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Lone pair

About: Lone pair is a(n) research topic. Over the lifetime, 7142 publication(s) have been published within this topic receiving 173785 citation(s). The topic is also known as: non-bonding pair & Lonepair.
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Journal ArticleDOI
Abstract: We present the development of a force field for simulation of nucleic acids and proteins. Our approach began by obtaining equilibrium bond lengths and angles from microwave, neutron diffraction, and prior molecular mechanical calculations, torsional constants from microwave, NMR, and molecular mechanical studies, nonbonded parameters from crystal packing calculations, and atomic charges from the fit of a partial charge model to electrostatic potentials calculated by ab initio quantum mechanical theory. The parameters were then refined with molecular mechanical studies on the structures and energies of model compounds. For nucleic acids, we focused on methyl ethyl ether, tetrahydrofuran, deoxyadenosine, dimethyl phosphate, 9-methylguanine-l-methylcytosine hydrogen-bonded complex, 9-methyladenine-l-methylthymine hydrogen-bonded complex, and 1,3-dimethyluracil base-stacked dimer. Bond, angle, torsional, nonbonded, and hydrogen-bond parameters were varied to optimize the agreement between calculated and experimental values for sugar pucker energies and structures, vibrational frequencies of dimethyl phosphate and tetrahydrofuran, and energies for base pairing and base stacking. For proteins, we focused on 4>,'lt maps of glycyl and alanyl dipeptides, hydrogen-bonding interactions involving the various protein polar groups, and energy refinement calculations on insulin. Unlike the models for hydrogen bonding involving nitrogen and oxygen electron donors, an adequate description of sulfur hydrogen bonding required explicit inclusion of lone pairs. There are two fundamental problems in simulating the struc­ tural and energetic properties of molecules: the first is how to choose an analytical been placed E(R) which correctly describes the energy of the system in terms of its 3N degrees of freedom. The second is how the simulation can search or span conforma­ tional space (R) in order to answer questions posed by the scientist interested in the properties of the system. For complex systems, solution to the first problem are an es­ sential first step in attacking the second problem, and thus, considerable effort has been placed in developing analytical functions that are simple enough to allow one to simulate the properties of complex molecules yet accurate enough to obtain meaningful estimates for structures and energies. In the case of the structures and thermodynamic stabilities of saturated hydrocarbons in inert solvents or the gas phase, the first problem has been essentially solved by molecular mechanics ap­ proaches of Allinger, I Ermer and Lifson,2 and their co-workers. However, for polar and ionic molecules in condensed phases, unsolved questions remain as to the best form of the analytical function E(R). In the area of proteins and peptides, seminal work has come from the Scheraga 3 and Lifson 4 schools. The Scheraga group has used both crystal packing (intermolecular) and con­ formational properties of peptides to arrive at force fields ECEPP, UNECEPP, and EPEN for modeling structural and thermodynamic properties of peptides and proteins. Levitt, using the energy refinement software developed in the Lifson group, has proposed a force field for proteins based on calculations on lysozyme,S and Gelin and Karplus have adapted this software along with many parameters from the Scheraga studies to do molecular dynamics

4,261 citations


Journal ArticleDOI
David O'Hagan1Institutions (1)
TL;DR: Fundamental aspects of the C-F bond are explored to rationalise the geometry, conformation and reactivity of individual organofluorine compounds.
Abstract: Fluorine is the most electronegative element in the periodic table. When bound to carbon it forms the strongest bonds in organic chemistry and this makes fluorine substitution attractive for the development of pharmaceuticals and a wide range of speciality materials. Although highly polarised, the C–F bond gains stability from the resultant electrostatic attraction between the polarised Cδ+ and Fδ– atoms. This polarity suppresses lone pair donation from fluorine and in general fluorine is a weak coordinator. However, the C–F bond has interesting properties which can be understood either in terms of electrostatic/dipole interactions or by considering stereoelectronic interactions with neighbouring bonds or lone pairs. In this tutorial review these fundamental aspects of the C–F bond are explored to rationalise the geometry, conformation and reactivity of individual organofluorine compounds.

2,223 citations


Journal ArticleDOI
TL;DR: The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding that offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.
Abstract: Short oxygen-halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short C-X...O-Y interaction (C-X is a carbon-bonded chlorine, bromine, or iodine, and O-Y is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X...O distance is less than or equal to the sums of the respective van der Waals radii (3.27 A for Cl...O, 3.37 A for Br...O, and 3.50 A for I...O) and can conform to the geometry seen in small molecules, with the C-X...O angle approximately 165 degrees (consistent with a strong directional polarization of the halogen) and the X...O-Y angle approximately 120 degrees . Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized pi -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.

1,320 citations


Journal ArticleDOI
TL;DR: Experimental as well as computational studies indicate that halogen and other sigma-hole interactions can be competitive with hydrogen bonding, which itself can be viewed as a subset of s Sigma-hole bonding.
Abstract: A halogen bond is a highly directional, electrostatically-driven noncovalent interaction between a region of positive electrostatic potential on the outer side of the halogen X in a molecule R–X and a negative site B, such as a lone pair of a Lewis base or the π-electrons of an unsaturated system. The positive region on X corresponds to the electronically-depleted outer lobe of the half-filled p-type orbital of X that is involved in forming the covalent bond to R. This depletion is labeled a σ-hole. The resulting positive electrostatic potential is along the extension of the R–X bond, which accounts for the directionality of halogen bonding. Positive σ-holes can also be found on covalently-bonded Group IV–VI atoms, which can similarly interact electrostatically with negative sites. Since positive σ-holes often exist in conjunction with negative potentials on other portions of the atom's surface, such atoms can interact electrostatically with both nucleophiles and electrophiles, as has been observed in surveys of crystallographic structures. Experimental as well as computational studies indicate that halogen and other σ-hole interactions can be competitive with hydrogen bonding, which itself can be viewed as a subset of σ-hole bonding.

1,211 citations


Journal ArticleDOI
TL;DR: A σ-hole bond is a noncovalent interaction between a covalently-bonded atom of Groups IV-VII and a negative site, e.g. a lone pair of a Lewis base or an anion.
Abstract: A σ-hole bond is a noncovalent interaction between a covalently-bonded atom of Groups IV–VII and a negative site, e.g. a lone pair of a Lewis base or an anion. It involves a region of positive electrostatic potential, labeled a σ-hole, on the extension of one of the covalent bonds to the atom. The σ-hole is due to the anisotropy of the atom's charge distribution. Halogen bonding is a subset of σ-hole interactions. Their features and properties can be fully explained in terms of electrostatics and polarization plus dispersion. The strengths of the interactions generally correlate well with the magnitudes of the positive and negative electrostatic potentials of the σ-hole and the negative site. In certain instances, however, polarizabilities must be taken into account explicitly, as the polarization of the negative site reaches a level that can be viewed as a degree of dative sharing (coordinate covalence). In the gas phase, σ-hole interactions with neutral bases are often thermodynamically unfavorable due to the relatively large entropy loss upon complex formation.

1,135 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20228
2021207
2020176
2019183
2018204
2017232