1
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de la Puente M, Laage D. Impact of interfacial curvature on molecular properties of aqueous interfaces. J Chem Phys 2024; 160:234504. [PMID: 38888129 DOI: 10.1063/5.0210884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024] Open
Abstract
The curvature of soft interfaces plays a crucial role in determining their mechanical and thermodynamic properties, both at macroscopic and microscopic scales. In the case of air/water interfaces, particular attention has recently focused on water microdroplets, due to their distinctive chemical reactivity. However, the specific impact of curvature on the molecular properties of interfacial water and interfacial reactivity has so far remained elusive. Here, we use molecular dynamics simulations to determine the effect of curvature on a broad range of structural, dynamical, and thermodynamical properties of the interface. For a droplet, a flat interface, and a cavity, we successively examine the structure of the hydrogen-bond network and its relation to vibrational spectroscopy, the dynamics of water translation, rotation, and hydrogen-bond exchanges, and the thermodynamics of ion solvation and ion-pair dissociation. Our simulations show that curvature predominantly impacts the hydrogen-bond structure through the fraction of dangling OH groups and the dynamics of interfacial water molecules. In contrast, curvature has a limited effect on solvation and ion-pair dissociation thermodynamics. For water microdroplets, this suggests that the curvature alone cannot fully account for the distinctive reactivity measured in these systems, which are of great importance for catalysis and atmospheric chemistry.
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Affiliation(s)
- M de la Puente
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - D Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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2
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Benayad Z, David R, Stirnemann G. Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials. Proc Natl Acad Sci U S A 2024; 121:e2322040121. [PMID: 38809704 PMCID: PMC11161780 DOI: 10.1073/pnas.2322040121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
While RNA appears as a good candidate for the first autocatalytic systems preceding the emergence of modern life, the synthesis of RNA oligonucleotides without enzymes remains challenging. Because the uncatalyzed reaction is extremely slow, experimental studies bring limited and indirect information on the reaction mechanism, the nature of which remains debated. Here, we develop neural network potentials (NNPs) to study the phosphoester bond formation in water. While NNPs are becoming routinely applied to nonreactive systems or simple reactions, we demonstrate how they can systematically be trained to explore the reaction phase space for complex reactions involving several proton transfers and exchanges of heavy atoms. We then propagate at moderate computational cost hundreds of nanoseconds of a variety of enhanced sampling simulations with quantum accuracy in explicit solvent conditions. The thermodynamically preferred reaction pathway is a concerted, dissociative mechanism, with the transient formation of a metaphosphate transition state and direct participation of water solvent molecules that facilitate the exchange of protons through the nonbridging phosphate oxygens. Associative-dissociative pathways, characterized by a much tighter pentacoordinated phosphate, are higher in free energy. Our simulations also suggest that diprotonated phosphate, whose reactivity is never directly assessed in the experiments, is significantly less reactive than the monoprotonated species, suggesting that it is probably never the reactive species in normal pH conditions. These observations rationalize unexplained experimental results and the temperature dependence of the reaction rate, and they pave the way for the design of more efficient abiotic catalysts and activating groups.
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Affiliation(s)
- Zakarya Benayad
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, Université Paris-Cité, 75005Paris, France
- PASTEUR, Département de Chimie, École Normale Supérieure, Paris Sciences et Lettres University, Sorbonne University, CNRS, 75005Paris, France
| | - Rolf David
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, Université Paris-Cité, 75005Paris, France
- PASTEUR, Département de Chimie, École Normale Supérieure, Paris Sciences et Lettres University, Sorbonne University, CNRS, 75005Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, Université Paris-Cité, 75005Paris, France
- PASTEUR, Département de Chimie, École Normale Supérieure, Paris Sciences et Lettres University, Sorbonne University, CNRS, 75005Paris, France
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3
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Tiwary P. Modeling prebiotic chemistries with quantum accuracy at classical costs. Proc Natl Acad Sci U S A 2024; 121:e2408742121. [PMID: 38809708 PMCID: PMC11161769 DOI: 10.1073/pnas.2408742121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Affiliation(s)
- Pratyush Tiwary
- Institute for Physical Science and Technology, University of Maryland, College Park, MD20742
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
- University of Maryland Institute for Health Computing, Bethesda, MD20852
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4
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Murke S, Chen W, Pezzotti S, Havenith M. Tuning Acid-Base Chemistry at an Electrified Gold/Water Interface. J Am Chem Soc 2024; 146:12423-12430. [PMID: 38599583 PMCID: PMC11082902 DOI: 10.1021/jacs.3c13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
Acid-base reactions are ubiquitous in solution chemistry, as well as in electrochemistry. However, macroscopic concepts derived in solutions, such as pKa and pH, differ significantly at electrified metal-aqueous interfaces due to specific solvation and applied voltage. Here, we measure the pKa values of an amino acid, glycine, at a gold/water interface under a varying applied voltage by means of spectroscopic titration. With the help of simulations, we propose a general model to understand potential-dependent shifts in pKa values in terms of local hydrophobicity and electric fields. These parameters can be tuned by adjusting the metal surface and applied voltage, respectively, offering promising, but still unexplored, paths to regulate reactivity. Our results change the focus with respect to common interpretations based on, for example, apparent local pH effects and open interesting perspectives for electrochemical reaction steering.
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Affiliation(s)
| | | | | | - Martina Havenith
- Department of Physical Chemistry
II, Ruhr University Bochum, D-44801 Bochum, Germany
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5
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Wen M, Chang X, Xu Y, Chen D, Chu Q. Determining the mechanical and decomposition properties of high energetic materials (α-RDX, β-HMX, and ε-CL-20) using a neural network potential. Phys Chem Chem Phys 2024; 26:9984-9997. [PMID: 38477375 DOI: 10.1039/d4cp00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Molecular simulations of high energetic materials (HEMs) are limited by efficiency and accuracy. Recently, neural network potential (NNP) models have achieved molecular simulations of millions of atoms while maintaining the accuracy of density functional theory (DFT) levels. Herein, an NNP model covering typical HEMs containing C, H, N, and O elements is developed. The mechanical and decomposition properties of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), hexahydro-1,3,5-trinitro-1,3,5-triazine (HMX), and 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (CL-20) are determined by employing the molecular dynamics (MD) simulations based on the NNP model. The calculated results show that the mechanical properties of α-RDX, β-HMX, and ε-CL-20 agree with previous experiments and theoretical results, including cell parameters, equations of state, and elastic constants. In the thermal decomposition simulations, it is also found that the initial decomposition reactions of the three crystals are N-NO2 homolysis, corresponding radical intermediates formation, and NO2-induced reactions. This decomposition trajectory is mainly divided into two stages separating from the peak of NO2: pyrolysis and oxidation. Overall, the NNP model for C/H/N/O elements in this work is an alternative reactive force field for RDX, HMX, and CL-20 HEMs, and it opens up new potential for future kinetic study of nitramine explosives.
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Affiliation(s)
- Mingjie Wen
- State Key Laboratory of Explosion Science and Safety Protection, Beijing Institute of Technology, Beijing 100081, P. R. China.
| | - Xiaoya Chang
- State Key Laboratory of Explosion Science and Safety Protection, Beijing Institute of Technology, Beijing 100081, P. R. China.
| | - Yabei Xu
- State Key Laboratory of Explosion Science and Safety Protection, Beijing Institute of Technology, Beijing 100081, P. R. China.
| | - Dongping Chen
- State Key Laboratory of Explosion Science and Safety Protection, Beijing Institute of Technology, Beijing 100081, P. R. China.
| | - Qingzhao Chu
- State Key Laboratory of Explosion Science and Safety Protection, Beijing Institute of Technology, Beijing 100081, P. R. China.
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6
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de la Puente M, Gomez A, Laage D. Neural Network-Based Sum-Frequency Generation Spectra of Pure and Acidified Water Interfaces with Air. J Phys Chem Lett 2024; 15:3096-3102. [PMID: 38470065 DOI: 10.1021/acs.jpclett.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The affinity of hydronium ions (H3O+) for the air-water interface is a crucial question in environmental chemistry. While sum-frequency generation (SFG) spectroscopy has been instrumental in indicating the preference of H3O+ for the interface, key questions persist regarding the molecular origin of the SFG spectral changes in acidified water. Here we combine nanosecond long neural network (NN) reactive simulations of pure and acidified water slabs with NN predictions of molecular dipoles and polarizabilities to calculate SFG spectra of long reactive trajectories including proton transfer events. Our simulations show that H3O+ ions cause two distinct changes in phase-resolved SFG spectra: first, a low-frequency tail due to the vibrations of H3O+ and its first hydration shell, analogous to the bulk proton continuum, and second, an enhanced hydrogen-bonded band due to the ion-induced static field polarizing molecules in deeper layers. Our calculations confirm that changes in the SFG spectra of acidic solutions are caused by hydronium ions preferentially residing at the interface.
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Affiliation(s)
- Miguel de la Puente
- PASTEUR, Department of Chemistry, École Normale Supérieur, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Axel Gomez
- PASTEUR, Department of Chemistry, École Normale Supérieur, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieur, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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7
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Chang X, Wu Y, Chu Q, Zhang G, Chen D. Ab Initio Driven Exploration on the Thermal Properties of Al-Li Alloy. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38497105 DOI: 10.1021/acsami.4c01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Al-Li alloys are feasible and promising additives in advanced energy and propellant systems due to the significantly enhanced heat release and increased specific impulse. The thermal properties of Al-Li alloys directly determine the manufacturing, storage safety, and ignition delay of propellants. In this study, a neural network potential (NNP) is developed to investigate the thermal behaviors of Al-Li alloys from an atomistic perspective. The novel NNP demonstrates an excellent predictive ability for energy, atomic force, mechanical behaviors, phonon vibrations, and dynamic evolutions. A series of NNP-based molecular dynamics simulations are performed to investigate the effect of Li doping on the thermal properties of Al-Li alloys. All calculated results for Al-Li alloys are consistent with experimental values for Al, ensuring their validity in predicting Al-Li interactions. The simulation results suggest that a minor increment in the Li content results in a slight change in the melting point, thermal expansion, and radical distribution functions. These three properties are associated with the lattice characteristics; nonetheless, it causes a substantial reduction in thermal conductivity, which is related to the physical properties of the elements. The lower thermal conductivity allows heat accumulation on the particle surface, thereby speeding up the surface premelt and ignition. This provides an alternative atomic explanation for the improved combustion performance of Al-Li alloys. These findings integrate insights from the field of alloy material science into crucial combustion applications, serving as an atomistic guide for developing manufacturing techniques.
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Affiliation(s)
- Xiaoya Chang
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Yongchao Wu
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Qingzhao Chu
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Gang Zhang
- Institute of High Performance Computing Agency for Science Technology and Research (A*STAR), Singapore 138632, Singapore
| | - Dongping Chen
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China
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8
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Ben-Amotz D. Interfacial chemical reactivity enhancement. J Chem Phys 2024; 160:084704. [PMID: 38391019 DOI: 10.1063/5.0186945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Interfacial enhancements of chemical reaction equilibria and rates in liquid droplets are predicted using a combined theoretical and experimental analysis strategy. Self-consistent solutions of reaction and adsorption equilibria indicate that interfacial reactivity enhancement is driven primarily by the adsorption free energy of the product (or activated complex). Reactant surface activity has a smaller indirect influence on reactivity due to compensating reactant interfacial concentration and adsorption free energy changes, as well as adsorption-induced depletion of the droplet core. Experimental air-water interfacial adsorption free energies and critical micelle concentration correlations provide quantitative surface activity estimates as a function of molecular structure, predicting an increase in interfacial reactivity with increasing product size and decreasing product polarity, aromaticity, and charge (but less so for anions than cations). Reactions with small, neutral, or charged products are predicted to have little reactivity enhancement at an air-water interface unless the product is rendered sufficiently surface active by, for example, interactions with interfacial water dangling OH groups, charge transfer, or voltage fluctuations.
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Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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9
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Prisle NL. Surfaces of Atmospheric Droplet Models Probed with Synchrotron XPS on a Liquid Microjet. Acc Chem Res 2024; 57:177-187. [PMID: 38156821 PMCID: PMC10795169 DOI: 10.1021/acs.accounts.3c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Indexed: 01/03/2024]
Abstract
ConspectusThe atmosphere is a key part of the earth system comprising myriad chemical species in all basic forms of matter. Ubiquitous nano- and microscopic aerosol particles and cloud droplets suspended in the air play crucial roles in earth's climate and the formation of air pollution. Surfaces are a prominent part of aerosols and droplets, due to the high surface area to bulk volume ratios, but very little is known about their specific properties. Many atmospheric compounds are surface-active, leading to enhanced surface concentrations in aqueous solutions. Their distribution between the surface and bulk may determine heterogeneous chemistry and many other properties of aerosol and cloud droplets, but has not been directly observed.We used X-ray photoelectron spectroscopy (XPS) to obtain direct molecular-level information on the surface composition and structure of aqueous solutions of surface-active organics as model systems for atmospheric aerosol and cloud droplets. XPS is a vacuum-based technique enabled for volatile aqueous organic samples by the application of a high-speed liquid microjet. In combination with brilliant synchrotron X-rays, the chemical specificity of XPS allows distinction between elements in different chemical states and positions within molecular structures. We used core-level C 1s and N 1s signals to identify the alkyl and hydrophilic groups of atmospheric carboxylic acids, alkyl-amines, and their conjugate acids and bases. From this, we infer changes in the orientation of surface-adsorbed species and quantify their relative abundances in the surface. XPS-derived surface enrichments of the organics follow trends expected from their surface activities and we observed a preferential orientation at the surface with the hydrophobic alkyl chains pointing increasingly outward from the solution at higher concentrations. This provides a first direct experimental observation of well-established concepts of surface adsorption and confirms the soundness of the method.We mapped relative abundances of conjugate acid-base pairs in the aqueous solution surfaces from the respective intensities of distinctive XPS signals. For each pair, the protonation equilibrium was significantly shifted toward the neutral form in the surface, compared to the bulk solution, across the full pH range. This represents an apparent shift of the pKa in the surface, which may be toward either higher or lower pH, depending on whether the acid or base form of the pair is the neutral species. The surface shifts are broadly consistent with the relative differences in surface enrichment of the individual acid and base conjugates in binary aqueous solutions, with additional contributions from nonideal interactions in the surface. In aqueous mixtures of surface-active carboxylate anions with ammonium salts at near-neutral pH, we found that the conjugate carboxylic acids were further strongly enhanced. This occurs as the coadsorption of weakly basic carboxylate anions and weakly acidic ammonium cations forms ion-pair surface layers with strongly enhanced local abundances, increasing the probability of net proton transfer according to Le Chatelier's principle. The effect is stronger when the evaporation of ammonia from the surface further contributes to irreversibly perturb the protonation equilibrium, leaving a surplus of carboxylic acid. These surface-specific effects may profoundly influence atmospheric chemistry mediated by aqueous aerosols and cloud droplets but are currently not taken into account in atmospheric models.
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Affiliation(s)
- Nønne L. Prisle
- Center for Atmospheric Research, University of Oulu, P.O. Box 4500, Oulu 90014, Finland
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10
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de la Puente M, Laage D. How the Acidity of Water Droplets and Films Is Controlled by the Air-Water Interface. J Am Chem Soc 2023; 145:25186-25194. [PMID: 37938132 DOI: 10.1021/jacs.3c07506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Acidity is a key determinant of chemical reactivity in atmospheric aqueous aerosols and water microdroplets used for catalysis. However, many fundamental questions about these systems have remained elusive, including how their acidity differs from that of bulk solutions, the degree of heterogeneity between their core and surface, and how the acid-base properties are affected by their size. Here, we perform hybrid density functional theory (DFT)-quality neural network-based molecular simulations with explicit nuclear quantum effects and combine them with an analytic model to describe the pH and self-ion concentrations of droplets and films for sizes ranging from nm to μm. We determine how the acidity of water droplets and thin films is controlled by the properties of the air-water interface and by their surface-to-volume ratio. We show that while the pH is uniform in each system, hydronium and hydroxide ions exhibit concentration gradients that span the two outermost molecular layers, enriching the interface with hydronium cations and depleting it with hydroxide anions. Acidity depends strongly on the surface-to-volume ratio for system sizes below a few tens of nanometers, where the core becomes enriched in hydroxide ions and the pH increases as a result of hydronium stabilization at the interface. These results obtained for pure water systems have important implications for our understanding of chemical reactivity in atmospheric aerosols and for catalysis in aqueous microdroplets.
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Affiliation(s)
- Miguel de la Puente
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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11
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Pereira RW, Ramabhadran RO. Accurate Computation of Aqueous p Kas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box p K-Yay Method. J Phys Chem A 2023; 127:9121-9138. [PMID: 37862610 DOI: 10.1021/acs.jpca.3c02977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.
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Affiliation(s)
- Roshni W Pereira
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
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12
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Zhang W, Zhou L, Yan T, Chen M. Speciation of La 3+-Cl - Complexes in Hydrothermal Fluids from Deep Potential Molecular Dynamics. J Phys Chem B 2023; 127:8926-8937. [PMID: 37812657 DOI: 10.1021/acs.jpcb.3c05428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The stability of rare earth element (REE) complexes plays a crucial role in quantitatively assessing their hydrothermal migration and transformation. However, reliable data are lacking under high-temperature hydrothermal conditions, which hampers our understanding of the association behavior of REE. Here a deep learning potential model for the LaCl3-H2O system in hydrothermal fluids is developed based on the first-principles density functional theory calculations. The model accurately predicts the radial distribution functions compared to ab initio molecular dynamics (AIMD) simulations. Furthermore, species of La-Cl complexes, the dissociation pathway of the La-Cl complexes dissociation process, and the potential of mean forces and corresponding association constants (logK) for LaCln3-n (n = 1-4) are extensively investigated under a wide range of temperatures and pressures. Empirical density models for logK calculation are fitted with these data and can accurately predict logK data from both experimental results and AIMD simulations. The distribution of La-Cl species is also evaluated across a wide range of temperatures, pressures, and initial chloride concentration conditions. The results show that La-Cl complexes are prone to forming in a low-density solution, and the number of bonded Cl- ions increases with rising temperature. In contrast, in a high-density solution, La3+ dominates and becomes the more prevalent species.
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Affiliation(s)
- Wei Zhang
- School of Geography and Environmental Science (School of Karst Science), Guizhou Normal University, Guiyang 550025, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550025, China
- Research Center of Karst Ecological Civilization, Guizhou Normal University, Guiyang 550025, China
| | - Li Zhou
- School of Geography and Environmental Science (School of Karst Science), Guizhou Normal University, Guiyang 550025, China
| | - Tinggui Yan
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, China
| | - Mohan Chen
- HEDPS, CAPT, College of Engineering and School of Physics, Peking University, Beijing 100871, China
- AI for Science Institute, Beijing 100080, China
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13
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Zeng J, Zhang D, Lu D, Mo P, Li Z, Chen Y, Rynik M, Huang L, Li Z, Shi S, Wang Y, Ye H, Tuo P, Yang J, Ding Y, Li Y, Tisi D, Zeng Q, Bao H, Xia Y, Huang J, Muraoka K, Wang Y, Chang J, Yuan F, Bore SL, Cai C, Lin Y, Wang B, Xu J, Zhu JX, Luo C, Zhang Y, Goodall REA, Liang W, Singh AK, Yao S, Zhang J, Wentzcovitch R, Han J, Liu J, Jia W, York DM, E W, Car R, Zhang L, Wang H. DeePMD-kit v2: A software package for deep potential models. J Chem Phys 2023; 159:054801. [PMID: 37526163 PMCID: PMC10445636 DOI: 10.1063/5.0155600] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/03/2023] [Indexed: 08/02/2023] Open
Abstract
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.
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Affiliation(s)
- Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | - Denghui Lu
- HEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Pinghui Mo
- College of Electrical and Information Engineering, Hunan University, Changsha, People’s Republic of China
| | - Zeyu Li
- Yuanpei College, Peking University, Beijing 100871, People’s Republic of China
| | - Yixiao Chen
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08540, USA
| | - Marián Rynik
- Department of Experimental Physics, Comenius University, Mlynská Dolina F2, 842 48 Bratislava, Slovakia
| | - Li’ang Huang
- Center for Quantum Information, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| | | | - Shaochen Shi
- ByteDance Research, Zhonghang Plaza, No. 43, North 3rd Ring West Road, Haidian District, Beijing, People’s Republic of China
| | | | - Haotian Ye
- Yuanpei College, Peking University, Beijing 100871, People’s Republic of China
| | - Ping Tuo
- AI for Science Institute, Beijing 100080, People’s Republic of China
| | - Jiabin Yang
- Baidu, Inc., Beijing, People’s Republic of China
| | | | - Yifan Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | | | - Qiyu Zeng
- Department of Physics, National University of Defense Technology, Changsha, Hunan 410073, People’s Republic of China
| | | | - Yu Xia
- ByteDance Research, Zhonghang Plaza, No. 43, North 3rd Ring West Road, Haidian District, Beijing, People’s Republic of China
| | | | - Koki Muraoka
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yibo Wang
- DP Technology, Beijing 100080, People’s Republic of China
| | | | - Fengbo Yuan
- DP Technology, Beijing 100080, People’s Republic of China
| | - Sigbjørn Løland Bore
- Hylleraas Centre for Quantum Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway
| | | | - Yinnian Lin
- Wangxuan Institute of Computer Technology, Peking University, Beijing 100871, People’s Republic of China
| | - Bo Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, People’s Republic of China
| | - Jiayan Xu
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, Belfast BT9 5AG, United Kingdom
| | - Jia-Xin Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Chenxing Luo
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
| | - Yuzhi Zhang
- DP Technology, Beijing 100080, People’s Republic of China
| | | | - Wenshuo Liang
- DP Technology, Beijing 100080, People’s Republic of China
| | - Anurag Kumar Singh
- Department of Data Science, Indian Institute of Technology, Palakkad, Kerala, India
| | - Sikai Yao
- DP Technology, Beijing 100080, People’s Republic of China
| | - Jingchao Zhang
- NVIDIA AI Technology Center (NVAITC), Santa Clara, California 95051, USA
| | | | - Jiequn Han
- Center for Computational Mathematics, Flatiron Institute, New York, New York 10010, USA
| | - Jie Liu
- College of Electrical and Information Engineering, Hunan University, Changsha, People’s Republic of China
| | | | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | | | - Han Wang
- Author to whom correspondence should be addressed:
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14
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Huo J, Chen J, Liu P, Hong B, Zhang J, Dong H, Li S. Microscopic Mechanism of Proton Transfer in Pure Water under Ambient Conditions. J Chem Theory Comput 2023. [PMID: 37365994 DOI: 10.1021/acs.jctc.3c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Water molecules and the associated proton transfer (PT) are prevalent in chemical and biological systems and have been a hot research topic. Spectroscopic characterization and ab initio molecular dynamics (AIMD) simulations have previously revealed insights into acidic and basic liquids. Presumably, the situation in the acidic/basic solution is not necessarily the same as in pure water; in addition, the autoionization constant for water is only 10-14 under ambient conditions, making the study of PT in pure water challenging. To overcome this issue, we modeled periodic water box systems containing 1000 molecules for tens of nanoseconds based on a neural network potential (NNP) with quantum mechanical accuracy. The NNP was generated by training a dataset containing the energies and atomic forces of 17 075 configurations of periodic water box systems, and these data points were calculated at the MP2 level that considers electron correlation effects. We found that the size of the system and the duration of the simulation have a significant impact on the convergence of the results. With these factors considered, our simulations showed that hydronium (H3O+) and hydroxide (OH-) ions in water have distinct hydration structures, thermodynamic and kinetic properties, e.g., the longer-lasting and more stable hydrated structure of OH- ions than that of H3O+, as well as a significantly higher free energy barrier for the OH--associated PT than that of H3O+, leading the two to exhibit completely different PT behaviors. Given these characteristics, we further found that PT via OH- ions tends not to occur multiple times or between many molecules. In contrast, PT via H3O+ can synergistically occur among multiple molecules and prefers to adopt a cyclic pattern among three water molecules, while it occurs mostly in a chain pattern when more water molecules are involved. Therefore, our studies provide a detailed and solid microscopic explanation for the PT process in pure water.
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Affiliation(s)
- Jun Huo
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Jianghao Chen
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Pei Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
| | - Benkun Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
| | - Jian Zhang
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, China
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15
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Angle KJ, Grassian VH. Direct quantification of changes in pH within single levitated microdroplets and the kinetics of nitrate and chloride depletion. Chem Sci 2023; 14:6259-6268. [PMID: 37325137 PMCID: PMC10266444 DOI: 10.1039/d2sc06994f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/11/2023] [Indexed: 06/17/2023] Open
Abstract
The hygroscopicity and pH of aqueous microdroplets and smaller aerosols control their impacts on human health and the climate. Nitrate depletion and chloride depletion through the partitioning of HNO3 and HCl into the gas phase are processes that are enhanced in micron-sized and smaller aqueous droplets and this depletion influences both hygroscopicity and pH. Despite a number of studies, uncertainties remain about these processes. While acid evaporation and the loss of HCl or HNO3 have been observed during dehydration, there is a question as to the rate of acid evaporation and whether this can occur in fully hydrated droplets at higher relative humidity (RH). To directly elucidate the kinetics of nitrate and chloride depletion through evaporation of HNO3 and HCl, respectively at high RH, single levitated microdroplets are probed with cavity-enhanced Raman spectroscopy. Using glycine as a novel in situ pH probe, we are able to simultaneously measure changes in microdroplet composition and pH over timescales of hours. We find that the loss of chloride from the microdroplet is faster than that of nitrate, and the calculated rate constants infer that depletion is limited by the formation of HCl or HNO3 at the air-water interface and subsequent partitioning into the gas phase.
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Affiliation(s)
- Kyle J Angle
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
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16
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Chang X, Chu Q, Chen D. Monitoring the melting behavior of boron nanoparticles using a neural network potential. Phys Chem Chem Phys 2023; 25:12841-12853. [PMID: 37165915 DOI: 10.1039/d3cp00571b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The melting behavior of metal additives is fundamental for various propulsion and energy-conversion applications. A neural network potential (NNP) is proposed to examine the size-dependent melting behaviors of boron nanoparticles. Our NNP model is proven to possess a desirable computational efficiency and retain ab initio accuracy, allowing investigation of the physicochemical properties of bulk boron crystals from an atomic perspective. In this work, a series of NNP-based molecular dynamics simulations were conducted and numerical evidence of the size-dependent melting behavior of boron nanoparticles with diameters from 3 to 6 nm was reported for the first time. Evolution of the intermolecular energy and the Lindemann index are used to monitor the melting process. A liquid layer forms on the particle surface and further expands with increased temperature. Once the liquid layer reaches the core region, the particle is completely molten. The reduced melting temperature of the boron nanoparticle decreases with its particle size following a linear relationship with reciprocal size, similar to other commonly used metals (Al and Mg). Additionally, boron nanoparticles are more sensitive to particle size than Al particles and less sensitive than Mg particles. These findings provide an atomistic perspective for developing manufacturing techniques and tailoring combustion performance in practical applications.
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Affiliation(s)
- Xiaoya Chang
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Qingzhao Chu
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Dongping Chen
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
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17
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Xia D, Chen J, Xie HB, Zhong J, Francisco JS. Counterintuitive Oxidation of Alcohols at Air-Water Interfaces. J Am Chem Soc 2023; 145:4791-4799. [PMID: 36795890 DOI: 10.1021/jacs.2c13661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
This study shows that the oxidation of alcohols can rapidly occur at air-water interfaces. It was found that methanediols (HOCH2OH) orient at air-water interfaces with a H atom of the -CH2- group pointing toward the gaseous phase. Counterintuitively, gaseous hydroxyl radicals do not prefer to attack the exposed -CH2- group but the -OH group that forms hydrogen bonds with water molecules at the surface via a water-promoted mechanism, leading to the formation of formic acids. Compared with gaseous oxidation, the water-promoted mechanism at the air-water interface significantly lowers free-energy barriers from ∼10.7 to ∼4.3 kcal·mol-1 and therefore accelerates the formation of formic acids. The study unveils a previously overlooked source of environmental organic acids that are bound up with aerosol formation and water acidity.
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Affiliation(s)
- Deming Xia
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hong-Bin Xie
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jie Zhong
- School of Petroleum Engineering and School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Joseph S Francisco
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6316, United States
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18
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Wan Z, Fang Y, Liu Z, Francisco JS, Zhu C. Mechanistic Insights into the Reactive Uptake of Chlorine Nitrate at the Air-Water Interface. J Am Chem Soc 2023; 145:944-952. [PMID: 36595549 DOI: 10.1021/jacs.2c09837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
It is well-known that the aqueous-phase processing of chlorine nitrate (ClONO2) plays a crucial role in ozone depletion. However, many of the physical and chemical properties of ClONO2 at the air-water interface or in bulk water are unknown or not understood on a microscopic scale. Here, the solvation and hydrolysis of ClONO2 at the air-water interface and in bulk water at 300 K were investigated by classical and ab initio molecular dynamics (AIMD) simulations combined with free energy methods. Our results revealed that ClONO2 prefers to accumulate at the air-water interface rather than in the bulk phase. Specifically, halogen bonding interactions (ClONO2)Cl···O(H2O) were found to be the predominant interactions between ClONO2 and H2O. Moreover, metadynamics-biased AIMD simulations revealed that ClONO2 hydrolysis is catalyzed at the air-water interface with an activation barrier of only ∼0.2 kcal/mol; additionally, the difference in free energy between the product and reactant is only ∼0.1 kcal/mol. Surprisingly, the near-barrierless reaction and the comparable free energies of the reactant and product suggested that the ClONO2 hydrolysis at the air-water interface is reversible. When the temperature is lowered from 300 to 200 K, the activation barrier for the ClONO2 hydrolysis at the air-water interface is increased to ∼5.4 kcal/mol. These findings have important implications for the interpretation of experiments.
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Affiliation(s)
- Zhengyi Wan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Yeguang Fang
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing100190, People's Republic of China
| | - Ziao Liu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States.,Department of Earth & Environmental Science, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing100190, People's Republic of China
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19
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Molecular dynamics simulations of LiCl ion pairs in high temperature aqueous solutions by deep learning potential. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Young TA, Johnston-Wood T, Zhang H, Duarte F. Reaction dynamics of Diels-Alder reactions from machine learned potentials. Phys Chem Chem Phys 2022; 24:20820-20827. [PMID: 36004770 DOI: 10.1039/d2cp02978b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent advances in the development of reactive machine-learned potentials (MLPs) promise to transform reaction modelling. However, such methods have remained computationally expensive and limited to experts. Here, we employ different MLP methods (ACE, NequIP, GAP), combined with automated fitting and active learning, to study the reaction dynamics of representative Diels-Alder reactions. We demonstrate that the ACE and NequIP MLPs can consistently achieve chemical accuracy (±1 kcal mol-1) to the ground-truth surface with only a few hundred reference calculations. These strategies are shown to enable routine ab initio-quality classical and quantum dynamics, and obtain dynamical quantities such as product ratios and free energies from non-static methods. For ambimodal reactions, product distributions were found to be strongly dependent on the QM method and less so on the type of dynamics propagated.
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Affiliation(s)
- Tom A Young
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | | | - Hanwen Zhang
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Fernanda Duarte
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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21
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Zheng RH, Wei WM. Sum-frequency vibrational spectroscopy of methanol at interfaces due to Fermi resonance. Phys Chem Chem Phys 2022; 24:27204-27211. [DOI: 10.1039/d2cp01808j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We present a theoretical method of studying sum-frequency vibrational spectroscopy for the CH3 group of methanol at interfaces due to Fermi resonance, which provides a novel and untraditional point of view with respect to traditional approaches.
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Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing, 100190, P. R. China
| | - Wen-Mei Wei
- School of Basic Medical Science, Anhui Medical University, Hefei, Anhui, 230032, P. R. China
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