1
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Goswami A, Kohata A, Okazoe T, Huang H, Aida T. Fluoro-Crown Ether Phosphate as Efficient Cell-Permeable Drug Carrier by Disrupting Hydration Layer. J Am Chem Soc 2024; 146:23406-23411. [PMID: 39082642 DOI: 10.1021/jacs.4c06464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Fast and direct permeation of drug molecules is crucial for effective biotherapeutics. Inspired by a recent finding that fluorous compounds disrupt the hydrogen-bonded network of water, we developed fluoro-crown ether phosphate CyclicFP-X. This compound acts as a fast cell-permeating agent, enabling direct delivery of various bioactive cargos (X) into cancer cells without endocytic entrapment. In contrast, its nonfluorinated cyclic analog (CyclicP-X) failed to achieve cellular internalization. Although the acyclic fluorous analog AcyclicFP-X was internalized, this process occurred slowly owing to the involvement of an endocytic trapping pathway. Designed with a high fluorine density, CyclicFP-X exhibits compactness, polarity, and high-water solubility, facilitating lipid vesicle fusion by disrupting their hydration layers. Raman spectroscopy confirmed the generation of dangling -OH bonds upon addition of CyclicFP-OH to water. Furthermore, conjugating CyclicFP-X with fluorouracil (FU, an anticancer drug) via a reductively cleavable disulfide linker (CyclicFP-SS-FU) demonstrated the general utility of fluoro-crown ether phosphate as a potent carrier for biotherapeutics.
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Affiliation(s)
- Abir Goswami
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ai Kohata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Okazoe
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Yokohama Technical Center, AGC Inc., 1-1 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hubiao Huang
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takuzo Aida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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2
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Panuszko A, Śmiechowski M, Pieloszczyk M, Malinowski A, Stangret J. Weakly Hydrated Solute of Mixed Hydrophobic-Hydrophilic Nature. J Phys Chem B 2024; 128:6352-6361. [PMID: 38913837 PMCID: PMC11228977 DOI: 10.1021/acs.jpcb.4c02429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/26/2024]
Abstract
Infrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane (MSM). In the hydration sphere of MSM, there are two types of populations of water molecules: a significant share of water molecules weakly bonded to the sulfone group and a smaller share of water molecules strongly bonded to each other around the methyl groups of MSM. The very weak hydrogen bond of water molecules with the hydrophilic group causes the extended network of water hydrogen bonds to be not "anchored" on the sulfone group, and consequently, the MSM hydration shell is labile.
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Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Maciej Pieloszczyk
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Adrian Malinowski
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Faculty
of Chemistry, Gdańsk University of
Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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3
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Samuel AZ, Sugiyama K, Takeyama H. Direct intracellular detection of biomolecule specific bound-water with Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121870. [PMID: 36116410 DOI: 10.1016/j.saa.2022.121870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Lipids, proteins, and nucleic acids have closely associated water molecules (Bound water), which exhibit considerably different physical properties compared to bulk water. Here we investigate the possibility of resolving Raman spectra of the specific hydration shell of these biomolecules in intracellular regions using Raman imaging. Lipids and proteins + nucleic acids Raman spectral components resolved in the analysis showed associated water spectral features, which are uniquely different from that of bulk water. These spectral profiles agree with water spectral profile observed in the case of corresponding hydrated pure biomolecules. The results show the prospects of Raman imaging in examining intracellular hydration in biomolecules and its functional relation.
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Affiliation(s)
- Ashok Zachariah Samuel
- Research Organization for Nano and Life Innovations, Waseda University, 513, Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan.
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovations, Waseda University, 513, Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Japan, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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4
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Gulotty EM, Sanadhya S, Tucker ZD, Moghaddam SS, Ashfeld BL. Controlling phase separation behavior of thermo-responsive ionic liquids through the directed distribution of anionic charge. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Shen Y, Liu L, Zheng Q, Zhao X, Han Y, Guo Q, Wang Y. Quantitative insights into tightly and loosely bound water in hydration shells of amino acids. SOFT MATTER 2021; 17:10080-10089. [PMID: 34714904 DOI: 10.1039/d1sm01234g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The hydration of amino acids closely correlates the hydration of peptides and proteins and is critical to their biological functions. However, complete and quantitative understanding about the hydration of amino acids is lacking. Here, tightly and loosely bound water of 20 zwitterionic amino acids are quantitatively distinguished and determined by Raman spectroscopy with multivariate curve resolution (Raman-MCR) and differential scanning calorimetry (DSC). The total hydration water obtained from Raman-MCR and the tightly bound water determined by DSC have certain relevance, but they do not exactly correspond. In particular, Pro, Arg and Lys exhibit larger number of tightly bound water molecules (4.02-6.59), showing a significant influence on the onset transition temperature and the melting enthalpy values of water molecules, which provides direct evidence for their unique functions associated with biological water. Asn, Ser, Thr, Met, His and Glu have a smaller number of tightly bound water molecules (0.30-1.31), whilst the other remaining 11 amino acids only contain loosely bound water molecules. Four exceptional amino acids Ile, Leu, Phe and Val show fewer tightly bound water molecules but a higher number of loosely bound water molecules. As for the hydration shell structure, most amino acids except Pro and Trp enhance tetrahedral water structure and H-bonds relative to pure water and at least 1.9% of the hydration water molecules associated with the amino acids show non-hydrogen-bonded OH defects. This work combines two effective experimental techniques to reveal the hydration water structure and quantitatively analyze two kinds of bound water molecules of 20 amino acids.
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Affiliation(s)
- Yutan Shen
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lu Liu
- Institute of Theoretical Chemistry, Jilin University, 130012, P. R. China
| | - Qiancheng Zheng
- Institute of Theoretical Chemistry, Jilin University, 130012, P. R. China
| | - Xi Zhao
- Institute of Theoretical Chemistry, Jilin University, 130012, P. R. China
| | - Yuchun Han
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
| | - Qianjin Guo
- Key Laboratory of Molecular Reaction Dynamics and Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
| | - Yilin Wang
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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6
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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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7
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Bilodeau CL, Lau EY, Roush DJ, Snyder MA, Cramer SM. Behavior of Water Near Multimodal Chromatography Ligands and Its Consequences for Modulating Protein-Ligand Interactions. J Phys Chem B 2021; 125:6112-6120. [PMID: 34097423 DOI: 10.1021/acs.jpcb.1c01549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multimodal chromatography is a powerful approach for purifying proteins that uses ligands containing multiple modes of interaction. Recent studies have shown that selectivity in multimodal chromatographic separations is a function of the ligand structure and geometry. Here, we performed molecular dynamics simulations to explore how the ligand structure and geometry affect ligand-water interactions and how these differences in solution affect the nature of protein-ligand interactions. Our investigation focused on three chromatography ligands: Capto MMC, Nuvia cPrime, and Prototype 4, a structural variant of Nuvia cPrime. First, the solvation characteristics of each ligand were quantified via three metrics: average water density, fluctuations, and residence time. We then explored how solvation was perturbed when the ligand was bound to the protein surface and found that the probability of the phenyl ring dewetting followed the order: Capto MMC > Prototype 4 > Nuvia cPrime. To explore how these differences in dewetting affect protein-ligand interactions, we calculated the probability of each ligand binding to different types of residues on the protein surface and found that the probability of binding to a hydrophobic residue followed the same order as the dewetting behavior. This study illustrates the role that wetting and dewetting play in modulating protein-ligand interactions.
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Affiliation(s)
- Camille L Bilodeau
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Edmond Y Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - David J Roush
- Biologics Process R&D, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mark A Snyder
- Process Chromatography Division, Bio-Rad Laboratories, 6000 James Watson Drive, Hercules, California 94547, United States
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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8
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Shen Y, Liu B, Cui J, Xiang J, Liu M, Han Y, Wang Y. Hydration Shell Changes in Surfactant Aggregate Transitions Revealed by Raman-MCR Spectroscopy. J Phys Chem Lett 2020; 11:7429-7437. [PMID: 32803982 DOI: 10.1021/acs.jpclett.0c02140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydration states of many self-assemblies directly relate to their structures and functions. Here, we use Raman multivariate curve resolution (Raman-MCR) assisted by differential scanning calorimetry and nuclear magnetic resonance to explore the hydration properties of aggregates formed by three cationic ammonium surfactants, trimethylene-1,3-bis(dodecyldimethylammonium bromide) (12-3-12(Br)2), didodecyldimethylammonium bromide (DDAB), and dodecyltrimethylammonium bromide (DTAB). For 12-3-12(Br)2, the transitions from spherical to rodlike and wormlike micelles lead to about 20% and 60% dehydration and gradually weaken water tetrahedral order and H-bond in hydration shells for both headgroup and hydrophobic chain. As to DDAB, unilamellar vesicles contain two kinds of hydration water species, but multicompartment vesicles exhibit decreased water order and weaker H-bond. DTAB only forms spherical micelles and its hydration structure is similar to that of the 12-3-12(Br)2 spherical micelles. This work provides a basis to explore the hydration states of complex biological self-assemblies.
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Affiliation(s)
- Yutan Shen
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Bin Liu
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jie Cui
- Analysis and Test Center, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, P. R. China
| | - Junfeng Xiang
- Analysis and Test Center, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, P. R. China
| | - Meirong Liu
- Analysis and Test Center, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, P. R. China
| | - Yuchun Han
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yilin Wang
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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9
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Biswas S, Mallik BS. Aqueous hydroxyl group as the vibrational probe to access the hydrophobicity of amide derivatives. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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10
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Mendes de Oliveira D, Zukowski SR, Palivec V, Hénin J, Martinez-Seara H, Ben-Amotz D, Jungwirth P, Duboué-Dijon E. Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys Chem Chem Phys 2020; 22:24014-24027. [DOI: 10.1039/d0cp02987d] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We combine Raman-MCR vibrational spectroscopy experiments with ab initio and classical MD simulations to gain molecular insights into carboxylate–cation binding.
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Affiliation(s)
| | | | - Vladimir Palivec
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
| | - Jérôme Hénin
- CNRS, Université de Paris
- UPR 9080
- Laboratoire de Biochimie Théorique
- 13 Rue Pierre et Marie Curie
- Paris
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
| | - Dor Ben-Amotz
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
| | - Elise Duboué-Dijon
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
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11
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Biswas A, Priyadarsini A, Mallik BS. Dynamics and Spectral Response of Water Molecules around Tetramethylammonium Cation. J Phys Chem B 2019; 123:8753-8766. [DOI: 10.1021/acs.jpcb.9b05466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
| | - Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
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12
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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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13
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Franck JM, Han S. Overhauser Dynamic Nuclear Polarization for the Study of Hydration Dynamics, Explained. Methods Enzymol 2018; 615:131-175. [PMID: 30638529 DOI: 10.1016/bs.mie.2018.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We outline the physical properties of hydration water that are captured by Overhauser Dynamic Nuclear Polarization (ODNP) relaxometry and explore the insights that ODNP yields about the water and the surface that this water is coupled to. As ODNP relies on the pairwise cross-relaxation between the electron spin of a spin probe and a proton nuclear spin of water, it captures the dynamics of single-particle diffusion of an ensemble of water molecules moving near the spin probe. ODNP principally utilizes the same physics as other nuclear magnetic resonance (NMR) relaxometry (i.e., relaxation measurement) techniques. However, in ODNP, electron paramagnetic resonance (EPR) excites the electron spins probes and their high net polarization acts as a signal amplifier. Furthermore, it renders ODNP parameters highly sensitive to water moving at rates commensurate with the EPR frequency of the spin probe (typically 10GHz). Also, ODNP selectively enhances the NMR signal contributions of water moving within close proximity to the spin label. As a result, ODNP can capture ps-ns movements of hydration waters with high sensitivity and locality, even in samples with protein concentrations as dilute as 10 µM. To date, the utility of the ODNP technique has been demonstrated for two major applications: the characterization of the spatial variation in the properties of the hydration layer of proteins or other surfaces displaying topological diversity, and the identification of structural properties emerging from highly disordered proteins and protein domains. The former has been shown to correlate well with the properties of hydration water predicted by MD simulations and has been shown capable of evaluating the hydrophilicity or hydrophobicity of a surface. The latter has been demonstrated for studies of an interhelical loop of proteorhodopsin, the partial structure of α-synuclein embedded at the lipid membrane surface, incipient structures adopted by tau proteins en route to fibrils, and the structure and hydration profile of a transmembrane peptide. This chapter focuses on offering a mechanistic understanding of the ODNP measurement and the molecular dynamics encoded in the ODNP parameters. In particular, it clarifies how the electron-nuclear dipolar coupling encodes information about the molecular dynamics in the nuclear spin self-relaxation and, more importantly, the electron-nuclear spin cross-relaxation rates. The clarification of the molecular dynamics underlying ODNP should assist in establishing a connection to theory and computer simulation that will offer far richer interpretations of ODNP results in future studies.
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Affiliation(s)
- John M Franck
- Department of Chemistry, Syracuse University, Syracuse, NY, United States.
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, United States; Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, United States
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14
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Wu X, Lu W, Streacker LM, Ashbaugh HS, Ben-Amotz D. Temperature-Dependent Hydrophobic Crossover Length Scale and Water Tetrahedral Order. J Phys Chem Lett 2018; 9:1012-1017. [PMID: 29420897 DOI: 10.1021/acs.jpclett.7b03431] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Experimental Raman multivariate curve resolution and molecular dynamics simulations are performed to demonstrate that the vibrational frequency and tetrahedrality of water molecules in the hydration-shells of short-chain alcohols differ from those of pure water and undergo a crossover above 100 °C (at 30 MPa) to a structure that is less tetrahedral than pure water. Our results demonstrate that the associated crossover length scale decreases with increasing temperature, suggesting that there is a fundamental connection between the spectroscopically observed crossover and that predicted to take place around idealized purely repulsive solutes dissolved in water, although the water structure changes in the hydration-shells of alcohols are far smaller than those associated with an idealized "dewetting" transition.
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Affiliation(s)
- Xiangen Wu
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences , Wuhan 430074, China
| | - Wanjun Lu
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences , Wuhan 430074, China
| | - Louis M Streacker
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University , New Orleans, Louisiana 70118, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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15
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Smirnov A, Zubrienė A, Manakova E, Gražulis S, Matulis D. Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding. PeerJ 2018; 6:e4412. [PMID: 29503769 PMCID: PMC5831161 DOI: 10.7717/peerj.4412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/04/2018] [Indexed: 11/28/2022] Open
Abstract
The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure.
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Affiliation(s)
- Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Saulius Gražulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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16
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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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17
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Moreno-Gómez N, Vargas EF, Buchner R. The effect of alkyl-chain branching on the hydration and ion association of tetrabutylammonium cations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.09.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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18
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Daly CA, Streacker LM, Sun Y, Pattenaude SR, Hassanali AA, Petersen PB, Corcelli SA, Ben-Amotz D. Decomposition of the Experimental Raman and Infrared Spectra of Acidic Water into Proton, Special Pair, and Counterion Contributions. J Phys Chem Lett 2017; 8:5246-5252. [PMID: 28976760 DOI: 10.1021/acs.jpclett.7b02435] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Textbooks describe excess protons in liquid water as hydronium (H3O+) ions, although their true structure remains lively debated. To address this question, we have combined Raman and infrared (IR) multivariate curve resolution spectroscopy with ab initio molecular dynamics and anharmonic vibrational spectroscopic calculations. Our results are used to resolve, for the first time, the vibrational spectra of hydrated protons and counterions and reveal that there is little ion-pairing below 2 M. Moreover, we find that isolated excess protons are strongly IR active and nearly Raman inactive (with vibrational frequencies of ∼1500 ± 500 cm-1), while flanking water OH vibrations are both IR and Raman active (with higher frequencies of ∼2500 ± 500 cm-1). The emerging picture is consistent with Georg Zundel's seminal work, as well as recent ultrafast dynamics studies, leading to the conclusion that protons in liquid water are primarily hydrated by two flanking water molecules, with a broad range of proton hydrogen bond lengths and asymmetries.
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Affiliation(s)
- Clyde A Daly
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Louis M Streacker
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Yuchen Sun
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Shannon R Pattenaude
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Ali A Hassanali
- Condensed Matter and Statistical Physics, International Centre for Theoretical Physics , Strada Costiera, 11, I-34151 Trieste, Italy
| | - Poul B Petersen
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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19
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Zukowski SR, Mitev PD, Hermansson K, Ben-Amotz D. CO 2 Hydration Shell Structure and Transformation. J Phys Chem Lett 2017; 8:2971-2975. [PMID: 28598626 DOI: 10.1021/acs.jpclett.7b00971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The hydration-shell of CO2 is characterized using Raman multivariate curve resolution (Raman-MCR) spectroscopy combined with ab initio molecular dynamics (AIMD) vibrational density of states simulations, to validate our assignment of the experimentally observed high-frequency OH band to a weak hydrogen bond between water and CO2. Our results reveal that while the hydration-shell of CO2 is highly tetrahedral, it is also occasionally disrupted by the presence of entropically stabilized defects associated with the CO2-water hydrogen bond. Moreover, we find that the hydration-shell of CO2 undergoes a temperature-dependent structural transformation to a highly disordered (less tetrahedral) structure, reminiscent of the transformation that takes place at higher temperatures around much larger oily molecules. The biological significance of the CO2 hydration shell structural transformation is suggested by the fact that it takes place near physiological temperatures.
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Affiliation(s)
- Samual R Zukowski
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Pavlin D Mitev
- Department of Chemistry-Ångström, Uppsala University , Box 538, S-75121 Uppsala, Sweden
| | - Kersti Hermansson
- Department of Chemistry-Ångström, Uppsala University , Box 538, S-75121 Uppsala, Sweden
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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20
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Bradford SM, Fisher EA, Meli MV. Ligand Shell Composition-Dependent Effects on the Apparent Hydrophobicity and Film Behavior of Gold Nanoparticles at the Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9790-9796. [PMID: 27594307 DOI: 10.1021/acs.langmuir.6b02238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanoparticles with well-defined interfacial energy and wetting properties are needed for a broad range of applications involving nanoparticle self-assembly including the formation of superlattices, stability of Pickering emulsions, and for the control of nanoparticle interactions with biological membranes. Theoretical, simulated, and recent experimental studies have found nanometer-scale chemical heterogeneity to have important effects on hydrophobic interactions. Here we report the study of 4 nm gold nanoparticles with compositionally well-defined mixed ligand shells of hydroxyl-(OH) and methyl-(CH3) terminated alkylthiols as Langmuir films. Compositions ranging from 0-25% hydroxyl were examined and reveal nonmonotonic changes in particle hydrophobicity at the air-water interface. Unlike nanoparticles capped exclusively with a methyl-terminated alkylthiol, extensive particle aggregation is found for ligand shells containing <2% hydroxyl-terminated chains. This aggregation was lessened upon increasing the quantity of OH-terminated chains. Nanoparticles capped with 25% OH yield films of well-separated nanoparticles exhibiting a fluid-phase regime in the surface pressure vs area isotherm. Compression-expansion hysteresis, monolayer collapse, and mean nanoparticle area measurements support the TEM-observed changes in film morphology. Such clear changes in the hydrophobicity of nanoparticles based on very small changes in the ligand shell composition are shown to impact the process of interfacial nanoparticle self-assembly and are an important demonstration of nanoscale wetting with consequences in both materials and biological applications of nanoparticles that require tunable hydrophobicity.
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Affiliation(s)
- Stephen M Bradford
- Department of Chemistry and Biochemistry, Mount Allison University , 63C York Street, Sackville, New Brunswick E4L 1E2, Canada
| | - Elizabeth A Fisher
- Department of Chemistry and Biochemistry, Mount Allison University , 63C York Street, Sackville, New Brunswick E4L 1E2, Canada
| | - M-Vicki Meli
- Department of Chemistry and Biochemistry, Mount Allison University , 63C York Street, Sackville, New Brunswick E4L 1E2, Canada
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21
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22
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Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907;
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23
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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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24
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Affiliation(s)
- Joshua A. Long
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Blake M. Rankin
- 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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25
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Varanasi SR, Guskova OA, John A, Sommer JU. Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration. J Chem Phys 2015; 142:224308. [DOI: 10.1063/1.4922322] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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