1
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Li Y, Li Z, Misra RP, Liang C, Gillen AJ, Zhao S, Abdullah J, Laurence T, Fagan JA, Aluru N, Blankschtein D, Noy A. Molecular transport enhancement in pure metallic carbon nanotube porins. NATURE MATERIALS 2024; 23:1123-1130. [PMID: 38937586 DOI: 10.1038/s41563-024-01925-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 05/16/2024] [Indexed: 06/29/2024]
Abstract
Nanofluidic channels impose extreme confinement on water and ions, giving rise to unusual transport phenomena strongly dependent on the interactions at the channel-wall interface. Yet how the electronic properties of the nanofluidic channels influence transport efficiency remains largely unexplored. Here we measure transport through the inner pores of sub-1 nm metallic and semiconducting carbon nanotube porins. We find that water and proton transport are enhanced in metallic nanotubes over semiconducting nanotubes, whereas ion transport is largely insensitive to the nanotube bandgap value. Molecular simulations using polarizable force fields highlight the contributions of the anisotropic polarizability tensor of the carbon nanotubes to the ion-nanotube interactions and the water friction coefficient. We also describe the origin of the proton transport enhancement in metallic nanotubes using deep neural network molecular dynamics simulations. These results emphasize the complex role of the electronic properties of nanofluidic channels in modulating transport under extreme nanoscale confinement.
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Affiliation(s)
- Yuhao Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Zhongwu Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Rahul Prasanna Misra
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chenxing Liang
- Walker Department of Mechanical Engineering, Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Alice J Gillen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Vivani Medical Inc., Emeryville, CA, USA
| | - Sidi Zhao
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- School of Engineering, University of California Merced, Merced, CA, USA
| | - Jobaer Abdullah
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Narayana Aluru
- Walker Department of Mechanical Engineering, Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA.
| | - Daniel Blankschtein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
- School of Natural Sciences, University of California Merced, Merced, CA, USA.
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2
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Savin AV, Kivshar YS. Stabilization of hydrogen-bonded molecular chains by carbon nanotubes. CHAOS (WOODBURY, N.Y.) 2024; 34:043111. [PMID: 38572948 DOI: 10.1063/5.0197401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
We study numerically nonlinear dynamics of several types of molecular systems composed of hydrogen-bonded chains placed inside carbon nanotubes with open edges. We demonstrate that carbon nanotubes provide a stabilization mechanism for quasi-one-dimensional molecular chains via the formation of their secondary structures. In particular, a polypeptide chain (Gly)N placed inside a carbon nanotube can form a stable helical chain (310-, α-, π-, and β-helix) with parallel chains of hydrogen-bonded peptide groups. A chain of hydrogen fluoride molecules ⋯FH⋯FH⋯FH can form a hydrogen-bonded zigzag chain. Remarkably, we demonstrate that for molecular complexes (Gly)N∈CNT and (FH)N∈CNT, the hydrogen-bonded chains will remain stable even at T=500 K. Thus, our results suggest that the use of carbon nanotubes with encapsulated hydrogen fluoride molecules may be important for the realization of high proton conductivity at high temperatures.
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Affiliation(s)
- Alexander V Savin
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
- Academic Department of Innovational Materials and Technologies Chemistry, Plekhanov Russian University of Economics, Moscow 117997, Russia
| | - Yuri S Kivshar
- Nonlinear Physics Center, Research School of Physics, Australian National University, Canberra, ACT 2601, Australia
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3
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Aluru NR, Aydin F, Bazant MZ, Blankschtein D, Brozena AH, de Souza JP, Elimelech M, Faucher S, Fourkas JT, Koman VB, Kuehne M, Kulik HJ, Li HK, Li Y, Li Z, Majumdar A, Martis J, Misra RP, Noy A, Pham TA, Qu H, Rayabharam A, Reed MA, Ritt CL, Schwegler E, Siwy Z, Strano MS, Wang Y, Yao YC, Zhan C, Zhang Z. Fluids and Electrolytes under Confinement in Single-Digit Nanopores. Chem Rev 2023; 123:2737-2831. [PMID: 36898130 PMCID: PMC10037271 DOI: 10.1021/acs.chemrev.2c00155] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification to new gas permeable materials for water electrolyzers and energy-storage devices. SDNs also present unique opportunities to achieve ultrasensitive and selective chemical sensing at the single-ion and single-molecule limit. In this review article, we summarize the progress on nanofluidics of SDNs, with a focus on the confinement effects that arise in these extremely narrow nanopores. The recent development of precision model systems, transformative experimental tools, and multiscale theories that have played enabling roles in advancing this frontier are reviewed. We also identify new knowledge gaps in our understanding of nanofluidic transport and provide an outlook for the future challenges and opportunities at this rapidly advancing frontier.
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Affiliation(s)
- Narayana R Aluru
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Fikret Aydin
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Daniel Blankschtein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Alexandra H Brozena
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Samuel Faucher
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - John T Fourkas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Hao-Kun Li
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Yuhao Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zhongwu Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Arun Majumdar
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Joel Martis
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Rahul Prasanna Misra
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Tuan Anh Pham
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Haoran Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - Archith Rayabharam
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Mark A Reed
- Department of Electrical Engineering, Yale University, 15 Prospect Street, New Haven, Connecticut06520, United States
| | - Cody L Ritt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Eric Schwegler
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zuzanna Siwy
- Department of Physics and Astronomy, Department of Chemistry, Department of Biomedical Engineering, University of California, Irvine, Irvine92697, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Yun-Chiao Yao
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Cheng Zhan
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Ze Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
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4
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Nagatsuka N, Shibata N, Muratani T, Watanabe K. Proton Configuration in Water Chain on Pt(533). J Phys Chem Lett 2022; 13:7660-7666. [PMID: 35959992 DOI: 10.1021/acs.jpclett.2c01378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this paper, a wetting behavior of Pt(533) is studied by using heterodyne-detected vibrational sum-frequency generation spectroscopy under an ultrahigh-vacuum condition at 145 K. The imaginary parts of the surface nonlinear susceptibility (Imχ(2)) of the H-bonded OH stretching region are successfully obtained for submonolayer water coverage that show negative bands indicating H-down (proton pointing to the substrate) configurations both for the water at the step and at the terrace. The growth manner of the Imχ(2) signal with coverage and the results of an isotopic dilution are consistent with a model in which a one-dimensional (1D) chain at the step forms a "zigzag" structure that contains H-down orientations. This finding resolves the previous controversy in the literature concerning the proton configuration in the 1D water chain at the step.
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Affiliation(s)
- Naoki Nagatsuka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Noboru Shibata
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Toya Muratani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazuya Watanabe
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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5
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Naeini VF, Baniassadi M, Foroutan M, Rémond Y, George D. Decisive structural elements in water and ion permeation through mechanosensitive channels of large conductance: insights from molecular dynamics simulation. RSC Adv 2022; 12:17803-17816. [PMID: 35765322 PMCID: PMC9201702 DOI: 10.1039/d2ra02284b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
In this paper, a series of equilibrium molecular dynamics simulations (EMD), steered molecular dynamics (SMD), and computational electrophysiology methods are carried out to explore water and ion permeation through mechanosensitive channels of large conductance (MscL). This research aims to identify the pore-lining side chains of the channel in different conformations of MscL homologs by analyzing the pore size. The distribution of permeating water dipole angles through the pore domains enclosed by VAL21 and GLU104 demonstrated that water molecules are oriented toward the charged oxygen headgroups of GLU104 from their hydrogen atoms to retain this interaction in a stabilized fashion. Although, this behavior was not perceived for VAL21. Numerical assessments of the secondary structure clarified that, during the ion permeation, in addition to the secondary structure alterations, the structure of Tb-MscL would also undergo significant conformational changes. It was elucidated that VAL21, GLU104, and water molecules accomplish a fundamental task in ion permeation. The mentioned residues hinder ion permeation so that the pulling SMD force is increased remarkably when the ions permeate through the domains enclosed by VAL21 and GLU102. The hydration level and potassium diffusivity in the hydrophobic gate of the transmembrane domain were promoted by applying the external electric field. Furthermore, the implementation of an external electric field altered the distribution pattern for potassium ions in the system while intensifying the accumulation of Cl− in the vicinity of ARG11 and ARG98. Graphical representation of the most determinant pore-lining side chains of Tb-MscL along with the solid surfaces depicting the spatial shape of the interior pore.![]()
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Affiliation(s)
- Vahid Fadaei Naeini
- Division of Machine Elements, Luleå University of Technology 97187 Luleå Sweden
| | - Majid Baniassadi
- School of Mechanical Engineering, College of Engineering, University of Tehran Tehran Iran.,University of Strasbourg, ICube Laboratory/CNRS 2 Rue Boussingault 67000 Strasbourg France
| | - Masumeh Foroutan
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran Tehran Iran
| | - Yves Rémond
- University of Strasbourg, ICube Laboratory/CNRS 2 Rue Boussingault 67000 Strasbourg France
| | - Daniel George
- University of Strasbourg, ICube Laboratory/CNRS 2 Rue Boussingault 67000 Strasbourg France
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6
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Corti HR, Appignanesi GA, Barbosa MC, Bordin JR, Calero C, Camisasca G, Elola MD, Franzese G, Gallo P, Hassanali A, Huang K, Laria D, Menéndez CA, de Oca JMM, Longinotti MP, Rodriguez J, Rovere M, Scherlis D, Szleifer I. Structure and dynamics of nanoconfined water and aqueous solutions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:136. [PMID: 34779954 DOI: 10.1140/epje/s10189-021-00136-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.
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Affiliation(s)
- Horacio R Corti
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina.
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - Marcia C Barbosa
- Institute of Physics, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil
| | - J Rafael Bordin
- Department of Physics, Institute of Physics and Mathematics, 96050-500, Pelotas, RS, Brazil
| | - Carles Calero
- Secció de Física Estadística i Interdisciplinària - Departament de Física de la Matèria Condensada, Universitat de Barcelona & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - M Dolores Elola
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària - Departament de Física de la Matèria Condensada, Universitat de Barcelona & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - Ali Hassanali
- Condensed Matter and Statistical Physics Section (CMSP), The International Center for Theoretical Physics (ICTP), Trieste, Italy
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Daniel Laria
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cintia A Menéndez
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - Joan M Montes de Oca
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - M Paula Longinotti
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier Rodriguez
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de General San Martín, San Martín, Buenos Aires, Argentina
| | - Mauro Rovere
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - Damián Scherlis
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Igal Szleifer
- Biomedical Engineering Department, Northwestern University, Evanston, USA
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7
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Kronberg R, Laasonen K. Dynamics and Surface Propensity of H + and OH - within Rigid Interfacial Water: Implications for Electrocatalysis. J Phys Chem Lett 2021; 12:10128-10134. [PMID: 34636561 PMCID: PMC8543677 DOI: 10.1021/acs.jpclett.1c02493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Facile solvent reorganization promoting ion transfer across the solid-liquid interface is considered a prerequisite for efficient electrocatalysis. We provide first-principles insight into this notion by examining water self-ion dynamics at a highly rigid NaCl(100)-water interface. Through extensive density functional theory molecular dynamics simulations, we demonstrate for both acidic and alkaline solutions that Grotthuss dynamics is not impeded by a rigid water structure. Conversely, decreased proton transfer barriers and a striking propensity of H3O+ and OH- for stationary interfacial water are found. Differences in the ideal hydration structure of the ions, however, distinguish their behavior at the water contact layer. While hydronium can maintain its optimal solvation, the preferentially hypercoordinated hydroxide is repelled from the immediate vicinity of the surface due to interfacial coordination reduction. This has implications for alkaline hydrogen electrosorption in which the formation of undercoordinated OH- at the surface is proposed to contribute to the observed sluggish kinetics.
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Dammak H, Brieuc F, Geneste G, Torrent M, Hayoun M. Isotope effect on hydrogen bond symmetrization in hydrogen and deuterium fluoride crystals by molecular dynamics simulation. Phys Chem Chem Phys 2019; 21:3211-3217. [PMID: 30681084 DOI: 10.1039/c8cp06949b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The isotope effect on the collective proton/deuteron transfer in hydrogen and deuterium fluoride crystals has been investigated at 100 K by ab initio quantum-thermal-bath path-integral molecular dynamics (QTB-PIMD) simulation. The deuterons within a planar zigzag chain of the orthorhombic structure simultaneously flip between covalent and hydrogen bonds due to the barrier crossing through tunnelling. The height of the corresponding static barrier normalized for one deuteron is 29.2 meV. In the HF crystal, all the protons are located at the center of the heavy-atom distance. This evidences the symmetrization of the H-bonds, and indicates that the proton zero-point energy is above the barrier top. The decrease of the heavy-atom distance due to quantum fluctuations in both HF and DF crystals corresponds to a large decrease and an increase of the hydrogen and covalent bond lengths, respectively. Upon deuteration, the increase of the heavy-atom distance (Ubbelohde effect) is in agreement with experimental data.
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Affiliation(s)
- Hichem Dammak
- Laboratoire Structures Propriétés et Modélisation des Solides, CentraleSupélec, CNRS, Université Paris-Saclay, F 91190 Gif-sur-Yvette, France.
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9
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Sirkin YAP, Hassanali A, Scherlis DA. One-Dimensional Confinement Inhibits Water Dissociation in Carbon Nanotubes. J Phys Chem Lett 2018; 9:5029-5033. [PMID: 30113846 DOI: 10.1021/acs.jpclett.8b02183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The effect of nanoconfinement on the self-dissociation of water constitutes an open problem whose elucidation poses a serious challenge to experiments and simulations alike. In slit pores of width ≈1 nm, recent first-principles calculations have predicted that the dissociation constant of H2O increases by almost 2 orders of magnitude [ Muñoz-Santiburcio and Marx, Phys. Rev. Lett. 2017 , 119 , 056002 ]. In the present study, quantum mechanics-molecular mechanics simulations are employed to compute the dissociation free-energy profile of water in a (6,6) carbon nanotube. According to our results, the equilibrium constant Kw drops by 3 orders of magnitude with respect to the bulk phase value, at variance with the trend predicted for confinement in two dimensions. The higher barrier to dissociation can be ascribed to the undercoordination of the hydroxide and hydronium ions in the nanotube and underscores that chemical reactivity does not exhibit a monotonic behavior with respect to pore size but may vary substantially with the characteristic length scale and dimensionality of the confining media.
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Affiliation(s)
- Yamila A Perez Sirkin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Buenos Aires C1428EHA , Argentina
| | - Ali Hassanali
- Condensed Matter and Statistical Physics , International Centre for Theoretical Physics , I-34151 Trieste , Italy
| | - Damián A Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Ciudad Universitaria , Buenos Aires C1428EHA , Argentina
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10
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Li F, Li Z, Li S, Fang W, Sun C, Men Z. Influence of the hydrogen bond quantum nature in liquid water and heavy water on stimulated Raman scattering. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 199:462-464. [PMID: 29133131 DOI: 10.1016/j.saa.2017.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Abstract
Stimulated Raman scattering (SRS) of liquid water and heavy water have been investigated using Nd:YAG laser. The SRS spectra of liquid heavy water indicate that ice-VII and ice-VIII structures are formed by shock-induced compression (SIC) in forward and backward directions, respectively. Simultaneously, the SRS spectra reveal of liquid water that only ice-VII structure is formed in the backward direction. The difference in ice structures formed by SIC in liquid water and heavy water could be attributed to the effect of the hydrogen bond quantum nature with H+. SRS spectra of 2M NaOH water solution with ice-VII and ice-VIII structures have been successfully obtained in forward and backward, respectively, as OH- greatly reduce the quantum nature of hydrogen bonds by neutralizing H+ in water. The hydrogen bond quantum nature is important for understanding isotope calibration test structure and isotopic effect.
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Affiliation(s)
- Fabing Li
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Zhanlong Li
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Shuo Li
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Wenhui Fang
- School of Science, Changchun University of Science and Technology, Changchun 130012, China
| | - Chenglin Sun
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Zhiwei Men
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China.
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11
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Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer. Nat Chem 2018. [DOI: 10.1038/s41557-018-0010-2] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Li C, Meckler SM, Smith ZP, Bachman JE, Maserati L, Long JR, Helms BA. Engineered Transport in Microporous Materials and Membranes for Clean Energy Technologies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:1704953. [PMID: 29315857 DOI: 10.1002/adma.201704953] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/12/2017] [Indexed: 05/25/2023]
Abstract
Many forward-looking clean-energy technologies hinge on the development of scalable and efficient membrane-based separations. Ongoing investment in the basic research of microporous materials is beginning to pay dividends in membrane technology maturation. Specifically, improvements in membrane selectivity, permeability, and durability are being leveraged for more efficient carbon capture, desalination, and energy storage, and the market adoption of membranes in those areas appears to be on the horizon. Herein, an overview of the microporous materials chemistry driving advanced membrane development, the clean-energy separations employing them, and the theoretical underpinnings tying membrane performance to membrane structure across multiple length scales is provided. The interplay of pore architecture and chemistry for a given set of analytes emerges as a critical design consideration dictating mass transport outcomes. Opportunities and outstanding challenges in the field are also discussed, including high-flux 2D molecular-sieving membranes, phase-change adsorbents as performance-enhancing components in composite membranes, and the need for quantitative metrologies for understanding mass transport in heterophasic materials and in micropores with unusual chemical interactions with analytes of interest.
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Affiliation(s)
- Changyi Li
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, CA, 94720, USA
| | - Stephen M Meckler
- Department of Chemistry, The University of California, Berkeley, CA, 94720, USA
| | - Zachary P Smith
- Department of Chemical Engineering, The Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jonathan E Bachman
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, CA, 94720, USA
| | - Lorenzo Maserati
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Jeffrey R Long
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, CA, 94720, USA
- Department of Chemistry, The University of California, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Brett A Helms
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
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13
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Sakti AW, Nishimura Y, Chou CP, Nakai H. Density-Functional Tight-Binding Molecular Dynamics Simulations of Excess Proton Diffusion in Ice Ih, Ice Ic, Ice III, and Melted Ice VI Phases. J Phys Chem A 2017; 122:33-40. [DOI: 10.1021/acs.jpca.7b10664] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | | | | | - Hiromi Nakai
- CREST, Japan Science and Technology Agency, Tokyo 102-0075, Japan
- ESICB, Kyoto University, Kyoto 615-8520, Japan
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14
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He X, Zhang F, Liu J, Fang G, Wang S. Homogenous graphene oxide-peptide nanofiber hybrid hydrogel as biomimetic polysaccharide hydrolase. NANOSCALE 2017; 9:18066-18074. [PMID: 29131232 DOI: 10.1039/c7nr06525f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cellulose, an impressive potential sustainable fuel, is difficult to hydrolyze because of the protection of β-1,4-glycosidic bonds through the tight hydrogen bonding network. In this study, homogenous graphene oxide (GO)-peptide nanofiber hybrid hydrogels (GO-PNFs) were designed as a β-glycosyl hydrolase mimetic to achieve efficient degradation of cellobiose and cellopentaose. For comparison, free peptides, graphene oxide mixed with free peptides (GO-peptdies) and self-assembled peptide nanofibers (PNFs) were also studied for their activity as a hydrolase mimetics for degradation of cellobiose. Among these materials, GO-PNFs showed the highest hydrolysis activity. Transmission electron microscopy, atomic force microscopy, fluorescence analysis, circular dichroism spectroscopies, X-ray diffraction, Raman spectra and computational modeling were used to interpret the difference in activity mechanism in these artificially designed enzymes. These investigations suggested that high catalytic performance of GO-PNFs toward cellobiose and cellopentaose hydrolysis could be attributed to the formation of nanofiber structures of peptides, optimal molecular conformation and less steric hindrance to access the substrate. More importantly, GO not only served as a platform for attaching PNFs, but also created a hydrophobic microenvironment and facilitated proton transfer, an essential step in catalytic hydrolysis, thus enhancing catalytic activity. All these provided insights into the potential use of peptides and GO hybrid composite nanoenzymes in efficient cellulose hydrolysis.
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Affiliation(s)
- Xingxing He
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
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15
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Affiliation(s)
- Jesse G. McDaniel
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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16
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Geneste G, Hermet J, Dezanneau G. Reply to the 'Comment on "Proton transport in barium stannate: classical, semi-classical and quantum regime"'. Phys Chem Chem Phys 2017; 19:21191-21209. [PMID: 28758646 DOI: 10.1039/c7cp02385e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We respond to the erroneous criticisms about our modeling of proton transport in barium stannate [G. Geneste et al., Phys. Chem. Chem. Phys., 2015, 17, 19104]. In this previous work, we described, on the basis of density-functional calculations, proton transport in the classical and semi-classical regimes, and provided arguments in favor of an adiabatic picture for proton transfer at low temperature. We re-explain here our article (with more detail and precision), the content of which has been distorted in the Comment, and reiterate our arguments in this reply. We refute all criticisms. They are completely wrong in the context of our article. Even though a few of them are based on considerations probably true in some metals, they make no sense here since they do not correspond to the content of our work. It has not been understood in the Comment that two competitive configurations, associated with radically different transfer mechanisms, have been studied in our work. It has also not been understood in the Comment that the adiabatic regime described for transfer occurs in the protonic ground state, in a very-low barrier configuration with the protonic ground state energy larger than the barrier. Serious confusion has been made in the Comment with the case of H in metals like Nb or Ta, leading to the introduction of the notion of (protonic) "excited-state proton transfer", relevant for H in some metals, but (i) that does not correspond to the (ground state) adiabatic transfers here described, and (ii) that does not correspond to what is commonly described as the "adiabatic limit for proton transfer" in the scientific literature. We emphasize, accordingly, the large differences between proton transfer in the present oxide and hydrogen jumps in metals like Nb or Ta, and the similarities between proton transfer in the present oxide and in acid-base solutions. We finally describe a scenario for proton transfer in the present oxide regardless of the temperature regime.
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17
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Goto T, Beć KB, Ozaki Y. Interpretation of the à ← X̃ transition of hydrated protons in aqueous solutions observed in the far-UV region with quantum chemical calculations. Phys Chem Chem Phys 2017; 19:21490-21499. [DOI: 10.1039/c7cp01766a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A substantial blue-shift of the first electronic transition band of liquid water with a H2SO4 concentration (0–14.4 M) observed in the far-UV region.
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Affiliation(s)
- Takeyoshi Goto
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
| | - Krzysztof B. Beć
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
| | - Yukihiro Ozaki
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
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18
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Zhang Q, He X, Han A, Tu Q, Fang G, Liu J, Wang S, Li H. Artificial hydrolase based on carbon nanotubes conjugated with peptides. NANOSCALE 2016; 8:16851-16856. [PMID: 27714071 DOI: 10.1039/c6nr05015h] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
An artificial enzyme was constructed by attaching short peptides with active sites (SHELKLKLKL, WLKLKLKL) onto carbon nanotubes (CNT). It was found that the combination of SHE amino acids was essential to form a catalytic triad. W was also incorporated into this artificial enzyme and acted as a substrate binding site, thus producing an enzyme model with synergism of 67.7% catalytic groups and 32.3% binding groups, CNT-(SHE/W)2:1-LKLKLKL. When the peptide SHELKLKLKL was attached with the catalytic triad site close to the surface of CNT, the composite had higher activity than a leucine-attached system terminated with the catalytic triad site, suggesting that CNT not only served as a platform for attaching active amino acids, but also created a hydrophobic microenvironment and facilitated the proton transfer process to enhance the catalytic activity. The artificial enzyme exhibited Michaelis-Menten behaviour, indicating that it was indeed a mimic of the corresponding natural enzyme. This work showed that a well-designed combination of CNT and short peptides containing active sites can mimic a natural enzyme.
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Affiliation(s)
- Qiang Zhang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Xingxing He
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Ailing Han
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Qingxia Tu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Guozhen Fang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Jifeng Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Haibo Li
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China
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19
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Rossi M, Ceriotti M, Manolopoulos DE. Nuclear Quantum Effects in H(+) and OH(-) Diffusion along Confined Water Wires. J Phys Chem Lett 2016; 7:3001-3007. [PMID: 27440483 DOI: 10.1021/acs.jpclett.6b01093] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The diffusion of protons and hydroxide ions along water wires provides an efficient mechanism for charge transport that is exploited by biological membrane channels and shows promise for technological applications such as fuel cells. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we focus on two aspects of this process that are often disregarded because of their high computational cost: the use of first-principles potential energy surfaces and the treatment of the nuclei as quantum particles. We consider proton and hydroxide ions in finite water wires using density functional theory augmented with an apolar cylindrical confining potential. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition that takes explicitly into account the delocalization of the charge in the Grotthus-like mechanism. We include nuclear quantum effects (NQEs) through the thermostated ring polymer molecular dynamics method and model finite system size effects by considering Langevin dynamics on the potential of mean force of the charged species, allowing us to extract the same "universal" diffusion coefficient from simulations with different wire sizes. In the classical case, diffusion coefficients depend significantly on the potential energy surface, in particular on how dispersion forces modulate water-water distances. NQEs, however, make the diffusion less sensitive to the underlying potential and geometry of the wire.
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Affiliation(s)
- Mariana Rossi
- Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
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20
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Agmon N, Bakker HJ, Campen RK, Henchman RH, Pohl P, Roke S, Thämer M, Hassanali A. Protons and Hydroxide Ions in Aqueous Systems. Chem Rev 2016; 116:7642-72. [PMID: 27314430 DOI: 10.1021/acs.chemrev.5b00736] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
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Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
| | - Richard H Henchman
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Peter Pohl
- Johannes Kepler University Linz , Institute of Biophysics, Gruberstrasse 40, 4020 Linz, Austria
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Material Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015, Lausanne, Switzerland
| | - Martin Thämer
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ali Hassanali
- CMSP Section, The Abdus Salaam International Center for Theoretical Physics , I-34151 Trieste, Italy
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21
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Striolo A, Michaelides A, Joly L. The Carbon-Water Interface: Modeling Challenges and Opportunities for the Water-Energy Nexus. Annu Rev Chem Biomol Eng 2016; 7:533-56. [DOI: 10.1146/annurev-chembioeng-080615-034455] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Providing clean water and sufficient affordable energy to all without compromising the environment is a key priority in the scientific community. Many recent studies have focused on carbon-based devices in the hope of addressing this grand challenge, justifying and motivating detailed studies of water in contact with carbonaceous materials. Such studies are becoming increasingly important because of the miniaturization of newly proposed devices, with ubiquitous nanopores, large surface-to-volume ratio, and many, perhaps most of the water molecules in contact with a carbon-based surface. In this brief review, we discuss some recent advances obtained via simulations and experiments in the development of carbon-based materials for applications in water desalination. We suggest possible ways forward, with particular emphasis on the synergistic combination of experiments and simulations, with simulations now sometimes offering sufficient accuracy to provide fundamental insights. We also point the interested reader to recent works that complement our short summary on the state of the art of this important and fascinating field.
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Affiliation(s)
- Alberto Striolo
- Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology, and Department of Physics and Astronomy, University College London, London WC1H 0AH, United Kingdom
| | - Laurent Joly
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, France
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22
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Ceriotti M, Fang W, Kusalik PG, McKenzie RH, Michaelides A, Morales MA, Markland TE. Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges. Chem Rev 2016; 116:7529-50. [DOI: 10.1021/acs.chemrev.5b00674] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Michele Ceriotti
- Laboratory
of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Wei Fang
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Peter G. Kusalik
- Department
of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Ross H. McKenzie
- School
of Mathematics and Physics, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Angelos Michaelides
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Miguel A. Morales
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
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23
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Abstract
The quantum electrodynamics theory of water put forward by Del Giudice and colleagues provides a useful foundation for a new science of water for life. The interaction of light with liquid water generates quantum coherent domains in which the water molecules oscillate between the ground state and an excited state close to the ionizing potential of water. This produces a plasma of almost free electrons favoring redox reactions, the basis of energy metabolism in living organisms. Coherent domains stabilized by surfaces, such as membranes and macromolecules, provide the excited interfacial water that enables photosynthesis to take place, on which most of life on Earth depends. Excited water is the source of superconducting protons for rapid intercommunication within the body. Coherent domains can also trap electromagnetic frequencies from the environment to orchestrate and activate specific biochemical reactions through resonance, a mechanism for the most precise regulation of gene function.
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Affiliation(s)
- Mae-Wan Ho
- Institute of Science in Society , London , UK
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24
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Clark JK, Habenicht BF, Paddison SJ. Ab initio molecular dynamics simulations of aqueous triflic acid confined in carbon nanotubes. Phys Chem Chem Phys 2015; 16:16465-79. [PMID: 24983213 DOI: 10.1039/c4cp01066c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ab initio molecular dynamics simulations were performed to investigate the effects of nanoscale confinement on the structural and dynamical properties of aqueous triflic acid (CF3SO3H). Single-walled carbon nanotubes (CNTs) with diameters ranging from ∼11 to 14 Å were used as confinement vessels, and the inner surface of the CNT were either left bare or fluorinated to probe the influence of the confined environment on structural and dynamical properties of the water and triflic acidic. The systems were simulated at hydration levels of n = 1-3 H2O/CF3SO3H. Proton dissociation expectedly increased with increasing hydration. Along with the level of hydration, hydrogen bond connectivity between the triflic acid molecules, both directly and via a single water molecule, played a role on proton dissociation. Direct hydrogen bonding between the CF3SO3H molecules, most commonly found in the larger bare CNT, also promoted interactions between water molecules allowing for greater separation of the dissociated protons from the CF3SO3(-) as the hydration level was increased. However, this also resulted in a decrease in the overall proportion of dissociated protons. The confinement dimensions altered both the hydrogen bond network and the distribution of water molecules where the H2O in the fluorinated CNTs tended to form small clusters with less proton dissociation at n = 1 and 2 but the highest at n = 3. In the absence of nearby hydrogen bond accepting sites from H2O or triflic acid SO3H groups, the water molecules formed weak hydrogen bonds with the fluorine atoms. In the bare CNT systems, these involved the CF3 groups of triflic acid and were more frequently observed when direct hydrogen bonding between CF3SO3H hindered potential hydrogen bonding sites. In the fluorinated tubes, interactions with the covalently bound fluorine atoms of the CNT wall dominated which appear to stabilize the hydrogen bond network. Increasing the hydration level increased the frequency of the OH···F (CNT) hydrogen bonding which was highly pronounced in the smaller fluorinated CNT indicating an influence on the confinement dimensions on these interactions.
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Affiliation(s)
- Jeffrey K Clark
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA.
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25
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Chen J, Ren X, Li XZ, Alfè D, Wang E. On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study. J Chem Phys 2015; 141:024501. [PMID: 25028021 DOI: 10.1063/1.4886075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
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Affiliation(s)
- Ji Chen
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| | - Xinguo Ren
- Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, People's Republic of China
| | - Xin-Zheng Li
- School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Dario Alfè
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | - Enge Wang
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
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26
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Theoretical investigations on Zundel cation present inside boron-nitride nanotubes: Effect of confinement and hydrogen bonding. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2014.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Giberti F, Hassanali AA, Ceriotti M, Parrinello M. The Role of Quantum Effects on Structural and Electronic Fluctuations in Neat and Charged Water. J Phys Chem B 2014; 118:13226-35. [DOI: 10.1021/jp507752e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Federico Giberti
- Department
of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Ali A. Hassanali
- The Abdus Salaam International Center for Theoretical Physics, Condensed Matter Physics Section, Strada Costiera 11, I-34151 Trieste, Italy
| | - Michele Ceriotti
- Laboratory of Computational
Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Parrinello
- Department
of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, via G. Buffi 13, CH-6900 Lugano, Switzerland
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28
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Effect of confinement on the structure and energetics of Zundel cation present inside the hydrophobic carbon nanotubes: an ab initio study. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1576-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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30
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Clark II JK, Paddison SJ. Ab initio molecular dynamics simulations of water and an excess proton in water confined in carbon nanotubes. Phys Chem Chem Phys 2014; 16:17756-69. [DOI: 10.1039/c4cp00415a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Ohba T, Chaban VV. A Highly Viscous Imidazolium Ionic Liquid inside Carbon Nanotubes. J Phys Chem B 2014; 118:6234-40. [DOI: 10.1021/jp502798e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Tomonori Ohba
- Graduate
School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan
| | - Vitaly V. Chaban
- MEMPHYS
- Center for Biomembrane Physics, Syddansk Universitet, Odense M, 5230, Denmark
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32
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McKenzie RH, Bekker C, Athokpam B, Ramesh SG. Effect of quantum nuclear motion on hydrogen bonding. J Chem Phys 2014; 140:174508. [DOI: 10.1063/1.4873352] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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33
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Wikfeldt KT, Michaelides A. Communication: ab initio simulations of hydrogen-bonded ferroelectrics: collective tunneling and the origin of geometrical isotope effects. J Chem Phys 2014; 140:041103. [PMID: 25669494 DOI: 10.1063/1.4862740] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ab initio simulations that account for nuclear quantum effects have been used to examine the order-disorder transition in squaric acid, a prototypical H-bonded antiferroelectric crystal. Our simulations reproduce the >100 K difference in transition temperature observed upon deuteration as well as the strong geometrical isotope effect observed on intermolecular separations within the crystal. We find that collective transfer of protons along the H-bonding chains - facilitated by quantum mechanical tunneling - is critical to the order-disorder transition and the geometrical isotope effect. This sheds light on the origin of isotope effects and the importance of tunneling in squaric acid which likely extends to other H-bonded ferroelectrics.
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Affiliation(s)
- K T Wikfeldt
- Science Institute, University of Iceland, Nordita, Stockholm, Sweden and University College London, London WC1E 6BT, United Kingdom
| | - A Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
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34
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Bekçioğlu G, Allolio C, Ekimova M, Nibbering ETJ, Sebastiani D. Competition between excited state proton and OH− transport via a short water wire: solvent effects open the gate. Phys Chem Chem Phys 2014; 16:13047-51. [DOI: 10.1039/c4cp00970c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the acid–base proton exchange reaction in a microsolvated bifunctional chromophore by means of quantum chemical calculations.
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Affiliation(s)
- Gül Bekçioğlu
- Physics Department
- Freie Universität Berlin
- 14195 Berlin, Germany
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
| | - Christoph Allolio
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle (Saale), Germany
| | - Maria Ekimova
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie
- D-12489 Berlin, Germany
| | - Erik T. J. Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie
- D-12489 Berlin, Germany
| | - Daniel Sebastiani
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle (Saale), Germany
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35
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Abstract
The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and (1)H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water.
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36
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Lu D. Accelerating water transport through a charged SWCNT: a molecular dynamics simulation. Phys Chem Chem Phys 2013; 15:14447-57. [PMID: 23884179 DOI: 10.1039/c3cp51855h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The properties of a nanotube, such as the hydrophobicity and charge of the surface, can significantly affect water transport behavior. However, our knowledge of the effects of charge density, dipole orientation, frequency of flipping, and movement behavior on water flow through carbon nanotubes (CNTs) is far from adequate. This study is aimed at gaining insight into the transport of single-file water molecules in a charged carbon nanotube. It was shown that the water chains inside the charged nanotube exhibit bipolar properties. The water dipoles are parallel to the z-axis, and point toward (D-defect) and away from (L-defect) the center of the nanotube for a negatively charged nanotube and a positively charged one, respectively. Compared with a pristine single-wall carbon nanotube (SWCNT), the charged nanotubes, including both positively charged and negatively charged, favor the water-filling process due to electrostatic interactions. According to the dipole distribution in the nanotube, the water dipole only flips in the middle region because of the bipolar nature of water chains. Additionally, flipping of the entire water chain is inhibited, which allows for the enhanced water flux. A negatively charged single-walled carbon nanotube (N-SWCNT) accelerated water transport by tuning the single-file flow from a "hopping" to a "continuous" mode, thus decreasing the energy barrier. The hydrogen bonds between water molecules inside the nanotube are also strengthened in the negatively charged nanotube, favoring water transport. Any distortion of uniformity will lead to additional energy barriers to water flux. Our results provide a comprehensive view of molecular events underpinning the water transport inside a SWCNT, which may be of assistance in creating innovative designs for water nanochannels.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China.
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37
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Quantum simulation of low-temperature metallic liquid hydrogen. Nat Commun 2013; 4:2064. [DOI: 10.1038/ncomms3064] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 05/26/2013] [Indexed: 11/08/2022] Open
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