Article
Astronomy & Astrophysics
N. A. Tsyganenko, V. A. Andreeva, M. Sitnov, G. K. Stephens, J. W. Gjerloev, X. Chu, O. A. Troshichev
Summary: The evolution of the low-latitude magnetosphere over the substorm cycle was reconstructed using a high-resolution 3D representation of the magnetic field and data mining. The study quantified the magnetospheric state using four indices and showed that the intensification and collapse of the inner tail current during specific substorm events led to large-scale dipolarization of the field. The system then recovered and returned to its pre-substorm state.
JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS
(2021)
Article
Biochemical Research Methods
Yanqiang Han, Zhilong Wang, Zhiyun Wei, Jinyun Liu, Jinjin Li
Summary: A neural network-based approach, NN-TMFCC, has been developed to accelerate energy and atomic force calculations of proteins with high precision and efficiency.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Chemistry, Multidisciplinary
Katja-Sophia Csizi, Markus Reiher
Summary: Quantum mechanics/molecular mechanics (QM/MM) hybrid models are used to study chemical phenomena in complex molecular environments. While this approach allows for large system sizes at moderate computational costs, constructing the models manually can be tedious. Therefore, developing automated procedures for QM/MM model construction is desired. This article reviews the current state of QM/MM modeling with a focus on automation, covering MM model parametrization, QM region selection, and embedding schemes.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Physical
S. David Tilley
Summary: In order to achieve cost-effective solar hydrogen production on a large scale, materials that are abundant, low-cost, and easily processed are necessary. This article argues that cuprous oxide shows strong potential for practical water splitting on a large scale, and emphasizes recent research directions for improving efficiency and durability, such as the interfaces of the Cu2O light absorber, protective overlayers, and co-catalysts. It proposes translating high-efficiency thin-film device architectures into photocatalytic sheets or particles as a disruptive approach to solar hydrogen generation, offering opportunities for new scientific discoveries.
ACS ENERGY LETTERS
(2023)
Review
Pharmacology & Pharmacy
Xiang Tong, Tao Liu, Zhenzhen Li, Sitong Liu, Hong Fan
Summary: The use of budesonide-formoterol as needed may reduce severe exacerbations in patients with mild persistent asthma, showing significant differences compared to using short-acting beta(2)-agonist alone. The daily dose of budesonide in the budesonide-formoterol group was significantly lower than in the budesonide group, and there was no difference in adverse events among the three groups.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Chemistry, Physical
Christoph Brunken, Markus Reiher
Summary: A protocol for the fully automated construction of quantum mechanical-classical hybrid models has been introduced, extending a previous approach on system-focused atomistic models. The QM/SFAM approach evaluates the QM region based on first principles to accurately describe atomic forces, allowing for high fidelity and complete automation. This method eliminates dependence on pre-existing parameters and enables convenient redefinition of the QM region during molecular exploration through a local reparametrization scheme.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Nick S. Blunt, Joan Camps, Ophelia Crawford, Robert Izsak, Sebastian Leontica, Arjun Mirani, Alexandra E. Moylett, Sam A. Scivier, Christoph Sunderhauf, Patrick Schopf, Jacob M. Taylor, Nicole Holzmann
Summary: Computational chemistry is crucial for the pharmaceutical industry, and quantum computing is a rapidly advancing technology that promises to revolutionize computational capabilities in chemical research. This article explores the potential applications of quantum computation in pharmaceutical problems, specifically in simulating molecules. The authors provide estimates of the quantum computational cost for simulating a protein-drug complex and highlight recent advancements in quantum algorithms that significantly reduce the required resources.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Social Issues
Mekuria Haile Teklemariam
Summary: This paper suggests that contextual strategy development for application diffusion should be based on the stage of mobile applications adoption already reached in a country. A total of 77 countries were categorized into Initial, Fast-Adoption, and Maturity clusters based on adoption rates and speeds over four years. Through panel data models, the study examines effective variables in enhancing global apps adoption and the differential policy effectiveness of determinant factors on adoption in different clusters. The conclusion indicates that countries should tailor their mobile apps inclusiveness strategy to their context of apps adoption, with each stage having its own effective strategy choice sets.
TECHNOLOGY IN SOCIETY
(2021)
Editorial Material
Cardiac & Cardiovascular Systems
Jian Huang, Jun Pan, Zitao Wang, Dongjin Wang, Jingyu Chen
Summary: Although pregnancy is not recommended in pulmonary arterial hypertension, some women still insist on childbirth. Surgical treatments, especially for those complicated with Eisenmenger syndrome, remain controversial. Two cases of severe pulmonary arterial hypertension complicated with Eisenmenger syndrome underwent successful bilateral lung transplantation combined with surgical atrioventricular defect correction, showing no obvious complications at the 1-year follow-up. This suggests that this combined strategy is feasible and warrants further investigation.
ANNALS OF THORACIC SURGERY
(2021)
Article
Physics, Mathematical
Juan J. Omiste, Rosario Gonzalez-Ferez, Rafael Ortega
Summary: In this study, the interaction between a linear molecule with azimuthal symmetry and external fields is investigated. By analyzing the behavior of closed orbits, a semi-theoretical method is developed to detect classical monodromy, and its effectiveness is numerically demonstrated.
JOURNAL OF MATHEMATICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Kingsley Y. Wu, David Doan, Marco Medrano, Chia-en A. Chang
Summary: The study used MD simulations to investigate the dynamics and conformational changes of A beta 42 peptides, highlighting the influence of force field and initial structures on the obtained results.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Timothy J. Giese, Darrin M. York
Summary: We used the modified Bigeleisen-Mayer equation to calculate kinetic isotope effect values for non-enzymatic phosphoryl transfer reactions. The modified equation includes the ratio of vibrational frequencies and the effect of isotopic substitution on the activation free energy. We developed a practical method to estimate the frequency ratio correction directly from umbrella sampling, which avoids the need for normal mode analysis. This method provides a new tool for calculating kinetic isotope effects in complex chemical reactions in the condensed phase.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Nanoscience & Nanotechnology
Changwei Dang, Sining Yun, Yongwei Zhang, Jiaoe Dang, Yinhao Wang, Zhuolei Liu, Yingying Deng, Guangping Yang, Jingjing Yang
Summary: The study designs a biphasic heterogeneous nano-hybrid electrocatalyst with optimized electronic structure and abundant catalytic sites using interface engineering tactic. The designed electrocatalyst demonstrates superior electrocatalytic activity and electrochemical stability, showing potential applications in photovoltaic and water splitting.
MATERIALS TODAY NANO
(2022)
Article
Chemistry, Physical
Myra Biedermann, Diddo Diddens, Andreas Heuer
Summary: This article demonstrates the application of the reactive step molecular dynamics simulation method in two different atomistic, chemically reactive systems, modeling transitions from reactant to product molecules based on quantum chemical information. The method is capable of capturing kinetic vs thermodynamic control effects of chemical reactions and shows excellent agreement when compared with traditional simulation methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Daniel Conde, Pablo F. Garrido, Martin Calvelo, Angel Pineiro, Rebeca Garcia-Fandino
Summary: This article investigates the behavior of self-assembled cyclic peptide nanotubes using molecular dynamics simulations and compares the performance of four different classical force fields in simulating these highly constrained peptides. Two methods to slow down the fastest degrees of freedom are also tested to improve simulation efficiency, and subtle differences are observed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Michele Nottoli, Patrizia Mazzeo, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: Hybrid TDDFT/MM approaches are popular for describing electronic transitions of molecules in solution or complex matrices. However, when combined with a polarisable force field, problems may arise. This paper presents a possible solution by introducing a Delta SCF formulation, which is expected to be particularly suitable for accurately describing charge-transfer states.
Article
Chemistry, Physical
Edoardo Cignoni, Lorenzo Cupellini, Benedetta Mennucci
Summary: We propose a machine learning strategy to calculate the excitonic properties of light harvesting complexes. By combining molecular dynamics simulations with ML prediction of the excitonic Hamiltonian, the proposed model can account for geometric fluctuations and electrostatic interactions. The model is trained on chlorophylls but can extrapolate beyond the training set, and its accuracy is demonstrated through simulations of absorption spectra in different environments.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Patrizia Mazzeo, Shaima Hashem, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: In this study, we propose a new method that combines the accuracy of a polarizable embedding QM/MM approach with the computational efficiency of an excited-state self-consistent field method to investigate the excited-state dynamics of molecules embedded in complex matrices. We apply this method to the photoactivation of the blue-light-using flavin (BLUF) domain of the AppA protein and demonstrate the presence of a proton-coupled electron transfer (PCET) process, which has been suggested in other BLUF proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Javier Cerezo, Cristina Garcia-Iriepa, Fabrizio Santoro, Isabelle Navizet, Giacomo Prampolini
Summary: In this study, the absorption spectrum of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH) in water was investigated computationally. The results show that non-adiabatic couplings, molecular structure, and interactions with the surrounding environment all play important roles in determining the spectral shape of 5,5-CprOxyLH. The use of quantum dynamics simulations and a mixed quantum classical protocol allows for an accurate description of these effects and provides a good agreement with experimental results.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Giacomo Prampolini, Marco Campetella, Alessandro Ferretti
Summary: The interplay between the inter-molecular interactions of catechol and the intra-molecular hydrogen bond affecting its conformational dynamics is investigated through a multi-level computational approach. Quantum mechanical calculations are used to characterize the potential energy surface of catechol and its interaction with surrounding solvent molecules, which is then used to develop a derived force-field for molecular dynamics simulations. The results reveal significant differences in the conformational behavior of catechol in solvated and isolated forms, and the stability of the intra-molecular hydrogen bond depends on the solvent environment.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Shaima Hashem, Giovanni Battista Alteri, Lorenzo Cupellini, Benedetta Mennucci
Summary: We use a combination of microsecond MD simulations and (polarizable) QM/MM calculations of NMR, FTIR, and UV-vis spectra to confirm the structure of the light-activated form of AppA photoreceptor. Our simulations demonstrate that the observed spectral features are directly linked to the tautomer form of glutamine, supporting the PCET mechanism. Furthermore, we observe small but significant structural changes in AppA, which propagate from the flavin binding pocket to the protein surface.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Laura Pedraza-Gonzalez, Edoardo Cignoni, Jacopo D'Ascenzi, Lorenzo Cupellini, Benedetta Mennucci
Summary: In response to varying light conditions, light-harvesting complexes (LHCs) undergo conformational changes to protect the photosynthetic organism from excessive light irradiation. Activation of the non-photochemical quenching (NPQ) mechanism is triggered by the acidification of the thylakoid lumen, resulting in a switch from a light-harvesting state to a quenched state. The pH sensitivity of the complex is driven by protonation of specific residues, and the quenching mechanism is controlled by a charge-transfer process controlled by the protein conformation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Javier Cerezo, Sheng Gao, Nicola Armaroli, Francesca Ingrosso, Giacomo Prampolini, Fabrizio Santoro, Barbara Ventura, Mariachiara Pastore
Summary: We conducted a joint experimental and theoretical study on the steady-state spectroscopy and time-resolved emission of the coumarin C153 dye in methanol. The lowest energy excited state of this molecule exhibits an intramolecular charge transfer, which results in significant shifts in the time-resolved emission spectra due to the methanol reorganization dynamics. By applying a novel computational protocol that combines the Ad-MD|gVH approach with nonequilibrium molecular dynamics simulations, we achieved accurate predictions of the transient emission spectral shapes, including both vibronic and solvent effects. The overall agreement between the calculated spectra and the experimental results demonstrates the effectiveness of our approach, although some deviations were found at low energies and in the sub-ps timescale due to fast solvent dynamics and experimental time resolution limitations.
Review
Chemistry, Multidisciplinary
Michele Nottoli, Mattia Bondanza, Patrizia Mazzeo, Lorenzo Cupellini, Carles Curutchet, Daniele Loco, Louis Lagardere, Jean-Philip Piquemal, Benedetta Mennucci, Filippo Lipparini
Summary: This article describes the development, implementation, and application of a polarizable QM/MM strategy based on the AMOEBA polarizable force field for calculating molecular properties and performing dynamics of molecular systems embedded in complex matrices. The authors demonstrate that this technology is well-understood and mature, and it can be efficiently implemented using advanced numerical methods and linear scaling techniques. The polarizable QM/AMOEBA approach has a wide range of applications, including predicting spectroscopies and performing multiscale ab initio molecular dynamics simulations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Physical
G. Medrano, E. Bainglass, O. Andreussi
Summary: Continuum solvation models are important in condensed matter simulations to characterize materials interfaces in wet electrified environments at reduced computational cost. However, implementing these models in plane-wave simulation packages for complex and heterogeneous environments is still challenging. This study proposes a double-cell formalism to address these challenges by separating the simulation cell for the continuum environment from the one for the electronic-structure simulation, allowing for larger simulation cell without increasing computational time.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Chemistry, Physical
M. Vasanthapandiyan, Shagun Singh, Fernanda Bononi, Oliviero Andreussi, Naiwrit Karmodak
Summary: The computational modeling of electrochemical interfaces and their applications in electrocatalysis has received great attention, but accurate atomistic descriptions at the electrode/electrolyte interfaces are still challenging. This review presents an overview of different computational models developed over the years to study the thermodynamics and kinetics of electrochemical reactions in the presence of an electrified catalyst surface. Various continuum solvation approaches and thermodynamic and kinetic modeling methods are discussed, along with their applications and the incorporation of machine learning models.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Vladislav Slama, Lorenzo Cupellini, Vincenzo Mascoli, Nicoletta Liguori, Roberta Croce, Benedetta Mennucci
Summary: This study uncovers the molecular mechanism for the formation and tuning of exciton-CT interactions in Lhca4 through molecular dynamics, multiscale quantum chemical calculations, and spectral simulations. The study shows that the coupling between exciton and CT states is extremely sensitive to tiny variations in the Chl dimer arrangement, explaining both the red-shifted bands and the switch between conformations with blue and red emission observed in single-molecule spectroscopy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Amanda Arcidiacono, Davide Accomasso, Lorenzo Cupellini, Benedetta Mennucci
Summary: This study utilizes QM/MM surface hopping nonadiabatic dynamics to investigate the excited-state decay of canthaxanthin in OCP, revealing possible pathways for structural changes and photoactivation.
Article
Chemistry, Physical
Daniele Padula, Alessandro Landi, Giacomo Prampolini
Summary: Recent advances in non-fullerene acceptors have improved the efficiency of organic photovoltaics. This study computationally characterizes the supramolecular structure and electron transfer properties of a promising non-fullerene acceptor and its derivatives. The findings suggest that alkyl side chains primarily impact crystal packing rather than dynamic disorder, leading to improved electron transfer integrals and charge mobilities.