Article
Chemistry, Physical
Raymond Weldon, Feng Wang
Summary: This study investigates two methods to convert flexible models into rigid models. The rigid model can be created based on the Model's Geometry (MG) without molecular interaction or the ensemble averaged geometry (EG) under specific thermodynamic conditions. While the MG model is more straightforward, it has relatively poor performance compared to the EG model, which behaves similarly to the corresponding flexible model (FL model) and agrees better with experiments. The difference between the EG and FL models is mainly due to flexibility, and the MG and EG models have different dipole moments in the condensed phase.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Shuang Luo, Yakang Jin, Ran Tao, Haiyang Li, Chu Li, Jun Wang, Zhigang Li
Summary: This study investigates the microscopic mechanism of ion rejection during the freezing of aqueous NaCl solutions through molecular dynamics simulations, finding that the rejection of ions by ice is determined by the competition between energy barrier at the ice-water interface and thermal effects. The ion rejection rate increases with temperature, and Na+ is rejected at a higher rate than Cl- due to differences in hydration energy. The role of temperature in freeze desalination applications of ion rejection is also discussed.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Wen Zhao, Hu Qiu, Wanlin Guo
Summary: In this study, a machine learning potential for water confined in graphene nanocapillaries was developed using deep neural networks trained on quantum mechanical density-functional theory (DFT) calculations. This potential offers near-DFT accuracy at a much lower computational cost and accurately reproduces a wide range of properties, opening the door to simulations of nanoconfined water with large system sizes and time scales at near-DFT accuracy.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Polymer Science
Vladimir Yu. Rudyak, Daniil E. Larin, Elena N. Govorun
Summary: This study investigates the microphase separation and self-assembly of random multiblock copolymers composed of A and B homo-oligomers using computer simulations. The correlations between different types of macromonomers are controlled by the reaction probabilities. The results suggest that an increase in the Flory-Huggins parameter chi leads to microphase separation into lamellar structures or irregularly arranged domains.
Article
Polymer Science
Vladimir Yu. Rudyak, Daniil E. Larin, Elena N. Govorun
Summary: The microphase separation of random multiblock copolymers composed of A and B homo-oligomers was studied by computer simulations, revealing that the correlations between the composition and sequence of copolymers are controlled by reaction probabilities, resulting in different microphase separations for different sequences.
Article
Polymer Science
Albert L. L. Kwansa, Rakhee C. C. Pani, Joseph A. A. DeLoach, Arianna Tieppo, Eric J. J. Moskala, Steven T. T. Perri, Yaroslava G. G. Yingling
Summary: Plasticizers improve the flexibility and durability of polymer materials by reducing glass transition and cold flex temperatures. However, the migration and exudation of plasticizers from polymer materials have hindered the development of efficient and safe plasticizers. This study used molecular dynamics simulations validated by experiment to investigate the molecular mechanism of exudation of different plasticizers from PVC, and found that plasticizer-PVC compatibility was the main determinant of exudation.
Article
Materials Science, Multidisciplinary
H. Zhang, Y. P. Feng, Y. J. Wang, Y. L. Tang, Y. L. Zhu, X. L. Ma
Summary: Through three-dimensional phase field simulations and experimental verification, various types of phase (domain) structures were found in (110)-oriented PbTiO3 thin films, and a temperature-misfit strain phase diagram was determined. The study demonstrates that the misfit strain can be used to control the structure and properties of the films, providing theoretical guidance for strain engineering of high-index (110)-oriented PbTiO3 thin films.
Article
Geosciences, Multidisciplinary
Zhongshi Zhang, Eystein Jansen, Stefan Pieter Sobolowski, Odd Helge Ottera, Gilles Ramstein, Chuncheng Guo, Aleksi Nummelin, Mats Bentsen, Caoyi Dong, Xijin Wang, Huijun Wang, Zhengtang Guo
Summary: Climate model simulations suggest that changes in global sea level modify atmospheric and oceanic circulation. The recent increase in global mean sea-level rise presents a challenge in assessing its climate impacts, but previous warmer periods with higher sea levels provide a unique opportunity to investigate climate effects. Simulations show that a rise in sea level reorganizes atmospheric and oceanic circulations, and even a slight increase in global mean sea level can cause substantial adjustments in the global climate.
Article
Chemistry, Physical
Satoki Ishiai, Katsuhiro Endo, Kenji Yasuoka
Summary: In this study, two types of graph neural network models, GCN and TeaNet, were applied to classify the structures of LJ systems and water systems. Both models satisfy invariance, but TeaNet can recognize molecular geometry more efficiently and can build novel order parameters without manual operation.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Gaurav Vishwakarma, Bijesh K. Malla, Soham Chowdhury, Sakshi Pradip Khandare, Thalappil Pradeep
Summary: Acetaldehyde in dilute solution can form geminal diol under normal atmospheric conditions. This study discovers the existence of stable acetaldehyde clathrate hydrate (CH) in ultrahigh vacuum at cryogenic temperatures. The formation of CH was confirmed using infrared spectroscopy and mass spectrometry. This finding suggests the possibility of stable CH phase for acetaldehyde in interstellar and cometary environments.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Geochemistry & Geophysics
Chong Liu, Victor M. Calo, Klaus Regenauer-Lieb, Manman Hu
Summary: The mechanism for selecting mineral precipitation patterns is still unclear. This study uses a phase-field model to explore the effects of diffusion parameters on dendritic morphologies and provides a criterion for distinguishing different dendrites. The model successfully reproduces classified dendrites in the field and has potential applications in geological exploration and industrial settings.
JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH
(2023)
Article
Chemistry, Medicinal
Samaneh Davoudi, Koen Raemdonck, Kevin Braeckmans, An Ghysels
Summary: This study demonstrates the impact of liposome curvature and lipid composition on their passive permeability through molecular dynamics simulations. The results show that curvature increases water permeability but decreases permeability for permeants with mixed energy profiles. Fatty acids decrease membrane thickness and area per lipid, leading to increased permeability, while cholesterol has the opposite effect. Therefore, fatty acids and cholesterol have opposing effects on permeability.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Malgorzata J. Zimon, Fausto Martelli
Summary: This study investigates the heterogeneous crystallization of high-pressure glassy water using (plastic) ice VII as a substrate through molecular dynamics simulations. A martensitic phase transition from (plastic) ice VII to (plastic) fcc crystal is observed. The presence of long-living icosahedral structures and the role of molecular rotations in achieving heterogeneous crystallization are found. This work provides new insights into the properties of water.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Jirf Skvara, Ivo Nezbeda
Summary: The thermodynamic and structural properties of TIP4P/ice water have been studied in the vicinity of the expected second critical point, revealing bimodal distribution in density histograms and anomalous behavior in isothermal compressibility, indicating the presence of a critical point.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Multidisciplinary Sciences
Aleks Reinhardt, Bingqing Cheng
Summary: By combining machine learning methods and advanced free-energy techniques, this study successfully predicts and calculates the phase diagram of water at three levels of hybrid density-functional theory, showing good agreement with experimental results, especially at pressures below 8000 bar. The research demonstrates the completeness of the experimental water phase diagram in the region considered, provides a feasibility of predicting a polymorphic system's phase diagram from first principles, and tests the limits of quantum-mechanical calculations through a thermodynamic approach.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Yaoguang Zhai, Alessandro Caruso, Sigbjorn Loland Bore, Zhishang Luo, Francesco Paesani
Summary: Deep neural network (DNN) potentials have gained popularity in computer simulations of molecular systems. This study combines the computational efficiency of the DeePMD framework and the accuracy of the MB-pol potential to train a DNN potential for large-scale simulations of water. The DNN potential can reproduce MB-pol results for liquid water but lacks accuracy for vapor-liquid equilibrium properties. Attempts to include many-body effects result in a new DNN potential that accurately reproduces vapor-liquid equilibrium properties but loses accuracy in liquid properties.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Raja Ghosh, Francesco Paesani
Summary: Photoactive organic and hybrid organic-inorganic materials exhibit interesting photophysical properties upon interaction with light. A theoretical model that accurately describes the structure-photophysics-property relationships is crucial for understanding these materials. This perspective introduces a unified theoretical framework and discusses excitonic and polaronic photophysical signatures in different materials using the Multiparticle Holstein Formalism. The integration of advanced computational methods with the Multiparticle Holstein Formalism is expected to identify new design strategies for next-generation energy materials.
Article
Chemistry, Medicinal
Samiran Sen, Morten Ledum, Sigbjorn Loland Bore, Michele Cascella
Summary: Hamiltonian hybrid particle-field molecular dynamics is an efficient method for studying large soft matter systems. In this work, the method is extended to constant-pressure simulations and the calculation of internal pressure is reformulated to account for particle distribution. The resulting model accurately describes the physics of systems under pressure and successfully reproduces experimental results.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Morten Ledum, Samiran Sen, Sigbjorn Loland Bore, Michele Cascella
Summary: Hybrid particle-field molecular dynamics is a molecular simulation strategy that couples particles to a density field. The Hamiltonian hybrid particle-field method has been expanded and generalized to establish compatibility with any local soft pair potential. The mean-field regime observed in hybrid particle-field simulations is determined by the systems considered, and the Hamiltonian hybrid particle-field model has been shown to effectively capture all properties of the Gaussian Core model.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Xuanyu Zhu, Marc Riera, Ethan F. Bull-Vulpe, Francesco Paesani
Summary: Using the MB-pol theoretical/computational framework, we have introduced a new family of data-driven many-body potential energy functions (PEFs) for water, named MB-pol(2023). By employing larger training sets and adopting sophisticated machine-learned representations, the MB-pol(2023) PEFs achieve sub-chemical accuracy in modeling hexamer isomers and outperform existing PEFs in describing water clusters in the gas phase. Moreover, the MB-pol(2023) PEFs show remarkable agreement with experimental results for various properties of liquid water, improving upon the original MB-pol PEF and closing the gap with experimental measurements.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(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
Lesheng Li, Marcos Calegari F. Andrade, Roberto Car, Annabella Selloni, Emily A. Carter
Summary: In this study, the influence of different TiS2 surface terminations on its interface with water was revealed through deep potential molecular dynamics simulations. Zigzag-L was identified as the only interface that favors water dissociation thermodynamically and kinetically, with the coexistence of four-fold-coordinated Ti and one-fold-coordinated S atoms on the surface playing a crucial role in proton transfer. This work provides new insights for the future design and optimization of TiS2-based CDI devices for water desalination.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Multidisciplinary
Thomas M. Rayder, Filip Formalik, Simon M. Vornholt, Hilliary Frank, Seryeong Lee, Maytham Alzayer, Zhihengyu Chen, Debabrata Sengupta, Timur Islamoglu, Francesco Paesani, Karena W. Chapman, Randall Q. Snurr, Omar K. Farha
Summary: Carbon capture, storage, and utilization (CCSU) is an opportunity to reduce carbon emissions and combat global climate change. Metal-organic frameworks (MOFs) have shown great potential as effective CO2 sorbents in CCSU through gas adsorption. Understanding the properties of MOF pores and their dynamic behavior during sorption can lead to the development of more efficient CCSU materials.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Sigbjrn Lland Bore, Francesco Paesani
Summary: Since the early 1900s, scientists have been trying to understand the stability of ice polymorphs in water's phase diagram. This study combines the MB-pol data-driven many-body potential for water with advanced enhanced-sampling algorithms to simulate water's phase diagram with a high level of realism. The study provides insights into the role of enthalpic, entropic, and nuclear quantum effects in shaping the free-energy landscape of water and bridges the gap between experiments and simulations.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Ching-Hwa Ho, Mason L. L. Valentine, Zhijie Chen, Haomiao Xie, Omar Farha, Wei Xiong, Francesco Paesani
Summary: This study investigates the water adsorption mechanism in the hydrophilic metal-organic framework NU-1500-Cr using molecular dynamics simulations and infrared spectroscopy. It is found that water initially adsorbs at the open Cr3+ sites and then forms water chains that gradually fill the framework. The insights gained from this study can contribute to the design of efficient water harvesting materials.
COMMUNICATIONS CHEMISTRY
(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
Marc Riera, Christopher Knight, Ethan F. Bull-Vulpe, Xuanyu Zhu, Henry Agnew, Daniel G. A. C. Smith, Andrew Simmonett, Francesco Paesani
Summary: MBX is a C++ library that implements many-body potential energy functions (PEFs) within the many-body energy (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be used as a standalone package or integrated with other molecular simulation software as an energy/force engine. It allows for classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations combining conventional force fields and MB-nrg PEFs for diverse systems.
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
Ruihan Zhou, Marc Riera, Francesco Paesani
Summary: We introduce a data-driven many-body energy potential energy function (MB-nrg PEF) to accurately describe the energetics and structural properties of N-methylacetamide (NMA), as well as the NMA-water interactions. The results show that the MB-nrg PEF is able to accurately represent many-body effects in both gas and liquid phases, making it a promising molecular model for predictive simulations of biomolecular systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Materials Science, Multidisciplinary
Zhihengyu Chen, Ching-Hwa Ho, Xiaoliang Wang, Simon M. Vornholt, Thomas M. Rayder, Timur Islamoglu, Omar K. Farha, Francesco Paesani, Karena W. Chapman
Summary: CALF-20, a metal-organic framework, shows selective CO2 physisorption. This study reveals that CALF-20 undergoes a structure transformation when exposed to humid environments, resulting in a new polymorph. The transformation is reversible, and the original structure can be regenerated. Computational evaluation indicates that the new polymorph has a higher CO2 heat of adsorption, potentially leading to improved CO2 sorption selectivity at low partial pressures.
ACS MATERIALS LETTERS
(2023)
