scholarly journals Synthon robustness by C-F groups in halogen substituted N-benzylideneanilines

2014 ◽  
Vol 70 (a1) ◽  
pp. C1811-C1811
Author(s):  
Gurpreet Kaur ◽  
Angshuman Roy Choudhury
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Topological Analysis ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor ◽  
The Impact ◽  
Organic Fluorine

The arrangement of the molecules in their crystal structure is controlled by the non-covalent intermolecular interactions other than the effectual space filling. The role of strong hydrogen bonds in guiding the crystal packing is well-known in the literature. But, how significant are the weak interactions in the field of crystal engineering, has yet not been fully understood. Our aim is to comprehend the nature and strength of the weak interactions involving fluorine in guiding the packing of small organic molecules in their respective crystal structure. The reason being the controversies, which are involved regarding the interactions offered by "organic fluorine"[1] and also due to the importance of these interactions in the pharmaceutical industry. Some of the research groups indicate the incapability of interactions offered by fluorine in the formation of supramolecular motifs, whereas other groups have indicated that substantial role is being played by fluorine in constructing the lattice through C-H···F, C-F···F and C-F···π interactions in the presence and absence of strong hydrogen bond donor and acceptor groups. To understand more about these interactions, we have chosen a model system of halogen substituted N-benzylideneanilines[2]. In this system, we have analysed the impact of fluorine mediated interactions on the crystal packing by having fluorine as a substituent on both the phenyl rings. Then the robustness of the synthons offered by organic fluorine has been anticipated in the same system, but with one of the substituent as chlorine or bromine in either of the phenyl ring. It has been observed that the replacement of the non-interacting fluorine by its heavier analogue has not altered the supramolecular motif, which was formed by the other fluorine. But the crystal packing has been found to be completely altered in the molecules where the interacting fluorine was replaced by its heavier analogue. Salient features of our computational studies, which include the calculation of the stabilization energies of the studied dimers using MP2 method and their topological analysis using AIM2000, to support the experimental observations will also be presented to highlight the sturdiness of the synthons formed by so called "organic fluorine".

scholarly journals "Organic Fluorine" and its Importance in Crystal Engineering

2014 ◽  
Vol 70 (a1) ◽  
pp. C669-C669
Author(s):  
Angshuman Roy Choudhury ◽  
Gurpreet Kaur ◽  
Maheswararao Karanam ◽  
Sandhya Patel
Keyword(s):  
Crystal Engineering ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Crystal Lattices ◽  
Organic Systems ◽  
Organic Solid ◽  
Group A ◽  
Number Of Publications ◽  
Organic Fluorine

The phrase "Organic fluorine" [1] was introduced by Dunitz and Taylor in 1997 to identify the C–F bonds in organic systems. Different research groups have used the phrase to glorify or deny the influence of C–F bond in crystal lattices. Once Dunitz stated that "Organic Fluorine: Odd Man Out" and Howard et al. questioned the role of "Organic fluorine" in crystal engineering. While some researchers have refuted the role of "organic fluorine" in crystal packing; the others indicated the importance of the interactions involving the same group. A number of publications have shown the importance of "Organic fluorine" in influencing crystal packing. We have been interested in the area of weak interactions in organic solid state chemistry since 1999 [2]; especially interactions involving "Organic fluorine". The study is being conducted following a systematic approach and is still in progress. We have looked at the structures of a number if tetrahydroisoquinoline derivatives, a number of differently substituted imines, phenyleacetanilydes, benzanilides and azobenzenes [3] etc. in order to elucidate the influence of "Organic fluorine" in crystal engineering both in the presence and in the absence of strong hydrogen bonding functional groups present within the molecule. A short summary of our observations will be highlighted in the presentation.

Evaluation of fluorine-mediated intermolecular interactions in tetrafluorinated tetrahydroisoquinoline derivatives: synthesis and computational studies

2020 ◽  
Vol 76 (4) ◽  
pp. 604-617
Author(s):  
Labhini Singla ◽  
Hare Ram Yadav ◽  
Angshuman Roy Choudhury
Keyword(s):  
Intermolecular Interactions ◽  
Organic Molecules ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Strong Hydrogen Bond ◽  
Supramolecular Synthons ◽  
Wide Range ◽  
Organic Fluorine ◽  
Insight Into

Intermolecular interactions involving the aromatic C—F group in the absence of other strong hydrogen bond acceptors is the theme of this article. Weak interactions involving fluorine are known to generate various supramolecular synthons, thereby altering the crystal structures of small organic molecules. It is demonstrated that the weak interactions involving organic fluorine play a major role in directing crystal packing of highly flexible organic molecules like diphenyl tetrahydroisoquinolines reported herein. The intramolecular C—H...F hydrogen bonds are found to be significant in controlling the molecular conformation in specific cases wheras the intermolecular interactions involving the C—F groups result in a wide range of supramolecular synthons involving C—H...F and C—F...F—C interactions. The interactions are studied computationally to provide insight into their energies and the topology of the interactions is studied using Atoms in Molecules. C—H...F—C interactions are found to be quite stabilizing in nature with the stabilization energy of −13.9 kcal mol−1.

scholarly journals Towards computer-guided tuning of the crystal packing of porous organic cages

2014 ◽  
Vol 70 (a1) ◽  
pp. C667-C667
Author(s):  
Angeles Pulido ◽  
Ming Liu ◽  
Paul Reiss ◽  
Anna Slater ◽  
Sam Chong ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Molecular Sieves ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Aromatic Aldehydes ◽  
Lattice Energy ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Computational Techniques

Among microporous materials, there has been an increasing recent interest in porous organic cage (POC) crystals, which can display permanent intrinsic (molecular) and extrinsic (crystal network) porosity. These materials can be used as molecular sieves for gas separation and potential applications as enzyme mimics have been suggested since they exhibit structural response toward guest molecules[1]. Small structural modifications of the initial building blocks of the porous organic molecules can lead to quite different molecular assembly[1]. Moreover, the crystal packing of POCs is based on weak molecular interactions and is less predictable that other porous materials such as MOFs or zeolites.[2] In this contribution, we show that computational techniques -molecular conformational searches and crystal structure prediction- can be successfully used to understand POC crystal packing preferences. Computational results will be presented for a series of closely related tetrahedral imine- and amine-linked porous molecules, formed by [4+6] condensation of aromatic aldehydes and cyclohexyl linked diamines. While the basic cage is known to have one strongly preferred crystal structure, the presence of small alkyl groups on the POC modifies its crystal packing preferences, leading to extensive polymorphism. Calculations were able to successfully identify these trends as well as to predict the structures obtained experimentally, demonstrating the potential for computational pre-screening in the design of POCs within targeted crystal structures. Moreover, the need of accurate molecular (ab initio calculations) and crystal (based on atom-atom potential lattice energy minimization) modelling for computer-guided crystal engineering will be discussed.

The Interplay among Molecular Structures, Crystal Symmetries and Lattice Energy Landscapes Revealed by Unsupervised Machine Learning: A Closer Look at Pyrrole Azaphenacenes

2019 ◽  
Author(s):  
Jack Yang ◽  
Nathan Li ◽  
Sean Li
Keyword(s):  
Crystal Structure ◽  
Machine Learning ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Similarity Index ◽  
Lattice Energy ◽  
Molecular Structures ◽  
Machine Learning Techniques ◽  
Specific Reference ◽  
Energy Landscapes

The ability to perform large-scale crystal structure predictions (CSP) have significantly advanced the synthesis of functional molecular solids by designs. In our recent work [Chem. Mater., 30, 4361 (2018)], we demonstrated our latest developments in organic CSPs by screening a set of 28 pyrrole azaphenacene isomers which led to one new molecule with higher thermodynamic stability and carrier mobilities in its crystalline form, compared to the one reported experimentally. Hereby, using the lattice energy landscapes for pyrrole azaphenacenes as examples, we applied machine-learning techniques to statistically reveal in more details, on how molecular symmetry and Z' values translate to the crystal packing landscapes, which in terms affect the coverage of landscape through quasi-random crystal structure samplings. A recurring theme in crystal engineering is to identify the probabilities of targeting isostructures to a specific reference crystal upon chemical functionalisations. For this, we propose here a global similarity index in conjunction with the Energy-Density Isostructurality (EDI) map to analyse the lattice energy landscapes for halogen substituted pyrrole azaphenacenes. A continue effort in the field is to accelerate CSPs for sampling a much wider chemical space for high-throughput material screenings, we propose a potential solution to this challenge drawn upon this study. Our work will hopefully stimulate the crystal engineering community in adapting a more statistically-oriented approach in understanding crystal packing of organic molecules in the age of digitisation.

New polymorphs of an old drug: conformational and synthon polymorphism of 5-nitrofurazone

2016 ◽  
Vol 72 (2) ◽  
pp. 263-273 ◽  
Author(s):  
Dorota Pogoda ◽  
Jan Janczak ◽  
Veneta Videnova-Adrabinska
Keyword(s):  
Hydrogen Bond ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Molecular Organization ◽  
Hydrogen Bond Donor ◽  
Scanning Calorimetry ◽  
Geometrical Isomers ◽  
Crystal Forms ◽  
Donor And Acceptor ◽  
Polymorphic Forms

Two new polymorphic forms of 5-nitrofurazone (5-nitro-2-furaldehyde semicarbazone) have been synthesized and structurally characterized by single-crystal and powder X-ray diffraction methods, vibrational spectroscopy (FT–IR and temperature Raman), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and Hirshfeld surface analysis. The compound crystallizes in three different polymorphic formsP21/a(polymorph α),P21(polymorph β) andP21/c(polymorph γ), the crystal structures of two of which (polymorphs β and γ) represent new structure determinations. The solid-state molecular organization in the three crystal forms is analyzed and discussed in terms of molecular conformation, crystal packing and hydrogen-bonded networks. All three crystals are formed fromtransgeometrical isomers, but the molecular conformation of the α-polymorph issyn–anti–anti–anti, while that of β- and γ-polymorphs issyn–anti–syn–syn. As a consequence of this the hydrogen-bond donor and acceptor sites of the molecules are oriented differently, which in turn results in different hydrogen-bond connectivity and packing patterns.

scholarly journals Towards an understanding of the propensity for crystalline hydrate formation by molecular compounds

IUCrJ ◽  
2016 ◽  
Vol 3 (6) ◽  
pp. 430-439 ◽  
Author(s):  
Alankriti Bajpai ◽  
Hayley S. Scott ◽  
Tony Pham ◽  
Kai-Jie Chen ◽  
Brian Space ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Crystal Packing ◽  
Hydrate Formation ◽  
Crystalline Hydrate ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Screening Experiments ◽  
Group Form ◽  
Structural Database ◽  
Molecular Compounds

Hydrates are technologically important and ubiquitous yet they remain a poorly understood and understudied class of molecular crystals. In this work, we attempt to rationalize propensity towards hydrate formation through crystallization studies of molecules that lack strong hydrogen-bond donor groups. A Cambridge Structural Database (CSD) survey indicates that the statistical occurrence of hydrates in 124 molecules that contain five- and six-memberedN-heterocyclic aromatic moieties is 18.5%. However, hydrate screening experiments on a library of 11N-heterocyclic aromatic compounds with at least two acceptor moieties and no competing hydrogen-bond donors or acceptors reveals that over 70% of this group form hydrates, suggesting that extrapolation from CSD statistics might, at least in some cases, be deceiving. Slurrying in water and exposure to humidity were found to be the most effective discovery methods. Electrostatic potential maps and/or analysis of the crystal packing in anhydrate structures was used to rationalize why certain molecules did not readily form hydrates.

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry

2002 ◽  
Vol 58 (3) ◽  
pp. 407-422 ◽  
Author(s):  
Frank H. Allen ◽  
W. D. Samuel Motherwell
Keyword(s):  
Organic Chemistry ◽  
Crystal Structure ◽  
Crystal Chemistry ◽  
Crystal Engineering ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Cambridge Structural Database ◽  
Software Systems ◽  
Wide Range ◽  
Structural Database

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

scholarly journals The Isocyanide Complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd, Pt; X = Cl, Br) as Tectons in Crystal Engineering Involving Halogen Bonds

Crystals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 799
Author(s):  
Maria V. Kashina ◽  
Daniil M. Ivanov ◽  
Mikhail A. Kinzhalov
Keyword(s):  
Dft Calculations ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Topological Analysis ◽  
Electron Localization ◽  
Halogen Bonds ◽  
Isocyanide Ligands ◽  
1D Chains

The isocyanide complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd; X = Cl, Br; M = Pt; X = Br) form isomorphous crystal structures exhibiting the Cl/Br and Pd/Pt exchanges featuring 1D chains upon crystallisation. Crystal packing is supported by the C–X···X–C halogen bonds (HaBs), C–H···X–C hydrogen bonds (HB), X···M semicoordination, and C···C contacts between the C atoms of aryl isocyanide ligands. The results of DFT calculations and topological analysis indicate that all the above contact types belong to attractive noncovalent interactions. A projection of the electron localization function (ELF) and an inspection of the electron density (ED) and the electrostatic potential (ESP) reveal the amphiphilic nature of X atoms playing the role of HaB donors, HaB and HB acceptors, and a nucleophilic partner in X···M semicoordination.

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides

2017 ◽  
Vol 73 (5) ◽  
pp. 805-819 ◽  
Author(s):  
Pradip Kumar Mondal ◽  
Hare Ram Yadav ◽  
Angshuman Roy Choudhury ◽  
Deepak Chopra
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Topological Analysis ◽  
Quantitative Characterization ◽  
Supramolecular Synthons ◽  
Molecular Scaffold ◽  
Substituted Benzamides ◽  
Organic Fluorine

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp2—H...F—Csp2interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp2—F...F—Csp2contacts.

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