Hydrogen bonding in DNA base complexes

Powell, B. M.; Martel, P.

doi:10.1016/s0006-3495(81)84851-5

Cited by 9 publications

(5 citation statements)

References 22 publications

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“…Quite unrealistic potential functions of the (6-exp) type have been proposed in Ref. (24) where electrostatic interactions have not been taken into account. The parameters for H-bonds have been chosen from frequencies of normal modes in 1-methylthymine and cytosine monohydrate crystals while other parameters are taken from other papers.…”

Section: Calculation Proceduresmentioning

confidence: 99%

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

Poltev

Shulyupina

1986

Journal of Biomolecular Structure and Dynamics

117

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Energy of interaction between nitrogen bases of nucleic acid has been calculated as a function of parameters determining the mutual position of two bases. Refined atom-atom potential functions are suggested. These functions contain terms proportional to the first (electrostatics), sixth (or tenth for the atoms forming a hydrogen bond) and twelfth (repulsion of all atoms) powers of interatomic distance. Calculations have shown that there are two groups of minima of the base interaction energy. The minima of the first group correspond to coplanar arrangement of the base pairs and hydrogen bond formation. The minima of the second group correspond to the position of bases one above the other in almost parallel planes. There are 28 energy minima corresponding to the formation of coplanar pairs with two (three for the G:C pair) almost linear N-H . . . O and (or) N-H . . . N hydrogen bonds. The position of nitrogen bases paired by two such H-bonds in any crystal of nucleic acid component in polynucleotide complexes and in tRNA is close to the position in one of these minima. Besides, for each pair there are energy minima corresponding to the formation of a single N-H . . . O or N-H . . . N and one C-H . . . O or C-H . . . N hydrogen bond. The form of potential surface in the vicinity of minima has been characterized. The results of calculations agree with the experimental data and with more rigorous calculations based on quantum-mechanical approach.

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Section: Calculation Proceduresmentioning

confidence: 99%

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

Poltev

Shulyupina

1986

Journal of Biomolecular Structure and Dynamics

117

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“…50,51 Nevertheless, some attention also has been dedicated to the applicability of hydrogen bonds in molecular modelling of cooperative systems, [52][53][54][55][56][57][58][59][60][61][62][63] wherein the origin of life based on DNA structure certainly is the most remarkable, incisive, and thorough investigation focus. [64][65][66][67][68][69] Notoriously all these researches provide a summary of the 'state of the art for hydrogen bonds', 70 although it must be remembered that its evidence is the greatest goal in any investigation type. [71][72][73][74] Over all these years, a lot of definitions for hydrogen bond [75][76][77][78][79][80][81][82][83] have been documented by famous scientists, such as Lewis, 84 Pauling, 85 Huggins, 86 Pimentel and McClellan, 87 Latimer and Rodebush 88 as well as Coulson and Danielson.…”

Section: Introductionmentioning

confidence: 99%

Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H^−δ⋯H^+δdihydrogen bonds

Oliveira

2013

Phys. Chem. Chem. Phys.

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In this paper, the intermolecular structural study asserted by the vibrational analysis in the stretch frequencies of hydrogen bonds (π···H) and dihydrogen bonds (H(-δ)···H(+δ)) have definitively been revisited by means of calculations carried out by Density Functional Theory (DFT) and topological parameters derived from the classic treatise of the Quantum Theory of Atoms in Molecules (QTAIM). As a matter of fact the π···H hydrogen bond is formed between the hydrofluoric acid and the C≡C bond of the acetylene, but the QTAIM calculations revealed a distortion in this interaction due to the formation of the ternary complex C(2)H(2)···2(HF). Although the π bonds of ethylene (C(2)H(4)), propylene (C(2)H(3)(CH(3))), and t-butylene (C(2)H(2)(CH(3))(2)) are considered proton acceptors, two hydrogen-bond types--π···H and C···H--can be observed. Over and above the analysis of the π hydrogen bonds, theoretical arguments also were used to discuss the red-shifts in the stretch frequencies of the binary dihydrogen complexes formed by BeH(2)···HX with X = F, Cl, CN, and CCH. Although a vibrational blue-shift in the stretch frequency of the H-C bond of HCF(3) due to the formation of the BeH(2)···HCF(3) dihydrogen complex was obtained, unmistakable red-shifts were detected in LiH···HCF(3), MgH(2)···HCF(3), and NaH···HCF(3). Moreover, the alkali-halogen bonds were identified in relation to the formation of the trimolecular systems NaH···2(HCF(3)) and NaH···2(HCCl(3)). At last, theoretical calculations and QTAIM molecular integrations were used to study a novel class of dihydrogen-bonded complexes (mC(2)H(5)(+)···nMgH(2) with m = 1 or 2 and n = 1 or 2) based in the insight that MgH(2) can bind with the non-localized hydrogen H(+δ) of the ethyl cation (C(2)H(5)(+)). In an overview, QTAIM calculations were applied to evaluate the molecular topography, charge density, as well as to interpret the shifted frequencies either to red or blue caused by the formation of the hydrogen bonds and dihydrogen bonds.

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“…The persistence and stability of OFs guarantee the predominant advantages for their potential use as active components of permanent or long-term equipment under harsh circumstances. As a complementary advantage, OFs constructed from a reversible self-assembly with noncovalent bonds would meet the demand for sustainable materials. − On the other hand, the emerging requirements for eco-friendly, temporary, or use-once materials and devices have to be satisfied by reversible supramolecular tectons, which dominate the bottom-up principles of evolution from substances to materials and life , by hydrogen bonds and van der Waals forces etc. Various hydrogen bonds, including halogen···H, O···H, N···H, and π···H, have been applied to explore persistant, porous, and luminescent materials. − One of the most improtant strategies to construct hydrogen bonds − is fluorination, which has been used to effectively optimize the optoelectronic properties of aromatics due to the extremely special electronegativity and polarizability of F atoms.…”

Section: Introductionmentioning

confidence: 99%

Wide-Gap 1D-, 2D-, and 3D-Hydrogen-Bonded Organic Frameworks Hierarchically Weaved by Macrocyclic Supramolecular Multifluorine Tectons

Bai

Wang

et al. 2021

Crystal Growth & Design

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A series of 1D-, 2D-, and 3D-hydrogen-bonded organic frameworks (1D-, 2D-, and 3D-HOFs) force-driven by macrocyclic multifluorine tectons (F-tectons) was constructed on the basis of burgeoning multifluorinated diaminoterephthalates (25, 345, and 26). Crystalline 25 gave ladder-shaped 1D-HOFs containing one kind of macrocyclic F-tecton looped by two F···H(CH3) hydrogen bonds in competition with strong π···π and π···H(CH3) interactions. Crystalline 345 gave layer-by-layer translational 2D-HOFs containing hierarchically macrocyclic F-tectons looped by 8-fold hydrogen bonds, including three F···H(CH3), three O···HN and two ArC···H(CH3) prior to weak π···π interactions. Crystalline 26 possessed 2-fold interpenetrated 3D-HOFs containing hierarchically macrocyclic F-tectons looped by F···H(CH3), ArH···F, and ArH···F···H(CH3) hydrogen bonds and interpenatrated by strong π···π interactions. In addition to that, the electron-withdrawing multifluorination of diaminoterephthalates caused an optical blue shift with wide optical energy gaps (2.43–2.51 eV) for 25, 345, and 26 in solution and a wide optical band gap (2.31 eV) for 345 in the film state. The multifluorination effect confirms an interesting trend that more F atoms bring in deeper highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO) energy levels (345 vs 25/26) and also regioisomerism confirms that farther F atoms bring in deeper HOMO/LUMO energy levels (25 vs 26).

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Hydrogen bonding in DNA base complexes

Cited by 9 publications

References 22 publications

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H^−δ⋯H^+δdihydrogen bonds

Wide-Gap 1D-, 2D-, and 3D-Hydrogen-Bonded Organic Frameworks Hierarchically Weaved by Macrocyclic Supramolecular Multifluorine Tectons

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Hydrogen bonding in DNA base complexes

Cited by 9 publications

References 22 publications

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H−δ⋯H+δdihydrogen bonds

Wide-Gap 1D-, 2D-, and 3D-Hydrogen-Bonded Organic Frameworks Hierarchically Weaved by Macrocyclic Supramolecular Multifluorine Tectons

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Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H^−δ⋯H^+δdihydrogen bonds