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Title: Size-Expanded yDNA bases: An Ab Initio Study

Abstract

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show thatmore » yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.« less

Authors:
 [1];  [1];  [2];  [1]
  1. ORNL
  2. Wroclaw University of Technology, Poland
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Center for Nanophase Materials Sciences; Center for Computational Sciences
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC)
OSTI Identifier:
1003296
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Physical Chemistry B; Journal Volume: 110; Journal Issue: 12
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; AROMATICS; DNA; ELECTRONIC STRUCTURE; NUCLEIC ACIDS; SYNTHESIS

Citation Formats

Fuentes-Cabrera, Miguel A, Sumpter, Bobby G, Lipkowski, Pawel, and Wells, Jack C. Size-Expanded yDNA bases: An Ab Initio Study. United States: N. p., 2006. Web. doi:10.1021/jp057356n.
Fuentes-Cabrera, Miguel A, Sumpter, Bobby G, Lipkowski, Pawel, & Wells, Jack C. Size-Expanded yDNA bases: An Ab Initio Study. United States. doi:10.1021/jp057356n.
Fuentes-Cabrera, Miguel A, Sumpter, Bobby G, Lipkowski, Pawel, and Wells, Jack C. Sun . "Size-Expanded yDNA bases: An Ab Initio Study". United States. doi:10.1021/jp057356n.
@article{osti_1003296,
title = {Size-Expanded yDNA bases: An Ab Initio Study},
author = {Fuentes-Cabrera, Miguel A and Sumpter, Bobby G and Lipkowski, Pawel and Wells, Jack C},
abstractNote = {xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.},
doi = {10.1021/jp057356n},
journal = {Journal of Physical Chemistry B},
number = 12,
volume = 110,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
  • The size-expanded DNA bases, xA, xC, xG, and xT, are benzo-homologue forms of the natural DNA bases; i.e., their structure can be seen as the fusion of a natural base and a benzene ring. Recently, a variety of DNAs, known as xDNAs, have been synthesized in which size-expanded and natural bases are paired. In this paper we use second-order Moeller-Plesset perturbation theory and density functional theory to investigate the structural and electronic properties of xA, xC, xG, and xT and their natural counterparts. We find that whereas natural and size-expanded bases have both nonplanar amino groups the latter have alsomore » nonplanar aromatic rings. When density functional theory is used to investigate the electronic properties of size-expanded and natural bases, it is found that the HOMO-LUMO gap of the size-expanded bases is smaller than that of the natural bases. Also, xG should be easier to oxidize than G.« less
  • Naptho-homologated DNA bases have been recently used to build a new type of size expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naptho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like form of naptho-thymine (yyT) and naptho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crickmore » pairing. However, the canonical-like species of naptho-guanine (yyG) and naptho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphto-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naptho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.« less
  • We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less
  • The structures, force constants, and relative acidities of a series of molecules that mimic the geometries of terminal and bridging hydroxyl groups in various substituted zeolites and clays are calculated by ab initio molecular orbital methods. The molecules are structural analogs of disiloxane H[sub 3]T-O-TH[sub 3], and the protonated form H[sub 3]T, Si, Al, B, and P. Also included are H[sub 3]/SiO[sup [minus]] and H[sub 3]SiOH that mimic terminal hydroxyl groups that occur at the zeolite surface and defect sites. Results are presented for restricted Hartree-Fock (RHF) calculations at levels of theory that range from the minimal RHF/STO-3G to double-more » and triple-zeta basis sets with multiple polarization functions. The study shows that the structures of the molecules converge toward limiting values at the higher levels of theory. The theoretical trend in acidity of the terminal and bridging hydroxyls, as determined by the proton affinity, the length of the O-H bond, the charge on the hydroxyl proton, and the O-H stretching force constants and frequencies, is presented and is in agreement with experimental determinations. The calculated proton affinity is also shown to depend on the basis set size; however, the acidity trend is well reproduced at all levels of theory except RHF/STO-3G. 38 refs., 7 figs., 15 tabs.« less
  • Hartree-Fock calculations of the molecular geometry and electronic properties (ionization potentials) of bare Ni[sub n] clusters (n = 3, 7, 13, and 25) and nickel clusters bearing a chemisorbed CH[sub 3] radical are reported. A basis of double-zeta quality on light atoms including carbon and a model core potential along with double-zeta plus polarization auxiliary basis sets for nickel atoms have been used. Computed properties serve to assess cluster-size convergence when nickel atoms core electrons are described with [1s-3d] pseudopotentials. In spite of their simplicity, results with these potentials are in good agreement with previously reported theoretical and experimental datamore » on seven-atom clusters. This suggests that the cluster-model approach to surface bonding using simple pseudopotentials can lead to meaningful results and tractable computational times when applied to larger chemisorbed organic molecules. Thus, this approach may be adequate to help find out direct experimental evidence of the interfacial bonding for grafted structures obtained under cathodic electropolymerization of acrylonitrile on nickel surfaces. 1 fig., 5 tabs.« less