Comparative analysis of electrostatic potential maxima and minima on molecular surfaces, as determined by three methods and a variety of basis sets

Riley, Kevin E.; Tran, Khanh-An; Lane, Pat; Murray, Jane S.; Politzer, Peter

doi:10.1016/j.jocs.2016.03.010

Cited by 72 publications

(55 citation statements)

References 64 publications

(116 reference statements)

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“…(All calculations to be reported are at the density functional M06-2X/6-31G* level, using the Gaussian 09 [32] and WFA-SAS [33] codes. The 6-31G* basis set has been demonstrated to give reliable electrostatic potentials [34].) In Figure 1a, note the positive potential on the outside of the bromine, along the extension of the P-Br bond; its most positive value (the local V S,max ) is 5 kcal/mol.…”

Section: A Brief History Of the σ-Holementioning

confidence: 99%

σ-Hole Interactions: Perspectives and Misconceptions

2017

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After a brief discussion of the σ-hole concept and the significance of molecular electrostatic potentials in noncovalent interactions, we draw attention to some common misconceptions that are encountered in that context: (1) Since the electrostatic potential reflects the contributions of both the nuclei and the electrons, it cannot be assumed that negative potentials correspond to "electron-rich" regions and positive potentials to "electron-poor" ones; (2) The electrostatic potential in a given region is determined not only by the electrons and nuclei in that region, but also by those in other portions of the molecule, especially neighboring ones; (3) A σ-hole is a region of lower electronic density on the extension of a covalent bond, not an electrostatic potential; (4) Noncovalent interactions are between positive and negative regions, which are not necessarily associated with specific atoms, so that "close contacts" between atoms do not always indicate the actual interactions.Keywords: σ-holes; noncovalent interactions; electrostatic potential; close contacts A Brief History of the σ-HoleThe σ-hole concept was introduced by Clark in the context of halogen bonding, at a conference in 2005 [1], although it did not appear in the chemical literature until 2007 [2]. Halogen bonding involves a favorable noncovalent interaction between a covalently-bonded halogen and a negative site, such as a lone pair. Such interactions were already known to experimentalists in the 19th century [3,4], and were studied extensively in the 20th [5][6][7][8][9][10], with crystallography playing a major role [10][11][12][13]. Nevertheless the basis for halogen bonding was not really understood. It was frequently rationalized as "charge transfer" from an electron "donor" (e.g., the lone pair) to an "acceptor" (the halogen), invoking the valence bond formalism of Mulliken [14] (which was later put in molecular orbital terms by Flurry [15,16]).However, the halogen is the most electronegative atom in each row of the periodic table, and a singly-bonded halogen atom is generally viewed as being negative in character. So why should it interact attractively with a donor of electronic charge? It was in fact pointed out long ago [7,17] that Mulliken's charge-transfer formalism was not intended to be an elucidation of the bonding in a ground-state noncovalent complex; it was purely a mathematical modeling of the transition of the ground-state complex to a low-lying excited state. The existence of halogen bonding was thus viewed by many as an enigma.The key to resolving the enigma was the molecular electrostatic potential. This is the potential V(r) that is created at any point r in the space of a molecule by its nuclei and electrons, given rigorously by Equation (1):Z A is the charge on nucleus A, located at R A , and ρ(r) is the molecule's electronic density. Regions in which V(r) is positive, indicating the dominance of the nuclear contribution, are attractive to

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Section: A Brief History Of the σ-Holementioning

confidence: 99%

σ-Hole Interactions: Perspectives and Misconceptions

2017

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“…It has recently been shown that this basis set size is sufficient for these purposes. 24 Differential electron densities (DED) defined as the difference between the complex electron density and the sum of the monomer electron densities as well as ESPs along the main intermolecular coordinate were calculated at the HF/cc-pVTZ level, all using Gaussian09 25 and Molekel4.3 26 programs. Dipole moments were calculated at the HF/cc-pVDZ level of theory.…”

Section: Electrostatic Potentialsmentioning

confidence: 99%

B–H⋯π: a nonclassical hydrogen bond or dispersion contact?

Fanfrlík

Pecina

Řezáč

et al. 2017

Phys. Chem. Chem. Phys.

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Highlighting research from the Computational Chemistry group of Prof. Pavel Hobza, IOCB Prague, Czech Republic B-H … π: a nonclassical hydrogen bond or dispersion contact?Herein, we re-interpret the nature of B−H … π contacts between closo-C 2 B 10 H 12 carborane and phenyl in Ir-dithiolene-phosphine complexes. These interaction motifs have recently been crystallographically observed and proposed as a new type of electrostatically driven nonclassical hydrogen bonding. By means of advanced quantum chemistry on model systems, we disprove such an explanation on the basis of electrostatic potential (ESP, see figure) which shows an electrostatic repulsion. We find that the formation of the B−H … π interaction motif is due to an attractive dispersion energy term. As featured in:See

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“…Molecular electronic densities are computed at the B3LYP/6-311G* level of theory [41]. Electrostatic potentials are computed using the Spartan molecular electronic structure program [42].…”

Section: Methodsmentioning

confidence: 99%

“…Electrostatic potentials are computed using the Spartan molecular electronic structure program [42]. The V S,max value, which represents the maximum potential value on the halogen, is a convenient measure of the magnitude of the size of a σ-hole, and is used extensively throughout this work [41].…”

Section: Methodsmentioning

confidence: 99%

Strength and Character of R–X···π Interactions Involving Aromatic Amino Acid Sidechains in Protein-Ligand Complexes Derived from Crystal Structures in the Protein Data Bank

Riley

Tran

2017

Crystals

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Abstract:Here, we investigate the strengths of R-X···π interactions, involving both chlorine and bromine, in model systems derived from protein-ligand complexes found in the PDB. We find that the strengths of these interactions can vary significantly, with binding energies ranging from −2.01 to −3.60 kcal/mol. Symmetry adapted perturbation theory (SAPT) analysis shows that, as would be expected, dispersion plays the largest role in stabilizing these R-X···π interactions, generally accounting for about 50% to 80% of attraction. R-Br···π interactions are, for the most part, found to be stronger than R-Cl···π interactions, although the relative geometries of the interacting pair and the halogen's chemical environment can also have a strong impact. The two factors that have the strongest impact on the strength of these R-X···π interactions is the distance between the halogen and the phenyl plane as well as the size of the halogen σ-hole.

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Comparative analysis of electrostatic potential maxima and minima on molecular surfaces, as determined by three methods and a variety of basis sets

Cited by 72 publications

References 64 publications

σ-Hole Interactions: Perspectives and Misconceptions

σ-Hole Interactions: Perspectives and Misconceptions

B–H⋯π: a nonclassical hydrogen bond or dispersion contact?

Strength and Character of R–X···π Interactions Involving Aromatic Amino Acid Sidechains in Protein-Ligand Complexes Derived from Crystal Structures in the Protein Data Bank

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