Article
Multidisciplinary Sciences
Prasun Pal, Sandipan Chakraborty, Biman Jana
Summary: This study investigates the specific binding of different types of antifreeze proteins to ice, along with the structure of their hydration layer and the properties of solvation water. It reveals that the hydration layer of globular AFP is semiclathrate-like, contrasting with the ice-like hydration layer of hyperactive AFP. These findings suggest a differential design in the ice-binding surface of antifreeze proteins that may contribute to their varying antifreeze activity.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Chemistry, Physical
Li Han, Haipeng Wang, Wensheng Cai, Xueguang Shao
Summary: The study investigated the change in the structure of water during ice growth in polyproline (PPro) solutions using near-infrared spectroscopy and molecular dynamics simulations. The results show that only high concentrations of PPro solutions can effectively inhibit ice growth. When PPro exhibits an antifreeze effect, the spectral intensity of hydrated water associated with PPro in a solution is weakened. The experiments and simulations reveal the critical role of interfacial water in the antifreeze activity of PPro.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Li Han, Haipeng Wang, Wensheng Cai, Xueguang Shao
Summary: The molecular mechanism of how polyproline inhibits ice growth and exhibits antifreeze activity was investigated through spectroscopy and molecular dynamics simulations. The results demonstrate that high concentrations of PPro inhibit ice growth by weakening the interfacial water between the ice crystal and hydrophobic groups of PPro.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Review
Chemistry, Multidisciplinary
Jing Guo, Ying Jiang
Summary: Water-solid interfaces play crucial roles in chemical and physical processes. With the use of scanning probe microscopy, molecular-level understanding of water structure and dynamics on solid surfaces has been achieved. The development of high-resolution microscopy and atomic force microscopy has enabled the study of hydrogen positions and proton transfer dynamics.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Chengcheng Zhang, Jinpeng Gao, Jeanne Hankett, Prabodh Varanasi, Charles O. Kerobo, Shouxun Zhao, Zhan Chen
Summary: The study highlights the significant impact of sizing solutions on the wettability and interfacial adhesion of composites. Surface-sensitive sum frequency generation (SFG) spectroscopy offers valuable insights into the complex structures of sizing solutions at solid-liquid interfaces, enabling a more accurate understanding of the structure-wettability relationship. This detailed understanding of interactions between sizing agents and substrates promotes informed and optimized selections of sizing formulations.
Article
Energy & Fuels
Cong Chen, Yue Zhang, Jingyue Sun, Yang Liu, Yan Qin, Zheng Ling, Weiguo Liu, Weizhong Li
Summary: In this study, molecular dynamics simulations were performed to investigate the inhibition behavior of Tenebrio molitor antifreeze protein (TmAFP) on methane hydrate growth. The results showed that TmAFP adsorbs on the hydrate growth surface, trapping the central gas in half hydrate cages, thereby inhibiting hydrate growth.
Review
Chemistry, Multidisciplinary
Eunchan Kim, Donghwan Kim, Kyungwon Kwak, Yuki Nagata, Mischa Bonn, Minhaeng Cho
Summary: Understanding water interactions with graphene is crucial in various applications. Vibrational sum frequency generation (VSFG) spectroscopy is capable of elucidating the hydrogen-bonding structure of water at the graphene-water interface. Specifically, increasing the number of graphene layers reveals water molecules with non-H-bonded, dangling OH groups, which correlate with the water adhesion energy of graphene. VSFG spectroscopy is a valuable technique for measuring water adhesion energy on confined interfaces.
Article
Chemistry, Multidisciplinary
Wei Ma, Yang Li, Christopher Y. H. Chao, Chi Yan Tso, Baoling Huang, Weihong Li, Shuhuai Yao
Summary: This study presents a novel icephobic surface combining superhydrophobicity and photothermal effect, achieving outstanding anti-icing performance at extremely low temperatures by enhancing solar-thermal conversion. Additionally, the simple, scalable fabrication method of this surface provides great potential for diverse applications.
CELL REPORTS PHYSICAL SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Omar Teschke, Jose Roberto Castro, Wyllerson Evaristo Gomes, David Mendez Soares
Summary: Experimental studies show that interfacial water structure exhibits specific cluster profiles, which expand over time to form structures of around 70 nm. Additionally, the dielectric permittivity at the interface may have an oscillating profile, describing spatial steps in force vs distance curves.
Article
Multidisciplinary Sciences
Guoying Bai, Jinhao Hu, Sijia Qin, Zipeng Qi, Hening Zhuang, Fude Sun, Youhua Lu, Shenglin Jin, Dong Gao, Jianjun Wang
Summary: In this study, a small molecule of fulvic acid (FA) with strong hydration ability was found to enable non-vitreous cellular cryopreservation by reducing ice growth during freezing and promoting ice melting during thawing. The ice-control properties of FA can be attributed to its strong bondage to water molecules. Furthermore, FA was found to be absorbed by red blood cells (RBCs) and mainly locate on membranes, suggesting its contribution to cell protection through stabilizing membranes.
Review
Engineering, Biomedical
Nishaka William, Sophia Mangan, Rob N. Ben, Jason P. Acker
Summary: One of the key challenges in subzero storage is controlling ice nucleation or recrystallization. Nature provides examples of organisms that can sustain subphysiological temperatures for extended periods of time, and by studying their proteins, we now have access to compounds and materials for biopreservation applications. This research can synergize with other advancements in cryobiology, making it a timely topic for review.
ANNUAL REVIEW OF BIOMEDICAL ENGINEERING
(2023)
Article
Chemistry, Physical
Tong Zhang, Zhi-Chao Huangfu, Yuqin Qian, Zhou Lu, Hong Gao, Yi Rao
Summary: In this work, broadband heterodyne detection was used to study the frequency-dependent spectral phases in interfacial electronic spectroscopy. It was found that the often-used Au thin film is not a suitable reference for frequency-dependent phases.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Multidisciplinary Sciences
Sayantan Chatterjee, Daria Maltseva, Yelena Kan, Elnaz Hosseini, Grazia Gonella, Mischa Bonn, Sapun H. Parekh
Summary: Lipid-protein interactions strongly influence protein condensation, suggesting a role of lipid in modulating condensate formation in cells.
Article
Crystallography
Wentao Yang, Yucong Liao, Qi Shi, Zhaoru Sun
Summary: Antifreeze glycoproteins (AFGPs) are powerful inhibitors of ice recrystallization and have been widely studied. However, there is still controversy about the molecular mechanism of how they inhibit ice growth, particularly the group responsible for binding AFGPs to ice. In this study, molecular dynamics simulations are used to investigate the atomistic details of AFGP8 binding to ice. The results show that AFGP8 can bind to ice through backbone dominant binding, disaccharide dominant binding, and weak binding. Hydrogen-bonding and hydrophobic groups contribute equally to the binding and synergistically promote it. The work provides valuable insights into the ice growth inhibition mechanism of AFGP8, which can aid in the design of efficient cryoprotectants.
Article
Agriculture, Multidisciplinary
Madison Fomich, Vermont P. Dia, Uvinduni I. Premadasa, Benjamin Doughty, Hari B. Krishnan, Tong Wang
Summary: The study investigated the ice recrystallization inhibition (IRI) activity of soy protein isolate (SPI) hydrolysates and determined that the F1 fraction (4-14 kDa) had the highest IRI activity. Vibrationalsum frequency generation (VSFG) analysis indicated that the molecular interactions at the water/air interface were linked to IRI activity.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Physical
Shuwen Yue, Marc Riera, Raja Ghosh, Athanassios Z. Panagiotopoulos, Francesco Paesani
Summary: Building upon previous work, this study introduces a second generation of data-driven many-body models for CO2 and systematically assesses the impact of CO2-CO2 interactions on the models' ability to predict equilibrium properties. By fitting reference energies calculated at the coupled cluster level, a series of models are constructed. The use of charge model 5 and scaling of two-body energies lead to more accurate descriptions of CO2 properties. The findings highlight the importance of training set quality in developing transferable, data-driven models.
JOURNAL OF CHEMICAL PHYSICS
(2022)
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
Biophysics
Arpa Hudait, James H. Hurley, Gregory A. Voth
Summary: In the late stages of the HIV-1 life cycle, the membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. The release of the virion requires the interaction between Gag lattice and ESCRT machinery at the viral budding site, followed by the assembly of downstream ESCRT-III factors. However, the molecular details of upstream ESCRT assembly dynamics remain unclear. In this study, molecular simulations were used to investigate the interactions between Gag, ESCRT-I, ESCRT-II, and membrane, revealing the mechanisms by which upstream ESCRTs assemble at the viral budding site.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Brodie L. Ranzau, Kartik L. Rallapalli, Mallory Evanoff, Francesco Paesani, Alexis C. Komor
Summary: Base editors are genome editing tools that modify nucleobases in DNA to enable precise base conversions. Adenine base editors convert A.T base pairs to G.C base pairs by using an adenosine deaminase enzyme. Previous experiments showed that the wild-type TadA enzyme had no activity on DNA, but we demonstrated that it can perform base editing in both bacterial and mammalian cells.
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, Multidisciplinary
Baorui Cheng, Yu Zhong, Yuqing Qiu, Suriyanarayanan Vaikuntanathan, Jiwoong Park
Summary: Generating electricity from a salinity gradient, known as osmotic power, has been made possible with the development of ultrathin membranes that have molecule-specific short-range interactions. These membranes have demonstrated giant gateable osmotic power with a record high power density. Molecular dynamics simulations have confirmed that the functionalized nanopores in these membranes are small enough for high selectivity and large enough for fast cross-membrane transport, enabling reversible gateable operation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(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
Yuanhui Pan, Ching-Hwa Ho, Francesco Paesani, Raja Ghosh
Summary: Covalent organic frameworks (COFs) are 2D organic materials with unique electronic and transport properties. In this study, the impact of interlayer stacking arrangements on the electronic structure and coherence of polarons in donor-acceptor COFs was investigated through density functional theory and multiparticle Holstein formalism simulations. It was found that the stacking arrangement significantly influences the transport properties, with varying behavior from metallic to highly localized states. The extent of charge delocalization is sensitive to the type and precise arrangement of interlayer stacking and donor-acceptor fragments in the COF structure. The results suggest that interlayer interactions can aid in enhancing charge delocalization and guide the design of new COF structures for potential applications in organic electronics.
CHEMISTRY OF MATERIALS
(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
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)
Article
Materials Science, Multidisciplinary
Jierui Zhang, Francesco Paesani, Martina Lessio
Summary: Studies have shown that incorporating hydrophilic functional groups into the UiO-66 metal-organic framework (MOF) can improve its water uptake ability at low relative humidity (RH). This computational study provides insights into the adsorption mechanism of water in UiO-66 and its functionalized derivatives, revealing the preferential interaction sites and the formation of localized water clusters inside the octahedral pores. The presence of functional groups allows water to cluster in the pores at lower RH, making the MOF a more efficient water harvester.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)