1
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Abate C, Giuffrè O, Amadeo A, Saija F, Cassone G, Foti C. Experimental and computational study on morin and its complexes with Mg 2+, Mn 2+, Zn 2+, and Al 3+: Coordination and antioxidant properties. J Inorg Biochem 2024; 258:112635. [PMID: 38852294 DOI: 10.1016/j.jinorgbio.2024.112635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/20/2024] [Accepted: 06/02/2024] [Indexed: 06/11/2024]
Abstract
Morin (MRN), an intriguing bioflavonol, has received increasing interest for its antioxidant properties, as have its metal complexes (Mz+-MRN). Understanding their antioxidant behavior is critical to assess their pharmaceutical, nutraceutical potential, and therapeutic impact in the design of advanced antioxidant drugs. To this end, knowing the speciation of different H+-MRN and Mz+-MRN is pivotal to understand and compare their antioxidant ability. In this work, the protonation constant values of MRN under physiological ionic strength and temperature conditions (I = 0.15 mol L-1 and t = 37 °C), determined by UV-vis spectrophotometric titrations, are introduced. Thus, a reliable speciation model on H+-MRN species in aqueous solution is presented, which exhibits five stable forms depending on pH, supplemented by quantum-mechanical calculations useful to determine the proton affinities of each functional group and corresponding deprotonation order. Furthermore, potentiometry and UV-vis spectrophotometry have been exploited to determine the thermodynamic interaction parameters of MRN with different metal cations (Mg2+, Mn2+, Zn2+, Al3+). The antioxidant ability of H+-MRN and Mz+-MRN has been evaluated by the 2,2'-diphenyl-1-benzopyran-4-one (DPPH) method, and the Zn2+-MRN system has proven to afford the most potent antioxidant effect. Ab initio molecular dynamics simulations of Mz+-MRN species at all possible chelation sites and under explicit water solvation allowed for the fine characterization not only of the metal chelation modalities of MRN in explicit water, but also of the role played by the local water environment around the metal cations. Those microscopic patterns reveal to be informative on the different antioxidant capabilities recorded experimentally.
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Affiliation(s)
- Chiara Abate
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.
| | - Ottavia Giuffrè
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy; CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Alessandro Amadeo
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy; Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Giuseppe Cassone
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy.
| | - Claudia Foti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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2
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Creazzo F, Luber S. Water-air interface revisited by means of path-integral ab initio molecular dynamics. Phys Chem Chem Phys 2024; 26:21290-21302. [PMID: 39078670 PMCID: PMC11305098 DOI: 10.1039/d4cp02500h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 07/21/2024] [Indexed: 07/31/2024]
Abstract
Although nuclear quantum effects (NQEs) have been considered on bulk liquid water, the impact of these latter on the air-water interface has not yet been reported. Herein, by performing and comparing ab initio molecular dynamics (AIMD) and path integral AIMD (PI-AIMD) simulations, we reveal the impact of NQEs on structural, dynamical and electronic properties as well as IR spectra of the air-water interface at room temperature. NQEs, being able to describe a more accurate proton delocalization in H-bonded system than AIMD, reveal a different structural arrangement and dynamical behaviour of both bulk and interfacial water molecules in comparison to AIMD results. A more de-structured and de-bound water arrangement and coordination are identified when the quantum nature of nuclei are considered for both bulk and interfacial water molecules. Structural properties, such as inter-/intra-molecular bond lengths, coordination numbers and H-bonding angles of bulk and interfacial water molecules here calculated, are affected by NQEs mitigating the overstructured description given by AIMD. Further evidences of an AIMD overstructured description of bulk water are in the computed IR spectra, where an increased absorption peak intensity and an increased strength of the hydrogen-bond network are alleviated by NQEs. In addition, NQEs show a valuable impact on the electronic structure of the air-water interface, reducing the total valence bandwidth and the electronic energy band-gap when passing from bulk to interfacial water. This work proves how NQEs significantly affect properties and features of the air-water interface, that are essential to accurately describe H-bonded interfacial systems.
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Affiliation(s)
- Fabrizio Creazzo
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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3
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Zlobin A, Smirnov I, Golovin A. Dynamic interchange between two protonation states is characteristic of active sites of cholinesterases. Protein Sci 2024; 33:e5100. [PMID: 39022909 PMCID: PMC11255601 DOI: 10.1002/pro.5100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/28/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024]
Abstract
Cholinesterases are well-known and widely studied enzymes crucial to human health and involved in neurology, Alzheimer's, and lipid metabolism. The protonation pattern of active sites of cholinesterases influences all the chemical processes within, including reaction, covalent inhibition by nerve agents, and reactivation. Despite its significance, our comprehension of the fine structure of cholinesterases remains limited. In this study, we employed enhanced-sampling quantum-mechanical/molecular-mechanical calculations to show that cholinesterases predominantly operate as dynamic mixtures of two protonation states. The proton transfer between two non-catalytic glutamate residues follows the Grotthuss mechanism facilitated by a mediator water molecule. We show that this uncovered complexity of active sites presents a challenge for classical molecular dynamics simulations and calls for special treatment. The calculated proton transfer barrier of 1.65 kcal/mol initiates a discussion on the potential existence of two coupled low-barrier hydrogen bonds in the inhibited form of butyrylcholinesterase. These findings expand our understanding of structural features expressed by highly evolved enzymes and guide future advances in cholinesterase-related protein and drug design studies.
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Affiliation(s)
- Alexander Zlobin
- Institute for Drug DiscoveryLeipzig University Medical SchoolLeipzigGermany
- Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Ivan Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussia
| | - Andrey Golovin
- Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussia
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
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4
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Zheng X, Pei Q, Tan J, Bai S, Luo Y, Ye S. Local electric field in nanocavities dictates the vibrational relaxation dynamics of interfacial molecules. Chem Sci 2024; 15:11507-11514. [PMID: 39055024 PMCID: PMC11268483 DOI: 10.1039/d4sc02463j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/16/2024] [Indexed: 07/27/2024] Open
Abstract
Plasmonic nanocavities enable the generation of strong light-matter coupling and exhibit great potential in plasmon-mediated chemical reactions (PMCRs). Although an electric field generated by nanocavities (E n) has recently been reported, its effect on the vibrational energy relaxation (VER) of the molecules in the nanocavities has not been explored. In this study, we reveal the impact of an electric field sensed by molecules (para-substituted thiophenol derivatives) in a nanocavity (E f) on VER processes by employing advanced time-resolved femtosecond sum frequency generation vibrational spectroscopy (SFG-VS) supplemented by electrochemical measurements. The magnitude of E n is almost identical (1.0 ± 0.2 V nm-1) beyond the experimental deviation while E f varies from 0.3 V nm-1 to 1.7 V nm-1 depending on the substituent. An exponential correlation between E f and the complete recovery time of the ground vibrational C[double bond, length as m-dash]C state (T 2) of the phenyl ring is observed. Substances with a smaller T 2 are strongly correlated with the reported macroscopic chemical reactivity. This finding may aid in enriching the current understanding of PMCRs and highlights the possibility of regulating vibrational energy flow into desired reaction coordinates by using a local electric field.
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Affiliation(s)
- Xiaoxuan Zheng
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China Hefei Anhui 230026 China
| | - Quanbing Pei
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China Hefei Anhui 230026 China
| | - Junjun Tan
- Hefei National Laboratory, University of Science and Technology of China Hefei Anhui 230088 China
| | - Shiyu Bai
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China Hefei Anhui 230026 China
| | - Yi Luo
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China Hefei Anhui 230026 China
- Hefei National Laboratory, University of Science and Technology of China Hefei Anhui 230088 China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China Hefei Anhui 230026 China
- Hefei National Laboratory, University of Science and Technology of China Hefei Anhui 230088 China
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5
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Torre MF, Amadeo A, Cassone G, Tommasini M, Mráziková K, Saija F. Water Dimer under Electric Fields: An Ab Initio Investigation up to Quantum Accuracy. J Phys Chem A 2024; 128:5490-5499. [PMID: 38976361 DOI: 10.1021/acs.jpca.4c01553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
It is well-established that strong electric fields (EFs) can align water dipoles, partially order the H-bond network of liquid water, and induce water splitting and proton transfers. To illuminate the fundamental behavior of water under external EFs, we present the first benchmark, to the best of our knowledge, of DFT calculations of the water dimer exposed to intense EFs against coupled cluster calculations. The analyses of the vibrational Stark effect and electron density provide a consistent picture of the intermolecular charge transfer effects driven along the H-bond by the increasing applied field at all theory levels. However, our findings prove that at extreme field regimes (∼1-2 V/Å) DFT calculations significantly exaggerate by ∼10-30% the field-induced strengthening of the H-bond, both within the GGA, hybrid GGA, and hybrid meta-GGA approximations. Notably, a linear correlation emerges between the vibrational Stark effect on OH stretching and H-bond strengthening: a 1 kcal mol-1 increase corresponds to an 80 cm-1 red-shift in OH stretching frequency.
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Affiliation(s)
- Marco Francesco Torre
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, 98166 Messina, Italy
| | - Alessandro Amadeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, 98166 Messina, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
| | - Matteo Tommasini
- Dipartimento di Chimica, Materiali e Ing. Chimica "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Klaudia Mráziková
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czechia
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
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6
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Zhang P, Chen C, Feng M, Sun C, Xu X. Hydroxide and Hydronium Ions Modulate the Dynamic Evolution of Nitrogen Nanobubbles in Water. J Am Chem Soc 2024; 146:19537-19546. [PMID: 38949461 DOI: 10.1021/jacs.4c06641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
It has been widely recognized that the pH environment influences the nanobubble dynamics and hydroxide ions adsorbed on the surface may be responsible for the long-term survival of the nanobubbles. However, understanding the distribution of hydronium and hydroxide ions in the vicinity of a bulk nanobubble surface at a microscopic scale and the consequent impact of these ions on the nanobubble behavior remains a challenging endeavor. In this study, we carried out deep potential molecular dynamics simulations to explore the behavior of a nitrogen nanobubble under neutral, acidic, and alkaline conditions and the inherent mechanism, and we also conducted a theoretical thermodynamic and dynamic analysis to address constraints related to simulation duration. Our simulations and theoretical analyses demonstrate a trend of nanobubble dissolution similar to that observed experimentally, emphasizing the limited dissolution of bulk nanobubbles in alkaline conditions, where hydroxide ions tend to reside slightly farther from the nanobubble surface than hydronium ions, forming more stable hydrogen bond networks that shield the nanobubble from dissolution. In acidic conditions, the hydronium ions preferentially accumulating at the nanobubble surface in an orderly manner drive nanobubble dissolution to increase the entropy of the system, and the dissolved nitrogen molecules further strengthen the hydrogen bond networks of systems by providing a hydrophobic environment for hydronium ions, suggesting both entropy and enthalpy effects contribute to the instability of nanobubbles under acidic conditions. These results offer fresh insights into the double-layer distribution of hydroxide and hydronium near the nitrogen-water interface that influences the dynamic behavior of bulk nanobubbles.
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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
| | - Changsheng Chen
- 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
| | - Muye Feng
- School of Mechanical and Power Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Chao Sun
- 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
- New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing 100084, China
| | - 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
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7
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Pullanchery S, Kulik S, Schönfeldová T, Egan CK, Cassone G, Hassanali A, Roke S. pH drives electron density fluctuations that enhance electric field-induced liquid flow. Nat Commun 2024; 15:5951. [PMID: 39009573 PMCID: PMC11251051 DOI: 10.1038/s41467-024-50030-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 06/26/2024] [Indexed: 07/17/2024] Open
Abstract
Liquid flow along a charged interface is commonly described by classical continuum theory, which represents the electric double layer by uniformly distributed point charges. The electrophoretic mobility of hydrophobic nanodroplets in water doubles in magnitude when the pH is varied from neutral to mildly basic (pH 7 → 11). Classical continuum theory predicts that this increase in mobility is due to an increased surface charge. Here, by combining all-optical measurements of surface charge and molecular structure, as well as electronic structure calculations, we show that surface charge and molecular structure at the nanodroplet surface are identical at neutral and mildly basic pH. We propose that the force that propels the droplets originates from two factors: Negative charge on the droplet surface due to charge transfer from and within water, and anisotropic gradients in the fluctuating polarization induced by the electric field. Both charge density fluctuations couple with the external electric field, and lead to droplet flow. Replacing chloride by hydroxide doubles both the charge conductivity via the Grotthuss mechanism, and the droplet mobility. This general mechanism deeply impacts a plethora of processes in biology, chemistry, and nanotechnology and provides an explanation of how pH influences hydrodynamic phenomena and the limitations of classical continuum theory currently used to rationalize these effects.
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Affiliation(s)
- S Pullanchery
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - S Kulik
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - T Schönfeldová
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - C K Egan
- International Centre for Theoretical Physics, Trieste, Italy
| | - G Cassone
- Institute for Physical-Chemical Processes, Italian National Research Council (IPCF-CNR), Messina, Italy
| | - A Hassanali
- International Centre for Theoretical Physics, Trieste, Italy.
| | - S Roke
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Institute of Materials Science and Engineering (IMX), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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8
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Verduci R, Creazzo F, Tavella F, Abate S, Ampelli C, Luber S, Perathoner S, Cassone G, Centi G, D'Angelo G. Water Structure in the First Layers on TiO 2: A Key Factor for Boosting Solar-Driven Water-Splitting Performances. J Am Chem Soc 2024; 146:18061-18073. [PMID: 38909313 DOI: 10.1021/jacs.4c05042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
The water hydrogen-bonded network is strongly perturbed in the first layers in contact with the semiconductor surface. Even though this aspect influences the outer-sphere electron transfer, it was not recognized that it is a crucial factor impacting the solar-driven water-splitting performances. To fill this gap, we have selected two TiO2 anatase samples (with and without B-doping), and by extensive experimental and computational investigations, we have demonstrated that the remarkable 5-fold increase in water-splitting photoactivity of the B-doped sample cannot be ascribed to effects typically associated to enhanced photocatalytic properties, such as band gap, heterojunctions, crystal facets, and other aspects. Studying these samples by combining FTIR measurements under controlled humidity with first-principles simulations sheds light on the role and nature of the first-layer water structure in contact with the photocatalyst surfaces. It turns out that the doping hampers the percolation of tetrahedrally coordinated water molecules while enhancing the population of topological H-bond defects forming approximately linear H-bonded chains. This work unveils how doping the semiconductor surface affects the local electric field, determining the water splitting rate by influencing the H-bond topologies in the first water layers. This evidence opens new prospects for designing efficient photocatalysts for water splitting.
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Affiliation(s)
- Rosaria Verduci
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science (MIFT), University of Messina, V.le F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Fabrizio Creazzo
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Francesco Tavella
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, ERIC aisbl and CASPE/INSTM, 98166 Messina, Italy
| | - Salvatore Abate
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, ERIC aisbl and CASPE/INSTM, 98166 Messina, Italy
| | - Claudio Ampelli
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, ERIC aisbl and CASPE/INSTM, 98166 Messina, Italy
| | - Sandra Luber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Siglinda Perathoner
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, ERIC aisbl and CASPE/INSTM, 98166 Messina, Italy
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Gabriele Centi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, ERIC aisbl and CASPE/INSTM, 98166 Messina, Italy
| | - Giovanna D'Angelo
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science (MIFT), University of Messina, V.le F. Stagno d'Alcontres 31, 98166 Messina, Italy
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9
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Chen C, Lu J, Zhang B, Liang T, Xiao F. Study on synergistic hydrogen generation from aluminum-based composites in different forms of water. Phys Chem Chem Phys 2024; 26:15987-15998. [PMID: 38775056 DOI: 10.1039/d3cp05429b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The environmental suitability of hydrogen storage materials is significantly influenced by the way aluminum reacts synchronously with water, ice, and water steam. The straightforward ball milling process was used to synthesize Al-based composite materials with carbon nanotubes (CNTs) or graphene oxide (GO). The reactivity of the composites in various types of water was investigated. The Al/Bi/CNT and Al/Bi/GO composites may react in liquid water, low-temperature ice, and high-temperature steam. The hydrolysis promotion of Al-based composites by CNTs is superior to that of GO, whether in liquid water at 20 °C or ice at -20 °C. The maximum hydrogen generation rate of Al/Bi/CNT composites can reach 34.6 mL g-1 s-1 at 20 °C. The hydrogen generation volume of Al/Bi/CNT can reach 700 mL g-1 in 15 min on ice at -20 °C. Moreover, the ignition temperature and ignition delay time of Al/Bi/CNT are shorter than those of Al/Bi/GO in high-temperature steam. The hydrogen generation volume from Al/Bi/CNT at 200 °C can reach 853 mL g-1. These may originate from the unique one-dimensional nanostructure of CNTs, which provides more surface area or reaction sites during the hydrolysis of the composite.
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Affiliation(s)
- Chong Chen
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, Shanxi, China.
| | - Jiaxin Lu
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, Shanxi, China.
| | - Bobo Zhang
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, Shanxi, China.
| | - Taixin Liang
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, Shanxi, China.
| | - Fei Xiao
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, Shanxi, China.
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10
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Sun L, Wang J, Chen Y. Coalescence of multiple droplets induced by a constant DC electric field. PLoS One 2024; 19:e0300925. [PMID: 38593131 PMCID: PMC11003697 DOI: 10.1371/journal.pone.0300925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/06/2024] [Indexed: 04/11/2024] Open
Abstract
In this work, the electro-coalescence process of three nanodroplets under a constant DC electric field is investigated via molecular dynamics simulations (MD), aiming to explore the electric manipulation of multiple droplets coalescence on the molecular level. The symmetrical and asymmetrical dynamic evolutions of electrocoalescence process can be observed. Our MD simulations show that there are two types of critical electric fields to induce the special dynamics. The chain configuration can be formed, when one of the critical electric field is exceeded, referred to as Ecc. On the other hand, there is another critical electric field to change the coalescence pattern from complete coalescence to partial coalescence, the so-called Ecn. Finally, we find that the use of the pulsed DC electric field can overcome the drawbacks of the constant DC electric field in the crude oil industry, and the mechanisms behind the suppressed effect of the water chain or non-coalescence are further revealed.
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Affiliation(s)
- Liwei Sun
- School of Mechanical Engineering, Changchun Automobile Industry Institute, Changchun, China
| | - Jian Wang
- College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yanhui Chen
- School of Mechanical Engineering, Changchun Automobile Industry Institute, Changchun, China
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11
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Cassone G, Martelli F. Electrofreezing of liquid water at ambient conditions. Nat Commun 2024; 15:1856. [PMID: 38424051 PMCID: PMC10904787 DOI: 10.1038/s41467-024-46131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Water is routinely exposed to external electric fields. Whether, for example, at physiological conditions, in contact with biological systems, or at the interface of polar surfaces in countless technological settings, water responds to fields on the order of a few V Å-1 in a manner that is under intense investigation. Dating back to the 19th century, the possibility of solidifying water upon applying electric fields - a process known as electrofreezing - is an alluring promise that has canalized major efforts since, with uncertain outcomes. Here, we perform long (up to 500 ps per field strength) ab initio molecular dynamics simulations of water at ambient conditions under external electric fields. We show that fields of 0.10 - 0.15 V Å-1 induce electrofreezing to a ferroelectric amorphous phase which we term f-GW (ferroelectric glassy water). The transition occurs after ~ 150 ps for a field of 0.15 V Å-1 and after ~ 200 ps for a field of 0.10 V Å-1 and is signaled by a structural and dynamic arrest and the suppression of the fluctuations of the hydrogen bond network. Our work reports evidence of electrofreezing of bulk liquid water at ambient conditions and therefore impacts several fields, from fundamental chemical physics to biology and catalysis.
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Affiliation(s)
- Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council, Viale F. Stagno d'Alcontres 37, Messina, 98158, Italy.
| | - Fausto Martelli
- IBM Research Europe, Keckwik Lane, Daresbury, WA4 4AD, UK.
- Department of Chemical Engineering, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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12
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Moncada F, Quintero W, Posada E, Pettersson LGM, Reyes A. A nuclear configuration interaction approach to study nuclear spin effects: an application to ortho- and para- 3 He 2 @C 60. Chemphyschem 2024; 25:e202300498. [PMID: 38055206 DOI: 10.1002/cphc.202300498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023]
Abstract
We introduce a non-orthogonal configuration interaction approach to investigate nuclear quantum effects on energies and densities of confined fermionic nuclei. The Hamiltonian employed draws parallels between confined systems and many-electron atoms, where effective non-Coulombic potentials represent the interactions of the trapped particles. One advantage of this method is its generality, as it offers the potential to study the nuclear quantum effects of various confined species affected by effective isotropic or anisotropic potentials. As a first application, we analyze the quantum states of two 3 He atoms encapsulated in C60 . At the Hartree-Fock level, we observe the breaking of spin and spatial symmetries. To ensure wavefunctions with the correct symmetries, we mix the broken-symmetry Hartree-Fock states within the non-orthogonal configuration interaction expansion. Our proposed approach predicts singly and triply degenerate ground states for the singlet (para-3 He2 @C60 ) and triplet (ortho-3 He2 @C60 ) nuclear spin configurations, respectively. The ortho-3 He2 @C60 ground state is 5.69 cm-1 higher in energy than the para-3 He2 @C60 ground state. The nuclear densities obtained for these states exhibit the icosahedral symmetry of the C60 embedding potential. Importantly, our calculated energies for the lowest 85 states are in close agreement with perturbation theory results based on a harmonic oscillator plus rigid rotor model of 3 He2 @C60 .
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Affiliation(s)
- Félix Moncada
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91, Stockholm, Sweden
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
| | - William Quintero
- Doctorado en Fisicoquímica Molecular, Universidad Andres Bello, Santiago de Chile, Chile
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
| | - Edwin Posada
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, USA
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
| | - Lars G M Pettersson
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91, Stockholm, Sweden
| | - Andrés Reyes
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
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13
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Pathak B, Kesari S, Patwari GN. Enticing a Proton using Single Ammonia Molecule as Bait. J Phys Chem B 2024; 128:1022-1028. [PMID: 38240575 DOI: 10.1021/acs.jpcb.3c06761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
In microhydrated acid-solvent clusters, deprotonation of an acid is assisted by a critical number of solvent molecules and a solvent electric field. Born-Oppenheimer molecular dynamics simulations reveal that trifluoroacetic acid undergoes spontaneous proton transfer in water clusters, with the critical number being five. Acetic acid and phenol, on the other hand, do not dissociate even in the presence of a large number of water molecules (in excess of 40). The addition of a single ammonia molecule to the water cluster, which interacts directly with the protic group, lowers the critical number of solvent water molecules required for proton transfer to three and seven in the case of acetic acid and phenol, respectively. The population of the undissociated and the proton-transferred structures get dispersed to form separate islands on the electric field versus the O-H distance representation with the cusp representing the critical values. The critical electric fields for the spontaneous proton transfer are around 254, 237, and 318 MV cm-1 for trifluoroacetic acid, acetic acid, and phenol, respectively. In the case of phenol, the free energy profiles suggest that proton transfer to the ammonia moiety embedded in water promotes proton transfer efficiently due to the higher basicity of ammonia and enhanced hydrogen bonding network of solvent water, vis-à-vis phenol-ammonia clusters.
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Affiliation(s)
- Bijaya Pathak
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Shaivi Kesari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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14
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Siddiqui SA, Stuyver T, Shaik S, Dubey KD. Designed Local Electric Fields-Promising Tools for Enzyme Engineering. JACS AU 2023; 3:3259-3269. [PMID: 38155642 PMCID: PMC10752214 DOI: 10.1021/jacsau.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 12/30/2023]
Abstract
Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings. Subsequently, the advances made so far in optimizing enzymatic electric fields through targeted mutations are discussed critically and concisely. The Perspective ends with an outlook on some anticipated evolutions of the field in the near future. Among others, we offer some pointers on how the recent data science/machine learning revolution, engulfing all science disciplines, could potentially provide robust and principled tools to facilitate rapid inference of electric field effects, as well as the translation between optimal electrostatic environments and corresponding chemical modifications.
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Affiliation(s)
- Shakir Ali Siddiqui
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
| | - Thijs Stuyver
- Ecole Nationale Supérieure de
Chimie de Paris, Université PSL, CNRS, Institute of Chemistry for Life and Health
Sciences, 75 005 Paris, France
| | - Sason Shaik
- Institute of Chemistry, Edmond J Safra Campus,
The Hebrew University of Jerusalem, Givat Ram, Jerusalem,
9190400, Israel
| | - Kshatresh Dutta Dubey
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
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15
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Ajide MT, English NJ. Nonequilibrium Ab Initio Molecular Dynamics Simulation of Water Splitting at Fe 2O 3-Hematite/Water Interfaces in an External Electric Field. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:24088-24105. [PMID: 38148852 PMCID: PMC10749450 DOI: 10.1021/acs.jpcc.3c05119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/28/2023]
Abstract
In the exploration of the optimal material for achieving the photoelectrochemical dissociation of water into hydrogen, hematite (α-Fe2O3) emerges as a highly promising candidate for proof-of-concept demonstrations. Recent studies suggest that the concurrent application of external electric fields could enhance the photoelectrochemical (PEC) process. To delve into this, we conducted nonequilibrium ab initio molecular dynamics (NE-AIMD) simulations in this study, focusing on hematite-water interfaces at room temperature under progressively stronger electric fields. Our findings reveal intriguing evidence of water molecule adsorption and dissociation, as evidenced by an analysis of the structural properties of the hydrated layered surface of the hematite-water interface. Additionally, we scrutinized intermolecular structures using radial distribution functions (RDFs) to explore the interaction between the hematite slab and water. Notably, the presence of a Grotthuss hopping mechanism became apparent as the electric field strength increased. A comprehensive discussion based on intramolecular geometry highlighted aspects such as hydrogen-bond lengths, H-bond angles, average H-bond numbers, and the observed correlation existing among the hydrogen-bond strength, bond-dissociation energy, and H-bond lifetime. Furthermore, we assessed the impact of electric fields on the librational, bending, and stretching modes of hydrogen atoms in water by calculating the vibrational density of states (VDOS). This analysis revealed distinct field effects for the three characteristic band modes, both in the bulk region and at the hematite-water interface. We also evaluated the charge density of active elements at the aqueous hematite surface, delving into field-induced electronic charge-density variations through the Hirshfeld charge density analysis of atomic elements. Throughout this work, we drew clear distinctions between parallel and antiparallel field alignments at the hematite-water interface, aiming to elucidate crucial differences in local behavior for each surface direction of the hematite-water interface.
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Affiliation(s)
- Mary T. Ajide
- School of Chemical &
Bioprocess Engineering, University College
Dublin, Belfield, Dublin 4, Ireland
| | - Niall J. English
- School of Chemical &
Bioprocess Engineering, University College
Dublin, Belfield, Dublin 4, Ireland
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16
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Li K, Chen B, Li M, Jiang L, Song Y, Yang M. Facilitation of Hydrate Dissociation and Structural Evolution by Major Marine Anions under Static Electric Fields. J Phys Chem B 2023; 127:10447-10457. [PMID: 37991934 DOI: 10.1021/acs.jpcb.3c06012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Electric fields have been proven to be capable of significantly affecting the equilibrium state of hydrates. In this study, the thermodynamic properties and structural changes of methane hydrate (MH) in various anion solutions in an electric field at 0.7 V/nm were investigated by molecular dynamics simulations. The presence of anions significantly enhances the instability of methane hydrates under electric fields, leading to a staged dissociation process. First, the anions coexist with MH to form a temporary metastable structure under the action of an electric field. Then, the migration of anions causes the dissociation of nearby hydrates and the formation of flow channels in the hydrate layer, which leads to the complete dissociation of MH after a period. The promotive effects of F-, Br-, I-, and Cl- ions were close, while SO42- was relatively weak. The anions are still in hydration shells in the MH phase, but the structure of the hydration shells differs slightly from that in solution (the coordination numbers of I- and SO42- ions increased). The migration resistances of multiple anions to cross the surface of the hydrate layer are similar. However, inside the hydrate phase, the anions with a larger radius have a higher migration resistance. It is difficult for SO42- ions to migrate inside the hydrate phase, and they tend to form a metastable structure on the hydrate surface. Combining our previous studies, SrCl2 solution has the best hydrate promotion under an electric field environment.
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Affiliation(s)
- Kehan Li
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian 116024, China
| | - Bingbing Chen
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian 116024, China
| | - Mingjun Li
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian 116024, China
| | - Lanlan Jiang
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian 116024, China
| | - Yongchen Song
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian 116024, China
| | - Mingjun Yang
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian 116024, China
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17
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Yadav P, Kumar P. External electric field, a potential catalyst for C-N cross-coupling reaction. Phys Chem Chem Phys 2023. [PMID: 38047469 DOI: 10.1039/d3cp04723g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The present work investigates the role of the external electric field (EEF) in boosting the C-N cross-coupling reaction between 2-chlorobenzoic acid and propylamine, by computing the reaction rates and energy barrier. The investigation suggests that the reaction can become barrierless by choosing an electric field in the appropriate direction, resulting in a quadrillionfold increase in the reaction rate in the presence of an EEF. We also found that the efficiency of the electric field depends on the dipole moment of the reactants, and hence, the results of the present work are general in nature and should be applicable to a variety of C-N cross-coupling reactions.
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Affiliation(s)
- Priyanka Yadav
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
| | - Pradeep Kumar
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
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18
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Rashid MAM, Rahman M, Acter T, Uddin N. Identifying the acidic or basic behavior of surface water: a QM/MM-MD study. Phys Chem Chem Phys 2023; 25:31194-31205. [PMID: 37955174 DOI: 10.1039/d3cp02080k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Controversies on the water surface were theoretically addressed with the help of large scale quantum mechanical molecular dynamics (QMMD) simulations on water surface model systems with and without excess hydroniums and hydroxides. It was revealed that the thermodynamic surface structures of these ions strongly depend on their location and dipole orientation. Fast hydronium diffusion by proton transfer establishes a wider kinetic depth distribution (∼6 Å) than that predicted by its thermodynamic affinity for the water surface, while slow hydroxide is shallowly trapped below the outermost molecular layer (3-4 Å). In addition, the anisotropic orientation of surface water dipole can generate a substantial magnitude of surface potential, which extends to a depth of a few molecular layers. With these distinctively different surface properties of two ions and water molecules, the seemingly contradictory observations of acidic and negatively charged water surfaces may be successfully explained. That is, the negative surface charge of neutral water mostly stems from intrinsic water properties such as water dipole orientation and electron density spillage at the surface, rather than surface OH- ions. The enhanced acidity of the water surface can be attributed in large part to the kinetic depth profile of ion density in addition to static thermodynamic origin. Furthermore, the different depth profiles of the two ions may differently affect the surface-sensitive spectroscopic observations.
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Affiliation(s)
- Md Al Mamunur Rashid
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Mofizur Rahman
- Research and Development Center, Berger Paints Bangladesh Limited, Berger House, Dhaka-1230, Bangladesh
| | - Thamina Acter
- Department of Mathematical and Physical Sciences, East West University, Aftabnagar, Dhaka-1212, Bangladesh
| | - Nizam Uddin
- Department of Nutrition and Food Engineering, Daffodil International University, Birulia, Dhaka-1216, Bangladesh.
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19
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Di Pino S, Donkor ED, Sánchez VM, Rodriguez A, Cassone G, Scherlis D, Hassanali A. ZundEig: The Structure of the Proton in Liquid Water from Unsupervised Learning. J Phys Chem B 2023; 127:9822-9832. [PMID: 37930954 DOI: 10.1021/acs.jpcb.3c06078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The structure of the excess proton in liquid water has been the subject of lively debate on both experimental and theoretical fronts for the last century. Fluctuations of the proton are typically interpreted in terms of limiting states referred to as the Eigen and Zundel species. Here, we put these ideas under the microscope, taking advantage of recent advances in unsupervised learning that use local atomic descriptors to characterize environments of acidic water combined with advanced clustering techniques. Our agnostic approach leads to the observation of only one charged cluster and two neutral ones. We demonstrate that the charged cluster involving the excess proton is best seen as an ionic topological defect in water's hydrogen bond network, forming a single local minimum on the global free-energy landscape. This charged defect is a highly fluxional moiety, where the idealized Eigen and Zundel species are neither limiting configurations nor distinct thermodynamic states. Instead, the ionic defect enhances the presence of neutral water defects through strong interactions with the network. We dub the combination of the charged and neutral defect clusters as ZundEig, demonstrating that the fluctuations between these local environments provide a general framework for rationalizing more descriptive notions of the proton in the existing literature.
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Affiliation(s)
- Solana Di Pino
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Edward Danquah Donkor
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Veronica M Sánchez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alex Rodriguez
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- Dipartimento di Matematica e Geoscienze, Universitá degli Studi di Trieste, via Alfonso Valerio 12/1, 34127 Trieste, Italy
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council (CNR-IPCF), Viale Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Damian Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ali Hassanali
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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20
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Zhang Y, Jiang B. Universal machine learning for the response of atomistic systems to external fields. Nat Commun 2023; 14:6424. [PMID: 37827998 PMCID: PMC10570356 DOI: 10.1038/s41467-023-42148-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/01/2023] [Indexed: 10/14/2023] Open
Abstract
Machine learned interatomic interaction potentials have enabled efficient and accurate molecular simulations of closed systems. However, external fields, which can greatly change the chemical structure and/or reactivity, have been seldom included in current machine learning models. This work proposes a universal field-induced recursively embedded atom neural network (FIREANN) model, which integrates a pseudo field vector-dependent feature into atomic descriptors to represent system-field interactions with rigorous rotational equivariance. This "all-in-one" approach correlates various response properties like dipole moment and polarizability with the field-dependent potential energy in a single model, very suitable for spectroscopic and dynamics simulations in molecular and periodic systems in the presence of electric fields. Especially for periodic systems, we find that FIREANN can overcome the intrinsic multiple-value issue of the polarization by training atomic forces only. These results validate the universality and capability of the FIREANN method for efficient first-principles modeling of complicated systems in strong external fields.
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Affiliation(s)
- Yaolong Zhang
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, 230026, China
- École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Bin Jiang
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, 230026, China.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, 230088, China.
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21
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Cassone G, Saija F, Sponer J, Shaik S. The Reactivity-Enhancing Role of Water Clusters in Ammonia Aqueous Solutions. J Phys Chem Lett 2023; 14:7808-7813. [PMID: 37623433 PMCID: PMC10494223 DOI: 10.1021/acs.jpclett.3c01810] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/22/2023] [Indexed: 08/26/2023]
Abstract
Among the many prototypical acid-base systems, ammonia aqueous solutions hold a privileged place, owing to their omnipresence in various planets and their universal solvent character. Although the theoretical optimal water-ammonia molar ratio to form NH4+ and OH- ion pairs is 50:50, our ab initio molecular dynamics simulations show that the tendency of forming these ionic species is inversely (directly) proportional to the amount of ammonia (water) in ammonia aqueous solutions, up to a water-ammonia molar ratio of ∼75:25. Here we prove that the reactivity of these liquid mixtures is rooted in peculiar microscopic patterns emerging at the H-bonding scale, where the highly orchestrated motion of 5 solvating molecules modulates proton transfer events through local electric fields. This study demonstrates that the reaction of water with NH3 is catalyzed by a small cluster of water molecules, in which an H atom possesses a high local electric field, much like the effect observed in catalysis by water droplets [ PNAS 2023, 120, e2301206120].
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Affiliation(s)
- Giuseppe Cassone
- Institute
for Physical-Chemical Processes, Italian
National Research Council (CNR-IPCF), Viale Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Franz Saija
- Institute
for Physical-Chemical Processes, Italian
National Research Council (CNR-IPCF), Viale Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Jiri Sponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czechia
| | - Sason Shaik
- Institute
of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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22
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Khaldi O, Ferhi H, Larbi T, Jomni F, Ben Younes R. Dielectric response of high- κ hafnium oxide under finite electric field: nonlinearities from ab initio and experimental points of view. Phys Chem Chem Phys 2023; 25:22310-22318. [PMID: 37578192 DOI: 10.1039/d3cp01552a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Herein, we report on the dielectric-voltage nonlinearities under a constant electric field in metal insulator metal (MIM) capacitor-based hafnium oxide (HfO2) with respect to the frequency range. Via the Schottky emission mechanism obtained from the current-voltage characteristic (I-V), we calculated the optical dielectric constant εr,opt for different external DC bias values. The extracted εr,opt revealed a quadratic dependence on the applied external field. This confirmed that such dependence is a common feature of high-κ oxides in the low and high frequency ranges. The results were correlated with the ab initio calculations using the finite field (FF) method as implemented in the CRYSTAL 17 code. Good agreement between the results from the FF method, I-V plots, as well as the UV-visible spectrometry is observed. To assess any change in the dielectric constant upon the application of an external electric field, several parameters such as exchange-correlation functional, basis sets (BSs), as well as supercell expansion factor (N) were tested. The corresponding parameters have a great influence on the macroscopic electron density and voltage along the field direction and thus on the optical response. For N > 2 and rich basis sets, the hybrid functional B3LYP revealed good agreement with the experimental results as compared to other Hamiltonian's forms such as LDA, PW-GGA and HF.
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Affiliation(s)
- Othmen Khaldi
- University of Tunis El Manar, Laboratory of Materials, Organization and Properties, LMOP(LR99ES17), 2092, Tunis, Tunisia.
| | - Hanen Ferhi
- University of Gafsa, Laboratory of Technology, Energy and Innovative Materials, Department of Physics, Faculty of Sciences of Gafsa, 2112, Gafsa, Tunisia
| | - Tarek Larbi
- University of Tunis El Manar, Laboratory of Nanomaterials, Nanotechnology and Energy, 2092, Tunis, Tunisia
| | - Fethi Jomni
- University of Tunis El Manar, Laboratory of Materials, Organization and Properties, LMOP(LR99ES17), 2092, Tunis, Tunisia.
| | - Rached Ben Younes
- University of Gafsa, Laboratory of Technology, Energy and Innovative Materials, Department of Physics, Faculty of Sciences of Gafsa, 2112, Gafsa, Tunisia
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23
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Conti Nibali V, Maiti S, Saija F, Heyden M, Cassone G. Electric-field induced entropic effects in liquid water. J Chem Phys 2023; 158:2889002. [PMID: 37154276 DOI: 10.1063/5.0139460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/13/2023] [Indexed: 05/10/2023] Open
Abstract
Externally applied electric fields in liquid water can induce a plethora of effects with wide implications in electrochemistry and hydrogen-based technologies. Although some effort has been made to elucidate the thermodynamics associated with the application of electric fields in aqueous systems, to the best of our knowledge, field-induced effects on the total and local entropy of bulk water have never been presented so far. Here, we report on classical TIP4P/2005 and ab initio molecular dynamics simulations measuring entropic contributions carried by diverse field intensities in liquid water at room temperature. We find that strong fields are capable of aligning large fractions of molecular dipoles. Nevertheless, the order-maker action of the field leads to quite modest entropy reductions in classical simulations. Albeit more significant variations are recorded during first-principles simulations, the associated entropy modifications are small compared to the entropy change involved in the freezing phenomenon, even at intense fields slightly beneath the molecular dissociation threshold. This finding further corroborates the idea that electrofreezing (i.e., the electric-field-induced crystallization) cannot take place in bulk water at room temperature. In addition, here, we propose a molecular-dynamics-based analysis (3D-2PT) that spatially resolves the local entropy and the number density of bulk water under an electric field, which enables us to map their field-induced changes in the environment of reference H2O molecules. By returning detailed spatial maps of the local order, the proposed approach is capable of establishing a link between entropic and structural modifications with atomistic resolution.
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Affiliation(s)
- Valeria Conti Nibali
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, 98166 Messina, Italy
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
| | - Sthitadhi Maiti
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
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24
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Datar A, Wright C, Matthews DA. Theoretical Investigation of the X-ray Stark Effect in Small Molecules. J Phys Chem A 2023; 127:1576-1587. [PMID: 36787229 DOI: 10.1021/acs.jpca.2c08311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We have studied the Stark effect in the soft x-ray region for various small molecules by calculating the field-dependent x-ray absorption spectra. This effect is explained in terms of the response of molecular orbitals (core and valence), the molecular dipole moment, and the molecular geometry to the applied electric field. A number of consistent trends are observed linking the computed shifts in absorption energies and intensities with specific features of the molecular electronic structure. We find that both the virtual molecular orbitals (valence and/or Rydberg) as well as the core orbitals contribute to observed trends in a complementary fashion. This initial study highlights the potential impact of x-ray Stark spectroscopy as a tool to study electronic structure and environmental perturbations at a submolecular scale.
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Affiliation(s)
- Avdhoot Datar
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Catherine Wright
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Devin A Matthews
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
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25
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Chen B, Li K, Sun H, Jiang L, Yang M, Song Y. Promoting Effect of Common Marine Cations on Hydrate Dissociation and Structural Evolution under a Static Electric Field. J Phys Chem B 2023; 127:698-709. [PMID: 36629388 DOI: 10.1021/acs.jpcb.2c05382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Natural gas hydrate, a potential energy resource, is attracting worldwide attention. In this study, we propose a new method of hydrate dissociation which uses seawater and electrostatic fields (SE method) cooperatively. The hydrate molecular dissociation mechanism of gas hydrate is a key issue in studying the kinetic properties of gas hydrate using the SE method. Therefore, molecular dynamics simulations were used to investigate the thermodynamic properties and structural changes of methane hydrate (MH) in multiple kinds of salt solutions under an electrostatic field. The results show that the electric field can drive cations into the MH phase to form a series of random semiopen cages, which are essentially temporary and metastable. The variation in free energy indicates that it is more difficult for divalent cations to enter the hydrate phase than monovalent cations, meaning that the hydrate structures formed with divalent cations are more unstable. Then, the ion current occurred in the hydrate phase (called ion migration in this study), which greatly accelerated hydrate dissociation. In contrast, the promotion effect of cations with the same charge on MH dissociation is as follows: Sr2+ > K+ ≈ Na+ > Ca2+ ≈ Mg2+. In general, the presence of common marine cations enhanced the promotion effect of the electric field on gas hydrate dissociation.
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Affiliation(s)
- Bingbing Chen
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian116024, China
| | - Kehan Li
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian116024, China
| | - Huiru Sun
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian116024, China
| | - Lanlan Jiang
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian116024, China
| | - Mingjun Yang
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian116024, China
| | - Yongchen Song
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian116024, China
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Feng K, Wang J, Hao S, Xie J. Molecular Dynamics Study of Interfacial Micromechanical Behaviors of 6H-SiC/Al Composites under Uniaxial Tensile Deformation. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:404. [PMID: 36770365 PMCID: PMC9919560 DOI: 10.3390/nano13030404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
This paper investigated the micromechanical behavior of different 6H-SiC/Al systems during the uniaxial tensile loading by using molecular dynamics simulations. The results showed that the interface models responded diversely to the tensile stress when the four low-index surfaces of the Al were used as the variables of the joint surfaces. In terms of their stress-strain properties, the SiC(0001)/Al(001) models exhibited the highest tensile strength and the smallest elongation, while the other models produced certain deformations to relieve the excessive strain, thus increasing the elongation. The SiC(0001)/Al(110) models exhibited the largest elongations among all the models. From the aspect of their deformation characteristics, the SiC(0001)/Al(001) model performed almost no plastic deformation and dislocations during the tensile process. The deformation of the SiC(0001)/Al(110) model was dominated by the slip of the 1/6 <112> Shockley partial dislocations, which contributed to the intersecting stacking faults in the model. The SiC(0001)/Al(111) model produced a large number of dislocations under the tensile loading. Dislocation entanglement was also found in the model. Meanwhile, a unique defect structure consisting of three 1/6 <110> stair-rod dislocations and three stacking faults were found in the model. The plastic deformation in the SiC(0001)/Al(112) interface model was restricted by the L-C lock and was carried out along the 1/6 <110> stair-rod dislocations' direction. These results reveal the interfacial micromechanical behaviors of the 6H-SiC/Al composites and demonstrate the complexity of the deformation systems of the interfaces under stress.
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Affiliation(s)
- Kai Feng
- School of Physics and Microelectronics, Zhengzhou University, Zhengzhou 450052, China
| | - Jiefang Wang
- School of Physics and Microelectronics, Zhengzhou University, Zhengzhou 450052, China
| | - Shiming Hao
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Jingpei Xie
- School of Materials Science and Engineering, Henan University of Science and Technology, Luoyang 471023, China
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Liu J, Liu R, Cao Y, Chen M. Solvation structures of calcium and magnesium ions in water with the presence of hydroxide: a study by deep potential molecular dynamics. Phys Chem Chem Phys 2023; 25:983-993. [PMID: 36519362 DOI: 10.1039/d2cp04105g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The solvation structures of calcium (Ca2+) and magnesium (Mg2+) ions with the presence of hydroxide (OH-) ion in water are essential for understanding their roles in biological and chemical processes but have not been fully explored. Ab initio molecular dynamics (AIMD) is an important tool to address this issue, but two challenges exist. First, an accurate description of OH- from AIMD needs an appropriate exchange-correlation functional. Second, a long trajectory is needed to reach an equilibrium state for the Ca2+-OH- and Mg2+-OH- ion pairs in aqueous solutions. Herein, we adopt a deep potential molecular dynamics (DPMD) method to simulate 1 ns trajectories for the Ca2+-OH- and Mg2+-OH- ion pairs in water; the DPMD method provides efficient machine-learning-based models that have the accuracy of the SCAN exchange-correlation functional within the framework of density functional theory. The solvation structures of the cations and the OH- in terms of three different species have been systematically investigated. On the one hand, we find that OH- have more significant effects on the solvation structure of Ca2+ than that of Mg2+. We observe that the OH- substantially affects the orientation angles of water molecules surrounding the cation. Through the time correlation functions, we conclude that the water molecules in the first solvation shell of Ca2+ change their preferred orientation faster than those of Mg2+. On the other hand, with the presence of the cation in the first solvation shell of OH-, we find that the hydrogen bonds of OH- are severely altered, and the adjacent water molecules of OH- are squeezed. The two cations have substantially different effects on the solvation structure of OH-. Our work provides new insight into the solvation structures of Ca2+ and Mg2+ in water with the presence of OH-.
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Affiliation(s)
- Jianchuan Liu
- HEDPS, CAPT, College of Engineering and School of Physics, Peking University, Beijing, 100871, China.
| | - Renxi Liu
- HEDPS, CAPT, College of Engineering and School of Physics, Peking University, Beijing, 100871, China. .,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yu Cao
- HEDPS, CAPT, College of Engineering and School of Physics, Peking University, Beijing, 100871, China.
| | - Mohan Chen
- HEDPS, CAPT, College of Engineering and School of Physics, Peking University, Beijing, 100871, China. .,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
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28
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Lamaire A, Cools-Ceuppens M, Bocus M, Verstraelen T, Van Speybroeck V. Quantum Free Energy Profiles for Molecular Proton Transfers. J Chem Theory Comput 2022; 19:18-24. [PMID: 36563337 PMCID: PMC9835831 DOI: 10.1021/acs.jctc.2c00874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although many molecular dynamics simulations treat the atomic nuclei as classical particles, an adequate description of nuclear quantum effects (NQEs) is indispensable when studying proton transfer reactions. Herein, quantum free energy profiles are constructed for three typical proton transfers, which properly take NQEs into account using the path integral formalism. The computational cost of the simulations is kept tractable by deriving machine learning potentials. It is shown that the classical and quasi-classical centroid free energy profiles of the proton transfers deviate substantially from the exact quantum free energy profile.
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29
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Cassone G, Sponer J, Sponer JE, Saija F. Electrofreezing of Liquid Ammonia. J Phys Chem Lett 2022; 13:9889-9894. [PMID: 36255376 PMCID: PMC9619927 DOI: 10.1021/acs.jpclett.2c02576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 05/25/2023]
Abstract
Here we prove that, in addition to temperature and pressure, another important thermodynamic variable permits the exploration of the phase diagram of ammonia: the electric field. By means of (path integral) ab initio molecular dynamics simulations, we predict that, upon applying intense electric fields on ammonia, the electrofreezing phenomenon occurs, leading the liquid toward a novel ferroelectric solid phase. This study proves that electric fields can generally be exploited as the access key to otherwise-unreachable regions in phase diagrams, unveiling the existence of new condensed-phase structures. Furthermore, the reported findings have manifold practical implications, from the safe storage and transportation of ammonia to the understanding of the solid structures this compound forms in planetary contexts.
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Affiliation(s)
- Giuseppe Cassone
- Institute
for Chemical-Physical Processes, National
Research Council of Italy, Viale F. Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Jiri Sponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czechia
- Regional
Center of Advanced Technologies and Materials, The Czech Advanced
Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 77900 Olomouc, Czechia
| | - Judit E. Sponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czechia
| | - Franz Saija
- Institute
for Chemical-Physical Processes, National
Research Council of Italy, Viale F. Stagno d’Alcontres 37, 98158 Messina, Italy
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30
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Bhateja Y, Ghosh R, Sponer J, Majumdar S, Cassone G. A Cr 2O 3-doped graphene sensor for early diagnosis of liver cirrhosis: a first-principles study. Phys Chem Chem Phys 2022; 24:21372-21380. [PMID: 36043859 DOI: 10.1039/d2cp01793h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liver cirrhosis is among the leading causes of death worldwide. Because of its asymptomatic evolution, timely diagnosis of liver cirrhosis via non-invasive techniques is currently under investigation. Among the diagnostic methods employing volatile organic compounds directly detectable from breath, sensing of limonene (C10H16) represents one of the most promising strategies for diagnosing alcohol liver diseases, including cirrhosis. In the present work, by means of state-of-the-art Density Functional Theory calculations including the U correction, we present an investigation on the sensing capabilities of a chromium-oxide-doped graphene (i.e., Cr2O3-graphene) structure toward limonene detection. In contrast with other structures such as g-triazobenzol (g-C6N6) monolayers and germanane, which revealed their usefulness in detecting limonene via physisorption, the proposed Cr2O3-graphene heterostructure is capable of undergoing chemisorption upon molecular approaching of limonene over its surface. In fact, a high adsorption energy is recorded (∼-1.6 eV). Besides, a positive Moss-Burstein effect is observed upon adsorption of limomene on the Cr2O3-graphene heterostructure, resulting in a net increase of the bandgap (∼50%), along with a sizeable shift of the Fermi level toward the conduction band. These findings pave the way toward the experimental validation of such predictions and the employment of Cr2O3-graphene heterostructures as sensors of key liver cirrhosis biomarkers.
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Affiliation(s)
- Yuvam Bhateja
- Dept. of Physics, Politecnico Di Milano, Piazza Leonardo da Vinci, 32, 20133 Milano, Italy.
| | - Ritam Ghosh
- Nil Ratan Sircar Medical College and Hospital, Raja Bazar 138, 700014 Kolkata, India
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czechia
| | - Sanhita Majumdar
- Center of Excellence for Green Energy and Sensor Systems, Indian Institute of Engineering Science and Technology, Shibpur, Botanical Garden Road, 711103 Howrah, India.
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy, Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy.
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31
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Amante G, Sponer JE, Sponer J, Saija F, Cassone G. A Computational Quantum-Based Perspective on the Molecular Origins of Life’s Building Blocks. ENTROPY 2022; 24:e24081012. [PMID: 35892991 PMCID: PMC9394336 DOI: 10.3390/e24081012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022]
Abstract
The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter—including its quantum nature—under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schro¨dinger equation at different levels of approximation (i.e., density functional theory)—such as ab initio molecular dynamics—and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life.
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Affiliation(s)
- Gabriele Amante
- Department of Mathematical and Computer Science, Physical Sciences and Earth Sciences, Università degli Studi di Messina, V. le F. Stagno d’Alcontres 31, 98166 Messina, Italy;
| | - Judit E. Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Franz Saija
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
- Correspondence: (F.S.); (G.C.)
| | - Giuseppe Cassone
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
- Correspondence: (F.S.); (G.C.)
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32
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Thomsen B, Shiga M. Structures of liquid and aqueous water isotopologues at ambient temperature from ab initio path integral simulations. Phys Chem Chem Phys 2022; 24:10851-10859. [PMID: 35504275 DOI: 10.1039/d2cp00499b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The heavy hydrogen isotopes D and T are found in trace amounts in water, and when their concentration increases they can play an intricate role in modulating the physical properties of the liquid. We present an analysis of the microscopic structures of ambient light water (H2O(l)), heavy water (D2O(l)), T2O(l), HDO(aq) and HTO(aq) studied by ab initio path integral molecular dynamics (PIMD). Unlike previous ab initio PIMD investigations of H2O(l) and D2O(l) [Chen et al., Phys. Rev. Lett., 2003, 91, 215503] [Machida et al., J. Chem. Phys., 2017, 148, 102324] we find that D2O(l) is more structured than H2O(l), as is predicted by the experiment. The agreement between the experiment and our simulation for H2O(l) and D2O(l) allows us to accurately predict the intra- and intermolecular structures of T2O(l) HDO(aq) and HTO(aq). T2O(l) is found to have a similar intermolecular structure to that of D2O(l), while the intramolecular structure is more compact, giving rise to a smaller dipole moment than those of H2O(l) and D2O(l). For the mixed isotope species, HDO(aq) and HTO(aq), we find smaller dipole moments and fewer hydrogen bonds when compared with the pure species H2O and D2O. We can attribute this effect to the relative compactness of the mixed isotope species, which results in a lower dipole moment than that of the pure species.
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Affiliation(s)
- Bo Thomsen
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba, 277-0871, Japan.
| | - Motoyuki Shiga
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba, 277-0871, Japan.
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33
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Schneider AL, Albrecht AV, Huang K, Germann MW, Poon GMK. Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields. Life (Basel) 2022; 12:life12050666. [PMID: 35629334 PMCID: PMC9143812 DOI: 10.3390/life12050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/22/2022] Open
Abstract
Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers, particularly DNA, well into the µs timescale. The continued utility of these forcefields depends in part on expanding the residue set in step with advancing nucleic acid chemistry and biology. A key step in parameterizing new residues is charge derivation which is self-consistent with the existing residues. As atomic charges are derived by fitting against molecular electrostatic potentials, appropriate structural models are critical. Benchmarking against the existing charge set used in current AMBER nucleic acid forcefields, we report that quantum mechanical models of deoxynucleosides, even at a high level of theory, are not optimal structures for charge derivation. Instead, structures from molecular mechanics minimization yield charges with up to 6-fold lower RMS deviation from the published values, due to the choice of such an approach in the derivation of the original charge set. We present a contemporary protocol for rendering self-consistent charges as well as optimized charges for a panel of nine non-canonical residues that will permit comparison with literature as well as studying the dynamics of novel DNA polymers.
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Affiliation(s)
- Amelia L. Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Amanda V. Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
| | - Gregory M. K. Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
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34
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Li C, Paesani F, Voth GA. Static and Dynamic Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature with Path Integral Simulations at Ambient Temperature. J Chem Theory Comput 2022; 18:2124-2131. [PMID: 35263110 PMCID: PMC9059465 DOI: 10.1021/acs.jctc.1c01223] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the overstructuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. We find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature.
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Affiliation(s)
- Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, Materials Science and Engineering, and San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637
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35
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Binding of Arsenic by Common Functional Groups: An Experimental and Quantum-Mechanical Study. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Arsenic is a well-known contaminant present in different environmental compartments and in human organs and tissues. Inorganic As(III) represents one of the most dangerous arsenic forms. Its toxicity is attributed to its great affinity with the thiol groups of proteins. Considering the simultaneous presence in all environmental compartments of other common functional groups, we here present a study aimed at evaluating their contribution to the As(III) complexation. As(III) interactions with four (from di- to hexa-) carboxylic acids, five (from mono- to penta-) amines, and four amino acids were evaluated via experimental methods and, in simplified systems, also by quantum-mechanical calculations. Data were analyzed also with respect to those previously reported for mixed thiol-carboxylic ligands to evaluate the contribution of each functional group (-SH, -COOH, and -NH2) toward the As(III) complexation. Formation constants of As(III) complex species were experimentally determined, and data were analyzed for each class of ligand. An empirical relationship was reported, taking into account the contribution of each functional group to the complexation process and allowing for a rough estimate of the stability of species in systems where As(III) and thiol, carboxylic, or amino groups are involved. Quantum-mechanical calculations allowed for the evaluation and the characterization of the main chelation reactions of As(III). The potential competitive effects of the investigated groups were evaluated using cysteine, a prototypical species possessing all the functional groups under investigation. Results confirm the higher binding capabilities of the thiol group under different circumstances, but also indicate the concrete possibility of the simultaneous binding of As(III) by the thiol and the carboxylic groups.
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36
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Li C, Voth GA. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J Chem Theory Comput 2022; 18:599-604. [PMID: 34982562 PMCID: PMC8864787 DOI: 10.1021/acs.jctc.1c01085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ab initio molecular dynamics (AIMD) has become one of the most popular and robust approaches for modeling complicated chemical, liquid, and material systems. However, the formidable computational cost often limits its widespread application in simulations of the largest-scale systems. The situation becomes even more severe in cases where the hydrogen nuclei may be better described as quantized particles using a path integral representation. Here, we present a computational approach that combines machine learning with recent advances in path integral contraction schemes, and we achieve a 2 orders of magnitude acceleration over direct path integral AIMD simulation while at the same time maintaining its accuracy.
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37
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Liu N, Wu Q, Li Q, Scheiner S. Promotion of TH 3 (T = Si and Ge) group transfer within a tetrel bond by a cation-π interaction. Phys Chem Chem Phys 2022; 24:1113-1119. [PMID: 34927648 DOI: 10.1039/d1cp05323j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The possibility of the transfer of the TH3 group across a tetrel bond is considered by ab initio calculations. The TB is constructed by pairing PhTH3 (Ph = phenyl; T = Si and Ge) with bases NH3, NHCH2, and the C3N2H4 carbene. The TH3 moves toward the base but only by a small amount in these dimers. However, when a Be2+ or Mg2+ dication is placed above the phenyl ring, the tetrel bond strength is greatly magnified reaching up to nearly 100 kcal mol-1. This dication also induces a much higher degree of transfer which can be best categorized as half-transfer for the two N-bases and a near complete transfer for the carbene.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Qiaozhuo Wu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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38
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Creazzo F, Luber S. Water-Assisted Chemical Route Towards the Oxygen Evolution Reaction at the Hydrated (110) Ruthenium Oxide Surface: Heterogeneous Catalysis via DFT-MD and Metadynamics Simulations. Chemistry 2021; 27:17024-17037. [PMID: 34486184 PMCID: PMC9293344 DOI: 10.1002/chem.202102356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 11/15/2022]
Abstract
Notwithstanding that RuO2 is a promising catalyst for the oxygen evolution reaction (OER), a plethora of fundamental details on its catalytic properties are still elusive, severely limiting its large‐scale deployment. It is also established experimentally that corrosion and wettability of metal oxides can, in fact, enhance the catalytic activity for OER owing to the formation of a hydrated surface layer. However, the mechanistic interplay between surface wettability, interfacial water dynamics and OER across RuO2, and what degree these processes are correlated are still debated. Herein, spin‐polarized Density Functional Theory Molecular Dynamics (DFT‐MD) simulations, coupled with advanced enhanced sampling methods in the well‐tempered metadynamics framework, are applied to gain a global understanding of RuO2 aqueous interface (explicit water solvent) in catalyzing the OER, and hence possibly help in the design of novel catalysts in the context of photochemical water oxidation. The present study quantitatively assesses the free‐energy barriers behind the OER at the (110)‐RuO2 catalyst surface revealing plausible pathways composing the reaction network of the O2 evolution. In particular, OER is investigated at room temperature when such a surface is exposed to both gas‐phase and liquid‐phase water. Albeit a unique efficient pathway has been identified in the gas‐phase OER, a surprisingly lowest‐free‐energy‐requiring reaction route is possible when (110)‐RuO2 is in contact with explicit liquid water. By estimating the free‐energy surfaces associated to these processes, we reveal a noticeable water‐assisted OER mechanism which involves a crucial proton‐transfer‐step assisted by the local water environment. These findings pave the way toward the systematic usage of DFT‐MD coupled with metadynamics techniques for the fine assessment of the activity of catalysts, considering finite‐temperature and explicit‐solvent effects.
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Affiliation(s)
- Fabrizio Creazzo
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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Cassone G, Sponer J, Saija F. Molecular dissociation and proton transfer in aqueous methane solution under an electric field. Phys Chem Chem Phys 2021; 23:25649-25657. [PMID: 34782902 DOI: 10.1039/d1cp04202e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methane-water mixtures are ubiquitous in our solar system and they have been the subject of a wide variety of experimental, theoretical, and computational studies aimed at understanding their behaviour under disparate thermodynamic scenarios, up to extreme planetary ice conditions of pressures and temperatures [Lee and Scandolo, Nat. Commun., 2011, 2, 185]. Although it is well known that electric fields, by interacting with condensed matter, can produce a range of catalytic effects which can be similar to those observed when material systems are pressurised, to the best of our knowledge, no quantum-based computational investigations of methane-water mixtures under an electric field have been reported so far. Here we present a study relying upon state-of-the-art ab initio molecular dynamics simulations where a liquid aqueous methane solution is exposed to strong oriented static and homogeneous electric fields. It turns out that a series of field-induced effects on the dipoles, polarisation, and the electronic structure of both methane and water molecules are recorded. Moreover, upon increasing the field strength, increasing fractions of water molecules are not only re-oriented towards the field direction, but are also dissociated by the field, leading to the release of oxonium and hydroxyde ions in the mixture. However, in contrast to what is observed upon pressurisation (∼50 GPa), where the presence of the water counterions triggers methane ionisation and other reactions, methane molecules preserve their integrity up to the strongest field explored (i.e., 0.50 V Å-1). Interestingly, neither the field-induced molecular dissociation of neat water (i.e., 0.30 V Å-1) nor the proton conductivity typical of pure aqueous samples at these field regimes (i.e., 1.3 S cm-1) are affected by the presence of hydrophobic interactions, at least in a methane-water mixture containing a molar fraction of 40% methane.
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Affiliation(s)
- Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy.
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolska 135, 61265 Brno, Czech Republic
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy.
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40
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Thomsen B, Shiga M. Ab initio study of nuclear quantum effects on sub- and supercritical water. J Chem Phys 2021; 155:194107. [PMID: 34800944 DOI: 10.1063/5.0071857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The structures of water in the ambient, subcritical, and supercritical conditions at various densities were studied systematically by ab initio path integral molecular dynamics simulations. It was found that the nuclear quantum effects (NQEs) have a significant impact on the structure of hydrogen bonds in close contact, not only in the ambient condition but also in the sub- and supercritical conditions. The NQEs on the structure beyond the hydrogen bond contact are important in ambient water, but not much for water in the sub- and supercritical conditions. The NQEs are furthermore important for determining the number of hydrogen bonds in the ambient conditions, and this role is, however, diminished in the sub- and supercritical conditions. The NQEs do, nevertheless, show their importance in determining the intramolecular structure of water and the close contact structures of the hydrogen bonds, even at sub- and supercritical conditions. Using the RPBE-D3 functional, the computed radial distribution functions for ambient water are in excellent agreement with experimental data, upgrading our previous results using the BLYP-D2 functional [Machida et al., J. Chem. Phys. 148, 102324 (2018)]. The computed radial distribution functions for water in the sub- and supercritical conditions were carefully compared with experiment. In particular, we found that the first peak in hydrogen pair distribution functions matches only when the NQEs are taken into account.
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Affiliation(s)
- Bo Thomsen
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Motoyuki Shiga
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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41
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Daivis PJ, Hansen JS, Todd BD. Electropumping of nanofluidic water by linear and angular momentum coupling: theoretical foundations and molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:25003-25018. [PMID: 34739012 DOI: 10.1039/d1cp04139h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this article we review the relatively new phenomenon of electropumping in nanofluidic systems, in which nonzero net flow results when polar molecules are rotated by external electric fields. The flow is a consequence of coupling of the spin angular momentum of molecules with their linear streaming momentum. By devising confining surfaces that are asymmetric - specifically one surface is more hydrophobic compared to the other - unidirectional flow results and so pumping can be achieved without the use of pressure gradients. We first cover the historical background to this phenomenon and follow that with a detailed theoretical description of the governing hydrodynamics. Following that we summarise work that has applied this phenomenon to pump water confined to planar nanochannels, semi-functionalised single carbon nanotubes and concentric carbon nanotubes. We also report on the energy efficiency of this pumping technique by comparisons with traditional flows of planar Couette and Poiseuille flow, with the surprising conclusion that electropumping at the nanoscale is some 4 orders of magnitude more efficient than pumping by Poiseuille flow.
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Affiliation(s)
- Peter J Daivis
- School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia.
| | - J S Hansen
- "Glass and Time", IMFUFA, Department of Science and Environment, Roskilde University, Roskilde 4000, Denmark.
| | - B D Todd
- Department of Mathematics, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia.
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42
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Pei Z, Qiao Q, Gong C, Wei D, Coote ML. Electrostatic effects in N-heterocyclic carbene catalysis: revealing the nature of catalysed decarboxylation. Phys Chem Chem Phys 2021; 23:24627-24633. [PMID: 34719698 DOI: 10.1039/d1cp04444c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum chemistry is used to investigate the nature of protonated N-heterocyclic carbene (NHC·H+) catalysed decarboxylation recently reported by Zhang et al. (ACS Catal., 2021, 11, 3443-3454). Our results show that there are strong electrostatic effects within the NHC·H+ catalysed decarboxylation, and these dominate hydrogen bonding. At the same time, energy decomposition analyses and comparison between the original NHC·H+ catalyst and a truncated form reveal that stabilizing dispersion interactions are also critical, as is induction. We also show that the electrostatic effects and their associated catalytic effects can be further enhanced using charged functional groups.
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Affiliation(s)
- Zhipeng Pei
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Qinyu Qiao
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Cunxi Gong
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Donghui Wei
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Michelle L Coote
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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Previti E, Foti C, Giuffrè O, Saija F, Sponer J, Cassone G. Ab initio molecular dynamics simulations and experimental speciation study of levofloxacin under different pH conditions. Phys Chem Chem Phys 2021; 23:24403-24412. [PMID: 34693952 DOI: 10.1039/d1cp03942c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Levofloxacin is an extensively employed broad-spectrum antibiotic belonging to the fluoroquinolone class. Despite the extremely wide usage of levofloxacin for a plethora of diseases, the molecular characterization of this antibiotic appears quite poor in the literature. Moreover, the acid-base properties of levofloxacin - crucial for the design of efficient removal techniques from wastewaters - have never extensively been investigated so far. Here we report on a study on the behavior of levofloxacin under standard and diverse pH conditions in liquid water by synergistically employing static quantum-mechanical calculations along with experimental speciation studies. Furthermore, with the aim of characterizing the dynamics of the water solvation shells as well as the protonation and deprotonation mechanisms, here we present the unprecedented quantum-based simulation of levofloxacin in aqueous environments by means of state-of-the-art density-functional-theory-based molecular dynamics. This way, we prove the cooperative role played by the aqueous hydration shells in assisting the proton transfer events and, more importantly, the key place held by the nitrogen atom binding the methyl group of levofloxacin in accepting excess protons eventually present in water. Finally, we also quantify the energetic contribution associated with the presence of a H-bond internal to levofloxacin which, on the one hand, stabilizes the ground-state molecular structure of this antibiotic and, on the other, hinders the first deprotonation step of this fluoroquinolone. Among other things, the synergistic employment of quantum-based calculations and speciation experiments reported here paves the way toward the development of targeted removal approaches of drugs from wastewaters.
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Affiliation(s)
- Emanuele Previti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Salita Sperone 31, 98166 Messina, Italy.
| | - Claudia Foti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Salita Sperone 31, 98166 Messina, Italy.
| | - Ottavia Giuffrè
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Salita Sperone 31, 98166 Messina, Italy.
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), Viale Stagno d'Alcontres 37, 98158 Messina, Italy.
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czechia
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), Viale Stagno d'Alcontres 37, 98158 Messina, Italy.
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Dan L, Zhang K, Huang Z, Wang F, Wang Q, Li J. Molecular-level evaluation of ionic transport under external electric fields in biological dielectric liquids. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Shenderovich IG, Denisov GS. Modeling of the Response of Hydrogen Bond Properties on an External Electric Field: Geometry, NMR Chemical Shift, Spin-Spin Scalar Coupling. Molecules 2021; 26:molecules26164967. [PMID: 34443575 PMCID: PMC8399935 DOI: 10.3390/molecules26164967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/15/2022] Open
Abstract
The response of the geometric and NMR properties of molecular systems to an external electric field has been studied theoretically in a wide field range. It has been shown that this adduct under field approach can be used to model the geometric and spectral changes experienced by molecular systems in polar media if the system in question has one and only one bond, the polarizability of which significantly exceeds the polarizability of other bonds. If this requirement is met, then it becomes possible to model even extreme cases, for example, proton dissociation in hydrogen halides. This requirement is fulfilled for many complexes with one hydrogen bond. For such complexes, this approach can be used to facilitate a detailed analysis of spectral changes associated with geometric changes in the hydrogen bond. For example, in hydrogen-bonded complexes of isocyanide C≡15N-1H⋯X, 1J(15N1H) depends exclusively on the N-H distance, while δ(15N) is also slightly influenced by the nature of X.
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Affiliation(s)
- Ilya G. Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
- Department of Physics, St. Petersburg State University, 198504 St. Petersburg, Russia;
- Correspondence:
| | - Gleb S. Denisov
- Department of Physics, St. Petersburg State University, 198504 St. Petersburg, Russia;
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46
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Cassone G, Sponer J, Saija F. Ab Initio Molecular Dynamics Studies of the Electric-Field-Induced Catalytic Effects on Liquids. Top Catal 2021. [DOI: 10.1007/s11244-021-01487-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Electric Field and Temperature Effects on the Ab Initio Spectroscopy of Liquid Methanol. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11125457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although many H-bonded systems have been extensively investigated by means of infrared (IR) spectroscopy, the vibrational response to externally applied electric fields of polar liquids remains poorly investigated. However, local electric fields along with quantum-mechanical interactions rule the behavior of H-bonded samples at the molecular level. Among the many H-bonded systems, liquid methanol holds a key place in that it exhibits a very simple H-bond network where, on average, each molecule acts as a single H-bond donor and, at the same time, as a single H-bond acceptor. Here we report on the IR spectra emerging from a series of state-of-the-art ab initio molecular dynamics simulations of bulk liquid methanol under the action of static and homogeneous electric fields. In addition, the same analysis is here conducted in the absence of the external field and for different temperatures. Although some electric-field-induced effects resemble the response of other polar liquids (such as the global contraction of the IR spectrum upon field exposure), it turns out that, distinctly from water, the “electrofreezing” phenomenon is unlikely to happen in liquid methanol. Finally, we provide atomistic analyses magnifying the completely different nature of electric-field- and temperature-induced effects on bulk liquid methanol and on its vibrational response.
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48
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Qin J, Liu Z, Zhao W, Wang D, Zhang Y, Zhong Y, Zhang X, Wang Z, Hu C, Liu J. Hydrogen Transportation Behaviour of V-Ni Solid Solution: A First-Principles Investigation. MATERIALS (BASEL, SWITZERLAND) 2021; 14:2603. [PMID: 34067643 PMCID: PMC8155835 DOI: 10.3390/ma14102603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022]
Abstract
Hydrogen embrittlement causes deterioration of materials used in metal-hydrogen systems. Alloying is a good option for overcoming this issue. In the present work, first-principles calculations were performed to systematically study the effects of adding Ni on the stability, dissolution, trapping, and diffusion behaviour of interstitial/vacancy H atoms of pure V. The results of lattice dynamics and solution energy analyses showed that the V-Ni solid solutions are dynamically and thermodynamically stable, and adding Ni to pure V can reduce the structural stability of various VHx phases and enhance their resistance to H embrittlement. H atoms preferentially occupy the characteristic tetrahedral interstitial site (TIS) and the octahedral interstitial site (OIS), which are composed by different metal atoms, and rapidly diffuse along both the energetically favourable TIS → TIS and OIS → OIS paths. The trapping energy of monovacancy H atoms revealed that Ni addition could help minimise the H trapping ability of the vacancies and suppress the retention of H in V. Monovacancy defects block the diffusion of H atoms more than the interstitials, as determined from the calculated H-diffusion barrier energy data, whereas Ni doping contributes negligibly toward improving the H-diffusion coefficient.
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Affiliation(s)
- Jiayao Qin
- Guangxi Key Laboratory of Information Materials, School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin 541004, China; (J.Q.); (Z.L.); (D.W.); (Y.Z.); (Y.Z.)
- Key Laboratory of Advanced Energy Storage Materials of Guangdong Province, School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China;
| | - Zhigao Liu
- Guangxi Key Laboratory of Information Materials, School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin 541004, China; (J.Q.); (Z.L.); (D.W.); (Y.Z.); (Y.Z.)
| | - Wei Zhao
- Key Laboratory of Advanced Energy Storage Materials of Guangdong Province, School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China;
| | - Dianhui Wang
- Guangxi Key Laboratory of Information Materials, School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin 541004, China; (J.Q.); (Z.L.); (D.W.); (Y.Z.); (Y.Z.)
| | - Yanli Zhang
- Guangxi Key Laboratory of Information Materials, School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin 541004, China; (J.Q.); (Z.L.); (D.W.); (Y.Z.); (Y.Z.)
| | - Yan Zhong
- Guangxi Key Laboratory of Information Materials, School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin 541004, China; (J.Q.); (Z.L.); (D.W.); (Y.Z.); (Y.Z.)
| | - Xiaohui Zhang
- College of Materials and Chemical Engineering, Hezhou University, Hezhou 542899, China;
| | - Zhongmin Wang
- Guangxi Key Laboratory of Information Materials, School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin 541004, China; (J.Q.); (Z.L.); (D.W.); (Y.Z.); (Y.Z.)
- College of Materials and Chemical Engineering, Hezhou University, Hezhou 542899, China;
| | - Chaohao Hu
- Guangxi Key Laboratory of Information Materials, School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin 541004, China; (J.Q.); (Z.L.); (D.W.); (Y.Z.); (Y.Z.)
| | - Jiangwen Liu
- Key Laboratory of Advanced Energy Storage Materials of Guangdong Province, School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China;
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Shenderovich IG. 1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution. Molecules 2021; 26:molecules26051390. [PMID: 33806666 PMCID: PMC7961616 DOI: 10.3390/molecules26051390] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its 31P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this 31P chemical shift. This approach has been tested on a variety of the metals of groups 8-12 and molecular structures. General recommendations for appropriate basis sets are reported.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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50
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Thomsen B, Shiga M. Nuclear quantum effects on autoionization of water isotopologs studied by ab initio path integral molecular dynamics. J Chem Phys 2021; 154:084117. [PMID: 33639728 DOI: 10.1063/5.0040791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this study, we investigate the nuclear quantum effects (NQEs) on the acidity constant (pKA) of liquid water isotopologs under the ambient condition by path integral molecular dynamics (PIMD) simulations. We compared simulations using a fully explicit solvent model with a classical polarizable force field, density functional tight binding, and ab initio density functional theory, which correspond to empirical, semiempirical, and ab initio PIMD simulations, respectively. The centroid variable with respect to the proton coordination number of a water molecule was restrained to compute the gradient of the free energy, which measures the reversible work of the proton abstraction for the quantum mechanical system. The free energy curve obtained by thermodynamic integration was used to compute the pKA value based on probabilistic determination. This technique not only reproduces the pKA value of liquid D2O experimentally measured (14.86) but also allows for a theoretical prediction of the pKA values of liquid T2O and aqueous HDO and HTO, which are unknown due to their scarcity. It is also shown that the NQEs on the free energy curve can result in a downshift of 4.5 ± 0.9 pKA units in the case of liquid water, which indicates that the NQEs plays an indispensable role in the absolute determination of pKA. The results of this study can help inform further extensions into the calculation of the acidity constants of isotope substituted species with high accuracy.
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Affiliation(s)
- Bo Thomsen
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Motoyuki Shiga
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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