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 …

Numerical methods for electronic structure calculations of materials

Y Saad, JR Chelikowsky, SM Shontz - SIAM review, 2010 - SIAM
The goal of this article is to give an overview of numerical problems encountered when
determining the electronic structure of materials and the rich variety of techniques used to …

Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

P Mignon, S Loverix, J Steyaert… - Nucleic Acids …, 2005 - academic.oup.com
The interplay between aromatic stacking and hydrogen bonding in nucleobases has been
investigated via high-level quantum chemical calculations. The experimentally observed …

How well can new-generation density functional methods describe stacking interactions in biological systems?

Y Zhao, DG Truhlar - Physical Chemistry Chemical Physics, 2005 - pubs.rsc.org
We compare the performance of four recently developed DFT methods (MPW1B95,
MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods …

Nature of base stacking: reference quantum‐chemical stacking energies in ten unique B‐DNA base‐pair steps

J Šponer, P Jurečka, I Marchan… - … A European Journal, 2006 - Wiley Online Library
Base‐stacking energies in ten unique B‐DNA base‐pair steps and some other
arrangements were evaluated by the second‐order Møller–Plesset (MP2) method, complete …

Aromatic− aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues

S Aravinda, N Shamala, C Das… - Journal of the …, 2003 - ACS Publications
Aromatic− aromatic interactions between phenylalanine side chains in peptides have been
probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val …

Design and NMR characterization of active analogues of compstatin containing non-natural amino acids

B Mallik, M Katragadda, LA Spruce… - Journal of Medicinal …, 2005 - ACS Publications
We present new findings in our drug discovery effort to develop an anticomplement
therapeutic. We have designed several active analogues of compstatin by altering its amino …

An intramembrane aromatic network determines pentameric assembly of Cys-loop receptors

S Haeger, D Kuzmin, S Detro-Dassen, N Lang… - Nature structural & …, 2010 - nature.com
Cys-loop receptors are pentameric ligand-gated ion channels (pLGICs) that mediate fast
synaptic transmission. Here functional pentameric assembly of truncated fragments …

Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in …

J Isaksson, S Acharya, J Barman, P Cheruku… - Biochemistry, 2004 - ACS Publications
The structural preorganization of isosequential ssDNA and ssRNA hexamers d/r (GAAAAC)
1 [J. Am. Chem. Soc. 2003, 125, 9948] have been investigated by NMR and molecular …

Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids

LR Rutledge, LS Campbell-Verduyn… - Chemical physics letters, 2007 - Elsevier
MP2/6-31G∗(0.25) gas-phase potential energy surfaces of stacked dimers between the four
aromatic amino acids and the natural (DNA or RNA) nucleobases were considered as a …