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Nieuwland C, Almacellas D, Veldhuizen MM, de Azevedo Santos L, Poater J, Fonseca Guerra C. Multiple hydrogen-bonded dimers: are only the frontier atoms relevant? Phys Chem Chem Phys 2024; 26:11306-11310. [PMID: 38054332 PMCID: PMC11022277 DOI: 10.1039/d3cp05244c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulation in the monomers.
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Affiliation(s)
- Celine Nieuwland
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
| | - David Almacellas
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Catalonia, Spain
| | - Mac M Veldhuizen
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
| | - Lucas de Azevedo Santos
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
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Bella G, Holub J, Bruno G, Nicolò F, Santoro A. Mononuclear or Coordination Polymer Complexes? Both Are Possible for 3,6,9-Trioxaundecanedioic Acid. Molecules 2023; 28:7410. [PMID: 37959829 PMCID: PMC10650274 DOI: 10.3390/molecules28217410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Investigating the driving forces leading to the formation of a specific supramolecular architecture among a wide spectrum of all the possibly obtainable structures is not an easy task. The contemporary literature provides several models for correctly predicting the thermodynamically accessible structures that can originate from a library of building blocks. Definitions are rigid by their very nature, so their application may sometimes require a shift in perspective. In the study presented herein, we describe the crystal structures of three metallo-supramolecular architectures assembled from deprotonated derivatives of 3,6,9-trioxaundecanedioic acid and Mn(II), Co(II) and Zn(II). In the Mn(II) case, the complexation resulted in a complex of a discrete/heptacoordinated nature, whereas the other two structures appeared as helical polymers. To explain such an anomaly, in this work, we describe how the interplay between the flexibility of the ligand spacer and the number of coordinating atoms involved determines the divergent or convergent organisation of the final coordination architecture.
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Affiliation(s)
- Giovanni Bella
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy; (G.B.); (G.B.); (F.N.)
| | - Jan Holub
- Department of Inorganic Chemistry, University of Chemistry and Technology, Prague, CZ-16628 Prague, Czech Republic;
| | - Giuseppe Bruno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy; (G.B.); (G.B.); (F.N.)
| | - Francesco Nicolò
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy; (G.B.); (G.B.); (F.N.)
| | - Antonio Santoro
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy; (G.B.); (G.B.); (F.N.)
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Bella G, Milone M, Bruno G, Santoro A. Which DFT factors influence the accuracy of 1H, 13C and 195Pt NMR chemical shift predictions in organopolymetallic square-planar complexes? New scaling parameters for homo- and hetero-multimetallic compounds and their direct applications. Phys Chem Chem Phys 2022; 24:26642-26658. [DOI: 10.1039/d2cp02773a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Because of their chemical heterogeneity, stereochemical complexity and the presence of heavy atoms involving orbitals with high quantum number L, organopolymetallic complexes require considerable focus during their NMR spectral interpretation.
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Affiliation(s)
- Giovanni Bella
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
- Department of Health Science, University of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Marco Milone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Giuseppe Bruno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Antonio Santoro
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
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Chen L, Dang J, Du J, Wang C, Mo Y. Hydrogen and Halogen Bonding in Homogeneous External Electric Fields: Modulating the Bond Strengths. Chemistry 2021; 27:14042-14050. [PMID: 34319620 DOI: 10.1002/chem.202102284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/28/2022]
Abstract
Recent years have witnessed various fascinating phenomena arising from the interactions of noncovalent bonds with homogeneous external electric fields (EEFs). Here we performed a computational study to interpret the sensitivity of intrinsic bond strengths to EEFs in terms of steric effect and orbital interactions. The block-localized wavefunction (BLW) method, which combines the advantages of both ab initio valence bond (VB) theory and molecular orbital (MO) theory, and the subsequent energy decomposition (BLW-ED) approach were adopted. The sensitivity was monitored and analyzed using the induced energy term, which is the variation in each energy component along the EEF strength. Systems with single or multiple hydrogen (H) or halogen (X) bond(s) were also examined. It was found that the X-bond strength change to EEFs mainly stems from the covalency change, while generally the steric effect rules the response of H-bonds to EEFs. Furthermore, X-bonds are more sensitive to EEFs, with the key difference between H- and X-bonds lying in the charge transfer interaction. Since phenylboronic acid has been experimentally used as a smart linker in EEFs, switchable sensitivity was scrutinized with the example of the phenylboronic acid dimer, which exhibits two conformations with either antiparallel or parallel H-bonds, thereby, opposite or consistent responses to EEFs. Among the studied systems, the quadruple X-bonds in molecular capsules exhibit remarkable sensitivity, with its interaction energy increased by -95.2 kJ mol-1 at the EEF strength 0.005 a.u.
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Affiliation(s)
- Li Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Juan Du
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience & Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC 27401, USA
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Trapani M, Castriciano MA, Collini E, Bella G, Cordaro M. Supramolecular BODIPY based dimers: synthesis, computational and spectroscopic studies. Org Biomol Chem 2021; 19:8118-8127. [PMID: 34473180 DOI: 10.1039/d1ob01433a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthetic procedures for the preparation of supramolecular BODIPY dimers decorated with complementary patterns able to induce the formation of a triple hydrogen bond through mutual interactions are here reported. The BODIPY and styryl-equipped BODIPY species have been suitably functionalized in meso position with 2,6-diacetamido-4-pyridyl and 1-butyl-6-uracyl moieties. Dimers and monomers have been subjected to computational and photophysical investigations in solvent media. Various peculiarities concerning the effects of the interaction geometry on the stability of the H-bonded systems have also been investigated. The combination of modelling and experimental data provides a paradigm for improving and refining the BODIPY synthetic pathway to have chromophoric architectures with a programmable supramolecular identity. Furthermore, the possibility of assembling dimers of different dyes through H-bonds could be appealing for a systematic investigation of the principal factors affecting the dynamics of the energy migration and possibly driving coherent transfer mechanisms. Our work highlights how the chemical versatility of these dyes can be exploited to design new BODIPY-based supramolecular architectures.
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Affiliation(s)
- Mariachiara Trapani
- CNR-ISMN, Istituto per lo Studio dei Materiali Nanostrutturati, c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy
| | - Maria Angela Castriciano
- CNR-ISMN, Istituto per lo Studio dei Materiali Nanostrutturati, c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy
| | - Elisabetta Collini
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Giovanni Bella
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy.
| | - Massimiliano Cordaro
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy.
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Intermolecular Forces Driving Hexamethylenetetramine Co-Crystal Formation, a DFT and XRD Analysis. Molecules 2021; 26:molecules26195746. [PMID: 34641290 PMCID: PMC8510214 DOI: 10.3390/molecules26195746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Interest in co-crystals formation has been constantly growing since their discovery, almost a century ago. Such success is due to the ability to tune the physical-chemical properties of the components in solid state by avoiding a change in their molecular structure. The properties influenced by the co-crystals formation range from an improvement of mechanical features and chemical stability to different solubility. In the scientific research area, the pharmacological field is undoubtedly one of those in which an expansion of the co-crystal knowledge can offer wide benefits. In this work, we described the crystalline structure of hexamethylenetetramine co-crystallized with the isophthalic acid, and we compared it with another co-crystal, showing the same components but different stoichiometry. To give a wider overview on the nature of the interactions behind the observed crystal packing and to rationalize the reasons of its formation, a computational analysis on such structures was carried out.
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