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Trevitt CR, Yashwanth Kumar DR, Fowler NJ, Williamson MP. Interactions between the protein barnase and co-solutes studied by NMR. Commun Chem 2024; 7:44. [PMID: 38418894 PMCID: PMC10902301 DOI: 10.1038/s42004-024-01127-0] [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: 11/05/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.
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Affiliation(s)
- Clare R Trevitt
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
- Certara UK Ltd, Level 2-Acero, 1 Concourse Way, Sheffield, S1 3BJ, UK
| | | | - Nicholas J Fowler
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
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2
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Bredt AJ, Kim Y, Mendes de Oliveira D, Urbina AS, Slipchenko LV, Ben-Amotz D. Expulsion of Hydroxide Ions from Methyl Hydration Shells. J Phys Chem B 2022; 126:869-877. [PMID: 35077175 DOI: 10.1021/acs.jpcb.1c08420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The affinity of hydroxide ions for methyl hydration shells is assessed using a combined experimental and theoretical analysis of tert-butyl alcohol (TBA) dissolved in pure water and aqueous NaOH and NaI. The experimental results are obtained using Raman multivariate curve resolution (Raman-MCR) and a new three-component total least squares (Raman-TLS) spectral decomposition strategy used to highlight vibrational perturbations resulting from interactions between TBA and aqueous ions. The experiments are interpreted and extended with the aid of effective fragment potential molecular dynamics (EFP-MD) simulations, as well as Kirkwood-Buff calculations and octanol/water partition measurements, to relate TBA-ion distribution functions to TBA solubility changes. The combined experimental and simulation results reveal that methyl group hydration shells more strongly expel hydroxide than iodide anions, whose populations near the methyl groups of TBA are predicted to be correlated with sodium counterion localization near the TBA hydroxyl group.
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Affiliation(s)
- Aria J Bredt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yongbin Kim
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Andres S Urbina
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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3
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Rogers BA, Okur HI, Yan C, Yang T, Heyda J, Cremer PS. Weakly hydrated anions bind to polymers but not monomers in aqueous solutions. Nat Chem 2022; 14:40-45. [PMID: 34725491 DOI: 10.1038/s41557-021-00805-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023]
Abstract
Weakly hydrated anions help to solubilize hydrophobic macromolecules in aqueous solutions, but small molecules comprising the same chemical constituents precipitate out when exposed to these ions. Here, this apparent contradiction is resolved by systematically investigating the interactions of NaSCN with polyethylene oxide oligomers and polymers of varying molecular weight. A combination of spectroscopic and computational results reveals that SCN- accumulates near the surface of polymers, but is excluded from monomers. This occurs because SCN- preferentially binds to the centre of macromolecular chains, where the local water hydrogen-bonding network is disrupted. These findings suggest a link between ion-specific effects and theories addressing how hydrophobic hydration is modulated by the size and shape of a hydrophobic entity.
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Affiliation(s)
- Bradley A Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Halil I Okur
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey
| | - Chuanyu Yan
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Tinglu Yang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Dejvice, Czech Republic
| | - Paul S Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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4
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5
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Roy S, Patra A, Palit DK, Mondal JA. Interaction of Zwitterionic Osmolyte Trimethylamine N-oxide (TMAO) with Molecular Hydrophobes: An Interplay of Hydrophobic and Electrostatic Interactions. J Phys Chem B 2021; 125:10939-10946. [PMID: 34570979 DOI: 10.1021/acs.jpcb.1c05694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interaction of trimethylamine N-oxide (TMAO) with charged/uncharged moieties of proteins and lipids is an important elementary step toward the multifaceted biofunctions of TMAO. Using minimum area Raman difference spectroscopy (MA-RDS) of aqueous TMAO (1.0 M) in the presence of deuterated molecular hydrophobes (e.g., deuterated tetramethylammonium cation (d-TMA+) and tert-butylalcohol (d-TBA)), we show that TMAO exhibits two distinct motifs of interaction with the cationic (d-TMA+) and uncharged (d-TBA) hydrophobes. Specifically, the trimethylammonium moiety of TMAO undergoes van der Waals attraction with the tert-butyl group of d-TBA, which is governed by their mutual hydrophobic interaction with water. This makes their methyl groups less exposed to water. In contrast, for the cationic hydrophobe (d-TMA+), TMAO interacts electrostatically via its negatively charged-oxygen, which in turn orients the TMAO-methyls away from the hydrophobe (d-TMA+), keeping them exposed to water.
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Affiliation(s)
- Subhadip Roy
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Trombay, Mumbai 400085, India
| | - Animesh Patra
- School of Chemistry, Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz (E), Mumbai 400098, India
| | - Dipak K Palit
- School of Chemistry, Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz (E), Mumbai 400098, India
| | - Jahur Alam Mondal
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Trombay, Mumbai 400085, India
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6
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Drexler CI, Cracchiolo OM, Myers RL, Okur HI, Serrano AL, Corcelli SA, Cremer PS. Local Electric Fields in Aqueous Electrolytes. J Phys Chem B 2021; 125:8484-8493. [PMID: 34313130 DOI: 10.1021/acs.jpcb.1c03257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vibrational Stark shifts were explored in aqueous solutions of organic molecules with carbonyl- and nitrile-containing constituents. In many cases, the vibrational resonances from these moieties shifted toward lower frequency as salt was introduced into solution. This is in contrast to the blue-shift that would be expected based upon Onsager's reaction field theory. Salts containing well-hydrated cations like Mg2+ or Li+ led to the most pronounced Stark shift for the carbonyl group, while poorly hydrated cations like Cs+ had the greatest impact on nitriles. Moreover, salts containing I- gave rise to larger Stark shifts than those containing Cl-. Molecular dynamics simulations indicated that cations and anions both accumulate around the probe in an ion- and probe-dependent manner. An electric field was generated by the ion pair, which pointed from the cation to the anion through the vibrational chromophore. This resulted from solvent-shared binding of the ions to the probes, consistent with their positions in the Hofmeister series. The "anti-Onsager" Stark shifts occur in both vibrational spectroscopy and fluorescence measurements.
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Affiliation(s)
| | - Olivia M Cracchiolo
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | | | - Halil I Okur
- Department of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
| | - Arnaldo L Serrano
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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7
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Xu X, Xia Y, Qian J, Yu H, Zhong Y, Wang F, Zhou C, Ni H. Roles of Proton in the Formation of Particles: Soap‐free Emulsion Polymerization of Styrene using AIBN and Potassium Persulfate as Initiators. ChemistrySelect 2021. [DOI: 10.1002/slct.202004321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiuhang Xu
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
| | - Yunfei Xia
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
| | - Jiajia Qian
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
| | - Haihua Yu
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
| | - Yangyang Zhong
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
| | - Chuan Zhou
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
| | - Henmei Ni
- School of Chemistry and Chemical Engineering Southeast University Southeast University Road 2 Jiangning, Nanjing 211189 China
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8
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Interfacial ion specificity modulates hydrophobic interaction. J Colloid Interface Sci 2020; 578:135-145. [PMID: 32521353 DOI: 10.1016/j.jcis.2020.05.091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 11/21/2022]
Abstract
HYPOTHESIS Ion specificity is crucial in assembly and aggregation of polymers in water driven by hydrophobic interaction. An increasing number of studies have suggested that specific ion adsorption and consequent impact on interfacial water molecules should play an important role in modulating hydrophobic interaction. EXPERIMENTS Here, bubble probe atomic force microscopy (AFM) combined with theoretical modeling analysis was applied to quantify hydrophobic interactions involving three model polymers in solutions containing different ions. FINDINGS For polystyrene, the hydrophobic interaction's decay length D0 was reduced from 0.75 nm to 0.60 nm by introducing weakly hydrated cations (e.g., K+ and NH4+), while varying anion type had little effect. For poly(methyl methacrylate) and polydimethylsiloxane, anion specificity was demonstrated more evident in shortening the hydrophobic interaction range, with D0 decreasing from 0.63 nm to 0.50 nm and from 0.72 nm to 0.58 nm respectively when strongly hydrated F- or Cl- was replaced by weakly hydrated I-. Such results could arise from specific ion adsorption at water/polymer interface which disrupts the water structuring effect. From the nanomechanical perspective, this work has revealed the importance of interfacial ion specificity in modulating hydrophobic interaction, which offers novel implications for tuning assembly behavior of macromolecules in relevant engineering applications such as micelle formation and foam stabilization.
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9
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Francisco OA, Glor HM, Khajehpour M. Salt Effects on Hydrophobic Solvation: Is the Observed Salt Specificity the Result of Excluded Volume Effects or Water Mediated Ion-Hydrophobe Association? Chemphyschem 2020; 21:484-493. [PMID: 31944529 DOI: 10.1002/cphc.201901000] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/14/2020] [Indexed: 12/30/2022]
Abstract
The solubility of hydrophobic molecules in water is sensitive to salt addition in an ion-specific manner. Such "salting-out" and "salting-in" properties have been shown to be a major contributor to the measured ion-specific Hofmeister effects that are observed in many biophysical phenomena. Various theoretical models have suggested a number of disparate mechanisms for salting-out (salting-in) of hydrophobic moieties, the most popular of which include preferential interaction, water-mediated association, and electrostriction models. However, a complete molecular level description of this ion-specificity is not yet available. This work investigates the ion-specific nature of hydrophobic solvation by studying how sodium and chloride salts affect the thermodynamics of 1,2-hexanediol micellization. The results of this study are analyzed in terms of scaled-particle theory and we show that salt addition can affect hydrophobic solvation in two modalities: salt addition changes the cavitation free energy; salt addition also influences the solvent-solute interaction energy by changing the hydration of the hydrophobic solute. These two effects are salt specific in nature and we suggest that for small hydrophobic solutes these effects are the main cause of salt-specific Hofmeister effects on their solubility.
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Affiliation(s)
| | - Hayden M Glor
- Department of Chemistry, University of Manitoba, Canada
| | - Mazdak Khajehpour
- University of Manitoba, 468 Parker Bldg., Winnipeg, Manitoba, R3T2 N2, Canada.,Department of Chemistry, University of Manitoba, Canada
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10
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Buchner R, Wachter W, Hefter G. Systematic Variations of Ion Hydration in Aqueous Alkali Metal Fluoride Solutions. J Phys Chem B 2019; 123:10868-10876. [DOI: 10.1021/acs.jpcb.9b09694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Wolfgang Wachter
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Glenn Hefter
- Chemistry Department, Murdoch University, Murdoch, WA 6150, Australia
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11
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Abstract
Hydration-shell vibrational spectroscopy provides an experimental window into solute-induced water structure changes that mediate aqueous folding, binding, and self-assembly. Decomposition of measured Raman and infrared (IR) spectra of aqueous solutions using multivariate curve resolution (MCR) and related methods may be used to obtain solute-correlated spectra revealing solute-induced perturbations of water structure, such as changes in water hydrogen-bond strength, tetrahedral order, and the presence of dangling (non-hydrogen-bonded) OH groups. More generally, vibrational-MCR may be applied to both aqueous and nonaqueous solutions, including multicomponent mixtures, to quantify solvent-mediated interactions between oily, polar, and ionic solutes, in both dilute and crowded fluids. Combining vibrational-MCR with emerging theoretical modeling strategies promises synergetic advances in the predictive understanding of multiscale self-assembly processes of both biological and technological interest.
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Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
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12
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Kananenka AA, Hestand NJ, Skinner JL. OH-Stretch Raman Multivariate Curve Resolution Spectroscopy of HOD/H2O Mixtures. J Phys Chem B 2019; 123:5139-5146. [DOI: 10.1021/acs.jpcb.9b02686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexei A. Kananenka
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Nicholas J. Hestand
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - J. L. Skinner
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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13
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Morawietz T, Marsalek O, Pattenaude SR, Streacker LM, Ben-Amotz D, Markland TE. The Interplay of Structure and Dynamics in the Raman Spectrum of Liquid Water over the Full Frequency and Temperature Range. J Phys Chem Lett 2018; 9:851-857. [PMID: 29394069 DOI: 10.1021/acs.jpclett.8b00133] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
While many vibrational Raman spectroscopy studies of liquid water have investigated the temperature dependence of the high-frequency O-H stretching region, few have analyzed the changes in the Raman spectrum as a function of temperature over the entire spectral range. Here, we obtain the Raman spectra of water from its melting to boiling point, both experimentally and from simulations using an ab initio-trained machine learning potential. We use these to assign the Raman bands and show that the entire spectrum can be well described as a combination of two temperature-independent spectra. We then assess which spectral regions exhibit strong dependence on the local tetrahedral order in the liquid. Further, this work demonstrates that changes in this structural parameter can be used to elucidate the temperature dependence of the Raman spectrum of liquid water and provides a guide to the Raman features that signal water ordering in more complex aqueous systems.
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Affiliation(s)
- Tobias Morawietz
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Ondrej Marsalek
- Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Shannon R Pattenaude
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Louis M Streacker
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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14
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Lee E, Choi JH, Cho M. The effect of Hofmeister anions on water structure at protein surfaces. Phys Chem Chem Phys 2018; 19:20008-20015. [PMID: 28722047 DOI: 10.1039/c7cp02826a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To understand the effects of specific ions on protein-water interactions and the thermodynamic stability of proteins in salt solutions, we use a molecular dynamics (MD) simulation to examine the water structure, orientational distribution, and dynamics near the surface of ubiquitin. In particular, we consider NaCl, NaBF4, NaSCN, and NaClO4 salt solutions containing ubiquitin, where the anions of the latter three salts are well-known chaotropic ions in the Hofmiester anion series. The number of hydrogen bonds (H-bonds) per water molecule is found to decrease significantly at the ubiquitin-water interface, indicating a significant disruption of the water H-bonding network. The distribution of the water H-bond numbers near the protein surface is modulated by dissolved ions, and the extent of the ion effect on the H-bonding network structure follows the order of the Hofmeister anion series, while there are no specific ion effects on water properties at distances larger than 5 Å from the protein surface. From detailed analyses of the surface area, volume, and root-mean-square deviation (RMSD) of ubiquitin, we show that changes in the properties of the protein could originate from the disruption of the water H-bond network induced by ions with a higher affinity for the protein surface instead of direct protein residue-ion interactions. An interesting observation made here is that the orientational distribution of water molecules at the protein-water interface is close to random, but there is a slight preference for interfacial water molecules with a straddle structure within 2.5 Å of the protein surface, where one of the two OH groups points away from the protein surface and the other points toward the surface. In addition, comparing the MD simulation results for ubiquitin solutions with dissolved NaSCN and KSCN, we show that Na+ affects the water H-bonding structure at the protein surface more than K+. It is clear that the H-bonding network structure of water more than one water layer away from the protein surface is not distinguishably different from that of neat water. We thus anticipate that the present work will provide insights into the scale of specific ion effects on the H-bonding structure and orientational distribution of water in the vicinity of protein surfaces in aqueous solutions.
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Affiliation(s)
- Euihyun Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea.
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15
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Matt SM, Ben-Amotz D. Influence of Intermolecular Coupling on the Vibrational Spectrum of Water. J Phys Chem B 2018; 122:5375-5380. [PMID: 29298478 DOI: 10.1021/acs.jpcb.7b11063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah M. Matt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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16
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Ju SW, Zhang N, Wang ZQ, Zhang RT, Zeng DW, Shao XP, Lin K. Contacted Ion Pairs in Aqueous CuCl2 by the Combination of Ratio Spectra, Difference Spectra, Second Order Difference Spectra in the UV-Visible Spectra. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1711211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Si-wen Ju
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - Ning Zhang
- College of Science, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhi-qiang Wang
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - Rui-ting Zhang
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - De-wen Zeng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Xiao-peng Shao
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - Ke Lin
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
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17
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Zdrali E, Chen Y, Okur HI, Wilkins DM, Roke S. The Molecular Mechanism of Nanodroplet Stability. ACS NANO 2017; 11:12111-12120. [PMID: 29224343 DOI: 10.1021/acsnano.7b05100] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mixtures of nano- and microscopic oil droplets in water have recently been rediscovered as miniature reaction vessels in microfluidic environments and are important constituents of many environmental systems, food, personal care, and medical products. The oil nanodroplet/water interface stabilized by surfactants determines the physicochemical properties of the droplets. Surfactants are thought to stabilize nanodroplets by forming densely packed monolayers that shield the oil phase from the water. This idea has been inferred from droplet stability measurements in combination with molecular structural data obtained from extended planar interfaces. Here, we present a molecular level investigation of the surface structure and stability of nanodroplets and show that the surface structure of nanodroplets is significantly different from that of extended planar interfaces. Charged surfactants form monolayers that are more than 1 order of magnitude more dilute than geometrically packed ones, and there is no experimental correlation between stability and surfactant surface density. Moreover, dilute negatively charged surfactant monolayers produce more stable nanodroplets than dilute positively charged and dense geometrically packed neutral surfactant monolayers. Droplet stability is found to depend on the relative cooperativity between charge-charge, charge-dipole, and hydrogen-bonding interactions. The difference between extended planar interfaces and nanoscale interfaces stems from a difference in the thermally averaged total charge-charge interactions in the two systems. Low dielectric oil droplets with a size smaller than the Debye length in oil permit repulsive interactions between like charges from opposing interfaces in small droplets. This behavior is generic and extends up to the micrometer length scale.
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Affiliation(s)
- Evangelia Zdrali
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Yixing Chen
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Halil I Okur
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - David M Wilkins
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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18
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Abstract
This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.
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Affiliation(s)
- Matthew B Hillyer
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
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19
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Kurniawan N, van Kempen THS, Sonneveld S, Rosalina TT, Vos BE, Jansen KA, Peters GWM, van de Vosse FN, Koenderink GH. Buffers Strongly Modulate Fibrin Self-Assembly into Fibrous Networks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6342-6352. [PMID: 28558246 PMCID: PMC5489959 DOI: 10.1021/acs.langmuir.7b00527] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/27/2017] [Indexed: 05/20/2023]
Abstract
Fibrin is a plasma protein with a central role in blood clotting and wound repair. Upon vascular injury, fibrin forms resilient fibrillar networks (clots) via a multistep self-assembly process, from monomers, to double-stranded protofibrils, to a branched network of thick fibers. In vitro, fibrin self-assembly is sensitive to physicochemical conditions like the solution pH and ionic strength, which tune the strength of the noncovalent driving forces. Here we report a surprising finding that the buffer-which is necessary to control the pH and is typically considered to be inert-also significantly influences fibrin self-assembly. We show by confocal microscopy and quantitative light scattering that various common buffering agents have no effect on the initial assembly of fibrin monomers into protofibrils but strongly hamper the subsequent lateral association of protofibrils into thicker fibers. We further find that the structural changes are independent of the molecular structure of the buffering agents as well as of the activation mechanism and even occur in fibrin networks formed from platelet-poor plasma. This buffer-mediated decrease in protofibril bundling results in a marked reduction in the permeability of fibrin networks but only weakly influences the elastic modulus of fibrin networks, providing a useful tuning parameter to independently control the elastic properties and the permeability of fibrin networks. Our work raises the possibility that fibrin assembly in vivo may be regulated by variations in the acute-phase levels of bicarbonate and phosphate, which act as physiological buffering agents of blood pH. Moreover, our findings add a new example of buffer-induced effects on biomolecular self-assembly to recent findings for a range of proteins and lipids.
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Affiliation(s)
- Nicholas
A. Kurniawan
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Thomas H. S. van Kempen
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Stijn Sonneveld
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
| | - Tilaï T. Rosalina
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Bart E. Vos
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
| | - Karin A. Jansen
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
| | - Gerrit W. M. Peters
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Frans N. van de Vosse
- Department of Biomedical
Engineering & Institute for Complex
Molecular Systems, and Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Systems Biophysics, AMOLF, Amsterdam 1009 DB, The Netherlands
- E-mail:
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20
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Sharker KK, Islam MN, Das S. Counterion Effect on Krafft Temperature and Related Properties of Octadecyltrimethylammonium Bromide. J SURFACTANTS DETERG 2017. [DOI: 10.1007/s11743-017-1957-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Trimethylamine N-oxide stabilizes proteins via a distinct mechanism compared with betaine and glycine. Proc Natl Acad Sci U S A 2017; 114:2479-2484. [PMID: 28228526 DOI: 10.1073/pnas.1614609114] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report experimental and computational studies investigating the effects of three osmolytes, trimethylamine N-oxide (TMAO), betaine, and glycine, on the hydrophobic collapse of an elastin-like polypeptide (ELP). All three osmolytes stabilize collapsed conformations of the ELP and reduce the lower critical solution temperature (LSCT) linearly with osmolyte concentration. As expected from conventional preferential solvation arguments, betaine and glycine both increase the surface tension at the air-water interface. TMAO, however, reduces the surface tension. Atomically detailed molecular dynamics (MD) simulations suggest that TMAO also slightly accumulates at the polymer-water interface, whereas glycine and betaine are strongly depleted. To investigate alternative mechanisms for osmolyte effects, we performed FTIR experiments that characterized the impact of each cosolvent on the bulk water structure. These experiments showed that TMAO red-shifts the OH stretch of the IR spectrum via a mechanism that was very sensitive to the protonation state of the NO moiety. Glycine also caused a red shift in the OH stretch region, whereas betaine minimally impacted this region. Thus, the effects of osmolytes on the OH spectrum appear uncorrelated with their effects upon hydrophobic collapse. Similarly, MD simulations suggested that TMAO disrupts the water structure to the least extent, whereas glycine exerts the greatest influence on the water structure. These results suggest that TMAO stabilizes collapsed conformations via a mechanism that is distinct from glycine and betaine. In particular, we propose that TMAO stabilizes proteins by acting as a surfactant for the heterogeneous surfaces of folded proteins.
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22
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Okur HI, Hladílková J, Rembert KB, Cho Y, Heyda J, Dzubiella J, Cremer PS, Jungwirth P. Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions. J Phys Chem B 2017; 121:1997-2014. [PMID: 28094985 DOI: 10.1021/acs.jpcb.6b10797] [Citation(s) in RCA: 416] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood. This situation could have been summarized as follows: Many chemists used the Hofmeister series as a mantra to put a label on ion-specific behavior in various environments, rather than to reach a molecular level understanding and, consequently, an ability to predict a particular effect of a given salt ion on proteins in solutions. In this Feature Article we show that the cationic and anionic Hofmeister series can now be rationalized primarily in terms of specific interactions of salt ions with the backbone and charged side chain groups at the protein surface in solution. At the same time, we demonstrate the limitations of separating Hofmeister effects into independent cationic and anionic contributions due to the electroneutrality condition, as well as specific ion pairing, leading to interactions of ions of opposite polarity. Finally, we outline the route beyond Hofmeister chemistry in the direction of understanding specific roles of ions in various biological functionalities, where generic Hofmeister-type interactions can be complemented or even overruled by particular steric arrangements in various ion binding sites.
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Affiliation(s)
- Halil I Okur
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Jana Hladílková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic.,Division of Theoretical Chemistry, Lund University , P.O.B. 124, SE-22100 Lund, Sweden
| | | | - Younhee Cho
- Department of Chemistry, Texas A&M University , College Station 77843, Texas, United States
| | - Jan Heyda
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Department of Physical Chemistry, University of Chemistry and Technology, Prague , Technická 5, 16628 Prague 6, Czech Republic
| | - Joachim Dzubiella
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Institut für Physik, Humboldt-Universität zu Berlin , Newtonstrasse 15, 12489 Berlin, Germany
| | | | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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23
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Bye JW, Baxter NJ, Hounslow AM, Falconer R, Williamson MP. Molecular Mechanism for the Hofmeister Effect Derived from NMR and DSC Measurements on Barnase. ACS OMEGA 2016; 1:669-679. [PMID: 31457155 PMCID: PMC6640789 DOI: 10.1021/acsomega.6b00223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/10/2016] [Indexed: 05/27/2023]
Abstract
The effects of sodium thiocyanate, sodium chloride, and sodium sulfate on the ribonuclease barnase were studied using differential scanning calorimetry (DSC) and NMR. Both measurements reveal specific and saturable binding at low anion concentrations (up to 250 mM), which produces localized conformational and energetic effects that are unrelated to the Hofmeister series. The binding of sulfate slows intramolecular motions, as revealed by peak broadening in 13C heteronuclear single quantum coherence spectroscopy. None of the anions shows significant binding to hydrophobic groups. Above 250 mM, the DSC results are consistent with the expected Hofmeister effects in that the chaotropic anion thiocyanate destabilizes barnase. In this higher concentration range, the anions have approximately linear effects on protein NMR chemical shifts, with no evidence for direct interaction of the anions with the protein surface. We conclude that the effects of the anions on barnase are mediated by solvent interactions. The results are not consistent with the predictions of the preferential interaction, preferential hydration, and excluded volume models commonly used to describe Hofmeister effects. Instead, they suggest that the Hofmeister anion effects on both stability and solubility of barnase are due to the way in which the protein interacts with water molecules, and in particular with water dipoles, which are more ordered around sulfate anions and less ordered around thiocyanate anions.
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Affiliation(s)
- Jordan W. Bye
- Department
of Chemical and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, U.K.
| | - Nicola J. Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
| | - Robert
J. Falconer
- Department
of Chemical and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, U.K.
| | - Mike P. Williamson
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
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24
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Barrett A, Imbrogno J, Belfort G, Petersen PB. Phosphate Ions Affect the Water Structure at Functionalized Membrane Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9074-9082. [PMID: 27506305 DOI: 10.1021/acs.langmuir.6b01936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antifouling surfaces improve function, efficiency, and safety in products such as water filtration membranes, marine vehicle coatings, and medical implants by resisting protein and biofilm adhesion. Understanding the role of water structure at these materials in preventing protein adhesion and biofilm formation is critical to designing more effective coatings. Such fouling experiments are typically performed under biological conditions using isotonic aqueous buffers. Previous studies have explored the structure of pure water at a few different antifouling surfaces, but the effect of electrolytes and ionic strength (I) on the water structure at antifouling surfaces is not well studied. Here sum frequency generation (SFG) spectroscopy is used to characterize the interfacial water structure at poly(ether sulfone) (PES) and two surface-modified PES films in contact with 0.01 M phosphate buffer with high and low salt (Ionic strength, I= 0.166 and 0.025 M, respectively). Unmodified PES, commonly used as a filtration membrane, and modified PES with a hydrophobic alkane (C18) and with a poly(ethylene glycol) (PEG) were used. In the low ionic strength phosphate buffer, water was strongly ordered near the surface of the PEG-modified PES film due to exclusion of phosphate ions and the creation of a surface potential resulting from charge separation between phosphate anions and sodium cations. However, in the high ionic strength phosphate buffer, the sodium and potassium chloride (138 and 3 mM, respectively) in the phosphate buffered saline screened this charge and substantially reduced water ordering. A much smaller water ordering and subsequent reduction upon salt addition was observed for the C18-modified PES, and little water structure change was seen for the unmodified PES. The large difference in water structuring with increasing ionic strength between widely used phosphate buffer and phosphate buffered saline at the PEG interface demonstrates the importance of studying antifouling coatings in the same aqueous environment for which they are designed. These results further suggest that strong long-range water structuring is limited in high ionic strength environments, such as within cells, facilitating chemical and biological reactions and processes.
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Affiliation(s)
- Aliyah Barrett
- Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14850, United States
| | - Joseph Imbrogno
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Poul B Petersen
- Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14850, United States
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25
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Ahmed M, Singh AK, Mondal JA. Hydrogen-bonding and vibrational coupling of water in a hydrophobic hydration shell as observed by Raman-MCR and isotopic dilution spectroscopy. Phys Chem Chem Phys 2016; 18:2767-75. [DOI: 10.1039/c5cp07014g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman multivariate curve resolution (Raman-MCR) spectroscopy reveals the perturbation of vibrational coupling of water in a hydrophobic hydration shell.
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Affiliation(s)
- Mohammed Ahmed
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
| | - Ajay K. Singh
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
| | - Jahur A. Mondal
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
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26
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Abstract
Understanding interactions between inorganic nanoparticles (NPs) is central to comprehension of self-organization processes and a wide spectrum of physical, chemical, and biological phenomena. However, quantitative description of the interparticle forces is complicated by many obstacles that are not present, or not as severe, for microsize particles (μPs). Here we analyze the sources of these difficulties and chart a course for future research. Such difficulties can be traced to the increased importance of discreteness and fluctuations around NPs (relative to μPs) and to multiscale collective effects. Although these problems can be partially overcome by modifying classical theories for colloidal interactions, such an approach fails to manage the nonadditivity of electrostatic, van der Waals, hydrophobic, and other interactions at the nanoscale. Several heuristic rules identified here can be helpful for discriminating between additive and nonadditive nanoscale systems. Further work on NP interactions would benefit from embracing NPs as strongly correlated reconfigurable systems with diverse physical elements and multiscale coupling processes, which will require new experimental and theoretical tools. Meanwhile, the similarity between the size of medium constituents and NPs makes atomic simulations of their interactions increasingly practical. Evolving experimental tools can stimulate improvement of existing force fields. New scientific opportunities for a better understanding of the electronic origin of classical interactions are converging at the scale of NPs.
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Affiliation(s)
- Carlos A Silvera Batista
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA. Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ronald G Larson
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA. Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA. Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA. Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA. Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA. Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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27
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Huang K, Gast S, Ma CD, Abbott NL, Szlufarska I. Comparison between Free and Immobilized Ion Effects on Hydrophobic Interactions: A Molecular Dynamics Study. J Phys Chem B 2015; 119:13152-9. [DOI: 10.1021/acs.jpcb.5b05220] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Sebastian Gast
- Institute
of Chemical Engineering, University of Stuttgart, Stuttgart 70199, Germany
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28
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Specific ion interactions with aromatic rings in aqueous solutions: Comparison of molecular dynamics simulations with a thermodynamic solute partitioning model and Raman spectroscopy. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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29
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How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory. Proc Natl Acad Sci U S A 2015; 112:9270-5. [PMID: 26170324 DOI: 10.1073/pnas.1511780112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is currently the consensus belief that protective osmolytes such as trimethylamine N-oxide (TMAO) favor protein folding by being excluded from the vicinity of a protein, whereas denaturing osmolytes such as urea lead to protein unfolding by strongly binding to the surface. Despite there being consensus on how TMAO and urea affect proteins as a whole, very little is known as to their effects on the individual mechanisms responsible for protein structure formation, especially hydrophobic association. In the present study, we use single-molecule atomic force microscopy and molecular dynamics simulations to investigate the effects of TMAO and urea on the unfolding of the hydrophobic homopolymer polystyrene. Incorporated with interfacial energy measurements, our results show that TMAO and urea act on polystyrene as a protectant and a denaturant, respectively, while complying with Tanford-Wyman preferential binding theory. We provide a molecular explanation suggesting that TMAO molecules have a greater thermodynamic binding affinity with the collapsed conformation of polystyrene than with the extended conformation, while the reverse is true for urea molecules. Results presented here from both experiment and simulation are in line with earlier predictions on a model Lennard-Jones polymer while also demonstrating the distinction in the mechanism of osmolyte action between protein and hydrophobic polymer. This marks, to our knowledge, the first experimental observation of TMAO-induced hydrophobic collapse in a ternary aqueous system.
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30
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Stojanoski V, Chow DC, Fryszczyn B, Hu L, Nordmann P, Poirel L, Sankaran B, Prasad BVV, Palzkill T. Structural Basis for Different Substrate Profiles of Two Closely Related Class D β-Lactamases and Their Inhibition by Halogens. Biochemistry 2015; 54:3370-80. [PMID: 25938261 DOI: 10.1021/acs.biochem.5b00298] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OXA-163 and OXA-48 are closely related class D β-lactamases that exhibit different substrate profiles. OXA-163 hydrolyzes oxyimino-cephalosporins, particularly ceftazidime, while OXA-48 prefers carbapenem substrates. OXA-163 differs from OXA-48 by one substitution (S212D) in the active-site β5 strand and a four-amino acid deletion (214-RIEP-217) in the loop connecting the β5 and β6 strands. Although the structure of OXA-48 has been determined, the structure of OXA-163 is unknown. To further understand the basis for their different substrate specificities, we performed enzyme kinetic analysis, inhibition assays, X-ray crystallography, and molecular modeling. The results confirm the carbapenemase nature of OXA-48 and the ability of OXA-163 to hydrolyze the oxyimino-cephalosporin ceftazidime. The crystal structure of OXA-163 determined at 1.72 Å resolution reveals an expanded active site compared to that of OXA-48, which allows the bulky substrate ceftazidime to be accommodated. The structural differences with OXA-48, which cannot hydrolyze ceftazidime, provide a rationale for the change in substrate specificity between the enzymes. OXA-163 also crystallized under another condition that included iodide. The crystal structure determined at 2.87 Å resolution revealed iodide in the active site accompanied by several significant conformational changes, including a distortion of the β5 strand, decarboxylation of Lys73, and distortion of the substrate-binding site. Further studies showed that both OXA-163 and OXA-48 are inhibited in the presence of iodide. In addition, OXA-10, which is not a member of the OXA-48-like family, is also inhibited by iodide. These findings provide a molecular basis for the hydrolysis of ceftazidime by OXA-163 and, more broadly, show how minor sequence changes can profoundly alter the active-site configuration and thereby affect the substrate profile of an enzyme.
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Affiliation(s)
| | | | | | | | - Patrice Nordmann
- §Medical and Molecular Microbiology "Emerging Antibiotic Resistance" Unit, Department of Medicine, Faculty of Science, University of Fribourg, 1700 Fribourg, Switzerland
| | - Laurent Poirel
- §Medical and Molecular Microbiology "Emerging Antibiotic Resistance" Unit, Department of Medicine, Faculty of Science, University of Fribourg, 1700 Fribourg, Switzerland
| | - Banumathi Sankaran
- ∥Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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31
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Gibb CLD, Oertling EE, Velaga S, Gibb BC. Thermodynamic Profiles of Salt Effects on a Host–Guest System: New Insight into the Hofmeister Effect. J Phys Chem B 2015; 119:5624-38. [DOI: 10.1021/acs.jpcb.5b01708] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Corinne L. D. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Estelle E. Oertling
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Santhosh Velaga
- 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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32
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Benjamin I. Correlating structure and thermodynamics of hydrophobic–hydrophilic ion pairs in water. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Rembert KB, Okur HI, Hilty C, Cremer PS. An NH moiety is not required for anion binding to amides in aqueous solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3459-3464. [PMID: 25764296 DOI: 10.1021/acs.langmuir.5b00127] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herein, we use a combination of thermodynamic and spectroscopic measurements to investigate the interactions of Hofmeister anions with a thermoresponsive polymer, poly(N,N-diethylacrylamide) (PDEA). This amide-based polymer does not contain an NH moiety in its chemical structure and, thus, can serve as a model to test if anions bind to amides in the absence of an NH site. The lower critical solution temperature (LCST) of PDEA was measured as a function of the concentration for 11 sodium salts in aqueous solutions, and followed a direct Hofmeister series for the ability of anions to precipitate the polymer. More strongly hydrated anions (CO3(2-), SO4(2-), S2O3(2-), H2PO4(-), F(-), and Cl(-)) linearly decreased the LCST of the polymer with increasing the salt concentration. Weakly hydrated anions (SCN(-), ClO4(-), I(-), NO3(-), and Br(-)) increased the LCST at lower salt concentrations but salted the polymer out at higher salt concentrations. Proton nuclear magnetic resonance (NMR) was used to probe the mechanism of the salting-in effect and showed apparent binding between weakly hydrated anions (SCN(-) and I(-)) and the α protons of the polymer backbone. Additional experiments performed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy found little change in the amide I band upon the addition of salt, which is consistent with very limited, if any, interactions between the salt ions and the carbonyl moiety of the amide. These results support a molecular mechanism for ion-specific effects on proteins and model amides that does not specifically require an NH group to interact with the anions for the salting-in effect to occur.
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34
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He L, Lin F, Li X, Sui H, Xu Z. Interfacial sciences in unconventional petroleum production: from fundamentals to applications. Chem Soc Rev 2015; 44:5446-94. [DOI: 10.1039/c5cs00102a] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
With the ever increasing demand for energy to meet the needs of growth in population and improvement in the living standards, in particular in developing countries, the abundant unconventional oil reserves (about 70% of total world oil), such as heavy oil, oil/tar sands and shale oil, are playing an increasingly important role in securing global energy supply.
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Affiliation(s)
- Lin He
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin
- P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Feng Lin
- Department of Chemical and Materials Engineering
- University of Alberta
- Edmonton
- Canada
| | - Xingang Li
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin
- P. R. China
- National Engineering Research Centre of Distillation Technology
| | - Hong Sui
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin
- P. R. China
- National Engineering Research Centre of Distillation Technology
| | - Zhenghe Xu
- Department of Chemical and Materials Engineering
- University of Alberta
- Edmonton
- Canada
- Institute of Nuclear and New Energy Technology
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35
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Hemmateenejad B, Shojaeifard Z, Shamsipur M, Neymeyr K, Sawall M, Mohajeri A. Solute-induced perturbation of methanol–water association. RSC Adv 2015. [DOI: 10.1039/c5ra13514a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chemometric analysis of the IR and UV-Vis absorbance data revealed the pronounced effect of the stability of the associated methanol–water cluster in mixtures of solvents.
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Affiliation(s)
| | | | - M. Shamsipur
- Department of Chemistry
- Razi University
- Kermanshah
- Iran
| | - K. Neymeyr
- Institute of Mathematics
- Rostock University
- Rostock
- Germany
- Leibniz Institute for Catalysis
| | - M. Sawall
- Institute of Mathematics
- Rostock University
- Rostock
- Germany
- Leibniz Institute for Catalysis
| | - A. Mohajeri
- Department of Chemistry
- Shiraz University
- Shiraz
- Iran
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dos Santos AP, Figueiredo W, Levin Y. Ion specificity and micellization of ionic surfactants: a Monte Carlo study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4593-4598. [PMID: 24702657 DOI: 10.1021/la500710t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We developed a simulation method that allows us to calculate the critical micelle concentrations for ionic surfactants in the presence of different salts. The results are in good agreement with the experimental data. The simulations are performed on a simple cubic lattice. The anionic interactions with the alkyl chains are taken into account based on the previously developed theory of the interfacial tensions of hydrophobic interfaces: the kosmotropic anions do not interact with the hydrocarbon tails of ionic surfactants, while chaotropic anions interact with the alkyl chains through a dispersion potential proportional to the anionic polarizability.
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Affiliation(s)
- Alexandre P dos Santos
- Departamento de Física, Universidade Federal de Santa Catarina , Florianópolis, Santa Catarina 88040-900, Brazil
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Ben-Amotz D, Rankin BM, Widom B. Molecular Aggregation Equilibria. Comparison of Finite Lattice and Weighted Random Mixing Predictions. J Phys Chem B 2014; 118:7878-85. [PMID: 24654770 DOI: 10.1021/jp5003337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dor Ben-Amotz
- Purdue University, Department of Chemistry, West Lafayette, Indiana 47907, United States
| | - Blake M. Rankin
- Purdue University, Department of Chemistry, West Lafayette, Indiana 47907, United States
| | - B. Widom
- Cornell University, Department of Chemistry, Ithaca, New York 14853, United States
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Scheu R, Chen Y, de Aguiar HB, Rankin BM, Ben-Amotz D, Roke S. Specific Ion Effects in Amphiphile Hydration and Interface Stabilization. J Am Chem Soc 2014; 136:2040-7. [DOI: 10.1021/ja4120117] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rüdiger Scheu
- Laboratory
for Fundamental BioPhotonics (LBP), Institute of Bio-Engineering (IBI),
School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Station 17, CH-1015 Lausanne, Switzerland
| | - Yixing Chen
- Laboratory
for Fundamental BioPhotonics (LBP), Institute of Bio-Engineering (IBI),
School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Station 17, CH-1015 Lausanne, Switzerland
| | - Hilton B. de Aguiar
- Laboratory
for Fundamental BioPhotonics (LBP), Institute of Bio-Engineering (IBI),
School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Station 17, CH-1015 Lausanne, Switzerland
| | - Blake M. Rankin
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Dor Ben-Amotz
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Sylvie Roke
- Laboratory
for Fundamental BioPhotonics (LBP), Institute of Bio-Engineering (IBI),
School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Station 17, CH-1015 Lausanne, Switzerland
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Ahmed M, Namboodiri V, Singh AK, Mondal JA, Sarkar SK. How Ions Affect the Structure of Water: A Combined Raman Spectroscopy and Multivariate Curve Resolution Study. J Phys Chem B 2013; 117:16479-85. [DOI: 10.1021/jp4100697] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Mohammed Ahmed
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - V. Namboodiri
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Ajay K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Jahur A. Mondal
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Sisir K. Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
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Rankin BM, Ben-Amotz D. Analysis of Molecular Aggregation Equilibria Using Random Mixing Statistics. J Phys Chem B 2013; 117:15667-74. [PMID: 23957847 DOI: 10.1021/jp406413b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Blake M. Rankin
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Dor Ben-Amotz
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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