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Fan Y, Wang L, Putnis CV, Zhang W. Direct Nanoscale Imaging Reveals the Mechanism by Which Organic Acids Dissolve Vivianite through Proton and Ligand Effects. Inorg Chem 2024; 63:6909-6921. [PMID: 38564449 DOI: 10.1021/acs.inorgchem.4c00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The coprecipitation of iron (Fe) and phosphorus (P) in natural environments limits their bioavailability. Plant root-secreted organic acids can dissolve Fe-P precipitates, but the molecular mechanism underlying mobilizing biogenic elements from highly insoluble inorganic minerals remains poorly understood. Here, we investigated vivianite (Fe3(PO4)2·8H2O) dissolution by organic acids (oxalic acid (OA), citric acid (CA), and 2'-dehydroxymugineic acid (DMA)) at three different pH values (4.0, 6.0, and 8.0). With increasing pH, the vivianite dissolution efficiency by OA and CA was decreased while that by DMA was increased, indicating various dissolution mechanisms of different organic acids. Under acidic conditions, weak ligand OA (HC2O4- > C2O42- at pH 4.0 and C2O42- at pH 6.0) dissolved vivianite through the H+ effect to form irregular pits, but under alkaline condition (pH 8.0), the completely deprotonated OA was insufficient to dissolve vivianite. At pH 4.0, CA (H2Cit- > HCit2- > H3Cit) dissolved vivianite to form irregular pits through a proton-promoted mechanism, while at pH 6.0 (HCit2- > Cit3-) and pH 8.0 (Cit3-), CA dissolved vivianite to form near-rhombohedral pits through a ligand-promoted mechanism. At three pH values ((H0)DMA3- > (H1)DMA2- at pH 4.0, (H0)DMA3- at pH 6.0, and (H0)DMA3- and one deprotonated imino at pH 8.0), strong ligand DMA dissolved vivianite to form near-rhombohedral pits via ligand-promoted mechanisms. Raman spectroscopy showed that the deprotonated carboxyl groups (COO-) and imino groups were bound to Fe on the vivianite (010) face. The surface free energy of vivianite coated with OA decreased from 29.32 mJ m-2 to 24.23 mJ m-2 and then to 13.47 mJ m-2 with increasing pH, and that coated with CA resulted in a similar pH-dependent vivianite surface free-energy decrease while that coated with DMA increased the vivianite surface free energy from 31.92 mJ m-2 to 39.26 mJ m-2 and then to 49.93 mJ m-2. Density functional theory (DFT)-based calculations confirmed these findings. Our findings provide insight into the mechanism by which organic acids dissolved vivianite through proton and ligand effects.
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Affiliation(s)
- Yuke Fan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christine V Putnis
- Institut für Mineralogie, University of Münster, 48149 Münster, Germany
- School of Molecular and Life Sciences, Curtin University, Perth 6845, Australia
| | - Wenjun Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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2
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Rao BK. Site specific interactions of amino acids with (ZnO) 12 cluster: Density functional approach. J Biomol Struct Dyn 2022; 40:13325-13333. [PMID: 34613890 DOI: 10.1080/07391102.2021.1987327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Stability and electronic properties of bio-hybrid molecules are investigated in the framework of the first-principles density functional theory. The site-specific interactions between (ZnO)12 nano-cluster and arginine/aspartic acid are investigated. There are partially ionic and covalent bonds between the interacting atoms, higher binding energy 8.86 eV is observed at -COOH site of arginine, and 7.60 eV at -CN site of aspartic acid during the interaction with a nano-cluster. Higher HOMO-LUMO gap 4.3 eV is found in arginine, and smaller 2.6 eV in a cluster, it becomes zero with -COOH site of arginine, and 0.8 eV at -CN site of aspartic acid during the formation of bio-hybrids, i.e. highly stable amino acids arg/asp-nano-cluster (ZnO)12 bio-hybrids are formed with small forbidden energy-gap. This study will support in the formation of drugs which will improve the response in wound healing, immune functioning in burn injuries, and in the treatment of bone dysfunction.HighlightsThe binding energy is higher in a bio-hybrid at -COOH site of Arg, and -CN site of Asp.HOMO-LUMO gap is higher in a pristine Arg (4.3 eV), smaller in a cluster (2.6 eV), zero gap in a bio-hybrid with -COOH site of Arg, smaller 0.8 eV at -CN site of Asp.Higher binding energy is found with the small forbidden energy-gap of bio-hybrid molecules.This study will support in the formation of drugs which will improve the response in wound healing, immune functioning in burn injuries, and in the treatment of bone dysfunction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Keshav Rao
- Department of Applied Physics, Shri Shankaracharya Technical Campus, Bhilai, Chhattisgarh, India
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3
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Chen Z, Zhu M, Cai M, Xu L, Weng Y. Palladium-Catalyzed C(sp 3)–H Arylation and Alkynylation of Peptides Directed by Aspartic Acid (Asp). ACS Catal 2021. [DOI: 10.1021/acscatal.1c01417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhuo Chen
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Meijie Zhu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Mengwei Cai
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Lulu Xu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
| | - Yiyi Weng
- College of Pharmaceutical Sciences, Zhejiang University of Technology, 310014 Hangzhou, P. R. China
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4
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Jones F, Rohl AL. Using Molecular Modelling to Understand and Predict the Impact of Organic Additives as Crystal Growth Modifiers. Aust J Chem 2020. [DOI: 10.1071/ch19388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Empirical molecular modelling was used to investigate the impact of organic additives on crystal morphology and inhibition. The replacement energy was found to correlate reasonably well with the degree of inhibition as determined from conductivity data. The replacement energy was also able to predict the barium sulfate face on which additive adsorption was most likely. While the ability of the organic functional groups to sit in the vacant sulfate lattice positions (the so-called ‘lattice matching’ criteria) appears intuitively sensible, it was found that this is not a sufficient criterion to predict real behaviour. A better criterion is the overall replacement energy as it takes into consideration the number of Ba–Oorganic interactions and whether the adsorption process overall is energetically favourable (by including the hydration energy of the ions). Thus, the replacement energy can successfully predict the effect of organic molecules on the crystal growth modification of barium sulfate.
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5
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Affiliation(s)
- Alexander G. Shtukenberg
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Michael D. Ward
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Bart Kahr
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
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6
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Xue Z, Shen Q, Liang L, Shen JW, Wang Q. Adsorption Behavior and Mechanism of SCA-1 on a Calcite Surface: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11321-11331. [PMID: 28666388 DOI: 10.1021/acs.langmuir.7b01217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The crystallization mechanism for natural mineral, especially the role of biological molecules in biomineralization, is still under debate. Protein adsorption on material surfaces plays a key role in biomineralization. In this article, molecular dynamics (MD) simulations were performed to systematically investigate the adsorption behavior of struthio camelus eggshell protein struthiocalcin-1 (SCA-1) on the calcite (104) surface with several different starting orientations in an explicit water environment. For each binding configuration, detailed adsorption behaviors and a mechanism were presented with the analysis of interaction energy, binding residues, hydrogen bonding, and structures (such as DSSP, dipole moment, and the electrostatic potential calculation). The results indicate that the positively charged and polar residues are the dominant residues for protein adsorption on the calcite (104) surface, and the strong electrostatic interaction drives the binding of model protein to the surface. The hydrogen bond bridge was found to play an important role in surface interactions as well. These results also demonstrate that SCA-1 is relatively rigid in spite of strong adsorption with few structural changes in α-helix and β-sheet contents. The results of the orientation calculation suggest that the dipole moment of the protein tends to remain parallel to calcite in most stable cases, which was confirmed by electrostatic potential isosurfaces analysis.
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Affiliation(s)
- Zhengyang Xue
- Department of Chemistry, Zhejiang University , Hangzhou 310027, People's Republic of China
| | - Qiying Shen
- School of Medicine, Hangzhou Normal University , Hangzhou 310016, People's Republic of China
| | - Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University , Hangzhou, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University , Hangzhou 310016, People's Republic of China
| | - Qi Wang
- Department of Chemistry, Zhejiang University , Hangzhou 310027, People's Republic of China
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7
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Nealon GL, Brown DH, Jones F, Parkinson G, Ogden MI. An azobenzene-based photoswitchable crystal growth modifier. CrystEngComm 2017. [DOI: 10.1039/c6ce02514e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An azobenzene derivative reversibly switches to a less effective crystal growth modifier of calcite when irradiated by UV light.
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Affiliation(s)
- Gareth L. Nealon
- Department of Chemistry and Nanochemistry Research Institute
- Curtin University
- Perth
- Australia
- Centre for Microscopy
| | - David H. Brown
- Department of Chemistry and Nanochemistry Research Institute
- Curtin University
- Perth
- Australia
| | - Franca Jones
- Department of Chemistry and Nanochemistry Research Institute
- Curtin University
- Perth
- Australia
| | - Gordon Parkinson
- Fuels and Energy Technology Institute
- Curtin University
- Perth
- Australia
| | - Mark I. Ogden
- Department of Chemistry and Nanochemistry Research Institute
- Curtin University
- Perth
- Australia
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8
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Wang L, Qin L, Putnis CV, Ruiz-Agudo E, King HE, Putnis A. Visualizing Organophosphate Precipitation at the Calcite-Water Interface by in Situ Atomic-Force Microscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:259-268. [PMID: 26636475 DOI: 10.1021/acs.est.5b05214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Esters of phosphoric acid constitute a large fraction of the total organic phosphorus (OP) in the soil environment and, thus, play an important role in the global phosphorus cycle. These esters, such as glucose-6-phosphate (G6P), exhibit unusual reactivity toward various mineral particles in soils, especially those containing calcite. Many important processes of OP transformation, including adsorption, hydrolysis, and precipitation, occur primarily at mineral-fluid interfaces, which ultimately governs the fate of organophosphates in the environment. However, little is known about the kinetics of specific mineral-surface-induced adsorption and precipitation of organophosphates. Here, by using in situ atomic-force microscopy (AFM) to visualize the dissolution of calcite (1014) faces, we show that the presence of G6P results in morphology changes of etch pits from the typical rhombohedral to a fan-shaped form. This can be explained by a site-selective mechanism of G6P-calcite surface interactions that stabilize the energetically unfavorable (0001) or (0112) faces through step-specific adsorption of G6P. Continuous dissolution at calcite (1014)-water interfaces caused a boundary layer at the calcite-water interface to become supersaturated with respect to a G6P-Ca phase that then drives the nucleation and growth of a G6P-Ca precipitate. Furthermore, after the introduction of the enzyme alkaline phosphatase (AP), the precipitates were observed to contain a mixture of components associated with G6P-Ca, amorphous calcium phosphate (ACP)-hydroxyapatite (HAP) and dicalcium phosphate dihydrate (DCPD). These direct dynamic observations of the transformation of adsorption- and complexation-surface precipitation and enzyme-mediated pathways may improve the mechanistic understanding of the mineral-interface-induced organophosphate sequestration in the soil environment.
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Affiliation(s)
- Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University , Wuhan 430070, China
| | - Lihong Qin
- College of Resources and Environment, Huazhong Agricultural University , Wuhan 430070, China
| | - Christine V Putnis
- Institut für Mineralogie, University of Münster , 48149 Münster, Germany
- Nanochemistry Research Institute, Department of Chemistry, Curtin University , Perth, Western Australia 6845, Australia
| | - Encarnación Ruiz-Agudo
- Department of Mineralogy and Petrology, University of Granada , Fuentenueva s/n, Granada 18071, Spain
| | - Helen E King
- Department of Earth Sciences, Utrecht University , 3584 CD Utrecht, The Netherlands
| | - Andrew Putnis
- Institut für Mineralogie, University of Münster , 48149 Münster, Germany
- The Institute for Geoscience Research (TIGeR), Curtin University , Perth, Western Australia 6102, Australia
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9
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Boon MP, Freeman S, Ogden MI, Oliveira A, Richmond WR, Skelton BW, Jones F. The many roles of mellitic acid during barium sulfate crystallization. Faraday Discuss 2015; 179:343-57. [PMID: 25877791 DOI: 10.1039/c4fd00211c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The various roles of mellitic acid during barium sulfate crystallization from nucleation to mesocrystal formation are explored and elucidated.
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Affiliation(s)
- Matthew P Boon
- Department of Chemistry, Curtin University, Bentley, WA 6102, Australia.
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10
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Wang L, Putnis CV, Ruiz-Agudo E, Hövelmann J, Putnis A. In situ imaging of interfacial precipitation of phosphate on Goethite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4184-4192. [PMID: 25763812 DOI: 10.1021/acs.est.5b00312] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Adsorption and subsequent immobilization of orthophosphate on iron oxides is of considerable importance in soil fertility and eutrophication studies. Here, in situ atomic force microscopy (AFM) has been used to probe the interaction of phosphate-bearing solutions with goethite, α-FeOOH, (010) cleavage surfaces. During the dissolution of goethite we observed simultaneous nucleation of nanoparticles (1.0-3.0 nm in height) of iron phosphate (Fe-P) phases at the earliest nucleation stages, subsequent aggregation to form secondary particles (about 6.0 nm in height) and layered precipitates under various pH values and ionic strengths relevant to acid soil solution conditions. The heterogeneous nucleation rates of Fe-P precipitates at phosphate concentrations ranging from 5.0 to 50.0 mM were quantitatively defined. Enhanced goethite dissolution in the presence of high concentration NaCl or AlCl3 leads to a rapid increase in Fe-P nucleation rates, whereas low concentration MgCl2 inhibits goethite dissolution, this in turn influences Fe-P nucleation. Moreover, kinetic data analyses show that low concentrations of citrate caused an increase in the nucleation rate of Fe-P phases. However, at higher concentrations of citrate, nucleation acceleration was reversed with much longer induction times to form Fe-P nuclei. These in situ observations may improve the mechanistic understanding of processes resulting in phosphate immobilization by goethite-rich acid soils in the presence of various inorganic and organic additive molecules.
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Affiliation(s)
- Lijun Wang
- †College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christine V Putnis
- ‡Institut für Mineralogie, University of Münster, 48149 Münster, Germany
- §Department of Chemistry, Curtin University, P.O. Box U1987, Perth, Washington 6845, Australia
| | | | - Jörn Hövelmann
- ‡Institut für Mineralogie, University of Münster, 48149 Münster, Germany
| | - Andrew Putnis
- ‡Institut für Mineralogie, University of Münster, 48149 Münster, Germany
- ⊥The Institute for Geoscience Research (TIGeR), Curtin University, Perth, Washington 6102, Australia
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11
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Bak JS. Lignocellulose depolymerization occurs via an environmentally adapted metabolic cascades in the wood-rotting basidiomycete Phanerochaete chrysosporium. Microbiologyopen 2014; 4:151-66. [PMID: 25470354 PMCID: PMC4335982 DOI: 10.1002/mbo3.228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 01/06/2023] Open
Abstract
Plant biomass can be utilized by a lignocellulose-degrading fungus, Phanerochaete chrysosporium, but the metabolic and regulatory mechanisms involved are not well understood. A polyomics-based analysis (metabolomics, proteomics, and transcriptomics) of P. chrysosporium has been carried out using statistically optimized conditions for lignocellulolytic reaction. Thirty-nine metabolites and 123 genes (14 encoded proteins) that consistently exhibited altered regulation patterns were identified. These factors were then integrated into a comprehensive map that fully depicts all signaling cascades involved in P. chrysosporium. Despite the diversity of these cascades, they showed complementary interconnection among themselves, ensuring the efficiency of passive biosystem and thereby yielding energy expenditure for the cells. Particularly, many factors related to intracellular regulatory networks showed compensating activity in homeostatic lignocellulolysis. In the main platform of proactive biosystem, although several deconstruction-related targets (e.g., glycoside hydrolase, ureidoglycolate hydrolase, transporters, and peroxidases) were systematically utilized, well-known supporters (e.g., cellobiose dehydrogenase and ferroxidase) were rarely generated.
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Affiliation(s)
- Jin Seop Bak
- Department of Chemical and Biomolecular Engineering, Advanced Biomass R&D Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Republic of Korea
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12
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Bak JS. Extracellular breakdown of lignocellulosic biomass by Dichomitus squalens: peroxidation-based platform and homeostatic regulation. Biotechnol Lett 2014; 37:349-58. [DOI: 10.1007/s10529-014-1676-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/09/2014] [Indexed: 11/24/2022]
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13
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Goh CY, Baldini L, Casnati A, Jones F, Mocerino M, Ogden MI, Sansone F, Ungaro R. Upper-rim acidic peptidocalixarenes as crystal growth modifiers. Supramol Chem 2014. [DOI: 10.1080/10610278.2014.891738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ching Yong Goh
- Department of Chemistry, Curtin University, GPO Box U 1987, Perth 6845, Australia
| | - Laura Baldini
- Dipartimento di Chimica, Università degli Studi di Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Alessandro Casnati
- Dipartimento di Chimica, Università degli Studi di Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Franca Jones
- Department of Chemistry, Curtin University, GPO Box U 1987, Perth 6845, Australia
| | - Mauro Mocerino
- Department of Chemistry, Curtin University, GPO Box U 1987, Perth 6845, Australia
| | - Mark I. Ogden
- Department of Chemistry, Curtin University, GPO Box U 1987, Perth 6845, Australia
| | - Francesco Sansone
- Dipartimento di Chimica, Università degli Studi di Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Rocco Ungaro
- Dipartimento di Chimica, Università degli Studi di Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
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14
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Qin L, Zhang W, Lu J, Stack AG, Wang L. Direct imaging of nanoscale dissolution of dicalcium phosphate dihydrate by an organic ligand: concentration matters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:13365-13374. [PMID: 24251349 DOI: 10.1021/es402748t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Unraveling the kinetics and mechanisms of sparingly soluble calcium orthophosphate (Ca-P) dissolution in the presence of organic acids at microscopic levels is important for an improved understanding in determining the effectiveness of organic acids present in most rhizosphere environments. Herein, we use in situ atomic force microscopy (AFM) coupled with a fluid reaction cell to image dissolution on the (010) face of brushite, CaHPO4 · 2H2O, in citrate-bearing solutions over a broad concentration range. We directly measure the dependence of molecular step retreat rate on citrate concentration at various pH values and ionic strengths, relevant to soil solution conditions. We find that low concentrations of citrate (10-100 μM) induced a reduction in step retreat rates along both the [100]Cc and [101]Cc directions. However, at higher concentrations (exceeding 0.1 mM), this inhibitory effect was reversed with step retreat speeds increasing rapidly. These results demonstrate that the concentration-dependent modulation of nanoscale Ca-P phase dissolution by citrate may be applied to analyze the controversial role of organic acids in enhancing Ca-P mineral dissolution in a more complex rhizosphere environment. These in situ observations may contribute to resolving the previously unrecognized interactions of root exudates (low molecular weight organic acids) and sparingly soluble Ca-P minerals.
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Affiliation(s)
- Lihong Qin
- College of Resources and Environment, Huazhong Agricultural University , Wuhan 430070, China
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15
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Xu Z, Yang Y, Wang Z, Mkhonto D, Shang C, Liu ZP, Cui Q, Sahai N. Small molecule-mediated control of hydroxyapatite growth: Free energy calculations benchmarked to density functional theory. J Comput Chem 2013; 35:70-81. [DOI: 10.1002/jcc.23474] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/01/2013] [Accepted: 10/06/2013] [Indexed: 02/04/2023]
Affiliation(s)
- Zhijun Xu
- Department of Polymer Science; 170 University Avenue; University of Akron; Akron Ohio 44325-3909
| | - Yang Yang
- Department of Chemistry and Biochemistry; 201 Mullica Hill Road; Rowan University; Glassboro New Jersey 08028
| | - Ziqiu Wang
- Department of Polymer Science; 170 University Avenue; University of Akron; Akron Ohio 44325-3909
| | - Donald Mkhonto
- Council for Scientific and Industrial Research; Meiring Naude Road Brumeria 0184 South Africa
| | - Cheng Shang
- Department of Chemistry; Key Laboratory of Computational Physical Science (Ministry of Education); Fudan University; Shanghai 200433 People's Republic China
| | - Zhi-Pan Liu
- Department of Chemistry; Key Laboratory of Computational Physical Science (Ministry of Education); Fudan University; Shanghai 200433 People's Republic China
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute; 1101 University Avenue; University of Wisconsin; Madison Wisconsin 53706
| | - Nita Sahai
- Department of Polymer Science; 170 University Avenue; University of Akron; Akron Ohio 44325-3909
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16
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Han G, Thirunahari S, Shan Chow P, Tan RBH. Resolving the longstanding riddle of pH-dependent outcome of glycine polymorphic nucleation. CrystEngComm 2013. [DOI: 10.1039/c2ce26594j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Jones F, Ogden MI. Crystal Growth and Molecular Crystal Growth Modification. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Wang L, Ruiz-Agudo E, Putnis CV, Menneken M, Putnis A. Kinetics of calcium phosphate nucleation and growth on calcite: implications for predicting the fate of dissolved phosphate species in alkaline soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:834-42. [PMID: 22136106 DOI: 10.1021/es202924f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Unraveling the kinetics of calcium orthophosphate (Ca-P) precipitation and dissolution is important for our understanding of the transformation and mobility of dissolved phosphate species in soils. Here we use an in situ atomic force microscopy (AFM) coupled with a fluid reaction cell to study the interaction of phosphate-bearing solutions with calcite surfaces. We observe that the mineral surface-induced formation of Ca-P phases is initiated with the aggregation of clusters leading to the nucleation and subsequent growth of Ca-P phases on calcite, at various pH values and ionic strengths relevant to soil solution conditions. A significant decrease in the dissolved phosphate concentration occurs due to the promoted nucleation of Ca-P phases on calcite surfaces at elevated phosphate concentrations and more significantly at high salt concentrations. Also, kinetic data analyses show that low concentrations of citrate caused an increase in the nucleation rate of Ca-P phases. However, at higher concentrations of citrate, nucleation acceleration was reversed with much longer induction times to form Ca-P nuclei. These results demonstrate that the nucleation-modifying properties of small organic molecules may be scaled up to analyze Ca-P dissolution-precipitation processes that are mediated by a more complex soil environment. This in situ observation, albeit preliminary, may contribute to an improved understanding of the fate of dissolved phosphate species in diverse soil systems.
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Affiliation(s)
- Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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19
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Jones F. Infrared investigation of barite and gypsum crystallization: Evidence for an amorphous to crystalline transition. CrystEngComm 2012. [DOI: 10.1039/c2ce25918d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Baynton A, Ogden MI, Raston CL, Jones F. Barium sulfate crystallization dependence on upper rim calix[4]arene functional groups. CrystEngComm 2012. [DOI: 10.1039/c1ce06083j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Chen CL, Qi J, Zuckermann RN, DeYoreo JJ. Engineered biomimetic polymers as tunable agents for controlling CaCO3 mineralization. J Am Chem Soc 2011; 133:5214-7. [PMID: 21417474 DOI: 10.1021/ja200595f] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In nature, living organisms use peptides and proteins to precisely control the nucleation and growth of inorganic minerals and sequester CO(2)via mineralization of CaCO(3). Here we report the exploitation of a novel class of sequence-specific non-natural polymers called peptoids as tunable agents that dramatically control CaCO(3) mineralization. We show that amphiphilic peptoids composed of hydrophobic and anionic monomers exhibit both a high degree of control over calcite growth morphology and an unprecedented 23-fold acceleration of growth at a peptoid concentration of only 50 nM, while acidic peptides of similar molecular weight exhibited enhancement factors of only ∼2 or less. We further show that both the morphology and rate controls depend on peptoid sequence, side-chain chemistry, chain length, and concentration. These findings provide guidelines for developing sequence-specific non-natural polymers that mimic the functions of natural peptides or proteins in their ability to direct mineralization of CaCO(3), with an eye toward their application to sequestration of CO(2) through mineral trapping.
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Affiliation(s)
- Chun-Long Chen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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Baynton A, Chandler BD, Jones F, Nealon G, Ogden MI, Radomirovic T, Shimizu GKH, Taylor JM. Phosphonate additives do not always inhibit crystallization. CrystEngComm 2011. [DOI: 10.1039/c0ce00338g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Yang X, Xie B, Wang L, Qin Y, Henneman ZJ, Nancollas GH. Influence of magnesium ions and amino acids on the nucleation and growth of hydroxyapatite. CrystEngComm 2011. [DOI: 10.1039/c0ce00470g] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Raiteri P, Gale JD. Water Is the Key to Nonclassical Nucleation of Amorphous Calcium Carbonate. J Am Chem Soc 2010; 132:17623-34. [DOI: 10.1021/ja108508k] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Paolo Raiteri
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Julian D. Gale
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
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Hamm LM, Wallace AF, Dove PM. Molecular Dynamics of Ion Hydration in the Presence of Small Carboxylated Molecules and Implications for Calcification. J Phys Chem B 2010; 114:10488-95. [DOI: 10.1021/jp9108893] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laura M. Hamm
- Department of Geosciences, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061
| | - Adam F. Wallace
- Department of Geosciences, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061
| | - Patricia M. Dove
- Department of Geosciences, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061
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Dowling R, Davey RJ, Curtis RA, Han G, Poornachary SK, Chow PS, Tan RBH. Acceleration of crystal growth rates: an unexpected effect of tailor-made additives. Chem Commun (Camb) 2010; 46:5924-6. [DOI: 10.1039/c0cc00336k] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Subnanometer atomic force microscopy of peptide-mineral interactions links clustering and competition to acceleration and catastrophe. Proc Natl Acad Sci U S A 2009; 107:11-5. [PMID: 20018743 DOI: 10.1073/pnas.0908205107] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vitro observations have revealed major effects on the structure, growth, and composition of biomineral phases, including stabilization of amorphous precursors, acceleration and inhibition of kinetics, and alteration of impurity signatures. However, deciphering the mechanistic sources of these effects has been problematic due to a lack of tools to resolve molecular structures on mineral surfaces during growth. Here we report atomic force microscopy investigations using a system designed to maximize resolution while minimizing contact force. By imaging the growth of calcium-oxalate monohydrate under the influence of aspartic-rich peptides at single-molecule resolution, we reveal how the unique interactions of polypeptides with mineral surfaces lead to acceleration, inhibition, and switching of growth between two distinct states. Interaction with the positively charged face of calcium-oxalate monohydrate leads to formation of a peptide film, but the slow adsorption kinetics and gradual relaxation to a well-bound state result in time-dependent effects. These include a positive feedback between peptide adsorption and step inhibition described by a mathematical catastrophe that results in growth hysteresis, characterized by rapid switching from fast to near-zero growth rates for very small reductions in supersaturation. Interactions with the negatively charged face result in formation of peptide clusters that impede step advancement. The result is a competition between accelerated solute attachment and inhibition due to blocking of the steps by the clusters. The findings have implications for control of pathological mineralization and suggest artificial strategies for directing crystallization.
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Carboxylated molecules regulate magnesium content of amorphous calcium carbonates during calcification. Proc Natl Acad Sci U S A 2009; 106:21511-6. [PMID: 19955417 DOI: 10.1073/pnas.0906741106] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With the realization that many calcified skeletons form by processes involving a precursor phase of amorphous calcium carbonate (ACC), a new paradigm for mineralization is emerging. There is evidence the Mg content in biogenic ACC is regulated by carboxylated (acidic) proteins and other macromolecules, but the physical basis for such a process is unknown. We test the hypothesis that ACC compositions express a systematic relationship to the chemistry of carboxyl-rich biomolecules. A series of inorganic control experiments were conducted to establish the dependence of Mg/Ca ratios in ACC on solution composition. We then determined the influence of a suite of simple carboxylated organic acids on Mg content. Molecules with a strong affinity for binding Ca compared with Mg promote the formation of Mg-enriched ACC that is compositionally equivalent to high-magnesium calcites and dolomite. Measurements show Mg/Ca ratios are controlled by a predictable dependence upon the binding properties of the organic molecules. The trend appears rooted in the conformation and electrostatic potential topology of each molecule, but dynamic factors also may be involved. The dependence suggests a physical basis for reports that specific sequences of calcifying proteins are critical to modulating mineralization. Insights from this study may provide a plausible explanation for why some biogenic carbonates and carbonaceous cements often contain higher Mg signatures than those that are possible by classical crystal growth processes. The findings reiterate the controls of microenvironment on mineralization and suggest an origin of compositional offsets, or vital effects, long recognized by the paleoclimate community.
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Weaver ML, Qiu SR, Hoyer JR, Casey WH, Nancollas GH, De Yoreo JJ. Surface aggregation of urinary proteins and aspartic Acid-rich peptides on the faces of calcium oxalate monohydrate investigated by in situ force microscopy. Calcif Tissue Int 2009; 84:462-73. [PMID: 19294448 PMCID: PMC2688023 DOI: 10.1007/s00223-009-9223-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Accepted: 01/11/2009] [Indexed: 12/02/2022]
Abstract
The growth of calcium oxalate monohydrate in the presence of Tamm-Horsfall protein (THP), osteopontin, and the 27-residue synthetic peptides (DDDS)(6)DDD and (DDDG)(6)DDD (D = aspartic acid, S = serine, and G = glycine) was investigated via in situ atomic force microscopy. The results show that these four growth modulators create extensive deposits on the crystal faces. Depending on the modulator and crystal face, these deposits can occur as discrete aggregates, filamentary structures, or uniform coatings. These proteinaceous films can lead to either the inhibition of or an increase in the step speeds (with respect to the impurity-free system), depending on a range of factors that include peptide or protein concentration, supersaturation, and ionic strength. While THP and the linear peptides act, respectively, to exclusively increase and inhibit growth on the (101) face, both exhibit dual functionality on the (010) face, inhibiting growth at low supersaturation or high modulator concentration and accelerating growth at high supersaturation or low modulator concentration. Based on analyses of growth morphologies and dependencies of step speeds on supersaturation and protein or peptide concentration, we propose a picture of growth modulation that accounts for the observations in terms of the strength of binding to the surfaces and steps and the interplay of electrostatic and solvent-induced forces at the crystal surface.
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Affiliation(s)
- Matthew L. Weaver
- Department of Chemistry, University of California, Davis, CA 95616 USA
- Department of Geology, University of California, Davis, CA 95616 USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - S. Roger Qiu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - John R. Hoyer
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - William H. Casey
- Department of Chemistry, University of California, Davis, CA 95616 USA
- Department of Geology, University of California, Davis, CA 95616 USA
| | - George H. Nancollas
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260 USA
| | - James J. De Yoreo
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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Harding JH, Duffy DM, Sushko ML, Rodger PM, Quigley D, Elliott JA. Computational Techniques at the Organic−Inorganic Interface in Biomineralization. Chem Rev 2008; 108:4823-54. [DOI: 10.1021/cr078278y] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- John H. Harding
- Department of Engineering Materials, University of Sheffield, Sheffield, U.K
| | | | | | | | | | - James A. Elliott
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, U.K
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De Yoreo JJ, Wierzbicki A, Dove PM. New insights into mechanisms of biomolecular control on growth of inorganic crystals. CrystEngComm 2007. [DOI: 10.1039/b713006f] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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