Article
Chemistry, Physical
C. P. Lamas, J. R. Espinosa, M. M. Conde, J. Ramirez, P. Montero de Hijes, E. G. Noya, C. Vega, E. Sanz
Summary: The seeding method is an approximate approach that combines molecular dynamics simulations with classical nucleation theory to study crystallization. By following a mislabelling criterion to select the threshold, consistency between seeding and rigorous methods can be achieved. This work supports the use of seeding for fast and reasonably accurate nucleation rate estimates in crystallization studies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Xiaorong Zhao, Yuying Liu, Dongdong Lin, Weiduo Zhu, Nan Ma, Wen Wu Xu, Wenhui Zhao, Yunxiang Sun, Xiao Cheng Zeng
Summary: This study uses molecular dynamics simulations to investigate the thermodynamic behavior of monolayer salt solution in subnanofluidic devices. The simulations demonstrate that the effective Coulombic interactions among Na+/Cl- ions have a strong impact on the behavior of the monolayer ionic aqueous solution. The findings reveal that the effective charges of the ions determine whether they dissolve in the monolayer water, assemble into nanocrystals, or exhibit gas-like behavior in the form of nanobubbles.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
A. R. Finney, M. Salvalaglio
Summary: Molecule- and particle-based simulations are used to test classical nucleation theory. The variational approach to Markov processes is applied to determine the suitability of different reaction coordinates for studying crystallization from supersaturated colloid suspensions. The results show that collective variables that correlate with the number of particles in the condensed phase, the system potential energy, and approximate configurational entropy are the most appropriate order parameters.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemical Research Methods
C. R. Soares, Y. M. H. Goncalves, B. A. C. Horta, A. G. Barreto Jr, F. W. Tavares
Summary: Molecular dynamics simulations were used to investigate the initial stage of phase separation mechanisms for an oversaturated electrolytic solution. A low computational cost methodology was developed to determine the simulation frames where the first ionic clusters are formed. The growth of the clusters identified with this methodology was analyzed until the end of the simulation. The change in phase separation mechanism due to increasing oversaturation underscores the importance of precise determination of the driving force and concentration limits for phase separation.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Physics, Multidisciplinary
Ignacio Sanchez-Burgos, Jorge R. Espinosa
Summary: This study provides the first direct estimation of the interfacial free energy of NaCl-saturated solution on several crystallographic planes. The results show high anisotropy between different crystal orientations, with values ranging from 100 to 150 mJ m-2.
PHYSICAL REVIEW LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Hyerim Hwang, Yong Chan Cho, Sooheyong Lee, Yun-Hee Lee, Seongheun Kim, Yongjae Kim, Wonhyuk Jo, Patrick Duchstein, Dirk Zahn, Geun Woo Lee
Summary: Experimental evidence indicates the formation of dense liquid regions in NaCl bulk solution at unprecedentedly high levels of supersaturation, providing new insights into the detailed mechanism of two-step nucleation for many other aqueous solutions. The evolution of solute clusters and breakage of hydration in highly supersaturated conditions were observed, leading to a better understanding of the early stages of nucleation.
Article
Chemistry, Physical
Annalisa Polidori, Ruth F. Rowlands, Anita Zeidler, Mathieu Salanne, Henry E. Fischer, Burkhard Annighofer, Stefan Klotz, Philip S. Salmon
Summary: The structure of a concentrated solution of NaCl in D2O and the coordination environment of the chloride ion were investigated through experimental and simulation studies. It was found that increased pressure resulted in an increase in coordination numbers and a decrease in self-diffusion coefficients. Contact ion pairs were observed under all conditions, with the exchange mechanism between water molecules and Na+ changing as state conditions varied.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Hyung Joong Kim, Jong Hoon Kim, Jong Seok Jeong, Chang youn Moon, Sahn Nahm, Ki Min Nam, Jucheol Park, Young Heon Kim
Summary: In this study, the nucleation and crystallization of Bi particles on c-Bi2S3 and a-Bi12TiO20 matrices were investigated using in situ transmission electron microscopy (TEM) analysis. It was found that the growth process followed a two-step nucleation mechanism and was influenced by the matrix, leading to different morphologies and atomic structures of Bi particles on different matrices.
Article
Chemistry, Physical
Wilberth A. Narvaez, Eric C. Wu, Sanghyun J. Park, Mariah Gomez, Benjamin J. Schwartz
Summary: By using ultrafast spectroscopy and molecular dynamics simulations, the localization dynamics of excess electrons in aqueous NaCl solutions are investigated. The results show that the electrons prefer to localize at pre-existing trap sites, and the presence of concentrated electrolytes has little impact on the localization behavior.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Zhang Xie, Zheng Li, Jingyuan Li, Jianlong Kou, Jun Yao, Jintu Fan
Summary: By conducting all-atom molecular dynamics simulations, it was discovered that the distribution and behavior of gas molecules in aqueous solutions can be regulated by the direction of external electric fields, which alters hydrogen bonds between water molecules at the solid-water interface. This finding reveals a new mechanism for controlling gas dissolution and accumulation in aqueous solutions, with potential applications in drug synthesis, microfluidic device design, and natural gas extraction.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Engineering, Chemical
Leif-Thore Deck, Marco Mazzotti
Summary: The stochastic nature of ice nucleation poses a challenge in the freezing and freeze-drying processes of biopharmaceuticals in vials. This study presents a method to estimate nucleation kinetic parameters and their uncertainty in order to facilitate model-based freezing process design. The methodology accounts for both the inherent stochasticity and variability in nucleation sites among vials, and the extended model demonstrates good agreement with experimental data.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Chemistry, Inorganic & Nuclear
Shuo Chen, Yu Zhang, Qingyuan Chen, Chunchun Zhang, Meng Zhang, Kui Yu
Summary: This study presents a pathway for the formation of semiconductor magic-size clusters (MSCs) in aqueous solutions and provides an in-depth understanding of their formation mechanism.
INORGANIC CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Xu Jiang, Shanshan He, Gang Han, Jun Long, Songwei Li, Cher Hon Lau, Sui Zhang, Lu Shao
Summary: In this study, a method was developed to synthesize monodispersed ZIF-8 nanocrystals with unique dopamine surface decoration layer in situ, which went through a triple-stage crystallization process to form a rhombic dodecahedron structure. The resulting ZIF-8-DA nanocrystals maintained their crystallinity and abundant microporosity, leading to enhanced gas permeability and selectivity in mixed-matrix membranes.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Physics, Multidisciplinary
Igor G. Likhachev, Vladimir Pustovoy, Boris A. Usievich
Summary: This paper presents a technique for comparing refractive indices of low concentration solutions by using direct spectral detection. The study compares low and ultra-low NaCl concentrations with water controls prepared through serial dilution. The results suggest that the mixing method has a significant impact on the refractive indices of the solutions.
FRONTIERS IN PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Nikita Orekhov, Nikolay Kondratyuk, Mikhail Logunov, Alexandra Timralieva, Vladimir Shilovskikh, Ekaterina Skorb
Summary: This study provides molecular insights into the self-assembly of melamine cyanurate in aqueous solution and identifies mechanisms of aggregation. The research suggests that the formation of small M-CA complexes is mainly stabilized through aromatic p-p stacking rather than hydrogen bond formation. It also demonstrates that changing the concentration ratio of M to CA leads to a variation in the structure of critical nuclei, indicating a potential for the programmable design of functional supramolecular materials.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Chemistry, Physical
Jack Weis, Francesco Sciortino, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti
Summary: Recent experiments and numerical simulations have provided support to the hypothesis that a second critical point exists in deeply supercooled water. In particular, a study has found that a liquid-liquid critical point can be located using a model parameterized solely based on ab initio calculations. This finding is important for understanding the phase behavior of supercooled water.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Pablo M. Piaggi, Jack Weis, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, Roberto Car
Summary: Molecular simulations based on machine-learning models and density-functional theory have provided insights into the mechanism of homogeneous ice nucleation. The results are in good agreement with experimental measurements, and the impact of factors such as thermodynamic driving force, interfacial free energy, and stacking disorder on nucleation rates has been studied.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Anirban Mondal, Dina Kussainova, Shuwen Yue, Athanassios Z. Panagiotopoulos
Summary: Researchers developed a deep potential machine learning model for simulating chemical reactions in molten alkali carbonate-hydroxide electrolyte containing dissolved CO2. They tested the model against density functional theory calculations and found it accurately simulated the reactions in the melt and extended the observation time.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Athanassios Z. Panagiotopoulos, Shuwen Yue
Summary: This article summarizes recent simulation work on the dynamics of aqueous electrolytes. It shows that full-charge, nonpolarizable models for water and ions predict solution dynamics that are too slow, while models with reduced charges have issues describing certain dynamic phenomena. Polarizable models, when appropriately parametrized, show promise but may miss important physical effects. First-principles calculations are emerging to capture polarization, charge transfer, and chemical transformations in solution. Machine-learning models trained on first-principles data offer promise for accurate and transferable modeling of electrolyte solution dynamics.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Physics, Multidisciplinary
Thomas E. Gartner III, Pablo M. Piaggi, Roberto Car, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti
Summary: The study provides preliminary evidence of liquid-liquid phase transition in water using molecular simulation techniques and a neural network model based on density functional theory calculations.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Thomas J. Longo, Nikolay A. Shumovskyi, Betul Uralcanc, Sergey. V. V. Buldyrev, Mikhail A. Anisimov, Pablo G. Debenedetti
Summary: The separation of substances into different phases is a common and important phenomenon in nature and has scientific and technological significance. When the species involved can interconvert, the presence of a strong external force can result in equal amounts of both alternative species and the observation of steady-state, restricted phase separation. This study uses simulations to investigate the formation of such mesoscale steady-state structures in binary mixtures that exhibit both equilibrium and forced interconversion, and shows that a nonequilibrium thermodynamic theory can explain the main trends and observations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Athanassios Z. Panagiotopoulos
Summary: This paper investigates the phase and aggregation behavior of linear chains composed of hydrophilic and hydrophobic blocks. The phase and conformational transitions of patterned chains are important for understanding liquid-liquid separation of biomolecular condensates and have applications in cellular biophysics, surfactants, and polymers. The key finding of this study is that certain chain architectures can exhibit both finite-size aggregate formation and phase separation under appropriate conditions of temperature and concentration. The computational approach used in this study involves histogram-reweighting grand canonical Monte Carlo simulations, which are described in detail.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Ignacio Sanchez-Burgos, Maria Carolina Muniz, Jorge R. Espinosa, Athanassios Z. Panagiotopoulos
Summary: In this study, the Deep Potential methodology was used to investigate the phase transition of liquid water to vapor. The machine learning model was trained on ab initio energies and forces based on the SCAN density functional. Various properties, such as surface tension, saturation pressure, and enthalpy of vaporization, were computed and compared with experimental data and a classical model. The results showed a deviation in nucleation rates due to an underestimation of surface tension in the Deep Potential model, and also revealed a preferential orientation of water molecules in the liquid-vapor interface.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Reha Mathur, Maria Carolina Muniz, Shuwen Yue, Roberto Car, Athanassios Z. Panagiotopoulos
Summary: In this work, distinct first-principles-based machine-learning models of CO2 were constructed, allowing for stable interfacial system simulation, prediction of vapor-liquid equilibrium properties, and improved computational efficiency. The SCAN and SCAN-rvv10 models exhibit temperature shifts, while the BLYP-D3 model performs better for liquid phase and vapor-liquid equilibrium properties, and the PBE-D3 model is better suited for predicting transport properties.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Pablo M. Piaggi, Roberto Car, Frank H. Stillinger, Pablo G. Debenedetti
Summary: Understanding the behavior of chiral molecules in condensed phase is crucial for biology and various technological applications. In this study, molecular dynamics simulations were used to investigate a chiral molecular model with second-order symmetry-breaking phase transition and determine the critical temperature. The finite-size scaling behavior of the order parameter suggests compatibility with the 3D Ising universality class. The presence of a free energy barrier indicates a suppressed fluctuation between the enantiomers, which could explain the origin of biological homochirality.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Pablo M. Piaggi, Thomas E. Gartner III, Roberto Car, Pablo G. Debenedetti
Summary: The possible existence of a liquid-liquid critical point in deeply supercooled water has been debated. Mishima and Stanley studied the melting curves of different ice polymorphs and suggested that the critical point lies between the melting curves of ice III and ice V. However, our molecular dynamics simulations and machine learning model based on ab initio calculations show that the melting curves of ices III, IV, V, VI, and XIII are supercritical and do not intersect the liquid-liquid transition locus. We conclude that the scenario in which the melting curves are supercritical is favored by the most recent computational and experimental evidence.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Maria Carolina Muniz, Roberto Car, Athanassios Z. Panagiotopoulos
Summary: A deep potential neural network (DPMD) model based on the MB-pol potential for water was developed, which can combine accuracy and transferability if sufficient attention is given to the construction of a representative training set for the target system.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Physics, Multidisciplinary
Chunyi Zhang, Shuwen Yue, Athanassios Z. Panagiotopoulos, Michael L. Klein, Xifan Wu
Summary: The dielectric permittivity of salt water decreases as more salt is dissolved, which is explained by saturation in the dielectric response of solvent water molecules. By using an advanced deep neural network (DNN) based on density functional theory data, the dielectric permittivity of sodium chloride solutions is studied. The computed decrease in dielectric permittivity as a function of concentration, using the DNN approach, agrees well with experimental results. The dominant effect causing this decrease is the intrusion of ionic hydration shells into the solvent hydrogen-bond network, disrupting dipolar correlations among water molecules and suppressing the collective response of solvent waters.
PHYSICAL REVIEW LETTERS
(2023)
Meeting Abstract
Biophysics
Ushnish Rana, Ke Xu, Amal Narayanan, Mackenzie T. Walls, Jose L. Avalos, Athanassios Z. Panagiotopoulos, Clifford P. Brangwynne
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Athanassios Z. Panagiotopoulos, Shuwen Yue
Summary: This Perspective article discusses recent simulation work on aqueous electrolyte dynamics. Full-charge, nonpolarizable models for water and ions tend to underestimate solution dynamics compared to experiments. Models with reduced charges perform better for diffusivities and viscosities, but struggle with other dynamic phenomena like crystal nucleation rates. Polarizable models show promise, but may still miss important effects like charge transfer. First-principles calculations are emerging to capture polarization, charge transfer, and transformations in solution, while machine-learning models trained on such data can accurately model electrolyte solution dynamics.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)