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Zhi H, Wang F, Zhang X, Cai Q, Chen M, Shi Y, Feng L. Green, pH-Sensitive, Highly Stretchable, and Hydrogen Bond-Dominated Ionogel for Wound Healing Activity. ACS APPLIED BIO MATERIALS 2024; 7:498-507. [PMID: 38149601 DOI: 10.1021/acsabm.3c01146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Traditional hydrogel dressings generally have poor mechanical properties and stability when subjected to external stress due to the undesirable chain entanglement structure of their single valence bond compositions. Therefore, it is particularly important to develop a type of gel dressing with good mechanical strength, stability, and environment-friendly monitoring. In this work, a transparent, pH-sensitive, highly stretchable, and biocompatible anthocyanidin ionogel dressing was prepared, realizing green and accurate detection. Attributed to the antibacterial activity of the ionic liquid, the biocompatibility of the pectin, and the ability to scavenge free radicals of the anthocyanidin, the ionogel dressing exhibited excellent re-epithelialization in the 14 day wound healing process. Besides, changes in pH values monitoring of the ionogel over 3 days coincided with normal wound exudate. The obtained ionogel also showed good water retention, swelling properties, mechanical stretchability, and 5 week stability, illustrating great potential in wound dressings.
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Affiliation(s)
- Hui Zhi
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Fengya Wang
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaobo Zhang
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qinxin Cai
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Meng Chen
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yushu Shi
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Liang Feng
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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2
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Moradkhani M, Naghipour A, Tyula YA, Abbasi S. Competition of hydrogen, tetrel, and halogen bonds in COCl 2-HOX (X=F, Cl, Br, I) complexes. J Mol Graph Model 2023; 122:108482. [PMID: 37058996 DOI: 10.1016/j.jmgm.2023.108482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/23/2023] [Accepted: 04/03/2023] [Indexed: 04/16/2023]
Abstract
The present study investigates the competition between hydrogen, halogen, and tetrel bonds from the interaction of COCl2 with HOX using quantum chemistry simulations at the MP2/aug-cc-pVTZ computational level, in which five configurations were optimized, including adducts I -V. Two hydrogen bonds, two halogen bonds, and two tetrel bonds were obtained for five forms of adducts. The compounds were investigated using spectroscopic, geometry, and energy properties. Adduct I complexes are more stable than others, and adduct V halogen bonded complexes are more stable than adduct II complexes. These results are in agreement with their NBO and AIM results. The stabilization energy of the XB complexes depends on the nature of both the Lewis acid and base. The stretching frequency of the O-H bond in adducts I, II, III, and IV displayed a redshift, and a blue shift was observed in adduct V. The results for the O-X bond showed a blue shift in adducts I and III and a red shift in adducts II, IV, and V. The nature and characteristics of three types of interactions are investigated via NBO analysis and atoms in molecules (AIM).
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Affiliation(s)
| | - Ali Naghipour
- Department of Chemistry, Faculty of Science, Ilam University, Ilam, 69315-516, Iran.
| | - Yunes Abbasi Tyula
- Department of Chemistry, Faculty of Science, Ilam University, Ilam, 69315-516, Iran
| | - Shahryar Abbasi
- Department of Chemistry, Faculty of Science, Ilam University, Ilam, 69315-516, Iran
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3
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Kazimir A, Schwarze B, Lönnecke P, Jelača S, Mijatović S, Maksimović-Ivanić D, Hey-Hawkins E. Metallodrugs against Breast Cancer: Combining the Tamoxifen Vector with Platinum(II) and Palladium(II) Complexes. Pharmaceutics 2023; 15:pharmaceutics15020682. [PMID: 36840003 PMCID: PMC9959148 DOI: 10.3390/pharmaceutics15020682] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/19/2023] Open
Abstract
The luminal A-subtype of breast cancer, where the oestrogen receptor α (ERα) is overexpressed, is the most frequent one. The prodrug tamoxifen (1) is the clinically used agent, inhibiting the ERα activity via the formation of several active metabolites, such as 4-hydroxytamoxifen (2) or 4,4'-dihydroxytamoxifen (3). In this study, we present the tamoxifen derivative 4-[1,1-bis(4-methoxyphenyl)but-1-en-2-yl]-2,2'-bipyridine (4), which was combined with platinum or palladium dichloride, the former a well-known scaffold in anticancer treatment, to give [PtCl2(4-κ2N,N')] (5) or [PdCl2(4-κ2N,N'] (6). To prevent fast exchange of weakly coordinating chlorido ligands in aqueous solution, a bulky, highly stable and hydrophobic nido-carborate(-2) ([C2B9H11]2-) was incorporated. The resulting complexes [3-(4-κ2N,N')-3,1,2-PtC2B9H11] (7) and [3-(4-κ2N,N')-3,1,2-PdC2B9H11] (8) exhibit a dramatic change in electronic and biological properties compared to 5 and 6. Thus, 8 is highly selective for triple-negative MDA-MB-231 cells (IC50 = 3.7 μM, MTT test), while 7 is completely inactive against this cell line. The observed cytotoxicity of compounds 4-6 and 8 against this triple-negative cell line suggests off-target mechanisms rather than only ERα inhibition, for which these compounds were originally designed. Spectroscopic properties and electronic structures of the metal complexes were investigated for possible explanations of the biological activities.
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Affiliation(s)
- Aleksandr Kazimir
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany
| | - Benedikt Schwarze
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, 04107 Leipzig, Germany
| | - Peter Lönnecke
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany
| | - Sanja Jelača
- Department of Immunology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia
| | - Sanja Mijatović
- Department of Immunology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia
| | - Danijela Maksimović-Ivanić
- Department of Immunology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia
| | - Evamarie Hey-Hawkins
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany
- Correspondence:
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4
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Putro PA, Maddu A, Hardhienata H, Isnaeni I, Ahmad F, Dipojono HK. Revealing the incorporation of an NH 2 group into the edge of carbon dots for H 2O 2 sensing via the C-N⋯H hydrogen bond interaction. Phys Chem Chem Phys 2023; 25:2606-2617. [PMID: 36602293 DOI: 10.1039/d2cp04097b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We investigated hydrogen peroxide (H2O2) sensing on NH2-functionalized carbon dots (Cdots) for three different -NH2 positions, and the N atom was found to be the active site using a quantum computational approach. B3LYP and 6-31G(d,p) were used for density functional theory (DFT) ground state calculations, whereas CAM-B3LYP and the same basis set were used in time-dependent density functional theory (TD-DFT) excited state calculations. Structural optimization showed that the H2O2 is chemisorbed on 1-sim via a C-N⋯H hydrogen bond interaction with an adsorption energy of -10.61 kcal mol-1. Mulliken atomic charge distributions and electrostatic potential (ESP) analysis were both used to determine reactivity of the molecules at the atomic level. For in-depth analysis of the ground states, we utilized Frontier molecular orbital (FMO) theory, quantum theory of atoms in molecules (QTAIM), and non-covalent interaction (NCI) index analysis. In addition, we also present UV-vis absorption spectra and charge transfer lengths to understand the mechanism of H2O2 sensing in excited states. Based on the molecular and electronic properties of the NH2-Cdots, it was shown that 1-sim is a potential candidate for use as an electrochemical sensor for H2O2 sensing. Whereas 3-sim is believed to be a potential candidate for use as an optical sensor of H2O2 based on the UV-vis characteristics via photoinduced charge transfer.
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Affiliation(s)
- Permono Adi Putro
- Department of Physics, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia. .,Department of Physics, Faculty of Science, Universitas Mandiri, Subang, 41211, Indonesia
| | - Akhiruddin Maddu
- Department of Physics, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia.
| | - Hendradi Hardhienata
- Department of Physics, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia.
| | - Isnaeni Isnaeni
- Research Center for Photonics, National Research and Innovation Agency, Banten, 15314, Indonesia
| | - Faozan Ahmad
- Department of Physics, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia.
| | - Hermawan Kresno Dipojono
- Department of Engineering Physics, Faculty of Industrial Technology, Bandung Institute of Technology, Bandung, 40132, Indonesia.,Research Center for Nanoscience and Nanotechnology, Bandung Institute of Technology, Bandung, 40132, Indonesia
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5
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Fast Quantum Approach for Evaluating the Energy of Non-Covalent Interactions in Molecular Crystals: The Case Study of Intermolecular H-Bonds in Crystalline Peroxosolvates. Molecules 2022; 27:molecules27134082. [PMID: 35807323 PMCID: PMC9268483 DOI: 10.3390/molecules27134082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Energy/enthalpy of intermolecular hydrogen bonds (H-bonds) in crystals have been calculated in many papers. Most of the theoretical works used non-periodic models. Their applicability for describing intermolecular H-bonds in solids is not obvious since the crystal environment can strongly change H-bond geometry and energy in comparison with non-periodic models. Periodic DFT computations provide a reasonable description of a number of relevant properties of molecular crystals. However, these methods are quite cumbersome and time-consuming compared to non-periodic calculations. Here, we present a fast quantum approach for estimating the energy/enthalpy of intermolecular H-bonds in crystals. It has been tested on a family of crystalline peroxosolvates in which the H∙∙∙O bond set fills evenly (i.e., without significant gaps) the range of H∙∙∙O distances from ~1.5 to ~2.1 Å typical for strong, moderate, and weak H-bonds. Four of these two-component crystals (peroxosolvates of macrocyclic ethers and creatine) were obtained and structurally characterized for the first time. A critical comparison of the approaches for estimating the energy of intermolecular H-bonds in organic crystals is carried out, and various sources of errors are clarified.
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6
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Hammami F, Issaoui N. A DFT Study of the Hydrogen Bonded Structures of Pyruvic Acid–Water Complexes. FRONTIERS IN PHYSICS 2022. [DOI: 10.3389/fphy.2022.901736] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The molecular geometries of the possible conformations of pyruvic acid–water complexes (PA-(H2O)n = 1–4) have been fully optimized at DFT/B3LYP/6-311G++ (d, p) levels of calculation. Among several optimized molecular clusters, we present here the most stable molecular arrangements obtained when one, two, three, and four water molecules are hydrogen-bonded to a central pyruvic acid molecule. Appropriate topological and geometrical parameters are considered primary indicators of H-bond strength. Atoms in molecules analysis shows that pyruvic acid can form a ring structure with water, and the molecular structures are stabilized by both strong O–H⋅⋅⋅O and C–H⋅⋅⋅O hydrogen bonds. In large clusters, classical O–H⋅⋅⋅O hydrogen bonds still exist between water molecules, and a cage-like structure is built around some parts of the central molecule of pyruvic acid.
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7
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Bezerra LL, Oliveira FGS, dos Santos LPM, de Sant’Ana HB, Feitosa FX, Correia AN, Schwarzacher W, Marinho ES, de Lima-Neto P, Monteiro NDKV. Electrochemical and theoretical investigation on the behavior of the Co2+ ion in three eutectic solvents. J Mol Graph Model 2022; 112:108137. [DOI: 10.1016/j.jmgm.2022.108137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
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8
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Veríssimo de Oliveira R, Lima Bezerra L, Gomes Sousa N, Xavier Feitosa F, Batista de Sant'Ana H, Nunes Correia A, de Lima-Neto P, Monteiro NK. Analysis of the behavior of Sn2+ and In3+ ions in DES and in water: A theoretical approach. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Buldashov IA, Medvedev AG, Mikhaylov AA, Churakov AV, Lev O, Prikhodchenko PV. Non-covalent interactions of the hydroperoxo group in crystalline adducts of organic hydroperoxides and their potassium salts. CrystEngComm 2022. [DOI: 10.1039/d2ce01017h] [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
X-ray diffraction of three new stable cocrystals of potassium salts of organic hydroperoxides with molecular hydroperoxides reveals strong charge-assisted ROO−⋯HOOR H-bonds.
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Affiliation(s)
- Ivan A. Buldashov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
- Faculty of Chemistry, National Research University Higher School of Economics, Miasnitskaya Str. 20, Moscow 101000, Russia
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Ovadia Lev
- The Casali Center, The Institute of Chemistry, and The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
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10
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A Comprehensive Experimental and Theoretical Study on the [{(η 5-C 5H 5) 2Zr[P(µ-PNEt 2) 2P(NEt 2) 2P]}] 2O Crystalline System. Molecules 2021; 26:molecules26237282. [PMID: 34885860 PMCID: PMC8658821 DOI: 10.3390/molecules26237282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
The structure of tetraphosphetane zirconium complex C52H100N8OP10Zr21 was determined by single crystal X-ray diffraction analysis. The crystal belongs to the monoclinic system, space group P21/c, with a = 19.6452(14), b = 17.8701(12), c = 20.7963(14)Å, α = γ = 90°, β = 112.953(7)°, V = 6722.7(8)Å3, Z = 4. The electronic structure of the organometallic complex has been characterized within the framework of Quantum Chemical Topology. The topology of the Electron Localization Function (ELF) and the electron density according to the Quantum Theory of Atoms in Molecules (QTAIM) show no covalent bonds involving the Zr atom, but rather dative, coordinate interactions between the metal and the ligands. This is the first reported case of a Zr complex stabilized by an oxide anion, anionic cyclopentadienyl ligands and rare tetraphosphetane anions.
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11
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Chitosan biofilms: Insights for the selective electromembrane extraction of fluoroquinolones from biological samples. Anal Chim Acta 2021; 1179:338832. [PMID: 34535259 DOI: 10.1016/j.aca.2021.338832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/21/2022]
Abstract
A selective electromembrane extraction procedure for the extraction of Enrofloxacin, Marbofloxacin and Flumequine, usually employed as antibiotic in veterinarian use, is proposed by using a chitosan biofilm, composed by 60% (w/w) chitosan and 40% (w/w) Aliquat®336, as active biopolymeric support. The interaction mechanism occurring between the target drugs and the biopolymer has been deeply studied using the Quantum Theory of Atoms in Molecules. The obtained results show the interaction between the extracted fluoroquinolones and the biomembrane is stabilized by two hydrogen bonds formed between both the carboxyl and keto groups of the drugs with both the amine and hydroxyl groups of glucosamine in the biopolymer. The energetic results agree with the high extraction efficiency obtained for Marbofloxacin, Enrofloxacin and Flumequine in terms of enrichment factors (83, 82 and 58, respectively) in presence of other fluoroquinolones. Under optimum conditions, the proposed electromembrane extraction method exhibits wide linear ranges of 4.2-200 μg L-1, 5.6-200 μg L-1 and 5.1-200 μg L-1, respectively; low limits of detection close to 1.3 μg L-1 and appropriate repeatability (relative standard deviation values 4-7%).
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12
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Rozenberg M, Fausto R, Reva I. Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119323. [PMID: 33508682 DOI: 10.1016/j.saa.2020.119323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH2) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.
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Affiliation(s)
- M Rozenberg
- The Hebrew University of Jerusalem, Department of Inorganic and Analytical Chemistry, Jerusalem, Givat Ram 91904, Israel.
| | - R Fausto
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - I Reva
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal; University of Coimbra, CIEPQPF, Department of Chemical Engineering, 3030-790 Coimbra, Portugal.
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Two Faces of Water in the Formation and Stabilization of Multicomponent Crystals of Zwitterionic Drug-Like Compounds. Symmetry (Basel) 2021. [DOI: 10.3390/sym13030425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Two new hydrated multicomponent crystals of zwitterionic 2-aminonicotinic acid with maleic and fumaric acids have been obtained and thoroughly characterized by a variety of experimental (X-ray analysis and terahertz Raman spectroscopy) and theoretical periodic density functional theory calculations, followed by Bader analysis of the crystalline electron density) techniques. It has been found that the Raman-active band in the region of 300 cm−1 is due to the vibrations of the intramolecular O-H...O bond in the maleate anion. The energy/enthalpy of the intermolecular hydrogen bonds was estimated by several empirical approaches. An analysis of the interaction networks reflects the structure-directing role of the water molecule in the examined multicomponent crystals. A general scheme has been proposed to explain the proton transfer between the components during the formation of multicomponent crystals in water. Water molecules were found to play the key role in this process, forming a “water wire” between the COOH group of the dicarboxylic acid and the COO– group of the zwitterion and the rendering crystal lattice of the considered multicomponent crystals.
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14
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Medvedev AG, Churakov AV, Prikhodchenko PV, Lev O, Vener MV. Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions. Molecules 2020; 26:E26. [PMID: 33374602 PMCID: PMC7793138 DOI: 10.3390/molecules26010026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 01/22/2023] Open
Abstract
Despite the technological importance of urea perhydrate (percarbamide) and sodium percarbonate, and the growing technological attention to solid forms of peroxide, fewer than 45 peroxosolvates were known by 2000. However, recent advances in X-ray diffractometers more than tripled the number of structurally characterized peroxosolvates over the last 20 years, and even more so, allowed energetic interpretation and gleaning deeper insight into peroxosolvate stability. To date, 134 crystalline peroxosolvates have been structurally resolved providing sufficient insight to justify a first review article on the subject. In the first chapter of the review, a comprehensive analysis of the structural databases is carried out revealing the nature of the co-former in crystalline peroxosolvates. In the majority of cases, the coformers can be classified into three groups: (1) salts of inorganic and carboxylic acids; (2) amino acids, peptides, and related zwitterions; and (3) molecular compounds with a lone electron pair on nitrogen and/or oxygen atoms. The second chapter of the review is devoted to H-bonding in peroxosolvates. The database search and energy statistics revealed the importance of intermolecular hydrogen bonds (H-bonds) which play a structure-directing role in the considered crystals. H2O2 always forms two H-bonds as a proton donor, the energy of which is higher than the energy of analogous H-bonds existing in isostructural crystalline hydrates. This phenomenon is due to the higher acidity of H2O2 compared to water and the conformational mobility of H2O2. The dihedral angle H-O-O-H varies from 20 to 180° in crystalline peroxosolvates. As a result, infinite H-bonded 1D chain clusters are formed, consisting of H2O2 molecules, H2O2 and water molecules, and H2O2 and halogen anions. H2O2 can form up to four H-bonds as a proton acceptor. The third chapter of the review is devoted to energetic computations and in particular density functional theory with periodic boundary conditions. The approaches are considered in detail, allowing one to obtain the H-bond energies in crystals. DFT computations provide deeper insight into the stability of peroxosolvates and explain why percarbamide and sodium percarbonate are stable to H2O2/H2O isomorphic transformations. The review ends with a description of the main modern trends in the synthesis of crystalline peroxosolvates, in particular, the production of peroxosolvates of high-energy compounds and mixed pharmaceutical forms with antiseptic and analgesic effects.
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Affiliation(s)
- Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
| | - Ovadia Lev
- The Casali Center of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia
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Di Muzio S, Ramondo F, Gontrani L, Ferella F, Nardone M, Benassi P. Choline Hydrogen Dicarboxylate Ionic Liquids by X-ray Scattering, Vibrational Spectroscopy and Molecular Dynamics: H-Fumarate and H-Maleate and Their Conformations. Molecules 2020; 25:E4990. [PMID: 33126573 PMCID: PMC7663696 DOI: 10.3390/molecules25214990] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/18/2020] [Accepted: 10/24/2020] [Indexed: 11/30/2022] Open
Abstract
We explore the structure of two ionic liquids based on the choline cation and the monoanion of the maleic acid. We consider two isomers of the anion (H-maleate, the cis-isomer and H-fumarate, the trans-isomer) having different physical chemical properties. H-maleate assumes a closed structure and forms a strong intramolecular hydrogen bond whereas H-fumarate has an open structure. X-ray diffraction, infrared and Raman spectroscopy and molecular dynamics have been used to provide a reliable picture of the interactions which characterize the structure of the fluids. All calculations indicate that the choline cation prefers to connect mainly to the carboxylate group through OH⋯O interactions in both the compounds and orient the charged head N(CH3)3+ toward the negative portion of the anion. However, the different structure of the two anions affects the distribution of the ionic components in the fluid. The trans conformation of H-fumarate allows further interactions between anions through COOH and CO2- groups whereas intramolecular hydrogen bonding in H-maleate prevents this association. Our theoretical findings have been validated by comparing them with experimental X-ray data and infrared and Raman spectra.
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Affiliation(s)
- Simone Di Muzio
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
| | - Fabio Ramondo
- Department of Chemistry, University of Rome La Sapienza, P.le A. Moro 5, 00185 Rome, Italy;
| | - Lorenzo Gontrani
- Department of Chemistry, University of Rome La Sapienza, P.le A. Moro 5, 00185 Rome, Italy;
| | - Francesco Ferella
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
- INFN, Gran Sasso National Laboratories, I-67100 Assergi (AQ), Italy
| | - Michele Nardone
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
| | - Paola Benassi
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
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16
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Halogen bonds on substituted dibromonitrobenzene derivatives. J Mol Model 2020; 26:319. [PMID: 33104901 DOI: 10.1007/s00894-020-04566-3] [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: 05/21/2020] [Accepted: 10/08/2020] [Indexed: 10/23/2022]
Abstract
Halogen bonding is a noncovalent interaction that has attracted great attention because of its importance in several areas, such as photonics, nonlinear optics, pharmaceutical products, supramolecular engineering, biochemistry, protein-ligand complexes, and polymer interactions. In this context, we describe the synthesis, molecular structure, supramolecular arrangement, and theoretical calculations of five dibromonitrobenzene derivatives, which present different halogen atoms substituted. The solid-state characterization was carried out by X-ray diffraction with the contribution of Hirshfeld surfaces for analysis of molecular interactions. The frontier molecular orbital, molecular electrostatic potential, and quantum theory of atoms in molecules were carried out at the M06-2X/6-311+G(d,p) level of theory. Those observed halogen interactions indicate the crystalline solid-state stabilization for the dibromonitrobenzene derivatives.
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17
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Quiñonero D, Alkorta I, Elguero J. Metastable Dianions and Dications. Chemphyschem 2020; 21:1597-1607. [PMID: 32314864 DOI: 10.1002/cphc.202000172] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
A theoretical study of metastable dianions and dications has been carried out at the CCSD(T)//MP2 level. MX3 2- and LX4 2- (M=Li and Na, L=Be and Mg, X=F and Cl) have been considered as dianions, M3 X2+ (M=Li and Na, X=F and Cl), YH3 2+ and ZH4 2+ (Y=F and Cl and Z=O, S) as dications. Minima structures are found in all cases, but they are less stable than the corresponding dissociated pair of mono-ions. The dissociation profile of the molecules in two mono-ions has been explored showing in all cases a maximum that prevent their spontaneous dissociation. The strength and nature of the chemical bond in the dianions and dications have been analyzed with the QTAIM, NBO and LMOEDA method and compared to the corresponding monoanions and monocations.
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Affiliation(s)
- David Quiñonero
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3. 28006, Madrid, Spain
| | - Jose Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3. 28006, Madrid, Spain
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18
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Ahmed E, Karothu DP, Pejov L, Commins P, Hu Q, Naumov P. From Mechanical Effects to Mechanochemistry: Softening and Depression of the Melting Point of Deformed Plastic Crystals. J Am Chem Soc 2020; 142:11219-11231. [DOI: 10.1021/jacs.0c03990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ejaz Ahmed
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | | | - Ljupčo Pejov
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, POB 8600, 4036 Stavanger, Norway
- Institute of Chemistry, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, MK-1000 Skopje, Macedonia
| | - Patrick Commins
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Qichi Hu
- Bruker Nano Surfaces Division, 112 Robin Hill Road, Santa Barbara, California 93117, United States
| | - Panče Naumov
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
- Radcliffe Institute for Advanced Study, Harvard University, 10 Garden Street, Cambridge, Massachusetts 02138, United States
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19
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Voronin AP, Surov AO, Churakov AV, Parashchuk OD, Rykounov AA, Vener MV. Combined X-ray Crystallographic, IR/Raman Spectroscopic, and Periodic DFT Investigations of New Multicomponent Crystalline Forms of Anthelmintic Drugs: A Case Study of Carbendazim Maleate. Molecules 2020; 25:E2386. [PMID: 32455564 PMCID: PMC7287603 DOI: 10.3390/molecules25102386] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Synthesis of multicomponent solid forms is an important method of modifying and fine-tuning the most critical physicochemical properties of drug compounds. The design of new multicomponent pharmaceutical materials requires reliable information about the supramolecular arrangement of molecules and detailed description of the intermolecular interactions in the crystal structure. It implies the use of a combination of different experimental and theoretical investigation methods. Organic salts present new challenges for those who develop theoretical approaches describing the structure, spectral properties, and lattice energy Elatt. These crystals consist of closed-shell organic ions interacting through relatively strong hydrogen bonds, which leads to Elatt > 200 kJ/mol. Some technical problems that a user of periodic (solid-state) density functional theory (DFT) programs encounters when calculating the properties of these crystals still remain unsolved, for example, the influence of cell parameter optimization on the Elatt value, wave numbers, relative intensity of Raman-active vibrations in the low-frequency region, etc. In this work, various properties of a new two-component carbendazim maleate crystal were experimentally investigated, and the applicability of different DFT functionals and empirical Grimme corrections to the description of the obtained structural and spectroscopic properties was tested. Based on this, practical recommendations were developed for further theoretical studies of multicomponent organic pharmaceutical crystals.
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Affiliation(s)
- Alexander P. Voronin
- Department of Physical Chemistry of Drugs, G.A. Krestov Institute of Solution Chemistry of RAS, 153045 Ivanovo, Russia; (A.P.V.); (A.O.S.)
| | - Artem O. Surov
- Department of Physical Chemistry of Drugs, G.A. Krestov Institute of Solution Chemistry of RAS, 153045 Ivanovo, Russia; (A.P.V.); (A.O.S.)
| | - Andrei V. Churakov
- Department of Crystal Chemistry and X-ray Diffraction, N.S. Kurnakov Institute of General and Inorganic Chemistry of RAS, 119991 Moscow, Russia;
| | - Olga D. Parashchuk
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alexey A. Rykounov
- Theoretical Department, FSUE “RFNC-VNIITF Named after Academ. E.I. Zababakhin”, 456770 Snezhinsk, Russia;
| | - Mikhail V. Vener
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, 125047 Moscow, Russia
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20
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On the metal ion selectivity of PNP-lariat ether—an insight from density functional theory calculations. Struct Chem 2020. [DOI: 10.1007/s11224-020-01542-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Si MK, Saha A, Ganguly B. Exploiting σ-hole interaction to design small uncharged ligand molecules to stabilize G-quadruplex-DNA: a computational study. J Mol Model 2020; 26:38. [PMID: 32008146 DOI: 10.1007/s00894-019-4282-2] [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: 07/16/2019] [Accepted: 12/19/2019] [Indexed: 11/28/2022]
Abstract
Small neutral seleno molecules were designed to stabilize G-quadruplex-DNA to accelerate the death of cancer cells. A new approach was considered in this study to design new ligands to stabilize G-quadruplex-DNA using the non-covalent σ-hole interaction. The systematic study has been performed with ligands in the absence and presence of σ-hole interaction to stabilize G-tetrad. Fluorine-substituted seleno ligands interact with the bases of G-quadruplex strongly with the σ-holes present in the ligands. The binding of the fluorinated ligands FSeCF2SeCF2 SeF2(4) (~75.0 kcal/mol) is stronger than that of BRACO-19 (~70.0 kcal/mol) calculated at the same level of theory with G-tetrad. It is reported that BRACO-19 is employed to inhibit the enzymatic activity of telomerase. The calculated results also reveal the importance of optimum chain length of ligands to achieve a better binding ability with G-tetrad. The MESP calculations and AIM analysis corroborate the trends of binding of these ligand molecules with G-quadruplexes. The small neutral molecules possess considerable advantage to pass through the lipid bilayer of the cell membrane by passive transport and are of choice in biological research and for clinical trials. Graphical AbtractSmall neutral ligands with σ-holes can stabilize G-quadruplex to inhibit enzymatic activity of telomerase.
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Affiliation(s)
- Mrinal Kanti Si
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat, 364002, India
| | - Anusuya Saha
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat, 364002, India.
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22
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Medvedev AG, Grishanov DA, Churakov AV, Mikhaylov AA, Lev O, Prikhodchenko PV. Hydroperoxo double hydrogen bonding: stabilization of hydroperoxo complexes exemplified by triphenylsilicon and triphenylgermanium hydroperoxides. CrystEngComm 2020. [DOI: 10.1039/c9ce01882d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Triphenylsilicon and germanium hydroperoxo complexes were characterized by single crystal X-ray analysis revealing hydroperoxo double hydrogen bonding.
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Affiliation(s)
- Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Dmitry A. Grishanov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
- The Casali Center
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Ovadia Lev
- The Casali Center
- the Institute of Chemistry and The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Jerusalem 91904
- Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
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23
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de Paula RLG, Duarte VS, Fernandes FS, Vaz WF, Ribeiro IN, Osório FAP, Valverde C, Oliveira GR, Napolitano HB. A Comprehensive Topological Analysis on a New Bromine-Chalcone with Potential Nonlinear Optical Properties. J Phys Chem A 2019; 123:8632-8643. [DOI: 10.1021/acs.jpca.9b06066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Renata Layse G. de Paula
- Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, 75132-40 Anápolis, Goiás, Brazil
| | - Vitor S. Duarte
- Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, 75132-40 Anápolis, Goiás, Brazil
- Centro de Pesquisa e Eficiência Energética, CAOA Montadora de Veículos- LTDA, 75184-000 Anápolis, Goiás, Brazil
| | - Fernanda S. Fernandes
- Instituto de Química, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
| | - Wesley F. Vaz
- Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, 75132-40 Anápolis, Goiás, Brazil
| | - Italo N. Ribeiro
- Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, 75132-40 Anápolis, Goiás, Brazil
| | - Francisco A. P. Osório
- Instituto de Física, Universidade Federal de Goiás, 74690-900 Goiânia, Goiás, Brazil
- Pontifícia Universidade Católica de Goiás, 74175-120 Goiânia, Goiás, Brazil
| | - Clodoaldo Valverde
- Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, 75132-40 Anápolis, Goiás, Brazil
- Laboratório de Modelagem Molecular Aplicada e Simulação, Universidade Paulista, 74845-090 Goiânia, Goiás, Brazil
| | - Guilherme R. Oliveira
- Instituto de Química, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
| | - Hamilton B. Napolitano
- Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, 75132-40 Anápolis, Goiás, Brazil
- Laboratório de Novos Materiais, Centro Universitário de Anápolis, 75075-010 Anápolis, Goiás, Brazil
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24
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Saha A, Si MK, Ganguly B. A new strategy to generate super and hyper acids with simple organic molecules exploiting σ-hole interaction. Phys Chem Chem Phys 2019; 21:17772-17778. [PMID: 31368467 DOI: 10.1039/c9cp03881g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Super and hyper acidity can be achieved using σ-hole non-covalent interactions with simple organic systems. The σ-hole interaction can stabilize the conjugate base of acids to such an extent that cyclopentadiene yields a ΔHacid of 256 kcal mol-1, which is ∼100 kcal mol-1 lower than the reported results. The hyper acidic value of 209.0 kcal mol-1 of organic acids has been achieved without electron-withdrawing substituents rather exploiting only σ-hole interaction. Remarkably, the 1st and 2nd acidity values (∼229 kcal mol-1) of comparable strength in the hyperacid range have been observed for the first time using DFT computations. The simple organic acids were predicted to reach the pKa values in the range of -7.3 to -7.8 in DMSO, which is remarkably lower than previous reports. These stable anions can be a potential candidate for application as an effective electrolyte in lithium-ion batteries.
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Affiliation(s)
- Anusuya Saha
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat 364002, India.
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25
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Zhai L, Otani Y, Ohwada T. Uncovering the Networks of Topological Neighborhoods in β-Strand and Amyloid β-Sheet Structures. Sci Rep 2019; 9:10737. [PMID: 31341215 PMCID: PMC6656768 DOI: 10.1038/s41598-019-47151-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/11/2019] [Indexed: 12/02/2022] Open
Abstract
Although multiple hydrophobic, aromatic π–π, and electrostatic interactions are proposed to be involved in amyloid fibril formation, the precise interactions within amyloid structures remain poorly understood. Here, we carried out detailed quantum theory of atoms-in-molecules (QTAIM) analysis to examine the hydrophobic core of amyloid parallel and antiparallel β-sheet structures, and found the presence of multiple inter-strand and intra-strand topological neighborhoods, represented by networks of through-space bond paths. Similar bond paths from side chain to side chain and from side chain to main chain were found in a single β-strand and in di- and tripeptides. Some of these bond-path networks were enhanced upon β-sheet formation. Overall, our results indicate that the cumulative network of weak interactions, including various types of hydrogen bonding (X-H—Y; X, Y = H, C, O, N, S), as well as non-H-non-H bond paths, is characteristic of amyloid β-sheet structure. The present study postulated that the presence of multiple through-space bond-paths, which are local and directional, can coincide with the attractive proximity effect in forming peptide assemblies. This is consistent with a new view of the van der Waals (vdW) interactions, one of the origins of hydrophobic interaction, which is updating to be a directional intermolecular force.
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26
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Korabel'nikov D, Zhuravlev YN. The nature of the chemical bond in oxyanionic crystals based on QTAIM topological analysis of electron densities. RSC Adv 2019; 9:12020-12033. [PMID: 35516991 PMCID: PMC9063545 DOI: 10.1039/c9ra01403a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/09/2019] [Indexed: 11/21/2022] Open
Abstract
The QTAIM topological analysis of the calculated electron densities in oxyanionic crystals revealed the covalency criteria for metal–oxygen and hydrogen bonds.
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Affiliation(s)
| | - Yuriy N. Zhuravlev
- Institute of Fundamental Sciences
- Kemerovo State University
- Kemerovo
- Russia
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27
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Churakov AV, Grishanov DA, Medvedev AG, Mikhaylov AA, Tripol'skaya TA, Vener MV, Navasardyan MA, Lev O, Prikhodchenko PV. Cyclic dipeptide peroxosolvates: first direct evidence for hydrogen bonding between hydrogen peroxide and a peptide backbone. CrystEngComm 2019. [DOI: 10.1039/c9ce00892f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crystal structures of cyclic dipeptide peroxosolvates provide valuable insight into the non-redox interaction of hydrogen peroxide with the peptide backbone.
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Affiliation(s)
- Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Dmitry A. Grishanov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Tatiana A. Tripol'skaya
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
- Department of Quantum Chemistry
| | - Mger A. Navasardyan
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Ovadia Lev
- The Casali Center of Applied Chemistry
- The Institute of Chemistry
- The Hebrew University of Jerusalem
- Jerusalem 91904
- Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
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28
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Beyramabadi SA, Khashi M, Morsali A, Gharib A, Chegini H. Experimental and Computational Investigations of 4-((E)-(2-Amino-5- Nitrophenylimino)Methyl)-5- (Hydroxymethyl)-2-Methylpyridin-3-Ol Schiff Base Derived from Vitamin B6. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618060112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Aghazadeh Meshgi M, Zaitsev KV, Vener MV, Churakov AV, Baumgartner J, Marschner C. Hypercoordinated Oligosilanes Based on Aminotrisphenols. ACS OMEGA 2018; 3:10317-10330. [PMID: 30198007 PMCID: PMC6120741 DOI: 10.1021/acsomega.8b01402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/17/2018] [Indexed: 05/05/2023]
Abstract
The hypercoordinated silicon chlorides ClSi[(o-OC6H4)3N] (3) and ClSi[(OC6H2Me2CH2)3N] (5) were used for the synthesis of catenated derivatives (Me3Si)3SiSi[(o-OC6H4)3N] (9), (Me3Si)3SiSiMe2SiMe2Si(SiMe3)2Si[(o-OC6H4)3N] (11), and (Me3Si)3SiSi[(OC6H2Me2CH2)3N] (13) in reactions with (Me3Si)3SiK·THF (7) or (Me3Si)3SiK·[18-crown-6] (8). It was found that the nature of the (Me3Si)3SiK solvate determines the product of interaction, resulting in the formation of (Me3Si)3Si(CH2)4OSi[(OC6H2Me2CH2)3N] (12) or 13. Compounds obtained were characterized using multinuclear NMR and UV-vis spectroscopy and mass spectrometry. The molecular structures of 3, 9, and 11-13 were investigated by single-crystal X-ray analysis, featuring hypercoordinated Si atoms in a trigonal-bipyramidal coordination environment with O atoms in the equatorial plane. The structure of the side product [N(CH2C6H2Me2O)3Si]2O (6) was also studied, indicating highly tetrahedrally distorted trigonal-bipyramidal environment at the Si atoms, which was confirmed by crystal density functional theory calculations indicating the very weak Si ← N interaction. The Si···N interatomic distances span a broad range (2.23-2.78 Å). The dependence of structural and NMR parameters for hypercoordinated catenated compounds from the type of the ligand was established.
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Affiliation(s)
- Mohammad Aghazadeh Meshgi
- Institute
of Inorganic Chemistry, Graz University
of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Kirill V. Zaitsev
- Department
of Chemistry, Moscow State University, Leninskye Gory 1, Moscow 119991, Russia
- E-mail: (K.V.Z.)
| | - Mikhail V. Vener
- Department
of Quantum Chemistry, Mendeleev University
of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia
| | - Andrei V. Churakov
- N.S.
Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr., 31, 119991 Moscow, Russia
| | - Judith Baumgartner
- Institute
of Inorganic Chemistry, Graz University
of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Christoph Marschner
- Institute
of Inorganic Chemistry, Graz University
of Technology, Stremayrgasse 9, 8010 Graz, Austria
- E-mail: (C.M.)
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30
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Lohrman J, Vázquez-Montelongo EA, Pramanik S, Day VW, Hix MA, Bowman-James K, Cisneros GA. Characterizing Hydrogen-Bond Interactions in Pyrazinetetracarboxamide Complexes: Insights from Experimental and Quantum Topological Analyses. Inorg Chem 2018; 57:9775-9778. [DOI: 10.1021/acs.inorgchem.8b00627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica Lohrman
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Erik A. Vázquez-Montelongo
- Department of Chemistry, University of North Texas, 1508 W Mulberry Street, Denton, Texas 76201, United States
| | - Subhamay Pramanik
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Victor W. Day
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Mark A. Hix
- Department of Chemistry, University of North Texas, 1508 W Mulberry Street, Denton, Texas 76201, United States
| | - Kristin Bowman-James
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, 1508 W Mulberry Street, Denton, Texas 76201, United States
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31
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Quiñonero D. Sigma-hole carbon-bonding interactions in carbon-carbon double bonds: an unnoticed contact. Phys Chem Chem Phys 2018; 19:15530-15540. [PMID: 28581553 DOI: 10.1039/c7cp01780d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this manuscript, we combine high-level ab initio calculations on some small complexes and a CSD survey to analyze the existence of unprecedented noncovalent carbon bonds in X2C[double bond, length as m-dash]CH2Y systems (Y = electron-rich atom or group). The methylene group is usually seen as a weak hydrogen bond donor when interacting with an electron-rich atom. However, we demonstrate that when the electron-rich atom is located equidistant from the two H atoms and along the C[double bond, length as m-dash]C bond a σ-hole noncovalent carbon-bonding interaction is established, instead of a bifurcated hydrogen bond, as derived from Atoms-in-Molecules (AIM) and Natural bond orbital (NBO) analyses. The physical nature of the interaction has been analyzed using the Symmetry Adapted Perturbation Theory (SAPT) method. The results indicate that electrostatics is very important followed by either the induction or dispersion terms in anionic and neutral complexes, respectively. In addition the CSD analysis reveals the existence of such interactions, giving reliability to our calculations, which are much more numerous for neutral than for anionic Y systems.
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Affiliation(s)
- D Quiñonero
- Department de Química, Universitat de les Illes Balears, Crta. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain.
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32
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Surov AO, Voronin AP, Vener MV, Churakov AV, Perlovich GL. Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac. CrystEngComm 2018. [DOI: 10.1039/c8ce01458b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.
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Affiliation(s)
- Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | | | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences
- Moscow
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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33
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Vener MV, Chernyshov IY, Rykounov AA, Filarowski A. Structural and spectroscopic features of proton hydrates in the crystalline state. Solid-state DFT study on HCl and triflic acid hydrates. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1380860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M. V. Vener
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Moscow, Russia
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - I. Yu. Chernyshov
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Moscow, Russia
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A. A. Rykounov
- Theoretical Department, Russian Federal Nuclear Center – All-Russian Research Institute of Technical Physics (RFNC-VNIITF), Snezhinsk, Russia
| | - A. Filarowski
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
- Department of Physics, Industrial University of Tyumen, Tyumen, Russia
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34
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Pejov L, Panda MK, Moriwaki T, Naumov P. Probing Structural Perturbation in a Bent Molecular Crystal with Synchrotron Infrared Microspectroscopy and Periodic Density Functional Theory Calculations. J Am Chem Soc 2017; 139:2318-2328. [DOI: 10.1021/jacs.6b11212] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ljupčo Pejov
- Institute
of Chemistry, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, MK−1000 Skopje, Macedonia
| | - Manas K. Panda
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Taro Moriwaki
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Panče Naumov
- Institute
of Chemistry, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, MK−1000 Skopje, Macedonia
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35
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Pordel M, Chegini H, Ramezani S, Daee M. New fluorescent heterocyclic systems from imidazo[1,2- a ]pyridine: Design, synthesis, spectral studies and quantum-chemical investigations. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Sobczyk L, Chudoba D, Tolstoy PM, Filarowski A. Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding. Molecules 2016; 21:E1657. [PMID: 27918442 PMCID: PMC6273268 DOI: 10.3390/molecules21121657] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.
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Affiliation(s)
- Lucjan Sobczyk
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
| | - Dorota Chudoba
- Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
| | - Peter M Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University, St. Petersburg 198504, Russia.
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
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37
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Effects of the crystal structure and thermodynamic stability on solubility of bioactive compounds: DFT study of isoniazid cocrystals. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Specific features of the extra strong intermolecular hydrogen bonds in crystals: Insights from the theoretical charge density analysis. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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39
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Manin AN, Voronin AP, Shishkina AV, Vener MV, Churakov AV, Perlovich GL. Influence of Secondary Interactions on the Structure, Sublimation Thermodynamics, and Solubility of Salicylate:4-Hydroxybenzamide Cocrystals. Combined Experimental and Theoretical Study. J Phys Chem B 2015; 119:10466-77. [PMID: 26258951 DOI: 10.1021/acs.jpcb.5b05082] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cocrystal screening of 4-hydroxybenzamide with a number of salicylates (salicylic acid, SA; 4-aminosalicylic acid, PASA; acetylsalicylic acid, ASA; and salicylsalicylic acid, SSA) was conducted to confirm the formation of two cocrystals, [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1). Their structures were determined using single-crystal X-ray diffraction, and the hydrogen-bond network topology was studied. Thermodynamic characteristics of salicylic acid cocrystal sublimation were obtained experimentally. It was proved that PASA cocrystallization with 4-OHBZA makes the drug more stable and prevents the irreversible process of decarboxylation of PASA resulting in formation of toxic 3-aminophenol. The pattern of non-covalent interactions in the cocrystals is described quantitatively using solid-state density functional theory followed by Bader analysis of the periodic electron density. It has been found that the total energy of secondary interactions between synthon atoms and the side hydroxyl group of the acid molecule in [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1) cocrystals is comparable to the energy of the primary acid-amide heterosynthon. The theoretical value of the sublimation enthalpy of [SA+4-OHBZA], 231 kJ/mol, agrees fairly well with the experimental one, 272 kJ/mol. The dissolution experiments with [SA+4-OHBZA] have proved that the relatively large cocrystal stability in relation to the stability of its components has a negative effect on the dissolution rate and equilibrium solubility. The [PASA+4-OHBZA] (1:1) cocrystal showed an enhancement of apparent solubility compared to that of the corresponding pure active pharmaceutical ingredient, while their intrinsic dissolution rates are comparable.
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Affiliation(s)
- Alex N Manin
- †G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 1, Academicheskaya, 153045 Ivanovo, Russian Federation
| | - Alexander P Voronin
- †G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 1, Academicheskaya, 153045 Ivanovo, Russian Federation
| | - Anastasia V Shishkina
- ‡Mendeleev University of Chemical Technology, 9, Miusskaya Square, 125047 Moscow, Russia
| | - Mikhail V Vener
- ‡Mendeleev University of Chemical Technology, 9, Miusskaya Square, 125047 Moscow, Russia
| | - Andrei V Churakov
- §Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia
| | - German L Perlovich
- †G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 1, Academicheskaya, 153045 Ivanovo, Russian Federation
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40
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Synthesis, Spectral Studies and Quantum-Chemical Investigations on the Powerful Fluorophores: Imidazo[4,5-a]acridines. J Fluoresc 2015; 25:1235-43. [DOI: 10.1007/s10895-015-1611-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/30/2015] [Indexed: 10/23/2022]
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41
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QTAIM study of substituent effects on the intramolecular hydrogen bond in 3,3′-dihydroxy-4,4′-[5-methyl-1,3-phenylenebis(nitrilomethylidyne)]-bis-phenol. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.11.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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Del Bene JE, Alkorta I, Elguero J. The Pnicogen Bond in Review: Structures, Binding Energies, Bonding Properties, and Spin-Spin Coupling Constants of Complexes Stabilized by Pnicogen Bonds. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_8] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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43
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Surov AO, Voronin AP, Simagina AA, Churakov AV, Skachilova SY, Perlovich GL. Saccharin salts of biologically active hydrazone derivatives. NEW J CHEM 2015. [DOI: 10.1039/c5nj01532d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Crystal structures, solubility and formation thermodynamics of saccharin salts with biologically active hydrazone derivatives were investigated.
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Affiliation(s)
- Artem O. Surov
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | - Alexander P. Voronin
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | - Anna A. Simagina
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | | | | | - German L. Perlovich
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
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44
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Marin-Luna M, Sanchez-Sanz G, O'Sullivan P, Rozas I. Guanidine complexes of platinum: a theoretical study. J Phys Chem A 2014; 118:5540-7. [PMID: 24988181 DOI: 10.1021/jp504483x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have studied theoretically the complexes of model N-phenylguanidine/ium derivatives with PtCl3(-) and PtCl2 in different coordinating modes (mono- and bidentate) with different N atoms of the guanidine/ium moiety using the B3LYP/6-31+G** and LANL2DZ mixed basis set. This will aid the understanding of the complexation between platinum and the guanidine or guanidinium moiety in order to design dual anticancer agents that combine a guanidine-based DNA minor groove binder and a cisplatin-like moiety. Calculated interaction and relative energies, analysis of the electron density, and examination of the orbital interactions indicate that the most stable type of complex is that with a monodentate interaction between PtCl3(-) and guanidinium established through one of the NH2 groups. Next, we optimized the structure of three bis-guanidinium diaromatic systems developed in our group as DNA minor groove binders and their complexation with PtCl3(-), finding that the formation of Pt complexes of these minor groove binders is favorable and would produce stable monodentate coordinated systems.
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Affiliation(s)
- Marta Marin-Luna
- Departamento de Química Orgánica, Universidad de Murcia , Facultad de Química, Regional Campus of International Excellence "Campus Mare Nostrum", Espinardo, 30100 Murcia, Spain
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45
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Manin AN, Voronin AP, Manin NG, Vener MV, Shishkina AV, Lermontov AS, Perlovich GL. Salicylamide cocrystals: screening, crystal structure, sublimation thermodynamics, dissolution, and solid-state DFT calculations. J Phys Chem B 2014; 118:6803-14. [PMID: 24861612 DOI: 10.1021/jp5032898] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new cocrystal of 2-hydroxybenzamide (A) with 4-acetamidobenzoic acid (B) has been obtained by the DSC screening method. Thermophysical analysis of the aggregate [A:B] has been conducted and a fusion diagram has been plotted. Cocrystal formation from melts was studied by using thermomicroscopy. A cocrystal single-crystal was grown and its crystal structure was determined. The pattern of noncovalent interactions has been quantified using the solid-state DFT computations coupled with the Bader analysis of the periodic electron density. The sublimation processes of A-B cocrystal have been studied and its thermodynamic functions have been calculated. The classical method of substance transfer by inert gas-carrier was chosen to investigate sublimation processes experimentally. The lattice energy is found to be 143 ± 4 kJ/mol. It is lower than the sum of the corresponding values of the cocrystal pure components. The theoretical value of the lattice energy, 156 kJ/mol, is in reasonable agreement with the experimental one. A ternary phase diagram of solubility (A-B-ethanol) has been plotted and the areas with solutions for growing thermodynamically stable cocrystals have been determined.
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Affiliation(s)
- Alex N Manin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences , 1, Academicheskaya, 153045 Ivanovo, Russia
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46
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Alkorta I, Elguero J, Del Bene JE. Characterizing Traditional and Chlorine-Shared Halogen Bonds in Complexes of Phosphine Derivatives with ClF and Cl2. J Phys Chem A 2014; 118:4222-31. [DOI: 10.1021/jp503436f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ibon Alkorta
- Instituto de Química
Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto de Química
Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
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47
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Varadwaj PR, Varadwaj A, Jin BY. Significant evidence of C⋯O and C⋯C long-range contacts in several heterodimeric complexes of CO with CH3–X, should one refer to them as carbon and dicarbon bonds! Phys Chem Chem Phys 2014; 16:17238-52. [DOI: 10.1039/c4cp01775g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An illustrated example of a ‘dicarbon bond’ formed between a pair of two carbon atoms of the OC⋯CH3–Cl3intermolecular complex, one corresponding to the methylated carbon in 1,1,1-trichloro-ethane (CH3–Cl3) and one to the carbon in the carbon dioxide (CO) molecule.
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Affiliation(s)
| | - Arpita Varadwaj
- Department of Chemistry
- National Taiwan University
- Taipei, Taiwan
| | - Bih-Yaw Jin
- Department of Chemistry
- National Taiwan University
- Taipei, Taiwan
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48
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Blanco F, Kelly B, Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J, Rozas I. Non-Covalent Interactions: Complexes of Guanidinium with DNA and RNA Nucleobases. J Phys Chem B 2013; 117:11608-16. [DOI: 10.1021/jp407339v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fernando Blanco
- Molecular Design
Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences
Institute, University of Dublin, Trinity College, Trinity College, 152-160 Pearse Street, Dublin 2, Ireland
| | - Brendan Kelly
- School of Chemistry,
Trinity Biomedical Sciences Institute, Trinity College, Trinity College, 152-160 Pearse Street, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences Research Center & IOCB, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Cristina Trujillo
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences Research Center & IOCB, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Ibon Alkorta
- Instituto de Química
Médica, IQM-CSIC, Juan de la
Cierva 3, 28006 Madrid, Spain
| | - Jose Elguero
- Instituto de Química
Médica, IQM-CSIC, Juan de la
Cierva 3, 28006 Madrid, Spain
| | - Isabel Rozas
- School of Chemistry,
Trinity Biomedical Sciences Institute, Trinity College, Trinity College, 152-160 Pearse Street, Dublin 2, Ireland
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49
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Alkorta I, Elguero J, Del Bene JE. Pnicogen bonded complexes of PO2X (X = F, Cl) with nitrogen bases. J Phys Chem A 2013; 117:10497-503. [PMID: 24044522 DOI: 10.1021/jp407097e] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An ab initio MP2/aug'-cc-pVTZ study has been carried out on complexes formed between PO2X (X = F and Cl) as the Lewis acids and a series of nitrogen bases ZN, including NH3, H2C═NH, NH2F, NP, NCH, NCF, NF3, and N2. Binding energies of these complexes vary from -10 to -150 kJ/mol, and P-N distances from 1.88 to 2.72 Å. Complexes ZN:PO2F have stronger P(...)N bonds and shorter P-N distances than the corresponding complexes ZN:PO2Cl. Charge transfer from the N lone pair through the π-hole to the P-X and P-O σ* orbitals leads to stabilization of these complexes, although charge-transfer energies can be evaluated only for complexes with binding energies less than -71 kJ/mol. Complexation of PO2X with the strongest bases leads to P···N bonds with a significant degree of covalency, and P-N distances that approach the P-N distances in the molecules PO2NC and PO2NH2. In these complexes, the PO2X molecules distort from planarity. Changes in (31)P absolute chemical shieldings upon complexation do not correlate with changes in charges on P, although they do correlate with the binding energies of the complexes. EOM-CCSD spin-spin coupling constants (1p)J(P-N) are dominated by the Fermi-contact term, which is an excellent approximation to total J. (1p)J(P-N) values are small at long distances, increase as the distance decreases, but then decrease at short P-N distances. At the shortest distances, values of (1p)J(P-N) approach (1)J(P-N) for the molecules PO2NC and PO2NH2.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC) , Juan de la Cierva, 3, 28006 Madrid, Spain
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50
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Vener MV, Shishkina AV, Rykounov AA, Tsirelson VG. Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis. J Phys Chem A 2013; 117:8459-67. [PMID: 23924151 DOI: 10.1021/jp405119x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.
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Affiliation(s)
- Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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