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Ralph H Scheicher - One of the best experts on this subject based on the ideXlab platform.
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physisorption of dna Nucleobases on h bn and graphene vdw corrected dft calculations
Journal of Physical Chemistry C, 2013Co-Authors: Yun Ki Choi, Ralph H ScheicherAbstract:Using local, semilocal, and van der Waals energy-corrected density-functional theory (PBE + vdW) calculations, we present a comparative study of DNA Nucleobases [guanine (G), adenine (A), thymine (T), and cytosine (C)] adsorbed on hexagonal boron nitride (h-BN) sheet and graphene. We find that, despite the very different electronic properties of BN sheet and graphene, the various nucleobase molecules have rather similar binding energies on the two types of sheets. The calculated binding energies of the four Nucleobases using the local, semilocal, and PBE + vdW schemes are in the range of 0.54–0.75, 0.06–0.15, and 0.93–1.18 eV, respectively. In particular, the PBE + vdW scheme predicts not only a binding energy predominantly determined by vdW interactions between the base molecules and their substrates decreasing in the order of G > A > T > C but also a very weak hybridization between the molecular levels of the Nucleobases and the π-states of the BN sheet or graphene. This physisorption of G, A, T, and C ...
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physisorption of dna Nucleobases on h bn and graphene vdw corrected dft calculations
arXiv: Mesoscale and Nanoscale Physics, 2013Co-Authors: Junho Lee, Yun Ki Choi, Ralph H Scheicher, Hyunjung Kim, Junhyung ChoAbstract:We present a comparative study of DNA Nucleobases [guanine (G), adenine (A), thymine (T), and cytosine (C)] adsorbed on hexagonal boron nitride (\textit{h}-BN) sheet and graphene, using local, semilocal, and van der Waals (vdW) energy-corrected density-functional theory (DFT) calculations. Intriguingly, despite the very different electronic properties of BN sheet and graphene, we find rather similar binding energies for the various nucleobase molecules when adsorbed on the two types of sheets. The calculated binding energies of the four Nucleobases using the local, semilocal, and DFT+vdW schemes are in the range of 0.54 ${\sim}$ 0.75 eV, 0.06 ${\sim}$ 0.15 eV, and 0.93 ${\sim}$ 1.18 eV, respectively. In particular, the DFT+vdW scheme predicts not only a binding energy predominantly determined by vdW interactions between the base molecules and their substrates decreasing in the order of G$>$A$>$T$>$C, but also a very weak hybridization between the molecular levels of the Nucleobases and the ${\pi}$-states of the BN sheet or graphene. This physisorption of G, A, T, and C on the BN sheet (graphene) induces a small interfacial dipole, giving rise to an energy shift in the work function by 0.11 (0.22), 0.09 (0.15), $-$0.05 (0.01), and 0.06 (0.13) eV, respectively.
Bernhard Lippert - One of the best experts on this subject based on the ideXlab platform.
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promotion of rare nucleobase tautomers by metal binding
Dalton Transactions, 2009Co-Authors: Bernhard Lippert, Deepali GuptaAbstract:Metal binding to ligands with the potential of existing in different tautomeric structures can dramatically alter the tautomeric equilibrium by stabilizing a particular, frequently minor, tautomer. The assumption that metal complexation of a minor tautomer is chemically irrelevant because of its very low abundance is misleading and in many cases wrong. In fact, from available X-ray structural data on metal–nucleobase complexes it is evident that metal binding to rare, as opposed to preferred tautomers, is anything but an exception. This “promotion of rare tautomers” through metal coordination is of particular biological relevance in the case of Nucleobases because any deviation from Watson–Crick base pairing is potentially mutagenic. In recent years models of “metal-stabilized rare nucleobase tautomers” have been characterized for all common DNA Nucleobases, including by X-ray crystallography. Though metal binding causes relatively minor structural changes in the Nucleobases, electronic changes as expressed by acid–base properties, for example, can be substantial. In this perspective article the biological consequences of the occupation of nucleobase sites by a metal entity and the altered acid–base chemistry of the nucleobase with regard to base mismatch formation, prevention of base pairing, and acid–base catalysis in nucleic acids are examined. Although not relevant to biology, the behaviour of the unsubstituted parent Nucleobases is illuminating in this respect and therefore included.
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metal stabilized rare tautomers and mispairs of dna bases n6 metalated adenine and n4 metalated cytosine theoretical and experimental views
Journal of Physical Chemistry A, 1999Co-Authors: Leonid Gorb, Jiři Sponer, Jerzy Leszczynski, Bernhard LippertAbstract:Crystal structure studies indicate that metalation of the exocyclic amino group of cytosine and adenine Nucleobases by PtII and HgII entities, respectively, induces protonation of a nucleobase ring nitrogen atom, and hence, causes a proton shift from an exocyclic to an endocyclic N atom. This metal-assisted process thus leads to the generation of rare nucleobase tautomers. In principle, such processes can lead to the stabilization of mispairs. The present study reports the first quantum chemical analysis of the metal-assisted tautomerization. The calculations clearly demonstrate that metalation of the exocyclic amino group of Nucleobases significantly increases the protonation energy of the aromatic rings of Nucleobases by about 30−34 kcal/mol for the PtII adduct and by about 10−14 kcal/mol for the HgII adduct. The calculations suggest that this kind of metalation could, besides the structural changes of DNA, significantly enhance the probability of formation of mispairs in DNA. In the course of the study...
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STRUCTURAL ASPECTS OF PT COMPLEXES CONTAINING MODEL Nucleobases
Coordination Chemistry Reviews, 1996Co-Authors: Ennio Zangrando, Fabio Pichierri, Lucio Randaccio, Bernhard LippertAbstract:Abstract Compounds of Pt(II) and Pt(IV)-containing Nucleobases as ligands (also including a few related ligands) are summarized and described, according to the nuclearity of the complexes. The large amount of available crystallographic data allows geometrical parameters such as bond lengths and angles, angular distortions, torsional angles related to the nucleobase plane orientations etc., to be derived with relatively high accuracy. Simple relationships between some of these parameters are reported and discussed. On mononuclear Pt complexes containing one or more nucleobase ligands a simple descriptive statistical analysis has been performed. The structural properties of polynuclear, often heteronuclear species have also been reviewed where the Nucleobases, particularly pyrimidines, act as polydentate-often bridging-ligands. A simple MO theoretical analysis of the metal-metal interaction in homo- and heterodinuclear species allows the degree of the intermetallic bond formation to be rationalized and the correlation of the qualitative results with the experimental metal-metal distances. Cyclic polynuclear species, which appear to be a new expanding field in the chemistry of Pt-nucleobase complexes, are also described.
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On Metal-Modified Nucleobase Triples and Quartets
Zeitschrift für Naturforschung B, 1993Co-Authors: André Schreiber, Edda C. Hillgeris, Bernhard LippertAbstract:Linking three Nucleobases by two metal ions M of linear coordination geometry leads to metal-modified base triples. With M = trans-(amine)₂Ptᴵᴵ, the bases are forced into an essentially coplanar fashion with interbase H bonding maintained in many cases. The model nucleobase triples described here are of general composition {[trans-(amine)₂PtB]₂(9-MeA)}ⁿ⁺ with two Nucleobases B bound via Pt to N1 and N7 of 9-methyladenine (9-MeA). The X-ray structure of a precursor, ([trans-(CH₃H₂)₂PtCl]₂(9-MeA)}(ClO₄)₂, is briefly described. The generation of metalated, cyclic nucleobase quartets and their expected structures are discussed and ways towards larger macrocyclic metal compounds are pointed out.
Thomas Carell - One of the best experts on this subject based on the ideXlab platform.
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a one pot water compatible synthesis of pyrimidine Nucleobases under plausible prebiotic conditions
Chemical Communications, 2019Co-Authors: Hidenori Okamura, Sidney Becker, Niklas Tiede, Stefan Wiedemann, Jonas Feldmann, Thomas CarellAbstract:Herein, we report a new prebiotically plausible pathway towards a pyrimidine nucleobase in continuous manner. The route involves simultaneous methylation and carbamoylation of cyanoacetylene-derived α,β-unsaturated thioamide with N-methyl-N-nitrosourea (MNU) in aqueous media. This provides S-methylpyrimidinone in one-pot, which can be converted into a variety of 4-substituted pyrimidine Nucleobases including cytosine and uracil.
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The chemistries and consequences of DNA and RNA methylation and demethylation.
RNA Biology, 2017Co-Authors: Franziska R. Traube, Thomas CarellAbstract:Chemical modification of Nucleobases plays an important role for the control of gene expression on different levels. That includes the modulation of translation by modified tRNA-bases or silencing and reactivation of genes by methylation and demethylation of cytosine in promoter regions. Especially dynamic methylation of adenine and cytosine is essential for cells to adapt to their environment or for the development of complex organisms from a single cell. Errors in the cytosine methylation pattern are associated with most types of cancer and bacteria use methylated Nucleobases to resist antibiotics. This Point of View wants to shed light on the known and potential chemistry of DNA and RNA methylation and demethylation. Understanding the chemistry of these processes on a molecular level is the first step towards a deeper knowledge about their regulation and function and will help us to find ways how nucleobase methylation can be manipulated to treat diseases.
Daniel M Neumark - One of the best experts on this subject based on the ideXlab platform.
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time resolved radiation chemistry femtosecond photoelectron spectroscopy of electron attachment and photodissociation dynamics in iodide nucleobase clusters
Physical Chemistry Chemical Physics, 2019Co-Authors: Alice Kunin, Daniel M NeumarkAbstract:Iodide–nucleobase (I−·N) clusters studied by time-resolved photoelectron spectroscopy (TRPES) are an opportune model system for examining radiative damage of DNA induced by low-energy electrons. By initiating charge transfer from iodide to the nucleobase and following the dynamics of the resulting transient negative ions (TNIs) with femtosecond time resolution, TRPES provides a novel window into the chemistry triggered by the attachment of low-energy electrons to Nucleobases. In this Perspective, we examine and compare the dynamics of electron attachment, autodetachment, and photodissociation in a variety of I−·N clusters, including iodide–uracil (I−·U), iodide–thymine (I−·T), iodide–uracil–water (I−·U·H2O), and iodide–adenine (I−·A), to develop a more unified representation of our understanding of nucleobase TNIs. The experiments probe whether dipole-bound or valence-bound TNIs are formed initially and the subsequent time evolution of these species. We also provide an outlook for forthcoming applications of TRPES to larger iodide-containing complexes to enable the further investigation of microhydration dynamics in Nucleobases, as well as electron attachment and photodissociation in more complex nucleic acid constituents.
Yun Ki Choi - One of the best experts on this subject based on the ideXlab platform.
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physisorption of dna Nucleobases on h bn and graphene vdw corrected dft calculations
Journal of Physical Chemistry C, 2013Co-Authors: Yun Ki Choi, Ralph H ScheicherAbstract:Using local, semilocal, and van der Waals energy-corrected density-functional theory (PBE + vdW) calculations, we present a comparative study of DNA Nucleobases [guanine (G), adenine (A), thymine (T), and cytosine (C)] adsorbed on hexagonal boron nitride (h-BN) sheet and graphene. We find that, despite the very different electronic properties of BN sheet and graphene, the various nucleobase molecules have rather similar binding energies on the two types of sheets. The calculated binding energies of the four Nucleobases using the local, semilocal, and PBE + vdW schemes are in the range of 0.54–0.75, 0.06–0.15, and 0.93–1.18 eV, respectively. In particular, the PBE + vdW scheme predicts not only a binding energy predominantly determined by vdW interactions between the base molecules and their substrates decreasing in the order of G > A > T > C but also a very weak hybridization between the molecular levels of the Nucleobases and the π-states of the BN sheet or graphene. This physisorption of G, A, T, and C ...
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physisorption of dna Nucleobases on h bn and graphene vdw corrected dft calculations
arXiv: Mesoscale and Nanoscale Physics, 2013Co-Authors: Junho Lee, Yun Ki Choi, Ralph H Scheicher, Hyunjung Kim, Junhyung ChoAbstract:We present a comparative study of DNA Nucleobases [guanine (G), adenine (A), thymine (T), and cytosine (C)] adsorbed on hexagonal boron nitride (\textit{h}-BN) sheet and graphene, using local, semilocal, and van der Waals (vdW) energy-corrected density-functional theory (DFT) calculations. Intriguingly, despite the very different electronic properties of BN sheet and graphene, we find rather similar binding energies for the various nucleobase molecules when adsorbed on the two types of sheets. The calculated binding energies of the four Nucleobases using the local, semilocal, and DFT+vdW schemes are in the range of 0.54 ${\sim}$ 0.75 eV, 0.06 ${\sim}$ 0.15 eV, and 0.93 ${\sim}$ 1.18 eV, respectively. In particular, the DFT+vdW scheme predicts not only a binding energy predominantly determined by vdW interactions between the base molecules and their substrates decreasing in the order of G$>$A$>$T$>$C, but also a very weak hybridization between the molecular levels of the Nucleobases and the ${\pi}$-states of the BN sheet or graphene. This physisorption of G, A, T, and C on the BN sheet (graphene) induces a small interfacial dipole, giving rise to an energy shift in the work function by 0.11 (0.22), 0.09 (0.15), $-$0.05 (0.01), and 0.06 (0.13) eV, respectively.
