Article
Chemistry, Physical
Jessica Bowles, Sascha Jahnigen, Rodolphe Vuilleumier, Florent Calvo, Carine Clavaguera, Federica Agostini
Summary: The vibrational spectrum of alanine amino acid was computationally determined in different environments and phases using molecular dynamics trajectories and an optimized polarizable force field. The analysis revealed significant differences between the spectra of neutral and zwitterionic forms of alanine in the gas phase, and provided insights into the molecular origins of vibrational bands in condensed phases.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Xingxu Yan, Chengyan Liu, Chaitanya A. Gadre, Lei Gu, Toshihiro Aoki, Tracy C. Lovejoy, Niklas Dellby, Ondrej L. Krivanek, Darrell G. Schlom, Ruqian Wu, Xiaoqing Pan
Summary: The study shows that space- and angle-resolved vibrational spectroscopy in a transmission electron microscope can map the vibrational spectra of individual crystal defects, revealing changes in energy and intensity of acoustic vibration modes restricted to a few nanometers around the defect. The capabilities of a state-of-the-art transmission electron microscope open the door to directly mapping phonon propagation around defects, offering valuable guidance for engineering the thermal properties of materials.
Article
Multidisciplinary Sciences
Kuo-Yang Chiang, Takakazu Seki, Chun-Chieh Yu, Tatsuhiko Ohto, Johannes Hunger, Mischa Bonn, Yuki Nagata
Summary: The dielectric properties of interfacial water on subnanometer length scales have been studied using surface-specific sum-frequency generation spectra. Experimental and simulated results reveal a drastic change in the interfacial dielectric constant in the subnanometer interfacial water region, leading to the formation of an electric triple-layer at charged planar interfaces.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Alican Gulsevin, Jens Meiler
Summary: The AmphiScan protocol is a tool developed to predict the interaction of amphipathic helices with membranes, with features of fast, accurate, and highly customizable.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Daniel Konstantinovsky, Elsa C. Y. Yan, Sharon Hammes-Schiffer
Summary: The chemistry of interfaces is different from that of the bulk. Calculation of interfacial properties depends on the definition of the interface, which can yield ambiguous results. Voronoi tessellation provides a method to explicitly define interfaces and boundaries in molecular systems. This method has broad applications in spectroscopy and can provide insights into various systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Jie Wang, Liangjie Fu, Huaming Yang, Xiaochao Zuo, Di Wu
Summary: This study integrated density functional theory with dispersion scheme (DFT-D) and various experimental methods to investigate the intercalation of dimethyl sulfoxide (DMSO) in kaolinite with and without hydration. It highlighted the kinetic, thermodynamic, and structural impacts of hydration, showing that water molecules significantly promote intercalation of DMSO into kaolinite due to favorable intercalation energy enabled by effective hydrogen bonding.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Paulina Maczugowska, Paulina Zawadzka, Krzysztof Halagan, Marcin Pastorczak, Joanna Sadlej, Marcin Kozanecki
Summary: In this study, water clusters formed in organic liquid matrices with different polarities were investigated using infrared absorption spectroscopy, Molecular Dynamics simulations, and Density Functional Theory calculations. The correlation between experiments and computations at a high level of accuracy was presented for the first time. The results revealed that a higher polarity of the organic matrix favored the formation of stable, small, and cyclic water clusters, while water molecules in nonpolar matrices tended to undergo phase separation on a macroscopic scale. The size of the water clusters strongly depended on the water content in the matrix.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Tao E. Li, Abraham Nitzan, Joseph E. Subotnik
Summary: Recent experiments have shown that the properties of molecules can be altered inside an optical Fabry-Perot microcavity under collective vibrational strong coupling conditions, but this phenomenon is not yet well understood theoretically. By studying the effect of the cavity environment on the nonlinear optical response of the molecular subsystem, researchers have found that a strong excitation pulse to the lower hybrid light-matter state leads to significantly enhanced molecular nonlinear absorption within the cavity. This polariton-enhanced multiphoton absorption also results in an ultrashort polariton lifetime under strong illumination. The mechanism by which energy is transferred to higher vibrationally excited dark states is expected to be observed experimentally in different molecular systems and cavities.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Patrick Ober, Sophia H. H. Kolbinger, Ellen H. G. Backus, Mischa Bonn
Summary: The charge and composition of a solid surface are affected by the composition of the aqueous phase due to ion-specific interactions between ions and the surface. This study investigates ion-specific interactions at the fluorite-water interface using surface-sensitive vibrational sum frequency generation spectroscopy and flow experiments. The flow-induced change in dissolved ion concentration at the surface alters chemical equilibria and influences the surface potential, which is probed using the vibrational sum frequency generation intensity in the OH stretch region. The study identifies charge screening and ion-specific effects, including surface adsorption, by analyzing the vibrational sum frequency generation intensity and its flow-induced change for different salts.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Multidisciplinary
Nathan L. Odendahl, Phillip L. Geissler
Summary: Experiments and simulations have shown that liquid water's surfaces can exhibit similar structural features to crystalline ice surfaces. These findings deepen our understanding of ice-like structures at the liquid's boundary and suggest the presence of quasi-ice layers at the surface of liquid water above the melting point.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Polymer Science
Carlo Andrea Massa, Francesco Puosi, Antonio Tripodo, Dino Leporini
Summary: The vibrational dynamics of a model polymer glass is studied using Molecular Dynamics simulations, focusing on the soft monomers and their tendency to form quasi-local clusters with strong anisotropy in shape. Limited size systems were used to better understand the role of these soft monomers.
Article
Chemistry, Physical
Nazanin Dehdasht-Heidari, Behzad Shareghi, Sadegh Farhadian, Lida Momeni
Summary: This study investigates the interaction between safranal and pepsin under physiological conditions, revealing that safranal can alter the structure and function of pepsin, with non-covalent reactions playing a critical role in this interaction.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Piotr Beldowski, Maciej Przybylek, Przemyslaw Raczynski, Andra Dedinaite, Krzysztof Gorny, Florian Wieland, Zbigniew Dendzik, Alina Sionkowska, Per M. Claesson
Summary: The lubrication mechanism in synovial fluid and joints relies on intermolecular interactions, with albumin being a major component with important electrostatic properties. Divalent cations, particularly Ca2+, are found to increase the affinity between hyaluronan and albumin, aiding in charge compensation. Molecular dynamics analysis reveals structurally and energetically characterized binding sites for hyaluronate in the presence of various ions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Edward Ditler, Sandra Luber
Summary: Vibrational spectroscopy is an important experimental technique for characterizing molecules and materials, but the interpretation of experimental results can be challenging. Computational studies using molecular dynamics simulations provide a valuable tool for understanding and predicting experimental results. This review article summarizes the field of vibrational spectroscopy using first-principles molecular dynamics and highlights recent advances in simulation techniques.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Multidisciplinary Sciences
Alexander Y. Hwang, Rohit Chikkaraddy, David -Benjamin Grys, Oren A. Scherman, Jeremy J. Baumberg, Bart de Nijs
Summary: Nanoconfined few-molecule water clusters are important systems for studying hydrogen bonding, but most experiments are limited to cryogenic temperatures. This study shows that combining Raman spectroscopy with the molecular nanocapsule cucurbituril allows for the sequestration and analysis of water clusters at ambient conditions. The technique provides high-resolution vibrational spectra and can track specific isotopic exchanges inside the water clusters.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Chemical
Maximilian Cohen, Dionisios G. Vlachos
Summary: Mechanistic modeling provides insights into catalytic reactions. The Energy Span Model (ESM) and its modified version (MESA) offer methods to analyze complex reaction networks with parallel pathways. The cycle plot method is proposed for visual reaction pathways analysis. MESA is consistent with microkinetic modeling results and extends the ESM to heterogeneous catalysts using collision theory.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Mehdi Zare, Pavel A. Kots, Stavros Caratzoulas, Dionisios G. Vlachos
Summary: The density and conformation of polyethylene at the interface with Pt(111) are influenced by the length, side chain length, and concentration of the polymer. Short chains are mostly located on the Pt surface, while longer chains exhibit broader conformational distributions. Branching significantly affects the conformations of long chains and can lead to a wider carbon product distribution upon C-C bond cleavage.
Article
Nanoscience & Nanotechnology
Yung Wei Hsiao, Darien K. Nguyen, Kewei Yu, Weiqing Zheng, Panagiotis Dimitrakellis, Dionisios G. Vlachos
Summary: We use a nonthermal, He/O-2 atmospheric plasma as an efficient method of surface functionalization for activated carbons. Plasma treatment rapidly increases the surface oxygen content of the activated carbon, introducing a diverse range of carbonyl and carboxyl functionalities. This surface functionalization improves the catalytic synthesis, reducing particle size, suppressing agglomerate formation, and increasing metal dispersion, leading to improved yield of biofuel replacement compound.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Engineering, Chemical
Nawaf M. Alghamdi, Dionisios G. Vlachos, S. Mani Sarathy
Summary: This study presents a thermodynamically consistent, density functional theory (DFT)-based parametrized microkinetic model that predicts CO oxidation on Rh at stoichiometric and lean conditions. The model accurately simulates experimental data and literature data collected under different conditions. This microkinetic mechanism can contribute to optimizing three-way catalysts to reduce CO emissions and propose cheaper alternative catalysts.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Chemistry, Medicinal
Bharat Medasani, Sashank Kasiraju, Dionisios G. G. Vlachos
Summary: Microkinetic modeling is a valuable tool for combining microscale atomistic data with macroscale reactor observables. This paper introduces an open-source microkinetic modeling toolkit called OpenMKM, which is primarily designed for heterogeneous catalytic reactions but can also be used for homogeneous reactions. OpenMKM is built on top of the Cantera software and allows users to input reaction mechanisms in human-readable files or use automatic generators. It provides built-in interfaces for solving ordinary differential equations and differential-algebraic equations, and offers various ideal reactors and energy balance options. OpenMKM also integrates with pMuTT for thermochemistry input file generation and RenView for visualization and reaction pathway analysis.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Pavel A. Kots, Panagiota A. Doika, Brandon C. Vance, Sean Najmi, Dionisios G. Vlachos
Summary: In this study, the hydrocracking of high-density polyethylene was investigated using a bifunctional Pt/Al2O3 and modified mordenite acid catalyst. Mass transport limitations affect polymer diffusion into mordenite pores, while initial reaction intermediates are formed on the zeolite's outer surface. Recrystallization and desilication of mordenite improve polymer conversion and shift the product distribution maximum. The nature of mesopores and total Bronsted acidity significantly impact zeolite activity and selectivity, indicating the importance of the hierarchical structure of mesoporous mordenite zeolites in plastic waste hydrocracking.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Fabio Cameli, Panagiotis Dimitrakellis, Dionisios G. Vlachos
Summary: A modular, biphasic plasma reactor is used to convert underutilized gas streams into liquid fuels and hydrogen for decentralized chemical processing. By selectively upgrading ethane into ethanol, methanol, and acetic acid in a catalyst-free, continuous plasma microreactor, a plasma-assisted path is established to generate oxygenates. This process also produces H-2 coproduction as well as CO2 and C2H4. The carbon selectivity in this process can be as high as >70% C2H5OH, CH3OH, and CH3COOH, and up to 1.3 and 1 mu mol min(-1) of liquid C2H5OH and CH3OH can be obtained. This low carbon footprint, electrified, modular, and intensified process has the potential to valorize underutilized shale gas resources in remote areas.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Yuqing Luo, Esun Selvam, Dionisios G. Vlachos, Marianthi Ierapetritou
Summary: The growing amount of plastic waste poses a threat to the environment. Polyethylene terephthalate (PET) is widely used in fibers and packaging, making it one of the most common plastics. Recent research has proposed chemical recycling and upcycling methods to produce valuable products from PET waste. This study evaluates the environmental and economic performance of various technologies, including microwave-assisted heterogeneous glycolysis, through techno-economic analysis and life cycle assessment. The results show that the microwave-assisted glycolysis process can reduce production costs and emissions compared to traditional routes, making it an effective method for handling distributed PET waste.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Borja Hernandez, Pavel Kots, Esun Selvam, Dionisios G. Vlachos, Marianthi G. Ierapetritou
Summary: This study compares the techno-economics and life cycle assessment of different thermochemical depolymerization technologies for generating various products from LDPE waste. Pyrolysis followed by conversion to lubricant oils is the most profitable technology, while hydrogenolysis has the lowest CO2 emissions at large scales. Hydrocracking is environmentally friendly but requires optimization of the supply chain. Gasification and hydrothermal liquefaction have high emissions, requiring carbon capture systems. Lowering sorting costs, collecting waste near big cities, building large plants, and achieving high selectivity to value-added products are critical for successful plastic waste management.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Gwendolyn J. Gregory, Cong Wang, Sunitha Sadula, Sam Koval, Raul F. Lobo, Dionisios G. Vlachos, Eleftherios Terry Papoutsakis
Summary: There is limited research on microbial deconstruction or functionalization of polyolefin's recalcitrant backbone. However, microbes can utilize polyolefin deconstruction products. In this study, researchers combined chemical catalysis and bioconversion to valorize polyethylene (PE) deconstruction products. They found microbial consortia derived from soil from local recycling plants that can utilize the PE-deconstruction product mix as the sole carbon source.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Darien K. Nguyen, Vibin Vargheese, Vinson Liao, Panagiotis Dimitrakellis, Sagar Sourav, Weiqing Zheng, Dionisios G. Vlachos
Summary: The study demonstrates that nonthermal, atmospheric He/O-2 plasma (NTAP) is an efficient and controllable method for removing organic ligands like PVP from nanoparticles, without altering the shape and size of the nanoparticles, making it a more efficient alternative to traditional calcination.
Article
Computer Science, Interdisciplinary Applications
Xue Zong, Jonathan Lym, Dionisios G. Vlachos
Summary: DescMAP is a Python-based software that automates the selection of descriptors, the generation of volcano maps, and the identification of active sites for structure-sensitive reactions. It enables quick screening of potential catalysts and can be applied to other complex chemistries.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Engineering, Chemical
Arnav Mittal, Souryadeep Bhattacharyya, Matthew Marino, Tai-Ying Chen, Pierre Desir, Marianthi Ierapetritou, Dionisios G. Vlachos
Summary: Liquid-liquid microchannels have high mass transfer rates but low throughput. To increase productivity, scaling up the channels by increasing diameter is crucial. However, predicting flow patterns and mass transfer rates with varying diameter while accounting for solvent effects is lacking in the literature. In this study, we develop machine learning models to predict flow patterns and mass transfer rates, considering solvent properties and channel diameter, using experimental and computational fluid dynamics data combined with literature-mined data.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Cong Wang, Sagar Sourav, Kewei Yu, Yeonsu Kwak, Weiqing Zheng, Dionisios G. Vlachos
Summary: This study successfully electrifies the dry reforming of methane using metal-free doped ceria catalysts and microwave radiation, providing new insights and methods for carbon-free syngas production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Cong Wang, Sagar Sourav, Kewei Yu, Yeonsu Kwak, Weiqing Zheng, Dionisios G. Vlachos
Summary: This study focuses on the decarbonization of Syngas production through the electrification of dry reforming of methane. By selectively coupling microwave radiation to metal-free doped ceria catalysts, excellent performance is achieved. The insights gained from this study can guide the design of catalysts and process intensification for carbon-free syngas production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)