1
|
Hübner O, Thusek J, Himmel HJ. Pyridine Dimers and Their Low-Temperature Isomerization: A High-Resolution Matrix-Isolation Spectroscopy Study. Angew Chem Int Ed Engl 2023; 62:e202218042. [PMID: 36633004 DOI: 10.1002/anie.202218042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
The bonding between two neutral aromatic compounds, especially small ones, has been controversially debated in the last decades, and terms like "π-stacking" had to be revised. Surprisingly, despite of many experimental and computational work, there is still no clear consensus about the structure of and the bonding in the pyridine dimer. In this work, for different isomeric forms of the pyridine dimer, the structures and bonding were elucidated by combining high-resolution matrix-isolation spectroscopic results with quantum-chemical calculations. High-resolution IR spectra of Ne matrices at 4 K containing pyridine were recorded for different concentrations and upon annealing to 10 and 12 K, relying on three isotopologues of pyridine. The spectra show the presence of hydrogen-bonded, T-shaped, and stacked forms of weakly-bound pyridine dimers. Among these, the hydrogen-bonded isomer is identified as the lowest-energy form. The results provide for the first time conclusive information about the interaction between two pyridine dimers.
Collapse
Affiliation(s)
- Olaf Hübner
- Inorganic Chemistry, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Jean Thusek
- Inorganic Chemistry, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Hans-Jörg Himmel
- Inorganic Chemistry, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| |
Collapse
|
2
|
Tan SL, Cardoso LNF, de Souza MVN, Wardell SMSV, Wardell JL, Tiekink ERT. Experimental and computational evidence for stabilising parallel, offset π[C(O)N(H)NC]⋯π(phenyl) interactions in acetohydrazide derivatives. CrystEngComm 2022. [DOI: 10.1039/d1ce01492g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stabilising π[C(O)N(H)NC]⋯π(phenyl) interactions are described.
Collapse
Affiliation(s)
- Sang Loon Tan
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Laura N. F. Cardoso
- Instituto de Tecnologia em Fármacos Farmanguinhos, FIOCRUZ Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, Brazil
| | - Marcus V. N. de Souza
- Instituto de Tecnologia em Fármacos Farmanguinhos, FIOCRUZ Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, Brazil
| | | | - James L. Wardell
- Department of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen, AB24 3UE, Scotland, UK
| | - Edward R. T. Tiekink
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| |
Collapse
|
3
|
A triorganotin(IV) cocrystal with pyridinic phosphoramide: crystal structure and DFT calculations. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-020-01461-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
4
|
García-Raso A, Terrón A, Fiol JJ, López-Zafra A, Massanet B, Frontera A, Barceló-Oliver M. Modified-amino acid/peptide pyrimidine analogs: synthesis, structural characterization and DFT studies of N-(pyrimidyl)gabapentine and N-(pyrimidyl)baclofen. NEW J CHEM 2021. [DOI: 10.1039/d1nj04639j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
H-Bonding networks and π–π and halogen bonding interactions in the crystal structures of N-modified amino acid pyrimidine analogs are investigated using DFT calculations and X-ray crystallography analysis.
Collapse
Affiliation(s)
- Angel García-Raso
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Angel Terrón
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Juan J. Fiol
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Adela López-Zafra
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Bárbara Massanet
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Miquel Barceló-Oliver
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| |
Collapse
|
5
|
Blagojević Filipović JP, Hall MB, Zarić SD. Stacking interactions of resonance-assisted hydrogen-bridged rings and C 6-aromatic rings. Phys Chem Chem Phys 2020; 22:13721-13728. [PMID: 32529195 DOI: 10.1039/d0cp01624a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings were systematically studied by analyzing crystal structures in the Cambridge Structural Database (CSD). The interaction energies were calculated by quantum-chemical methods. Although the interactions are stronger than benzene/benzene stacking interactions (-2.7 kcal mol-1), the strongest calculated RAHB/benzene stacking interaction (-3.7 kcal mol-1) is significantly weaker than the strongest calculated RAHB/RAHB stacking interaction (-4.7 kcal mol-1), but for a particular composition of RAHB rings, RAHB/benzene stacking interactions can be weaker or stronger than the corresponding RAHB/RAHB stacking interactions. They are also weaker than the strongest calculated stacking interaction between five-membered saturated hydrogen-bridged rings and benzene (-4.4 kcal mol-1) and between two five-membered saturated hydrogen-bridged rings (-4.9 kcal mol-1). SAPT energy decomposition analyses show that the strongest attractive term in RAHB/benzene stacking interactions is dispersion, however, it is mostly canceled by a repulsive exchange term; hence the geometries of the most stable structures are determined by an electrostatic term.
Collapse
Affiliation(s)
| | - Michael B Hall
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
| |
Collapse
|
6
|
Maroń AM, Choroba K, Małecki JG, Kula S, Malicka E. Platinum(II) coordination compound with 4′-[4-(dimethylamino)phenyl]-2,2′:6′,2″-terpyridine – The new insight into the luminescence behavior and substituent effect. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
7
|
Ninković D, Blagojević Filipović JP, Hall MB, Brothers EN, Zarić SD. What Is Special about Aromatic-Aromatic Interactions? Significant Attraction at Large Horizontal Displacement. ACS CENTRAL SCIENCE 2020; 6:420-425. [PMID: 32232142 PMCID: PMC7099588 DOI: 10.1021/acscentsci.0c00005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Indexed: 05/22/2023]
Abstract
High-level ab initio calculations show that the most stable stacking for benzene-cyclohexane is 17% stronger than that for benzene-benzene. However, as these systems are displaced horizontally the benzene-benzene attraction retains its strength. At a displacement of 5.0 Å, the benzene-benzene attraction is still ∼70% of its maximum strength, while benzene-cyclohexane attraction has fallen to ∼40% of its maximum strength. Alternatively, the radius of attraction (>2.0 kcal/mol) for benzene-benzene is 250% larger than that for benzene-cyclohexane. Thus, at relatively large distances aromatic rings can recognize each other, a phenomenon that helps explain their importance in protein folding and supramolecular structures.
Collapse
Affiliation(s)
- Dragan
B. Ninković
- Innovation
Center of the Faculty of Chemistry in Belgrade, Studentski trg 12-16, Belgrade 11001, Serbia
| | | | - Michael B. Hall
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
- E-mail:
| | - Edward N. Brothers
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874, Doha, Qatar
| | - Snežana D. Zarić
- Faculty
of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11000, Serbia
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874, Doha, Qatar
- E-mail:
| |
Collapse
|
8
|
Malenov DP, Aladić AJ, Zarić SD. Stacking interactions of borazine: important stacking at large horizontal displacements and dihydrogen bonding governed by electrostatic potentials of borazine. Phys Chem Chem Phys 2019; 21:24554-24564. [PMID: 31663532 DOI: 10.1039/c9cp02966d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Potential energy surfaces of borazine-benzene and borazine-borazine stacking interactions were studied by performing DFT, CCSD(T)/CBS and SAPT calculations. The strongest borazine-benzene stacking was found in a parallel-displaced geometry, with a CCSD(T)/CBS interaction energy of -3.46 kcal mol-1. The strongest borazine-borazine stacking has a sandwich geometry, with a CCSD(T)/CBS interaction energy of -3.57 kcal mol-1. The study showed that borazine forms significant stacking interactions at large horizontal displacements (over 4.5 Å), with energies of -2.20 kcal mol-1 for the borazine-benzene and -1.96 kcal mol-1 for the borazine-borazine system. The strength of interactions and their geometrical preferences can be rationalized by observing the electrostatic potentials of borazine and benzene, which is in agreement with SAPT analysis showing that electrostatics is the most important energy component for borazine stacking. All the interactions found in crystal structures of borazine and related compounds were identified either as potential curve minima or the geometries obtained from their optimizations. We also report a new dihydrogen bonding dimer with a CCSD(T)/CBS interaction energy of -2.37 kcal mol-1, which is encountered in the borazine crystal structures and enables the formation of additional simultaneous interactions that contribute to the overall stability of the crystals.
Collapse
Affiliation(s)
- Dušan P Malenov
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia.
| | | | | |
Collapse
|
9
|
Choroba K, Machura B, Raposo LR, Małecki JG, Kula S, Pająk M, Erfurt K, Maroń AM, Fernandes AR. Platinum(ii) complexes showing high cytotoxicity toward A2780 ovarian carcinoma cells. Dalton Trans 2019; 48:13081-13093. [PMID: 31411239 DOI: 10.1039/c9dt02894c] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
2,6-Bis(thiazol-2-yl)pyridines functionalized with 9-anthryl (L1), 9-phenanthryl (L2), and 1-pyrenyl (L3) groups were used for the preparation of [Pt(Ln)Cl]CF3SO3 (1-3). The constitution of the Pt(ii) complexes was determined by 1H and 13C NMR spectroscopy, HR-MS spectrometry, elemental analysis and X-ray analysis (for (1)). The electrochemical and photophysical properties of [Pt(Ln)Cl]CF3SO3 were compared with the behaviour of the Pt(ii) complexes with aryl-substituted 2,2':6',2''-terpyridine ligands. What is noteworthy is that the coordination ability of dtpy toward the Pt(ii) centre was investigated for the first time. All complexes were tested in vitro by MTS assay on four tumor cell lines, A2780 (ovarian carcinoma), HTC116 (colon rectal carcinoma), MCF7 (breast adenocarcinoma), and PC3 (prostate carcinoma) and on normal primary fibroblasts. Compounds (1-3) showed a dose dependent antiproliferative effect in the A2780 cell line with (3) > (2) > (1) and this loss of A2780 cell viability was due to a combination of an apoptotic cell death mechanism via mitochondria and autophagic cell death. Exposure to IC50 concentration of (2) induced an increase in the number of apoptotic nuclei and a depolarization of the mitochondrial membrane which is consistent with the induction of apoptosis while exposure to IC50 concentration of (3) showed an increase in the apoptotic nuclei with a slight hyperpolarization of the mitochondrial membrane that might indicate an initial step of apoptosis induction. The complexes (2) and (3) induce an increase in the production of intracellular ROS which is associated with the trigger of the apoptotic pathways. The ROS production was augmented by the presence of oxidants and correlated with an increase of oxygen radicals. The IC50 of (2) and (3) (4.4 μM and 2.9 μM, respectively) was similar to the IC50 of cisplatin (3.4 μM) in the A2780 cell line, which together with their low cytotoxicity in normal fibroblasts, demonstrates their potential for further studies.
Collapse
Affiliation(s)
- Katarzyna Choroba
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland.
| | - Barbara Machura
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland.
| | - Luis R Raposo
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
| | - Jan G Małecki
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland.
| | - Slawomir Kula
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland.
| | - Michał Pająk
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland.
| | - Karol Erfurt
- Department of Chemical Organic Technology and Petrochemistry, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland
| | - Anna M Maroń
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland.
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
| |
Collapse
|
10
|
Malenov DP, Zarić SD. Strong stacking interactions of metal–chelate rings are caused by substantial electrostatic component. Dalton Trans 2019; 48:6328-6332. [DOI: 10.1039/c9dt00182d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking interactions of metal–chelate rings are strong due to very strong electrostatic energy component.
Collapse
Affiliation(s)
- Dušan P. Malenov
- Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade
- Serbia
- Department of Chemistry
| | - Snežana D. Zarić
- Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade
- Serbia
- Department of Chemistry
| |
Collapse
|
11
|
Andrić JM, Antonijević IS, Janjić GV, Zarić SD. Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules. J Mol Model 2018; 24:60. [PMID: 29464387 DOI: 10.1007/s00894-017-3570-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/14/2017] [Indexed: 11/30/2022]
Abstract
Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.
Collapse
Affiliation(s)
- Jelena M Andrić
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Ivana S Antonijević
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Goran V Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia. .,Department of Chemistry, Texas A & M University at Qatar, P.O. Box 23874, Doha, Qatar.
| |
Collapse
|
12
|
Nagasaka M, Yuzawa H, Kosugi N. Intermolecular Interactions of Pyridine in Liquid Phase and Aqueous Solution Studied by Soft X-ray Absorption Spectroscopy. Z PHYS CHEM 2018. [DOI: 10.1515/zpch-2017-1054] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Intermolecular interactions of pyridine in liquid and in aqueous solution are studied by using soft X-ray absorption spectroscopy (XAS) at the C, N, and O K-edges. XAS of liquid pyridine shows that the N 1s→π* peak is blue shifted and the C 1s→π* peak of the meta and para sites is red shifted, respectively, as compared with XAS of pyridine gas. These shifts in liquid are smaller than those in clusters, indicating that the intermolecular interaction of liquid pyridine is weaker than that of pyridine cluster, as supported by the combination of quantum chemical calculations of the core excitation and molecular dynamics simulations of the liquid structure. On the other hand, XAS spectra of aqueous pyridine solutions (C5H5N)x(H2O)1−x
measured at different molar fractions show that in the pyridine rich region, x>0.7, the C and N 1s→π* peak energies are not so different from pure liquid pyridine (x=1.0). In this region, antiparallel displaced structures of pyridine molecules are dominant as in pure pyridine liquid. In the O K-edge XAS, the pre-edge peaks sensitive to the hydrogen bond (HB) network of water molecules show the red shift of −0.15 eV from that of bulk water, indicating that small water clusters with no large-scale HB network are formed in the gap space of structured pyridine molecules. In the water rich region, 0.7>x, the N 1s→π* peaks and the O 1s pre-edge peaks are blue shifted, and the C 1s→π* peaks of the meta and para sites are red-shifted by increasing molar fraction of water. The HB network of bulk water is dominant, but quantum chemical calculations indicate that small pyridine clusters with the HB interaction between the H atom in water and the N atom in pyridine are still existent even in very dilute pyridine solutions.
Collapse
Affiliation(s)
- Masanari Nagasaka
- Institute for Molecular Science and SOKENDAI (Graduate University for Advanced Studies) , Myodaiji, Okazaki 444-8585 , Japan
| | - Hayato Yuzawa
- Institute for Molecular Science , Myodaiji, Okazaki 444-8585 , Japan
| | - Nobuhiro Kosugi
- Institute for Molecular Science and SOKENDAI (Graduate University for Advanced Studies) , Myodaiji, Okazaki 444-8585 , Japan
| |
Collapse
|
13
|
Jacobs M, Greff Da Silveira L, Prampolini G, Livotto PR, Cacelli I. Interaction Energy Landscapes of Aromatic Heterocycles through a Reliable yet Affordable Computational Approach. J Chem Theory Comput 2018; 14:543-556. [DOI: 10.1021/acs.jctc.7b00602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Matheus Jacobs
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Leandro Greff Da Silveira
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
- Departamento
de Ciências Exatas e da Terra, Universidade Regional Integrada do Alto Uruguay e da Missões (URI), Avenida Assis Brasil 709, CEP 98400-00 Frederico Westphalen, Brazil
| | - Giacomo Prampolini
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Paolo Roberto Livotto
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Ivo Cacelli
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi
3, I-56124 Pisa, Italy
| |
Collapse
|
14
|
Malenov DP, Antonijević IS, Hall MB, Zarić SD. Stacking of cyclopentadienyl organometallic sandwich and half-sandwich compounds. Strong interactions of sandwiches at large offsets. CrystEngComm 2018. [DOI: 10.1039/c8ce00597d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
73% of stacking of Cp sandwiches in the CSD is at large offsets, since these interactions are relatively strong. Much weaker stacking between Cp half-sandwiches is surprising 60% of all stacks, due to more simultaneous interactions.
Collapse
Affiliation(s)
| | - Ivana S. Antonijević
- Institute of Chemistry
- Technology and Metallurgy
- University of Belgrade
- 11000 Belgrade
- Serbia
| | | | - Snežana D. Zarić
- Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade
- Serbia
- Department of Chemistry
| |
Collapse
|
15
|
Sierański T. Discovering the stacking landscape of a pyridine-pyridine system. J Mol Model 2017; 23:338. [PMID: 29124340 PMCID: PMC5680376 DOI: 10.1007/s00894-017-3496-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/09/2017] [Indexed: 10/24/2022]
Abstract
Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the interaction energies of the particular systems-one can learn how the pyridine dimer stability changes along with various geometrical parameters. Other calculations such as natural bond orbital and energy decomposition have also been applied. The interplay of two significant factors, electrostatic forces and electron correlation effects, have been evaluated. The role of π···π interactions in the stacked pyridine systems has also been confirmed, and surprisingly, this happened to be true even for the geometries where the formation of C-H···π interactions might be proposed instead. The combination of many different methods has revealed the complexity of the stacking interactions. Apart from providing a "literal new look" into pyridine interaction patterns another picture has emerged. A stacking interaction in a pyridine dimer system is perceived as a combination of many different sources of the interaction energy, including orbital ones, and this is true for many different geometries.
Collapse
Affiliation(s)
- Tomasz Sierański
- Institute of General and Ecological Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland.
| |
Collapse
|
16
|
|
17
|
Sanchez Montilva OC, Movilla F, Rodriguez MG, Di Salvo F. Synthesis, crystal structure and study of the crystal packing in the complex bis(4-aminopyridine-κN 1)dichloridocobalt(II). Acta Crystallogr C Struct Chem 2017; 73:399-406. [PMID: 28469066 DOI: 10.1107/s2053229617004880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Abstract
Despite the large number of reported crystalline structures of coordination complexes bearing pyridines as ligands, the relevance of π-π interactions among these hereroaromatic systems in the stabilization of their supramolecular structures and properties is not very well documented in the recent literature. The title compound, [CoCl2(C5H6N2)2], was obtained as bright-blue crystals suitable for single-crystal X-ray diffraction analysis from the reaction of 4-aminopyridine with cobalt(II) chloride in ethanol. The new complex was fully characterized by a variety of spectroscopic techniques and single-crystal X-ray diffraction. The crystal structure showed a tetrahedral complex stabilized mainly by bidimensional motifs constructed by π-π interactions with large horizontal displacements between the 4-aminopyridine units, and N-H...Cl hydrogen bonds. Other short contacts, such as C-H...Cl interactions, complete the three-dimensional arrangement. The supramolecular investigation was extended by statistical studies using the Cambridge Structural Database and a Hirshfeld surface analysis.
Collapse
Affiliation(s)
- Olga Carolina Sanchez Montilva
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Buenos Aires, Argentina
| | - Federico Movilla
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Buenos Aires, Argentina
| | - Maricel Gabriela Rodriguez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Buenos Aires, Argentina
| | - Florencia Di Salvo
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Buenos Aires, Argentina
| |
Collapse
|
18
|
Lu N, Wei RJ, Lin KY, Alagesan M, Wen YS, Liu LK. Weak hydrogen bonding and fluorous interactions in the chloride and bromide salts of 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:343-349. [PMID: 28378719 DOI: 10.1107/s2053229617004016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/13/2017] [Indexed: 11/10/2022]
Abstract
Neutralization of 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridine with hydrohalo acids HX (X = Cl and Br) yielded the pyridinium salts 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium chloride, C9H10F4NO+·Cl-, (1), and 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium bromide, C9H10F4NO+·Br-, (2), both carrying a fluorous side chain at the para position of the pyridinium ring. Single-crystal X-ray diffraction techniques revealed that (1) and (2) are isomorphous. The halide anions accept four hydrogen bonds from N-H, ortho-C-H and CF2-H groups. Two cations and two anions form a centrosymmetric dimeric building block, utilizing complimentary N-H...X...H-Csp3 connections. These dimers are further crosslinked, utilizing another complimentary Csp2-H...X...H-Csp2 connection. The pyridinium rings are π-stacked, forming columns running parallel to the a axis that make angles of ca 44-45° with the normal to the pyridinium plane. There are also supramolecular C-H...F-C interactions, namely bifurcated C-H...F and bifurcated C-F...H interactions; additionally, one type II C-F...F-C halogen bond has been observed.
Collapse
Affiliation(s)
- Norman Lu
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Rong Jyun Wei
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Kwan Yu Lin
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Mani Alagesan
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Yuh Sheng Wen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Ling Kang Liu
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| |
Collapse
|
19
|
Blagojević JP, Veljković DŽ, Zarić SD. Stacking interactions between hydrogen-bridged and aromatic rings: study of crystal structures and quantum chemical calculations. CrystEngComm 2017. [DOI: 10.1039/c6ce02045c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
20
|
An Y, Doney AC, Andrade RB, Wheeler SE. Stacking Interactions between 9-Methyladenine and Heterocycles Commonly Found in Pharmaceuticals. J Chem Inf Model 2016; 56:906-14. [DOI: 10.1021/acs.jcim.5b00651] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi An
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Analise C. Doney
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Rodrigo B. Andrade
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| |
Collapse
|
21
|
Very Strong Parallel Interactions Between Two Saturated Acyclic Groups Closed with Intramolecular Hydrogen Bonds Forming Hydrogen-Bridged Rings. CRYSTALS 2016. [DOI: 10.3390/cryst6040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
22
|
|
23
|
Yu TL, Hao PF, Shen JJ, Li HH, Fu YL. Stoichiometry-controlled structural and functional variation in two photochromic iodoargentates with a fast and wide range response. Dalton Trans 2016; 45:16505-16510. [DOI: 10.1039/c6dt03105f] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Two MCMP+/iodoargentate hybrids have been synthesized and they exhibit rare electron transfer photochromsim with a fast response rate, a wide response range and a long-lived charge-separated state, which is largely ascribed to the flexible aggregation of electron-deficient MCMP+ counterions.
Collapse
Affiliation(s)
- Tan-Lai Yu
- School of Chemistry & Material Science
- Shanxi Normal University
- Linfen 041004
- P. R. China
| | - Peng-Fei Hao
- School of Chemistry & Material Science
- Shanxi Normal University
- Linfen 041004
- P. R. China
| | - Jun-Ju Shen
- School of Chemistry & Material Science
- Shanxi Normal University
- Linfen 041004
- P. R. China
| | - Hui-Hui Li
- School of Chemistry & Material Science
- Shanxi Normal University
- Linfen 041004
- P. R. China
| | - Yun-Long Fu
- School of Chemistry & Material Science
- Shanxi Normal University
- Linfen 041004
- P. R. China
| |
Collapse
|
24
|
Ninković DB, Vojislavljević-Vasilev DZ, Medaković VB, Hall MB, Brothers EN, Zarić SD. Aliphatic–aromatic stacking interactions in cyclohexane–benzene are stronger than aromatic–aromatic interaction in the benzene dimer. Phys Chem Chem Phys 2016; 18:25791-25795. [DOI: 10.1039/c6cp03734h] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations.
Collapse
Affiliation(s)
- D. B. Ninković
- Innovation Center of Department of Chemistry
- 11000 Belgrade
- Serbia
- Department of Chemistry
- Texas A&M University at Qatar
| | | | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade
- Serbia
| | - M. B. Hall
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - E. N. Brothers
- Department of Chemistry
- Texas A&M University at Qatar
- Doha
- Qatar
| | - S. D. Zarić
- Department of Chemistry
- Texas A&M University at Qatar
- Doha
- Qatar
- Department of Chemistry
| |
Collapse
|
25
|
The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
|
26
|
Malenov DP, Ninković DB, Zarić SD. Stacking of metal chelates with benzene: can dispersion-corrected DFT be used to calculate organic-inorganic stacking? Chemphyschem 2015; 16:761-8. [PMID: 25630762 DOI: 10.1002/cphc.201402589] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Indexed: 11/06/2022]
Abstract
CCSD(T)/CBS energies for stacking of nickel and copper chelates are calculated and used as benchmark data for evaluating the performance of dispersion-corrected density functionals for calculating the interaction energies. The best functionals for modeling the stacking of benzene with the nickel chelate are M06HF-D3 with the def2-TZVP basis set, and B3LYP-D3 with either def2-TZVP or aug-cc-pVDZ basis set, whereas for copper chelate the PBE0-D3 with def2-TZVP basis set yielded the best results. M06L-D3 with aug-cc-pVDZ gives satisfying results for both chelates. Most of the tested dispersion-corrected density functionals do not reproduce the benchmark data for stacking of benzene with both nickel (no unpaired electrons) and copper chelate (one unpaired electron), whereas a number of these functionals perform well for interactions of organic molecules.
Collapse
Affiliation(s)
- Dušan P Malenov
- Innovation Center of the Department of Chemistry, Studentski trg 12-16, Belgrade (Serbia)
| | | | | |
Collapse
|
27
|
Khavasi HR, Mir Mohammad Sadegh B. Influence of N-heteroaromatic π–π stacking on supramolecular assembly and coordination geometry; effect of a single-atom change in the ligand. Dalton Trans 2015; 44:5488-502. [DOI: 10.1039/c4dt03518f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study on how the polarization of aromatic systems, through the introduction of a nitrogen heteroatom, affects the π–π interactions and crystal packing of mercury coordination compounds.
Collapse
|
28
|
Vojislavljević-Vasilev DZ, Janjić GV, Medaković VB, Blagojević JP, Zarić SD. Parallel water/aromatic interactions of non-coordinated and coordinated water. Chemphyschem 2014; 15:2386-96. [PMID: 24840235 DOI: 10.1002/cphc.201402004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/19/2014] [Indexed: 11/07/2022]
Abstract
The parallel interactions of non-coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel-down orientation in which one OH bond is parallel to the aromatic ring, whereas the other OH bond points to the plane of the ring. The interactions of aqua complexes with parallel-down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is -14.89 kcal mol(-1) . The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.
Collapse
|
29
|
Malenov DP, Ninković DB, Sredojević DN, Zarić SD. Stacking of Benzene with Metal Chelates: Calculated CCSD(T)/CBS Interaction Energies and Potential-Energy Curves. Chemphyschem 2014; 15:2458-61. [DOI: 10.1002/cphc.201402114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/20/2014] [Indexed: 11/12/2022]
|
30
|
Ninković DB, Andrić JM, Malkov SN, Zarić SD. What are the preferred horizontal displacements of aromatic–aromatic interactions in proteins? Comparison with the calculated benzene–benzene potential energy surface. Phys Chem Chem Phys 2014; 16:11173-7. [DOI: 10.1039/c3cp54474e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Stacking interactions of phenylalanine residues show preference for large offsets (3.5–5.0 Å), while the calculations show substantially strong interactions, of about −2.0 kcal mol−1.
Collapse
Affiliation(s)
| | - Jelena M. Andrić
- Innovation center of the Department of Chemistry
- 11000 Belgrade, Serbia
| | - Saša N. Malkov
- Department of Mathematics
- University of Belgrade
- 11000 Belgrade, Serbia
| | - Snežana D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A & M University at Qatar
| |
Collapse
|
31
|
Woziwodzka A, Gołuński G, Wyrzykowski D, Kaźmierkiewicz R, Piosik J. Caffeine and other methylxanthines as interceptors of food-borne aromatic mutagens: inhibition of Trp-P-1 and Trp-P-2 mutagenic activity. Chem Res Toxicol 2013; 26:1660-73. [PMID: 24102551 DOI: 10.1021/tx4002513] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Caffeine is one of the most important biologically active food components. In this article, we demonstrate that caffeine and other methylxanthines significantly reduce the mutagenic activity of two food-derived heterocyclic aromatic amines, Trp-P-1 and Trp-P-2 in the Salmonella typhimurium TA98 strain. Moreover, protection against Trp-P-1-induced mutagenicity was independent of liver S9 enzymatic fraction, suggesting that mechanisms other than modulation of mutagen bioactivation can contribute to the observed protective effects. UV-vis spectroscopy and computational studies revealed that methylxanthines intercept Trp-P-1 and Trp-P-2 in noncovalent molecular complexes, with association constants (KAC) in the 10(2) M(-1) range. Enthalpy values (ΔH about -30 kJ·mol(-1)) of mutagen-methylxanthine heterocomplexation obtained microcalorimetrically correspond to stacking (π-π) interactions. Finally, we demonstrated that the biological activity of Trp-P-1 and Trp-P-2 is strictly dependent on the presence of the mutagen in a free (unbound with methylxanthine) form, suggesting that mutagen sequestration in stacking heterocomplexes with methylxanthines can decrease its bioavailability and diminish its biological effects.
Collapse
Affiliation(s)
- Anna Woziwodzka
- Laboratory of Biophysics, Intercollegiate Faculty of Biotechnology UG-MUG , Kładki 24, 80-822 Gdańsk, Poland
| | | | | | | | | |
Collapse
|
32
|
Janjić GV, Ninković DB, Zarić SD. Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2013; 69:389-394. [PMID: 23873064 DOI: 10.1107/s2052519213013961] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/20/2013] [Indexed: 06/02/2023]
Abstract
Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.
Collapse
Affiliation(s)
- Goran V Janjić
- ICTM, University of Belgrade, Njegoševa 12, Belgrade 11000, Serbia
| | | | | |
Collapse
|