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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond. Int J Mol Sci 2022; 23:ijms23158816. [PMID: 35955945 PMCID: PMC9369011 DOI: 10.3390/ijms23158816] [Citation(s) in RCA: 2] [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: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX6 (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- Correspondence: (A.V.); (P.R.V.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
- Correspondence: (A.V.); (P.R.V.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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Carbon Quantum Dots’ Synthesis with a Strong Chemical Claw for Five Transition Metal Sensing in the Irving–Williams Series. NANOMATERIALS 2022; 12:nano12050806. [PMID: 35269294 PMCID: PMC8912369 DOI: 10.3390/nano12050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023]
Abstract
Carbon quantum dots (CQDs) are an excellent eco-friendly fluorescence material, ideal for various ecological testing systems. Herein, we establish uniform microwave synthesis of the group of carbon quantum dots with specific functionalization of ethylenediamine, diethylenetriamine, and three types of Trilon (A, B and C) with chelate claws -C-NH3. CQDs’ properties were studied and applied in order to sense metal cations in an aquatic environment. The results provide the determination of the fluorescence quench in dots by pollutant salts, which dissociate into double-charged ions. In particular, the chemical interactions with CQDs’ surface in the Irving–Williams series (IWs) via functionalization of the negatively charged surface were ascribed. CQD-En and CQD-Dien demonstrated linear fluorescence quenching in high metal cation concentrations. Further, the formation of claws from Trilon A, Trilon B, and C effectively caught the copper and nickel cations from the solution due to the complexation on CQDs’ surface. Moreover, CQD-Trilon C presented chelating properties of the surface and detected five cations (Cu2+, Ni2+, Ca2+, Mg2+, Zn2+) from 0.5 mg/mL to 1 × 10−7 mg/mL in the Irving–William’s series. Dependence was mathematically attributed as an equation (ML regression model) based on the constant of complex formation. The reliability of the data was 0.993 for the training database.
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Shang XY, An HY, Zhang T, Lin JH, Hao F, Yu DH, Xiao JC, Li TD. Evaluating and understanding the affinity of metal ions to water and ammonia using density functional theory calculation. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138398] [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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Portelinha J, Duay SS, Yu SI, Heilemann K, Libardo MDJ, Juliano SA, Klassen JL, Angeles-Boza AM. Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities. Chem Rev 2021; 121:2648-2712. [PMID: 33524257 DOI: 10.1021/acs.chemrev.0c00921] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The emergence of new pathogens and multidrug resistant bacteria is an important public health issue that requires the development of novel classes of antibiotics. Antimicrobial peptides (AMPs) are a promising platform with great potential for the identification of new lead compounds that can combat the aforementioned pathogens due to their broad-spectrum antimicrobial activity and relatively low rate of resistance emergence. AMPs of multicellular organisms made their debut four decades ago thanks to ingenious researchers who asked simple questions about the resistance to bacterial infections of insects. Questions such as "Do fruit flies ever get sick?", combined with pioneering studies, have led to an understanding of AMPs as universal weapons of the immune system. This review focuses on a subclass of AMPs that feature a metal binding motif known as the amino terminal copper and nickel (ATCUN) motif. One of the metal-based strategies of hosts facing a pathogen, it includes wielding the inherent toxicity of copper and deliberately trafficking this metal ion into sites of infection. The sudden increase in the concentration of copper ions in the presence of ATCUN-containing AMPs (ATCUN-AMPs) likely results in a synergistic interaction. Herein, we examine common structural features in ATCUN-AMPs that exist across species, and we highlight unique features that deserve additional attention. We also present the current state of knowledge about the molecular mechanisms behind their antimicrobial activity and the methods available to study this promising class of AMPs.
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Affiliation(s)
- Jasmin Portelinha
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Searle S Duay
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States.,Chemistry Department, Adamson University, 900 San Marcelino Street, Ermita, Manila 1000, Philippines
| | - Seung I Yu
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Kara Heilemann
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - M Daben J Libardo
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Samuel A Juliano
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Alfredo M Angeles-Boza
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States.,Institute of Material Science, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
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Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
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Gao M, Miao P, Han X, Sun C, Ma Y, Gao Y, Xu P. Hollow transition metal hydroxide octahedral microcages for single particle surface-enhanced Raman spectroscopy. Inorg Chem Front 2019. [DOI: 10.1039/c9qi00579j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Single M(OH)x (M = Fe, Co, Ni) hollow octahedral microcage particles are explored as novel SERS-active substrates for sensitive dye molecule detection.
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Affiliation(s)
- Mansha Gao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Peng Miao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Xijiang Han
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Cheng Sun
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Yan Ma
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Yali Gao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Ping Xu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
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Salerno G, Scarano S, Mamusa M, Consumi M, Giuntini S, Macagnano A, Nativi S, Fragai M, Minunni M, Berti D, Magnani A, Nativi C, Richichi B. A small heterobifunctional ligand provides stable and water dispersible core-shell CdSe/ZnS quantum dots (QDs). NANOSCALE 2018; 10:19720-19732. [PMID: 30256371 DOI: 10.1039/c8nr05566a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We describe a simple method to prepare water dispersible core-shell CdSe/ZnS quantum dots (QDs) 1 by capping QDs with a new thiol-containing heterobifunctional dicarboxylic ligand 4 (DHLA-EDADA). This ligand, obtained on a gram scale through a few synthetic steps, provides a compact layer on the QDs, whose hydrodynamic size in H2O is 15 nm ± 3 nm. The colloidal stability is dramatically enhanced with respect to the well-known (±) α-lipoic acid (DHLA). The ligand affinity towards QDs and the water dispersibility of nanocrystals 1 are addressed by the dithiol groups of DHLA, which chelate the zinc of the shell, and by the dicarboxylic groups of the ethylenediamine-N,N-diacetic acid (EDADA) residue, respectively. The effects of pH, buffer solutions, and biological medium on the stability of QDs 1 were assessed by monitoring the photoluminescence (PL) and hydrodynamic size over time. Highly fluorescent QD dispersions, stable over extended periods of time and over broad pH ranges and buffer types, were obtained. Furthermore, we show that the DHLA-EDADA ligand 4 also endows QDs with functional groups suitable for further conjugation and for metal ion detection. As a case study to illustrate the potential of our approach, we report the preparation and characterization of a highly luminescent orange light emitting polymer-QD 1 composite film.
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Affiliation(s)
- Gianluca Salerno
- Department of Chemistry 'Ugo Schiff', University of Florence, Via della Lastruccia 13, 50019 Sesto F.no, FI, Italy.
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Dalecki AG, Crawford CL, Wolschendorf F. Copper and Antibiotics: Discovery, Modes of Action, and Opportunities for Medicinal Applications. Adv Microb Physiol 2017; 70:193-260. [PMID: 28528648 DOI: 10.1016/bs.ampbs.2017.01.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Copper is a ubiquitous element in the environment as well as living organisms, with its redox capabilities and complexation potential making it indispensable for many cellular functions. However, these same properties can be highly detrimental to prokaryotes and eukaryotes when not properly controlled, damaging many biomolecules including DNA, lipids, and proteins. To restrict free copper concentrations, all bacteria have developed mechanisms of resistance, sequestering and effluxing labile copper to minimize its deleterious effects. This weakness is actively exploited by phagocytes, which utilize a copper burst to destroy pathogens. Though administration of free copper is an unreasonable therapeutic antimicrobial itself, due to insufficient selectivity between host and pathogen, small-molecule ligands may provide an opportunity for therapeutic mimicry of the immune system. By modulating cellular entry, complex stability, resistance evasion, and target selectivity, ligand/metal coordination complexes can synergistically result in high levels of antibacterial activity. Several established therapeutic drugs, such as disulfiram and pyrithione, display remarkable copper-dependent inhibitory activity. These findings have led to development of new drug discovery techniques, using copper ions as the focal point. High-throughput screens for copper-dependent inhibitors against Mycobacterium tuberculosis and Staphylococcus aureus uncovered several new compounds, including a new class of inhibitors, the NNSNs. In this review, we highlight the microbial biology of copper, its antibacterial activities, and mechanisms to discover new inhibitors that synergize with copper.
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Affiliation(s)
- Alex G Dalecki
- The University of Alabama at Birmingham, Birmingham, AL, United States
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Turrina A, Iulian Dugulan A, Collier JE, Walton RI, Casci JL, Wright PA. Synthesis and activation for catalysis of Fe-SAPO-34 prepared using iron polyamine complexes as structure directing agents. Catal Sci Technol 2017. [DOI: 10.1039/c7cy01269a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fe-SAPO-34 templated with Fe2+–polyamine complexes gives Fe3+ species upon calcination that are active for selective catalytic reduction of NOx with ammonia.
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Affiliation(s)
- Alessandro Turrina
- EaStCHEM School of Chemistry
- University of St. Andrews
- St. Andrews
- UK
- Johnson Matthey Technology Centre
| | - A. Iulian Dugulan
- Fundamental Aspects of Materials and Energy Group
- Delft University of Technology
- 2629 JB Delft
- The Netherlands
| | | | | | | | - Paul A. Wright
- EaStCHEM School of Chemistry
- University of St. Andrews
- St. Andrews
- UK
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Stępniewski A, Radoń M, Góra-Marek K, Broclawik E. Ammonia-modified Co(II) sites in zeolites: spin and electron density redistribution through the Co(II)-NO bond. Phys Chem Chem Phys 2016; 18:3716-29. [PMID: 26761131 DOI: 10.1039/c5cp07452e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic factors essential for the bonding of a non-innocent NO ligand to ammonia-modified Co(2+) sites in cobalt-exchanged zeolites are examined for small cluster models using DFT and advanced correlated wave function calculations. The analysis of charge transfer processes between the NO ligand and the cobalt center involves two protocols: valence-bond expansion of the multiconfiguration CASSCF wave function (in terms of fragment-localized active orbitals) and spin-resolved natural orbitals for chemical valence (SR-NOCV). Applicability of SR-NOCV analysis to transition metal complexes involving non-innocent fragments is critically assessed and the approach based on the CASSCF wave function turns out to be much more robust and systematic for all studied models. It is shown that the character and direction of electron density redistribution through the Co-N-O bond, quantified by relative share of the Co(II)-NO(0), Co(III)-NO(-), and Co(I)-NO(+) resonance structures in the total wave function, fully rationalize the activation of the N-O bond upon NH3 co-ligation (evidenced by calculated and measured red-shift of the NO stretching frequency and commonly ascribed to enhanced backdonation). The huge red-shift of νN-O is attributed to an effective electron transfer between the ammonia-modified Co(ii) centers and the NO antibonding π*-orbitals (related to the increased share of the Co(III)-NO(-) form). Unexpectedly, the effect is stronger for the singlet complex with three NH3 ligands than for that with five NH3 ligands bound to the cobalt center. Our results also indicate that high-efficiency electron transfers between the Co(ii) center and the NO ligand may be enabled for the selected spin state and disabled for the other spin state of the adduct. This illustrates how the cobalt center may serve to fine-tune the electronic communication between the NO ligand and its binding site.
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Affiliation(s)
- Adam Stępniewski
- Jerzy Haber Institute of Catalysis PAS, Niezapominajek 8, 30-239 Krakow, Poland.
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Varadwaj A, Varadwaj PR, Jin BY. Can an entirely negative fluorine in a molecule, viz. perfluorobenzene, interact attractively with the entirely negative site(s) on another molecule(s)? Like liking like! RSC Adv 2016. [DOI: 10.1039/c5ra27039a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study presents the possibility for the formation of attractive intermolecular interactions between various entirely negative Lewis bases, leading to the formation of the thirteen isolated binary complexes examined.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan 10617
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering
- School of Engineering
- The University of Tokyo
- Japan 113-8656
| | - Bih-Yaw Jin
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan 10617
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