1
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Jang YJ, Han JH, Min KS. Ferromagnetic chloro-bridged copper(II) coordination polymer: Synthesis, structure, magnetism, and DNA cleavage effects. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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2
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Pagliari A, Meyer AR, Solner V, Rosa JML, Hoerner M, Gauze Bonacorso H, Zanatta N, Martins MAP. Effect of Hydrogen Bonds and π...π-interactions on the Crystallization of Phenyl-perfluorophenyl Amides: Understanding the Self-organization of a Cocrystal. CrystEngComm 2022. [DOI: 10.1039/d2ce00231k] [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
A series of N-arylbenzamides containing amide group and phenyl−perfluorinated rings were used as the smallest molecules to investigate the direct influence of hydrogen bond and aromatic donor-acceptor complementarity in the...
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3
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Petelski AN, Marquez J, Pamies SC, Sosa GL, Peruchena NM. Understanding the Chloride Affinity of Barbiturates for Anion Receptor Design. Chemphyschem 2021; 22:665-674. [PMID: 33538090 DOI: 10.1002/cphc.202100008] [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: 01/06/2021] [Revised: 02/02/2021] [Indexed: 11/09/2022]
Abstract
Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in metal coordination chemistry. Yet their abilities to recognize anions remain unexplored. In this work, we were able to identify four structural features of barbiturates that are responsible for a certain anion affinity. The set of coordination interactions can be finely tuned with covalent decorations at the methylene group. DFT-D computations at the BLYP-D3(BJ)/aug-cc-pVDZ level of theory show that the C-H bond is as effective as the N-H bond to coordinate chloride. An analysis of the electron charge density at the C-H⋅⋅⋅Cl- and N-H⋅⋅⋅Cl- bond critical points elucidates their similarities in covalent character. Our results reveal that the special acidity of the C-H bond shows up when the methylene group moves out of the ring plane and it is mainly governed by the orbital interaction energy. The amide and carboxyl groups are the best choices to coordinate the ion when they act together with the C-H bond. We finally show how can we use this information to rationally improve the recognition capability of a small cage-like complex that is able to coordinate NaCl.
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Affiliation(s)
- Andre Nicolai Petelski
- Departamento de Ingeniería Química, Grupo de Investigación en Química Teórica y Experimental (QUITEX), Universidad Tecnológica Nacional, Facultad Regional Resistencia, French 414, H3500CHJ), Resistencia, Chaco, Argentina.,Instituto de Química Básica y Aplicada del Nordeste Argentino, IQUIBA-NEA, UNNE-CONICET, Avenida Libertad 5460, 3400, Corrientes, Argentina
| | - Josefina Marquez
- Departamento de Ingeniería Química, Grupo de Investigación en Química Teórica y Experimental (QUITEX), Universidad Tecnológica Nacional, Facultad Regional Resistencia, French 414, H3500CHJ), Resistencia, Chaco, Argentina
| | - Silvana Carina Pamies
- Departamento de Ingeniería Química, Grupo de Investigación en Química Teórica y Experimental (QUITEX), Universidad Tecnológica Nacional, Facultad Regional Resistencia, French 414, H3500CHJ), Resistencia, Chaco, Argentina
| | - Gladis Laura Sosa
- Departamento de Ingeniería Química, Grupo de Investigación en Química Teórica y Experimental (QUITEX), Universidad Tecnológica Nacional, Facultad Regional Resistencia, French 414, H3500CHJ), Resistencia, Chaco, Argentina.,Instituto de Química Básica y Aplicada del Nordeste Argentino, IQUIBA-NEA, UNNE-CONICET, Avenida Libertad 5460, 3400, Corrientes, Argentina
| | - Nélida María Peruchena
- Instituto de Química Básica y Aplicada del Nordeste Argentino, IQUIBA-NEA, UNNE-CONICET, Avenida Libertad 5460, 3400, Corrientes, Argentina.,Área de Química Física - Departamento de Química, Laboratorio de Estructura Molecular y Propiedades (LEMyP), Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460, 3400, Corrientes, Argentina
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4
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Zhou M, Springborg M. Theoretical study of the mechanism behind the site- and enantio-selectivity of C-H functionalization catalysed by chiral dirhodium catalyst. Phys Chem Chem Phys 2020; 22:9561-9572. [PMID: 32319983 DOI: 10.1039/d0cp00249f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C-H functionalization is very important for the synthesis of pharmaceuticals and complex natural products. Rhodium carbenoids, obtained when a dirhodium(ii) catalyst containing a crown formed by chiral ligands reacts with diazo compounds with both an electron donating group and an electron withdrawing group, play an important part in controlling site- and enantio-selectivity for functionalization of non-activated C-H bonds. It has earlier been demonstrated that the tertiary C-H bond is more favored to be functionalized inside the crown of the dirhodium catalyst with S-configuration ligands compared with the secondary and primary C-H bonds although the latter possess weaker steric effects. We argue that the higher site- and enantio-selectivity for some types of C-H bond functionalization can be related to intermolecular hydrogen bonding, steric hindrance, and weak interactions when the dirhodium catalyst is interacting with the chiral ligands.
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Affiliation(s)
- Meijuan Zhou
- Physical and Theoretical Chemistry Department, University of Saarland, 66123 Saarbrücken, Germany.
| | - Michael Springborg
- Physical and Theoretical Chemistry Department, University of Saarland, 66123 Saarbrücken, Germany. and Materials Science, Tianjin University, Tianjin 300072, China
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5
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Supramolecular self-assembly and thermodynamic properties of 5-aryl-1-(1,1-dimethylethyl)-1H-pyrazoles in the crystalline state. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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[2]Rotaxanes Bearing a Tetralactam Macrocycle: The Role of a Trifurcated Hydrogen Bond in the Crystalline State. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Petelski AN, Pamies SC, Sejas AG, Peruchena NM, Sosa GL. Impact of confinement in multimolecular inclusion compounds of melamine and cyanuric acid. Phys Chem Chem Phys 2019; 21:8205-8214. [PMID: 30854534 DOI: 10.1039/c8cp07705c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Supramolecular cavities can be found in clathrates and self-assembling capsules. In these computational experiments, we studied the effect of folding planar hydrogen-bonded supramolecules of melamine (M) and cyanuric acid (CA) into stable cage-like quartets. Based on dispersion-corrected density functional theory calculations at the ωB97XD/6-311++G(d,p) level, we show the flexibility of M and CA molecules to form free confined spaces. Our bonding analysis indicates that only CA can form a cage, which is more stable than its planar systems. We then studied the capacity of the complexes to host ionic and neutral monoatomic species like Na+, Cl- and Ar. The encapsulation energies range from -2 to -65 kcal mol-1. A detailed energy decomposition analysis (EDA) supports the fact that the triazine ring of CA is superior to the M one for capturing chloride ions. In addition, the EDA and the topology of the electron density, by means of the Atoms in Molecules (AIM) theory and electrostatic potential maps, reveal the nature of the host-guest interactions in the confined space. The CA cluster appears to be the best multimolecular inclusion compound because it can host the three species and keep its cage structure, and therefore it could also act as a dual receptor of the ionic pair Na+Cl-. We think these findings could inspire the design of new heteromolecular inclusion compounds based on triazines and hydrogen bonds.
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Affiliation(s)
- Andre Nicolai Petelski
- Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Departamento de Ingeniería Química, Facultad Regional Resistencia, Universidad Tecnológica Nacional, French 414 (H3500CHJ), Resistencia, Chaco, Argentina.
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8
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Carvalho LC, Bueno MA, de Oliveira BG. The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C 2H 2⋯HF and C 2H 4⋯HF small dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:438-455. [PMID: 30738351 DOI: 10.1016/j.saa.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C2H2⋯(HF), C2H2⋯2(HF), C2H2⋯4(HF), C2H4⋯(HF), C2H4⋯2(HF) and C2H4⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).
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9
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Grabowski SJ. A-H…σ Hydrogen Bonds: Dihydrogen and Cycloalkanes as Proton Acceptors. Chemphyschem 2019; 20:565-574. [PMID: 30645024 DOI: 10.1002/cphc.201900045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Indexed: 11/11/2022]
Abstract
ωB97XD/aug-cc-pVTZ calculations were performed for complexes of dihydrogen, cyclopropane, cyclobutane and cyclopentane, with simple proton donating species such as hydrogen fluoride, hydrogen chloride, water, hydrogen cyanide and acetylene. Numerous dependencies between geometrical, energetic and topological parameters of complexes considered were found, since various theoretical approaches were applied: Quantum Theory of 'Atoms in Molecules' (QTAIM), Natural Bond Orbital (NBO) method and energy decomposition analysis (EDA). It was confirmed that complexes of dihydrogen and cyclopropane are linked through the A-H…σ interactions that may be classified as hydrogen bonds. In the case of complexes of cyclobutane such hydrogen bonds are rather weak. Other type and also weak A-H…C hydrogen bonds are formed for complexes with cyclopentane.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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10
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Pagliari A, Orlando T, Salbego PRS, Zimmer G, Hörner M, Zanatta N, Bonacorso HG, Martins MAP. Supramolecular Packing of a Series of N-Phenylamides and the Role of NH···O=C Interactions. ACS OMEGA 2018; 3:13850-13861. [PMID: 31458083 PMCID: PMC6645157 DOI: 10.1021/acsomega.8b01801] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/03/2018] [Indexed: 05/25/2023]
Abstract
A series of seven N-phenylamides [R-C(O)NHPh, in which R: CH3, C(CH3)3, Ph, CF3, CCl3, CBr3, and H] were used as models in this study. Molecular packing and intermolecular interactions were evaluated by theoretical calculations, solution NMR, and quantum theory of atoms in molecules analyses. Crystallization mechanisms were proposed based on the energetic and topological parameters using the supramolecular cluster as demarcation. Concentration-dependent 1H NMR experiments corroborated the proposed interactions between molecules. For all compounds (except for R: H, which initially formed tetramers), layers (two-dimensional) or chains (one-dimensional) were formed in the first stage of the proposed crystallization mechanisms. The presence of strong intermolecular NH···O=C interactions promoted the first stages. The study in solution provided different values of association constant (K ass) governed by the hydrogen bond NH···O=C, showing that the stronger interactions are directly influenced by the substituent steric hindrance. A correlation between K ass(NH···O=C) from the solution and the NH···O=C interaction energy in the crystal showed a good trend.
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Affiliation(s)
- Anderson
B. Pagliari
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
| | - Tainára Orlando
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
| | - Paulo R. S. Salbego
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
| | - Geórgia
C. Zimmer
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
| | - Manfredo Hörner
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
| | - Nilo Zanatta
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
| | - Helio G. Bonacorso
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
| | - Marcos A. P. Martins
- Núcleo
de Química de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, Rio
Grande do Sul, Brazil
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11
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Alhameedi K, Karton A, Jayatilaka D, Thomas SP. Bond orders for intermolecular interactions in crystals: charge transfer, ionicity and the effect on intramolecular bonds. IUCRJ 2018; 5:635-646. [PMID: 30224966 PMCID: PMC6126646 DOI: 10.1107/s2052252518010758] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/24/2018] [Indexed: 05/30/2023]
Abstract
The question of whether intermolecular interactions in crystals originate from localized atom⋯atom interactions or as a result of holistic molecule⋯molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby-Gould bond indices are reported for intermolecular 'σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed. In contrast with conventional bond-order estimations, the new method separately estimates the ionic and covalent bond indices for atom⋯atom and molecule⋯molecule bond orders, which shed light on the nature of these interactions. A consistent trend in charge transfer from halogen/chalcogen bond-acceptor to bond-donor groups has been found in these intermolecular interaction regions via Hirshfeld atomic partitioning of the electron populations. These results, along with the 'conservation of bond orders' tested in the interaction regions, establish the significant role of localized atom⋯atom interactions in the formation of these intermolecular binding motifs.
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Affiliation(s)
- Khidhir Alhameedi
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
- College of Education for Pure Science, University of Karbala, Karbala, Iraq
| | - Amir Karton
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Sajesh P. Thomas
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
- Centre for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
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12
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Orlando T, Salbego PRS, Zimmer GC, Pagliari AB, Bender CR, Rodrigues LV, Bonacorso HG, Zanatta N, Berná J, Martins MAP. Conformer Distribution in Rotaxanes Containing Nonsymmetric Threads: A Systematic Approach. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800991] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Tainára Orlando
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Paulo R. S. Salbego
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Geórgia C. Zimmer
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Anderson B. Pagliari
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Caroline R. Bender
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Leticia V. Rodrigues
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Helio G. Bonacorso
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Nilo Zanatta
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
| | - Jose Berná
- Departmento de Química Orgánica; Faculdad de Química; Universidade de Murcia; 30100 Murcia Spain
| | - Marcos A. P. Martins
- Núcleo de Química de Heterociclos (NUQUIMHE); Departmento de Química; Unversidade Federal de Santa Maria; 97105-900 Santa Maria RS Brazil
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13
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Venkataramanan NS, Suvitha A. Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis. J Mol Graph Model 2018. [PMID: 29524753 DOI: 10.1016/j.jmgm.2018.02.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters.
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Affiliation(s)
| | - Ambigapathy Suvitha
- Department of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, 613 401, India
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14
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Sebastianelli P, Cometto PM, Pereyra RG. Systematic Characterization of Gas Phase Binary Pre-Nucleation Complexes Containing H2SO4 + X, [ X = NH3, (CH3)NH2, (CH3)2NH, (CH3)3N, H2O, (CH3)OH, (CH3)2O, HF, CH3F, PH3, (CH3)PH2, (CH3)2PH, (CH3)3P, H2S, (CH3)SH, (CH3)2S, HCl, (CH3)Cl)]. A Computational Study. J Phys Chem A 2018; 122:2116-2128. [DOI: 10.1021/acs.jpca.7b10205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paolo Sebastianelli
- Fa.M.A.F., Universidad Nacional de Córdoba, Medina Allende s/n, Ciudad Universitaria, X5000HUA Córdoba, Argentina
- FCEyN, Universidad Nacional de La Pampa, Uruguay 151, 6300 Santa Rosa, La Pampa, Argentina
| | - Pablo M. Cometto
- FCEyN, Universidad Nacional de La Pampa, Uruguay 151, 6300 Santa Rosa, La Pampa, Argentina
- Atmospheric Chemical Physics Laboratory, INCITAP-CONICET, Uruguay 151, 6300 Santa Rosa, La Pampa, Argentina
| | - Rodolfo G. Pereyra
- Fa.M.A.F., Universidad Nacional de Córdoba, Medina Allende s/n, Ciudad Universitaria, X5000HUA Córdoba, Argentina
- IFEG-CONICET, Medina Allende s/n, Ciudad
Universitaria, X5000HUA Córdoba, Argentina
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15
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Shen D, Su P, Wu W. What kind of neutral halogen bonds can be modulated by solvent effects? Phys Chem Chem Phys 2018; 20:26126-26139. [DOI: 10.1039/c8cp05358h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Halogen bonds with a large portion of polarization can be modulated by solvent effects.
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Affiliation(s)
- Dan Shen
- The State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
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16
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Zimmer GC, Pagliari AB, Bender CR, Salbego PRS, Orlando T, Hörner M, Zanatta N, Bonacorso HG, Martins MAP. Insights on conformation in the solid state: a case study – s-cis and/or s-trans crystallization of 5(3)-aryl-3(5)-carboxyethyl-1-tert-butylpyrazoles. CrystEngComm 2018. [DOI: 10.1039/c8ce00984h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformation adopted by COOEt group in solid state were influenced by supramolecular environment and intramolecular interaction for 1,3- and 1,5-regioisomers, respectively.
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Affiliation(s)
- Geórgia C. Zimmer
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Anderson B. Pagliari
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Caroline R. Bender
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Paulo R. S. Salbego
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Tainára Orlando
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Manfredo Hörner
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Nilo Zanatta
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Helio G. Bonacorso
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
| | - Marcos A. P. Martins
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- CEP 97105-900 Santa Maria
- Brazil
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17
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Johnstone TC, Nolan EM. Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography. J Am Chem Soc 2017; 139:15245-15250. [PMID: 28956921 PMCID: PMC5748154 DOI: 10.1021/jacs.7b09375] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.
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Affiliation(s)
- Timothy C. Johnstone
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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18
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Varadwaj A, Varadwaj PR, Yamashita K. Hybrid organic-inorganic CH3NH3PbI3perovskite building blocks: Revealing ultra-strong hydrogen bonding and mulliken inner complexes and their implications in materials design. J Comput Chem 2017; 38:2802-2818. [DOI: 10.1002/jcc.25073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/21/2017] [Accepted: 08/31/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering; The University of Tokyo 7-3-1; Hongo Bunkyo-ku 113-8656 Japan
- CREST-JST, 7 Gobancho; Chiyoda-ku Tokyo 102-0076 Japan
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering; The University of Tokyo 7-3-1; Hongo Bunkyo-ku 113-8656 Japan
- CREST-JST, 7 Gobancho; Chiyoda-ku Tokyo 102-0076 Japan
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering; The University of Tokyo 7-3-1; Hongo Bunkyo-ku 113-8656 Japan
- CREST-JST, 7 Gobancho; Chiyoda-ku Tokyo 102-0076 Japan
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19
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Matthies O, Grin Y, Kohout M. Absent Diamond-to-β-SnPhase Transition for Carbon: Quantum Chemical Topology Approach. ChemistrySelect 2017. [DOI: 10.1002/slct.201700828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Olga Matthies
- Max-Planck-Institut für Chemische Physik fester Stoffe; Nöthnitzer Straße 40 01187 Dresden Germany
| | - Yuri Grin
- Max-Planck-Institut für Chemische Physik fester Stoffe; Nöthnitzer Straße 40 01187 Dresden Germany
| | - Miroslav Kohout
- Max-Planck-Institut für Chemische Physik fester Stoffe; Nöthnitzer Straße 40 01187 Dresden Germany
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20
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Zheng S, Xu S, Wang G, Tang Q, Jiang X, Li Z, Xu Y, Wang R, Lin F. Proposed Hydrogen-Bonding Index of Donor or Acceptor Reflecting Its Intrinsic Contribution to Hydrogen-Bonding Strength. J Chem Inf Model 2017; 57:1535-1547. [DOI: 10.1021/acs.jcim.7b00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suqing Zheng
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
| | - Shaofang Xu
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
| | - Guitao Wang
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Qing Tang
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
| | - Xiaonan Jiang
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Zhanting Li
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Yong Xu
- Institute
of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science
Park, Guangzhou, Guangdong 510530, P. R. China
| | - Renxiao Wang
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Fu Lin
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
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21
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Mallov I, Johnstone TC, Burns DC, Stephan DW. A model for C–F activation by electrophilic phosphonium cations. Chem Commun (Camb) 2017. [DOI: 10.1039/c7cc04057a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The electrophilic phosphonium cation (EPC) salt [C10H6(CF3)PF(C6F5)2][B(C6F5)4] 4 exhibited structural and spectroscopic features evidencing an interaction between the CF3 and fluorophosphonium units. It thus models a key step in the proposed mechanism of main group C–F activation.
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Affiliation(s)
- Ian Mallov
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
| | | | - Darcy C. Burns
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
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22
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Karas LJ, Batista PR, Viesser RV, Tormena CF, Rittner R, de Oliveira PR. Trends of intramolecular hydrogen bonding in substituted alcohols: a deeper investigation. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp03572a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
NBO analyses were used to perform a deeper investigation on the effects that drive IAHB strength in substituted acyclic alcohols.
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Affiliation(s)
- Lucas J. Karas
- Conformational Analysis and Renewable Resources Laboratory
- Department of Chemistry and Biology
- Federal University of Technology-Paraná
- Curitiba
- Brazil
| | - Patrick R. Batista
- Conformational Analysis and Renewable Resources Laboratory
- Department of Chemistry and Biology
- Federal University of Technology-Paraná
- Curitiba
- Brazil
| | - Renan V. Viesser
- Physical Organic Chemistry Laboratory
- Institute of Chemistry
- University of Campinas
- 13083-970 Campinas
- Brazil
| | - Cláudio F. Tormena
- Physical Organic Chemistry Laboratory
- Institute of Chemistry
- University of Campinas
- 13083-970 Campinas
- Brazil
| | - Roberto Rittner
- Physical Organic Chemistry Laboratory
- Institute of Chemistry
- University of Campinas
- 13083-970 Campinas
- Brazil
| | - Paulo R. de Oliveira
- Conformational Analysis and Renewable Resources Laboratory
- Department of Chemistry and Biology
- Federal University of Technology-Paraná
- Curitiba
- Brazil
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