The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance

Guerra, Célia Fonseca; Bickelhaupt, F.; Snijders, J.G.; Baerends, E. J.

doi:10.1002/(sici)1521-3765(19991203)5:12<3581::aid-chem3581>3.0.co;2-y

Cited by 339 publications

(199 citation statements)

References 6 publications

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“…12͑a͔͒, at variance with the situation for AT where the corresponding bonds elongate by 0.02-0.05 Å due to the stronger charge-transfer interactions in the latter base pair. 14 The above BP86/TZ2P results agree well with the available data from literature that AF is rather weakly bound, by 3-4 kcal/mol, with hydrogen bond distances of 3.2-3.4 Å. Experimental data have, to our knowledge, not been reported.…”

Section: A Geometries and Hydrogen Bond Strengthssupporting

confidence: 89%

“…͑14͒ with ⌫ϭ ]: the electron-donor atoms of the N6 -H6"""O4 and N1"""H3-N3 hydrogen bonds ͑see Chart 1͒ lose 24 and 46 milielectrons while the N-H bonds gain up to 54 milielectrons. This charge-transfer picture was found before by Fonseca Guerra et al 14 but now, for the first time, we are able to separate the effect of Pauli repulsion between the lone pairs of the electron-donor atoms and the occupied N-H bonding orbitals (⌬Q Pauli in Fig. 6͒ from the bonding donor-acceptor interactions (⌬Q oi in Fig.…”

Section: Charge Redistribution Due To Hydrogen Bondingsupporting

confidence: 83%

“…12͑b͒, 14 We have shown previously that this intrinsic base-pairing interaction is affected neither by microsolvation of the major and minor grooves nor by the interaction between two stacked base pairs. Thus, the barrier for nucleotide insertion increases substantially if the stabilizing hydrogen bonds cannot be formed between the bases in the active site of the enzyme.…”

Section: A-f Versus A-t Interaction In Dna Polymerase's Active Sitementioning

confidence: 99%

“…14,15 For this purpose, the VDD method has been further developed such that the charge redistribution ⌬Q per atom can be decomposed into a component associated with the Pauli repulsion and a component associated with the bonding orbital interactions: ⌬Qϭ⌬Q Pauli ϩ⌬Q oi . Full details of our analyses and the new developments of the VDD method are reported, and we discuss the implications of our findings for the mechanism of DNA replication.…”

Section: Introductionmentioning

confidence: 99%

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Orbital interactions and charge redistribution in weak hydrogen bonds: The Watson–Crick AT mimic adenine-2,4-difluorotoluene

Guerra

Bickelhaupt

2003

The Journal of Chemical Physics

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The discovery by Kool and co-workers that 2,4-difluorotoluene ͑F͒ mimics thymine ͑T͒ in DNA replication has led to a controversy about the question if this mimic has the capability of forming hydrogen bonds with adenine ͑A͒. In the present study, we address not only the question about the strengths of the hydrogen bonds in AF as compared to those in AT but we focus in particular on the nature of these interactions. Thus, we have analyzed AF and AT at the BP86/TZ2P level of density functional theory ͑DFT͒. In line with previous experience, this approach is shown to achieve close agreement with the available data from ab initio computations and experiment: the complexation energy of AF ͑Ϫ3.2 kcal/mol͒ is confirmed to be much weaker indeed than that of AT ͑Ϫ13.0 kcal/mol͒. Interestingly, the weak hydrogen bonds in AF still possess a significant orbital interaction component that resembles the situation for the more strongly bound AT, as follows from ͑1͒ an analysis of the orbital electronic structure of AF and AT, ͑2͒ a quantitative decomposition of the A-F and A-T bond energies, as well as ͑3͒ a quantitative decomposition of the charge redistribution associated with the A-F and A-T interactions based on the Voronoi deformation density ͑VDD͒ method. The VDD method has been further developed such that the charge redistribution ⌬Q per atom can be decomposed into a component associated with the Pauli repulsive orbital interactions and a component associated with the bonding orbital interactions: ⌬Qϭ⌬Q Pauli ϩ⌬Q oi . Implications of our findings for the mechanism of DNA replication are discussed.

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Section: A Geometries and Hydrogen Bond Strengthssupporting

confidence: 89%

Section: Charge Redistribution Due To Hydrogen Bondingsupporting

confidence: 83%

Section: A-f Versus A-t Interaction In Dna Polymerase's Active Sitementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Orbital interactions and charge redistribution in weak hydrogen bonds: The Watson–Crick AT mimic adenine-2,4-difluorotoluene

Guerra

Bickelhaupt

2003

The Journal of Chemical Physics

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“…[25][26][27][28] The proton donor and proton acceptor groups in RAHBs are connected through a chain of p-conjugated double bonds, and the standard explanation of the noticeable strength of these interactions is based on a chemically intuitive reasoning in which the conjugated bonds display an equalization of lengths through a pseudo-ring. This description of RAHBs is consistent with the deeply rooted idea that the existence of equivalent resonance structures is a stabilizing feature of a molecular system.…”

Section: Introductionmentioning

confidence: 99%

The nature of resonance-assisted hydrogen bonds: a quantum chemical topology perspective

Guevara‐Vela

Romero-Montalvo

Costales

et al. 2016

Phys. Chem. Chem. Phys.

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Title: The nature of resonance-assisted hydrogen bonds: a quantum chemical topology perspectiveThis work addresses the nature of Resonance Assisted Hydrogen Bonds (RAHBs) by considering malonaldehyde whose H-bonded (closed) and non H-bonded (open) conformations are represented in the bottom and top of the seesaws respectively. Although delocalization indices are more uniform in the closed form (seesaw in the left), the number of delocalized electrons diminish on RAHB formation. The interaction is characterized by an increase/decrease in the intra-atomic/inter-atomic exchange energies as schematized with sparks in the highlighted seesaw in the right. The artwork is due to Mr Víctor Duarte Alaniz. indicate that the p-conjugated bonds allow for a larger adjustment of electron density throughout the H-bonded system as compared with non-conjugated carbonyl molecules. This rearrangement of charge distribution is a response to the electric field due to the H atom involved in the hydrogen bonding of the considered compounds. As opposed to the usual description of RAHB interactions, these HBs lead to a larger electron localisation in the system, and concomitantly to larger QTAIM charges which in turn lead to stronger electrostatic, polarization and charge transfer components of the interaction. Overall, the results presented here offer a new perspective on the cause of strengthening of these important interactions.

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Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

Šponer¹,

Leszczyński²,

Hobza³

2001

Biopolymers

429

357

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This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio‐base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C—H … O interbase contacts, sugar–base stacking, intrinsically nonplanar base pairs, out‐of‐plane hydrogen bonds, and amino–acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation–π interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 3–31, 2002; DOI 10.1002/bip.10048

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The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance

Abstract: atom upon formation of the base pair from the separate bases.

Cited by 339 publications

References 6 publications

Orbital interactions and charge redistribution in weak hydrogen bonds: The Watson–Crick AT mimic adenine-2,4-difluorotoluene

Orbital interactions and charge redistribution in weak hydrogen bonds: The Watson–Crick AT mimic adenine-2,4-difluorotoluene

The nature of resonance-assisted hydrogen bonds: a quantum chemical topology perspective

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

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