Article
Chemistry, Multidisciplinary
Anh L. P. Nguyen, Ekaterina I. Izgorodina
Summary: This study investigated the performance of the counterpoise (CP) correction by Boys and Bernardi in many-body clusters of organic compounds. It was found that the CP-corrected interaction energies were basis-set independent, unlike the electronic energies of individual molecules. The use of a small basis set showed excellent performance in predicting HF interaction energies.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Anders Brakestad, Peter Wind, Stig Rune Jensen, Luca Frediani, Kathrin Helen Hopmann
Summary: In this study, high-precision multiwavelet calculations were used to compute metal-ligand association energies for 27 transition metal complexes. The results showed that counterpoise corrections commonly used to correct for basis set superposition errors often lead to underbinding, especially when the association step involves a chemical transformation. Multiwavelets offer a promising alternative for computing electronic interaction energies free from any basis set errors, and can be conveniently applied to all types of reactions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Pedro Salvador, Istvan Mayer
Summary: The study introduces a new method based on the chemical Hamiltonian approach, which reduces basis set superposition error. Comparing with previous methods, it shows a significant simplification, but performs poorly with the aug-cc-pVDZ basis set.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2022)
Article
Chemistry, Physical
Montgomery Gray, Paige E. Bowling, John M. Herbert
Summary: This study systematically assesses the counterpoise (CP) procedure in density functional theory and finds that nearly complete-basis quality intermolecular interaction energies can be obtained using only double-zeta basis sets with CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions, which is important for large systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Donghan Wang, Wenze Li, Xu Dong, Hongzhi Li, LiHong Hu
Summary: This study proposes an interpretable noncovalent interaction (NCI) prediction model called TFRegNCI, based on RegNet feature extraction and a transformer encoder fusion strategy. The model achieves high accuracy and efficiency by using a transformer encoder for feature fusion and 2D inputs instead of 3D inputs. The addition of the visualization module, Grad-RAM, enhances the interpretability of the model by displaying feature maps and validating their significance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Polymer Science
Giuseppe Scherillo, Giuseppe Mensitieri, Antonio Baldanza, Valerio Loianno, Pellegrino Musto, Marianna Pannico, Andrea Correa, Antonio De Nicola, Giuseppe Milano
Summary: This study combines experimental and theoretical approaches to gain a molecular-scale understanding of the state of CO2 molecules absorbed in glassy poly(ether imide) (PEI), providing a comprehensive physicochemical picture.
Article
Chemistry, Multidisciplinary
Ctirad Cervinka
Summary: Five ionic liquids were used to benchmark the performance of quasi-harmonic DFT calculations, with PBE-D3 combined with a triple-zeta GTO basis set often yielding the most accurate predictions. The error cancellation between basis set superposition and PBE imperfections strongly affects the overall accuracy, unlike B3LYP/GTO calculations, hindering systematic convergence towards higher accuracy.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Asem Alenaizan
Summary: In this article, a simple approach is proposed to reduce the basis set requirement for accurate computation of interaction energies of bimolecular noncovalent complexes. The approach utilizes a distributed multipole expansion to assess the significance of basis functions at each atom. By moderately truncating the basis sets, computational cost is reduced without sacrificing accuracy. The approach proves to be successful for wavefunction-based methods and density functional theory approximation using the Dunning, Karlsruhe, and Jensen basis sets.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Engineering, Electrical & Electronic
Valentin Gherman, Lorenzo Ciampolini, Samuel Evain, Sebastien Ricavy
Summary: It is formally proven that conventional ECC decoders reinforced with weak-bit-flipping can achieve similar error correction capability as theoretical generalized-minimum-distance decoders. Weak-bit-flipping combined with SEC-DED or DEC-TED codes can significantly reduce the UBER. Weak-bit-information extracted from a 2T2R memory can greatly improve the UBER of a conventional decoder.
MICROELECTRONICS RELIABILITY
(2022)
Article
Multidisciplinary Sciences
Fatemeh Najafi, Farzaneh Farzad, Samaneh Pasban
Summary: The interaction between free amino acids and biocompatible nanoparticles is crucial for plasma-related biomedical applications. In this study, the effect of molecular polarity on the interaction between boron nitride nanosheets and amino acids was investigated using quantum mechanical calculations, classical MD simulations, and metadynamics simulations.
SCIENTIFIC REPORTS
(2022)
Article
Mechanics
Panxu Sun, Senpei Zhang, Yadan Yan, Dongwei Wang
Summary: This paper analyzes the source of truncation error in the complex mode superposition method for hysteretic damped systems with non-proportional characteristics, including truncation errors of external excitation load and Hilbert transform term. It obtains the approximate expression of high-order modal response and proposes a complex mode superposition method for mode static correction in non-proportionally damped systems.
INTERNATIONAL JOURNAL OF APPLIED MECHANICS
(2023)
Article
Chemistry, Physical
Han Chen, Chris-Kriton Skylaris
Summary: This work extends the energy decomposition analysis (EDA) method to metallic systems for the first time, by considering partially occupied molecular orbitals and using weighted orthogonalization. The method gives more weight to orbitals with higher occupancies and treats each fragment as metallic, providing a new paradigm and tool for studying interactions in metallic systems within large-scale DFT calculations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Inorganic & Nuclear
Nikita Y. Shmelev, Tesfu H. Okubazghi, Pavel A. Abramov, Vladislav Y. Komarov, Mariana I. Rakhmanova, Alexander S. Novikov, Artem L. Gushchin
Summary: Treating [(PPh3)AuCl] complex with silver triflate in dichloromethane leads to synthesis of dinuclear gold(I) complexes with high yields. Crystal structures show linear gold ions with twisted bipyridine ligands allowing aurophilic interactions. Photoluminescence in solid state with different emission colors and phosphorescent lifetimes is observed when excited at 300 nm.
DALTON TRANSACTIONS
(2021)
Article
Computer Science, Information Systems
Seonmin Koo, Chanjun Park, Jaehyung Seo, Seungjun Lee, Hyeonseok Moon, Jungseob Lee, Heuiseok Lim
Summary: Recently, there has been active research on Korean grammatical error correction in machine translation and automatic noise generation. However, there is a lack of a gold-standard test set for objective and official comparative analysis. This study proposes a gold-standard test set called K-NCT for Korean grammatical error correction, which uses a new error type classification guideline to improve accuracy. Quantitative analysis using a commercialization system and human evaluation shows that the proposed test set is well-balanced, diverse, and precise.
Article
Chemistry, Physical
Jun Zhang, Zhen Tang, Xiaoyong Zhang, Hong Zhu, Ruoqi Zhao, Yangyi Lu, Jiali Gao
Summary: A flexible self-consistent field method called target state optimization (TSO) is introduced for exploring electronic excited configurations and localized diabatic states. The method partitions molecular orbitals into different subspaces based on the excitation or localization pattern for a target state, avoid mixing of orbitals belonging to different subspaces. The TSO method can be applied in both Hartree-Fock theory and Kohn-Sham density functional theory (DFT). Comparisons with time-dependent density functional theory (TD-DFT) calculations show that TSO-DFT provides similar quality results for valence excited states of organic compounds with average errors of 0.5 and 0.4 eV, respectively, and superior performance for core excitation, doubly excited states, and charge-transfer states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Biochemistry & Molecular Biology
Annia Galano, Eduardo G. Guzman-Lopez, Russel J. Reiter
Summary: Melatonin and its derivatives have potential in antioxidant protection and neuroprotection, and chemistry research may lead to the discovery of new compounds. Research is also focused on the discovery of multifunctional pharmaceuticals for use in various diseases including neurodegenerative disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Mirzam Carreon-Gonzalez, Leonardo Munoz-Rugeles, Annik Vivier-Bunge, Juan Raul Alvarez-Idaboy
Summary: This study investigated the repairing antioxidant activity of eight different thiophenols for damaged leucine and tryptophane, and elucidated the corresponding reaction mechanisms. Thiophenols repair leucine in a similar manner to the one used by glutathione to repair carbon-centered radicals, and restore tryptophane via proton-coupled electron transfer and single electron transfer mechanisms.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Romina Castaneda-Arriaga, Adriana Perez-Gonzalez, Tiziana Marino, Nino Russo, Annia Galano
Summary: Phenolic acids in nopal can prevent the formation of hydroxyl free radicals by chelating copper ions, thereby reducing the harmful effects caused by oxidative stress.
Article
Biochemistry & Molecular Biology
Eduardo Gabriel Guzman-Lopez, Miguel Reina, Adriana Perez-Gonzalez, Misaela Francisco-Marquez, Luis Felipe Hernandez-Ayala, Romina Castaneda-Arriaga, Annia Galano
Summary: This article presents a computational protocol for designing new antioxidants with versatile behavior. The protocol, called CADMA-Chem, allows for the analysis of drug-like behavior, toxicity, manufacturability, versatile antioxidant protection, and receptor-ligand binding affinities. It is expected to accelerate the discovery of oral drugs that can prevent or slow down multifactorial human health disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Miguel Reina, Eduardo Gabriel Guzman-Lopez, Annia Galano
Summary: This study presents a set of new rasagiline derivatives that are designed to be antioxidant compounds for treating neurodegenerative disorders. Computational methods were used to produce and evaluate these derivatives, identifying three of them as the most promising with potential for better free radical scavenging and neuroprotective capabilities compared to rasagiline.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Physical
Cesar Millan-Pacheco, Iris N. Serratos, Sinai del Rosario Sanchez Gonzalez, Annia Galano
Summary: This study explored the molecular recognition between human COMT and two newly designed melatonin analogues, suggesting that these analogues may act as COMT inhibitors. The analysis of binding energies revealed that the binding energy between COMT and dm-115 is similar to that of L-dopa and slightly higher than that of dopamine.
THEORETICAL CHEMISTRY ACCOUNTS
(2022)
Review
Chemistry, Multidisciplinary
Adriana Perez-Gonzalez, Romina Castaneda-Arriaga, Eduardo Gabriel Guzman-Lopez, Luis Felipe Hernandez-Ayala, Annia Galano
Summary: This study systematically and rationally searched for chalcone derivatives with multifunctional behavior, using a computer-assisted protocol (CADMA-Chem). By selecting a subset of molecules with the best drug-like behavior, four chalcone derivatives were identified as promising candidates for multifunctional antioxidants with neuroprotective effects.
Article
Chemistry, Physical
Misaela Francisco-Marquez, Annia Galano
Summary: In this study, the reactions between limonene and various free radicals were investigated using density functional theory. It was found that the relative reactivity of the studied radicals towards limonene follows the order: (SH)-S-center dot > (OBr)-O-center dot > (OCH3)-O-center dot > (OOH)-O-center dot > (OOCH3)-O-center dot.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mirzam Carreon-Gonzalez, Juan Raul Alvarez-Idaboy
Summary: This study investigated the synergy between glutathione (GSH) and phenolic antioxidants using Quantum Chemistry and computational kinetics. The results showed that phenolic antioxidants can repair GSH through sequential proton loss electron transfer (SPLET) and proton-coupled electron transfer (PCET), enhancing antioxidant activity.
Article
Biochemistry & Molecular Biology
Eduardo Gabriel Guzman-Lopez, Miguel Reina, Luis Felipe Hernandez-Ayala, Annia Galano
Summary: Ferulic acid has beneficial effects on human health and 185 new derivatives were computationally designed using CADMA-Chem protocol. The chemical space of these derivatives was evaluated using selection and elimination scores based on ADME properties, toxicity, and synthetic accessibility. Twelve derivatives were further investigated and their potential as antioxidants and neuroprotectors was predicted and analyzed.
Article
Plant Sciences
Jose A. Gutierrez-Gonzalez, Araceli Perez-Vasquez, Martin Gonzalez-Andrade, Annia Galano, Jose L. Villasenor, Rachel Mata
Summary: Four new natural chemical entities were isolated from Ageratina grandifolia, along with 11 known compounds. The structures of these compounds were determined using various techniques. Compounds 8, 10, 11, and 12 showed high affinity for calmodulin and displayed potential therapeutic and research applications.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Biochemistry & Molecular Biology
Luis Felipe Hernandez-Ayala, Eduardo Gabriel Guzman-Lopez, Annia Galano
Summary: Quinoline and its derivatives have been shown to have diverse biological activities. In this study, 8536 quinoline derivatives were designed and screened using the CADMA-Chem protocol. The selected derivatives were further investigated for their acid-base, antioxidant and neuroprotective properties. The results indicate that some derivatives exhibit promising antioxidant and neuroprotective activities, making them potential candidates for the treatment of Alzheimer's and Parkinson's diseases.
Article
Chemistry, Multidisciplinary
Laura M. Castro-Gonzalez, Annia Galano, Juan Raul Alvarez-Idaboy
Summary: This study focuses on the free radical scavenging activity of sesamol derivatives, showing their potential as antioxidants, with single electron transfer and formal hydrogen atom transfer identified as the main reaction mechanisms.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Miguel Reina, Eduardo Gabriel Guzman-Lopez, Isabella Romeo, Tiziana Marino, Nino Russo, Annia Galano
Summary: A systematic search for new p-coumaric acid derivatives was conducted using a computer-assisted protocol, resulting in the selection of 10 derivatives with favorable drug-like behavior and lower toxicity. Three of these derivatives were identified as promising chemical antioxidants, potentially more effective than p-coumaric acid itself in combating oxidative stress. These findings suggest potential applications in developing new non-nitrocatechol inhibitors for Parkinson's disease treatment without the side effects of current inhibitors.
NEW JOURNAL OF CHEMISTRY
(2021)