Ground‐ and excited‐state properties of DNA base molecules from plane‐wave calculations using ultrasoft pseudopotentials

Preuss, M.; Schmidt, Wolf Gero; Seino, K.; Furthmüller, J.; Bechstedt, F.

doi:10.1002/jcc.10372

Cited by 92 publications

(114 citation statements)

References 85 publications

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“…Note also that since the straight line in Fig. 3 includes the theoretical values of bond lengths from [6], the above result implies that the latter values are good representations of the radii sum, R(sum).…”

Section: Bond Lengths In All the Molecules As Sums Of Atomic Covalentmentioning

confidence: 60%

“…Although he dealt with the bond lengths in the purines: adenine (A) and guanine (G) and the pyrimidines: thymine (T), cytosine (C) and uracil (U), he did not interpret these bonds. This article shows here that the existing bond lengths [4][5][6][7] (see Tabs. 1 and 2) in the above molecules and in ribose (Ri), deoxyribose (De) and phosphoric acid (Ph), correspond to the sums of the appropriate covalent radii of the five atoms, carbon, nitrogen, hydrogen, oxygen and phosphorus.…”

Section: Introductionmentioning

confidence: 80%

“…1), the CC bond length is around 1.40 Å and the CN bond length has values around 1.32 Å and 1.36 Å. A survey of the existing bond length data [4][5][6][7] (see Tabs. 1 and 2), shows that the CC, CN CH, NH, CO, OH and PO bonds in the above molecules do have some essentially fixed bond lengths, and in fact more than the three considered by Pauling.…”

Section: Atomic Covalent Radii and The Cn Bond Length In Adeninementioning

confidence: 99%

“…The above additivity of atomic radii was then tested for the distances between any two atoms in the skeletal structures of the molecular components of nucleic acids by comparing the data from [4][5][6][7] with the sums R(sum) of the appropriate atomic covalent radii in Fig. 2B.…”

Section: Bond Lengths In All the Molecules As Sums Of Atomic Covalentmentioning

confidence: 99%

“…2. The average values of the bond lengths [4][5][6][7] for the above molecules (from Tabs. 1 and 2) and the corresponding R(sum) for the various bonds are tabulated in Tab.…”

Section: Bond Lengths In All the Molecules As Sums Of Atomic Covalentmentioning

confidence: 99%

See 4 more Smart Citations

Structures of the Molecular Components in DNA and RNA with Bond Lengths Interpreted as Sums of Atomic Covalent Radii

Heyrovská¹

2008

TOSBJ

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Two dimensional layers of graphene are currently drawing a great attention in fundamental and applied nanoscience. Graphene consists of interconnected hexagons of carbon atoms as in graphite. This article presents for the first time the structures of graphene at the atomic level and shows how it differs from that of benzene, due to the difference in the double bond and resonance bond based radii of carbon. The carbon atom of an aliphatic compound such as methane has a longer covalent single bond radius as in diamond. All the atomic structures presented here have been drawn to scale.

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Section: Bond Lengths In All the Molecules As Sums Of Atomic Covalentmentioning

confidence: 60%

Section: Introductionmentioning

confidence: 80%

Section: Atomic Covalent Radii and The Cn Bond Length In Adeninementioning

confidence: 99%

Section: Bond Lengths In All the Molecules As Sums Of Atomic Covalentmentioning

confidence: 99%

“…2. The average values of the bond lengths [4][5][6][7] for the above molecules (from Tabs. 1 and 2) and the corresponding R(sum) for the various bonds are tabulated in Tab.…”

Section: Bond Lengths In All the Molecules As Sums Of Atomic Covalentmentioning

confidence: 99%

See 3 more Smart Citations

Structures of the Molecular Components in DNA and RNA with Bond Lengths Interpreted as Sums of Atomic Covalent Radii

Heyrovská¹

2008

TOSBJ

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Preliminary study on fiber splitting of bicomponent meltblown fibers

Sun

Zhang

Liu

et al. 2004

J of Applied Polymer Sci

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Side-by-side bicomponent meltblown fiber webs were developed on REICOFIL ® bicomponent (bico) meltblown line at The University of Tennessee's Textiles and Nonwovens Development Center (TANDEC), using polypropylene (PP), polyethylene (PE), polyethylene terephthalate (PET), polybutylene terephthalate (PBT), polyamide (PA), polytrimethylene terephthalate (PTT), and so forth. The posttreatment was performed by hydroentanglement to investigate the fiber-splitting behavior in this research. Microscopy analysis and SEM were applied to examine the web structure. The change in web property after posttreatment and the adhesion mechanism of the polymer interface were also addressed.

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Structure and Electronic Properties of Unnatural Base Pairs: The Role of Dispersion Interactions

2017

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Recent reports of the successful incorporation of unnatural base pairs (UBPs), such as d5SICS–dNaM, in the gene sequence and replication with DNA is an important milestone in synthetic biology. Followed by this, several other UBPs, such as dTPT3–dNaM, dTPT3–dFIMO, dTPT3–IMO, dTPT3–FEMO, FTPT3–NaM, FTPT3–FIMO, FTPT3–IMO, and FTPT3–FEMO, have demonstrated similar or better retention and fidelity inside cells. Of these base pairs, dNaM–dTPT3 has been optimized to be a better fit inside a pAIO plasmid. Based on both implicit and explicit dispersion‐corrected density functional theory (DFT) calculations, we show that although this set of UBPs is significantly diverse in elemental and structural configuration, the members do share a common trait of favoring a slipped parallel stacked dimer arrangement. Unlike the natural bases (A, T, G, C, and U), this set of UBPs has a negligible affinity for a Watson–Crick (WC)‐type planar structure because they are invariably more stable within slipped parallel stacked orientations. We also observed that all the UBPs have either similar or higher binding energies with the natural bases in similar stacked orientations. When arranged between two natural base pairs, the UBPs exhibited a binding energy similar to that of three‐base sequences of natural bases. Our computational data show that the most promising base pairs are 5SICS–NaM, TPT3–NaM, and TPT3–FEMO. These results are consistent with recent progress on experimental research into UBPs along with our previous calculations on the d5SICS–dNaM pair and, therefore, strengthen the hypothesis that hydrogen bonding might not be absolutely essential and that interbase stacking dispersion interactions play a key role in the stabilization of genetic materials.

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Ground‐ and excited‐state properties of DNA base molecules from plane‐wave calculations using ultrasoft pseudopotentials

Cited by 92 publications

References 85 publications

Structures of the Molecular Components in DNA and RNA with Bond Lengths Interpreted as Sums of Atomic Covalent Radii

Structures of the Molecular Components in DNA and RNA with Bond Lengths Interpreted as Sums of Atomic Covalent Radii

Preliminary study on fiber splitting of bicomponent meltblown fibers

Structure and Electronic Properties of Unnatural Base Pairs: The Role of Dispersion Interactions

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