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Wang R, Mehdi S, Zou Z, Tiwary P. Is the Local Ion Density Sufficient to Drive NaCl Nucleation from the Melt and Aqueous Solution? J Phys Chem B 2024; 128:1012-1021. [PMID: 38262436 DOI: 10.1021/acs.jpcb.3c06735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Even though nucleation is ubiquitous in different science and engineering problems, investigating nucleation is extremely difficult due to the complicated ranges of time and length scales involved. In this work, we simulate NaCl nucleation in both molten and aqueous environments using enhanced sampling of all-atom molecular dynamics with deep-learning-based estimation of reaction coordinates. By incorporating various structural order parameters and learning the reaction coordinate as a function thereof, we achieve significantly improved sampling relative to traditional ad hoc descriptions of what drives nucleation, particularly in an aqueous medium. Our results reveal a one-step nucleation mechanism in both environments, with reaction coordinate analysis highlighting the importance of local ion density in distinguishing solid and liquid states. However, although fluctuations in the local ion density are necessary to drive nucleation, they are not sufficient. Our analysis shows that near the transition states, descriptors such as enthalpy and local structure become crucial. Our protocol proposed here enables robust nucleation analysis and phase sampling and could offer insights into nucleation mechanisms for generic small molecules in different environments.
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Affiliation(s)
- Ruiyu Wang
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Shams Mehdi
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Ziyue Zou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Pratyush Tiwary
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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2
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Sun Q, He X, Fu Y. The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water. Molecules 2023; 28:5164. [PMID: 37446826 DOI: 10.3390/molecules28135164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular hydrogen bondings. During folding, hydrophobic interactions are regarded to be the driving forces, especially in the initial structural collapse of a protein. Additionally, folding is guided by the strong interactions within proteins, such as intramolecular hydrogen bondings related to the α-helices and β-sheets of proteins. Therefore, a protein is divided into the folding key (FK) regions related to intramolecular hydrogen bondings and the non-folding key (non-FK) regions. Various conformations are expected for FK and non-FK regions. Different from non-FK regions, it is necessary for FK regions to form the specific conformations in folding, which are regarded as the necessary folding pathways (or "beacons"). Additionally, sequential folding is expected for the FK regions, and the intermediate state is found during folding. They are reflected on the local basins in the free energy landscape (FEL) of folding. To demonstrate the structural model, molecular dynamics (MD) simulations are conducted on the folding pathway of the TRP-cage in water.
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Affiliation(s)
- Qiang Sun
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Xian He
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Yanfang Fu
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
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3
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Darojat Y, Aljalal A, Gasmi K, Aljundi IH, Mirsaleh-Kohan N, Al-Basheer W. Laser-Induced Shockwave Crystallization in Supersaturated Solutions and Conceivable Clustering in Undersaturated Aqueous Potassium Nitrate Solutions. ACS OMEGA 2022; 7:38400-38408. [PMID: 36340109 PMCID: PMC9631718 DOI: 10.1021/acsomega.2c03456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
In this study, a newly developed setup based on laser-induced shockwave crystallization coupled with electric conductivity monitoring was employed to study the growth of crystals in supersaturated solutions and to investigate possible clustering in undersaturated solutions of potassium nitrate (KNO3). A comparison was drawn between crystals induced by laser irradiation, by shockwaves, and spontaneously in terms of crystals' mean size, shape, and size distribution. The size distribution of produced crystals by shockwaves was also characterized in terms of laser irradiation time. The results show that produced crystals by shockwaves propagation have the sharpest size distribution and the smallest mean dimensions compared to crystals grown spontaneously or by direct laser induction. Real-time monitoring of nucleation was also performed in supersaturated solutions, while decrease in conductivity was observed in undersaturated solutions as a function of laser irradiation time.
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Affiliation(s)
- Yusron Darojat
- Department
of Physics, King Fahd University of Petroleum
& Minerals, Dhahran31261, Saudi Arabia
- Department
of Physics, Institut Teknologi Sumatera, Lampung35365, Indonesia
| | - Abdulaziz Aljalal
- Department
of Physics, King Fahd University of Petroleum
& Minerals, Dhahran31261, Saudi Arabia
| | - Khaled Gasmi
- Department
of Physics, King Fahd University of Petroleum
& Minerals, Dhahran31261, Saudi Arabia
- Interdisciplinary
Research Center for Intelligent Manufacturing and Robotics, King Fahd University of Petroleum & Minerals, Dhahran31261, Saudi Arabia
| | - Isam H. Aljundi
- Chemical
Engineering Department, King Fahd University
of Petroleum and Minerals, Dhahran31261, Saudi Arabia
- Interdisciplinary
Research Center of Membranes and Water Security, King Fahd University of Petroleum & Minerals, Dhahran31261, Saudi Arabia
| | - Nasrin Mirsaleh-Kohan
- Division
of Chemistry and Biochemistry, Texas Woman’s
University, Denton76204, Texas, United States
| | - Watheq Al-Basheer
- Department
of Physics, King Fahd University of Petroleum
& Minerals, Dhahran31261, Saudi Arabia
- Interdisciplinary
Research Center of Membranes and Water Security, King Fahd University of Petroleum & Minerals, Dhahran31261, Saudi Arabia
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Lenart VM, de Lara LS, Gómez SL, Turchiello RF. Study of brine-halite phase separation through optical constringence and molecular dynamics. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:57. [PMID: 35781758 DOI: 10.1140/epje/s10189-022-00214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
This work presents a study of the reciprocal dispersive power, also known as constringence or Abbe number of an aqueous solution of NaCl in a wide range of concentrations. The constringence exhibited a distinct behavior in the region close to the phase transition between a phase containing exclusively brine and a phase containing brine+halite. Molecular dynamics simulations of this system indicated the existence of halite formation below the known saturation curve, which agreed with the experimental measurements, indicating a crystal growth in the unsaturated region.
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Affiliation(s)
- Vinícius M Lenart
- Physics Department, Federal University of Technology of Paran'a, Doutor Washington Subtil Chueire, 330, Ponta Grossa, PR, 84017-220, Brazil
| | - Lucas S de Lara
- Department of Physics, State University of Ponta Grossa, Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
| | - Sergio L Gómez
- Department of Physics, State University of Ponta Grossa, Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
| | - Rozane F Turchiello
- Physics Department, Federal University of Technology of Paran'a, Doutor Washington Subtil Chueire, 330, Ponta Grossa, PR, 84017-220, Brazil.
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Bulutoglu PS, Wang S, Boukerche M, Nere NK, Corti DS, Ramkrishna D. An investigation of the kinetics and thermodynamics of NaCl nucleation through composite clusters. PNAS NEXUS 2022; 1:pgac033. [PMID: 36713321 PMCID: PMC9802385 DOI: 10.1093/pnasnexus/pgac033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/04/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023]
Abstract
Having a good understanding of nucleation is critical for the control of many important processes, such as polymorph selection during crystallization. However, a complete picture of the molecular-level mechanisms of nucleation remains elusive. In this work, we take an in-depth look at the NaCl homogeneous nucleation mechanism through thermodynamics. Distinguished from the classical nucleation theory, we calculate the free energy of nucleation as a function of two nucleus size coordinates: crystalline and amorphous cluster sizes. The free energy surface reveals a thermodynamic preference for a nonclassical mechanism of nucleation through a composite cluster, where the crystalline nucleus is surrounded by an amorphous layer. The thickness of the amorphous layer increases with an increase in supersaturation. The computed free energy landscape agrees well with the composite cluster-free energy model, through which phase specific thermodynamic properties are evaluated. As the supersaturation increases, there is a change in stability of the amorphous phase relative to the solution phase, resulting in a change from one-step to two-step mechanism, seen clearly from the free energy profile along the minimum free energy path crossing the transition curve. By obtaining phase-specific diffusion coefficients, we construct the full mesoscopic model and present a clear roadmap for NaCl nucleation.
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Affiliation(s)
- Pelin S Bulutoglu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | - Shiyan Wang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | - Moussa Boukerche
- Process Research and Development , AbbVie Inc, North Chicago, IL 60064, USA
| | - Nandkishor K Nere
- Process Research and Development , AbbVie Inc, North Chicago, IL 60064, USA
| | - David S Corti
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
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Villa AM, Doglia SM, De Gioia L, Natalello A, Bertini L. Fluorescence of KCl Aqueous Solution: A Possible Spectroscopic Signature of Nucleation. J Phys Chem B 2022; 126:2564-2572. [PMID: 35344657 PMCID: PMC8996234 DOI: 10.1021/acs.jpcb.2c01496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Ion pairing
in water solutions alters both the water hydrogen-bond network and
ion solvation, modifying the dynamics and properties of electrolyte
water solutions. Here, we report an anomalous intrinsic fluorescence
of KCl aqueous solution at room temperature and show that its intensity
increases with the salt concentration. From the ab initio density
functional theory (DFT) and time-dependent DFT modeling, we propose
that the fluorescence emission could originate from the stiffening
of the hydrogen bond network in the hydration shell of solvated ion-pairs
that suppresses the fast nonradiative decay and allows the slower
radiative channel to become a possible decay pathway. Because computations
suggest that the fluorophores are the local ion-water structures present
in the prenucleation phase, this band could be the signature of the
incoming salt precipitation.
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Affiliation(s)
- Anna Maria Villa
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Silvia Maria Doglia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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Sun Q, Wang W, Cui S. Directional nature of hydrophobic interactions: Implications for the mechanism of molecular recognition. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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