relationship between the gas …

Toward true DNA base-stacking energies: MP2, CCSD (T), and complete basis set calculations

P Hobza, J Šponer - Journal of the American Chemical Society, 2002 - ACS Publications
Stacking energies in low-energy geometries of pyrimidine, uracil, cytosine, and guanine
homodimers were determined by the MP2 and CCSD (T) calculations utilizing a wide range …

Potentials and algorithms for incorporating polarizability in computer simulations

SW Rick, SJ Stuart - Reviews in computational chemistry, 2002 - Wiley Online Library
Polarization refers to the redistribution of a particle's electron density due to an electric field.
In terms of molecular interactions, polarization leads to nonadditivity, since a molecule …

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4 ', 6-diaminide-2-phenylindole) and DNA base pairs. Ab …

D Řeha, M Kabelác, F Ryjácek, J Šponer… - Journal of the …, 2002 - ACS Publications
Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4, 6 '-
diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine⊙⊙⊙ …