Article
Multidisciplinary Sciences
Poutoum P. Samire, Bo Zhuang, Bertrand Legeret, Angel Baca-Porcel, Gilles Peltier, Damien Sorigue, Alexey Aleksandrov, Frederic Beisson, Pavel Mueller
Summary: Ongoing climate change is driving the search for renewable and carbon-neutral alternatives to fossil fuels. Pho-tocatalytic conversion of fatty acids to hydrocarbons by fatty acid photodecarboxylase (FAP) represents a promising route to green fuels. Chlorella variabilis FAP (CvFAP) has higher catalytic activity on n-octanoic acid, in part, due to an autocatalytic effect of its n-heptane product.
Article
Biochemistry & Molecular Biology
Phujinn Honorio, Supawadee Sainimnuan, Supa Hannongbua, Patchreenart Saparpakorn
Summary: The research discovered that protoberberine alkaloids isolated from natural resources are potent inhibitors of acetylcholinesterase (AChE) and have the potential to reduce symptoms of Alzheimer's disease. The key interactions of palmatine and berberine with AChE were identified as 7C-7C interactions with specific amino acids and H-bond interactions. In contrast, cyclanoline showed a different binding mode and preference for a deeper site within AChE.
CHEMICO-BIOLOGICAL INTERACTIONS
(2021)
Article
Chemistry, Physical
Miguel Jorge, Jose R. B. Gomes, Maria Cecilia Barrera
Summary: This paper investigates polarization effects in condensed phases and presents an improved and extended Self-Consistent Electrostatic Embedding (SCEE) method. The results demonstrate the importance of accounting for local solvation effects, particularly the formation of hydrogen bonds, in determining the extent of liquid phase polarization.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: A novel strategy was designed to compute TRIR spectra of photoreceptors by combining different types of molecular dynamics, revealing that the dynamic Stokes shift of flavin is ultrafast and mainly driven by the internal reorganization of the chromophore.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Engineering, Electrical & Electronic
Yuyao Lu, Geng Yang, Shenqiang Wang, Yuqi Zhang, Yihui Jian, Long He, Ting Yu, Huayu Luo, Depeng Kong, Yunlei Xianyu, Bo Liang, Tao Liu, Xiaoping Ouyang, Jicheng Yu, Xinyang Hu, Huayong Yang, Zhen Gu, Wei Huang, Kaichen Xu
Summary: A thin elastic conductive nanocomposite formed by cryogenically transferring laser-induced graphene to a hydrogel film can be used to create multifunctional sensors for on-skin monitoring and cardiac patches for in vivo detection.
NATURE ELECTRONICS
(2023)
Article
Biochemistry & Molecular Biology
Alexander Zlobin, Igor Diankin, Sergey Pushkarev, Andrey Golovin
Summary: Organophosphate hydrolases have potential as biotherapeutic agents for treating poisoning but require further engineering for practical use. Molecular modeling techniques can accurately model DFPase and provide insights into the DFP binding process.
Article
Biochemistry & Molecular Biology
Raul Alvarado, Gustavo Cardenas, Juan J. Nogueira, Nicolas Ramos-Berdullas, Marcos Mandado
Summary: This study simulated the permeation of dioxin-like pollutants through lipid membranes using CMD and umbrella sampling. The results showed that TCDD and TCDF reached energy minima at distances of 8 angstrom and 9.5 angstrom from the centre of the membrane, respectively. The interactions between the molecules and the lipid membrane were mainly governed by dispersion forces, independent of the toxicity of the molecules.
Article
Multidisciplinary Sciences
Isabela de Souza Gomes, Charles Abreu Santana, Leandro Soriano Marcolino, Leonardo Henrique Franca de Lima, Raquel Cardoso de Melo-Minardi, Roberto Sousa Dias, Sergio Oliveira de Paula, Sabrina de Azevedo Silveira
Summary: The study aims to utilize machine learning strategy along with docking, MM-PBSA calculations, and metadynamics to identify potential inhibitors for SARS-COV-2 main protease among FDA approved compounds. Six molecules were highlighted as potential inhibitors, with ambenonium being a novel candidate without previous literature documentation as an inhibitor for the SARS-COV-2 main protease.
Article
Chemistry, Physical
Anirban Chandra, Troy Loeffler, Henry Chan, Xiaoyu Wang, G. B. Stephenson, Michael J. Servis, Subramanian K. R. S. Sankaranarayanan
Summary: Exploring mesoscopic physical phenomena remains challenging for all-atom molecular dynamics simulations. Coarse-graining of all-atom models provides a solution to study mesoscale physics but without sacrificing desired structural features. In this study, a hybrid bond-order coarse-grained forcefield (HyCG) is proposed to model mesoscale aggregation in liquid-liquid mixtures. The potential is parameterized using a reinforcement learning algorithm and accurately captures critical fluctuations in binary extraction systems. This approach could be applied to explore inaccessible mesoscale phenomena with the developed potential model and training workflow.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Taichi Inagaki, Shinji Saito
Summary: In this paper, a new hybrid method called potential scaling HMC (PS-HMC) is introduced to study complex chemical processes. By modulating the trajectory and gradually flattening the potential energy surface, the PS-HMC method is capable of constructing the canonical ensemble with a multimodal distribution. Applications to different molecular processes demonstrate the feasibility and features of this new method.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Michele Nottoli, Riccardo Nifosi, Benedetta Mennucci, Filippo Lipparini
Summary: The study presents an implementation of a fully coupled polarizable QM/MM/continuum model based on the AMOEBA force field and the screening model. The model is linear scaling in memory requirements and computational cost, suitable for modeling large, complex systems. By investigating three variants of the green-fluorescent protein, the study demonstrates the overall computational cost and the effect of the continuum model on the convergence of computed properties, as well as the fundamental role of polarization effects.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Medicinal
Emmanuelle Bignon, Antonio Monari
Summary: This article investigates the RNA genome replication mechanism of the SARS-CoV-2 virus. Through calculations and simulations, the high efficiency of the viral polymerase and the unique active site of the enzyme are discovered. The results contribute to the future design of antiviral drugs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Alexander Zlobin, Julia Belyaeva, Andrey Golovin
Summary: Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations are widely used in computational biochemistry and enzymology. However, when it comes to certain scenarios in computational enzymology, the commonly used hydrogen-capping approach may not be sufficient. This study shows that the consequences of neglecting certain artifacts in QM/MM simulations can be severe and may lead to incorrect conclusions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Alexander Zlobin, Julia Belyaeva, Andrey Golovin
Summary: Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations are widely used in computational biochemistry and enzymology. However, when using QM/MM in computational enzymology, incorporating backbone atoms into the QM region can lead to artifacts that may significantly affect the results. Further research is needed to address these issues and improve the accuracy of simulations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
John P. Pederson, Jesse G. McDaniel
Summary: We propose a method that combines density functional theory and quantum mechanics/molecular mechanics to achieve long-range electrostatic embedding. By directly integrating the computed electrostatic potential from a particle-mesh Ewald grid, we are able to accurately evaluate integrals using standard DFT machinery. The benchmarks and evaluations demonstrate the importance of our algorithm in accurately calculating redox potentials in complex solvents such as ionic liquids.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Inorganic & Nuclear
Lianghu Gu, Lawrence M. Wolf, Walter Thiel, Christian W. Lehmann, Manuel Alcarazo
Article
Chemistry, Multidisciplinary
Dan Wu, Ya-Ting Wang, Wei-Hai Fang, Ganglong Cui, Walter Thiel
CHEMISTRY-AN ASIAN JOURNAL
(2018)
Article
Chemistry, Physical
Jie Liu, Walter Thiel
JOURNAL OF CHEMICAL PHYSICS
(2018)
Article
Chemistry, Physical
Pau Armengol, Lasse Sporkel, Ricard Gelabert, Miquel Moreno, Walter Thiel, Jose M. Lluch
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2018)
Article
Chemistry, Physical
Alec Owens, Andrey Yachmenev, Jochen Kuepper, Sergei N. Yurchenko, Walter Thiel
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Gui-Juan Cheng, Nikolaos Drosos, Bill Morandi, Walter Thiel
Article
Chemistry, Physical
Deniz Tuna, Lasse Spoerkel, Mario Barbatti, Walter Thiel
Article
Chemistry, Physical
Pavlo O. Dral, Mario Barbatti, Walter Thiel
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2018)
Article
Chemistry, Multidisciplinary
Xin Wu, Pavlo O. Dral, Axel Koslowski, Walter Thiel
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
Pin Xiao, Chun-Xiang Li, Wei-Hai Fang, Ganglong Cui, Walter Thiel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2018)
Article
Biochemistry & Molecular Biology
Gerhard Koenig, Frank C. Pickard, Jing Huang, Walter Thiel, Alexander D. MacKerell, Bernard R. Brooks, Darrin M. York
Article
Chemistry, Physical
Pavlo O. Dral, Xin Wu, Walter Thiel
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2019)
Article
Chemistry, Medicinal
Leon Wehrhan, Alexander Hillisch, Stefan Mundt, Adrian Tersteegen, Katharina Meier
Article
Multidisciplinary Sciences
Lluis Raich, Katharina Meier, Judith Guenther, Clara D. Christ, Frank Noe, Simon Olsson
Summary: Bromodomains are small protein modules that interact with acetylated marks in histones, crucial for gene expression regulation. A conserved transient state involving breaking of hydrogen bonds was discovered, serving as an allosteric regulatory switch potentially related to a recently unveiled mode of BD-DNA binding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Lea Seep, Anne Bonin, Katharina Meier, Holger Diedam, Andreas H. Goeller
Summary: This study compares three algorithms for generating conformer ensembles and finds that MD-derived maps are significantly influenced by macrocycles, charge states, and solvents, while post-optimized conformers using implicit solvent models have similar maps regardless of solvent. Post-optimized MD ensembles cover a larger conformational space than generator ensembles, with 3D polar surface area distributions being similar for all macrocycles except for one compound.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Michal Novotny, Matus Dubecky, Frantisek Karlicky
Summary: This paper investigates the accuracy of different DFT-based computational approaches in calculating the equilibrium lattice constants and exfoliation energy of hexagonal boron nitride (h-BN). The results are compared with experiments and reference QMC calculations to evaluate the accuracy of these computational methods.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega
Summary: The charge transfer dynamics in asymmetrically substituted indenotetracene molecules upon photo-excitation were investigated using real-time time-dependent density functional theory simulations. The study found that the electron-donating character of the substituents affects the overall electronic energy spacing and ultrafast charge transfer dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Vasilii Korotenko, Hendrik Zipse
Summary: The stability of various radicals and molecules has been studied using different theoretical methods, and good correlations between theoretical calculations and experimental results have been found. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have also been investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Oleg Egorov, Michael Rey, Dominika Viglaska, Andrei V. Nikitin
Summary: In this work, the rovibrational energy levels of four isotopologues of methylene were calculated using a new accurate ab initio potential energy surface. The accuracy of the calculations was improved by considering scalar relativistic effects, DBOC, and high-order electronic correlations. For the first time, all available experimental rovibrational transitions were reproduced with high accuracy, without any empirical corrections.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)