Review
Materials Science, Multidisciplinary
Zaiba Zafar, Sha-Sha Yi, Jin-Peng Li, Chuan-Qi Li, Yong-Fa Zhu, Amir Zada, Wei-Jing Yao, Zhong-Yi Liu, Xin-Zheng Yue
Summary: This review discusses the impact of defect architecture on photocatalytic activity and emphasizes the importance of defect engineering in the design of modern photocatalysts. By tuning the electronic microstructure and surface morphologies of semiconductors, efficiency of photocatalysts can be improved.
ENERGY & ENVIRONMENTAL MATERIALS
(2022)
Review
Chemistry, Multidisciplinary
Muhammad Faheem, Arshad Hussain, Muhammad Ali, Md. Abdul Aziz
Summary: Aluminum-sulfur batteries have become the most prominent battery technology due to their high theoretical capacity, eco-friendliness, economics, and abundance of aluminum as well as sulfur. Recent research has focused on different types of carbon as hosts for sulfur and controlling the aluminum polysulfide shuttling effect. Significant progress has been made in finding suitable electrolytes theoretically and experimentally, with some success using ionic liquid electrolytes. However, challenges such as oxide layer formation on aluminum, low cyclic stability, and high cost of electrolytes still need to be addressed to make aluminum-sulfur batteries a competitor to lithium-ion batteries.
Article
Chemistry, Multidisciplinary
Jaya Mehara, Adarsh Koovakattil Surendran, Teun van Wieringen, Deeksha Setia, Cina Foroutan-Nejad, Michal Straka, Lubomir Rulisek, Jana Roithova
Summary: Gold(II) complexes are not commonly used in catalyzing chemical transformations due to their easy oxidation or reduction to more stable gold(III) or gold(I) complexes. In this study, we investigated the thermodynamics, stability, and spectral properties of [Au-II(L)(X)](+) complexes (L=ligand, X=halogen) in the gas phase. It was found that bidentate and tridentate ligands with nitrogen donor atoms are the best choices for stabilizing gaseous [Au-II(L)(X)](+) complexes. Quantum chemical calculations revealed that the molecular and electronic structures, as well as the spectroscopic properties, of the investigated gold(II) complexes are similar to those of stable copper(II) complexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Engineering, Chemical
Shahab Alizadeh, Mahmoud Abdollahy, Ahmad Khodadadi Darban, Mehdi Mohseni
Summary: The extraction behavior of lanthanides (La3+ and Y3+) in nitric acid solution was studied using a bifunctional ionic liquid, and it was found that the ionic liquid had higher extraction capacity compared to a molecular extractant. The selectivity results were confirmed and interpreted using Density Functional Theory and the Conductor-like Screening Model. The ionic liquid was more efficient than the molecular extractant in the extraction of the ionic complexes of lanthanum and yttrium.
MINERALS ENGINEERING
(2022)
Article
Materials Science, Multidisciplinary
Changle Li, Song Lu, Sergiy Divinski, Levente Vitos
Summary: Grain boundary energy (GBE) and its temperature dependence in body-centered cubic (bcc) metals were investigated using ab initio calculations. A scaling relationship between the GBEs of the same grain boundary structure in different bcc metals was identified, with the scaling factor estimated by the ratio of low-index surface energy. The general GBEs of bcc metals at 0 K were predicted, and the predicted GBEs at elevated temperatures were found to be in good agreement with experimental data.
Article
Thermodynamics
Peng Liu, Bingjie Chen, Zepeng Li, Anthony Bennett, Salim Sioud, Heinz Pitsch, S. Mani Sarathy, L. William Roberts
Summary: The study investigates the chemical evolution of various functional groups in PAH and soot, revealing their sensitivity to temperature and different reaction pathways at different temperatures. Kinetic modeling and experimental data interpretation suggest a qualitative description of the formation of OPAH with the C-O-C functional group through the HACA-like pathway, while the evolution of PAH with different functional groups is captured through different reactions involving PAH radicals and C2H4/C2H3.
PROCEEDINGS OF THE COMBUSTION INSTITUTE
(2021)
Article
Chemistry, Analytical
Max Wamsley, Samadhi Nawalage, Juan Hu, Willard E. Collier, Dongmao Zhang
Summary: This article presents a first-principle model for analyzing the absorption and fluorescence of correlated samples. The model can fit the fluorescence intensity as a function of absorbance and provides a theoretical foundation for correction methods and quantitative mechanistic studies. The authors hope that this model will be widely adopted in both student education and various fluorescence applications.
ANALYTICAL CHEMISTRY
(2022)
Article
Physics, Multidisciplinary
Kamran Behnia
Summary: La1.67Sr0.33CuO4 is not a superconductor with a T-2 temperature dependence, while La1.71Sr0.29CuO4 exhibits superconductivity with a T-Linear term in its resistivity. The unusually large electron-electron collision rate above a critical doping may play a role in the emergence of these two distinct features.
Article
Chemistry, Physical
Masoumeh Ghalkhani, Roya Majidi, Esmail Sohouli
Summary: This study evaluated the interaction between clonazepam and zigzag carbon nanotubes (CNTs) and demonstrated the adsorption ability of CNTs for clonazepam molecules. The experimental results showed that clonazepam molecules can effectively interact with CNTs and be adsorbed onto the surface of CNTs. The presence of CNTs facilitated the redox reaction of clonazepam, resulting in sharper voltammograms. The findings suggest that CNTs are suitable for the fabrication of sensitive sensors for trace analysis of clonazepam or effective adsorbents for its removal from contaminated specimens.
Article
Nanoscience & Nanotechnology
Ellen Yan, Renata Balgley, Maureen B. Morla, Soonho Kwon, Charles B. Musgrave, Bruce S. Brunschwig, William A. Goddard, Nathan S. Lewis
Summary: Reductant-activated functionalization enhances the methylation of ceMoS2 and ceWS2 by introducing excess negative charge for nucleophilic attack reaction. The coverage of ceWS2 increases from 25% to 52% with the presence of reductant, while the methyl coverage on ceWS2 is about 20% lower than ceMoS2 at every potential. Density functional theory calculations show that methylation is thermodynamically and kinetically more favorable on 1T'-MoS2 than 1T'-WS2 due to the presence of more negative charge on 1T'-MoS2. However, this effect is moderated when the reactions are compared at constant charge, emphasizing the importance of comparing reactivity at nominally identical electrode potentials.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Physics, Condensed Matter
Ashwaq Abuhusain, Fahad Abdulaziz, M. Gandouzi, Abdullah S. Alshammari, M. Bouzidi, Mansour Mohamed, Z. R. Khan
Summary: This work investigates pure, Sr, and (Sr,Co) co-doped CdS systems through experimental and theoretical methods. Thin films of pure and co-doped CdS nanostructures were grown using sol-gel spin coating, with varying Co doping concentrations. X-ray diffractograms showed growth along the (002) plane and crystallite sizes of approximately 3-6 nm. The films exhibited band gaps of 2.30-2.48 eV, with a blue shift observed in the co-doped CdS compared to the Sr:CdS system. Density functional theory calculations revealed excellent agreement with the experimental results, and the (Sr,Co) co-doped CdS demonstrated spin polarization effects on the valence band, making it suitable for optoelectronics and spintronics applications.
PHYSICA B-CONDENSED MATTER
(2023)
Article
Multidisciplinary Sciences
Pawel Goj, Bartosz Handke, Pawel Stoch
Summary: Aluminum phosphates are versatile materials with potential applications in various industries. By using experimental and computational methods, the vibrational features of these materials were analyzed and related to their structures and compositions, providing valuable insights for their application and research.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Binod R. Giri, Aamir Farooq, Milan Szori, John M. Roscoe
Summary: This work presents the temperature dependence of the rate coefficients for the reactions between atomic bromine and xylenes. The experiments were conducted at various oxygen concentrations to assess its role in the reactions and compare the results with previous studies. The rate coefficients were found to be independent of the oxygen concentration and the temperature dependence was determined. Theoretical calculations revealed that the reactions proceed through a complex forming mechanism.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Shengjiang Zhang, Xiuniang Tan, Yan Zhou, Jinyang Liu, Xiangyao Liang, Xuehuan Ding, Guangmiao Lyu, Ying Wei, Junxin Chen, Yidan Mao, Jinmei Wu, Yushan Huang, Yusen Huang, Xuecai Tan, Zaiyin Huang
Summary: In this study, the thermodynamic properties of nano-cadmium sulphide (nano-CdS) were investigated, and it was found that the surface heat capacity of nano-CdS is influenced by the critical size, which is valuable for understanding the energy storage processes of nanomaterials.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
Dominik Legut, Andrzej Piotr Kadzielawa, Petr Panek, Kristyna Markova, Petra Vanova, Katerina Konecna, Sarka Langova
Summary: This study investigates the corrosion inhibition of mild steel by different ionic liquids in 1 M HCl solution. The inhibitory efficiency of 1-octyl-3-methylimidazolium salts is high, with a range of 80-92%, demonstrating a stronger effect than the anion type. Additionally, the alkyl chain length has a greater impact on the inhibition process than the type of anion present.
Article
Biochemistry & Molecular Biology
Linda Celeste Montemiglio, Elena Gugole, Ida Freda, Cecile Exertier, Lucia D'Auria, Cheng Giuseppe Chen, Alessandro Nicola Nardi, Gabriele Cerutti, Giacomo Parisi, Marco D'Abramo, Carmelinda Savino, Beatrice Vallone
Summary: This study analyzed the role of a cavity in substrate binding to OleP by mutating its volume. The results showed that inserting bulky residues into the cavity affected the binding properties of the enzyme and perturbed the conformational space of the substrate-enzyme complex. The study highlights the importance of this region in OleP substrate binding and suggests the potential to redirect its activity through this region.
Article
Chemistry, Physical
Cheng Giuseppe Chen, Mauro Giustini, Anita Scipioni, Andrea Amadei, Marco D'Abramo
Summary: We present an advanced theoretical-computational approach to simulate the electronic circular dichroism spectrum of the smallest chiral amino acid in water solution. The calculation results, compared with experimental data, demonstrate the effectiveness of our approach.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Leonardo Bo, Edoardo Milanetti, Cheng Giuseppe Chen, Giancarlo Ruocco, Andrea Amadei, Marco D'Abramo
Summary: The folding-unfolding thermodynamics of two mutants of Trp-cage miniprotein were characterized using extended molecular dynamics simulations and an advanced statistical-mechanical-based approach. The computational data accurately reproduced the experimental results for the thermophilic mutant, but the mesophilic mutant's thermodynamic behavior could not be reconstructed.
Article
Chemistry, Physical
Cheng Giuseppe Chen, Alessandro Nicola Nardi, Andrea Amadei, Marco D'Abramo
Summary: PyMM is a Python software package that applies the QM/MM approach using the perturbed matrix method in a simple and efficient way. It accurately describes the electronic properties of the system and provides various perturbed calculations and analyses for common electronic properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Maria Laura De Sciscio, Alessandro Nicola Nardi, Giacomo Parisi, Giovanni Bulfaro, Antonella Costanzo, Elena Gugole, Cecile Exertier, Ida Freda, Carmelinda Savino, Beatrice Vallone, Linda Celeste Montemiglio, Marco D'Abramo
Summary: We investigated the impact of structural dynamic conformational behavior on the catalytic activity of Cytochrome P450 OleP. By combining equilibrium-binding experiments and all-atom molecular dynamics simulations, we found that the closed-catalytic competent-form is favored under high-ionic strength conditions. Interestingly, different mechanisms can be used to explain this effect, depending on the chemistry of the cations.
Article
Chemistry, Multidisciplinary
Marta Monti, Maria Francisca Matus, Sami Malola, Alessandro Fortunelli, Massimiliano Aschi, Mauro Stener, Hannu Hakkinen
Summary: The water-soluble glutathione-protected [Au-25(GSH)(18)](-1) nanocluster was investigated using molecular dynamics simulations, essential dynamics analysis, and time-dependent density functional theory calculations. Conformational changes, weak interactions, and solvent effects, particularly hydrogen bonds, were found to significantly influence the optical response of the system. The analysis demonstrated the sensitive nature of the electronic circular dichroism to the presence of solvent and the active role of the solvent in forming a chiral solvation shell around the cluster. This work presents a successful strategy for studying chiral interfaces between metal nanoclusters and their environments, with potential applications in chiral electronic interactions with biomolecules.
Article
Chemistry, Multidisciplinary
Matteo Capone, Abhishek Sirohiwal, Massimiliano Aschi, Dimitrios A. Pantazis, Isabella Daidone
Summary: Photosystem-II (PSII) is a multi-subunit protein complex that performs oxygenic photosynthesis by harvesting sunlight. Studying the processes following light excitation has been challenging due to spectral congestion, ultrafast nature, and multi-component behavior. Using advanced computational multiscale approaches, researchers have identified two possible primary pathways to radical-pair formation, with significantly different kinetics. The dominant pathway is fast (short-range), but the existence of a slower (long-range) alternative pathway suggests the evolution of redundancy for other purposes related to the formation of oxidative species in PSII that drives water oxidation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Cheng Giuseppe Chen, Mauro Giustini, Marco D'Abramo, Andrea Amadei
Summary: In this paper, the dynamics of the emitting electronic excited state of aqueous indole were reconstructed, and its relaxation mechanism and kinetics were investigated with respect to the time-dependent fluorescence signal. Using recent results, the relaxation process in solution was modeled by transitions between two gas-phase singlet electronic states (L-1(a) and L-1(b)), which subsequently irreversibly relaxed to the gas-phase singlet dark state ((1)pi sigma*). A comparison with experimental data showed that the theoretical-computational model accurately reproduced all experimental observables.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
M. Monti, G. Brancolini, E. Coccia, D. Toffoli, A. Fortunelli, S. Corni, M. Stener, M. Aschi
Summary: The effects of the conformational dynamics of 2-PET protective ligands on the electronic circular dichroism (ECD) of chiral Au-38(SC2H4Ph)(24) clusters are investigated. ECD spectra are calculated using the first principle polTDDFT approach on a series of conformations extracted from MD simulations, and weighted to predict the final spectrum. The results show the importance of considering conformational effects in ECD modeling of chiral nanoclusters.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Massimiliano Aschi, Laura Palombi, Andrea Amadei
Summary: The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were successfully modeled using a theoretical-computational method combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations. The method accurately reproduced the experimental spectra and demonstrated its effectiveness in modeling spectral features in complex systems. The strategy involved performing a long timescale MD simulation, extracting relevant conformations, and calculating the ECD spectrum using the PMM approach.
Article
Biochemistry & Molecular Biology
Alessandro Nicola Nardi, Alessio Olivieri, Andrea Amadei, Riccardo Salvio, Marco D'Abramo
Summary: In this study, the kinetics of hydroxide-promoted hydrolysis of phosphoric diesters were modeled using a hybrid quantum/classical approach. The results suggest that the hydrolysis occurs through a concerted A(N)D(N) mechanism, with no formation of penta-coordinated intermediates. This modeling method has the potential to predict rate constants and reactivities/selectivities in complex environments.
Article
Biochemistry & Molecular Biology
Valentina Tedeschi, Giorgia Paldino, Josephine Alba, Emanuele Molteni, Fabiana Paladini, Rossana Scrivo, Mattia Congia, Alberto Cauli, Rosalba Caccavale, Marino Paroli, Manuela Di Franco, Loretta Tuosto, Rosa Sorrentino, Marco D'Abramo, Maria Teresa Fiorillo
Summary: The HLA-B*27 family of alleles is strongly associated with ankylosing spondylitis (AS), but some non-associated HLA-B*27 variants have been found. The quantity of presented epitopes, rather than the quality, may explain the difference. The ERAP1/2 haplotype and the B*27:05 allele play crucial roles in shaping the CD8+ T cell response to viral and self-B*27 peptides.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Isabella Daidone, Riccardo Foffi, Andrea Amadei, Laura Zanetti-Polzi
Summary: In this study, we applied a theoretical model to investigate the thermodynamic properties of supercooled water. Our model, which incorporates clusters of molecules beyond the first hydration shell, accurately describes the two distinct liquid states and shows good agreement with the results of other two-state models.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Maria Laura De Sciscio, Alessandro Nicola Nardi, Fabio Centola, Mara Rossi, Enrico Guarnera, Marco D'Abramo
Summary: In this work, a theoretical-computational method is used to study the deamidation reaction, a critical post-translational modification in proteins, using a simple model molecule in solution. The research highlights the importance of accurately considering environmental factors and developing precise kinetic models in order to correctly assess the overall kinetics of the deamidation reaction.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)