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van Dam A, van Schendel R, Gangarapu S, Zuilhof H, Smulders MMJ. DFT Study of Imine-Exchange Reactions in Iron(II)-Coordinated Pincers. Chemistry 2023; 29:e202301795. [PMID: 37560922 DOI: 10.1002/chem.202301795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/11/2023]
Abstract
The imine bond is among the most applied motifs in dynamic covalent chemistry. Although its uses are varied and often involve coordination to a transition metal for stability, mechanistic studies on imine exchange reactions so far have not included metal coordination. Herein, we investigated the condensation and transimination reactions of an Fe2+ -coordinated diimine pyridine pincer, employing wB97XD/6-311G(2d,2p) DFT calculations in acetonitrile. We first experimentally confirmed that Fe2+ is strongly coordinated by these pincers, and is thus a justified model ion. When considering a four-membered ring-shaped transition state for proton transfers, the required activation energies for condensation and transimination reaction exceeded the values expected for reactions known to be spontaneous at room temperature. The nature of the incoming and exiting amines and the substituents on the para-position of the pincer had no effect on this. Replacing Fe2+ with Zn2+ or removing it altogether did not reduce it either. However, the addition of two ethylamine molecules lowered the energy barriers to be compatible with experiment (19.4 and 23.2 kcal/mol for condensation and transimination, respectively). Lastly, the energy barrier of condensation of a non-coordinated pincer was significantly higher than found for Fe2+ -coordinating pincers, underlining the catalyzing effect of metal coordination on imine exchange reactions.
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Affiliation(s)
- Annemieke van Dam
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Robin van Schendel
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Satesh Gangarapu
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
- School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Tianjin, 300072, P.R. China
| | - Maarten M J Smulders
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
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2
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Lippert B, Sanz Miguel PJ. Beyond sole models for the first steps of Pt-DNA interactions: Fundamental properties of mono(nucleobase) adducts of PtII coordination compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Amino acid coordination complex mediates cisplatin entrapment within PEGylated liposome: An implication in colorectal cancer therapy. Int J Pharm 2022; 623:121946. [PMID: 35750277 DOI: 10.1016/j.ijpharm.2022.121946] [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: 03/16/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 11/22/2022]
Abstract
Cis-Diaminedichloroplatinum (cisplatin, CDDP) remained among the most widely used anti-cancer agents; however, management of the dose-limiting side effects is still a great hurdle to its therapeutic potential. In the framework of this investigation, novel approach was developed for CDDP encasement within liposome based on the formation of a coordination bond between the platinum (II) atom and a carboxylic group in aspartic acid (AA) and glutamic acid (GA). We have also compared two methods of preparation based on equilibration and conventional lipid film hydration. For this, first FTIR spectra of the conjugates confirmed coordination bond between Pt and the carboxylate moieties. The PEGylated liposomes composed of HSPC, cholesterol and DPPG had a size of 134 to 197 nm and negative zeta potential (-14.20 to -20.90 mv). Cytotoxicity study revealed IC50 values of <7 µg/ml for liposomes. In vivo plasma retention following iv administration indicated the potential of liposome in maintaining cisplatin levels within the circulation, while free cisplatin and cisplatin conjugates were promptly eliminated. Anti-tumor efficacy studies following iv injections at 3 mg/kg cisplatin weekly for three weeks in C26 tumor bearing BALB/c mice demonstrated the potential of the cisplatin liposomes in tumor growth inhibition. Pt-complexes were not as effective as liposomal formulations showing the crucial role of liposomes in maintaining cisplatin levels within blood circulation. Overall, the developed cisplatin liposome seems to be a promising therapeutic approach for targeting solid tumors.
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4
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Nieuwland C, Fonseca Guerra C. How the Chalcogen Atom Size Dictates the Hydrogen‐Bond Donor Capability of Carboxamides, Thioamides, and Selenoamides. Chemistry 2022; 28:e202200755. [PMID: 35322485 PMCID: PMC9324920 DOI: 10.1002/chem.202200755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 12/21/2022]
Abstract
The amino groups of thio‐ and selenoamides can act as stronger hydrogen‐bond donors than of carboxamides, despite the lower electronegativity of S and Se. This phenomenon has been experimentally explored, particularly in organocatalysis, but a sound electronic explanation is lacking. Our quantum chemical investigations show that the NH2 groups in thio‐ and selenoamides are more positively charged than in carboxamides. This originates from the larger electronic density flow from the nitrogen lone pair of the NH2 group towards the lower‐lying π*C=S and π*C=Se orbitals than to the high‐lying π*C=O orbital. The relative energies of the π* orbitals result from the overlap between the chalcogen np and carbon 2p atomic orbitals, which is set by the carbon‐chalcogen equilibrium distance, a consequence of the Pauli repulsion between the two bonded atoms. Thus, neither the electronegativity nor the often‐suggested polarizability but the steric size of the chalcogen atom determines the amide's hydrogen‐bond donor capability.
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Affiliation(s)
- Celine Nieuwland
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Leiden Institute of Chemistry Gorlaeus Laboratories Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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5
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Budow-Busse S, Chai Y, Müller SL, Daniliuc C, Seela F. The α-D-anomer of 2'-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis. Acta Crystallogr C Struct Chem 2021; 77:202-208. [PMID: 33949335 PMCID: PMC8097964 DOI: 10.1107/s2053229621003430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/30/2021] [Indexed: 11/23/2022] Open
Abstract
β-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2'-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2'-endo-C3'-exo twist (23T; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleosides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the 1H NMR spectrum, indicating a hindered rotation around the C4-N4 bond and a relatively short C-N bond in the solid state. Crystal packing is controlled by N-H...O and O-H...O contacts between the nucleobase and sugar moieties. Moreover, two weak C-H...N contacts (C1'-H1' and C3'-H3'A) are observed. A Hirshfeld surface analysis was carried out and the results support the intermolecular interactions observed by the X-ray analysis.
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Affiliation(s)
- Simone Budow-Busse
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Sebastian Lars Müller
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Constantin Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, Osnabrück 49069, Germany
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6
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Frańska M, Konował E. Unexpected cytosine-AuCl 4- interaction under electrospray ionization mass spectrometry conditions-Formation of cytosine-Au(I) complexes. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2020; 26:225-229. [PMID: 31801025 DOI: 10.1177/1469066719893233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interaction of cytosine with AuCl4-, under electrospray ionization mass spectrometric conditions, is discussed. On the basis of respective full scan mass spectra and product ion spectra, obtained in positive and negative ion mode, it has been deduced that cytosine is very prone to form Au(I)-containing complexes. The complexes may be formed in the gas phase by decomposition of Au(III)-containing complexes and also in the electrospray ionization source as a result of the occurrence of redox process. It has also been found that the interaction of cytosine with Au+ is stronger than that with Cu+ or Ag+, although taking into account the electrostatic attraction, it is not expected.
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Affiliation(s)
- Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo, Poznań, Poland
| | - Emilia Konował
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo, Poznań, Poland
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7
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Zhou X, Müller SL, Leonard P, Daniliuc C, Chai Y, Budow-Busse S, Seela F. Crystal structures of α-D and β-D anomeric 2′-Deoxycytidines decorated with octadiynyl side chains: Hydrogen bonding, crystal packing and impact of alkyne residues on physical properties. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.04.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Müller SL, Zhou X, Leonard P, Korzhenko O, Daniliuc C, Seela F. Functionalized Silver‐Ion‐Mediated α‐dC/β‐dC Hybrid Base Pairs with Exceptional Stability: α‐d‐5‐Iodo‐2′‐Deoxycytidine and Its Octadiynyl Derivative in Metal DNA. Chemistry 2019; 25:3077-3090. [DOI: 10.1002/chem.201805299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/04/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Sebastian Lars Müller
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Xinglong Zhou
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Oxana Korzhenko
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Constantin Daniliuc
- Institut für Organische ChemieUniversität Münster Corrensstrasse 40 48149 Münster Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für, Chemie neuer MaterialienUniversität Osnabrück Barbarastrasse 7 49069 Osnabrück Germany
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9
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Yu ZN, Zhang Z, Lv ZS, Liu MT, Zhang L, Wang AJ, Jiang LY, Feng JJ. Platinum69-cobalt31 alloyed nanosheet nanoassemblies as advanced bifunctional electrocatalysts for boosting ethylene glycol oxidation and oxygen reduction. J Colloid Interface Sci 2018; 525:216-224. [DOI: 10.1016/j.jcis.2018.04.050] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/25/2018] [Accepted: 04/11/2018] [Indexed: 11/26/2022]
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10
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Zhu XY, Zhang L, Yuan PX, Feng JJ, Yuan J, Zhang QL, Wang AJ. Hollow Ag 44Pt 56 nanotube bundles with high electrocatalytic performances for hydrogen evolution and ethylene glycol oxidation reactions. J Colloid Interface Sci 2018; 532:571-578. [PMID: 30114646 DOI: 10.1016/j.jcis.2018.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 01/23/2023]
Abstract
It is a main challenge to synthesize highly efficient and durable nanocatalysts towards hydrogen evolution reaction (HER) and alcohol oxidation reaction in energy conversion and storage. Herein, a green wet-chemical approach was developed to directly prepare hollow Ag44Pt56 nanotube bundles (H-Ag44Pt56 NTBs), utilizing 5-azacytosine as a structure-directing agent. The obtained electrocatalyst displayed superior catalytic activity and durability for HER in acid media, and the great improvement in catalytic performance for ethylene glycol oxidation reaction (EGOR) in the alkaline electrolyte, outperforming home-made Ag34Pt66 nanoparticles (NPs), Ag70Pt30 NPs, and commercial Pt/C catalysts. The high electrocatalytic characters are mainly attributed to the special nanostructures and the synergetic effects between the bimetals.
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Affiliation(s)
- Xiao-Yan Zhu
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Lu Zhang
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Pei-Xin Yuan
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jiu-Ju Feng
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Junhua Yuan
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Qian-Li Zhang
- School of Chemistry and Biological Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Ai-Jun Wang
- Key laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China.
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11
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Guo X, Leonard P, Ingale SA, Seela F. Gemcitabine, Pyrrologemcitabine, and 2'-Fluoro-2'-Deoxycytidines: Synthesis, Physical Properties, and Impact of Sugar Fluorination on Silver Ion Mediated Base Pairing. Chemistry 2017; 23:17740-17754. [PMID: 28906062 DOI: 10.1002/chem.201703427] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/05/2017] [Indexed: 01/06/2023]
Abstract
The stability of silver-mediated "dC-dC" base pairs relies not only on the structure of the nucleobase, but is also sensitive to structural modification of the sugar moiety. 2'-Fluorinated 2'-deoxycytidines with fluorine atoms in the arabino (up) and ribo (down) configuration as well as with geminal fluorine substitution (anticancer drug gemcitabine) and the novel fluorescent phenylpyrrolo-gemcitabine (ph PyrGem) have been synthesized. All the nucleosides display the recognition face of naturally occurring 2'-deoxycytidine. The nucleosides were converted into phosphoramidites and incorporated into 12-mer oligonucleotides by solid-phase synthesis. The addition of silver ions to DNA duplexes with a fluorine-modified "dC-dC" pair near the central position led to significant duplex stabilization. The increase in stability was higher for duplexes with fluorinated sugar residues than for those with an unchanged 2'-deoxyribose moiety. Similar observations were made for "dC-dT" pairs and to a minor extent for "dC-dA" pairs. The increase in silver ion mediated base-pair stability was reversed by annulation of a pyrrole ring to the cytosine moiety, as shown for 2'-fluorinated ph PyrGem in comparison with phenylpyrrolo-dC (ph PyrdC). This phenomenon results from stereoelectronic effects induced by fluoro substitution, which are transmitted from the sugar moiety to the silver ion mediated base pairs. The extent of the effect depends on the number of fluorine substituents, their configuration, and the structure of the nucleobase.
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Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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12
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Bai L, Gao C, Liu Q, Yu C, Zhang Z, Cai L, Yang B, Qian Y, Yang J, Liao X. Research progress in modern structure of platinum complexes. Eur J Med Chem 2017; 140:349-382. [PMID: 28985575 DOI: 10.1016/j.ejmech.2017.09.034] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/18/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
Abstract
Since the antitumor activity of cisplatin was discovered in 1967 by Rosenberg, platinum-based anticancer drugs have played an important role in chemotherapy in clinic. Nevertheless, platinum anticancer drugs also have caused severe side effects and cross drug resistance which limited their applications. Therefore, a significant amount of efforts have been devoted to developing new platinum-based anticancer agents with equal or higher antitumor activity but lower toxicity. Until now, a large number of platinum-based complexes have been prepared and extensively investigated in vitro and in vivo. Among them, some platinum-based complexes revealing excellent anticancer activity showed the potential to be developed as novel type of anticancer agents. In this account, we present such platinum-based anticancer complexes which owning various types of ligands, such as, amine carrier ligands, leaving groups, reactive molecule, steric hindrance groups, non-covalently binding platinum (II) complexes, Platinum(IV) complexes and polynuclear platinum complexes. Overall, platinum-based anticancer complexes reported recently years upon modern structure are emphasized.
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Affiliation(s)
- Linkui Bai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Chuanzhu Gao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
| | - Qinghua Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Congtao Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Zhuxin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Linxiang Cai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Bo Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yunxu Qian
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jian Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xiali Liao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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13
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Guo X, Seela F. Anomeric 2′-Deoxycytidines and Silver Ions: Hybrid Base Pairs with Greatly Enhanced Stability and Efficient DNA Mismatch Detection with α-dC. Chemistry 2017; 23:11776-11779. [DOI: 10.1002/chem.201703017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie; Institut für Chemie neuer Materialien; Universität Osnabrück; Barbarastrasse 7 49069 Osnabrück Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie; Institut für Chemie neuer Materialien; Universität Osnabrück; Barbarastrasse 7 49069 Osnabrück Germany
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14
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The exocyclic amino group of adenine in Pt II and Pd II complexes: a critical comparison of the X-ray crystallographic structural data and gas phase calculations. J Biol Inorg Chem 2017; 22:567-579. [PMID: 28315011 DOI: 10.1007/s00775-017-1448-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/28/2017] [Indexed: 12/30/2022]
Abstract
A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H2, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH+) and deprotonated forms (9MeA-H), free and metal-complexed, has been conducted. The metals are PtII and PdII, bonded to nitrogen-containing co-ligands (NH3, dien, bpy), with N1, N6, and N7 being the metal-binding sites, individually or in different combinations. The results obtained from gas phase calculations are critically compared with X-ray crystallography data, whenever possible. In the majority of cases, there is good qualitative agreement between calculated and experimentally determined C6-N6 bond lengths, but calculated values always show a trend to larger values, by 0.02-0.08 Å. Both methods indicate, with few exceptions, a high degree of double-bond character of C6-N6, consistent with an essentially sp2-hybridized N6 atom. The shortest values for C6-N6 distances in X-ray crystal structures are around 1.30 Å. Exceptions refer to cases in which DFT calculations suggest the existence of a hydrogen bond with N6H2 acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp3. Nevertheless, even in these cases the C6-N6 bond (1.392 Å) is still halfway between a typical C-N single bond (1.48 Å) and a typical C=N double bond (1.28 Å). This scenario is, however, not borne out by X-ray crystallographic results, and is attributed to the absence of counter anions and solvent molecules in the calculated structures.
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15
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Jana SK, Guo X, Mei H, Seela F. Robust silver-mediated imidazolo-dC base pairs in metal DNA: dinuclear silver bridges with exceptional stability in double helices with parallel and antiparallel strand orientation. Chem Commun (Camb) 2016; 51:17301-4. [PMID: 26463426 DOI: 10.1039/c5cc06734k] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new unprecedented metal-mediated base pair was designed that stabilizes reverse Watson-Crick DNA (parallel strand orientation, ps) as well as canonical Watson-Crick DNA (antiparallel strand orientation, aps). This base pair contains two imidazolo-dC units decorated with furan residues. Tm measurements and spectroscopic studies reveal that each silver-mediated furano-imidazolo-dC forms exceptionally stable duplexes with ps and aps chain orientation. This stability increase by a silver-mediated base pair is the highest reported so far for ps and aps DNA helices.
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Affiliation(s)
- Sunit Kumar Jana
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany and Institute for Nanobiomedical Technology and Membrane Biology, Sichuan University, No. 1 Keyuan 4th Road, Gaopengdadao, Chengdu 610041, P. R. China
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany and Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany.
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16
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Lippert B, Sanz Miguel PJ. The Renaissance of Metal-Pyrimidine Nucleobase Coordination Chemistry. Acc Chem Res 2016; 49:1537-45. [PMID: 27472006 DOI: 10.1021/acs.accounts.6b00253] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The significance of metal ions for the function and properties of DNA and RNA, long seen primarily under biological aspects and medicinal uses, has recently gained a renewed momentum. This is a consequence of the advent of novel applications in the fields of materials science, biotechnology, and analytical sensor chemistry that relate to the designed incorporation of transition metal ions into nucleic acid base pairs. Ag(+) and Hg(2+) ions, binding to pyrimidine (pym) nucleobases, represent major players in this development. Interestingly, these metal ions were the ones that some 60 years ago started the field! At the same time, the mentioned metal ions had demonstrated a "special relationship" with the pym nucleobases cytosine, thymine, and uracil! Parallel work conducted with oligonucleotides and model nucleobases fostered numerous significant details of these interactions, in particular when X-ray crystallography was involved, correcting earlier views occasionally. Our own activities during the past three to four decades have focused on, among others, the coordination chemistry of transition and main-group metal ions with pym model nucleobases, with an emphasis on Pt(II) and Pd(II). It has always been our goal to deduce, if possible, the potential relevance of our findings for biological processes. It is interesting to put our data, in particular for trans-a2Pt(II) (a = NH3 or amine), into perspective with those of other metal ions, notably Ag(+) and Hg(2+). Irrespective of major differences in kinetics and lability/inertness between d(8) and d(10) metal ions, there is also a lot of similarity in structural aspects as a result of the preferred linear coordination geometry of these species. Moreover, the apparent clustering of metal ions to the pym nucleobases, which is presumably essential for the formation of nanoclusters on oligonucleotide scaffolds, is impressively reflected in model systems, as are reasons for inter-nucleobase cross-links containing more than a single metal ion. The present understanding of these interrelationships is a consequence of intensive research carried out during the last 60 years by numerous laboratories. For space restrictions in this Account, it was impossible to adequately highlight the valuable contributions of all of the researchers in the field of metal-pym nucleobase interactions. Explicitly this refers to colleagues not cited in the references, e.g., R. Stuart Tobias, Robert Bau, R. Bruce Martin, Colin J. L. Lock, Katsuyuki Aoki, Helmut Sigel, and Michael J. Clarke, among others.
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Affiliation(s)
- Bernhard Lippert
- Fakultät
für Chemie und Chemische Biologie (CCB), Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Pablo J. Sanz Miguel
- Departamento
de Química Inorgánica, Instituto de Síntesis
Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
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Yin-Bandur L, Sanz Miguel PJ, Rodríguez-Santiago L, Sodupe M, Berghaus M, Lippert B. Multiple Condensation Reactions Involving PtII/PdII−OH2, Pt−NH3, and Cytosine−NH2Groups: New Twists in Cisplatin−Nucleobase Chemistry. Chemistry 2016; 22:13653-68. [DOI: 10.1002/chem.201602244] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Lu Yin-Bandur
- Fakultät Chemie und Chemische Biologie (CCB); Technische Universität Dortmund; Otto-Hahn-Str. 6 44221 Dortmund Germany
| | - Pablo J. Sanz Miguel
- Departamento de Química Inorgánica; Instituto de Sintesis Química y Catálisis Homogénea (ISQCH); Universidad de Zaragoza-CSIC; 50009 Zaragoza Spain
| | | | - Mariona Sodupe
- Department da Química; Universitat Autónoma Barcelona; Bellaterra 08193 Barcelona Spain
| | - Melanie Berghaus
- Fakultät Chemie und Chemische Biologie (CCB); Technische Universität Dortmund; Otto-Hahn-Str. 6 44221 Dortmund Germany
| | - Bernhard Lippert
- Fakultät Chemie und Chemische Biologie (CCB); Technische Universität Dortmund; Otto-Hahn-Str. 6 44221 Dortmund Germany
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Vellé A, Cebollada A, Lippert B, Sanz Miguel PJ. Topology of metallacalix[4]arenes with uracil and cytosine ligands: favorable and unfavorable assemblies. NEW J CHEM 2016. [DOI: 10.1039/c6nj00772d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A single isomer of many topologically possible ones! The experimentally isolated metallacalix[4]arenes based on pyrimidine nucleobases are the energetically more favorable.
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Affiliation(s)
- Alba Vellé
- Departamento de Química Inorgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- Universidad de Zaragoza-CSIC
- 50009 Zaragoza
- Spain
| | - Andrea Cebollada
- Departamento de Química Inorgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- Universidad de Zaragoza-CSIC
- 50009 Zaragoza
- Spain
| | - Bernhard Lippert
- Fakultät Chemie und Chemische Biologie (CCB)
- Technische Universität Dortmund
- 44221 Dortmund
- Germany
| | - Pablo J. Sanz Miguel
- Departamento de Química Inorgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- Universidad de Zaragoza-CSIC
- 50009 Zaragoza
- Spain
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Mulder JR, Guerra CF, Slootweg JC, Lammertsma K, Bickelhaupt FM. Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table. J Comput Chem 2015; 37:304-13. [DOI: 10.1002/jcc.24197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Joshua R. Mulder
- Department of Chemistry and Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1083 Amsterdam 1081 HV the Netherlands
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); VU University Amsterdam; De Boelelaan 1083 Amsterdam 1081 HV the Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); VU University Amsterdam; De Boelelaan 1083 Amsterdam 1081 HV the Netherlands
| | - J. Chris Slootweg
- Department of Chemistry and Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1083 Amsterdam 1081 HV the Netherlands
| | - Koop Lammertsma
- Department of Chemistry and Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1083 Amsterdam 1081 HV the Netherlands
- Department of Chemistry; University of Johannesburg, Auckland Pk Kingsway Campus; Auckland Pk ZA- 2006 South Africa
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); VU University Amsterdam; De Boelelaan 1083 Amsterdam 1081 HV the Netherlands
- Institute of Molecules and Materials (IMM), Radboud University Nijmegen; Heyendaalseweg 135 Nijmegen 6525 AJ the Netherlands
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Ibáñez S, Mihály B, Sanz Miguel PJ, Steinborn D, Pretzer I, Hiller W, Lippert B. The challenge of deciphering linkage isomers in mixtures of oligomeric complexes derived from 9-methyladenine and trans-(NH3)2Pt(II) units. Chemistry 2015; 21:5794-806. [PMID: 25737270 DOI: 10.1002/chem.201406378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Indexed: 11/11/2022]
Abstract
Metal coordination to N9-substituted adenines, such as the model nucleobase 9-methyladenine (9MeA), under neutral or weakly acidic pH conditions in water preferably occurs at N1 and/or N7. This leads, not only to mononuclear linkage isomers with N1 or N7 binding, but also to species that involve both N1 and N7 metal binding in the form of dinuclear or oligomeric species. Application of a trans-(NH3)2Pt(II) unit and restriction of metal coordination to the N1 and N7 sites and the size of the oligomer to four metal entities generates over 50 possible isomers, which display different feasible connectivities. Slowly interconverting rotamers are not included in this number. Based on (1)H NMR spectroscopic analysis, a qualitative assessment of the spectroscopic features of N1,N7-bridged species was attempted. By studying the solution behavior of selected isolated and structurally characterized compounds, such as trans-[PtCl(9MeA-N7)(NH3)2]ClO4⋅2H2O or trans,trans-[{PtCl(NH3)2}2(9MeA-N1,N7)][ClO4]2⋅H2O, and also by application of a 9MeA complex with an (NH3)3Pt(II) entity at N7, [Pt(9MeA-N7)(NH3)3][NO3]2, which blocks further cross-link formation at the N7 site, basic NMR spectroscopic signatures of N1,N7-bridged Pt(II) complexes were identified. Among others, the trinuclear complex trans-[Pt(NH3)2{μ-(N1-9MeA-N7)Pt(NH3)3}2][ClO4]6⋅2H2O was crystallized and its rotational isomerism in aqueous solution was studied by NMR spectroscopy and DFT calculations. Interestingly, simultaneous Pt(II) coordination to N1 and N7 acidifies the exocyclic amino group of the two 9MeA ligands sufficiently to permit replacement of one proton each by a bridging heterometal ion, Hg(II) or Cu(II), under mild conditions in water.
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Affiliation(s)
- Susana Ibáñez
- Fakultät Chemie und Chemische Biologie (CCB), Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund (Germany), Fax: (+49) 231-755-3797
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21
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Lüth MS, Freisinger E, Kampf G, Garijo Anorbe M, Griesser R, Operschall BP, Sigel H, Lippert B. Connectivity patterns and rotamer states of nucleobases determine acid-base properties of metalated purine quartets. J Inorg Biochem 2015; 148:93-104. [PMID: 25773716 DOI: 10.1016/j.jinorgbio.2015.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 10/24/2022]
Abstract
Potentiometric pH titrations and pD dependent (1)H NMR spectroscopy have been applied to study the acidification of the exocyclic amino group of adenine (A) model nucleobases (N9 position blocked by alkyl groups) when carrying trans-a2Pt(II) (with a=NH3 or CH3NH2) entities both at N1 and N7 positions. As demonstrated, in trinuclear complexes containing central A-Pt-A units, it depends on the connectivity pattern of the adenine bases (N7/N7 or N1/N1) and their rotamer states (head-head or head-tail), how large the acidifying effect is. Specifically, a series of trinuclear complexes with (A-N7)-Pt-(N7-A) and (A-N1)-Pt-(N1-A) cross-linking patterns and terminal 9-alkylguanine ligands (9MeGH, 9EtGH) have been analyzed in this respect, and it is shown that, for example, the 9MeA ligands in trans-,trans-,trans-[Pt(NH3)2(N7-9MeA-N1)2{Pt(NH3)2(9EtGH-N7)}2](ClO4)6·6H2O (4a) and trans-,trans-,trans-[Pt(NH3)2(N7-9EtA-N1)2{Pt(CH3NH2)2(9-MeGH-N7)}2](ClO4)6·3H2O (4b) are more acidic, by ca. 1.3 units (first pKa), than the linkage isomer trans-,trans-,trans-[Pt(CH3NH2)2(N1-9MeA-N7)2{Pt(NH3)2(9MeGH-N7)}2](NO3)6·6.25H2O (1b). Overall, acidifications in these types of complexes amount to 7-9 units, bringing the pKa values of such adenine ligands in the best case close to the physiological pH range. Comparison with pKa values of related trinuclear Pt(II) complexes having different co-ligands at the Pt ions, confirms this picture and supports our earlier proposal that the close proximity of the exocyclic amino groups in a head-head arrangement of (A-N7)-Pt-(N7-A), and the stabilization of the resulting N6H(-)⋯H2N6 unit, is key to this difference.
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Affiliation(s)
- Marc Sven Lüth
- Fakultät Chemie und Chemische Biologie (CCB), Technische Universität, Dortmund 44221 Dortmund, Germany; Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, 4056 Basel, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Gunnar Kampf
- Fakultät Chemie und Chemische Biologie (CCB), Technische Universität, Dortmund 44221 Dortmund, Germany; Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, 4056 Basel, Switzerland
| | - Marta Garijo Anorbe
- Fakultät Chemie und Chemische Biologie (CCB), Technische Universität, Dortmund 44221 Dortmund, Germany
| | - Rolf Griesser
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, 4056 Basel, Switzerland
| | - Bert P Operschall
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, 4056 Basel, Switzerland
| | - Helmut Sigel
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, 4056 Basel, Switzerland.
| | - Bernhard Lippert
- Fakultät Chemie und Chemische Biologie (CCB), Technische Universität, Dortmund 44221 Dortmund, Germany.
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Gómez-Iglesias P, Martín-Alvarez JM, Miguel D, Villafañe F. Amidino ligands obtained from the coupling of 1-methylcytosine and nitrile: a new method to incorporate biomolecules into luminescent Re(CO)3 complexes. Dalton Trans 2015; 44:17478-81. [DOI: 10.1039/c5dt03221k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Amidino chelating ligands obtained from the coupling of 1-methylcytosine with nitriles allow the incorporation of biologically relevant substrates into Re(CO)3 complexes.
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Affiliation(s)
- Patricia Gómez-Iglesias
- GIR MIOMeT-IU Cinquima-Química Inorgánica
- Facultad de Ciencias
- Campus Miguel Delibes
- Universidad de Valladolid
- 47011 Valladolid
| | - Jose Miguel Martín-Alvarez
- GIR MIOMeT-IU Cinquima-Química Inorgánica
- Facultad de Ciencias
- Campus Miguel Delibes
- Universidad de Valladolid
- 47011 Valladolid
| | - Daniel Miguel
- GIR MIOMeT-IU Cinquima-Química Inorgánica
- Facultad de Ciencias
- Campus Miguel Delibes
- Universidad de Valladolid
- 47011 Valladolid
| | - Fernando Villafañe
- GIR MIOMeT-IU Cinquima-Química Inorgánica
- Facultad de Ciencias
- Campus Miguel Delibes
- Universidad de Valladolid
- 47011 Valladolid
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