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Crystals
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Heterocyclic Organic Compounds: Crystal Structure and Their Properties
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Heterocyclic Organic Compounds: Crystal Structure and Their Properties

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Organic Crystalline Materials".

Deadline for manuscript submissions: 30 November 2024 | Viewed by 2846

Special Issue Editors

Prof. Dr. Etsuo Yonemochi

E-Mail Website
Guest Editor
School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo 142-8501, Japan
Interests: physicochemimcal properties; physical property analysis; crystal form; polymorph prediction
Special Issues, Collections and Topics in MDPI journals
Dr. Nagaraju Sakkani

E-Mail Website
Guest Editor Assistant
College of Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
Interests: organic synthesi; asymmetric organocatalysis; photocatalysis; medicinal chemsitry and process chemistry

Special Issue Information

Dear Colleagues,

In the realm of organic chemistry, heterocyclic compounds are intriguing and versatile entities. Their diverse array of structures, ranging from simple five-membered rings to complex fused systems, offers a vast playground for exploration. These compounds exhibit extensive applicative potential due to their presence of heteroatoms, extended conjugation, aromaticity, and hydrogen bonding. Notably, they are prevalent in numerous drugs, from antibiotics to anticancer agents, with over 75% of heterocyclic derivatives currently in clinical use. A recent survey revealed that, in 2021, around 36 new chemical entities (NCEs) containing heterocyclic compounds were approved by the US Food and Drug Administration (FDA).

The significance of heterocyclic compounds extends beyond mere chemical structures into the realms of materials science, pharmaceuticals, and agrochemicals. Several heterocyclic compounds serve as the key building blocks for numerous natural products, drug discovery, pharmaceuticals, and functional materials.

Various techniques exist to determine the structure of heterocyclic compounds. However, crystal structures provide complete information about the structure and orientation of molecules, including stereochemistry. This technique also yields crucial insights into their stability, reactivity, packing arrangements, bond lengths, angles, and intermolecular interactions. Consequently, crystallographic studies play an instrumental role in designing the next generation of heterocyclic molecules for discovery and material chemistry based on their targets. Therefore, both the synthesis of novel heterocyclic compounds and crystal studies represent an ideal approach for any drug discovery or material chemistry program.

Hence, the scope of this Special Issue, entitled "Heterocyclic Organic Compounds: Crystal Structure and Properties," is intentionally broad. It welcomes the submission of any type of paper (communication, original paper, perspective paper, review) regarding the synthesis of heterocyclic compounds, structural studies, biological activity applications, and new synthetic methodologies.

Dr. Nagaraju Sakkani
Prof. Dr. Etsuo Yonemochi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • heterocyclic compounds
  • biological activity
  • crystal structure
  • multicomponent reactions
  • new methodologies

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Published Papers (3 papers)

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Research

14 pages, 2662 KiB  
Article
Novel Crystalline Salts of 4-Piperidyl- and 4-Pyridylmethylamines Prepared by Catalytic Hydrogenation of 4-Pyridinecarbonitrile: Crystallographic Unit Cells Based on Powder XRD Patterns by Using the DASH Program Package
by János Madarász and László Hegedűs
Crystals 2024, 14(11), 938; https://doi.org/10.3390/cryst14110938 - 29 Oct 2024
Viewed by 492
Abstract
Structures of some hydrogenated products and intermediates, prepared by a heterogeneous Pd/C or Ru/C catalyst starting from 4-pyridinecarbonitrile (4PN), in water and in the presence of an acidic additive (HCl or H2SO4), were confirmed in various salt [...] Read more.
Structures of some hydrogenated products and intermediates, prepared by a heterogeneous Pd/C or Ru/C catalyst starting from 4-pyridinecarbonitrile (4PN), in water and in the presence of an acidic additive (HCl or H2SO4), were confirmed in various salt forms of 4-piperidylmethylamine (4PIPA) and 4-pyridylmethylamine (4PA). Crystallographic unit cell structure of the completely hydrogenated product salts (4PIPA·H2SO4 and 4PIPA·2HCl) showed a common double-protonated [4PIPA+2H]2+ divalent cation structure, also proved by FT-IR, and that of the 4PA·H2SO4 intermediate salt was also indexed and modeled by means of powder X-ray diffraction, applying the DASH 4.0 software package and crystal coordinates coming from former single-crystal X-ray structure determination. Formations of the anhydrous and hydrated forms of 4PA·0.5H2SO4·xH2O (x = 0 or x = 0.5, hemisulfates) were also studied by powder XRD and FT-IR spectroscopy for comparing these crystal structures. Full article
(This article belongs to the Special Issue Heterocyclic Organic Compounds: Crystal Structure and Their Properties)
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20 pages, 7589 KiB  
Article
Recurrent Supramolecular Patterns in a Series of Salts of Heterocyclic Polyamines and Heterocyclic Dicarboxylic Acids: Synthesis, Single-Crystal X-ray Structure, Hirshfeld Surface Analysis, Energy Framework, and Quantum Chemical Calculations
by Joanna Bojarska, Krzysztof Łyczko, Martin Breza and Adam Mieczkowski
Crystals 2024, 14(8), 733; https://doi.org/10.3390/cryst14080733 - 17 Aug 2024
Cited by 1 | Viewed by 875
Abstract
A series of novel salts based on aromatic polyamines and 2,3-pyrazinedicarboxylic acid, such as C10H12N6O5 (1), C10H9ClN6O4 (2), C11H10N8O [...] Read more.
A series of novel salts based on aromatic polyamines and 2,3-pyrazinedicarboxylic acid, such as C10H12N6O5 (1), C10H9ClN6O4 (2), C11H10N8O4 (3), and C14H17N16O5.5 (4) or 3,4-thiophenedicarboxylic acid, such as C10H10N4O4S (5), C10H9ClN4O4S (6), and C10H10N4O4S2 (7), were synthesized and characterized by single-crystal X-ray diffraction. All compounds crystallize in a monoclinic space group. The structure was subjected to complex Hirshfeld surface analysis, molecular electrostatic potential, enrichment ratio, and energy framework calculations. The influence of different cations on the packing of 3-carboxypyrazine-2-carboxylate and 4-carboxythiophene-3-carboxylate anions in the crystal lattice was studied. O…H/H…O interactions are the main contributor in all crystals. In addition, in a series of pyrazine-containing structures, N(C)…H/H…N(C) interactions have relevance, while in a series of thiophene-based compounds, C…H/H…C and S…H(O)/H(O)…S. In addition, Cl-based interactions are observed in compound 2. According to the enrichment ratio calculations, O…H/H…O and C…C are the most preferable interactions in all structures. The energy frameworks are dominated by the dispersive contribution, only in compound 3 is the electrostatic term dominant. The analyzed structures reveal intra- and intermolecular recurrent supramolecular synthons. In both series of crystals, the robust H-bonded centrosymmetric dimer R22(8) as homo- or as heterosynthon (in compounds 2, 3, 6, and 7) and the intramolecular synthon S(7) generated by O-H…O interactions (in compounds 2, 6, and 7) are present. The supramolecular patterns formed by π…π (C…C) and C-O(Cl,S)…C are also noticeable. Notably, a dual synthon linking the supramolecular chain via π…π interactions and the homosynthon R22(8) via N-H…N interactions is visible in both series of new salts. A library of H-bonding motifs at diverse levels of supramolecular architecture is provided. We extended the analysis of intramolecular H-bonding motifs to similar structures deposited in the Cambridge Structural Database. Another important feature is the existence of an intramolecular O…H…O bridge between two neighboring carboxylic groups as substituents in anions in compounds 3 and 5. In this context, we performed quantum theory of atoms-in-molecule calculations to reveal more details. Full article
(This article belongs to the Special Issue Heterocyclic Organic Compounds: Crystal Structure and Their Properties)
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23 pages, 12447 KiB  
Article
Novel Salts of Heterocyclic Polyamines and 5-Sulfosalicylic Acid: Synthesis, Crystal Structure, and Hierarchical Supramolecular Interactions
by Joanna Bojarska, Krzysztof Łyczko and Adam Mieczkowski
Crystals 2024, 14(6), 497; https://doi.org/10.3390/cryst14060497 - 24 May 2024
Cited by 1 | Viewed by 1011
Abstract
A series of novel salts of heterocyclic polyamines with 5-sulfosalicylic acid (C4H7N4+)(C7H5O6S−)∙2(H2O) (1), (C4H6ClN4+)(C7H5 [...] Read more.
A series of novel salts of heterocyclic polyamines with 5-sulfosalicylic acid (C4H7N4+)(C7H5O6S−)∙2(H2O) (1), (C4H6ClN4+)(C7H5O6S−)∙H2O (2), (C5H8N3+)(C7H5O6S−)∙H2O (3), (C5H7N6+)(C7H5O6S−)∙H2O (4), (C6H14N22+)(C7H4O6S2−)∙H2O (5), and (C14H19N2+)(C7H5O6S−) (6) have been successfully synthesized. Their crystal structures have been determined by single-crystal X-ray diffraction. Overall, compounds adopt a layered structure with aminium cations and 5-sulfosalicylic anions linked via water molecules. The solid-state architectures of these compounds are dominated by O(N,H)-H⋯O and N-H⋯N hydrogen bonds and stabilized by weak interconnects. C-Cl⋯π and S-O⋯π interactions, apart from π⋯π and C-H(O)⋯π, were reported. Diverse approaches were used to study the effect of substituents in the polyamines in solid-state arrangement. A Hirshfeld surface analysis, with associated 3D Hirshfeld surface maps and 2D fingerprint plots, molecular electrostatic potential, and energy frameworks were used to comprehensively investigate the nature and hierarchy of non-covalent interactions and inspect supramolecular differences. The contact enrichment ratio calculations provided deeper insight into the propensity of interconnects to influence crystal packing. The evaluation of the effects of H-bonding synthons resulting from different substituents in the polyamines on self-assemblies is also presented. In the context of crystal engineering, a specific intramolecular synthon via O-H⋯O observed in nearly all crystals can be employed in the pseudo-cyclic replacement strategy in the design of new molecules. Full article
(This article belongs to the Special Issue Heterocyclic Organic Compounds: Crystal Structure and Their Properties)
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