Article
Chemistry, Applied
Patrick Heasman, Aleksandar Y. Mehandzhiyski, Sarbani Ghosh, Igor Zozoulenko
Summary: Processing natural cellulose requires dissolution and regeneration. The crystallinity of re-generated cellulose does not match that of native cellulose, and the physical and mechanical properties of re-generated cellulose vary depending on the technique used. Molecular dynamics simulations were performed to simulate the regeneration of order in cellulose. The simulations show that cellulose chains have an affinity to align with each other on the nanosecond scale, but the end results still lack sufficient order. The time factor plays a major role in reclaiming the order of crystalline cellulose.
CARBOHYDRATE POLYMERS
(2023)
Article
Chemistry, Multidisciplinary
Punam Rattu, Bastien Belzunces, Taylor Haynes, Chris-Kriton Skylaris, Syma Khalid
Summary: The study investigates the impact of nanopores with hydrophobic constrictions on DNA translocation, finding that aromatic residues slow down the process. Stressed DNA strands exhibit greater variability in translocation rates, and the number of DNA entries into the pores correlates with pore width.
Article
Chemistry, Physical
Zhicheng Ye, Haiping Su, Cheng Lian, Jiajie Hu, Yazhuo Shang, Honglai Liu
Summary: The LCST behavior of block copolymer P(MEO(2)MA-b-OEGMA) is linearly related to its OEGMA block ratio, which is influenced by the hydrophilic effect and entropy effect of water. The dominant hydrophilic effect leads to a coil state at lower temperatures, while the prevailing entropy effect causes a globule state at higher temperatures, resulting in a coil-to-globule transition at the LCST where the competition between the two effects reaches a balance.
MOLECULAR SIMULATION
(2021)
Article
Chemistry, Multidisciplinary
Lorenzo Agosta, Daniel Arismendi-Arrieta, Mikhail Dzugutov, Kersti Hermansson
Summary: The hydrophobicity found in rare-earth oxides is intriguing. Despite its hydrophilic nature, the CeO2 (100) surface exhibits hydrophobic behavior when immersed in water. A detailed analysis of the water structure and dynamics reveals that the first water layer in contact with the hydroxylated CeO2 surface acts as a hydrophobic interface. This discovery introduces a new concept of hydrophobicity mediated by specific water patterns on a hydrophilic surface in water/rare-earth oxide interfaces.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Nuno Galamba
Summary: Using molecular dynamics, it was demonstrated that the hydration free energy of model hydrocarbons in supercooled water exhibits a convergence temperature. The hydration entropy and enthalpy minima are associated with structural differences between shell-bulk water, similar to those observed between low-density liquid and high-density liquid water.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Physics, Multidisciplinary
G. Monet, H. Berthoumieux, F. Bresme, A. Kornyshev
Summary: The study describes a minimal Landau-Ginzburg field theory for nanoconfined water and demonstrates how the interplay between boundary conditions and intrinsic bulk correlations affects the dielectric properties of confined water. The theoretical analysis is supported by molecular dynamics simulations and comparison with experimental data.
PHYSICAL REVIEW LETTERS
(2021)
Article
Agriculture, Multidisciplinary
Ya Wu, Jiayue Hu, Yikai Du, Gen Lu, Yingnan Li, Yujia Feng, Liting Chen, Yuhao Tu, Mengxiong Xiang, Yifan Gui, Tong Shu, Longjiang Yu
Summary: This study investigated the structure-activity relationship of Xylo-1 xylosidase under high-salt conditions and discovered that the presence of Na+ ions enhances the catalytic activity and stability of Xylo-1. The synergistic catalysis of Xylo-1 and xylanase was employed to produce xylose with high conversion yields, suggesting potential industrial applications.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Polymer Science
Jian Li, Bokai Zhang, Yushan Li
Summary: Polymer-related materials exhibit rich glassy behaviors at different length scales due to their various molecular structures and topological constraints. Recent studies have identified transient interpenetration of long-chain rings contributing to dynamic arrest on the center-of-mass level. Interpenetration of rings is proposed as an approach to facilitate glass formation in polymer melts. Our work investigates glass transition on the nanometer-scale segments influenced by permanent interpenetration of rings using molecular dynamics simulations. We find that decreasing chain length in the mechanically interlocked system is equivalent to inducing an effective chain stiffness on the subrings, providing a unified explanation for unique structural features and transient dynamic arrest. Furthermore, our work reveals a dynamic transition from weak to strong caging at the crossover temperature, deepening the understanding of induced stiffness on glass transition.
Article
Chemistry, Physical
Vladimir S. Farafonov, Michael Stich, Dmitry A. Nerukh
Summary: For the first time, a complete all-atom molecular dynamics (MD) model of virus MS2, including its protein outer shell, genomic RNA, and surrounding explicit aqueous solution, was built and tested. The model can be used for reconstructing other large biomolecular structures and studying the biology and dynamics of the MS2 virus and its interaction with host bacteria.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Alessandra Serva, Mathieu Salanne, Martina Havenith, Simone Pezzotti
Summary: Hydrophobic hydration at the metal/water interface is studied using constant applied potential molecular dynamics in this work. The study proposes an adaptation of the Lum-Chandler-Weeks theory to describe the free energy of hydrophobic hydration at the interface, showing a preference for outer-sphere adsorption of small hydrophobic solutes at the gold surface and higher free energy cost for hydrating larger hydrophobes at the interface compared to the bulk.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Aleksander E. P. Durumeric, Gregory A. Voth
Summary: Bottom-up CG molecular dynamics models, parameterized using complex effective Hamiltonians, are often optimized to approximate high dimensional data from atomistic simulations. However, human validation of these models may not differentiate between the CG model and the atomistic simulations. We propose using classification to estimate high dimensional errors and utilizing explainable machine learning to convey this information to scientists. This approach is demonstrated using Shapley additive explanations and two CG protein models, and may be valuable for assessing the accuracy of allosteric effects in CG models at the atomistic level.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Aiping Zhang, Kai Cui, Yuanyuan Tian, Tieying Wang, Xin He
Summary: This article investigates the impact behavior of binary nanodroplets on hydrophobic and superhydrophobic surfaces, using molecular dynamics simulations to directly capture and analyze the dynamic evolutions of droplets. It provides insights into the practical applications of droplet impact and contributes to advancements in this field.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Ujjal Kumar Sur
Summary: The behavior of water near hydrophobic surfaces and interfaces is crucial for understanding interfacial phenomena in biology and chemistry. In recent years, the scarcity of water density near hydrophobic interfaces has been extensively studied through experimental and theoretical methods. This review article summarizes fascinating experimental, computational, and theoretical studies aimed at a comprehensive understanding of this hydrophobic interfacial gap.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Materials Science, Multidisciplinary
Jintao Zhou, Heng Chen, Rulong Zhou, YuWei You, Fei Sun, Dongdong Li
Summary: In this study, first-principles calculations were conducted to investigate the formation and migration behaviors of point defects in TiD2, as well as its phase stability. The results showed that the formation energies of Ti vacancy (VTi) and D vacancy (VD) in TiD2 were 2.34 and 0.73 eV, respectively. The migration barriers of VD within ab plane and bc plane were 0.80 and 0.66 eV, respectively, which were much lower than those of the interstitial D atoms. Therefore, the predominant diffusion mechanism of D atom in TiD2 is vacancy hopping mechanism.
JOURNAL OF NUCLEAR MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Ruijie D. Teo, D. Peter Tieleman
Summary: The past century has seen waves of viral pandemics, increasing the importance of molecular simulation research. In this study, all-atom molecular dynamics were used to simulate an enterovirus-D68 capsid and its dependency on AMBER and CHARMM force fields was examined. Results showed that CHARMM36m and CHARMM36 produced secondary structures most consistent with protein structural data and sampled the largest conformational space.
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)