An all-atom empirical energy function for the simulation of nucleic acids

AD MacKerell Jr, J Wiorkiewicz-Kuczera… - Journal of the …, 1995 - ACS Publications
Nucleic acidparameters are developed for the all-atomempirical energy function used in the
CHARMM program. The parameters were determined by use of results for model …

Surface-enhanced Raman spectroscopic and density functional theory study of adenine adsorption to silver surfaces

B Giese, D McNaughton - The Journal of Physical Chemistry B, 2002 - ACS Publications
The surface-enhanced Raman spectra (SERS) of adenine and three deuterated analogues
adsorbed on colloids, electrochemically roughened electrodes, and vacuum deposited …

Geometric and energetic consequences of prototropy for adenine and its structural models–a review

ED Raczyńska, M Makowski, M Hallmann… - RSC advances, 2015 - pubs.rsc.org
Heterocycles containing one or more amidine moieties {–NH–C (R) N–} such as adenine
and its building blocks, imidazole, 4-aminopyrimidine, and purine, are excellent examples of …

A DFT study of the water-assisted intramolecular proton transfer in the tautomers of adenine

J Gu, J Leszczynski - The Journal of Physical Chemistry A, 1999 - ACS Publications
High level quantum chemistry calculations have been applied in order to explore the
intramolecular proton transfer process in the tautomers of adenine. The presence of …

Chiral sum frequency generation spectroscopy detects double-helix dna at interfaces

EA Perets, KB Olesen, ECY Yan - Langmuir, 2022 - ACS Publications
Many DNA-based technologies involve the immobilization of DNA and therefore require a
fundamental understanding of the DNA structure–function relationship at interfaces. We …

Matrix isolation FT-IR studies and ab initio calculations of hydrogen-bonded complexes of molecules modeling cytosine or isocytosine tautomers. 1. Pyridine and …

A Destexhe, J Smets, L Adamowicz… - The Journal of Physical …, 1994 - ACS Publications
An experimental method is described for a vibrational spectroscopic study of the H-bonding
properties of cytosines and isocytosines in low-temperature inert matrices. The method …

On the participation of photoinduced N–H bond fission in aqueous adenine at 266 and 220 nm: a combined ultrafast transient electronic and vibrational absorption …

GM Roberts, HJB Marroux, MP Grubb… - The Journal of …, 2014 - ACS Publications
A combination of ultrafast transient electronic absorption spectroscopy (TEAS) and transient
vibrational absorption spectroscopy (TVAS) is used to investigate whether photoinduced N …

IR spectra of guanine and hypoxanthine isolated molecules

GG Sheina, SG Stepanian, ED Radchenko… - Journal of Molecular …, 1987 - Elsevier
High resolution spectra of guanine, hypoxanthine, isocytosine, 2-aminopyrimidine and their
deutero-and methyl derivatives obtained in Ar matrices by the low temperature IR …

Protonation of nucleic acid bases. A comprehensive post-Hartree− Fock study of the energetics and proton affinities

Y Podolyan, L Gorb, J Leszczynski - The Journal of Physical …, 2000 - ACS Publications
The results of an ab initio post-Hartree− Fock study of the protonation of all nucleic acid
bases are reported. Rare tautomers of guanine and cytosine, which coexist in the gas phase …

Vibrational spectra of nucleic acid bases and their Watson–Crick pair complexes

R Santamaria, E Charro, A Zacarias… - Journal of …, 1999 - Wiley Online Library
The vibrational spectra of the nucleic acid bases adenine, thymine, guanine, and cytosine
are calculated in the frame of density functional theory (DFT). In particular we use the Kohn …