An ab initio study of DNA base pair hydrogen bonding: a comparison of plane-wave versus Gaussian-type function methods

Fellers, R. S.; Barsky, Daniel; Gygi, F.; Colvin, Michael E.

doi:10.1016/s0009-2614(99)00898-2

Cited by 32 publications

(31 citation statements)

References 31 publications

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“…First, the relaxed geometry of the G–C base-pair was determined, which determined the three hydrogen bond lengths of the duplex which were d(H C … O G ) = 1.74 Å, d(N C … H G ) = 1.89 Å and d(O C … H G ) = 1.91 Å, and are in excellent agreement with similar calculations [37–39]. …”

Section: Structuressupporting

confidence: 69%

“…Several theoretical investigations related to the hydrogen bond length and bond energy of DNA base-pairs have been performed [32–39] and comparisons made [37, 38] between different DFT exchange–correlation potentials (B3LYP, BLYP, BP86, PBE, PW91, etc). Tsuzuki and Lüthi [40] showed that PW91 performs best for interaction energies of weakly bound systems via van der Waals or hydrogen bond interactions.…”

Section: Structuresmentioning

confidence: 99%

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Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

Lee

Sankey²

2008

J. Phys.: Condens. Matter

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We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH 2 ) 2 )-guanidinium-phosphate-deoxyribose-cytosineguanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guaninecytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.

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Section: Structuressupporting

confidence: 69%

Section: Structuresmentioning

confidence: 99%

Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

Lee

Sankey²

2008

J. Phys.: Condens. Matter

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“…21 A recent DFT study of hydrogen bond cooperativity 22 took advantage of this and we refer the interested reader to the discussion therein. 3) There is no bias arising from wrong or improper choices of local-orbital basis set, simply because only one parameter (the number of plane waves) is increased until the results converge.…”

Section: ■ Theory and Methodsmentioning

confidence: 99%

Hydrogen-Bonding Networks from First-Principles: Exploring the Guanidine Crystal

2012

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Hydrogen bonding is among the most important interactions in molecular crystals, and examples are abundant. As a consequence of such interactions, many molecules crystallize in complex but intriguing structures, in contrast to the relatively simple packing principles of metallic or ionic solids. In this work, we present a computational approach based on plane-wave density-functional theory (DFT) and supercell techniques, aiming to understand and quantify hydrogen-bonded networks in the solid state and in two-, one-, and zero-dimensional fragments derived from the molecular crystal. With such methodology at hand, we investigate guanidine, a fitting example of a molecular crystal and an important compound for inorganic and organic chemistry alike. On the basis of our computations, we discuss the initially proposed layered structure of guanidine and identify both stabilizing and destabilizing cooperative interactions in the three crystalline dimensions.

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“…[16] An advan-A C H T U N G T R E N N U N G tage of PW-DFT is that it is inherently free from the basisset superposition error (BSSE), because plane-wave basis sets describe any point in the periodic supercell with the same quality in contrast to Gaussian orbitals spanning only a local region. [17] Geometries of infinite chains of N-centred BTA 3 and C= O-centred BTA 4 were optimised by using the PW-DFT approach. Since PW-DFT calculations are of inherently periodic nature, an N-or C=O-centred BTA dimeric unit was placed in an (a a c) orthorhombic supercell.…”

Section: Wwwchemeurjorgmentioning

confidence: 99%

Dynamic Supramolecular Polymers Based on Benzene‐1,3,5‐tricarboxamides: The Influence of Amide Connectivity on Aggregate Stability and Amplification of Chirality

Stals

Everts

Bruijn

et al. 2010

Chemistry A European J

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N‐Centred benzene‐1,3,5‐tricarboxamides (N‐BTAs) composed of chiral and achiral alkyl substituents were synthesised and their solid‐state behaviour and self‐assembly in dilute alkane solutions were investigated. A combination of differential scanning calorimetry (DSC), polarisation optical microscopy (POM) and X‐ray diffraction revealed that the chiral N‐BTA derivatives with branched 3,7‐dimethyloctanoyl chains were liquid crystalline and the mesophase was assigned as Colho. In contrast, N‐BTA derivatives with linear tetradecanoyl or octanoyl chains lacked a mesophase and were obtained as crystalline compounds. Variable‐temperature infrared spectroscopy showed the presence of threefold, intermolecular hydrogen bonding between neighbouring molecules in the mesophase of the chiral N‐BTAs. In the crystalline state at room temperature a more complicated packing between the molecules was observed. Ultraviolet and circular dichroism spectroscopy on dilute solutions of N‐BTAs revealed a cooperative self‐assembly behaviour of the N‐BTA molecules into supramolecular polymers with preferred helicity when chiral alkyl chains were present. Both the sergeants‐and‐soldiers as well as the majority‐rules principles were operative in stacks of N‐BTAs. In fact, the self‐assembly of N‐BTAs resembles closely that of their carbonyl (CO)‐centred counterparts, with the exception that aggregation is weaker and amplification of chirality is less pronounced. The differences in the self‐assembly of N‐ and CO‐BTAs were analysed by density functional theory (DFT) calculations. These reveal a substantially lower interaction energy between the monomeric units in the supramolecular polymers of N‐BTAs. The lower interaction energy is due to the higher energy penalty for rotation around the PhNH bond compared to the PhCO bond and the diminished magnitude of dipole–dipole interactions. Finally, we observed that mixed stacks are formed in dilute solution when mixing N‐BTAs and CO BTAs.

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An ab initio study of DNA base pair hydrogen bonding: a comparison of plane-wave versus Gaussian-type function methods

Cited by 32 publications

References 31 publications

Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

Hydrogen-Bonding Networks from First-Principles: Exploring the Guanidine Crystal

Dynamic Supramolecular Polymers Based on Benzene‐1,3,5‐tricarboxamides: The Influence of Amide Connectivity on Aggregate Stability and Amplification of Chirality

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