Review
Biochemistry & Molecular Biology
Bruna Clara De Simone, Marta Erminia Alberto, Tiziana Marino, Nino Russo, Marirosa Toscano
Summary: Computational studies on electrochromic systems have shown reliability and prediction abilities, aiding in the interpretation of experimental data and guiding the rational design of molecules with interesting electrochromic properties.
Article
Chemistry, Physical
Bora Karasulu, Jean-Marc Leyssale, Patrick Rowe, Cedric Weber, Carla de Tomas
Summary: In this study, the structure of carbon clusters spanning a wide range of sizes was systematically predicted using the stochastic ab initio random structure search algorithm (AIRSS) combined with geometry optimizations based on interatomic potentials. The transferability and predictive capability of seven widely used carbon potentials were tested, and the best performing potential, GAP-20, was employed to predict larger clusters in the nanometer scale. The complete cluster dataset obtained captures the evolution of topological properties with cluster size, including ordered and disordered structures, as well as predicting novel isomers.
Review
Engineering, Environmental
Yin Xu, Pan Xia, Chao Wang, Jie Cai, Haibo Li, Zhihong Ye, Hui Zhang
Summary: In the past decade, metal-organic frameworks (MOFs) have gained significant interest in various fields, especially in water purification, due to their large surface area, adjustable topologies, and high physicochemical tunability. This article provides a detailed overview of MOFs materials in heterogeneous advanced oxidation processes (AOPs) for water treatment, focusing on their activation of peroxide to generate reactive oxygen species (ROS) for organic contaminant removal. The article also summarizes the advancements in MOFs activated peroxide processes with photo-, electro-, and ultrasonic-assisted strategies, as well as discusses the specific behaviors, modulation strategies, role of reactive sites, and mechanism of ROS formation in these systems. The article concludes by highlighting the challenges in large-scale synthesis and industrial application of MOFs for peroxide activation, suggesting the great application potential of MOFs-based materials in environmental remediation.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Engineering, Environmental
Manman Wei, Fatma Marrakchi, Chuan Yuan, Xiaoxue Cheng, Ding Jiang, Fatemeh Fazeli Zafar, Yanxia Fu, Shuang Wang
Summary: In this study, activated carbon (ENAC) was prepared by NaOH activation using macroalgae as raw material, resulting in a material with a large surface area and total pore volume. The adsorption of tetracycline (TC) by ENAC followed the Langmuir model and pseudo-second-order kinetics, indicating its potential application in antibiotic removal from aqueous solutions.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Lotfi Sellaoui, Sarra Said, Mohamed Bouzidi, Abdullah Sarhan Alshammari, Ziaul Raza Khan, Mohamed Gandouzi, Carlos Schnorr, Guilherme Luiz Dotto, Luis Silva, Angelica Fatima Streit, Abdelmottaleb Ben Lamine, Alessandro Erto
Summary: In this research, activated carbon derived from sludge is used for the adsorption of Reactive Black 5 and Green Alizarin dyes in wastewater. The adsorption capacities and behavior of the dyes are studied at different temperatures. The results show that the activated carbon has good performance in removing these dyes, and physical models provide insights into the adsorption mechanism. The orientation and aggregation process of the dyes on carbon are identified. The impact of temperature on the adsorption process is also evaluated, indicating its relevance in dye removal.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Adam Yuile, Alexander Schulz, Erik Wiss, Jens Mueller, Steffen Wiese
Summary: This study conducted a theoretical analysis and thermal CFD simulation to evaluate the potential of reactive multilayer systems (rms) in bonding silicon chips and ceramic substrates. The analysis focused on the temperature and liquid fraction contours to understand the bonding process. The results provide valuable information for the design of test substrates in experimental investigations.
APPLIED SCIENCES-BASEL
(2022)
Article
Chemistry, Physical
Mao Su, Ji-Hui Yang, Zhi-Pan Liu, Xin-Gao Gong
Summary: In this study, the interface structures of the CdS/CdTe heterostructure were explored using a combination of the differential evolution algorithm and neural network potential. The stability of various interfacial structures with defects was assessed by considering the interfacial energies. It was found that under the Cd-poor condition, the CdS-like interface I was energetically more favorable and preferred to be defect-free. This research is of great significance for improving solar cell efficiencies and suppressing defect recombination at the interface.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Mao Su, Ji-Hui Yang, Zhi-Pan Liu, Xin-Gao Gong
Summary: This study presents a scheme to explore the interface structures of CdS/CdTe heterostructure by combining the differential evolution algorithm and the neural network potential. The research finds that the CdS-like interface I is more stable and tends to be defect-free under the Cd-poor condition, which may be beneficial for improving the efficiency of solar cells.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Agricultural Engineering
Rodrigo J. Martinez, Alina Z. Vela-Carrillo, Luis A. Godinez, Jose de Jesus Perez-Bueno, Irma Robles
Summary: This study examined the feasibility of using sugarcane bagasse, spent coffee-grounds, and orange peel activated carbons for the removal of methyl orange and methylene blue. The results showed that these three carbon materials can adsorb both dyes simultaneously and exhibit different adsorption capacities under different pH and initial concentrations. This is important for the treatment of wastewater containing mixed pollutants.
BIOMASS & BIOENERGY
(2023)
Article
Chemistry, Physical
Yegor M. Kedalo, Andrey A. Knizhnik, Boris V. Potapkin
Summary: The effectiveness of vibrational excitation for promoting reactions can be accurately described by the Fridman-Macheret (F-M) alpha-model, initially developed for gas-phase processes. However, it is also widely used to analyze the efficacy of vibrational excitation in heterogeneous processes, such as NH3 synthesis, CO2 reduction, and CH4 activation. In plasma-assisted heterogeneous processes, the contribution of highly vibrationally excited species to the reaction is emphasized. This study aims to determine whether the F-M model is applicable for the activation of N-2 molecules on the surfaces of Ru(113) and Ru(0001) using molecular dynamics with machine learning potential (MLP). The results indicate that the F-M model is a reasonable approximation for estimating the vibrational efficacy of highly excited states (v >= 7) that are crucial under non-equilibrium plasma conditions.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Haina Wang, Frank H. Stillinger, Salvatore Torquato
Summary: The Zhang-Torquato conjecture states that any realizable set of pair statistics, whether from a nonequilibrium or equilibrium system, can be achieved by equilibrium systems involving up to two-body interactions. The study shows that the unit-step function g(2) can be easily realized within a certain range of densities. For higher dimensions, the maximum terminal packing fraction can be achieved, and the large-r behaviors of the effective potentials are given by approximate expressions based on known conditions. These findings are important for the design of novel nanoparticle systems with density-dependent effective potentials, including exotic hyperuniform states of matter.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Engineering, Environmental
Jiahui Yu, Shuai Liu, Xueliang Mu, Gang Yang, Xiang Luo, Edward Lester, Tao Wu
Summary: By activating CO2 at the interfaces of Cu-ZrO2 and controlling the formation of highly dispersed Cu nanoclusters, the Cu-ZrO2 catalyst demonstrates superior catalytic activity and selectivity in the hydrogenation of CO2 to methanol.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Applied
Edward Stacey, Matthew G. Quesne, C. Richard A. Catlow
Summary: We conducted a comprehensive study on the calculated lattice and cohesive energies of pure silica zeolites and pure microporous alumino-phosphates (ALPOs). DFT-based molecular mechanical and quantum mechanical methods were employed to calculate lattice and cohesive energies. The results indicate that the siliceous zeolites and microporous ALPOs are metastable compared to α-Quartz and Berlinite, with the DFT methods yielding values closer to experimental data than interatomic potential based methods. However, for the ALPO systems, the DFT calculations give higher energies than interatomic potential based methods, deviating significantly from experimental values. Possible reasons for this discrepancy are discussed.
MICROPOROUS AND MESOPOROUS MATERIALS
(2023)
Article
Green & Sustainable Science & Technology
Moein Jahanbani Veshareh, Hamidreza M. Nick
Summary: This study suggests that using production water samples may not be suitable for studying reservoir souring, as they may not accurately reflect the sulfate reducing bacteria responsible for souring in the reservoir. The results indicate that a more accurate prediction of reservoir souring requires understanding the behavior of sulfate reducing bacteria in injection water and formation brine.
JOURNAL OF CLEANER PRODUCTION
(2021)
Article
Chemistry, Physical
Saheed A. Ganiyu, Oluwole Ajumobi, Abdulkadir Tanimu, Ismail Abdulazeez, Salawu Omobayo Adio, Qamarrudin Muhammad, Khalid Alhooshani
Summary: This study focused on the synthesis and application of activated carbon in removing DBT and DMDBT from isooctane, showing that the adsorbent synthesized from agricultural waste material exhibited high surface area and porosity. DFT calculations predict the selectivity of the activated carbon towards DMDBT, with results indicating that DMDBT preferentially adsorbs onto adsorbents with larger pore sizes and volumes. Thorough studies on the adsorbent's performance in removing organosulfur compounds revealed that process parameters such as pyrolysis temperature and ramping rate play crucial roles in determining the adsorbent's efficiency.
SURFACES AND INTERFACES
(2021)
Editorial Material
Biology
Andrea Perez-Villa, Fabio Pietrucci, A. Marco Saitta
PHYSICS OF LIFE REVIEWS
(2020)
Article
Chemistry, Physical
Paraskevi Gkeka, Gabriel Stoltz, Amir Barati Farimani, Zineb Belkacemi, Michele Ceriotti, John D. Chodera, Aaron R. Dinner, Andrew L. Ferguson, Jean-Bernard Maillet, Herve Minoux, Christine Peter, Fabio Pietrucci, Ana Silveira, Alexandre Tkatchenko, Zofia Trstanova, Rafal Wiewiora, Tony Lelievre
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Chemistry, Physical
Jonathan Amodeo, Fabio Pietrucci, Julien Lam
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Chemistry, Physical
Theo Magrino, Fabio Pietrucci, A. Marco Saitta
Summary: This study provides a quantitative microscopic description of the complex Strecker reaction by adopting a state-of-the-art ab initio computational approach. It reveals the step-by-step chemical pathway from Strecker precursors to glycine in solution and calculates the corresponding full free energy landscape, demonstrating agreement with experimental data and providing new insights into this crucial bottleneck for the emergence of life.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Alessandro Sinopoli, Ahmed Abotaleb, Fabio Pietrucci, Ivan Gladich
Summary: This study investigates the chemical conversion of CO2 at the vapor/liquid water interface using first-principles molecular dynamics simulations and an enhanced sampling technique. The results reveal the instability of the zwitterion and carbamate ions at the interface, indicating the need for novel solvents to overcome limitations of current absorbents in the design of cost-effective capture systems for low CO2 partial pressure conditions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Mathieu Moog, Fabio Pietrucci, A. Marco Saitta
Summary: The study utilized extensive ab initio molecular dynamics simulations to characterize the structural behavior of carbon dioxide fluids under geological conditions. It identified various disordered regimes, including polymeric and molecular forms, existing in the lower mantle.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Diana Nelli, Fabio Pietrucci, Riccardo Ferrando
Summary: This study investigates the diffusion mechanism of single-atom impurities in nanoalloys using two computational techniques and reveals unexpected diffusion pathways related to non-homogeneous compressive stress. The observed mechanism differs from previously identified vacancy-mediated diffusion processes.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Flavio Siro Brigiano, Maciej Gierada, Frederik Tielens, Fabio Pietrucci
Summary: This study investigates the mechanism of peptide bond formation over a silica surface in an aqueous environment, revealing a strong catalytic effect of the interface on the reaction.
Article
Multidisciplinary Sciences
Hadrien Vroylandt, Ludovic Goudenege, Pierre Monmarche, Fabio Pietrucci, Benjamin Rotenberg
Summary: We introduce a method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. By using a parametrization based on hidden auxiliary variables, this method recovers both the memory kernel and random noise, providing a reduced dynamical model for multidimensional collective variables. It allows for the accurate sampling of their long-time dynamical properties at a lower computational cost, and conveniently provides other observables beyond the memory kernel or velocity-autocorrelation function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Timothee Devergne, Theo Magrino, Fabio Pietrucci, A. Marco Saitta
Summary: The study investigates the use of advanced free-energy methods for predicting the thermodynamics, kinetics, and microscopic mechanisms of chemical reactions in solution. The researchers propose an ab initio protocol that combines machine learning with atomistic simulation methods to improve computational efficiency and avoid extrapolation risks. The results show that the proposed protocol achieves comparable accuracy to traditional ab initio methods with significantly reduced computational load.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Karen Palacio-Rodriguez, Fabio Pietrucci
Summary: This study focuses on constructing accurate mathematical models of complex system dynamics on a collective variable by using a simple and effective algorithm to estimate parameters from out-of-equilibrium molecular dynamics trajectories. By maximizing model likelihood based on short-time propagator expressions, the approach reconstructs thermodynamics and kinetics of activated processes such as free energy landscapes, diffusion coefficients, and kinetic rates. Compared to existing enhanced sampling methods, this method directly utilizes short unbiased trajectories at a competitive computational cost.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Karen Palacio-Rodriguez, Hadrien Vroylandt, Lukas S. Stelzl, Fabio Pietrucci, Gerhard Hummer, Pilar Cossio
Summary: Simulations with adaptive time-dependent bias allow efficient exploration of a system's conformational space, but alter the dynamic information. Infrequent metadynamics can recover the transition rate of crossing a barrier, but certain conditions must be met. To overcome these limitations, we use Kramers' theory to calculate the barrier-crossing rate with a time-dependent bias, and propose approximate analytical expressions for reproducing barrier-crossing time statistics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Alexandre Jedrecy, A. Marco Saitta, Fabio Pietrucci
Summary: The existence of a first-order phase transition between low-density liquid (LDL) and high-density liquid (HDL) forms of supercooled water has been a debated issue in physics and chemistry for the past three decades. Through computational study using the TIP4P/2005 force field, we determined the free-energy landscapes of supercooled water under various pressure and temperature conditions. Our simulations did not detect any barrier within the investigated timescales and system size for a discontinuous transition between LDL and HDL forms, until the onset of solid, non-diffusive amorphous forms.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Theo Magrino, Leon Huet, A. Marco Saitta, Fabio Pietrucci
Summary: Reaction coordinates are crucial for studying rare events in chemistry and physics. This paper critically evaluates the advantages and disadvantages of heuristic reaction coordinates compared to those optimized using reliable transition-path sampling data. The researchers used ab initio molecular dynamics simulations to study chloride SN2 substitution and developed a computational protocol that allows the unsupervised optimization of coordinates that account for solute and solvent contributions, leading to high-quality free-energy reconstruction without requiring chemical intuition.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Multidisciplinary
Fabio Pietrucci, Mauro Boero, Wanda Andreoni
Summary: Water pollution by heavy metals is a growing concern due to its severe environmental and health impacts. Natural materials, like spent coffee grains or fruit peels, are being explored as potential cheap alternatives for heavy metal removal. Molecular simulations show that hemicellulose may efficiently capture lead ions from water through spontaneous adsorption on specific functional groups.
