The Effect of Hydrogen Bonding on the Structures of Uracil and Some Methyl Derivatives Studied by Experiment and Theory.

Portalone, Gustavo; Bencivenni, L.; Colapietro, Marcello; Pieretti, Andrea; Ramondo, Fabio; Møller, Jørgen; Senning, Alexander; Yao, Xin‐Kan; Wang, Honggen; Tuchagues, J. P.; Ögren, Mattias

doi:10.3891/acta.chem.scand.53-0057

Cited by 99 publications

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“…As a part of a more general study of multiple-hydrogen-bonding DNA/RNA nucleobases as potential supramolecular reagents (Portalone et al, 1999;Portalone & Colapietro, 2007a, b), this work is a continuation of our studies on crystal adducts of DNA/RNA pyrimidine bases coupled with amino-derivatives of aromatic N-heterocycles via multiple hydrogen bonds to mimic the base-pairing of nucleic acids.…”

Section: S1 Commentmentioning

confidence: 95%

“…For a general approach to the use of multiple-hydrogenbonding DNA/RNA nucleobases as potential supramolecular reagents, see: Portalone et al (1999); Portalone & Colapietro (2007a,b and references therein). For the computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al (1990); Bernstein et al (1995); Motherwell et al (1999).…”

Section: Related Literaturementioning

confidence: 99%

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Acetoguanamine N,N-dimethylformamide solvate

Portalone

2008

Acta Cryst E

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Key indicators: single-crystal X-ray study; T = 298 K; mean (C-C) = 0.005 Å; R factor = 0.047; wR factor = 0.127; data-to-parameter ratio = 8.5.The structure of acetoguanamine (or 2,4-diamino-6-methyl-1,3,5-triazine) has been determined as the N,N-dimethylformamide solvate, C 4 H 7 N 5 ÁC 3 H 7 NO. The molecular components are associated in the crystal structure to form ribbons stabilized by three N-HÁ Á ÁN and one N-HÁ Á ÁO hydrogen bonds which involve NH groups as donors and the N atoms of the heterocyclic ring and the carbonyl O atom of the solvent as acceptors.

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Section: S1 Commentmentioning

confidence: 95%

Section: Related Literaturementioning

confidence: 99%

Acetoguanamine N,N-dimethylformamide solvate

Portalone

2008

Acta Cryst E

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“…3) is 4.8 pm/V. The absolute value of local piezocoefficient (d 33 ) eff was sufficiently high, varying between 3 and 10 pm/V depending on the location. These values are comparable to those of widely used piezoelectric materials ZnO 47 and AlN 48 and thus can be useful for microelectromechanical applications.…”

Section: Resultsmentioning

confidence: 85%

“…This model is in a full agreement with the earlier reported data. 33,37 However, taking into account hydrogen atoms and their effect on the final structure, we could calculate the lengths of hydrogen bonds and dipole moments of the individual thymine molecules (D % 4.5 Debye, see Table I) for the entire crystal structure. We could determine the polarization of thymine (as well as other physical parameters) in various volume partitions and directions.…”

Section: Modeling and Theoretical Analysismentioning

confidence: 99%

“…Crystal structure was explored by local density approximation (LDA) of density functional theory (DFT) with first-principle calculations on the base of AIMPRO code. 32,33,35 The basis set for each of the used atoms was taken from the AIMPRO library. 32 We used single point (SP) calculations as well geometrical optimization (total energy optimization).…”

Section: Molecular Modelingmentioning

confidence: 99%

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Local piezoresponse and polarization switching in nucleobase thymine microcrystals

Bdikin

Heredia

Neumayer

et al. 2015

Journal of Applied Physics

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Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectricbased applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field. V C 2015 AIP Publishing LLC. [http://dx

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Density functional theory study of the interaction between formamide and uracil

Duan

et al. 2006

Int J of Quantum Chemistry

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ABSTRACT:The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6-31G to 6-311ϩϩG(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven-membered rings; the others are eight-membered rings. The eight-membered ring is preferred over the seven-membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported.

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The Effect of Hydrogen Bonding on the Structures of Uracil and Some Methyl Derivatives Studied by Experiment and Theory.

Cited by 99 publications

References 0 publications

Acetoguanamine N,N-dimethylformamide solvate

Acetoguanamine N,N-dimethylformamide solvate

Local piezoresponse and polarization switching in nucleobase thymine microcrystals

Density functional theory study of the interaction between formamide and uracil

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