Highly Polar Stacking Interactions Wrap Inorganics in Organics: Lone-pair–-Hole Interactions between the PdO4 Core and Electron-deficient Arenes

2021 ◽  
Author(s):  
Yury Torubaev ◽  
Ivan V. Skabitsky ◽  
Anton V Rozhkov ◽  
Bartolome Galmes ◽  
Antonio Frontera ◽  
...  
Keyword(s):  
Lone Pair ◽  
Palladium Acetate ◽  
Stacking Interactions

Cocrystallization of the palladium acetate cluster Pd3(OAc)6 (abbreviated as [Pd3]) with electron-deficient iodine(I)-based perfluoroarenes (ArFI: iodopentafluorobenzene, 4-iodoheptafluorotoluene, 1,4-diiodotetrafluorobenzene, 1,2-diiodotetrafluorobenzene, and octafluoro-4,4’-diiodo-1,1-biphenyl) and iodine-free octafluoronaphthalene gave a series of six cocrystals...

scholarly journals Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs

2017 ◽  
Vol 45 (19) ◽  
pp. 11019-11032 ◽  
Author(s):  
Mohit Chawla ◽  
Edrisse Chermak ◽  
Qingyun Zhang ◽  
Janusz M. Bujnicki ◽  
Romina Oliva ◽  
...  
Keyword(s):  
Lone Pair ◽  
Stacking Interactions ◽  
Π Stacking ◽  
Functional Rnas

Concomitant polymorphic forms of 3-cyclopropyl-5-(2-hydrazinylpyridin-3-yl)-1,2,4-oxadiazole

2020 ◽  
Vol 76 (8) ◽  
pp. 836-844 ◽  
Author(s):  
Svitlana V. Shishkina ◽  
Irina S. Konovalova ◽  
Veronika R. Karpina ◽  
Svitlana S. Kovalenko ◽  
Sergiy M. Kovalenko ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Lone Pair ◽  
Lattice Energy ◽  
Structural Motif ◽  
Stacking Interactions ◽  
Centrosymmetric Dimer ◽  
Triclinic Structure ◽  
Isopropanol Solution ◽  
Polymorphic Forms ◽  
Head Type

The dipharmacophore compound 3-cyclopropyl-5-(2-hydrazinylpyridin-3-yl)-1,2,4-oxadiazole, C10H11N5O, was studied on the assumption of its potential biological activity. Two concomitant polymorphs were obtained on crystallization from isopropanol solution and these were thoroughly studied. Identical conformations of the molecules are found in both structures despite the low difference in energy between the four possible conformers. The two polymorphs differ crucially with respect to their crystal structures. A centrosymmetric dimer formed due to both stacking interactions of the `head-to-tail' type and N—H...N(π) hydrogen bonds is the building unit in the triclinic structure. The dimeric building units form an isotropic packing. In the orthorhombic polymorphic structure, the molecules form stacking interactions of the `head-to-head' type, which results in their organization in a column as the primary basic structural motif. The formation of N—H...N(lone pair) hydrogen bonds between two neighbouring columns allows the formation of a double column as the main structural motif. The correct packing motifs in the two polymorphs could not be identified without calculations of the pairwise interaction energies. The triclinic structure has a higher density and a lower (by 0.60 kcal mol−1) lattice energy according to periodic calculations compared to the orthorhombic structure. This allows us to presume that the triclinic form of 3-cyclopropyl-5-(2-hydrazinylpyridin-3-yl)-1,2,4-oxadiazole is the more stable.

scholarly journals The intermolecular interactions in the aminonitromethylbenzenes

2011 ◽  
Vol 9 (1) ◽  
pp. 94-105 ◽  
Author(s):  
Rafal Kruszynski ◽  
Tomasz Sieranski
Keyword(s):  
Hydrogen Bonds ◽  
Lone Pair ◽  
Quantum Mechanical ◽  
Stacking Interactions ◽  
Quantum Mechanical Calculations ◽  
Charge Redistribution ◽  
Intermolecular Hydrogen Bonds ◽  
Non Covalent Interactions ◽  
The One ◽  
Covalent Interactions

AbstractThe intermolecular non-covalent interactions in aminonitromethylbenzenes namely 2-methyl-4-nitroaniline, 4-methyl-3-nitroaniline, 2-methyl-6-nitroaniline, 4-amino-2,6-dinitrotoluene, 2-methyl-5-nitroaniline, 4-methyl-2-nitroaniline, 2,3-dimethyl-6-nitroaniline, 4,5-dimethyl-2-nitroaniline and 2-methyl-3,5-dinitroaniline were studied by quantum mechanical calculations at RHF/311++G(3df,2p) and B3LYP/311++G(3df,2p) level of theory. The calculations prove that solely geometrical study of hydrogen bonding can be very misleading because not all short distances (classified as hydrogen bonds on the basis of interaction geometry) are bonding in character. For studied compounds interaction energy ranges from 0.23 kcal mol−1 to 5.59 kcal mol−1. The creation of intermolecular hydrogen bonds leads to charge redistribution in donors and acceptors. The Natural Bonding Orbitals analysis shows that hydrogen bonds are created by transfer of electron density from the lone pair orbitals of the H-bond acceptor to the antibonding molecular orbitals of the H-bond donor and Rydberg orbitals of the hydrogen atom. The stacking interactions are the interactions of delocalized molecular π-orbitals of the one molecule with delocalized antibonding molecular π-orbitals and the antibonding molecular σ-orbital created between the carbon atoms of the second aromatic ring and vice versa.

Syntheses and Characterization of Two New Mixed-Ligand Bismuth(III) Complexes, Crystal Structure of [Bi(phen)2(NO3)(NCS)2(MeOH)]

2005 ◽  
Vol 60 (4) ◽  
pp. 389-392 ◽  
Author(s):  
Ali Morsali
Keyword(s):  
Lone Pair ◽  
Mixed Ligand ◽  
Bismuth Atom ◽  
Stacking Interactions ◽  
Coordination Geometry ◽  
Aromatic Rings ◽  
X Ray ◽  
X Ray Crystallography ◽  
Elemental Analyses

Complexes [Bi(phen)2(NO3)(NCS)2(MeOH)] and [Bi(phen)2(NO3)2(NCS)] have been synthesized and characterized by their IR spectra and elemental analyses. The structure of the [Bi(phen)2(NO3)(NCS)2(MeOH)] complex has been confirmed by X-ray crystallography. The Bi atoms are unsymmetrically eight-coordinated, N6O2. The arrangement of the ligands does not show a gap in the coordination geometry around the Bi(III) ion, indicating that its lone pair of electrons is not active. The thiocyanate ligands are coordinated to the bismuth atom via the nitrogen atom. There is π-π stacking interactions between the parallel aromatic rings belonging to adjacent chains

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

On the Crystal Chemistry of Inorganic Nitrides: Crystal-Chemical Parameters and Opportunities in the Exploration of Their Compositional Space

2020 ◽  
Author(s):  
Olivier Charles Gagné
Keyword(s):  
Functional Properties ◽  
A Priori ◽  
Lone Pair ◽  
Length Variation ◽  
Electronic Effects ◽  
Statistical Knowledge ◽  
Redox Active ◽  
Multiply Bonded ◽  
Jahn Teller ◽  
Compositional Space

The scarcity of nitrogen in Earth’s crust, combined with challenging synthesis, have made inorganic nitrides a relatively-unexplored class of compounds compared to their naturally-abundant oxide counterparts. To facilitate exploration of their compositional space via <i>a priori</i> modeling, and to help <i>a posteriori</i> structure verification not limited to inferring the oxidation state of redox-active cations, we derive a suite of bond-valence parameters and Lewis-acid strength values for 76 cations observed bonding to N<sup>3-</sup>, and further outline a baseline statistical knowledge of bond lengths for these compounds. We examine structural and electronic effects responsible for the functional properties and anomalous bonding behavior of inorganic nitrides, and identify promising venues for exploring uncharted compositional spaces beyond the reach of high-throughput computational methods. We find that many mechanisms of bond-length variation ubiquitous to oxide and oxysalt compounds (e.g., lone-pair stereoactivity, the Jahn-Teller and pseudo Jahn-Teller effects) are similarly pervasive in inorganic nitrides, and are occasionally observed to result in greater distortion magnitude than their oxide counterparts. We identify inorganic nitrides with multiply-bonded metal ions as a promising venue in heterogeneous catalysis, e.g. in the development of a post-Haber-Bosch process proceeding at milder reaction conditions, thus representing further opportunity in the thriving exploration of the functional properties of this emerging class of materials.<br>

The intermolecular anthracene-transfer in a regiospecific antipodal C60 difunctionalization

2020 ◽  
Author(s):  
Radu Talmazan ◽  
Klaus R. Liedl ◽  
Bernhard Kräutler ◽  
Maren Podewitz
Keyword(s):  
Noncovalent Interactions ◽  
Interaction Model ◽  
Alder Reaction ◽  
Diels Alder ◽  
Stacking Interactions ◽  
Pi Stacking ◽  
Diels Alder Reaction ◽  
Double Decker ◽  
Anthracene Molecule ◽  
New Strategies

We analyze the mechanism of the topochemically controlled difunctionalization of C60 and anthracene, where an anthracene molecule is transferred from one C60 monoadduct to another one under exclusive formation of equal amounts of C60 and the difficult to make antipodal C60 bisadduct. Our herein disclosed dispersion corrected DFT studies show the anthracene transfer to take place in a synchronous retro Diels-Alder/Diels-Alder reaction: an anthracene molecule dissociates from one fullerene under formation of an intermediate, while already undergoing stabilizing interactions with both neighboring fullerenes, facilitating the reaction kinetically. In the intermediate, a planar anthracene molecule is sandwiched between two neighboring fullerenes and forms equally strong "double-decker" type pi-pi stacking interactions with both of these fullerenes. Analysis with the distorsion interaction model shows that the anthracene unit of the intermediate is almost planar with minimal distorsions. This analysis sheds light on the existence of noncovalent interactions engaging both faces of a planar polyunsaturated ring and two convex fullerene surfaces in an unprecedented 'inverted sandwich' structure. Hence, it sheds light on new strategies to design functional fullerene based materials.<br>

An NBO-TS predictive approach for torquoselectivity of ring opening in 3-substituted cyclobutenes

2017 ◽  
Author(s):  
Arpita Yadav ◽  
Dasari L V K Prasad ◽  
Veejendra Yadav
Keyword(s):  
Transition State ◽  
Ring Opening ◽  
Natural Bond Orbital ◽  
Theoretical Calculations ◽  
Lone Pair ◽  
Product Distribution ◽  
Acceptor Substituent ◽  
Important Contributor ◽  
Predictive Approach ◽  
Donor Substituent

<p>The torquoselectivity, the inward or outward ring opening of 3-substituted cyclobutenes, is conventionally guided by the donor and/or acceptor ability of the substituent (S). It is typically predicted by estimating the respective ring opening transition state (TS) barriers. While there is no known dissent in regard to the outward rotation of electron-rich substituents from the approaches of TS calculations, the inward rotation was predicted for some electron-accepting substituents and outward for others. To address this divergence in predicting the torquoselectivity, we have used reliable orbital descriptors through natural bond orbital theoretical calculations and demonstrated that (a) interactions <i>n</i><i><sub>S</sub></i>→s*<sub>C3C4</sub> for a lone pair containing substituent, s<sub>S</sub>→s*<sub>C3C4</sub> for a s-donor substituent, s<sub>C3C4</sub>→p*<sub>S</sub> for a resonance-accepting substituent and s<sub>C3C4</sub>→s*<sub>S</sub> for a s-acceptor substituent constitute the true electronic controls of torquoselectivity, and (b) reversibility of the ring opening event is an additional important contributor to the observed product distribution.</p>

Bond-length distributions for ions bonded to oxygen: Metalloids and post-transition metals

2017 ◽  
Author(s):  
Olivier Charles Gagné ◽  
Frank Christopher Hawthorne
Keyword(s):  
Transition Metal ◽  
Transition Metals ◽  
Metal Ions ◽  
Bond Length ◽  
Lone Pair ◽  
Transition Metal Ions ◽  
Oxygen Lone Pair

Bond-length distributions are examined for thirty-three configurations of the metalloid ions and fifty-six configurations of the post-transition-metal ions bonded to oxygen. Lone-pair stereoactivity is discussed.

Bond-length distributions for ions bonded to oxygen: Metalloids and post-transition metals

2017 ◽  
Author(s):  
Olivier Charles Gagné ◽  
Frank Christopher Hawthorne
Keyword(s):  
Transition Metal ◽  
Transition Metals ◽  
Metal Ions ◽  
Bond Length ◽  
Lone Pair ◽  
Transition Metal Ions ◽  
Oxygen Lone Pair

Bond-length distributions are examined for thirty-three configurations of the metalloid ions and fifty-six configurations of the post-transition-metal ions bonded to oxygen. Lone-pair stereoactivity is discussed.

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