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Ilgen AG, Borguet E, Geiger FM, Gibbs JM, Grassian VH, Jun YS, Kabengi N, Kubicki JD. Bridging molecular-scale interfacial science with continuum-scale models. Nat Commun 2024; 15:5326. [PMID: 38909017 PMCID: PMC11193788 DOI: 10.1038/s41467-024-49598-y] [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: 12/27/2023] [Accepted: 06/07/2024] [Indexed: 06/24/2024] Open
Abstract
Solid-water interfaces are crucial for clean water, conventional and renewable energy, and effective nuclear waste management. However, reflecting the complexity of reactive interfaces in continuum-scale models is a challenge, leading to oversimplified representations that often fail to predict real-world behavior. This is because these models use fixed parameters derived by averaging across a wide physicochemical range observed at the molecular scale. Recent studies have revealed the stochastic nature of molecular-level surface sites that define a variety of reaction mechanisms, rates, and products even across a single surface. To bridge the molecular knowledge and predictive continuum-scale models, we propose to represent surface properties with probability distributions rather than with discrete constant values derived by averaging across a heterogeneous surface. This conceptual shift in continuum-scale modeling requires exponentially rising computational power. By incorporating our molecular-scale understanding of solid-water interfaces into continuum-scale models we can pave the way for next generation critical technologies and novel environmental solutions.
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Affiliation(s)
- Anastasia G Ilgen
- Geochemistry Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA.
| | - Eric Borguet
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Franz M Geiger
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California, La Jolla, CA, 92093, USA
| | - Young-Shin Jun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Nadine Kabengi
- Department of Geosciences, Georgia State University, Atlanta, GA, 30302, USA
| | - James D Kubicki
- Department of Earth, Environmental and Resource Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
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Park Y, Noda I, Jung YM. Novel Developments and Progress in Two-Dimensional Correlation Spectroscopy (2D-COS). APPLIED SPECTROSCOPY 2024:37028241255393. [PMID: 38872353 DOI: 10.1177/00037028241255393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
This first of the two-part series of the comprehensive survey review on the progress of the two-dimensional correlation spectroscopy (2D-COS) field during the period 2021-2022, covers books, reviews, tutorials, novel concepts and theories, and patent applications that appeared in the last two years, as well as some inappropriate use or citations of 2D-COS. The overall trend clearly shows that 2D-COS is continually growing and evolving with notable new developments. The technique is well recognized as a powerful analytical tool that provides deep insights into systems in many science fields.
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Affiliation(s)
- Yeonju Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, and Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon, Korea
| | - Isao Noda
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, USA
| | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, and Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon, Korea
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Park Y, Noda I, Jung YM. Diverse Applications of Two-Dimensional Correlation Spectroscopy (2D-COS). APPLIED SPECTROSCOPY 2024:37028241256397. [PMID: 38835153 DOI: 10.1177/00037028241256397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
This second of the two-part series of a comprehensive survey review provides the diverse applications of two-dimensional correlation spectroscopy (2D-COS) covering different probes, perturbations, and systems in the last two years. Infrared spectroscopy has maintained its top popularity in 2D-COS over the past two years. Fluorescence spectroscopy is the second most frequently used analytical method, which has been heavily applied to the analysis of heavy metal binding, environmental, and solution systems. Various other analytical methods including laser-induced breakdown spectroscopy, dynamic mechanical analysis, differential scanning calorimetry, capillary electrophoresis, seismologic, and so on, have also been reported. In the last two years, concentration, composition, and pH are the main effects of perturbation used in the 2D-COS fields, as well as temperature. Environmental science is especially heavily studied using 2D-COS. This comprehensive survey review shows that 2D-COS undergoes continuous evolution and growth, marked by novel developments and successful applications across diverse scientific fields.
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Affiliation(s)
- Yeonju Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, and Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon, Korea
| | - Isao Noda
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, USA
| | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, and Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon, Korea
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Kim D, Townsley S, Grassian VH. Vibrational spectroscopy as a probe of heterogeneities within geochemical thin films on macro, micro, and nanoscales. RSC Adv 2023; 13:28873-28884. [PMID: 37790106 PMCID: PMC10543985 DOI: 10.1039/d3ra05179j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023] Open
Abstract
Minerals play a critical role in the chemistry occurring along the interface of different environmental systems, including the atmosphere/geosphere and hydrosphere/geosphere. In the past few decades, vibrational spectroscopy has been used as a probe for studying interfacial geochemistry. Here, we compare four different vibrational methods for probing physical and chemical features across different mineral samples and length scales, from the macroscale to nanoscale. These methods include Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR), Optical Photothermal Infrared (O-PTIR), Atomic Force Microscopy-Infrared (AFM-IR) and micro-Raman spectroscopy. The emergence of these micro-spectroscopic probes has offered new insights into heterogeneities within geochemical thin films and particles. These developments represent an important step forward for analyzing environmental interfaces and thin films as often these are assumed to be physically and chemically homogeneous. By comparing and integrating data across these measurement techniques, new insights into sample differences and heterogeneities can be gained. For example, interrogation of the various mineral samples at smaller length scales is shown to be particularly informative in highlighting unique chemical environments, including for chemically complex, multicomponent samples such as Arizona Test Dust (AZTD), as well as differences due to crystal orientation.
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Affiliation(s)
- Deborah Kim
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Samantha Townsley
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
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Sit I, Fashina BT, Baldo AP, Leung K, Grassian VH, Ilgen AG. Formic and acetic acid p Ka values increase under nanoconfinement. RSC Adv 2023; 13:23147-23157. [PMID: 37533784 PMCID: PMC10390803 DOI: 10.1039/d2ra07944e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/22/2023] [Indexed: 08/04/2023] Open
Abstract
Organic acids are prevalent in the environment and their acidity and the corresponding dissociation constants can change under varying environmental conditions. The impact of nanoconfinement (when acids are confined within nanometer-scale domains) on physicochemical properties of chemical species is poorly understood and is an emerging field of study. By combining infrared and Raman spectroscopies with molecular dynamics (MD) simulations, we quantified the effect of nanoconfinement in silica nanopores on one of the fundamental chemical reactions-the dissociation of organic acids. The pKa of formic and acetic acids confined within cylindrical silica nanopores with 4 nm diameters were measured. MD models were constructed to calculate the shifts in the pKa values of acetic acid nanoconfined within 1, 2, 3, and 4 nm silica slit pores. Both experiments and MD models indicate a decrease in the apparent acid dissociation constants (i.e., increase in the pKa values) when organic acids are nanoconfined. Therefore, nanoconfinement stabilizes the protonated species. We attribute this observation to (1) a decrease in the average dielectric response of nanoconfined aqueous solutions where charge screening may be decreased; or (2) an increase in proton concentration inside nanopores, which would shift the equilibrium towards the protonated form. Overall, the results of this study provide the first quantification of the pKa values for nanoconfined formic and acetic acids and pave the way for a unifying theory predicting the impact of nanoconfinement on acid-base chemistry.
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Affiliation(s)
- Izaac Sit
- Department of Nanoengineering, University of California San Diego La Jolla CA 92093 USA
| | - Bidemi T Fashina
- Geochemistry Department, Sandia National Laboratories Albuquerque NM 87123 USA
| | - Anthony P Baldo
- Geochemistry Department, Sandia National Laboratories Albuquerque NM 87123 USA
| | - Kevin Leung
- Geochemistry Department, Sandia National Laboratories Albuquerque NM 87123 USA
| | - Vicki H Grassian
- Department of Chemistry & Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Anastasia G Ilgen
- Geochemistry Department, Sandia National Laboratories Albuquerque NM 87123 USA
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Sit I, Young MA, Kubicki JD, Grassian VH. Distinguishing different surface interactions for nucleotides adsorbed onto hematite and goethite particle surfaces through ATR-FTIR spectroscopy and DFT calculations. Phys Chem Chem Phys 2023. [PMID: 37470700 PMCID: PMC10395000 DOI: 10.1039/d3cp01200j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Geochemical interfaces can impact the fate and transport of aqueous species in the environment including biomolecules. In this study, we investigate the surface chemistry of adsorbed nucleotides on two different minerals, hematite and goethite, using infrared spectroscopy and density functional theory (DFT) calculations. Attenuated total reflectance-Fourier transform infrared spectroscopy is used to probe the adsorption of deoxyadenosine monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxycytidine monophosphate (dCMP), and deoxythymidine monophosphate (dTMP) onto either hematite or goethite particle surfaces. The results show preferential adsorption of the phosphate group to either surface. Remarkably, surface adsorption of the four nucleotides onto either hematite or goethite have nearly identical experimental spectra in the phosphate region (900 to 1200 cm-1) for each mineral surface yet are distinctly different between the two minerals, suggesting differences in binding of these nucleotides to the two mineral surfaces. The experimental absorption frequencies in the phosphate region were compared to DFT calculations for nucleotides adsorbed through the phosphate group to binuclear clusters in either a monodentate or bidentate bridging coordination. Although the quality of the fits suggests that both binding modes may be present, the relative amounts differ on the two surfaces with preferential bonding suggested to be monodentate coordination on hematite and bidentate bridging on goethite. Possible reasons for these differences are discussed.
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Affiliation(s)
- Izaac Sit
- Department of Nanoengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark A Young
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - James D Kubicki
- Department of Earth, Environmental & Resource Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA.
| | - Vicki H Grassian
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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Kim D, Grassian VH. Analysis of micro- and nanoscale heterogeneities within environmentally relevant thin films containing biological components, oxyanions and minerals using AFM-PTIR spectroscopy. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:484-495. [PMID: 36789672 DOI: 10.1039/d3em00005b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Minerals in groundwater interact with various chemical and biological species including organic matter, proteins, and prevalent oxyanions, resulting in surface coatings and thin films of these different components. Surface interactions and the surface adsorption of these components on both oxide and oxyhydroxide iron surfaces have been widely investigated using a variety of spectroscopic methods. Despite these numerous studies, there still remains uncertainty with respect to interactions between these individual components, as well as heterogeneities and phase segregations within these thin films. In this study, we investigate mixtures containing Fe-containing minerals, proteins, and oxyanions to better understand surface interactions and phase segregation using Atomic Force Microscopy PhotoThermal Infrared (AFM-PTIR) spectroscopy. The results of this study show that AFM-PTIR spectroscopy can identify both nano- and microscale heterogeneities present within these thin films that are difficult to discern with other more conventional techniques such as ATR-FTIR spectroscopy due to phase segregation and mineral surface interactions. Overall, AFM-PTIR spectroscopy provides insights into multi-component environmental films that are difficult to uncover using other methodologies. This method has the potential to differentiate between bound and unbound toxic species as well as biological components, including environmental DNA, which can be used to assess the fate and transport of these species in the environment.
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Affiliation(s)
- Deborah Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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Sit I, Quirk E, Hettiarachchi E, Grassian VH. Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15038-15049. [PMID: 36445255 PMCID: PMC9753757 DOI: 10.1021/acs.langmuir.2c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The fate of biomolecules in the environment depends in part on understanding the surface chemistry occurring at the biological-geochemical (bio-geo) interface. Little is known about how environmental DNA (eDNA) or smaller components, like nucleotides and oligonucleotides, persist in aquatic environments and the role of surface interactions. This study aims to probe surface interactions and adsorption behavior of nucleotides on oxide surfaces. We have investigated the interactions of individual nucleotides (dGMP, dCMP, dAMP, and dTMP) on TiO2 particle surfaces as a function of pH and in the presence of complementary and noncomplementary base pairs. Using attenuated total reflectance-Fourier transform infrared spectroscopy, there is an increased number of adsorbed nucleotides at lower pH with a preferential interaction of the phosphate group with the oxide surface. Additionally, differential adsorption behavior is seen where purine nucleotides are preferentially adsorbed, with higher surface saturation coverage, over their pyrimidine derivatives. These differences may be a result of intermolecular interactions between coadsorbed nucleotides. When the TiO2 surface was exposed to two-component solutions of nucleotides, there was preferential adsorption of dGMP compared to dCMP and dTMP, and dAMP compared to dTMP and dCMP. Complementary nucleotide base pairs showed hydrogen-bond interactions between a strongly adsorbed purine nucleotide layer and a weaker interacting hydrogen-bonded pyrimidine second layer. Noncomplementary base pairs did not form a second layer. These results highlight several important findings: (i) there is differential adsorption of nucleotides; (ii) complementary coadsorbed nucleotides show base pairing with a second layer, and the stability depends on the strength of the hydrogen bonding interactions and; (iii) the first layer coverage strongly depends on pH. Overall, the importance of surface interactions in the adsorption of nucleotides and the templating of specific interactions between nucleotides are discussed.
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Affiliation(s)
- Izaac Sit
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eleanor Quirk
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eshani Hettiarachchi
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Vicki H. Grassian
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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Mantri Y, Sit I, Zhou J, Grassian VH, Jokerst JV. Photoacoustic Enhancement of Ferricyanide-Treated Silver Chalcogenide-Coated Gold Nanorods. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:7605-7614. [PMID: 36249163 PMCID: PMC9563653 DOI: 10.1021/acs.jpcc.2c01727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plasmonic gold nanorods (AuNRs) are often employed as photoacoustic (PA) contrast agents due to their ease of synthesis, functionalization, and biocompatibility. These materials can produce activatable signals in response to a change in optical absorbance intensity or absorbance wavelength. Here, we report a surprising finding: Ag2S/Se-coated AuNRs have a ~40-fold PA enhancement upon addition of an oxidant but with no change in absorption spectra. We then study the mechanism underlying this enhancement. Electron micrographs and absorption spectra show good colloidal stability and retention of the core-shell structure after potassium hexacyanoferrate(III) (HCF) addition, ruling out aggregation and morphology-induced PA enhancement. X-ray diffraction data showed no changes, ruling out crystallographic phase changes upon HCF addition, thus leading to induced PA enhancement. Attenuated total reflectance-Fourier transform infrared spectroscopy and zeta potential analysis suggest that PA enhancement is driven by the irreversible displacement of hexadecyltrimethylammonium bromide with HCF. This is further confirmed using elemental mapping with energy-dispersive X-ray analysis. PA characterization after HCF addition showed a four-fold increase in the Grüneisen parameter (Γ), thus resulting in PA enhancement. The PA enhancement is not seen in uncoated AuNRs or spherical particles. Two possible mechanisms for PA enhancement are proposed: first, the photo-induced redox heating at the Ag2S/Se shell-HCF interface, resulting in an increase in temperature-dependent Γ, and second, an enhanced electrostriction response due to HCF adsorption on a layered plasmonic nanoparticle surface, resulting in a high thermal expansion coefficient (β) that is directly proportional to Γ.
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Affiliation(s)
- Yash Mantri
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Izaac Sit
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Jiajing Zhou
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jesse V Jokerst
- Department of Nanoengineering, Materials Science Program, and Department of Radiology, University of California San Diego, La Jolla, California 92093, United States
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