1
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Zhang P, Gardini AT, Xu X, Parrinello M. Intramolecular and Water Mediated Tautomerism of Solvated Glycine. J Chem Inf Model 2024; 64:3599-3604. [PMID: 38620066 DOI: 10.1021/acs.jcim.4c00273] [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: 04/17/2024]
Abstract
Understanding tautomerism and characterizing solvent effects on the dynamic processes pose significant challenges. Using enhanced-sampling molecular dynamics based on state-of-the-art deep learning potentials, we investigated the tautomeric equilibria of glycine in water. We observed that the tautomerism between neutral and zwitterionic glycine can occur through both intramolecular and intermolecular proton transfers. The latter proceeds involving a contact anionic-glycine-hydronium ion pair or separate cationic-glycine-hydroxide ion pair. These pathways with comparable barriers contribute almost equally to the reaction flux.
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Affiliation(s)
- Pengchao Zhang
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
- Atomistic Simulations, Italian Institute of Technology, Genova 16152, Italy
| | - Axel Tosello Gardini
- Atomistic Simulations, Italian Institute of Technology, Genova 16152, Italy
- Department of Materials Science, Università di Milano-Bicocca, 20126 Milano, Italy
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Michele Parrinello
- Atomistic Simulations, Italian Institute of Technology, Genova 16152, Italy
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2
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Murke S, Chen W, Pezzotti S, Havenith M. Tuning Acid-Base Chemistry at an Electrified Gold/Water Interface. J Am Chem Soc 2024; 146:12423-12430. [PMID: 38599583 PMCID: PMC11082902 DOI: 10.1021/jacs.3c13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
Acid-base reactions are ubiquitous in solution chemistry, as well as in electrochemistry. However, macroscopic concepts derived in solutions, such as pKa and pH, differ significantly at electrified metal-aqueous interfaces due to specific solvation and applied voltage. Here, we measure the pKa values of an amino acid, glycine, at a gold/water interface under a varying applied voltage by means of spectroscopic titration. With the help of simulations, we propose a general model to understand potential-dependent shifts in pKa values in terms of local hydrophobicity and electric fields. These parameters can be tuned by adjusting the metal surface and applied voltage, respectively, offering promising, but still unexplored, paths to regulate reactivity. Our results change the focus with respect to common interpretations based on, for example, apparent local pH effects and open interesting perspectives for electrochemical reaction steering.
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Affiliation(s)
| | | | | | - Martina Havenith
- Department of Physical Chemistry
II, Ruhr University Bochum, D-44801 Bochum, Germany
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3
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Energetic, conformational and vibrational features of the tripeptide (Gly)3. Data from MP2 and DFT calculations. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2022.113989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Water admixture triggers the self-assembly of the glycyl-glycine thin film at the presence of organic vapors. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Itaya R, Idei W, Nakamura T, Nishihara T, Kurihara R, Okamoto A, Tanabe K. Changes of C≡C Triple Bond Vibration that Disclosed Non-Canonical Cytosine Protonation in i-Motif-Forming Oligodeoxynucleotides. ACS OMEGA 2021; 6:31595-31604. [PMID: 34869984 PMCID: PMC8637604 DOI: 10.1021/acsomega.1c04074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/05/2021] [Indexed: 05/09/2023]
Abstract
Non-canonical protonation at cytosine (C) in DNA is related to a formation of second order DNA structures such as i-motif, which has a role in gene regulation. Although the detailed structural information is indispensable for comprehension of their functions in cells, the protonation status of C in complicated environments is still elusive. To provide a reporter system of non-canonical protonation, we focused on the molecular vibration that could be monitored using the Raman spectroscopy. We prepared a cytosine derivative (PC) with an acetylene unit as a Raman tag, and found that the Raman signal of acetylene in PC in oligodeoxynucleotides (ODNs) changed due to protonation at the cytosine ring which shortened an acetylene bond. The signal change in i-motif-forming ODNs was also observed in crowded environments with polyethylene glycol, evidencing protonation in i-motif DNA in complicated environments. This system would be one of tracking tools for protonation in DNA structures.
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Affiliation(s)
- Ryota Itaya
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Wakana Idei
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Takashi Nakamura
- Faculty
of Bioscience, Nagahama Institute of Bio-Science
and Technology, 1266
Tamura-cho, Nagahama 526-0829, Japan
| | - Tatsuya Nishihara
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Ryohsuke Kurihara
- School
of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Akimitsu Okamoto
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Kazuhito Tanabe
- Department
of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
- . Phone: +81-42-759-6229. Fax: +81-42-759-6493
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6
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Takemura S, Watanabe H, Nishihara T, Okamoto A, Tanabe K. Monitoring intracellular metal ion complexation with an acetylene-tagged ligand by Raman spectroscopy. RSC Adv 2020; 10:36119-36123. [PMID: 35517095 PMCID: PMC9056985 DOI: 10.1039/d0ra06329k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
We propose to monitor molecular vibrations to identify metal ion-ligand complexation by means of Raman spectroscopy, which has been applied to track vibrational modes of molecules and to obtain a structural fingerprint. We prepared ligand molecules for Zn2+ ion complexation with a dipycolylaminoethyl aniline (DPEA) skeleton and phenylacetylene unit as the Raman tag which showed a typical band around 2200 cm-1. Among the labeled ligands synthesized in this study, A-DPEA showed a strong band attributed to the acetylene unit at 2212 cm-1, while the addition of Zn2+ ion resulted in a band shift to 2220 cm-1 due to complex formation. The addition of other metal ions and titration experiments showed that A-DPEA bound with Zn2+ selectively with a dissociation constant (K d) that was estimated to be 0.22 μM. We also conducted cellular experiments and found that complexation between A-DPEA and Zn2+ also occurred in cells, with a shift in the Raman signal of the ligand from 2212 to 2215 cm-1. Thus, complex formation of the metal ion was identified by monitoring the Raman band shift.
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Affiliation(s)
- Seiya Takemura
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan +81-42-759-6493 +81-42-759-6229
| | - Hikaru Watanabe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan +81-42-759-6493 +81-42-759-6229
| | - Tatsuya Nishihara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan +81-42-759-6493 +81-42-759-6229
| | - Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
| | - Kazuhito Tanabe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan +81-42-759-6493 +81-42-759-6229
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7
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Nguyen TKN, Dumait N, Grasset F, Cordier S, Berthebaud D, Matsui Y, Ohashi N, Uchikoshi T. Zn-Al Layered Double Hydroxide Film Functionalized by a Luminescent Octahedral Molybdenum Cluster: Ultraviolet-Visible Photoconductivity Response. ACS APPLIED MATERIALS & INTERFACES 2020; 12:40495-40509. [PMID: 32786251 DOI: 10.1021/acsami.0c10487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A novel UV-Vis photodetector consisting of an octahedral molybdenum cluster-functionalized Zn2Al layered double hydroxide (LDH) has been successfully synthesized by co-precipitation and delamination methods under ambient conditions. The electrophoretic deposition process has been used as a low-cost, fast, and effective method to fabricate thin and transparent nanocomposite films containing a dense and regular layered structure. The study provided evidence that the presence of the Mo6 cluster units between the LDH does not affect the ionic conduction mechanism of the LDH, which linearly depends on the relative humidity and temperature. Moreover, the photocurrent response is remarkably extended to the visible domain. The reproducibility and stabilization of the photocurrent response caused by the Mo6 cluster-functionalized LDH have been verified upon light excitation at 540 nm. Additionally, it was demonstrated that the films show advantageously strong adherence properties for application requirements.
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Affiliation(s)
- Thi Kim Ngan Nguyen
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
- CNRS-Saint-Gobain-NIMS, UMI 3629, Laboratory for Innovative Key Materials and Structures (LINK), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Noée Dumait
- Univ. Rennes-CNRS-Institut des Sciences Chimiques de Rennes, UMR 6226, 35000 Rennes, France
| | - Fabien Grasset
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
- CNRS-Saint-Gobain-NIMS, UMI 3629, Laboratory for Innovative Key Materials and Structures (LINK), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Univ. Rennes-CNRS-Institut des Sciences Chimiques de Rennes, UMR 6226, 35000 Rennes, France
| | - Stéphane Cordier
- Univ. Rennes-CNRS-Institut des Sciences Chimiques de Rennes, UMR 6226, 35000 Rennes, France
| | - David Berthebaud
- CNRS-Saint-Gobain-NIMS, UMI 3629, Laboratory for Innovative Key Materials and Structures (LINK), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Yoshio Matsui
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Naoki Ohashi
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
- CNRS-Saint-Gobain-NIMS, UMI 3629, Laboratory for Innovative Key Materials and Structures (LINK), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Tetsuo Uchikoshi
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
- CNRS-Saint-Gobain-NIMS, UMI 3629, Laboratory for Innovative Key Materials and Structures (LINK), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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8
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Goby JD, Furuya K, Zimmermann E, Beller JA, Schmitt JM, Cortese M, Breit JF, Coffman JL. Feasibility of spectral pH measurement during the low-pH virus inactivation step of continuous therapeutic antibody production. Biotechnol Prog 2020; 36:e2988. [PMID: 32109000 DOI: 10.1002/btpr.2988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 12/20/2019] [Accepted: 02/06/2020] [Indexed: 11/10/2022]
Abstract
Acidic virus inactivation is commonly used during production of biotherapeutic products to provide virus safety in case of undetected virus contamination. Accurate pH measurement is required to ensure the product pH reaches a virus-inactivating level (typically 3.5-3.7), and a level post-inactivation that is appropriate for later purification steps (typically 5.5-7.5). During batch low-pH inactivation in discrete tanks, potentiometric glass probes are appropriate for measuring pH. During continuous inactivation for 2-3 weeks in an enclosed product stream, probe calibration drift and lag may lead to poor accuracy, and operational difficulties when compensating for drift. Monitoring the spectral response of compounds (indicators) in the product stream whose spectra are pH-sensitive offers a possible alternative way to measure pH without these drawbacks. Such indicators can already exist in the stream (intrinsic) or can be added (extrinsic). Herein are reported studies evaluating the feasibility of both.Promising ultraviolet screening results with the two extrinsics studied, thiamine and ascorbic acid, led to the addition of both to product stream samples titrated to different potentiometric pH values in the 3.3-4.5 range (a representative range encountered during continuous inactivation), and attempts to model pH using sample ultraviolet spectra. One model, based on variability in six spectral attributes, was able to predict pH of an independent sample set within ±0.07 units at the 95% confidence level. Since a typical inactivating pH tolerance is ±0.1 units, the results show that extrinsic indicators potentially can measure inactivation pH with sufficient accuracy. Suggested future steps and an alternative approach are presented.
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Affiliation(s)
- Jeffrey D Goby
- Analytical Science, Process Science, Boehringer Ingelheim Fremont Inc., Fremont, California, USA
| | - Kenji Furuya
- Analytical Science, Process Science, Boehringer Ingelheim Fremont Inc., Fremont, California, USA
| | - Eike Zimmermann
- Analytical Science, Process Science, Boehringer Ingelheim Fremont Inc., Fremont, California, USA.,Allogene, South San Francisco, California, USA
| | | | | | | | | | - Jonathan L Coffman
- Bioprocess Engineering, Process Science, Boehringer Ingelheim Fremont Inc., Fremont, California, USA.,Bioprocess Technology and Engineering group at AstraZeneca, Gaithersburg, Maryland, USA
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9
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Hernández B, Pflüger F, Ghomi M. Aspartate: An interesting model for analyzing dipole‐ion and ion pair interactions through its oppositely charged amine and acid groups. J Comput Chem 2020; 41:1402-1410. [DOI: 10.1002/jcc.26184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Belén Hernández
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)UMR 7369, Université de Reims, Faculté des Sciences Moulin de la Housse, Reims Cedex 2 France
- Université Sorbonne Paris Nord, UFR Santé‐Médecine‐Biologie HumaineGroupe de Biophysique Moléculaire Bobigny Cedex France
| | - Fernando Pflüger
- Université Sorbonne Paris Nord, UFR Santé‐Médecine‐Biologie HumaineGroupe de Biophysique Moléculaire Bobigny Cedex France
| | - Mahmoud Ghomi
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)UMR 7369, Université de Reims, Faculté des Sciences Moulin de la Housse, Reims Cedex 2 France
- Université Sorbonne Paris Nord, UFR Santé‐Médecine‐Biologie HumaineGroupe de Biophysique Moléculaire Bobigny Cedex France
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10
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Horikawa Y, Tokushima T, Takahashi O, Harada Y, Hiraya A, Shin S. Effect of amino group protonation on the carboxyl group in aqueous glycine observed by O 1s X-ray emission spectroscopy. Phys Chem Chem Phys 2018; 20:23214-23221. [DOI: 10.1039/c7cp08305j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The valence electronic structures of the amino acid glycine in aqueous solution were investigated in detail through X-ray emission spectroscopy at O 1s excitation under selective excitation conditions of the CO site in the carboxyl group.
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Affiliation(s)
| | | | - O. Takahashi
- Department of Chemistry
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Y. Harada
- Institute for Solid State Physics
- The University of Tokyo
- Kashiwa
- Japan
- Synchrotron Radiation Research Organization
| | - A. Hiraya
- Department of Physical Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - S. Shin
- Institute for Solid State Physics
- The University of Tokyo
- Kashiwa
- Japan
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11
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Glycine elicited self-assembly of amphiphilic star block copolymers with contradistinct hydrophobicities. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.06.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Hernández B, Pflüger F, Kruglik SG, Cohen R, Ghomi M. Protonation–deprotonation and structural dynamics of antidiabetic drug metformin. J Pharm Biomed Anal 2015; 114:42-8. [DOI: 10.1016/j.jpba.2015.04.041] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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