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Molecules
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Intermolecular Interactions in Crystal Lattice
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Intermolecular Interactions in Crystal Lattice

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 11272

Special Issue Editor

Dr. Jan Sýkora

E-Mail Website
Guest Editor
Institute of Chemical Process Fundamentals, Czech Academy of Sciences, Rozvojová 135, 16502 Prague, Czech Republic
Interests: heteronuclear NMR spectroscopy; HPLC separation methods; structure elucidation; NMR metabolomics; X-ray structure analysis

Special Issue Information

Dear Colleagues,

We recently celebrated the millionth crystal structure deposited in the Cambridge Structural Database. In the vast majority of cases, the crystal structure serves as a confirmation of a compound’s identity, and little attention is paid to the molecular interactions that hold molecules together forming a well-defined 3D framework. The intermolecular interactions, their direction, and strength predetermine the physical properties of the crystal. Regardless of the character of intermolecular interactions, a careful analysis of the possible intermolecular interactions of a given molecule enables their exploitation in crystal engineering. The design and preparation of different polymorphs, solvatomorphs or co-crystals is aimed at the adjustment of physical properties of the crystalline material required by specific applications.

The present Special Issue is focused on discussions on intermolecular interactions in crystal packing determined experimentally by means of X-ray and NMR crystallography.

Dr. Jan Sýkora
Guest Editor

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. Molecules is an international peer-reviewed open access semimonthly 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 2700 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

  • intermolecular interactions
  • crystal packing
  • X-ray crystallography
  • NMR crystallography
  • hydrogen bonds
  • π–π stacking
  • charge-transfer complex
  • crystal engineering
  • cocrystals

Published Papers (5 papers)

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Research

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18 pages, 4910 KiB  
Article
Enantiotropy of Simvastatin as a Result of Weakened Interactions in the Crystal Lattice: Entropy-Driven Double Transitions and the Transient Modulated Phase as Seen by Solid-State NMR Spectroscopy
by Jiri Brus, Jiri Czernek, Martina Urbanova and Ctirad Červinka
Molecules 2022, 27(3), 679; https://doi.org/10.3390/molecules27030679 - 20 Jan 2022
Cited by 1 | Viewed by 2220
Abstract
In crystalline molecular solids, in the absence of strong intermolecular interactions, entropy-driven processes play a key role in the formation of dynamically modulated transient phases. Specifically, in crystalline simvastatin, the observed fully reversible enantiotropic behavior is associated with multiple order–disorder transitions: upon cooling, [...] Read more.
In crystalline molecular solids, in the absence of strong intermolecular interactions, entropy-driven processes play a key role in the formation of dynamically modulated transient phases. Specifically, in crystalline simvastatin, the observed fully reversible enantiotropic behavior is associated with multiple order–disorder transitions: upon cooling, the dynamically disordered high-temperature polymorphic Form I is transformed to the completely ordered low-temperature polymorphic Form III via the intermediate (transient) modulated phase II. This behavior is associated with a significant reduction in the kinetic energy of the rotating and flipping ester substituents, as well as a decrease in structural ordering into two distinct positions. In transient phase II, the conventional three-dimensional structure is modulated by periodic distortions caused by cooperative conformation exchange of the ester substituent between the two states, which is enabled by weakened hydrogen bonding. Based on solid-state NMR data analysis, the mechanism of the enantiotropic phase transition and the presence of the transient modulated phase are documented. Full article
(This article belongs to the Special Issue Intermolecular Interactions in Crystal Lattice)
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17 pages, 6617 KiB  
Article
The Effect of Deoxyfluorination on Intermolecular Interactions in the Crystal Structures of 1,6-Anhydro-2,3-epimino-hexopyranoses
by Martin Jakubec, Ivana Císařová, Jindřich Karban and Jan Sýkora
Molecules 2022, 27(1), 278; https://doi.org/10.3390/molecules27010278 - 03 Jan 2022
Viewed by 1340
Abstract
The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, [...] Read more.
The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-Fax and C4-Feq epimines presented here. Full article
(This article belongs to the Special Issue Intermolecular Interactions in Crystal Lattice)
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14 pages, 1765 KiB  
Article
Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments
by Nghia Tuan Duong, Yoshitaka Aoyama, Katsumi Kawamoto, Toshio Yamazaki and Yusuke Nishiyama
Molecules 2021, 26(15), 4652; https://doi.org/10.3390/molecules26154652 - 31 Jul 2021
Cited by 8 | Viewed by 2111
Abstract
Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided [...] Read more.
Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine. Full article
(This article belongs to the Special Issue Intermolecular Interactions in Crystal Lattice)
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11 pages, 1163 KiB  
Article
Analyzing Discrepancies in Chemical-Shift Predictions of Solid Pyridinium Fumarates
by Martin Dračínský
Molecules 2021, 26(13), 3857; https://doi.org/10.3390/molecules26133857 - 24 Jun 2021
Cited by 3 | Viewed by 1820
Abstract
Highly accurate chemical-shift predictions in molecular solids are behind the success and rapid development of NMR crystallography. However, unusually large errors of predicted hydrogen and carbon chemical shifts are sometimes reported. An understanding of these deviations is crucial for the reliability of NMR [...] Read more.
Highly accurate chemical-shift predictions in molecular solids are behind the success and rapid development of NMR crystallography. However, unusually large errors of predicted hydrogen and carbon chemical shifts are sometimes reported. An understanding of these deviations is crucial for the reliability of NMR crystallography. Here, recently reported large deviations of predicted hydrogen and carbon chemical shifts of a series of solid pyridinium fumarates are thoroughly analyzed. The influence of the geometry optimization protocol and of the computational level of NMR calculations on the accuracy of predicted chemical shifts is investigated. Periodic calculations with GGA, meta-GGA and hybrid functionals are employed. Furthermore, molecular corrections at the coupled-cluster singles-and-doubles (CCSD) level are calculated. The effect of nuclear delocalization on the structure and NMR shielding is also investigated. The geometry optimization with a computationally demanding hybrid functional leads to a substantial improvement in proton chemical-shift predictions. Full article
(This article belongs to the Special Issue Intermolecular Interactions in Crystal Lattice)
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Review

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27 pages, 13983 KiB  
Review
The Phosphorus Bond, or the Phosphorus-Centered Pnictogen Bond: The Covalently Bound Phosphorus Atom in Molecular Entities and Crystals as a Pnictogen Bond Donor
by Pradeep R. Varadwaj, Arpita Varadwaj, Helder M. Marques and Koichi Yamashita
Molecules 2022, 27(5), 1487; https://doi.org/10.3390/molecules27051487 - 23 Feb 2022
Cited by 17 | Viewed by 3096
Abstract
The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a [...] Read more.
The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a nucleophile in another, or the same, molecular entity. It is the second member of the family of pnictogen bonds, formed by the second member of the pnictogen family of the periodic table. In this overview, we provide the reader with a snapshot of the nature, and possible occurrences, of phosphorus-centered pnictogen bonding in illustrative chemical crystal systems drawn from the ICSD (Inorganic Crystal Structure Database) and CSD (Cambridge Structural Database) databases, some of which date back to the latter part of the last century. The illustrative systems discussed are expected to assist as a guide to researchers in rationalizing phosphorus-centered pnictogen bonding in the rational design of molecular complexes, crystals, and materials and their subsequent characterization. Full article
(This article belongs to the Special Issue Intermolecular Interactions in Crystal Lattice)
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