Article
Chemistry, Multidisciplinary
Niklas F. Eisele, Rene Rahrt, Lamprini Giachanou, Fadi Shikho, Konrad Koszinowski
Summary: The chemistry of alkali-metal enolates, particularly their ion pairing, has been studied. Experiment and quantum chemical calculations reveal that the affinities between alkali-metal cations and enolate anions decrease as the alkali-metal cations increase in size. The electron density of carbonyl and/or nitrile groups of the enolates also affects the affinities.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Hiroki Hayashi, Satoshi Maeda, Tsuyoshi Mita
Summary: This article introduces the application of quantum chemical calculations in the development of synthetic methodologies. It can be used to analyze the reaction mechanisms of developed reactions and predict unknown reactions. The use of computational methods allows researchers to explore unknown reactions, catalysts, and synthetic routes more effectively before conducting time-consuming and costly experimental investigations.
Article
Chemistry, Multidisciplinary
Hiroki Hayashi, Satoshi Maeda, Tsuyoshi Mita
Summary: Quantum chemical calculations play a crucial role in the development of synthetic methodologies by analyzing reaction mechanisms and predicting unknown reactions. They drive the discovery of new methodologies through efficient computation, saving time and costs compared to experimental investigations, and enable the exploration of synthetic routes to complex molecules and catalyst design.
Article
Chemistry, Analytical
Wei Teng, Jin Xu, Jiuheng Yu, Sumin Cong, Xiufen Yan
Summary: The degradation mechanism of 2,4,6-trichlorophenol (2,4,6-TCP) by photocatalysts is not well understood. This study investigated the photoelectrocatalytic degradation of 2,4,6-TCP at the solid-liquid interface using TiO2 nanotube array electrodes supported by Ag nanoparticles. The results showed that the Ag/TiO2 electrode effectively enhanced the photoelectrocatalytic activity during the degradation of 2,4,6-TCP, and proposed two sequential pathways for its degradation.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2022)
Article
Environmental Sciences
Deming Xia, Jingwen Chen, Ya Wang, Tong Xu, Lihao Su, Hong-bin Xie, David T. Allen
Summary: The study shows that recombination of charged clusters/ions plays a crucial role in nucleation processes of organic acids and H2SO4. NH3 can stabilize MBTCA clusters and change ion compositions, leading to an increase in cluster formation rates. Although the proposed new mechanism cannot compete with traditional nucleation mechanisms currently, it may become significant in the future.
Article
Biochemistry & Molecular Biology
Hassan Rasouli, Seyed Mohammad Bagher Hosseini Ghazvini, Reza Yarani, Ali Altintas, Saber Ghafari Nikoo Jooneghani, Teodorico C. Ramalho
Summary: Alzheimer's disease is a major neurodegenerative disorder, and natural metabolites, such as alkaloids and flavonoids, have shown potential in preventing and improving its complications. However, the lack of data on the molecular mode of action and the ability to cross the blood-brain barrier limits the application of these compounds in AD therapy. This study used docking and quantum studies to determine the binding mode of flavonoids with protein kinases involved in AD pathogenesis, and found that quantum chemical descriptors can help correct virtual docking results and identify promising backbones for further development.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Yifan Zhang, Xianwei Hu, Fengguo Liu, Jiaxin Yang, Liyu Chen, Wenju Tao, Aimin Liu, Zhongning Shi, Zhaowen Wang
Summary: In this study, the reaction process and reaction mechanism of the aluminothermic reduction of NaVO3 to prepare aluminum-vanadium intermediate alloy were investigated by experimental analysis and quantum chemical calculations. The study found that the reduction process of NaVO3 was a multi-step process and temperature played a critical role. The results showed that aluminum first interacted with NaVO3 to form an intermediate complex through electrostatic interaction, leading to the formation of aluminum-vanadium intermediate alloy.
JOURNAL OF ALLOYS AND COMPOUNDS
(2023)
Article
Chemistry, Physical
Goncagul Serdaroglu, Nesimi Uludag, Erol Ercag, Paramasivam Sugumar, Parthasarathi Rajkumar
Summary: Various carbazole derivatives were synthesized and characterized, revealing the preferential intermolecular interactions of one compound, the factors contributing to the reduction of stabilization energy, and the highest binding affinity with a human enzyme. Antioxidant properties were also studied, indicating the potential of a specific compound. Additionally, molecular docking calculations were performed on enzymes to further understand the interactions of the synthesized compounds.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Nanoscience & Nanotechnology
Xinlu Liu, Ting Fu, Jianping Liu, Yinglin Wang, Yuwen Jia, Chao Wang, Xiaofei Li, Xintong Zhang, Yichun Liu
Summary: In this study, an efficient surface chemistry optimization of PbS CQDs for photovoltaics was achieved by annealing the CQD solution with concentrated lead halide ligands after conventional solution-phase ligand exchange. This strategy not only minimized CQD polydispersity and decreased aggregation, but also decreased trap-state density, leading to highly efficient solar cells. The research provides meaningful guidance for controlling ligand reactivity and realizing subtly purified CQDs.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Preeti Prajapati, Jaya Pandey, Poonam Tandon, Kirti Sinha, Manishkumar R. Shimpi
Summary: In this study, cocrystals of ezetimibe with L-proline were investigated to improve the physicochemical properties of ezetimibe. The cocrystal formed a zwitterionic structure with strong hydrogen bonding, leading to enhanced pharmacological properties.
FRONTIERS IN CHEMISTRY
(2022)
Article
Chemistry, Physical
H. da Silva, B. K. Kendrick, N. Balakrishnan
Summary: Quantum calculations are reported for the stereodynamic control of the H + D-2 <-> D + HD chemical reaction in the energy range of 1-50 K. The results show significant control over the reaction by selectively preparing the molecular state, including the possibility of turning the reaction completely on or off.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Analytical
Anne Stinn, Jens Furkert, Stefan H. E. Kaufmann, Pedro Moura-Alves, Michael Kolbe
Summary: The AhR is a highly conserved cellular sensor with important roles in various diseases, making it a promising target for drug development. Understanding the ligand binding properties is crucial for precise pharmacological interventions and targeted therapies.
Article
Environmental Sciences
Yuka Yokoyama, Hai-Bo Qin, Masato Tanaka, Yoshio Takahashi
Summary: Selenium, an important trace element in the environment, can interact with calcite and be absorbed at neutral pH. The study found that selenite can substitute for carbonate in calcite and be incorporated by a slight expansion of crystal volume, providing insights into selenium behavior in groundwater systems.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Physical
Lara A. Patel, Phuong Chau, Serena Debesai, Leah Darwin, Chris Neale
Summary: Computer-aided drug design has the potential to reduce the cost and effort in drug discovery. A new computational method called ligand-exchange Monte Carlo molecular dynamics is introduced, which combines molecular dynamics simulations and Monte Carlo-based ligand exchanges to optimize drug design. This method accurately calculates competitive binding free energies and identifies compounds with strong binding abilities.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Engineering, Environmental
Malgorzata Wolska-Pietkiewicz, Maria Jedrzejewska, Katarzyna Tokarska, Julia Wielgorska, Michal Chudy, Justyna Grzonka, Janusz Lewinski
Summary: Colloidal quantum dots (QDs) are important materials with unique physicochemical properties and potential applications. The development of efficient synthetic methods for ligand-free QDs is crucial for producing stable and dispersible quantum dot-based inks.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Physical
Peter Reinholdt, Jacob Kongsted, Filippo Lipparini
Summary: The article explores three strategies to approximate the QM/MM coupling based on multipole expansion techniques, benchmarking the implementations for accuracy and computational efficiency in calculating spectroscopic properties. The proposed strategies provide significant computational savings without compromising the accuracy of the calculated spectroscopic properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Miriam R. B. Porzberg, Laust Moesgaard, Catrine Johansson, Udo Oppermann, Jacob Kongsted, Jasmin Mecinovic
Summary: This study examines the binding scope of asymmetric dimethylarginine mimics by Spindlin1 and finds that the biomolecular recognition is not significantly affected. High-energy water molecules play an important role in the reader-histone association.
Article
Chemistry, Organic
Nurgul Bilgin, Laust Moesgaard, Marijn N. Maas, Jordi C. J. Hintzen, Apolonia Witecka, Jakub Drozak, Jacob Kongsted, Jasmin Mecinovic
Summary: The role of Ile71 residue in beta-actin on human SETD3 catalysis was examined. It was found that the 'secondary' Ile71 binding pocket regulates the substrate efficiency of beta-actin and can accommodate structurally diverse hydrophobic side chains. Water thermodynamics calculations revealed that high-energy water molecules occupy the Ile71 pocket and are released upon Ile71 binding, contributing to the formation of SETD3-beta A complex. These findings are important for the design and development of chemical probes targeting SETD3.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Physical
Salvatore Prioli, Daniel Wustner, Jacob Kongsted
Summary: In this study, the optical properties of cholestatrienol within the NPC2 binding pockets were simulated using response theory, and a change in CD signal was observed.
THEORETICAL CHEMISTRY ACCOUNTS
(2022)
Article
Medicine, Research & Experimental
Laust Moesgaard, Peter Reinholdt, Carsten Uhd Nielsen, Jacob Kongsted
Summary: Considerable effort has been devoted to the search for modulators of membrane transport proteins. This study focuses on the inhibitory effect of polysorbate 20 (PS20) on P-glycoprotein (P-gp) and aims to understand the underlying molecular mechanism. Molecular dynamics simulations revealed that the hydrophobic nature of PS20 drives its binding to the drug-binding domain of P-gp, resulting in the inhibition of the protein's function.
MOLECULAR PHARMACEUTICS
(2022)
Article
Biochemistry & Molecular Biology
Maria Szomek, Peter Reinholdt, Hanna-Loisa Walther, Holger A. Scheidt, Peter Mueller, Sebastian Obermaier, Bert Poolman, Jacob Kongsted, Daniel Wuestner
Summary: This study investigates the molecular interactions of natamycin and its antifungal activity. The results show that natamycin forms aggregates in aqueous solution and interacts with model membranes, leading to interference with the function of sterols in the membranes and membrane proteins. The study provides a mechanistic explanation for the selective action of natamycin.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Chemistry, Physical
Willem Van den Heuvel, Peter Reinholdt, Hans Jorgen Aa. Jensen, Jacob Kongsted
Summary: The polarizable density embedding model is combined with the multiconfigurational self-consistent field and MC-srDFT electronic structure methods to study solvatochromic shifts. Differences between linear-response and state-specific solvent shifts are analyzed, showing that the discrepancies arise not only from the different responses to polarizability but also from the static part of the environment potential.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Frederik Kamper Jorgensen, Peter Reinholdt, Erik Donovan Hedegard, Jacob Kongsted
Summary: In this paper, we extend the polarizable density embedding (PDE) model to include gauge including atomic orbitals (GIAOs) for calculating nuclear magnetic resonance (NMR) shielding constants within a density functional theory (DFT) framework. The PDE model divides the total system into fragments and uses anisotropic polarizabilities, inter-fragment two-electron Coulomb integrals, and a non-local repulsion operator to simulate quantum mechanics (QM) effects. We explore different approaches to handle the gauge dependency of the non-local operator and find that the PDE model outperforms the classical polarizable embedding (PE) model in terms of accuracy in certain scenarios.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Vildan A. Turkmen, Jordi C. J. Hintzen, Anthony Tumber, Laust Moesgaard, Eidarus Salah, Jacob Kongsted, Christopher J. Schofield, Jasmin Mecinovic
Summary: Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyze oxidation of proteins, and this study focuses on the substrate selectivity and inhibition of human ribosomal oxygenases (ROX) MINA53 and NO66. The results show that MINA53 and NO66 have narrow substrate selectivity compared to other human JmjC hydroxylases. Inhibition assays also suggest that the activities of MINA53/NO66 might be regulated in vivo by competition with non-oxidized proteins/peptides.
RSC CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Organic
Mads W. Mulberg, Mick Hornum, Peter Reinholdt, Brian Bjarke Jensen, Maria Szomek, Jonathan R. Brewer, Daniel Wuestner, Jacob Kongsted, Poul Nielsen
Summary: Fine-tuning of fluorophores is crucial for the development of next generation fluorescent dyes for microscopy. We report a robust and concise method for synthesizing 14 new Nile Red analogues with extended pi ring systems and diverse functionalities. These new fluorophores showed favorable two-photon excitation efficiency and general fluorescent properties. One derivative exhibited extreme solvent sensitivity and another showed significantly redshifted emission, large Stokes shift, and high two-photon brightness.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Nurguel Bilgin, Laust Moesgaard, Mohammad M. Rahman, Vildan A. Tuerkmen, Jacob Kongsted, Jasmin Mecinovic
Summary: In this study, we investigated the molecular recognition of histone H3 peptides with methacryllysine and crotonyllysine by the AF9 YEATS domain. Our findings suggest that AF9 YEATS has a higher binding affinity for crotonyllysine than methacryllysine, indicating its ability to distinguish between the two regioisomers. Molecular dynamics simulations revealed that the desolvation of the AF9 YEATS domain by crotonyllysine/methacryllysine contributes to the recognition of both epigenetic marks. These findings are important for the development of AF9 YEATS inhibitors, a promising area of biomedical research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Peter Reinholdt, Willem Van den Heuvel, Jacob Kongsted
Summary: The polarizable density embedding (PDE) model is an advanced fragment-based QM/QM embedding model that improves the description of electrostatics and includes non-electrostatic repulsion. We developed analytic geometric gradients for the PDE model to optimize the geometry of QM regions within large molecular environments. We also propose a hybrid PDE-LJ model that produces good quality solute-solvent structures for density functional theory (DFT) calculations.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Physical
Willem Van den Heuvel, Peter Reinholdt, Jacob Kongsted
Summary: The PDE model is expanded to include exchange and nonadditive exchange-correlation effects, resulting in the PDE-X model. The PDE-X model accurately captures the range dependence of solvent interaction and improves the accuracy of excitation energies for organic chromophores. The improved embedding description leads to systematic solvent effects that do not average out when applying configurational sampling.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Mays S. Q. Al-Fakhar, Nurgul Bilgin, Laust Moesgaard, Apolonia Witecka, Jakub Drozak, Jacob Kongsted, Jasmin Mecinovic
Summary: This study reveals that the amino acid Trp79 in beta-actin plays an important role in the catalytic activity of SETD3, and maintaining a bulky and hydrophobic amino acid at position 79 is crucial for efficient methylation of His73 by SETD3. The findings highlight the significance of the distant Trp79 binding site in efficient SETD3 catalysis, which contributes to the identification of new SETD3 substrates and the development of chemical probes targeting SETD3, an important biomolecule in biomedicine.
Article
Chemistry, Physical
Willem Van den Heuvel, Peter Reinholdt, Jacob Kongsted
Summary: The polarizable density embedding (PDE) model is extended to include exchange and nonadditive exchange-correlation in the embedding potential, resulting in the PDE-X model. This model accurately captures the range dependence of solvent interaction and significantly improves the accuracy of excitation energies for organic chromophores. The improved embedding description leads to systematic solvent effects that persist under configurational sampling.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)