Conference Agenda

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Session Overview
Session
MS-28: Theory and practice of supramolecular synthons in crystal engineering
Time:
Monday, 16/Aug/2021:
2:45pm - 5:10pm

Session Chair: Seiji Tsuzuki
Session Chair: Alessia Bacchi
Location: Club C

50 1st floor

Invited: Jindrich Fanfrlik (Czech Republic), Berta Gomez-Lor (Spain)


Session Abstract

Control of the molecular arrangement in the crystal is an important issue in research fields such as pharmaceuticals and organic electronic materials, since the molecular arrangement in the crystal greatly affects the physical properties of the organic crystal. Control of crystal structure using supramolecular synthons has been actively studied for decades. Recently, it is becoming possible to reveal the details of the intermolecular interactions of supramolecular synthons by high-level quantum chemical calculations. We invite contributions concerning analysis of intermolecular interactions of supramolecular synthons by theoretical and computational methods and applications of supramolecular synthons for crystal engineering.

For all abstracts of the session as prepared for Acta Crystallographica see PDF in Introduction, or individual abstracts below.


Introduction
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Presentations
2:45pm - 2:50pm

Introduction to session

Seiji Tsuzuki, Alessia Bacchi



2:50pm - 3:20pm

Modulation of halogen, chalcogen and pnictogen bonds by σ-hole tunning

Jindrich Fanfrlik

Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic

Propertios of halogen (X), chalcogen (E) and pnictogen (Pn) bonds can be modulated by changing (i) the nature of the X, E and Pn, (ii) the chemical environment of the X, E and Pn, and (iii) properties of the electron donor. Apart from small molecular complexes, this has been demonstrated in protein-ligand complexes, e.g. on a series of aldose reductase inhibitors. The counterintuitive ability of heteroboranes to form strong σ-hole interactions was found and attributed to the multicenter bonding. It breaks the classical electronegativity concept and results highly positive σ-holes on heterovetices that are incorporated into the skeleton via multicenter type of bonding. X, E and Pn elements in neutral heteroboranes can thus have highly positive σ-holes that are responsible for strong σ-hole interactions. The E···π, X···π, Pn···π and Pn···H-B types of σ-hole interactions of heteroboranes have been observed in the corresponding crystal packings. σ-Hole interactions can be used for designing protein-ligand interactions as well as for crystal engineering.

External Resource:
Video Link


3:20pm - 3:50pm

Benzothiadiazole-based luminescent stimuli-responsive materials: The role of “2S–2N” square synthon on their supramolecular arrangement and switchable behaviour

Berta Gómez-Lor, Marcelo Echeverri

Instituto de Ciencia de Materiales de Madrid, Madrid, Spain

Materials which switch their optical spectroscopic properties (i.e., color, fluorescence) upon physical external stimulation (i.e., pressure, temperature) arouse much interest owing to their potential applications in fields as varied as sensing, construction, recording, display technologies or rewritable paper [1]. In the quest for new organic stimuli responsive materials, the 2,1,3-benzothiadiazole moiety (BTD) have emerged as a promising building block, since the absorption and emission properties of this moiety is strongly influenced by its external environment. In the last few years several BTD-based chromogenic and fluorogenic materials have been reported, but although there are some recent exceptions, in most examples crystalline-to-amorphous transitions are in the origin of this behaviour. This fact prevents an in-depth study of the mechanism behind this process and limits the rational development of new chromophores with predesigned properties.

Herein we present a variety of BTD-derivatives, which crystallizes in different polymorphs with layer-like organization, exhibit distinct light emitting properties under UV illumination and can be readily interconverted by means of external stimuli [2, 3]. Through a joined crystallographic, spectroscopical and theoretical approach we have been able to unravel the origin of the polymorphic transformation and fluorogenic behavior.

In this communication we will discuss interesting design principles, to obtain novel BTD stimuli-responsive organic materials that we have been able to establish as a result of this study. A special emphasis will be placed on the role of “2S–2N” square synthon [4] in the supramolecular arrangement and switchable light emission properties of BTD derivatives.

[1] Roy, B.; Reddy, M. C.; Hazra, P. (2018) Chem. Sci. 9, 3592 [2] Echeverri, M.; Ruiz, C.; Gámez-Valenzuela, S.; Martín, I.; Delgado, M. C. R.; Gutiérrez-Puebla, E.; Monge, M. Á.; Aguirre-Díaz, L. M. & Gómez-Lor, B. (2020) J. Am. Chem. Soc. 142, 17147. [3] Echeverri, M.; Ruiz, C.; Gámez-Valenzuela, S.; Alonso-Navarro, M.; Gutierrez-Puebla, E.; Serrano, J. L.; Ruiz Delgado, M. C. & Gómez-Lor, B. (2020) ACS Appl. Mater. Interfaces 12, 10929. [4] Ams, M. R.; Trapp, N.; Schwab, A.; Milić, J. V.; Diederich, F. (2019) Chem. A Eur. J 25, 323.

External Resource:
Video Link


3:50pm - 4:10pm

Combining modified CCDC tools to predict multicomponent formation: co-crystals of nevirapine and benzoic derivatives

Rogeria Nunes Costa1, Duane Choquesillo-Lazarte2, Elna Pidcock3, Silvia Lucía Cuffini1, Lourdes Infantes4

1Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, 12231-280 São José dos Campos, Brazil; 2Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, 18100 Armilla, Granada, Spain; 3Cambridge Crystallographic Data Centre, Cambridge, CB2 1EZ, United Kingdom; 4Instituto de Química y Fisica Rocasolano, CSIS, 28006 Madrid, Spain

In the pharmaceutical area, the screening of multicomponent forms of a drug is a well-known strategy to assess new crystalline forms with improved physicochemical properties, such as solubility, dissolution, absorption, and others [1-3]. Among the possible multicomponent forms, co-crystals, salts, and solvates are obtained from the inclusion of other suitable molecules (co-formers) within the target molecule‘s crystalline structure. The process to obtain multicomponent crystalline forms of a drug could be an expensive and long-term process, since there is an infinity of possible co-former molecules, in addition to the large number of crystallization techniques that can be used [4]. Thus, it is necessary a strategy to help in the screening of new multicomponent forms of a target molecule through the rationalization of co-former selection, associated with lower consumption of materials and other costs, such as the final disposal of toxic waste. Aiming this, it is proposed a new methodology to optimize and to rationalize the co-former selection using knowledge-based supramolecular chemistry [5]. This new methodology aims to predict the formation of a multicomponent form through the evaluation of the molecular complementarity and the possible intermolecular interactions between the target molecule and the co-former through the use of three statistical tools developed by the Cambridge Crystallographic Data Centre (CCDC) [6]. The SFIMP (Statistical Analysis of Frequency of Interaction for Multicomponent Prediction) method [7] was developed based on the optimization of three CCDC tools – Molecular Complementarity (MC), Coordination Value likelihood calculation (CV), and H-Bond Propensity (HBP) [4, 8-10] – to perform a multicomponent analysis and to allow the combination of their results to obtain a single multicomponent score. Nevirapine (NVP), an antiretroviral drug that exhibits low-aqueous solubility, was used as the target molecule in this study. A bunch of 470 possible co-former molecules was evaluated and the multicomponent score obtained for each one was used to rank these molecules according to the possibility of forming a NVP multicomponent. The SFIMP method was validated through an experimental screening of new multicomponent forms of NVP. The results obtained from the prediction were used in the experimental screening and it enabled the obtention of four new co-crystals of NVP with benzoic acid, 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, and 2,5-dihydroxybenzoic acid [5, 11]. The crystalline structures of these new co-crystals were characterized through single-crystal and powder X-ray diffraction, and differential scanning calorimetry. The SFIMP method shows improvements compared to what is currently available in the CSD system for the analysis and prediction of multicomponent forms. Besides, the results show this methodology as a promising strategy to evaluate the possibility of multicomponent formation in new systems.

External Resource:
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4:10pm - 4:30pm

Gold(III) as an effective electrophilic site, namely coinage bond donor: assembly of AuCl4ˉ units into supramolecular anionic polymers

Giuseppe Resnati1, Andrea Daolio1, Andrea Pizzi1, Giancarlo Terraneo1, Maurizio Ursini1, Antonio Frontera2

1Politecnico di Milano, Milano, Italy; 2Universitat de les Illes Balears, Palma de Mallorca (Baleares), Spain

The distribution of the electron density at the outer regions of bonded atoms is anisotropic. This feature was first proposed for explaining the noncovalent interactions formed by bonded atoms early nineteen nineties [1] and now it is successfully used for rationalizing interactions of elements of all groups of the p block of the periodic table [2]. This mindset began to be extended to d block elements four years ago, being first applied to elements of group 11, then to elements of groups 10 and 12 [3]. For instance, some theoretical studies and experimental results have shown that gold can behave as an effective acceptor of electron density in some of its derivatives, e.g., attractive interactions, named coinage bond (CiB) [3], can be formed between donors of electron density and regions of most positive electrostatic potential at the outer surface of gold nanoparticles and halides.

In this communication we describe that gold can function as acceptor of electron density not only in neutral species, as mentioned above, but also in negatively charged species. It will be proven that the Au(III)∙∙∙nucleophile supramolecular synthon is quite robust and effectively controls the packing of ionic crystals. This synthon may complement the opportunities offered by the aurophilic interactions which are now dominating the interactional landscape of gold. Specifically, we report single crystal structures wherein AuCl4ˉ anions act as self-complementary tectons, chlorine and gold atoms functioning as donors and acceptors of electron density, respectively. Au and Cl atoms of different units form short Au∙∙∙Cl contacts and construct supramolecular anionic polymers (Figure) wherein gold forms a second CiB with a lone pair possessing atom (the oxygen of an ester group). The electrophilic role of gold and the attractive nature of Au∙∙∙Cl/O interactions will be proven by some modelling. A survey of the Cambridge Structural Database (CSD) will be reported suggesting that this behaviour is quite general. Indeed, a non-minor fraction of CSD structures containing the AuCl4ˉ anion show the presence of the Au∙∙∙nucleophile supramolecular synthon and the same holds for structures containing the AuBr4ˉ and Au(CN)4ˉ anions.

External Resource:
Video Link


4:30pm - 4:50pm

Experimental and ab initio molecular dynamics study of hydrogen bond systems in selected crystals

Leszek M. Malec, Mateusz Z. Brela, Katarzyna M. Stadnicka

Faculty of Chemistry of Jagiellonian University in Kraków, Gronostajowa 2, 30-387 Kraków, Poland

Crystal engineering requires precise insight into intermolecular interactions, which results in the crystal symmetry enabling the emergence of desired physical properties [1, 2]. Such a process is based on structural and thermodynamic information, and should also consider the possibility of polymorphism or phase transitions of engineered crystals [3, 4]. Therefore, the controlled synthesis and development of new multifunctional materials and pharmaceuticals should involve the understanding of the dynamics of their interaction networks. One of the most important and abundant intermolecular interactions in crystalline systems are the hydrogen bonds. Several classifications are available for H-bond description, which are based on geometrical parameters, spectroscopic features and charge density calculations. The analysis of different molecular arrangements formed via H-bonds is crucial to understand the stability of crystal phases and the origins of their physical properties [3-5].

In this investigation, the dynamics of complicated H-bond systems in selected crystals were studied using Born-Oppenheimer molecular dynamics (BOMD) simulations. Ab initio molecular dynamics computations provide on the flight evaluation of atomic force evolution using first-principles DFT calculations at every time step. BOMD simulations enable the characterization of solid-state phase dynamics in several statistical ensembles. The insight into crystal entropy and energy is given by the appropriate ensemble averages. The canonical ensemble (NVT) gives the possibility to study the temperature influence on the molecular motion, elastic properties as well as spectroscopic features. In addition, BOMD features allow considering the influence of anharmonicity and quantum effects at the vibrational spectra of examined materials.

In our computations, different cluster sizes were used for investigated H-bonded systems. The system dynamics were studied at different temperatures mainly in the NVT ensemble. Time and space correlations between molecular motions were analysed through the detailed study of interaction network changes along the obtained trajectories. The power spectra were used to investigate the spectroscopic features and the dynamics of considered H-bond systems. Additionally, the structural analysis based on X-ray diffraction experiments was performed, including H-bond propensities and coordination scores. These methods were used to assess the likelihood of specific H-bond formation, and the efficiency of entire H-bond systems according to donor and acceptor expected saturation.

[1] Tiekink, E. R. T., Vittal, J., Zaworotko, M., Ed. (2010). Organic Crystal Engineering: Frontiers in Crystal Engineering. Chichester: John Wiley & Sons, Ltd.
[2] Nangia, A. K. & Desiraju, G. R., (2019). Angew. Chem. Int. Ed. 58, 4100.
[3] Bernstein, J., Davey, R. J. & Henck, J.-O., (1999). Angew. Chem. Int. Ed. 38, 3440.
[4] Price, S. L., (2013). Acta Crystallogr. B69, 313.
[5] Aakeröy, C. B., Forbes, S. & Desper, J., (2014). CrystEngComm. 16, 5870.

Presented computations were performed using PL-Grid Infrastructure and resources provided by ACC Cyfronet AGH. The research was supported by the Polish National Science Centre, project PRELUDIUM 15 number 2018/29/N/ST3/00703 “Study of dynamics in the interaction networks of selected co-crystals”.

External Resource:
Video Link


4:50pm - 5:10pm

Thermally Actuating Multifunctional Molecular Crystals

Durga Prasad Karothu1, Rodrigo Ferreira1, Luca Catalano1, Ghada Dushaq2, Mahmoud Rasras2, Panče Naumov1

1Department of chemistry, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; 2Department of Electrical and Computer Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates

There has been a growing interest in mechanically responsive molecular crystals that show reversible and unusually large positive and negative thermal expansion triggered by external stimuli, a property which could be applied to the design of actuators for soft robotics, artificial muscles, and microfluidic and electrical devices [1]. However, controlling molecular motion to execute sufficiently larger and practically useful thermal expansion in crystals remains a formidable challenge, and strong deformation of such crystals usually results in their destruction [2]. Here we report a single crystal of simple organic compound which exhibits giant thermal expansion due to collective reorientation of molecules in the crystal lattice which is reversible after more than fifty heating and cooling cycles. Such atypical molecular motion, revealed by single crystal X-ray diffraction and microscopy analyses, drives an exceptionally large expansion of the crystal. The applicability of the material as an actuator with electrical properties is demonstrated by dielectric, capacitance, conductance and current measurements. The large shape change of the crystal, combined with remarkable durability and electrical properties, suggest that this material is a strong candidate for microscopic multifunctional thermal actuating devices.

External Resource:
Video Link


 
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