The Virial Field and Transferability in DNA Base‐Pairing

Bader, R. F. W.; Cortés‐Guzmán, Fernando

doi:10.1002/9783527629213.ch10

Cited by 9 publications

(4 citation statements)

References 57 publications

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“…No one viewing this picture can deny the existence of atoms in molecules nor question the role of the electron density as the vehicle for the transmission of chemical information methyl and methylene groups make additive, transferable contributions to the molecular properties in this series of molecules (Bader 1990). The diagram makes clear that corresponding groups have identifiable, transferable electron densities in spite of differing external potentials and that the densities of the groups determine their properties, a property verified many times over from both theory and experiment (Bader 2008(Bader , 2010Cortés-Guzmán and Bader 2003;Benabicha et al 2000;Flaig et al 2002;Kingsforf-Adaboh et al 2002;Flaig et al 1998;Scheins et al 2004;Bader and Bayles 2000;Bader et al 1994;Bader and Cortés-Guzmán 2009). No one viewing this picture can question the existence of atoms in molecules nor the role of the electron density in determining their chemistry.…”

Section: Epiloguementioning

confidence: 93%

On the non-existence of parallel universes in chemistry

Bader

2011

Found Chem

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This treatise presents thoughts on the divide that exists in chemistry between those who seek their understanding within a universe wherein the laws of physics apply and those who prefer alternative universes wherein the laws are suspended or 'bent' to suit preconceived ideas. The former approach is embodied in the quantum theory of atoms in molecules (QTAIM), a theory based upon the properties of a system's observable distribution of charge. Science is experimental observation followed by appeal to theory that, upon occasion, leads to new experiments. This is the path that led to the development of the molecular structure hypothesis-that a molecule is a collection atoms with characteristic properties linked by a network of bonds that impart a structure-a concept forged in the crucible of nineteenth century experimental chemistry. One hundred and fifty years of experimental chemistry underlie the realization that the properties of some total system are the sum of its atomic contributions. The concept of a functional group, consisting of a single atom or a linked set of atoms, with characteristic additive properties forms the cornerstone of chemical thinking of both molecules and crystals and Dalton's atomic hypothesis has emerged as the operational theory of chemistry. We recognize the presence of a functional group in a given system and predict its effect upon the static, reactive and spectroscopic properties of the system in terms of the characteristic properties assigned to that group. QTAM gives physical substance to the concept of a functional group.Keywords Electron density Á Atoms in molecules Á Molecular structure Á QTAIM Present day chemistryWe are at a cross-roads in chemistry, wherein we face a dichotomy in two important areas: in one we must choose between physics, as embodied in the quantum theory of atoms in Electronic supplementary material The online version of this article (

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Section: Epiloguementioning

confidence: 93%

On the non-existence of parallel universes in chemistry

Bader

2011

Found Chem

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“…It has been found 45 that employing the atom−atom contributions of only the atoms directly involved in the HB leads to an overestimation and that all of the atom−atom contributions in the DNA BP must be included to obtain an accurate picture. In addition to the DNA base pairing, 45 the atomic partitioning based on QTAIM has been used to assess the dissociation energies of the C−C bonds in aliphatic hydrocarbons, 46 quantify the strength of P− O bonds, 47 and analyze the energetic properties of ATP. 48,49 Our analysis of DNA BPs revealed the molecular regions that are more affected by electrostatic, exchange−correlation, and kinetic energy variations.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The transferability of the virial field in DNA base pairing has been explored by using the QTAIM approach based on the total density contribution. It has been found that employing the atom–atom contributions of only the atoms directly involved in the HB leads to an overestimation and that all of the atom–atom contributions in the DNA BP must be included to obtain an accurate picture. In addition to the DNA base pairing, the atomic partitioning based on QTAIM has been used to assess the dissociation energies of the C–C bonds in aliphatic hydrocarbons, quantify the strength of P–O bonds, and analyze the energetic properties of ATP. , …”

Section: Introductionmentioning

confidence: 99%

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Anatomy of Base Pairing in DNA by Interacting Quantum Atoms

Cuyacot

Durník

Foroutan‐Nejad

et al. 2020

J. Chem. Inf. Model.

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The formation of purine and pyrimidine base pairs (BPs), which contributes to shaping of the canonical and noncanonical 3D structures of nucleic acids, is one the most investigated phenomena in chemistry and life sciences. In this contribution, the anatomy of the bond energy (BDE) of the base-pairing interaction in 39 different arrangements found experimentally or predicted for DNA structures containing the four common nucleobases (A, C, G, T) in their neutral or protonated forms is described in light of the theory of interacting quantum atoms within the context of the quantum theory of atoms in molecules. The interplay of individual energy components involved in the three stages of the bond formation process (structural deformation, electron-density promotion, and intermolecular interaction) is studied. We recognized that for the neutral BPs, variations in the kinetic and electrostatic contributions to the BDE are rather negligible, leaving the exchange–correlation energy as the main stabilizing component. It is shown that the contribution of the exchange–correlation term can be recovered by including atoms that are formally assumed to be hydrogen bonded (primary interaction). In contrast, to recover the electrostatic component of interaction, one must consider both the primary and secondary (formally nonbonded atoms) interatomic interactions. The results of our study were employed to design new types of BPs with altered bonding anatomy. We demonstrate that improving the electrostatic characteristics of the BPs does not necessarily result in greater interaction energies if weak secondary hydrogen bonding is destroyed. However, the main tuning factor for systems with conserved interacting faces (primary interactions) is the electrostatic component of the interaction energy resulting from the secondary atom–atom electrostatics.

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Toward universal substituent constants: Transferability of group descriptors from the quantum theory of atoms in molecules

Lefrancois-Gagnon

Mawhinney

2021

J Comput Chem

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Traditionally, substituents are described not by their intrinsic properties, but by their effect elsewhere in a molecule. However, the quantum theory of atoms in molecules (QTAIM) provides a route to intrinsic substituent descriptors. Ideally, these descriptors would exhibit minimal change as the local environment changes, and hence be considered transferable. Whether this is true is an open question. Here, we evaluated the transferability of QTAIM functional group descriptors for 117 functional groups in a series of 17 substrates to determine whether descriptors obtained using hydrogen as substrate are transferable. The functional group volume has a strong, consistent, linear relationship throughout. All other hydrogen‐based group descriptors exhibit a relatively strong linear relationship with those in carbon‐based substrates and a reasonable linear relationship with those in non‐carbon‐based substrates. Outliers are readily interpretable in terms of substrate induced functional group geometry changes. As expected, directional descriptors lying along the substituent‐substrate axis are the least conserved.

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The Virial Field and Transferability in DNA Base‐Pairing

Cited by 9 publications

References 57 publications

On the non-existence of parallel universes in chemistry

On the non-existence of parallel universes in chemistry

Anatomy of Base Pairing in DNA by Interacting Quantum Atoms

Toward universal substituent constants: Transferability of group descriptors from the quantum theory of atoms in molecules

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