Remote Communication in a DNA‐Based Nanoswitch

Guerra, Célia Fonseca; Szekeres, Zsolt; Bickelhaupt, F. Matthias

doi:10.1002/chem.201101335

Cited by 23 publications

(10 citation statements)

References 31 publications

(18 reference statements)

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“…Apart from the peptide bond, the Asp−Arg dipeptide features a hydrogen bond between the carboxylic and an amino group. The charge transfer at a hydrogen bond from a charged system can be as large as 0.2 e per hydrogen bond, 62 so that the differences in the density due to neglecting the polarization via the hydrogen bond and the peptide bond can be the same order of magnitude. The restriction of integer number of electrons in the fragment calculations therefore leads to considerable differences in the density with respect to the supermolecular calculation.…”

Section: Treatment Of Charged Amino Acid Residues In 3-fdementioning

confidence: 99%

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

Kiewisch

Jacob

Visscher

2013

J. Chem. Theory Comput.

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The ability to calculate accurate electron densities of full proteins or of selected sites in proteins is a prerequisite for a fully quantum-mechanical calculation of protein-protein and protein-ligand interaction energies. Quantum-chemical subsystem methods capable of treating proteins and other biomolecular systems provide a route to calculate the electron densities of proteins efficiently and further make it possible to focus on specific parts. Here, we evaluate and extend the 3-partition frozen-density embedding (3-FDE) scheme [Jacob, C. R.; Visscher, L. J. Chem. Phys.2008, 128, 155102] for this purpose. In particular, we have extended this scheme to allow for the treatment of disulfide bridges and charged amino acid residues and have introduced the possibility to employ more general partitioning schemes. These extensions are tested both for the prediction of full protein electron densities and for focusing on the electron densities of a selected protein site. Our results demonstrate that 3-FDE is a promising tool for the fully quantum-chemical treatment of proteins.

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Section: Treatment Of Charged Amino Acid Residues In 3-fdementioning

confidence: 99%

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

Kiewisch

Jacob

Visscher

2013

J. Chem. Theory Comput.

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“…Fonseca Guerra et al. have demonstrated how to tune HBs in guanine‐cytosine dimers [27] and other Watson–Crick base pairs [28] . They have also developed design principles to rationally modulate the HBs in DDAA‐AADD (D=donor, A=acceptor, D−H⋅⋅⋅A) and DAA‐ADD dimers [29] .…”

Section: Introductionmentioning

confidence: 99%

Impact of Covalent Modifications on the Hydrogen Bond Strengths in Diaminotriazine Supramolecules

et al. 2022

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Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In this work, we have computationally investigated how substituents can be exploited to improve the binding strength of M supramolecules. Two types of covalent modifications were studied: the substitution of an H atom within an amine group −NHR, and the replacement of the whole −NH2 group (R=H, F, CH3 and COCH3). Through our dispersion‐corrected density functional theory computations, we explain which covalent modification will show the best self‐assembling capabilities, and why the binding energy is enhanced. Our charge density and molecular orbital analyses indicate that the best substituents are those that generate a charge accumulation on the endocyclic N atom, providing an improvement of the electrostatic attraction. At the same time the substituent assists the main N−H⋅⋅⋅N hydrogen bonds by interacting with the amino group of the other monomer. We also show how the selected group notably boosts the strength of hexameric rosettes. This research, therefore, provides molecular tools for the rational design of emerging materials based on uneven hydrogen‐bonded arrangements.

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“…10 In particular, NMR spectroscopy is one of the main techniques for experimentally characterizing H-bond interactions, 11,12 and computational studies have been devoted to explain the observations. 13−20 Previous theoretical studies have examined the effect on the H bonding of DNA base pair GC, 21 when anionic, neutral, or cationic substituents were introduced at the C8 position of guanine through a π-conjugated linker of acetylene units, − (CC) n − (see Chart 1). The computations demonstrated the possibility to build a supramolecular nanoswitch based on the DNA base pair GC that can be chemically switched in a remote way, over a distance of up to nearly 3 nm, between three states that differ in hydrogen-bond strength: weak, intermediate, and strong.…”

mentioning

confidence: 99%

NMR ¹H-Shielding Constants of Hydrogen-Bond Donor Reflect Manifestation of the Pauli Principle

Zarycz

Guerra

2018

J. Phys. Chem. Lett.

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NMR spectroscopy is one of the most useful methods for detection and characterization of hydrogen bond (H-bond) interactions in biological systems. For H bonds X–H···Y, where X and Y are O or N, it is generally believed that a decrease in 1H-shielding constants relates to a shortening of H-bond donor–acceptor distance. Here we investigated computationally the trend of 1H-shielding constants for hydrogen-bonded protons in a series of guanine C8-substituted GC pair model compounds as a function of the molecular structure. Furthermore, the electron density distribution around the hydrogen atom was analyzed with the Voronoi deformation density (VDD) method. Our findings demonstrate that 1H-shielding values of the hydrogen bond are determined by the depletion of charge around the hydrogen atom, which stems from the fact that electrons obey the Pauli exclusion principle.

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Remote Communication in a DNA‐Based Nanoswitch

Abstract: Nano-telegraph: It is shown quantum chemically how the hydrogen-bond strength of a DNA base pair can be remotely switched (across several nanometers) between three states (weak, intermediate, and strong) through a π-conjugated "organic wire".

Cited by 23 publications

References 31 publications

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

Impact of Covalent Modifications on the Hydrogen Bond Strengths in Diaminotriazine Supramolecules

NMR ¹H-Shielding Constants of Hydrogen-Bond Donor Reflect Manifestation of the Pauli Principle

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Remote Communication in a DNA‐Based Nanoswitch

Abstract: Nano-telegraph: It is shown quantum chemically how the hydrogen-bond strength of a DNA base pair can be remotely switched (across several nanometers) between three states (weak, intermediate, and strong) through a π-conjugated "organic wire".

Cited by 23 publications

References 31 publications

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

Impact of Covalent Modifications on the Hydrogen Bond Strengths in Diaminotriazine Supramolecules

NMR 1H-Shielding Constants of Hydrogen-Bond Donor Reflect Manifestation of the Pauli Principle

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NMR ¹H-Shielding Constants of Hydrogen-Bond Donor Reflect Manifestation of the Pauli Principle