Conformational differences and intermolecular C—H...N interactions in three polymorphs of a bis(pyridinyl)-substituted benzimidazole

The structural characterization of several polymorphic forms of a compound allow the interplay between molecular conformation and intermolecular interactions to be studied, which can contribute to the development of strategies for the rational preparation of materials with desirable properties and the tailoring of intermolecular interactions to produce solids with predictable characteristics of interest in crystal engineering. The crystal structures of two new polymorphs of 5,6-dimethyl-2-(pyridin-2-yl)-1-[(pyridin-2-yl)methyl]-1H-benzimidazole, C20H18N4, are reported. The previously reported polymorph, (1) [Geiger & DeStefano (2014).Acta Cryst.E70, o365], exhibits the space groupC2/c, whereas polymorphs (2) and (3) presented here are in thePnmaandP\overline{1} space groups, respectively. The molecular structures of the three forms differ in their orientations of the 2-(pyridin-2-yl)- and 1-[(pyridin-2-yl)methyl]- substituents. Density functional theory (DFT) calculations show that the relative energies of the molecule in the three conformations follows the order (1) < (2) < (3), with a spread of 10.6 kJ mol−1. An analysis of the Hirshfeld surfaces shows that the three polymorphs exhibit intermolecular C—H...N interactions, which can be classified into six types. Based on DFT calculations involving pairs of molecules having the observed interactions, the C—H...N energy in the systems explored is approximately −11.2 to −14.4 kJ mol−1.

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Polydopamine and eumelanin molecular structures investigated with ab initio calculations

Chemical Science ◽

10.1039/c6sc04692d ◽

2017 ◽

Vol 8 (2) ◽

pp. 1631-1641 ◽

Cited By ~ 67

Author(s):

Chun-Teh Chen ◽

Francisco J. Martin-Martinez ◽

Gang Seob Jung ◽

Markus J. Buehler

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Dft Calculations ◽

Ab Initio Calculations ◽

Ab Initio ◽

Density Functional ◽

Md Simulations ◽

Molecular Structures ◽

Brute Force ◽

Functional Theory

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

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Thiabendazole and Thiabendazole-Formic Acid Solvate: A Computational, Crystallographic, Spectroscopic and Thermal Study

Molecules ◽

10.3390/molecules25133083 ◽

2020 ◽

Vol 25 (13) ◽

pp. 3083 ◽

Cited By ~ 1

Author(s):

Andreia M. Tabanez ◽

Bernardo A. Nogueira ◽

Alberto Milani ◽

M. Ermelinda S. Eusébio ◽

José A. Paixão ◽

...

Keyword(s):

Dft Calculations ◽

Formic Acid ◽

Intermolecular Interactions ◽

Density Functional ◽

Intramolecular Interactions ◽

Conformational Space ◽

Scanning Calorimetry ◽

Trans Form ◽

Strong Basis ◽

Trans Conformer

Thiabendazole (TBZ) is a substance which has been receiving multiple important applications in several domains, from medicine and pharmaceutical sciences, to agriculture and food industry. Here, a comprehensive multi-technique investigation on the molecular and crystal properties of TBZ is reported. In addition, a new solvate of the compound is described and characterized structurally, vibrationally and thermochemically for the first time. Density functional theory (DFT) calculations were used to investigate the conformational space of thiabendazole (TBZ), revealing the existence of two conformers, the most stable planar trans form and a double-degenerated-by-symmetry gauche form, which is ~30 kJ mol−1 higher in energy than the trans conformer. The intramolecular interactions playing the major roles in determining the structure of the TBZ molecule and its conformational preferences were characterized. The UV-visible and infrared spectra of the isolated molecule (most stable trans conformer) were also calculated, and their assignment undertaken. The information obtained for the isolated molecule provided a strong basis for the understanding of the intermolecular interactions and properties of the crystalline compound. In particular, the infrared spectrum for the isolated molecule was compared with that of crystalline TBZ and the differences between the two spectra were interpreted in terms of the major intermolecular interactions existing in the solid state. The analysis of the infrared spectral data was complemented with vibrational results of up-to-date fully-periodic DFT calculations and Raman spectroscopic studies. The thermal behavior of TBZ was also investigated using differential scanning calorimetry (DSC) and thermogravimetry. Furthermore, a new TBZ–formic acid solvate [2-(1,3-thiazol-4-yl)benzimidazolium formate formic acid solvate] was synthesized and its crystal structure determined by X-ray diffraction. The Hirshfeld method was used to explore the intermolecular interactions in the crystal of the new TBZ solvate, comparing them with those present in the neat TBZ crystal. Raman spectroscopy and DSC studies were also carried out on the solvate to further characterize this species and investigate its temperature-induced desolvation.

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A theoretical study of weak interactions in phenylenediamine homodimer clusters

Physical Chemistry Chemical Physics ◽

10.1039/c6cp04922b ◽

2016 ◽

Vol 18 (42) ◽

pp. 29249-29257 ◽

Cited By ~ 16

Author(s):

Chengqian Yuan ◽

Haiming Wu ◽

Meiye Jia ◽

Peifeng Su ◽

Zhixun Luo ◽

...

Keyword(s):

Density Functional Theory ◽

Dft Calculations ◽

Intermolecular Interactions ◽

Density Functional ◽

Theoretical Study ◽

Natural Bond Orbital ◽

Weak Interactions ◽

Interaction Energies ◽

Functional Theory ◽

Weak Intermolecular Interactions

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

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Preparation of Zirconium Oxide Powder Using Zirconium Carboxylate Precursors

Advances in Physical Chemistry ◽

10.1155/2014/429751 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 4

Author(s):

Mohammed H. Al-Hazmi ◽

YongMan Choi ◽

Allen W. Apblett

Keyword(s):

Dft Calculations ◽

Density Functional ◽

Dissociative Adsorption ◽

Gravimetric Analysis ◽

X Ray Diffraction ◽

Functional Theory ◽

Experimental Findings ◽

Periodic Dft Calculations ◽

Good Agreement

Zirconia was prepared at low temperatures (<450°C) using single several source precursors based on zirconium carboxylates where the R groups were systematically varied. The combination of density functional theory (DFT) calculations and extensive characterization of the precursors (i.e., X-ray diffraction, thermal gravimetric analysis, infrared spectroscopy, and scanning electron microscopy) indicated that the carboxylic acid complexes may link the zirconium metal with a cis bidentate configuration. Periodic DFT calculations were performed to examine the interaction between monoclinic ZrO2 and propanoic acid. Dissociative adsorption takes place through the cis bidentate structure with an adsorption energy of −1.43 eV. Calculated vibrational frequencies using the optimized structure are in good agreement with experimental findings.

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Charge transfer complexes between 2-, 3- and 4-aminopyridines and some π-acceptors in the gas phase and in chloroform: DFT calculations

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633616500292 ◽

2016 ◽

Vol 15 (04) ◽

pp. 1650029 ◽

Cited By ~ 1

Author(s):

Nuha Ahmed Wazzan

Keyword(s):

Charge Transfer ◽

Dft Calculations ◽

Gas Phase ◽

Density Functional ◽

Molecular Structures ◽

Basis Set ◽

Charge Transfer Complexes ◽

Good Correspondence ◽

Electronic Distribution ◽

Picryl Chloride

This work reports density functional theory (DFT) calculations on the molecular structures, electronic distribution, and UV-Vis and IR spectroscopy analysis of charge transfer complexes between aminopyridines (APYs), namely 2-APY, 3-APY and 4-APY, as electron-donors and some [Formula: see text]-electron-acceptors, namely chloranil (CHL), tetracyanoethylene (TCNE) and picryl chloride (PC), formed in the gas phase at the B3LYP/6-31[Formula: see text]G(d,p) method/basis set, and in chloroform at the same method/basis set using PCM as solvation model. Good correspondence was generally obtained between the calculated parameters and the experimental ones.

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Experimental and theoretical investigations of selenium nuclear magnetic shielding tensors in Se–N heterocycles

Canadian Journal of Chemistry ◽

10.1139/v09-100 ◽

2009 ◽

Vol 87 (10) ◽

pp. 1546-1564 ◽

Cited By ~ 10

Author(s):

Andre Sutrisno ◽

Andy Y.H. Lo ◽

Joel A. Tang ◽

Jason L. Dutton ◽

Gregg J. Farrar ◽

...

Keyword(s):

Dft Calculations ◽

First Principles ◽

Density Functional ◽

Molecular Geometry ◽

Molecular Structures ◽

Magnetic Shielding ◽

First Principles Calculations ◽

Theoretical Investigations ◽

Intermolecular Contacts ◽

Nuclear Magnetic

A preliminary study involving solid-state 77Se NMR spectroscopy and first principles calculations of 77Se NMR parameters in Se–N heterocycles is reported. 77Se CP/MAS NMR spectra of the ring systems reveal expansive selenium chemical shift (CS) tensors, which are extremely sensitive to molecular geometry, symmetry, ligand substitution, and intermolecular contacts. For systems with known crystal structures, hybrid density functional theory (DFT) calculations of selenium nuclear magnetic shielding (NMS) tensors were carried out, and tensor orientations in the molecular frames examined. Additional DFT calculations of selenium NMS tensors are presented, along with a detailed analysis of pairs of occupied and virtual molecular orbitals that give rise to the Se NMS tensors. A new naturalized local molecular orbital (NLMO) analysis under the same DFT framework is also discussed. Collectively, the NMR data and first principles calculations provide understanding of the influences of electronic structure, bonding, and intermolecular interactions on the selenium NMS tensors, allowing for (i) prediction of unknown molecular structures and (ii) insight into the positions of the stereochemically active selenium lone pairs.

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A COMPARISON OF THE STEREOISOMERIC PENTA-COORDINATED PHOSPHORUS INTERMEDIATES FORMED FROM 19 DIMETHOXYL N-PHOSPHORYL AMINO ACIDS BY DFT CALCULATIONS

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633611006360 ◽

2011 ◽

Vol 10 (02) ◽

pp. 217-229

Author(s):

LIJIAO ZHAO ◽

TINGTING LIU ◽

RUGANG ZHONG

Keyword(s):

Amino Acids ◽

Dft Calculations ◽

Density Functional ◽

Molecular Structures ◽

Phosphoryl Group ◽

Hydroxyl Groups ◽

Functional Theory ◽

Important Species ◽

Ester Exchange ◽

Two Sides

N-phosphoryl amino acids (PAAs) are important species in the origin of life that self-catalyze and self-assemble into polypeptides and polynucleotides under mild conditions. Both experimental and theoretical studies have shown that a penta-coordinated phosphorus intermolecular mixed carboxylic-phosphoric anhydride (IMCPA) is formed as the common intermediate in these reactions. In this work, the mechanism for the formation of stereoisomeric IMCPAs from PAAs is investigated using density functional theory (DFT) calculations at the B3LYP/6-311+G(d,p) theoretical level. The molecular structures of the cis- and the trans-IMCPAs, as well as the transition states of the two stereochemical reaction pathways, were characterized in detail. The results showed that the hydroxyl groups of PAAs were situated in favorable positions for attacking the phosphorus atom from two sides of the phosphoryl group, resulting in the formation of the cis-IMCPA and the trans-IMCPA, respectively. The trans-isomers were predicted to be more likely to undergo a further reaction involving an ester exchange on the phosphorus than the cis-isomers. By comparing the relative energies of the IMCPAs and the activation energies, the trans-IMCPAs were computed to be more stable than the cis-IMCPAs, but the energy barriers for the formation of the trans- and the cis-isomers were similar. This work is expected to shed light on the stereochemical effect involved in the chemical evolution of biomolecules.

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Chemical Speciation of the System Cu(II)-Indomethacin in Ethanol and Water by UV-Vis Spectrophotometry

Journal of Chemistry ◽

10.1155/2016/9804162 ◽

2016 ◽

Vol 2016 ◽

pp. 1-12 ◽

Cited By ~ 4

Author(s):

Norma Rodríguez-Laguna ◽

Luis I. Reyes-García ◽

Rosario Moya-Hernández ◽

Alberto Rojas-Hernández ◽

Rodolfo Gómez-Balderas

Keyword(s):

Density Functional ◽

Equilibrium Constants ◽

Formation Constants ◽

Molecular Structures ◽

Therapeutic Effects ◽

Essential Information ◽

The Density Functional Theory ◽

Crucial Information ◽

Inflammatory Drugs

It has been proposed that the metal-drug complexes could be in fact the active agents displaying therapeutic effects of drugs. The characterization of the global formation equilibrium of complexes formed between metal ions and species with biological activity such as nonsteroidal anti-inflammatory drugs provides essential information to understand the mechanism of action of drugs. Since equilibrium constants determine the relative predominance of species, they provide crucial information to identify what complexes are more likely to be present in the system being responsible for the therapeutic effects of the drug. In this paper, the systems formed between copper and Indomethacin of different concentrations in ethanol or water were studied by UV-Vis spectrophotometry. The stoichiometry of the complexes Cu(II)–Indomethacin and their formation constants were investigated. Moreover, molecular structures of the Cu(II)–Indomethacin complexes were explored by means of the molecular modeling within the frame of the density functional theory.

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Polymerization Isomerism in Co-M (M = Cu, Ag, Au) Carbonyl Clusters: Synthesis, Structures and Computational Investigation

Molecules ◽

10.3390/molecules26061529 ◽

2021 ◽

Vol 26 (6) ◽

pp. 1529

Author(s):

Cristiana Cesari ◽

Beatrice Berti ◽

Francesco Calcagno ◽

Cristina Femoni ◽

Marco Garavelli ◽

...

Keyword(s):

Solid State ◽

Density Functional ◽

Molecular Structures ◽

Molar Ratio ◽

X Ray Diffraction ◽

Functional Theory ◽

Cluster Chemistry ◽

Molecular Weights ◽

Crystallization Conditions

The reaction of [Co(CO)4]− (1) with M(I) compounds (M = Cu, Ag, Au) was reinvestigated unraveling an unprecedented case of polymerization isomerism. Thus, as previously reported, the trinuclear clusters [M{Co(CO)4}2]− (M = Cu, 2; Ag, 3; Au, 4) were obtained by reacting 1 with M(I) in a 2:1 molar ratio. Their molecular structures were corroborated by single-crystal X-ray diffraction (SC-XRD) on isomorphous [NEt4][M{Co(CO)4}2] salts. [NEt4](3)represented the first structural characterization of 3. More interestingly, changing the crystallization conditions of solutions of 3, the hexanuclear cluster [Ag2{Co(CO)4}4]2− (5) was obtained in the solid state instead of 3. Its molecular structure was determined by SC-XRD as Na2(5)·C4H6O2, [PPN]2(5)·C5H12 (PPN = N(PPh3)2]+), [NBu4]2(5) and [NMe4]2(5) salts. 5 may be viewed as a dimer of 3 and, thus, it represents a rare case of polymerization isomerism (that is, two compounds having the same elemental composition but different molecular weights) in cluster chemistry. The phenomenon was further studied in solution by IR and ESI-MS measurements and theoretically investigated by computational methods. Both experimental evidence and density functional theory (DFT) calculations clearly pointed out that the dimerization process occurs in the solid state only in the case of Ag, whereas Cu and Au related species exist only as monomers.

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Intermolecular Interactions in Crystal Structures of Imatinib-Containing Compounds

International Journal of Molecular Sciences ◽

10.3390/ijms21238970 ◽

2020 ◽

Vol 21 (23) ◽

pp. 8970

Author(s):

Anna V. Vologzhanina ◽

Ivan E. Ushakov ◽

Alexander A. Korlyukov

Keyword(s):

Crystal Structures ◽

Intermolecular Interactions ◽

Tyrosine Kinases ◽

Density Functional ◽

Molecular Conformation ◽

Hydrophobic Interactions ◽

Density Functional Theory Calculations ◽

Molecular Surface ◽

Molecular Conformations ◽

Receptor Complexes

Imatinib, one of the most used therapeutic agents to treat leukemia, is an inhibitor that specifically blocks the activity of tyrosine kinases. The molecule of imatinib is flexible and contains several functional groups able to take part in H-bonding and hydrophobic interactions. Analysis of molecular conformations for this drug was carried out using density functional theory calculations of rotation potentials along single bonds and by analyzing crystal structures of imatinib-containing compounds taken from the Cambridge Structural Database and the Protein Data Bank. Rotation along the N-C bond in the region of the amide group was found to be the reason for two relatively stable molecular conformations, an extended and a folded one. The role of various types of intermolecular interactions in stabilization of the particular molecular conformation was studied in terms of (i) the likelihood of H-bond formation, and (ii) their contribution to the Voronoi molecular surface. It is shown that experimentally observed hydrogen bonds are in accord with the likelihood of their formation. The number of H-bonds in ligand-receptor complexes surpasses that in imatinib salts due to the large number of donors and acceptors of H-bonding within the binding pocket of tyrosine kinases. Contribution of hydrophilic intermolecular interactions to the Voronoi molecular surface is similar for both conformations, while π...π stacking is more typical for the folded conformation of imatinib.

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