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Jarończyk M, Ostrowski S, Dobrowolski JC. On Integral INICS Aromaticity of Pyridodiazepine Constitutional Isomers and Tautomers. Molecules 2023; 28:5684. [PMID: 37570653 PMCID: PMC10419959 DOI: 10.3390/molecules28155684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The structure, energetics, and aromaticity of c.a. 100 constitutional isomers and tautomers of pyrido[m,n]diazepines (m = 1, 2; n = 2, 3, 4, 5; m ≠ n) were studied at the B3LYP/cc-pVTZ level. The pyrido[1,3]diazepines appear the most, while pyrido[2,4]diazepines are the least stable (ca. 26 kcal/mol). In the pyrido[1,n]diazepine group (n = 2-5), the [1,5] isomers are higher in energy by ca. 4.5 kcal/mol and the [1,4] ones by ca. 7 kcal/mol, and the pyrido[1,2]diazepines are the least stable (ca. 20 kcal/mol). All the most stable pyrido[1,n]diazepines have N-atoms near the ring's junction bond but on opposite sites. The most stable [2,n]-forms are also those with the pyridine ring N6-atom near the junction bond. Surprisingly, for the [1,2]-, [1,3]-, and [1,4]-isomer condensation types of pyridine and diazepine rings, the same N9 > N7 > N6 > N8 stability pattern obeys. The stability remains similar in a water medium simulated with the Polarizable Continuum Model of the solvent and is conserved when calculated using the CAM-B3LYP or BHandHlyp functionals. The ring's aromaticity in the pyridine[m,n]diazepines was established based on the integral INICS index resulting from the NICSzz-scan curves' integration. The integral INICS index is physically justified through its relation to the ringcurrent as demonstrated by Berger, R.J.F., et al. Phys. Chem. Chem. Phys. 2022, 24, 624. The six-membered pyrido rings have negative INICSZZ indices and can be aromatic only if they are not protonated at the N-atom. All protonated pyrido and seven-membered rings exhibit meaningful positive INICSZZ values and can be assigned as antiaromatic. However, some non-protonated pyrido rings also have substantial positive INICSZZ indices and are antiaromatic. A weak linear correlation (R2 = 0.72) between the INICSZZ values of the pyridine I(6) and diazepine I(7) rings exists and is a consequence of the communication between the π-electron systems of the two rings. The juxtaposition of the INICS descriptor of the six- and seven-membered rings and diverse electron density parameters at the Ring Critical Points (RCP) revealed good correlations only with the Electrostatic Potentials from the electrons and nuclei (ESPe and ESPn). The relationships with other RCP parameters like electron density and its Laplacian, total energy, and the Hamiltonian form of kinetic energy density were split into two parts: one nearly constant for the six-membered rings and one linearly correlating for the seven-membered rings. Thus, most of the electron density parameters at the RCP of the six-membered rings of pyridodiazepines practically do not change with the diazepine type and the labile proton position. In contrast, those of the seven-membered rings display aromaticity changes in the antiaromatic diazepine with its ring structural modifications.
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Affiliation(s)
| | - Sławomir Ostrowski
- Institute of Chemistry and Nuclear Technology, 16 Dorodna Street, 03-195 Warsaw, Poland;
| | - Jan Cz. Dobrowolski
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
- Institute of Chemistry and Nuclear Technology, 16 Dorodna Street, 03-195 Warsaw, Poland;
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Theoretical study of nimetazepam, a real-life chiral molecule without an asymmetric carbon atom. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hoz ADL, Alkorta I, Elguero J. The mechanism of the reaction of hydrazines with α,β-unsaturated carbonyl compounds to afford hydrazones and 2-pyrazolines (4,5-dihydro-1H-pyrazoles): Experimental and theoretical results. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Núñez Alonso D, Pérez-Torralba M, Claramunt RM, Torralba MC, Delgado-Martínez P, Alkorta I, Elguero J, Roussel C. Regiospecific Synthesis and Structural Studies of 3,5-Dihydro-4 H-pyrido[2,3- b][1,4]diazepin-4-ones and Comparison with 1,3-Dihydro-2 H-benzo[ b][1,4]diazepin-2-ones. ACS OMEGA 2020; 5:25408-25422. [PMID: 33043221 PMCID: PMC7542844 DOI: 10.1021/acsomega.0c03843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/10/2020] [Indexed: 05/12/2023]
Abstract
Nine 3,5-dihydro-4H-pyrido[2,3-b][1,4]diazepin-4-ones (17-25), some of which contain fluoro-substituents, have been regiospecifically prepared by reaction of 2,3-diaminopyridines with ethyl aroylacetates. In two cases, open intermediates have been isolated and these are related to the reaction pathway. The X-ray crystal structure of 1-methyl-4-phenyl-3,5-dihydro-4H-pyrido[2,3-b][1,4]diazepin-4-one (23) has been solved (formula, C15H13N3O; crystal system, monoclinic; space group, C2/c). This is an asymmetric unit constituted by a single nonplanar molecule and its conformational enantiomer due to the presence of the seven-membered diazepin-2-one moiety, which introduces a certain degree of torsion in the adjacent pyridine ring. The 1H, 13C, 15N, and 19F NMR spectra were obtained and the chemical shifts, together with those of the previously published 1,3-dihydro-2H-benzo[b][1,4]diazepin-2-ones (1-16), i.e., a total of 544 values, were successfully compared with the chemical shifts calculated at the gauge invariant atomic orbital (GIAO)/Becke, three-parameter, Lee-Yang-Parr (B3LYP)/6-311++G(d,p) level. The seven-membered ring inversion barrier in 5-benzyl-2-phenyl-3,5-dihydro-4H-pyrido[2,3-b][1,4]diazepin-4-one (25) was determined and, in conjunction with the data from the literature, compared with the B3LYP/6-311++G(d,p) computed values. This allowed the determination of several structural effects. The rotation about the exocyclic N1-CR bond was also calculated and its dynamic properties were discussed.
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Affiliation(s)
- David Núñez Alonso
- Departamento
de Química Orgánica y Bio-Orgánica, Facultad
de Ciencias, UNED, Paseo Senda del Rey, 9, E-28040 Madrid, Spain
| | - Marta Pérez-Torralba
- Departamento
de Química Orgánica y Bio-Orgánica, Facultad
de Ciencias, UNED, Paseo Senda del Rey, 9, E-28040 Madrid, Spain
| | - Rosa M. Claramunt
- Departamento
de Química Orgánica y Bio-Orgánica, Facultad
de Ciencias, UNED, Paseo Senda del Rey, 9, E-28040 Madrid, Spain
| | - M. Carmen Torralba
- Departamento
de Química Inorgánica, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, E-28040 Madrid, Spain
| | - Patricia Delgado-Martínez
- Unidad
de Difracción de Rayos X−CAI Técnicas Físicas
y Químicas, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, E-28040 Madrid, Spain
| | - Ibon Alkorta
- Instituto
de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Christian Roussel
- Aix-Marseille
Univ., CNRS, Centrale Marseille, iSm2, 13397 Marseille, France
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Alkorta I, Elguero J. Theoretical studies of conformational analysis and intramolecular dynamic phenomena. Struct Chem 2019. [DOI: 10.1007/s11224-019-01370-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Janciene R, Mikulskiene G. The complete 1 H and 13 C NMR spectra assignments of N-(2-nitrobenzoyl)-1,5-benzodiazepin-2-one and dihydroquinazolino[3,2-α]benzodiazepine derivatives. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:968-974. [PMID: 31325185 DOI: 10.1002/mrc.4924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/24/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Regina Janciene
- Vilnius University Life Sciences Center, Institute of Biochemistry, Vilnius, Lithuania
| | - Gema Mikulskiene
- Vilnius University Life Sciences Center, Institute of Biochemistry, Vilnius, Lithuania
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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Nieto CI, Sanz D, Claramunt RM, Torralba MC, Torres MR, Alkorta I, Elguero J. Molecular structure in the solid state by X-ray crystallography and SSNMR and in solution by NMR of two 1,4-diazepines. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Nieto CI, Claramunt RM, Torralba MC, Torres MR, Elguero J. Crystal structure of (1 Z,4 Z)-2,4-dimethyl-3 H-benzo[ b][1,4]diazepine. Acta Crystallogr E Crystallogr Commun 2017; 73:647-650. [PMID: 28529767 PMCID: PMC5418775 DOI: 10.1107/s2056989017004972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/30/2017] [Indexed: 11/11/2022]
Abstract
The title compound, C11H12N2, is not planar due to the folding of the seven-membered ring. In the crystal, molecules are packed opposite each other to minimize the electronic repulsion but the long intermolecular distances indicate that no directional contacts are found.
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Martín O, Pérez-Torralba M, García MÁ, Claramunt RM, Torralba MC, Torres MR, Alkorta I, Elguero J. Static and Dynamic Properties of Fluorinated 4-Aryl-1,5-Benzodiazepinones. ChemistrySelect 2016. [DOI: 10.1002/slct.201600167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Olga Martín
- Departamento de Química Orgánica y Bio-Orgánica; Facultad de Ciencias; UNED; Senda del Rey 9 28040- Madrid Spain
| | - Marta Pérez-Torralba
- Departamento de Química Orgánica y Bio-Orgánica; Facultad de Ciencias; UNED; Senda del Rey 9 28040- Madrid Spain
| | - M. Ángeles García
- Departamento de Química Orgánica y Bio-Orgánica; Facultad de Ciencias; UNED; Senda del Rey 9 28040- Madrid Spain
| | - Rosa M. Claramunt
- Departamento de Química Orgánica y Bio-Orgánica; Facultad de Ciencias; UNED; Senda del Rey 9 28040- Madrid Spain
| | - M. Carmen Torralba
- Departamento de Química Inorgánica I; Facultad de Ciencias Químicas; UCM; Ciudad Universitaria s/n; 28040- Madrid Spain
| | - M. Rosario Torres
- CAI de Difracción de Rayos-X; Facultad de Ciencias Químicas; UCM; Ciudad Universitaria s/n; 28040- Madrid Spain
| | - Ibon Alkorta
- Instituto de Química Médica; Centro de Química Orgánica Manuel Lora-Tamayo; CSIC; Juan de la Cierva 3 28006- Madrid Spain
| | - José Elguero
- Instituto de Química Médica; Centro de Química Orgánica Manuel Lora-Tamayo; CSIC; Juan de la Cierva 3 28006- Madrid Spain
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Young J, Schäfer C, Solan A, Baldrica A, Belcher M, Nişanci B, Wheeler KA, R. Trivedi E, Török B, Dembinski R. Regioselective “hydroamination” of alk-3-ynones with non-symmetrical o-phenylenediamines. Synthesis of diversely substituted 3H-1,5-benzodiazepines via (Z)-3-amino-2-alkenones. RSC Adv 2016. [DOI: 10.1039/c6ra24291j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Reaction of alk-3-yn-1-ones with non-symmetricalo-phenylenediamines provides an effective method with high atom economy for the synthesis of diversely substituted 1,5-benzodiazepines and conjugated enaminones.
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Affiliation(s)
| | | | - Agnes Solan
- Department of Chemistry
- Oakland University
- Rochester
- USA
| | | | | | - Bilal Nişanci
- Department of Chemistry
- University of Massachusetts Boston
- Boston
- USA
| | | | | | - Béla Török
- Department of Chemistry
- University of Massachusetts Boston
- Boston
- USA
| | - Roman Dembinski
- Department of Chemistry
- Oakland University
- Rochester
- USA
- Centre of Molecular and Macromolecular Studies
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Dynamic Behavior of Clobazam on High-Performance Liquid Chromatography Chiral Stationary Phases. Chirality 2015; 28:17-21. [DOI: 10.1002/chir.22542] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/03/2015] [Accepted: 09/09/2015] [Indexed: 12/24/2022]
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14
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Obydennov DL, Sosnovskikh VY. The reaction of 6-substituted 4-pyrone-2-carboxylic acids with o-phenylenediamine. Synthesis and structure of 3-(1H-1,5-benzodiazepin-2(3Н)-ylidenemethyl)quinoxalin-2(1H)-ones. Chem Heterocycl Compd (N Y) 2015. [DOI: 10.1007/s10593-015-1696-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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An experimental and theoretical study of the structure of Lamotrigine in its neutral and protonated forms: evidence of Lamotrigine enantiomers. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.02.075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pérez-Torralba M, Claramunt RM, Angeles García M, López C, Torralba MC, Rosario Torres M, Alkorta I, Elguero J. Structure of 1,5-benzodiazepinones in the solid state and in solution: Effect of the fluorination in the six-membered ring. Beilstein J Org Chem 2013; 9:2156-67. [PMID: 24204428 PMCID: PMC3817505 DOI: 10.3762/bjoc.9.253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/24/2013] [Indexed: 12/22/2022] Open
Abstract
Two novel tetrafluorinated 1,5-benzodiazepinones were synthesized and their X-ray structures determined. 6,7,8,9-Tetrafluoro-4-methyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one crystallizes in the monoclinic P21/c space group and 6,7,8,9-tetrafluoro-1,4-dimethyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one in the triclinic P−1 space group. Density functional theory studies at the B3LYP/6-311++G(d,p) level were carried out on these compounds and on four non-fluorinated derivatives, allowing to calculate geometries, tautomeric energies and ring-inversion barriers, that were compared with the experimental results obtained by static and dynamic NMR in solution and in solid state.
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Affiliation(s)
- Marta Pérez-Torralba
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Paseo Senda del Rey 9, 28040-Madrid, Spain
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