1
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Lang X, Shi L, Zhao Z, Min W. Probing the structure of water in individual living cells. Nat Commun 2024; 15:5271. [PMID: 38902250 PMCID: PMC11190263 DOI: 10.1038/s41467-024-49404-9] [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: 10/16/2023] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
Water regulates or even governs a wide range of biological processes. Despite its fundamental importance, surprisingly little is known about the structure of intracellular water. Herein we employ a Raman micro-spectroscopy technique to uncover the composition, abundance and vibrational spectra of intracellular water in individual living cells. In three different cell types, we show a small but consistent population (~3%) of non-bulk-like water. It exhibits a weakened hydrogen-bonded network and a more disordered tetrahedral structure. We attribute this population to biointerfacial water located in the vicinity of biomolecules. Moreover, our whole-cell modeling suggests that all soluble (globular) proteins inside cells are surrounded by, on average, one full molecular layer (about 2.6 Angstrom) of biointerfacial water. Furthermore, relative invariance of biointerfacial water is observed among different single cells. Overall, our study not only opens up experimental possibilities of interrogating water structure in vivo but also provides insights into water in life.
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Affiliation(s)
- Xiaoqi Lang
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Lixue Shi
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
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2
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Xu N, Rosander P, Schäfer C, Lindgren E, Österbacka N, Fang M, Chen W, He Y, Fan Z, Erhart P. Tensorial Properties via the Neuroevolution Potential Framework: Fast Simulation of Infrared and Raman Spectra. J Chem Theory Comput 2024; 20:3273-3284. [PMID: 38572734 PMCID: PMC11044275 DOI: 10.1021/acs.jctc.3c01343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024]
Abstract
Infrared and Raman spectroscopy are widely used for the characterization of gases, liquids, and solids, as the spectra contain a wealth of information concerning, in particular, the dynamics of these systems. Atomic scale simulations can be used to predict such spectra but are often severely limited due to high computational cost or the need for strong approximations that limit the application range and reliability. Here, we introduce a machine learning (ML) accelerated approach that addresses these shortcomings and provides a significant performance boost in terms of data and computational efficiency compared with earlier ML schemes. To this end, we generalize the neuroevolution potential approach to enable the prediction of rank one and two tensors to obtain the tensorial neuroevolution potential (TNEP) scheme. We apply the resulting framework to construct models for the dipole moment, polarizability, and susceptibility of molecules, liquids, and solids and show that our approach compares favorably with several ML models from the literature with respect to accuracy and computational efficiency. Finally, we demonstrate the application of the TNEP approach to the prediction of infrared and Raman spectra of liquid water, a molecule (PTAF-), and a prototypical perovskite with strong anharmonicity (BaZrO3). The TNEP approach is implemented in the free and open source software package gpumd, which makes this methodology readily available to the scientific community.
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Affiliation(s)
- Nan Xu
- Institute
of Zhejiang University-Quzhou, Quzhou 324000, P. R. China
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, P. R. China
| | - Petter Rosander
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Christian Schäfer
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Eric Lindgren
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Nicklas Österbacka
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Mandi Fang
- Institute
of Zhejiang University-Quzhou, Quzhou 324000, P. R. China
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, P. R. China
| | - Wei Chen
- State
Key Laboratory of Multiphase Complex Systems, Institute of Process
Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yi He
- Institute
of Zhejiang University-Quzhou, Quzhou 324000, P. R. China
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, P. R. China
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Zheyong Fan
- College
of Physical Science and Technology, Bohai
University, Jinzhou 121013, P. R. China
| | - Paul Erhart
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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3
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Montero de Hijes P, Dellago C, Jinnouchi R, Schmiedmayer B, Kresse G. Comparing machine learning potentials for water: Kernel-based regression and Behler-Parrinello neural networks. J Chem Phys 2024; 160:114107. [PMID: 38506284 DOI: 10.1063/5.0197105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024] Open
Abstract
In this paper, we investigate the performance of different machine learning potentials (MLPs) in predicting key thermodynamic properties of water using RPBE + D3. Specifically, we scrutinize kernel-based regression and high-dimensional neural networks trained on a highly accurate dataset consisting of about 1500 structures, as well as a smaller dataset, about half the size, obtained using only on-the-fly learning. This study reveals that despite minor differences between the MLPs, their agreement on observables such as the diffusion constant and pair-correlation functions is excellent, especially for the large training dataset. Variations in the predicted density isobars, albeit somewhat larger, are also acceptable, particularly given the errors inherent to approximate density functional theory. Overall, this study emphasizes the relevance of the database over the fitting method. Finally, this study underscores the limitations of root mean square errors and the need for comprehensive testing, advocating the use of multiple MLPs for enhanced certainty, particularly when simulating complex thermodynamic properties that may not be fully captured by simpler tests.
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Affiliation(s)
- Pablo Montero de Hijes
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Josef-Holaubuek-Platz 2, 1090 Vienna, Austria
| | - Christoph Dellago
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
| | - Ryosuke Jinnouchi
- Toyota Central R&D Labs., Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | | | - Georg Kresse
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
- VASP Software GmbH, Berggasse 21, A-1090 Vienna, Austria
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4
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Maturi F, Raposo Filho RS, Brites CDS, Fan J, He R, Zhuang B, Liu X, Carlos LD. Deciphering Density Fluctuations in the Hydration Water of Brownian Nanoparticles via Upconversion Thermometry. J Phys Chem Lett 2024; 15:2606-2615. [PMID: 38420927 PMCID: PMC10926164 DOI: 10.1021/acs.jpclett.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
We investigate the intricate relationship among temperature, pH, and Brownian velocity in a range of differently sized upconversion nanoparticles (UCNPs) dispersed in water. These UCNPs, acting as nanorulers, offer insights into assessing the relative proportion of high-density and low-density liquid in the surrounding hydration water. The study reveals a size-dependent reduction in the onset temperature of liquid-water fluctuations, indicating an augmented presence of high-density liquid domains at the nanoparticle surfaces. The observed upper-temperature threshold is consistent with a hypothetical phase diagram of water, validating the two-state model. Moreover, an increase in pH disrupts the organization of water molecules, similar to external pressure effects, allowing simulation of the effects of temperature and pressure on hydrogen bonding networks. The findings underscore the significance of the surface of suspended nanoparticles for understanding high- to low-density liquid fluctuations and water behavior at charged interfaces.
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Affiliation(s)
- Fernando
E. Maturi
- Phantom-g,
CICECO - Aveiro Institute of Materials, Department of Physics, University of Aveiro, 3810-193 Aveiro, Portugal
- Institute
of Chemistry, São Paulo State University
(UNESP), 14800-060 Araraquara, SP, Brazil
| | - Ramon S. Raposo Filho
- Phantom-g,
CICECO - Aveiro Institute of Materials, Department of Physics, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlos D. S. Brites
- Phantom-g,
CICECO - Aveiro Institute of Materials, Department of Physics, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Jingyue Fan
- Department
of Chemistry, National University of Singapore, Singapore 117543
| | - Ruihua He
- Department
of Chemistry, National University of Singapore, Singapore 117543
| | - Bilin Zhuang
- Harvey
Mudd College, 301 Platt
Boulevard, Claremont, California 91711, United States
| | - Xiaogang Liu
- Department
of Chemistry, National University of Singapore, Singapore 117543
| | - Luís D. Carlos
- Phantom-g,
CICECO - Aveiro Institute of Materials, Department of Physics, University of Aveiro, 3810-193 Aveiro, Portugal
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5
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Kapil V, Kovács DP, Csányi G, Michaelides A. First-principles spectroscopy of aqueous interfaces using machine-learned electronic and quantum nuclear effects. Faraday Discuss 2024; 249:50-68. [PMID: 37799072 PMCID: PMC10845015 DOI: 10.1039/d3fd00113j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/18/2023] [Indexed: 10/07/2023]
Abstract
Vibrational spectroscopy is a powerful approach to visualising interfacial phenomena. However, extracting structural and dynamical information from vibrational spectra is a challenge that requires first-principles simulations, including non-Condon and quantum nuclear effects. We address this challenge by developing a machine-learning enhanced first-principles framework to speed up predictive modelling of infrared, Raman, and sum-frequency generation spectra. Our approach uses machine learning potentials that encode quantum nuclear effects to generate quantum trajectories using simple molecular dynamics efficiently. In addition, we reformulate bulk and interfacial selection rules to express them unambiguously in terms of the derivatives of polarisation and polarisabilities of the whole system and predict these derivatives efficiently using fully-differentiable machine learning models of dielectric response tensors. We demonstrate our framework's performance by predicting the IR, Raman, and sum-frequency generation spectra of liquid water, ice and the water-air interface by achieving near quantitative agreement with experiments at nearly the same computational efficiency as pure classical methods. Finally, to aid the experimental discovery of new phases of nanoconfined water, we predict the temperature-dependent vibrational spectra of monolayer water across the solid-hexatic-liquid phases transition.
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Affiliation(s)
- Venkat Kapil
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | | | - Gábor Csányi
- Engineering Laboratory, University of Cambridge, Cambridge, CB2 1PZ, UK
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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6
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LaCour RA, Heindel JP, Head-Gordon T. Predicting the Raman Spectra of Liquid Water with a Monomer-Field Model. J Phys Chem Lett 2023; 14:11742-11749. [PMID: 38116782 DOI: 10.1021/acs.jpclett.3c02873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The Raman spectrum of liquid water is quite complex, reflecting its strong sensitivity to the local environment of the individual waters. The OH-stretch region of the spectrum, which captures the influence of hydrogen bonding, has only just begun to be unraveled. Here we develop a model for predicting the Raman spectra of the OH-stretch region by considering how local electric fields distort the energy surface of each water monomer. We find that our model is capable of reproducing the bimodal nature of the main peak, with the shoulder at 3250 cm-1 resulting almost entirely from Fermi resonance. Furthermore, we capture the temperature and polarization dependence of the shoulder, which has proven to be difficult to obtain with previous methods, and analyze the origin of this dependence. We expect our model to be generally useful for understanding and predicting how Raman spectra change under different conditions and with different probe reporters beyond water.
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Affiliation(s)
- R Allen LaCour
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joseph P Heindel
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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7
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Clark JB, Bowling-Charles T, Proma SJ, Biswas B, Limmer DT, Allen HC. Structural evolution of water-in-propylene carbonate mixtures revealed by polarized Raman spectroscopy and molecular dynamics. Phys Chem Chem Phys 2023; 25:23963-23976. [PMID: 37644802 DOI: 10.1039/d3cp02181e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The liquid structure of systems wherein water is limited in concentration or through geometry is of great interest in various fields such as biology, materials science, and electrochemistry. Here, we present a combined polarized Raman and molecular dynamics investigation of the structural changes that occur as water is added incrementally to propylene carbonate (PC), a polar, aprotic solvent that is important in lithium-ion batteries. Polarized Raman spectra of PC solutions were collected for water mole fractions 0.003 ≤ χwater ≤ 0.296, which encompasses the solubility range of water in PC. The novel approach taken herein provides additional hydrogen bond and solvation characterization of this system that has not been achievable in previous studies. Analysis of the polarized carbonyl Raman band in conjunction with simulations demonstrated that the bulk structure of the solvent remained unperturbed upon the addition of water. Experimental spectra in the O-H stretching region were decomposed through Gaussian fitting into sub-bands and comparison to studies of dilute HOD in D2O. With the aid of simulations, we identified these different bands as water arrangements having different degrees of hydrogen bonding. The observed water structure within PC indicates that water tends to self-aggregate, forming a hydrogen bond network that is distinctly different from the bulk and dependent on concentration. For example, at moderate concentrations, the most likely aggregate structures are chains of water molecules, each with two hydrogen bonds.
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Affiliation(s)
- Jessica B Clark
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Tai Bowling-Charles
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Shamma Jabeen Proma
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Biswajit Biswas
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Kavli Energy NanoScience Institute, Berkeley, California 94720, USA
| | - Heather C Allen
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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8
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Atsango AO, Morawietz T, Marsalek O, Markland TE. Developing machine-learned potentials to simultaneously capture the dynamics of excess protons and hydroxide ions in classical and path integral simulations. J Chem Phys 2023; 159:074101. [PMID: 37581418 DOI: 10.1063/5.0162066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics simulations to model the bond breaking and formation involved in proton transfer and path-integral simulations to model the nuclear quantum effects relevant to light hydrogen atoms. These requirements result in a prohibitive computational cost, especially at the time and length scales needed to converge proton transport properties. Here, we present machine-learned potentials (MLPs) that can model both excess protons and hydroxide ions at the generalized gradient approximation and hybrid density functional theory levels of accuracy and use them to perform multiple nanoseconds of both classical and path-integral proton defect simulations at a fraction of the cost of the corresponding ab initio simulations. We show that the MLPs are able to reproduce ab initio trends and converge properties such as the diffusion coefficients of both excess protons and hydroxide ions. We use our multi-nanosecond simulations, which allow us to monitor large numbers of proton transfer events, to analyze the role of hypercoordination in the transport mechanism of the hydroxide ion and provide further evidence for the asymmetry in diffusion between excess protons and hydroxide ions.
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Affiliation(s)
- Austin O Atsango
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Ondrej Marsalek
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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9
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Bandyopadhyay A, Saha G, Mondal JA. Vibrational Coupling and Hydrogen-Bond Structure of Water in the Extended Hydration Shell of Metal Ions. J Phys Chem B 2023; 127:7174-7180. [PMID: 37530805 DOI: 10.1021/acs.jpcb.3c01883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Intra- and intermolecular vibrational coupling (VC) and hydrogen bonding (H-bonding) of water are sparsely understood in the hydration shell (HS) of a metal ion, though the corresponding knowledge for an anion is quite extensive. This is primarily due to the overwhelming effect of anions on water, which masks the subtle perturbing influence of most of the cations. Using Raman difference spectroscopy with simultaneous curve fitting (Raman-DS-SCF) in combination with isotopic dilution and polarized Raman spectroscopy, we have elucidated the VC and H-bonding of water in the HS of bi- and trivalent metal ions─Mg2+, Ca2+, La3+, Gd3+, Dy3+. Polarized Raman measurement of the HS water with VC "turned on" and "turned off" (using isotopically diluted water, HOD) reveals that water retains the intra- and intermolecular vibrational coupling in the HS of high-charge-density metal ions, which is in stark contrast to that of an anion. Hydration shell spectroscopy in HOD unambiguously shows that the average H-bonding of water becomes stronger in the HS than that of bulk water. The first HS water strongly donates two H-bonds to the second HS water (ν̅max ≈ 3200 cm-1) but weakly accepts a H-bond from the second HS water (ν̅max ≈ 3590 cm-1), which makes the HS water heterogeneous in terms of its H-bond structure. The weakly interacting OH (ν̅max 3585 cm-1 in HOD) red-shifts by ∼ 15 cm-1 while the VC is "turned on" (ν̅max ≈ 3600 cm-1 in H2O), revealing the intramolecular coupling of water in the HS of metal ions.
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Affiliation(s)
- Anisha Bandyopadhyay
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Trombay, Mumbai 400085, India
| | - Gunomoni Saha
- Department of Chemistry, Barrackpore Rastraguru Surendranath College, Kolkata -700120, India
| | - Jahur Alam Mondal
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Trombay, Mumbai 400085, India
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10
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Chen MS, Lee J, Ye HZ, Berkelbach TC, Reichman DR, Markland TE. Data-Efficient Machine Learning Potentials from Transfer Learning of Periodic Correlated Electronic Structure Methods: Liquid Water at AFQMC, CCSD, and CCSD(T) Accuracy. J Chem Theory Comput 2023; 19:4510-4519. [PMID: 36730728 DOI: 10.1021/acs.jctc.2c01203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Obtaining the atomistic structure and dynamics of disordered condensed-phase systems from first-principles remains one of the forefront challenges of chemical theory. Here we exploit recent advances in periodic electronic structure and provide a data-efficient approach to obtain machine-learned condensed-phase potential energy surfaces using AFQMC, CCSD, and CCSD(T) from a very small number (≤200) of energies by leveraging a transfer learning scheme starting from lower-tier electronic structure methods. We demonstrate the effectiveness of this approach for liquid water by performing both classical and path integral molecular dynamics simulations on these machine-learned potential energy surfaces. By doing this, we uncover the interplay of dynamical electron correlation and nuclear quantum effects across the entire liquid range of water while providing a general strategy for efficiently utilizing periodic correlated electronic structure methods to explore disordered condensed-phase systems.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California94305, United States
| | - Joonho Lee
- Department of Chemistry, Columbia University, New York, New York10027, United States
| | - Hong-Zhou Ye
- Department of Chemistry, Columbia University, New York, New York10027, United States
| | - Timothy C Berkelbach
- Department of Chemistry, Columbia University, New York, New York10027, United States
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York10010, United States
| | - David R Reichman
- Department of Chemistry, Columbia University, New York, New York10027, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California94305, United States
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11
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Das Mahanta D, Brown DR, Pezzotti S, Han S, Schwaab G, Shell MS, Havenith M. Local solvation structures govern the mixing thermodynamics of glycerol-water solutions. Chem Sci 2023; 14:7381-7392. [PMID: 37416713 PMCID: PMC10321518 DOI: 10.1039/d3sc00517h] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
Glycerol is a major cryoprotective agent and is widely used to promote protein stabilization. By a combined experimental and theoretical study, we show that global thermodynamic mixing properties of glycerol and water are dictated by local solvation motifs. We identify three hydration water populations, i.e., bulk water, bound water (water hydrogen bonded to the hydrophilic groups of glycerol) and cavity wrap water (water hydrating the hydrophobic moieties). Here, we show that for glycerol experimental observables in the THz regime allow quantification of the abundance of bound water and its partial contribution to the mixing thermodynamics. Specifically, we uncover a 1 : 1 connection between the population of bound waters and the mixing enthalpy, which is further corroborated by the simulation results. Therefore, the changes in global thermodynamic quantity - mixing enthalpy - are rationalized at the molecular level in terms of changes in the local hydrophilic hydration population as a function of glycerol mole fraction in the full miscibility range. This offers opportunities to rationally design polyol water, as well as other aqueous mixtures to optimize technological applications by tuning mixing enthalpy and entropy based on spectroscopic screening.
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Affiliation(s)
- Debasish Das Mahanta
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
- Department of Physics, Technische Universität Dortmund 44227 Dortmund Germany
| | - Dennis Robinson Brown
- Department of Chemical Engineering, University of California Santa Barbara California 93106-5080 USA
| | - Simone Pezzotti
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
| | - Songi Han
- Department of Chemical Engineering, University of California Santa Barbara California 93106-5080 USA
- Department of Chemistry and Biochemistry, University of California Santa Barbara California 93106-9510 USA
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
| | - M Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara California 93106-5080 USA
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
- Department of Physics, Technische Universität Dortmund 44227 Dortmund Germany
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12
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Bore SL, Paesani F. Realistic phase diagram of water from "first principles" data-driven quantum simulations. Nat Commun 2023; 14:3349. [PMID: 37291095 DOI: 10.1038/s41467-023-38855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/12/2023] [Indexed: 06/10/2023] Open
Abstract
Since the experimental characterization of the low-pressure region of water's phase diagram in the early 1900s, scientists have been on a quest to understand the thermodynamic stability of ice polymorphs on the molecular level. In this study, we demonstrate that combining the MB-pol data-driven many-body potential for water, which was rigorously derived from "first principles" and exhibits chemical accuracy, with advanced enhanced-sampling algorithms, which correctly describe the quantum nature of molecular motion and thermodynamic equilibria, enables computer simulations of water's phase diagram with an unprecedented level of realism. Besides providing fundamental insights into how enthalpic, entropic, and nuclear quantum effects shape the free-energy landscape of water, we demonstrate that recent progress in "first principles" data-driven simulations, which rigorously encode many-body molecular interactions, has opened the door to realistic computational studies of complex molecular systems, bridging the gap between experiments and simulations.
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Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
- Materials Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, 92093, USA.
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 92093, USA.
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13
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Pastorczak M, Duk K, Shahab S, Kananenka AA. Combinational Vibration Modes in H 2O/HDO/D 2O Mixtures Detected Thanks to the Superior Sensitivity of Femtosecond Stimulated Raman Scattering. J Phys Chem B 2023. [PMID: 37201478 DOI: 10.1021/acs.jpcb.3c01334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Overtones and combinational modes frequently play essential roles in ultrafast vibrational energy relaxation in liquid water. However, these modes are very weak and often overlap with fundamental modes, particularly in isotopologues mixtures. We measured VV and HV Raman spectra of H2O and D2O mixtures with femtosecond stimulated Raman scattering (FSRS) and compared the results with calculated spectra. Specifically, we observed the mode at around 1850 cm-1 and assigned it to H-O-D bend + rocking libration. Second, we found that the H-O-D bend overtone band and the OD stretch + rocking libration combination band contribute to the band located between 2850 and 3050 cm-1. Furthermore, we assigned the broad band located between 4000 and 4200 cm-1 to be composed of combinational modes of high-frequency OH stretching modes with predominantly twisting and rocking librations. These results should help in a proper interpretation of Raman spectra of aqueous systems as well as in the identification of vibrational relaxation pathways in isotopically diluted water.
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Affiliation(s)
- Marcin Pastorczak
- Institute of Physical Chemistry, Polish Academy of Sciences, Laser Centre, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Katsiaryna Duk
- Institute of Physical Chemistry, Polish Academy of Sciences, Laser Centre, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Samaneh Shahab
- Institute of Physical Chemistry, Polish Academy of Sciences, Laser Centre, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Alexei A Kananenka
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
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14
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Begušić T, Blake GA. Two-dimensional infrared-Raman spectroscopy as a probe of water's tetrahedrality. Nat Commun 2023; 14:1950. [PMID: 37029146 PMCID: PMC10082090 DOI: 10.1038/s41467-023-37667-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
Two-dimensional spectroscopic techniques combining terahertz (THz), infrared (IR), and visible pulses offer a wealth of information about coupling among vibrational modes in molecular liquids, thus providing a promising probe of their local structure. However, the capabilities of these spectroscopies are still largely unexplored due to experimental limitations and inherently weak nonlinear signals. Here, through a combination of equilibrium-nonequilibrium molecular dynamics (MD) and a tailored spectrum decomposition scheme, we identify a relationship between the tetrahedral order of liquid water and its two-dimensional IR-IR-Raman (IIR) spectrum. The structure-spectrum relationship can explain the temperature dependence of the spectral features corresponding to the anharmonic coupling between low-frequency intermolecular and high-frequency intramolecular vibrational modes of water. In light of these results, we propose new experiments and discuss the implications for the study of tetrahedrality of liquid water.
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Affiliation(s)
- Tomislav Begušić
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Geoffrey A Blake
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
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15
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Wang L, Morita A, North NM, Baumler SM, Springfield EW, Allen HC. Identification of Ion Pairs in Aqueous NaCl and KCl Solutions in Combination with Raman Spectroscopy, Molecular Dynamics, and Quantum Chemical Calculations. J Phys Chem B 2023; 127:1618-1627. [PMID: 36757371 DOI: 10.1021/acs.jpcb.2c07923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
This work summarizes a theoretical analysis of the perturbation on Raman spectra in aqueous NaCl and KCl solutions with the aim to detect ion pairs. The experimental Raman spectra, both polarized and depolarized, are perturbed by these ions to a comparable extent or somewhat less by KCl than NaCl. This result appears to be contrary to the molecular dynamics (MD) simulation showing that the isolated and separated ions of KCl should have a larger perturbation than NaCl, as the solvation shell of K+ is larger than that of Na+. The apparent discrepancy signifies the ion pair formation which is more substantial for KCl than NaCl. The MD simulations and quantum chemical calculations revealed that KCl forms ion pairs more than NaCl and that the ion pair formation reduces the perturbation on the Raman spectra more for KCl. The present analysis shows that the perturbed Raman spectra provide a useful sign to evaluate the ion pair formation in aqueous solutions.
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Affiliation(s)
- Lin Wang
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku Sendai 980-8578, Japan
| | - Akihiro Morita
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku Sendai 980-8578, Japan
| | - Nicole M North
- Department of Chemistry and Biochemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Stephen M Baumler
- Department of Chemistry and Biochemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Elliot W Springfield
- Department of Chemistry and Biochemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Heather C Allen
- Department of Chemistry and Biochemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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16
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Schienbein P. Spectroscopy from Machine Learning by Accurately Representing the Atomic Polar Tensor. J Chem Theory Comput 2023; 19:705-712. [PMID: 36695707 PMCID: PMC9933433 DOI: 10.1021/acs.jctc.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Vibrational spectroscopy is a key technique to elucidate microscopic structure and dynamics. Without the aid of theoretical approaches, it is, however, often difficult to understand such spectra at a microscopic level. Ab initio molecular dynamics has repeatedly proved to be suitable for this purpose; however, the computational cost can be daunting. Here, the E(3)-equivariant neural network e3nn is used to fit the atomic polar tensor of liquid water a posteriori on top of existing molecular dynamics simulations. Notably, the introduced methodology is general and thus transferable to any other system as well. The target property is most fundamental and gives access to the IR spectrum, and more importantly, it is a highly powerful tool to directly assign IR spectral features to nuclear motion─a connection which has been pursued in the past but only using severe approximations due to the prohibitive computational cost. The herein introduced methodology overcomes this bottleneck. To benchmark the machine learning model, the IR spectrum of liquid water is calculated, indeed showing excellent agreement with the explicit reference calculation. In conclusion, the presented methodology gives a new route to calculate accurate IR spectra from molecular dynamics simulations and will facilitate the understanding of such spectra on a microscopic level.
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17
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Dobrynina EA, Zykova VA, Adichtchev SV, Surovtsev NV. Gigahertz elastic modulus and OH stretching frequency correlate with Jones-Dole's B-coefficient in aqueous solutions of the Hofmeister series. J Chem Phys 2023; 158:034504. [PMID: 36681647 DOI: 10.1063/5.0130490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The ability of salts to change the macroscopic viscosity of their aqueous solutions is described by the Jones-Dole equation with B-coefficient for the linear concentration term. The sign and value of this coefficient are often considered as a measure of the salt's structure-making/breaking ability, while the validity of this assignment is still under discussion. Here, by applying Raman and Brillouin scattering spectroscopy to various salts from the Hofmeister series, we studied a possible relation between macroscopic Jones-Dole's B-coefficient and the microscopic dynamic response. Raman spectroscopy provides information about molecular vibrations and Brillouin spectroscopy about acoustic phonons with wavelengths of hundreds of nanometers. It has been found that Jones-Dole's B-coefficient correlates linearly with the coefficients, describing the concentration dependences of the average OH stretching frequency, real and imaginary parts of gigahertz elastic modulus. These relationships have been interpreted to mean that the OH stretching frequency is a measure of the ion-induced changes in the water network that cause changes in both viscosity and gigahertz relaxation. Depolarized inelastic light scattering revealed that the addition of structure-making ions not only changes the frequency of the relaxation peak but also increases the low-frequency part of the relaxation susceptibility. It was shown that the ion-induced increase in the gigahertz elastic modulus can be described by changes in the relaxational susceptibility without a noticeable change in the instantaneous elastic modulus. The isotropic Raman contribution associated with the tetrahedral-like environment of H2O molecule does not correlate with Jones-Dole's B-coefficient, suggesting a minor influence of these tetrahedral-like configurations on viscosity.
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Affiliation(s)
- E A Dobrynina
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - V A Zykova
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - S V Adichtchev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - N V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
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18
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Xu Y, Xing L, Cao X, Li D, Men Z, Li Z, Wang S, Sun C. Hydrogen bonding network dynamics of 1,2-propanediol-water binary solutions by Raman spectroscopy and stimulated Raman scattering. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 284:121825. [PMID: 36081192 DOI: 10.1016/j.saa.2022.121825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Raman spectroscopy and stimulated Raman scattering (SRS) were used to investigate the hydrogen bonding (HB) network in 1,2-propanediol (1,2-PD)-water binary solutions. Abnormal changes in hydrogen bonds (HBs) were detected when V1,2-PD (volume fraction of the1,2-PD) was 0.4. In the case of Raman spectroscopy, the HB strength of water is weakened and then strengthened with the increase of 1,2-PD volume fraction. In the case of SRS, two new peaks at 3283 cm-1 and 3319 cm-1 were appeared, which demonstrated the appearance of ice-like structures near the methyl group and the weakening of HBs. Based on these phenomena, the HB structure of this binary system underwent a transition from H2O-H2O to H2O-1,2-PD when the V1,2-PD was 0.4 as V1,2-PD increased. This work serves as a reference value for the study of HB networks in alcohol-water binary solutions.
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Affiliation(s)
- Yang Xu
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Lu Xing
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Xianwen Cao
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Dongfei Li
- College of Physics, Jilin Normal University, SiPing 136000, China
| | - Zhiwei Men
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China
| | - Zhanlong Li
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China.
| | - Shenghan Wang
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China; Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), College of Physics, Jilin University, Changchun 130012, China.
| | - Chenglin Sun
- Coherent Light and Atomic and Molecular Spectroscopy Laboratory, College of Physics, Jilin University, Changchun 130012, China.
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19
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Shanavas Rasheeda D, Martín Santa Daría A, Schröder B, Mátyus E, Behler J. High-dimensional neural network potentials for accurate vibrational frequencies: the formic acid dimer benchmark. Phys Chem Chem Phys 2022; 24:29381-29392. [PMID: 36459127 DOI: 10.1039/d2cp03893e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In recent years, machine learning potentials (MLP) for atomistic simulations have attracted a lot of attention in chemistry and materials science. Many new approaches have been developed with the primary aim to transfer the accuracy of electronic structure calculations to large condensed systems containing thousands of atoms. In spite of these advances, the reliability of modern MLPs in reproducing the subtle details of the multi-dimensional potential-energy surface is still difficult to assess for such systems. On the other hand, moderately sized systems enabling the application of tools for thorough and systematic quality-control are nowadays rarely investigated. In this work we use benchmark-quality harmonic and anharmonic vibrational frequencies as a sensitive probe for the validation of high-dimensional neural network potentials. For the case of the formic acid dimer, a frequently studied model system for which stringent spectroscopic data became recently available, we show that high-quality frequencies can be obtained from state-of-the-art calculations in excellent agreement with coupled cluster theory and experimental data.
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Affiliation(s)
- Dilshana Shanavas Rasheeda
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany.
| | - Alberto Martín Santa Daría
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Benjamin Schröder
- Universität Göttingen, Institut für Physikalische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany
| | - Edit Mátyus
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany.
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20
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Daru J, Forbert H, Behler J, Marx D. Coupled Cluster Molecular Dynamics of Condensed Phase Systems Enabled by Machine Learning Potentials: Liquid Water Benchmark. PHYSICAL REVIEW LETTERS 2022; 129:226001. [PMID: 36493459 DOI: 10.1103/physrevlett.129.226001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 06/17/2023]
Abstract
Coupled cluster theory is a general and systematic electronic structure method, but in particular the highly accurate "gold standard" coupled cluster singles, doubles and perturbative triples, CCSD(T), can only be applied to small systems. To overcome this limitation, we introduce a framework to transfer CCSD(T) accuracy of finite molecular clusters to extended condensed phase systems using a high-dimensional neural network potential. This approach, which is automated, allows one to perform high-quality coupled cluster molecular dynamics, CCMD, as we demonstrate for liquid water including nuclear quantum effects. The machine learning strategy is very efficient, generic, can be systematically improved, and is applicable to a variety of complex systems.
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Affiliation(s)
- János Daru
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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21
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Schönfeldová T, Dupertuis N, Chen Y, Ansari N, Poli E, Wilkins DM, Hassanali A, Roke S. Charge Gradients around Dendritic Voids Cause Nanoscale Inhomogeneities in Liquid Water. J Phys Chem Lett 2022; 13:7462-7468. [PMID: 35930807 DOI: 10.1021/acs.jpclett.2c01872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Water is the matrix of life and serves as a solvent for numerous physical and chemical processes. The origins of the nature of inhomogeneities that exist in liquid water and the time scales over which they occur remains an open question. Here, we report femtosecond elastic second harmonic scattering (fs-ESHS) of liquid water in comparison to an isotropic liquid (CCl4) and show that water is indeed a nonuniform liquid. The coherent fs-ESHS intensity was interpreted, using molecular dynamics simulations, as arising from charge density fluctuations with enhanced nanoscale polarizabilities around transient voids having an average lifetime of 300 fs. Although voids were also present in CCl4, they were not characterized by hydrogen bond defects and did not show strong polarizability fluctuations, leading to fs-ESHS of an isotropic liquid. The voids increased in number at higher temperatures above room temperature, in agreement with the fs-ESHS results.
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Affiliation(s)
- Tereza Schönfeldová
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nathan Dupertuis
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yixing Chen
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Narjes Ansari
- Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Emiliano Poli
- Condensed Matter and Statistical Physics (CMSP), The Abdus Salam International Center For Theoretical Physics, 34151 Trieste, Italy
| | - David M Wilkins
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Ali Hassanali
- Condensed Matter and Statistical Physics (CMSP), The Abdus Salam International Center For Theoretical Physics, 34151 Trieste, Italy
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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22
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Jung KA, Markland TE. 2D spectroscopies from condensed phase dynamics: Accessing third-order response properties from equilibrium multi-time correlation functions. J Chem Phys 2022; 157:094111. [DOI: 10.1063/5.0107087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and frequency dimensions in these spectroscopies provides access to rich information on the electronic and vibrational states present, the coupling between them, and the resulting rates at which they exchange energy that are obscured in linear spectroscopy, particularly for condensed phase systems that usually contain many overlapping features. While the exact quantum expression for the third-order response is well established it is incompatible with the methods that are practical for calculating the atomistic dynamics of large condensed phase systems. These methods, which include both classical mechanics and quantum dynamics methods that retain quantum statistical properties while obeying the symmetries of classical dynamics, such as LSC-IVR, Centroid Molecular Dynamics (CMD) and Ring Polymer Molecular Dynamics (RPMD) naturally provide short-time approximations to the multi-time symmetrized Kubo transformed correlation function. Here, we show how the third-order response can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions. We demonstrate the utility and accuracy of our approach by showing how it can be used to obtain the third-order response of a series of model systems using both classical dynamics and RPMD. In particular, we show that this approach captures features such as anharmonically induced vertical splittings and peak shifts while providing a physically transparent framework for understanding multidimensional spectroscopies.
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23
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Palchowdhury S, Mukherjee K, Maroncelli M. Rapid Water Dynamics Structures the OH-Stretching Spectra of Solitary Water in Ionic Liquids and Dipolar Solvents. J Chem Phys 2022; 157:084502. [DOI: 10.1063/5.0107348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In a recent study [ J. Phys. Chem. B 126, 4584 (2022)] we used infrared spectroscopy to investigate the solvation and dynamics of solitary water in ionic liquids and dipolar solvents. Complex shapes observed for water OH-stretching bands common to all high-polarity solvents were assigned to water in several solvation states. In the present study, classical molecular dynamics simulations of a single water molecule in four ionic liquids and three dipolar solvents were used to test and refine this interpretation. Consistent with past assignments, simulations show solitary water usually donates two hydrogen bonds to distinct solvent molecules. Such symmetrically solvated water produces the primary pair of peaks identified in the OH spectra of water in nearly all solvents. We had further proposed that additional features flanking this main peak are due to asymmetric solvation states, states in which only one OH group makes a hydrogen bond to solvent. Such states were found in significant concentrations in all of the systems simulated. Simulations of the OH stretching spectra using a semiclassical description and the vibrational map developed by Auer and Skinner [ J. Chem. Phys. 128, 224511 (2008)] provided semi-quantitative agreement with experiment. Analysis of species-specific spectra also confirmed assignment of the additional features in the experimental spectra to asymmetrically solvated water. The simulations also showed that rapid water motions cause a marked motional narrowing compared to the inhomogeneous limit, and that this narrowing is largely responsible for making the additional features due to minority solvation states manifest in the spectra.
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Affiliation(s)
- Souarv Palchowdhury
- The Pennsylvania State University - University Park Campus, United States of America
| | - Kallol Mukherjee
- The Pennsylvania State University - University Park Campus, United States of America
| | - Mark Maroncelli
- Department of Chemsitry, The Pennsylvania State University - University Park Campus, United States of America
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24
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Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
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25
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Brkljača Z, Butumović M, Bakarić D. Water does not dance as ions sing: A new approach in elucidation of ion-invariant water fluctuations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120907. [PMID: 35144056 DOI: 10.1016/j.saa.2022.120907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Aqueous solutions of salts composed from monovalent ions are explored using temperature-dependent FT-IR spectroscopy in transmission. Water combination band, being extremely sensitive to the network of hydrogen bonds due to the contribution of water librations (ρLH2O), is analyzed in uni- and multivariate fashion. Univariate analysis of the combination band maximum (νmax) reveals that perturbation of water hydrogen bond network by ions is primary driven by electrostatic interactions between water and ions. Using multivariate curve resolution with alternating least squares and evolving factor analysis this band is separated into two components that represent low- and high-density water. The observed asymmetry in their behavior is interpreted in terms of fluctuations of a hydrogen bond network of two water components. The significance of the found phenomenon is unambiguously confirmed by performing analogous analysis in the spectral range that contains partial signature of water linear bending (δHOH) and is free from ρLH2O, in which the asymmetry is absent. Additionally, we show that this phenomenon, namely ion-invariant behavior of water fluctuations, persists even in the regime of high ionic strengths. Although ions indeed participate in shaping of water hydrogen bond network, this straightforward approach shows that its temperature-dependent fluctuations are ion-independent.
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Affiliation(s)
- Zlatko Brkljača
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Marija Butumović
- Division of Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Danijela Bakarić
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
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26
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Kringle L, Thornley WA, Kay BD, Kimmel GA. Isotope effects on the structural transformation and relaxation of deeply supercooled water. J Chem Phys 2022; 156:084501. [DOI: 10.1063/5.0078796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We have examined the structure of supercooled liquid D2O as a function of temperature between 185 and 255 K using pulsed laser heating to rapidly heat and cool the sample on a nanosecond timescale. The liquid structure can be represented as a linear combination of two structural motifs, with a transition between them described by a logistic function centered at 218 K with a width of 10 K. The relaxation to a metastable state, which occurred prior to crystallization, exhibited nonexponential kinetics with a rate that was dependent on the initial structural configuration. When the temperature is scaled by the temperature of maximum density, which is an isostructural point of the isotopologues, the structural transition and the non-equilibrium relaxation kinetics of D2O agree remarkably well with those for H2O.
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Affiliation(s)
- Loni Kringle
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Wyatt A. Thornley
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Bruce D. Kay
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Greg A. Kimmel
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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27
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Machine-learning-based many-body energy analysis of argon clusters: Fit for size? Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Rogers BA, Okur HI, Yan C, Yang T, Heyda J, Cremer PS. Weakly hydrated anions bind to polymers but not monomers in aqueous solutions. Nat Chem 2022; 14:40-45. [PMID: 34725491 DOI: 10.1038/s41557-021-00805-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023]
Abstract
Weakly hydrated anions help to solubilize hydrophobic macromolecules in aqueous solutions, but small molecules comprising the same chemical constituents precipitate out when exposed to these ions. Here, this apparent contradiction is resolved by systematically investigating the interactions of NaSCN with polyethylene oxide oligomers and polymers of varying molecular weight. A combination of spectroscopic and computational results reveals that SCN- accumulates near the surface of polymers, but is excluded from monomers. This occurs because SCN- preferentially binds to the centre of macromolecular chains, where the local water hydrogen-bonding network is disrupted. These findings suggest a link between ion-specific effects and theories addressing how hydrophobic hydration is modulated by the size and shape of a hydrophobic entity.
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Affiliation(s)
- Bradley A Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Halil I Okur
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey
| | - Chuanyu Yan
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Tinglu Yang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Dejvice, Czech Republic
| | - Paul S Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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29
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Robalo JR, Mendes de Oliveira D, Ben-Amotz D, Vila Verde A. Influence of Methylene Fluorination and Chain Length on the Hydration Shell Structure and Thermodynamics of Linear Diols. J Phys Chem B 2021; 125:13552-13564. [PMID: 34875166 DOI: 10.1021/acs.jpcb.1c08601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interplay between the local hydration shell structure, the length of hydrophobic solutes, and their identity (perfluorinated or not) remains poorly understood. We address this issue by combining Raman-multivariate curve resolution (Raman-MCR) spectroscopy, simulation, and quantum-mechanical calculations to quantify the thermodynamics and the first principle interactions behind the formation of defects in the hydration shell of alkyl-diol and perfluoroalkyl-diol chains. The hydration shell of the fluorinated diols contains substantially more defects than that of the nonfluorinated diols; these defects are water hydroxy groups that do not donate hydrogen bonds and which either point to the solute (radial-dangling OH) or not (nonradial-dangling OH). The number of radial-dangling OH defects per carbon decreases for longer chains and toward the interior of the fluorinated diols, mainly due to less favorable electrostatics and exchange interactions; nonradial-dangling OH defects per carbon increase with chain length. In contrast, the hydration shell of the nonfluorinated diols only contains radial-dangling defects, which become more abundant toward the center of the chain and for larger chains, predominantly because of more favorable dispersion interactions. These results have implications for how the folding of macromolecules, ligand binding to biomacromolecules, and chemical reactions at water-oil interfaces could be modified through the introduction of fluorinated groups or solvents.
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Affiliation(s)
- João R Robalo
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
| | | | - Dor Ben-Amotz
- Purdue University, Department of Chemistry, West Lafayette, Indiana 47907, United States
| | - Ana Vila Verde
- University of Duisburg-Essen, Faculty of Physics, Lotharstrasse 1, 47057 Duisburg, Germany
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30
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Efimov YY. VIBRATIONAL SPECTRA OF WATER: ROLE OF EXTREMUMS IN THE ENERGY OF HYDROGEN BONDS O–H…O AND IN THE DEGENERACY OF THEIR GEOMETRIC STATES. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Liu J, He X. Ab initio molecular dynamics simulation of liquid water with fragment-based quantum mechanical approach under periodic boundary conditions. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai 200062, China
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32
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Cui X, Tang M, Wang M, Zhu T. Water as a probe for pH measurement in individual particles using micro-Raman spectroscopy. Anal Chim Acta 2021; 1186:339089. [PMID: 34756261 DOI: 10.1016/j.aca.2021.339089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
Atmospheric aerosol acidity impacts numerous physicochemical processes, but the determination of particle pH remains a significant challenge due to the nonconservative nature of the H+ concentration ([H+]). Traditional measurements have difficulty in describing the practical state of an aerosol because they comprise chemical components or hypotheses that change the nature of the particles. In this work, we present a direct pH measurement that uses water as a general probe to detect [H+] in individual particles by micro-Raman spectroscopy. Containing the vibrational bands of ions and water influenced by ions, the spectra of hydrated ion were decomposed from the solution spectra as standard spectra by multivariate curve resolution analysis. Meanwhile, ratios of hydrated ions were calculated between the Raman spectra and standard spectra to evaluate concentration profiles of each ion. It demonstrated that good quantitative models between the ratio and concentration for all ions including H+ can be built with correlation coefficients (R2) higher than 0.95 for the solutions. The method was further applied to individual particle pH measurement. The pH value of sulfate aerosol particles was calculated, and the standard error was 0.09 using pH values calculated from the [HSO4-]/[SO42-] as a reference. Furthermore, the applicability of the method was proven by detecting the pH value of chloride particles. Therefore, utilizing water, the most common substance, as the spectroscopic probe to measure [H+] without restriction of the ion system, this method has potential to measure the pH value of atmospheric particles with various compounds, although more work needs to be done to improve the sensitivity of the method.
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Affiliation(s)
- Xiaoyu Cui
- BIC-ESAT and SKL-ESPC, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Mingjin Tang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Mingjin Wang
- BIC-ESAT and SKL-ESPC, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tong Zhu
- BIC-ESAT and SKL-ESPC, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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33
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Sun T, Wyslouzil BE. Freezing of Dilute Aqueous-Alcohol Nanodroplets: The Effect of Molecular Structure. J Phys Chem B 2021; 125:12329-12343. [PMID: 34709826 DOI: 10.1021/acs.jpcb.1c06188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate vapor-liquid nucleation and subsequent freezing of aqueous-alcohol nanodroplets containing 1-pentanol, 1-hexanol, and their 3-isomers. The aerosols are produced in a supersonic nozzle, where condensation and freezing are characterized by static pressure and Fourier transform Infrared (FTIR) spectroscopy measurements. At fixed water concentrations, the presence of alcohol enables particle formation at higher temperatures since both the equilibrium vapor pressure above the critical clusters and the cluster interfacial free energy are decreased relative to the pure water case. The disappearance of a small free OH peak, observed for pure water droplets, when alcohols are added and shifts in the CH peaks as a function of alcohol chain length reveal varying surface partitioning preferences of the alcohols. Changes in the FTIR spectra during freezing, as well as changes in the ice component derived from self-modeling curve resolution analysis, show that 1-hexanol and 1-pentanol perturb freezing less than their branched isomers do. This behavior may reflect the molecular footprints of the alcohols, the available surface area of the droplets, and not only alcohol solubility. The presence of alcohols also lowers the freezing temperature relative to that of pure water, but when there is clear evidence for the formation of ice, the ice nucleation rates change by less than a factor of ∼2-3 for all cases studied.
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Affiliation(s)
- Tong Sun
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Barbara E Wyslouzil
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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34
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Wang Y, Li F, Fang W, Sun C, Men Z. Study of hydrogen bonding interactions in ethylene glycol-water binary solutions by Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119916. [PMID: 34020386 DOI: 10.1016/j.saa.2021.119916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
EG (ethylene glycol) is a good model system for the study of the fundamental hydrogen bonds in aqueous solutions. Using Raman spectroscopy, we have investigated the EG volume fraction induced variation in the hydrogen bonding interactions and conformations of EG-H2O (water) binary solutions. New hydrogen bonding networks is evidenced by the appearance of remarkable changes in Raman spectra and the full width at half maximum (FWHM) when the mixing volume ratio is 0.5. The H-bond in water molecules firstly strengthened and then weakened with the increasing concentration of EG. Meanwhile, the dominant association structure also changed from H2O-H2O to EG-H2O in binary solutions in this process. We provide a simple but effective method for studying EG-H2O binary solutions. It also has exciting potential prospects and can be easily extended to other mixing situations.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun 130012, China
| | - Fabing Li
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun 130012, China
| | - Wenhui Fang
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun 130012, China; School of Science, Changchun University of Science and Technology, Changchun 130022, China.
| | - Chenglin Sun
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun 130012, China
| | - Zhiwei Men
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun 130012, China.
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35
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Shepherd S, Lan J, Wilkins DM, Kapil V. Efficient Quantum Vibrational Spectroscopy of Water with High-Order Path Integrals: From Bulk to Interfaces. J Phys Chem Lett 2021; 12:9108-9114. [PMID: 34523941 DOI: 10.1021/acs.jpclett.1c02574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Vibrational spectroscopy is key in probing the interplay between the structure and dynamics of aqueous systems. To map different regions of experimental spectra to the microscopic structure of a system, it is important to combine them with first-principles atomistic simulations that incorporate the quantum nature of nuclei. Here we show that the large cost of calculating the quantum vibrational spectra of aqueous systems can be dramatically reduced compared with standard path integral methods by using approximate quantum dynamics based on high-order path integrals. Together with state-of-the-art machine-learned electronic properties, our approach gives an excellent description not only of the infrared and Raman spectra of bulk water but also of the 2D correlation and the more challenging sum-frequency generation spectra of the water-air interface. This paves the way for understanding complex interfaces such as water encapsulated between or in contact with hydrophobic and hydrophilic materials through robust and inexpensive surface-sensitive and multidimensional spectra with first-principles accuracy.
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Affiliation(s)
- Sam Shepherd
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Jinggang Lan
- Department of Chemistry, University of Zürich, Zürich 8057, Switzerland
| | - David M Wilkins
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Venkat Kapil
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW,United Kingdom
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36
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Keith JA, Vassilev-Galindo V, Cheng B, Chmiela S, Gastegger M, Müller KR, Tkatchenko A. Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems. Chem Rev 2021; 121:9816-9872. [PMID: 34232033 PMCID: PMC8391798 DOI: 10.1021/acs.chemrev.1c00107] [Citation(s) in RCA: 190] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Indexed: 12/23/2022]
Abstract
Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This Review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.
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Affiliation(s)
- John A. Keith
- Department
of Chemical and Petroleum Engineering Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Valentin Vassilev-Galindo
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Bingqing Cheng
- Accelerate
Programme for Scientific Discovery, Department
of Computer Science and Technology, 15 J. J. Thomson Avenue, Cambridge CB3 0FD, United Kingdom
| | - Stefan Chmiela
- Department
of Software Engineering and Theoretical Computer Science, Technische Universität Berlin, 10587, Berlin, Germany
| | - Michael Gastegger
- Department
of Software Engineering and Theoretical Computer Science, Technische Universität Berlin, 10587, Berlin, Germany
| | - Klaus-Robert Müller
- Machine
Learning Group, Technische Universität
Berlin, 10587, Berlin, Germany
- Department
of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul, 02841, Korea
- Max-Planck-Institut für Informatik, 66123 Saarbrücken, Germany
- Google Research, Brain Team, 10117 Berlin, Germany
| | - Alexandre Tkatchenko
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
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37
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Chen MS, Morawietz T, Mori H, Markland TE, Artrith N. AENET-LAMMPS and AENET-TINKER: Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials. J Chem Phys 2021; 155:074801. [PMID: 34418919 DOI: 10.1063/5.0063880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Machine-learning potentials (MLPs) trained on data from quantum-mechanics based first-principles methods can approach the accuracy of the reference method at a fraction of the computational cost. To facilitate efficient MLP-based molecular dynamics and Monte Carlo simulations, an integration of the MLPs with sampling software is needed. Here, we develop two interfaces that link the atomic energy network (ænet) MLP package with the popular sampling packages TINKER and LAMMPS. The three packages, ænet, TINKER, and LAMMPS, are free and open-source software that enable, in combination, accurate simulations of large and complex systems with low computational cost that scales linearly with the number of atoms. Scaling tests show that the parallel efficiency of the ænet-TINKER interface is nearly optimal but is limited to shared-memory systems. The ænet-LAMMPS interface achieves excellent parallel efficiency on highly parallel distributed-memory systems and benefits from the highly optimized neighbor list implemented in LAMMPS. We demonstrate the utility of the two MLP interfaces for two relevant example applications: the investigation of diffusion phenomena in liquid water and the equilibration of nanostructured amorphous battery materials.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Hideki Mori
- Department of Mechanical Engineering, College of Industrial Technology, 1-27-1 Nishikoya, Amagasaki, Hyogo 661-0047, Japan
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Nongnuch Artrith
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
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38
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Yao Y, Kanai Y. Nuclear Quantum Effect and Its Temperature Dependence in Liquid Water from Random Phase Approximation via Artificial Neural Network. J Phys Chem Lett 2021; 12:6354-6362. [PMID: 34231366 DOI: 10.1021/acs.jpclett.1c01566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report structural and dynamical properties of liquid water described by the random phase approximation (RPA) correlation together with the exact exchange energy (EXX) within density functional theory. By utilizing thermostated ring polymer molecular dynamics, we examine the nuclear quantum effects and their temperature dependence. We circumvent the computational limitation of performing direct first-principles molecular dynamics simulation at this high level of electronic structure theory by adapting an artificial neural network model. We show that the EXX+RPA level of theory accurately describes liquid water in terms of both dynamical and structural properties.
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Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
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39
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Miksch AM, Morawietz T, Kästner J, Urban A, Artrith N. Strategies for the construction of machine-learning potentials for accurate and efficient atomic-scale simulations. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abfd96] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Recent advances in machine-learning interatomic potentials have enabled the efficient modeling of complex atomistic systems with an accuracy that is comparable to that of conventional quantum-mechanics based methods. At the same time, the construction of new machine-learning potentials can seem a daunting task, as it involves data-science techniques that are not yet common in chemistry and materials science. Here, we provide a tutorial-style overview of strategies and best practices for the construction of artificial neural network (ANN) potentials. We illustrate the most important aspects of (a) data collection, (b) model selection, (c) training and validation, and (d) testing and refinement of ANN potentials on the basis of practical examples. Current research in the areas of active learning and delta learning are also discussed in the context of ANN potentials. This tutorial review aims at equipping computational chemists and materials scientists with the required background knowledge for ANN potential construction and application, with the intention to accelerate the adoption of the method, so that it can facilitate exciting research that would otherwise be challenging with conventional strategies.
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40
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Bredt AJ, Mendes de Oliveira D, Urbina AS, Slipchenko LV, Ben-Amotz D. Hydration and Seamless Integration of Hydrogen Peroxide in Water. J Phys Chem B 2021; 125:6986-6993. [PMID: 34133177 DOI: 10.1021/acs.jpcb.1c03107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Raman multivariate curve resolution is used to decompose the vibrational spectra of aqueous hydrogen peroxide (H2O2) into pure water, dilute H2O2, and concentrated H2O2 spectral components. The dilute spectra reveal four sub-bands in the OH stretch region, assigned to the OH stretch and Fermi resonant bend overtone of H2O2, and two nonequivalent OH groups on water molecules that donate a hydrogen bond to H2O2. At high concentrations, a spectral component resembling pure H2O2 emerges. Our results further demonstrate that H2O2 perturbs the structure of water significantly less than either methanol or sodium chloride of the same concentration, as evidenced by comparing the hydration-shell spectra of tert-butyl alcohol dissolved in the three aqueous solutions.
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Affiliation(s)
- Aria J Bredt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Andres S Urbina
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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41
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Altman RM, Richmond GL. Twist and Stretch: Assignment and Surface Charge Sensitivity of a Water Combination Band and Its Implications for Vibrational Sum Frequency Spectra Interpretations. J Phys Chem B 2021; 125:6717-6726. [DOI: 10.1021/acs.jpcb.1c03408] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Rebecca M. Altman
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Geraldine L. Richmond
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
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42
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Sun T, Ben-Amotz D, Wyslouzil BE. The freezing behavior of aqueous n-alcohol nanodroplets. Phys Chem Chem Phys 2021; 23:9991-10005. [PMID: 33870962 DOI: 10.1039/d0cp06131j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We generate water-rich aerosols containing 1-propanol and 1-pentanol in a supersonic nozzle to study the effects of these solutes on the freezing behavior of water. Condensation and freezing are characterized by two complementary techniques, pressure trace measurements and Fourier Transform Infrared spectroscopy. When 1-pentanol and 1-propanol are present, condensation occurs at higher temperatures because particle formation from the vapor phase is enhanced by the decrease in interfacial free energy of mixed aqueous-alcohol critical clusters relative to those of pure water. FTIR results suggest that when ∼6 nm radius droplets freeze, the tetrahedral structure of the ice is well preserved up to an overall alcohol mole fraction of 0.031 for 1-propanol and 0.043 for 1-pentanol. In this concentration range, the ice nucleation temperature decreases continuously with increasing 1-propanol concentration, whereas the onset of freezing is not significantly perturbed by 1-pentanol up to a mole fraction of 0.03. Furthermore, once freezing starts the ice nucleation rates in the aqueous-alcohol droplets are very close to those for pure water. In contrast, at the highest mole fractions of either alcohol it is not clear whether droplets freeze to form crystalline ice since the final state of the particles cannot be adequately characterized with the available experimental techniques.
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Affiliation(s)
- Tong Sun
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
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43
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Ahlers J, Adams EM, Bader V, Pezzotti S, Winklhofer KF, Tatzelt J, Havenith M. The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS. Biophys J 2021; 120:1266-1275. [PMID: 33515602 PMCID: PMC8059208 DOI: 10.1016/j.bpj.2021.01.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/21/2020] [Accepted: 01/19/2021] [Indexed: 01/09/2023] Open
Abstract
Formation of biomolecular condensates through liquid-liquid phase separation (LLPS) has emerged as a pervasive principle in cell biology, allowing compartmentalization and spatiotemporal regulation of dynamic cellular processes. Proteins that form condensates under physiological conditions often contain intrinsically disordered regions with low-complexity domains. Among them, the RNA-binding proteins FUS and TDP-43 have been a focus of intense investigation because aberrant condensation and aggregation of these proteins is linked to neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. LLPS occurs when protein-rich condensates form surrounded by a dilute aqueous solution. LLPS is per se entropically unfavorable. Energetically favorable multivalent protein-protein interactions are one important aspect to offset entropic costs. Another proposed aspect is the release of entropically unfavorable preordered hydration water into the bulk. We used attenuated total reflection spectroscopy in the terahertz frequency range to characterize the changes in the hydrogen bonding network accompanying the FUS enrichment in liquid-liquid phase-separated droplets to provide experimental evidence for the key role of the solvent as a thermodynamic driving force. The FUS concentration inside LLPS droplets was determined to be increased to 2.0 mM independent of the initial protein concentration (5 or 10 μM solutions) by fluorescence measurements. With terahertz spectroscopy, we revealed a dewetting of hydrophobic side chains in phase-separated FUS. Thus, the release of entropically unfavorable water populations into the bulk goes hand in hand with enthalpically favorable protein-protein interaction. Both changes are energetically favorable, and our study shows that both contribute to the thermodynamic driving force in phase separation.
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Affiliation(s)
- Jonas Ahlers
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Ellen M Adams
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Simone Pezzotti
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Martina Havenith
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany.
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44
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Morawietz T, Artrith N. Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications. J Comput Aided Mol Des 2021; 35:557-586. [PMID: 33034008 PMCID: PMC8018928 DOI: 10.1007/s10822-020-00346-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/26/2020] [Indexed: 01/13/2023]
Abstract
Atomistic simulations have become an invaluable tool for industrial applications ranging from the optimization of protein-ligand interactions for drug discovery to the design of new materials for energy applications. Here we review recent advances in the use of machine learning (ML) methods for accelerated simulations based on a quantum mechanical (QM) description of the system. We show how recent progress in ML methods has dramatically extended the applicability range of conventional QM-based simulations, allowing to calculate industrially relevant properties with enhanced accuracy, at reduced computational cost, and for length and time scales that would have otherwise not been accessible. We illustrate the benefits of ML-accelerated atomistic simulations for industrial R&D processes by showcasing relevant applications from two very different areas, drug discovery (pharmaceuticals) and energy materials. Writing from the perspective of both a molecular and a materials modeling scientist, this review aims to provide a unified picture of the impact of ML-accelerated atomistic simulations on the pharmaceutical, chemical, and materials industries and gives an outlook on the exciting opportunities that could emerge in the future.
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Affiliation(s)
- Tobias Morawietz
- Bayer AG, Pharmaceuticals, R&D, Digital Technologies, Computational Molecular Design, 42096 Wuppertal, Germany
| | - Nongnuch Artrith
- Department of Chemical Engineering, Columbia University, New York, NY 10027 USA
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45
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On the existence of soliton-like collective modes in liquid water at the viscoelastic crossover. Sci Rep 2021; 11:5417. [PMID: 33686146 PMCID: PMC7940660 DOI: 10.1038/s41598-021-84277-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/04/2021] [Indexed: 11/11/2022] Open
Abstract
The problem of large-density variations in supercooled and ambient water has been widely discussed in the past years. Recent studies have indicated the possibility of nanometer-sized density variations on the subpicosecond and picosecond time scales. The nature of fluctuating density heterogeneities remains a highly debated issue. In the present work, we address the problem of possible association of such density variations with the dynamics of terahertz longitudinal acoustic-like modes in liquid water. Our study is based on the fact that the subpicosecond dynamics of liquid water are essentially governed by the structural relaxation. Using a mode coupling theory approach, we found that for typical values of parameters of liquid water, the dynamic mechanism coming from the combination of the structural relaxation process and the finiteness of the amplitude of terahertz longitudinal acoustic-like mode gives rise to a soliton-like collective mode on a temperature-dependent nanometer length scale. The characteristics of this mode are consistent with the estimates of the amplitudes and temperature-dependent correlation lengths of density fluctuations in liquid water obtained in experiments and simulations. Thus, the fully dynamic mechanism could contribute to the formation and dynamics of fluctuating density heterogeneities. The soliton-like collective excitations suggested by our analysis may be relevant to different phenomena connected with supercooled water and can be expected to be associated with some ultrafast biological processes.
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Efimov YY, Naberukhin YI. Coupling of three intramolecular vibration modes of liquid H 2O molecules in the framework of the fluctuation theory of hydrogen bonding. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118772. [PMID: 32846302 DOI: 10.1016/j.saa.2020.118772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/30/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Vibrational spectra of liquid water contain a wealth of information about its structure and dynamics but there are no generally acknowledged interpretation of their band profiles, unfortunately. We have tried to calculate them taking into account only the coupling of three intramolecular vibrations in the set of H2O molecules with different initial oscillator frequencies and intensities. The matter is that each water molecule forms hydrogen bonds of different strengths; thus the OH stretching band spans several hundreds of wave numbers (the fluctuation theory of hydrogen bonding). This distribution overlaps with the similar band of the first overtone of the HOH bending frequencies thus triggering a Fermi resonance between three vibrations. There were some problems causing some simplifications in previous theoretical modeling of vibrational transitions in condensed water. To solve them we extract the statistical distribution of OH frequencies of H2O molecules directly from the experimental spectra of HOD molecules at the same conditions instead of defining it theoretically. Also the bending overtone is allowed to have non-zero intrinsic intensity when calculating the Fermi resonance. The test calculation of the isotropic component of the Raman spectrum which is most critical for interpretation shows that our algorithm can reproduces the characteristic peculiarities of the experiment. The spectrum consists of three non-Gaussian contours. The overtone of bending vibration, being strengthened by Fermi resonance, makes the greatest contribution to the dominating low-frequency spectrum component that was previously attributed to intermolecular coupling of adjacent OH oscillators by some authors. Further we plan to calculate similar band profiles in the IR and also Raman isotropic and anisotropic spectra of Н2О and D2О molecules within a wide temperature range for their quantitative comparison with experiment.
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Affiliation(s)
- Yu Ya Efimov
- Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia.
| | - Yu I Naberukhin
- Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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Laser diagnostics of self-organization of amphiphiles in aqueous solutions on the example of sodium octanoate. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Piskulich ZA, Thompson WH. Temperature Dependence of the Water Infrared Spectrum: Driving Forces, Isosbestic Points, and Predictions. J Phys Chem Lett 2020; 11:7762-7768. [PMID: 32852956 DOI: 10.1021/acs.jpclett.0c02301] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The temperature derivative of the infrared (IR) spectrum of HOD/D2O is directly calculated from simulations at a single temperature using a fluctuation theory approach. It is demonstrated, on the basis of an energetic decomposition of the derivative, that the blue shift with increasing temperature is associated with the competition between electrostatic and Lennard-Jones interactions. The same competition gives rise, where their contributions cancel, to a near isosbestic point. The derivative is further used to define an effective internal energy (and entropy) associated with the IR spectrum, and it is shown how a van't Hoff relation can be used to accurately predict the spectrum over a wide range of temperatures. These predictions also explain why a precise isosbestic point is not observed.
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Affiliation(s)
- Zeke A Piskulich
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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Chen MS, Zuehlsdorff TJ, Morawietz T, Isborn CM, Markland TE. Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments. J Phys Chem Lett 2020; 11:7559-7568. [PMID: 32808797 DOI: 10.1021/acs.jpclett.0c02168] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. Here, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore-environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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