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Li MS, Dong YW, Pang XY, Chai H, Wang X, Jiang W. The Influence of Small Biomolecules, Salts and Buffers on the Molecular Recognition of Amide Naphthotube in Aqueous Solutions. Chemistry 2023; 29:e202202972. [PMID: 36196913 DOI: 10.1002/chem.202202972] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 11/18/2022]
Abstract
We found the binding affinities of amide naphthotube to neutral organic molecules in water are not influenced by most of small biomolecules, inorganic salts, and PBS and Tris buffers but are reduced in HEPES buffer through competitive binding. Nevertheless, salts do change the binding affinities of amide naphthotube to charged molecules through a screening effect.
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Affiliation(s)
- Ming-Shuang Li
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Yi-Wei Dong
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Xin-Yu Pang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Hongxin Chai
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China.,Shenzhen Xinhua Middle School, Shenzhen, 518109, P. R. China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Wei Jiang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
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Kubik S. When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water. ChemistryOpen 2022; 11:e202200028. [PMID: 35373466 PMCID: PMC8977507 DOI: 10.1002/open.202200028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.
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Affiliation(s)
- Stefan Kubik
- Technische Universität KaiserslauternFachbereich Chemie – Organische ChemieErwin-Schrödinger-Straße 5467663KaiserslauternGermany
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Jordan JH, Ashbaugh HS, Mague JT, Gibb BC. Buffer and Salt Effects in Aqueous Host-Guest Systems: Screening, Competitive Binding, or Both? J Am Chem Soc 2021; 143:18605-18616. [PMID: 34704751 PMCID: PMC8587612 DOI: 10.1021/jacs.1c08457] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There are many open questions regarding the supramolecular properties of ions in water, a fact that has ramifications within any field of study involving buffered solutions. Indeed, as Pielak has noted (Buffers, Especially the Good Kind, Biochemistry, 2021, in press. DOI:10.1021/acs.biochem.1c00200) buffers were conceived of with little regard to their supramolecular properties. But there is a difficulty here; the mathematical models supramolecular chemists use for affinity determinations do not account for screening. As a result, there is uncertainty as to the magnitude of any screening effect and how this compares to competitive salt/buffer binding. Here we use a tetra-cation cavitand to compare halide affinities obtained using a traditional unscreened model and a screened (Debye-Hückel) model. The rule of thumb that emerges is that if ionic strength is changed by >1 order of magnitude─either during a titration or if a comparison is sought between two different buffered solutions─screening should be considered. We also build a competitive mathematical model showing that binding attenuation in buffer is largely due to competitive binding to the host by said buffer. For the system at hand, we find that the effect of competition is approximately twice that of the effect of screening (∼RT at 25 °C). Thus, for strong binders it is less important to account for screening than it is to account for competitive complexation, but for weaker binders both effects should be considered. We anticipate these results will help supramolecular chemists unravel the properties of buffers and so help guide studies of biomacromolecules.
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Affiliation(s)
- Jacobs H Jordan
- Agricultural Research Service Southern Regional Research Center, U.S. Department of Agriculture, New Orleans, Louisiana 70124, United States
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors. Molecules 2020; 26:molecules26010106. [PMID: 33379401 PMCID: PMC7796322 DOI: 10.3390/molecules26010106] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.
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Sayed M, Tom DM, Pal H. Multimode binding and stimuli responsive displacement of acridine orange dye complexed with p-sulfonatocalix[4/6]arene macrocycles. Phys Chem Chem Phys 2020; 22:13306-13319. [PMID: 32510077 DOI: 10.1039/d0cp00030b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Interaction of acridine orange (AOH+) dye with water soluble anionic p-sulfonatocalix[n]arene (SCXn) hosts, SCX4 and SCX6, having different cavity dimensions, has been investigated using multispectroscopic techniques. Intriguing modulation in the photophysical properties of AOH+ upon interaction with SCXn hosts indicate the formation of different host-guest complexes at different regions of the host concentrations. At lower host concentrations, AOH+ undergoes SCXn assisted aggregation, causing a drastic reduction in fluorescence intensity. At higher host concentrations, aggregated-AOH+-SCXn complexes disintegrate and monomeric-AOH+-SCXn exo and inclusion complexes are eventually formed, leading to a huge fluorescence enhancement finally. Observed effects are more pronounced with SCX6 as compared to SCX4 host. Time-resolved fluorescence studies indicate that at very high host concentrations, there is also a diffusion-controlled dynamic quenching for both monomeric-AOH+-SCXn exo and inclusion complexes, caused by the free SCXn present in the solution, a phenomenon not reported before for such host-guest systems. The aggregated-AOH+-SCXn complexes at lower host concentration were employed to investigate displacement study using an antiviral drug, 1-adamantanamine (AD) and a neurotransmitter, acetylcholine (AcCh), as the competitive binders cum external stimuli, which resulted in a drastic recovery of the fluorescence reduced initially due to aggregation process. Though both the AOH+-SCXn systems act as efficient supramolecular assemblies in sensing AD and AcCh as the analytes through fluorescence "OFF-ON" mechanism, the effect is more pronounced for AOH+-SCX4 system as compared to AOH+-SCX6. SCXn induced interesting modulation in the photophysical properties of AOH+ and the stimulus responsive dye displacement observed for aggregated-AOH+-SCXn systems can expectedly find applications in fluorescence OFF-ON sensing, supramolecular functional materials and similar others.
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Affiliation(s)
- Mhejabeen Sayed
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India. and Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India.
| | - Dona M Tom
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Haridas Pal
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India. and Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
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Basílio N, Pessêgo M, Acuña A, García‐Río L. Sulfonatocalixarene Counterion Exchange Binding Model in Action: Metal‐Ion Catalysis Through Host‐Guest Complexation. ChemCatChem 2019. [DOI: 10.1002/cctc.201901254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Nuno Basílio
- LAQV-REQUIMTEDepartamento de Química Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa Caparica 2829-516 Portugal
| | - Márcia Pessêgo
- LAQV-REQUIMTEDepartamento de Química Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa Caparica 2829-516 Portugal
| | - Angel Acuña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química FísicaUniversidad de Santiago Santiago 15782 Spain
| | - Luis García‐Río
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química FísicaUniversidad de Santiago Santiago 15782 Spain
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Garcia-Rio L, Basílio N, Francisco V. Counterion effect on sulfonatocalix[n]arene recognition. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2019-0305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Sulfonatocalixarenes, like other ionic receptors, possess counterions that can affect the molecular recognition process. In the present review it is shown that the competitive effect of the alkaline cations frequently used as counterions determines not only the magnitude of the external guest association constant, but also the stoichiometry of the complexes. Experimental evidences are shown about the interaction of the counterions with sulfonatocalixarene, allowing to quantify its association equilibrium constants. The counterions recognition will be a competitive process that must be taken into account when investigating the interaction of calixarenes with an external guests. When the external guest is a neutral molecule it will be possible to form ternary complexes where the counterion shows a competitive and cooperative effect. By increasing the size of the receptor, sulfonatocalix[6] and sulfonatocalix[8]arene, the complexity of the system is increased due to the formation of counterion complexes with stoichiometries 1:1 and 1:2. In the presence of an external guest, the formation of heteroternary complexes with 1:1:1 stoichiometries including a counterion and an organic cation will be possible.
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Affiliation(s)
- Luis Garcia-Rio
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Física , Universidad de Santiago , 15782 Santiago , Spain , Fax: +34 981595012
| | - Nuno Basílio
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departmento de Química, Faculdade de Ciências e Tecnologia , Universidade NOVA de Lisboa , 2829-516 Caparica , Portugal
| | - Vitor Francisco
- CNC – Center for Neurosciences and Cell Biology , University of Coimbra , 3004-517 Coimbra , Portugal
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Lavande N, Acuña A, Basílio N, Francisco V, Malkhede DD, Garcia-Rio L. A journey from calix[4]arene to calix[6] and calix[8]arene reveals more than a matter of size. Receptor concentration affects the stability and stoichiometric nature of the complexes. Phys Chem Chem Phys 2017; 19:13640-13649. [DOI: 10.1039/c7cp01889d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An in-depth study provides the basis for an accurate characterization of supramolecular systems based on p-sulfonatocalix[6,8]arenes.
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Affiliation(s)
- Nitin Lavande
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Física
- Universidad de Santiago
- 15782 Santiago
- Spain
- Department of Chemistry
| | - Angel Acuña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Física
- Universidad de Santiago
- 15782 Santiago
- Spain
| | - Nuno Basílio
- Laboratório Associado para a Química Verde (LAQV)
- Rede de Química e Tecnologia (REQUIMTE)
- Departmento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
| | - Vitor Francisco
- CNC – Center for Neurosciences and Cell Biology
- University of Coimbra
- 3004-517 Coimbra
- Portugal
| | | | - Luis Garcia-Rio
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Física
- Universidad de Santiago
- 15782 Santiago
- Spain
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Rodrigo AC, Laurini E, Vieira VMP, Pricl S, Smith DK. Effect of buffer at nanoscale molecular recognition interfaces – electrostatic binding of biological polyanions. Chem Commun (Camb) 2017; 53:11580-11583. [DOI: 10.1039/c7cc07413a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The electrostatic binding of polyanionic heparin by cationic receptors is highly dependent on the buffer in which the binding assay is carried out.
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Affiliation(s)
| | - Erik Laurini
- Simulation Engineering (MOSE) Laboratory
- Department of Engineering and Architectures (DEA)
- University of Trieste
- Trieste
- Italy
| | | | - Sabrina Pricl
- Simulation Engineering (MOSE) Laboratory
- Department of Engineering and Architectures (DEA)
- University of Trieste
- Trieste
- Italy
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Affiliation(s)
- Ching W. Chan
- Department of Chemistry, University of York, York, UK
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