scholarly journals Quantitative Lattice Energy Analysis of Intermolecular Interactions in Crystal Structures of Some Benzimidazole Derivatives

2020 ◽  
Vol 5 (1-2) ◽  
pp. 53-62
Author(s):  
Gopal Sharma ◽  
Rajni Kant
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Energy Analysis ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Molecular Packing ◽  
Benzimidazole Derivatives ◽  
Intermolecular Hydrogen Bonds ◽  
Centrosymmetric Dimers

The benzimidazole moiety found in a large number of biologically important drugs has not been completely realized as yet in respect of its strength and directionality of its molecular interactions. To understand the role played by the intermolecular interactions in the benzimidazole derivatives, lattice energy of a series of five important molecules has been computed and results accrued thereof have been discussed. Analysis of molecular packing based on the intermolecular interaction energies suggests existence of different molecular pairs that play an important role in the stabilization of the crystal structures. Interaction energy analysis of such motifs reveals that intermolecular interactions of the type N-H…N and C-H…N happen to be the major contributors to the stabilization of molecular packing in the unit cell. N-H…π and C-H…π type edge-to-face stacking interactions also contribute significantly to the stabilization of crystal packing. The pairs of N-H…N intermolecular hydrogen bonds link the molecules into centrosymmetric dimers making a contribution of -14 to -18.52 kcal/mol towards stabilization, whereas C-H…N bonds link the molecules into dimers in the energy range of -2 to -5 kcal/mol. Additionally, the role of π…π interactions has also been investigated in molecular stabilization.

scholarly journals Molecular Structures Polymorphism the Role of F…F Interactions in Crystal Packing of Fluorinated Tosylates

Crystals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 242 ◽  
Author(s):  
Dmitry E. Arkhipov ◽  
Alexander V. Lyubeshkin ◽  
Alexander D. Volodin ◽  
Alexander A. Korlyukov
Keyword(s):  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Total Contribution ◽  
X Ray ◽  
Weak Hydrogen Bonds ◽  
Intermolecular Bonding

The peculiarities of interatomic interactions formed by fluorine atoms were studied in four tosylate derivatives p-CH3C6H4OSO2CH2CF2CF3 and p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5, 7) using X-ray diffraction and quantum chemical calculations. Compounds p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) were crystallized in several polymorph modifications. Analysis of intermolecular bonding was carried out using QTAIM approach and energy partitioning. All compounds are characterized by crystal packing of similar type and the contribution of intermolecular interactions formed by fluorine atoms to lattice energy is raised along with the increase of their amount. The energy of intra- and intermolecular F…F interactions is varied in range 0.5–13.0 kJ/mol. Total contribution of F…F interactions to lattice energy does not exceed 40%. Crystal structures of studied compounds are stabilized mainly by C-H…O and C-H…F weak hydrogen bonds. The analysis of intermolecular interactions and lattice energies in polymorphs of p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) has shown that most stabilized are characterized by the least contribution of F…F interactions.

The role of non-covalent intermolecular interactions on the diversity of crystal packing in supramolecular dihalopyridine–silver(i) nitrate complexes

CrystEngComm ◽  
2020 ◽  
Vol 22 (45) ◽  
pp. 7962-7974
Author(s):  
Sunčica Roca ◽  
Lucija Hok ◽  
Robert Vianello ◽  
Mladen Borovina ◽  
Marijana Đaković ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Nitrate Complexes

The crystal structures of six novel Ag+ complexes with NO3− and dihalopyridines revealed intriguing differences that were interpreted by DFT calculations.

Crystal structures and Hirshfeld surface analysis of four 1,4-bis(methoxyphenyl)-2,3-diazabuta-1,3-dienes: comparisons of the intermolecular interactions in related compounds

2019 ◽  
Vol 234 (1) ◽  
pp. 59-71 ◽  
Author(s):  
Ligia R. Gomes ◽  
John N. Low ◽  
Nathasha R. de L. Correira ◽  
Thais C.M. Noguiera ◽  
Alessandra C. Pinheiro ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Dimensional Structure ◽  
Intermolecular Hydrogen Bonds ◽  
Π Interactions ◽  
Isomeric Compound ◽  
Related Compounds

Abstract The crystal structures of four azines, namely 1-3-bis(4-methoxyphenyl)-2,3-diaza-1,4-butadiene, 1, 1,3-bis(2,3-dimethoxyphenyl)-2,3-diaza-1,4-butadiene, 2, 1,3-bis(2-hydroxy-3-methoxyphenyl)-2,3-diaza-1,4-butadiene, 3, and 1,3-bis(2-hydroxy-4-methoxyphenyl)-2,3-diaza-1,4-butadiene, 4, are reported. Molecules of 3 and 4, and both independent molecules of 2, Mol A and Mol B, possess inversion centers. The central C=N–N=C units in each molecule is planar with an (E,E) conformation. The intermolecular interactions found in the four compounds are C–H···O, C–H–N, C–H---π and π---π interactions. However, there is no consistent set of intermolecular interactions for the four compounds. Compound, 1, has a two-dimensional undulating sheet structure, generated from C–H···O and C–H···N intermolecular hydrogen bonds. The only recognized intermolecular interaction in 2 is a C–H···O hydrogen bond, which results in a zig-zag chain of alternating molecules, Mol A and Mol B. While 3 forms a puckered sheet of molecules, solely via C–H···π interactions, its isomeric compound, 4, has a more elaborate three-dimensional structure generated from a combination of C–H···O hydrogen bonds, C–H···π and π···π interactions. The findings in this study, based on both PLATON and Hirshfeld approaches, for the four representative compounds match well the reported structural findings in the literature of related compounds, which are based solely on geometric parameters.

The lines-of-force landscape of interactions between molecules in crystals; cohesive versus tolerant and `collateral damage' contact

2010 ◽  
Vol 66 (3) ◽  
pp. 396-406 ◽  
Author(s):  
Angelo Gavezzotti
Keyword(s):  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Minimum Energy ◽  
Lattice Energy ◽  
Interaction Force ◽  
Coordination Shell ◽  
Geometrical Parameters ◽  
Interaction Energies ◽  
Organic Salts

A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule–molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in ∼ 9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO2, SO2). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom–atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care.

Qualitative and quantitative analysis of intermolecular interactions in xanthenedione derivatives

2018 ◽  
Vol 74 (7) ◽  
pp. 830-838
Author(s):  
Gayathri Purushothaman ◽  
Vijay Thiruvenkatam
Keyword(s):  
Intermolecular Interactions ◽  
Acetylcholinesterase Inhibitors ◽  
Lattice Energy ◽  
Boat Conformation ◽  
Qualitative And Quantitative Analysis ◽  
Structural Conformation ◽  
Hirshfeld Analysis ◽  
Conformational Geometry ◽  
Twisted Boat

The existence of intermolecular interactions and the conformational geometry adopted by molecules are related to biological activity. Xanthenedione molecules are promising and emerging antioxidants and acetylcholinesterase inhibitors. To examine the role of different functional groups involved in the intermolecular interactions and conformational geometries adopted in xanthenediones, a series of three substituted xanthenediones have been crystallized [9-(3-hydroxyphenyl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-1H-xanthene-1,8(2H)-dione, C23H26O4, 9-(5-bromo-2-methoxyphenyl)-3,3,6,6-tetramethyl-3,4,6,7-tetrahydro-2H-xanthene-1,8(5H,9H)-dione, C24H27BrO4, and 3,3,6,6-tetramethyl-9-(pyridin-2-yl)-3,4,6,7-tetrahydro-2H-xanthene-1,8(5H,9H)-dione, C22H25NO3] and their intermolecular interactions analyzedviaHirshfeld analysis. The results show that all the derivatives adopt the same structural conformation, where the central ring has a shallow boat conformation and the outer rings have a twisted boat conformation. The intermolecular interactions in the molecules are predominantly O—H...O, C—H...O and π–π interactions. The optimized structures of the derivatives from theoretical B3LYP/6-311G** calculations show a good correlation with the experimental structures. The lattice energy involved in the intermolecular interactions has been explored usingPIXELC.

Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing

2014 ◽  
Vol 70 (4) ◽  
pp. 681-696 ◽  
Author(s):  
Piyush Panini ◽  
K. N. Venugopala ◽  
Bharti Odhav ◽  
Deepak Chopra
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Biologically Active ◽  
Two Dimensional ◽  
Energy Calculations ◽  
X Ray ◽  
Fingerprint Plots

A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (AandB) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N—H]+...Cl−and [C—H]+...Cl−hydrogen bonds mainly stabilizes the crystal packing in both formsAandB, while in the case ofB·H2O [N—H]+...Owaterand Owater—H...Cl−hydrogen bonds along with [N—H]+...Cl−and [C—H]+...Cl−provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case ofA, form (I) (monoclinic) is more stable whereas forBit is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms ofAandBand its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. TheR/E(distance–energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organicR+and Cl−) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case ofA) or the hydrates (in the case ofB) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms ofAandBand its hydrate were observed to be different.

Similarities and differences in the crystal packing of halogen-substituted indole derivatives

2018 ◽  
Vol 74 (4) ◽  
pp. 376-384 ◽  
Author(s):  
Rahul Shukla ◽  
Paramveer Singh ◽  
Piyush Panini ◽  
Deepak Chopra
Keyword(s):  
Quantum Theory ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Topological Analysis ◽  
Indole Derivatives ◽  
Π Interactions ◽  
Supramolecular Motifs ◽  
Exchange Repulsion ◽  
Similarities And Differences

The role of different intermolecular interactions in the crystal structures of halogen-substituted indoles which are fused with six-membered or seven-membered cyclic rings is investigated here. Several crystal structures show isostructural characteristics due to the presence of similar supramolecular motifs. In the absence of any strong hydrogen bonds, the molecular packing of reported structures is primarily stabilized by the presence of non-classical N—H...π and C—H...π interactions in addition to C—H...X (X = F/Cl/Br) interactions. The nature and energetics of primary and secondary dimeric motifs are partitioned into the electrostatics, polarization, dispersion and exchange–repulsion components using the PIXEL method. Short and directional N—H...π interactions are further explored by a topological analysis of the electron density based on quantum theory of atoms in molecules.

A Comparison of the Enamino Carbonyl Conjugation Efficiency for Hydrogen Bonding Formation in Pyridone and Dihydropyridone Systems

2000 ◽  
Vol 55 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Teresa Borowiak ◽  
Irena Wolska ◽  
Artur Korzański ◽  
Wolfgang Milius ◽  
Wolfgang Schnick ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Steric Hindrance ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds

The crystal structures of two compounds containing enaminone heterodiene systems and forming intermolecular hydrogen bonds N-H·O are reported: 1) 3-ethoxycarbonyl-2-methyl-4-pyridone (hereafter ETPY) and 2) 3-ethoxycarbonyl-2-phenyl-6-methoxycarbonyl-5,6-di-hydro-4-pyridone (hereafter EPPY). The crystal packing is controlled by intermolecular hydro­ gen bonds N-H·O = C connecting the heteroconjugated enaminone groups in infinite chains. In ETPY crystals the intermolecular hydrogen bond involves the heterodienic pathway with the highest π-delocalization that is effective for a very short N·O distance of 2.701(9) Å (average from two molecules in the asymmetric unit). Probably due to the steric hindrance, the hydrogen bond in EPPY is formed following the heterodienic pathway that involves the ester C = O group, although π-delocalization along this pathway is less than that along the pyridone-part pathway resulting in a longer N·O distance of 2.886(3) Å

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