An extended Lennard-Jones potential energy function for diatomic molecules: Application to ground electronic states

Hajigeorgiou, Photos G.

doi:10.1016/j.jms.2010.07.003

Cited by 95 publications

(20 citation statements)

References 56 publications

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“…In terms of high-level theoretical calculations, there are a large number of papers and reviews dealing exclusively or predominately with these molecules, in the literature. [26][27][28][29][30][31][32][33][34][35] The lithium dimer (Li 2 ) is the second smallest stable homonuclear dimer next to H 2 . Spectra of Li 2 were observed and analysed in the 1930s.…”

Section: Introductionmentioning

confidence: 99%

Chemical bonding in Period 2 homonuclear diatomic molecules: a comprehensive relook

Das

Arunan

2019

J Chem Sci

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Theoretical and experimental studies of bonding in the main group homonuclear diatomic molecules have been pursued for many years, and they possess serious challenges for scientists. Most of the early experimental work have been carried out by Herzberg. 1,2 We take a relook at the bonding motifs of Period 2 homonuclear diatomic molecules (from Li 2 to Ne 2) using varieties of quantum chemical tools, commonly used for intermolecular bonding/interactions now. The methods employed include Atoms in Molecules (AIM), Non-covalent Index plot (NCI), Electrostatic potential (ESP), and Potential Acting on one Electron in a Molecule (PAEM). The spectroscopic constants i.e., equilibrium bond distances (r e), harmonic frequencies (x), bond dissociation energies (D e) have all been evaluated using high-level ab initio methods and critically compared with the experimental results. Multi-reference calculations (CASSCF) on B 2 and C 2 have been carried out as they have a large number of low lying electronic states. Bonding within these homonuclear diatomic molecules show all the diversities that are encountered in inter/intra-molecular bonding in chemistry. Based on the AIM analysis, these 8 homonuclear diatomic molecules could be divided into three different groups, based on the correlation between binding energy and the electron density at the bond critical point. However, PAEM/ESP analysis allows us to analyse all eight of them as one group having a good correlation between binding energy and the PAEM/ESP at the critical point between the two atoms. Our results highlight the arbitrariness in relying on some computational tools to characterize a bond as covalent (shared) or ionic/electrostatic (closed). In contrast, they also show the usefulness of the various methods in exploring similarities and differences in bonding. We propose that from Li 2 to Ne 2 , all homonuclear diatomic molecules are bound by 'chemical bonds'.

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Section: Introductionmentioning

confidence: 99%

Chemical bonding in Period 2 homonuclear diatomic molecules: a comprehensive relook

Das

Arunan

2019

J Chem Sci

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“…Molecular interaction field (MIF) calculations were performed by placing each probe at different GRID steps iteratively. Furthermore, total interaction energy ( E xyz ) as a sum of Lennard–Jones potential energy ( E lj ), electrostatic ( E el ) potential interactions, and hydrogen-bond ( E hb ) interactions was calculated at each grid point as shown in Equation (6) [ 134 , 135 ]:

…”

Section: Methodsmentioning

confidence: 99%

Combined Pharmacophore and Grid-Independent Molecular Descriptors (GRIND) Analysis to Probe 3D Features of Inositol 1,4,5-Trisphosphate Receptor (IP3R) Inhibitors in Cancer

Ismatullah¹,

Jabeen²

2021

IJMS

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Inositol 1, 4, 5-trisphosphate receptor (IP3R)-mediated Ca2+ signaling plays a pivotal role in different cellular processes, including cell proliferation and cell death. Remodeling Ca2+ signals by targeting the downstream effectors is considered an important hallmark in cancer progression. Despite recent structural analyses, no binding hypothesis for antagonists within the IP3-binding core (IBC) has been proposed yet. Therefore, to elucidate the 3D structural features of IP3R modulators, we used combined pharmacoinformatic approaches, including ligand-based pharmacophore models and grid-independent molecular descriptor (GRIND)-based models. Our pharmacophore model illuminates the existence of two hydrogen-bond acceptors (2.62 Å and 4.79 Å) and two hydrogen-bond donors (5.56 Å and 7.68 Å), respectively, from a hydrophobic group within the chemical scaffold, which may enhance the liability (IC50) of a compound for IP3R inhibition. Moreover, our GRIND model (PLS: Q2 = 0.70 and R2 = 0.72) further strengthens the identified pharmacophore features of IP3R modulators by probing the presence of complementary hydrogen-bond donor and hydrogen-bond acceptor hotspots at a distance of 7.6–8.0 Å and 6.8–7.2 Å, respectively, from a hydrophobic hotspot at the virtual receptor site (VRS). The identified 3D structural features of IP3R modulators were used to screen (virtual screening) 735,735 compounds from the ChemBridge database, 265,242 compounds from the National Cancer Institute (NCI) database, and 885 natural compounds from the ZINC database. After the application of filters, four compounds from ChemBridge, one compound from ZINC, and three compounds from NCI were shortlisted as potential hits (antagonists) against IP3R. The identified hits could further assist in the design and optimization of lead structures for the targeting and remodeling of Ca2+ signals in cancer.

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“…The transformation to the canonical form and its associated piecewise affine transformation between two different potential curves exploited in ref are distinctly different from the traditional process of constructing approximations to potential curves within a specified family of functions depending upon a finite number of free parameters . In the present work, it is shown how the two points of view can be perceived in stark contrast by applying the above transformation to the canonical form to three of the simplest classical algebraic potential forms, the Kratzer potential, , the Morse potential, , and both a classic , and a generalized Lennard-Jones potential, defined as follows. In the following definitions, D e = E ( R e ) denotes the well depth (dissociation energy for a diatomic molecule) for the potential, R e denotes the equilibrium separation distance of the nuclei for a diatomic molecule, and R am denotes the separation distance of the nuclei at which the attractive (Feynman) force has maximum magnitude, that is, the inflection point of E ( R ).…”

Section: Methodsmentioning

confidence: 99%

“…11,12 Furthermore, there is the potential for reducing computational costs associated with their application in molecular calculations for increasingly complex calculations in fields such as biochemistry and nanotechnology to name a few. [13][14][15][16][17] Three specific algebraic forms for representing pairwise interactions that were among the first introduced and have had a venerated history are the Lennard-Jones 18,19 which can be regarded as a special case of the Mie potential, 20 Kratzer 21,22 and Morse 23,24 potentials. These three potentials have continued popularity for widespread applications, primarily because of limited numbers of adjustable parameters and their abilities to account for the most important inherent characteristics of the potentials they are chosen to represent.…”

Section: Introductionmentioning

confidence: 99%

Morse, Lennard-Jones, and Kratzer Potentials: A Canonical Perspective with Applications

et al. 2016

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Canonical approaches are applied to classic Morse, Lennard-Jones, and Kratzer potentials. Using the canonical transformation generated for the Morse potential as a reference, inverse transformations allow the accurate generation of the Born-Oppenheimer potential for the H ion, neutral covalently bound H, van der Waals bound Ar, and the hydrogen bonded one-dimensional dissociative coordinate in a water dimer. Similar transformations are also generated using the Lennard-Jones and Kratzer potentials as references. Following application of inverse transformations, vibrational eigenvalues generated from the Born-Oppenheimer potentials give significantly improved quantitative comparison with values determined from the original accurately known potentials. In addition, an algorithmic strategy based upon a canonical transformation to the dimensionless form applied to the force distribution associated with a potential is presented. The resulting canonical force distribution is employed to construct an algorithm for deriving accurate estimates for the dissociation energy, the maximum attractive force, and the internuclear separations corresponding to the maximum attractive force and the potential well.

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An extended Lennard-Jones potential energy function for diatomic molecules: Application to ground electronic states

Cited by 95 publications

References 56 publications

Chemical bonding in Period 2 homonuclear diatomic molecules: a comprehensive relook

Chemical bonding in Period 2 homonuclear diatomic molecules: a comprehensive relook

Combined Pharmacophore and Grid-Independent Molecular Descriptors (GRIND) Analysis to Probe 3D Features of Inositol 1,4,5-Trisphosphate Receptor (IP3R) Inhibitors in Cancer

Morse, Lennard-Jones, and Kratzer Potentials: A Canonical Perspective with Applications

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