Article
Chemistry, Physical
Maciej Spiegel
Summary: Bee products are valuable substances with high levels of polyphenolic compounds that have been shown to reduce oxidative stress. This study found that while their immediate antioxidant activity is limited, they may support the role of pre-existing physiological reductants in the biological matrix. Pinocembrin was effective in repairing oxidatively damaged biological compounds.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Yihan Huang, Anthony S. Wexler, Keith J. Bein, Roland Faller
Summary: In this study, a new ReaxFF model was developed to describe the reactions involving phosphoenolpyruvate (PEP) in C4 plants and the atomic interactions in the P/C/O/H system. The model accurately described the structures and energetics of PEP systems and depicted the reactions between bicarbonate and PEP in solution. This provides potential insights for designing optimal carbon capture absorbents.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Ziyang Wei, John Mark P. Martirez, Emily A. Carter
Summary: This article introduces the random phase approximation (RPA) as a method for treating electron correlation, which has been shown to outperform standard density functional theory (DFT) approximations in cases such as extended surfaces. By using sub-system embedding schemes, the RPA can be used to simulate heterogeneous reactions at a reduced computational cost. The authors explore two embedded RPA approaches, periodic emb-RPA and cluster emb-RPA, and validate them in the H-2 dissociative adsorption on Cu(111) surface, finding that cluster emb-RPA accurately reproduces the energy profile while significantly reducing computational cost.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Condensed Matter
A. L. Kutepov
Summary: The atomic forces formulation, based on the Dirac-Kohn-Sham equation and the flexible (APW + lo/LAPW) + LO basis set, allows easy switching between different basis functions and local orbitals. The implementation takes into account small discontinuities at the muffin-tin sphere boundaries and demonstrates robustness in applications to materials with strong relativistic effects. Comparison with numerical differentiation of electronic free energy shows close agreement with deviations of 0.1% or less.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2021)
Article
Chemistry, Multidisciplinary
Felipe E. Gallegos, Lorena M. Meneses, Sebastian A. Cuesta, Juan C. Santos, Josefa Arias, Pamela Carrillo, Fernanda Pilaquinga
Summary: This study examines the interaction between silver clusters and monosaccharide molecules and identifies the most efficient reducing agent. Through geometry optimization and density functional theory, it is found that glyceraldehyde is the best reducing agent.
Article
Chemistry, Physical
Gavin A. McCarver, Robert J. Hinde
Summary: The article introduces a simulation method of the three-dimensional potential energy surface of the H2O-H van der Waals dimer, obtaining a series of potential energy values for specific geometric configurations through ab initio calculations. By using specific calculation methods and basis sets to minimize errors, a potential energy surface suitable for molecular dynamics simulations is established.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Vladimir Kolesar, Matus Dubecky
Summary: This article critically evaluates the accuracy of effective core potential (ECP)-based single-determinant fixed-node diffusion quantum Monte Carlo (SD FNDMC) in prototypical noncovalent closed-shell systems involving d-elements. The analysis reveals two practical findings for SD FNDMC in these systems. Firstly, in some systems, SD FNDMC shows large biases of interaction energy differences compared to a reliable reference, exceeding the target 2% relative error. Secondly, the leading error of SD FNDMC with ECPs is attributed to the higher nuclear charge of d-group atoms compared to sp elements, leading to increased bias in systems with higher electronic densities. Therefore, caution should be exercised when using SD FNDMC in systems with a large Z.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
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
Chemistry, Inorganic & Nuclear
Nidhi Awasthi, Rolly Yadav, Anamika Shukla, Devesh Kumar
Summary: This study investigates the hydroxylation of 4-nitrophenol by Cytochrome P450 metalloenzyme, revealing a single state reactivity pathway.
INORGANIC CHEMISTRY COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Yoshihiro Hayashi, Junichiro Shiomi, Junko Morikawa, Ryo Yoshida
Summary: This study presents an open-source library, RadonPy, that can automate the process of molecular dynamics simulations for a wide range of polymeric materials. By calculating various properties and validating the results with experimental data, the library provides a reliable tool for materials research. The study also identifies high thermal conductivity polymers and uncovers their underlying mechanisms. The construction of this database will contribute to the development of polymer informatics.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Materials Science, Multidisciplinary
Kevin Roccapriore, Andrey Bozhko, Gleb Nazarikov, Vladimir Drachev, Arkadii Krokhin
Summary: The presence of an ENZ layer in the dielectric layer affects the dispersion of surface plasmons and results in additional radiative losses. A strong electric field normal to the metal film impacts the electron density within the transition layer, causing a measurable shift in the plasmonic resonance.
Article
Chemistry, Physical
Amnon Stanger
Summary: When close to the molecular plane, the behavior of nucleus independent chemical shift (NICS) deviates from its behavior at larger distances. The maximal NICS values are obtained above the atoms, moving towards the center as the grid is elevated. This behavior is a result of the electron density influencing the current density and the induced magnetic field measured by the NICS.
Article
Chemistry, Applied
Shinya Hosokawa, Kentaro Kobayashi, Akihide Koura, Fuyuki Shimojo, Yasuhisa Tezuka, Jun-ichi Adachi, Yohei Onodera, Shinji Kohara, Hiroo Tajiri, Anand Chokkalingam, Toru Wakihara
Summary: The atomic structure of an Ag-containing 4A zeolite was investigated using pair distribution function analysis. The valence and conduction band electronic structures of this insulating material were measured using soft X-ray emission and absorption spectroscopies. Density functional theory (DFT) was used to determine the atomic structures and electronic states, and the results excellently reproduced the experimental data. The DFT calculation revealed half-filled charges on the Ag atoms in this zeolite, which may contribute to its antibacterial function.
MICROPOROUS AND MESOPOROUS MATERIALS
(2023)
Article
Computer Science, Interdisciplinary Applications
Shizhe Jiao, Zhenlin Zhang, Kai Wu, Lingyun Wan, Huanhuan Ma, Jielan Li, Sheng Chen, Xinming Qin, Jie Liu, Zijing Ding, Jinlong Yang, Yingzhou Li, Wei Hu, Lin Lin, Chao Yang
Summary: KSSOLV is a MATLAB toolbox for performing Kohn-Sham density functional theory (DFT) calculations with a plane-wave basis set. It is used to study the electronic structures of molecules and solids, and includes new functionalities and algorithms for improved performance.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Abbygale M. Strominger, Brooke L. Sutherland, Austin S. Flemming, Brendan C. Dutmer, Thomas M. Gilbert
Summary: Systematic computational studies on the reactions between aminoborane and different cyclopentadienes revealed that substitution at Sa and Sb positions increases barrier heights and reaction energies. Different regioselectivities were observed for CH3 and CF3 substituents, while F substitutions had varying effects on reaction energetics. The study also showed a preference for 2- and 4-substituted meta products over ortho/para products based on frontier molecular orbital calculations.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Medicinal
Daniel Sethio, Vasanthanathan Poongavanam, Ruisheng Xiong, Mohit Tyagi, Duc Duy Vo, Roland Lindh, Jan Kihlberg
Summary: Conformational analysis is crucial for the design of bioactive molecules, and it becomes even more challenging for macrocycles due to their unique characteristics. In this study, we simulated the conformations of five designed macrocycles and verified the results against experimental measurements. Our simulations accurately predicted the intramolecular interactions and revealed a solvent-induced conformational switch of the macrocyclic ring. This provides a foundation for the rational design of molecular chameleons that can adapt to different environments.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Francesco Bosia, Peikun Zheng, Alain Vaucher, Thomas Weymuth, Pavlo O. Dral, Markus Reiher
Summary: This work discusses the impact of various well-established semi-empirical approximations on calculation speed and their relation to data transfer rates. The study considers desktop computers, local high-performance computing, and remote cloud services to elucidate the effect on interactive calculations for different interfaces.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Robin Feldmann, Alberto Baiardi, Markus Reiher
Summary: This work introduces a generalized framework based on concepts from differential geometry for deriving exact and approximate Newton self-consistent field (SCF) orbital optimization algorithms. Within this framework, the augmented Roothaan-Hall (ARH) algorithm is extended to handle unrestricted electronic and nuclear-electronic calculations. The authors demonstrate that ARH offers a great balance between stability and computational cost for SCF problems that are difficult to converge using conventional first-order optimization strategies. For electronic calculations, ARH overcomes the slow convergence of orbitals in correlated molecules, illustrated by examples of iron-sulfur clusters. For nuclear-electronic calculations, ARH significantly improves convergence even for small molecules, as shown with a series of protonated water clusters.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
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)
Review
Biochemistry & Molecular Biology
Alberto Baiardi, Matthias Christandl, Markus Reiher
Summary: Molecular biology and biochemistry interpret microscopic processes in terms of molecular structures and interactions, which are quantum mechanical. However, computational solution of quantum mechanical equations is challenging. Classical mechanics is often used to understand molecular function, mapping electron and nucleus interactions onto classical surrogate potentials. This simplifies computation but ignores quantum correlations. This work discusses how quantum computation can improve simulations of biomolecules, considering both quantum mechanical and classical problems in molecular biology, as well as data-driven approaches of bioinformatics.
Article
Chemistry, Multidisciplinary
Matthew D. Wodrich, Ruben Laplaza, Nicolai Cramer, Markus Reiher, Clemence Corminboeuf
Summary: In this mini review, a computational pipeline developed in the framework of NCCR Catalysis is presented, which can successfully reproduce the enantiomeric ratios of homogeneous catalytic reactions. The pipeline is based on the SCINE Molassembler module, a graph-based software that provides molecular construction algorithms for all periodic table elements. With this pipeline, simultaneous functionalization and generation of ensembles of transition state conformers is possible, allowing exploration of the influence of various substituents on the overall enantiomeric ratio. This provides quick and reliable access to energetically low-lying transition states, which is crucial for in silico catalyst optimization.
Article
Chemistry, Multidisciplinary
Moritz Bensberg, Markus Reiher
Summary: Investigating a reactive chemical system with automated reaction network exploration algorithms allows for a more detailed understanding of the chemical mechanism compared to manual investigation. The proposed algorithm identifies and explores kinetically accessible regions of the reaction network in real-time, providing an unprecedented mechanistic picture. Using the example of the multi-component proline-catalyzed Michael addition reaction, the algorithm demonstrates its ability to uncover intricate details of the reaction mechanism.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Physical
Ignacio Fdez Galvan, Roland Lindh
Summary: In this study, a pseudodiabatic surrogate model is developed based on Gaussian process regression, which accurately reproduces the adiabatic surfaces and significantly reduces the computational effort required to obtain minimum energy crossing points using the restricted variance optimization method.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Marco Eckhoff, Markus Reiher
Summary: This paper introduces a machine learning potential (MLP) that can maintain high accuracy and requires little computational demand. By introducing element-embracing atom-centered symmetry functions (eeACSFs), MLPs can be trained for each individual system and uncertainty quantification can be used to continually adapt the MLP. Continual learning strategies are proposed to enable autonomous and on-the-fly training on a continuous stream of new data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Giovanni Li Manni, Ignacio Fdez. Galvan, Ali Alavi, Flavia Aleotti, Francesco Aquilante, Jochen Autschbach, Davide Avagliano, Alberto Baiardi, Jie J. Bao, Stefano Battaglia, Letitia Birnoschi, Alejandro Blanco-Gonzalez, Sergey I. Bokarev, Ria Broer, Roberto Cacciari, Paul B. Calio, Rebecca K. Carlson, Rafael Carvalho Couto, Luis Cerdan, Liviu F. Chibotaru, Nicholas F. Chilton, Jonathan Richard Church, Irene Conti, Sonia Coriani, Juliana Cuellar-Zuquin, Razan E. Daoud, Nike Dattani, Piero Decleva, Coen de Graaf, Mickael G. Delcey, Luca De Vico, Werner Dobrautz, Sijia S. Dong, Rulin Feng, Nicolas Ferre, Michael Filatov (Gulak), Laura Gagliardi, Marco Garavelli, Leticia Gonzalez, Yafu Guan, Meiyuan Guo, Matthew R. Hennefarth, Matthew R. Hermes, Chad E. Hoyer, Miquel Huix-Rotllant, Vishal Kumar Jaiswal, Andy Kaiser, Danil S. Kaliakin, Marjan Khamesian, Daniel S. King, Vladislav Kochetov, Marek Krosnicki, Arpit Arun Kumaar, Ernst D. Larsson, Susi Lehtola, Marie-Bernadette Lepetit, Hans Lischka, Pablo Lopez Rios, Marcus Lundberg, Dongxia Ma, Sebastian Mai, Philipp Marquetand, Isabella C. D. Merritt, Francesco Montorsi, Maximilian Morchen, Artur Nenov, Vu Ha Anh Nguyen, Yoshio Nishimoto, Meagan S. Oakley, Massimo Olivucci, Markus Oppel, Daniele Padula, Riddhish Pandharkar, Quan Manh Phung, Felix Plasser, Gerardo Raggi, Elisa Rebolini, Markus Reiher, Ivan Rivalta, Daniel Roca-Sanjuan, Thies Romig, Arta Anushirwan Safari, Aitor Sanchez-Mansilla, Andrew M. Sand, Igor Schapiro, Thais R. Scott, Javier Segarra-Marti, Francesco Segatta, Dumitru-Claudiu Sergentu, Prachi Sharma, Ron Shepard, Yinan Shu, Jakob K. Staab, Tjerk P. Straatsma, Lasse Kragh Sorensen, Bruno Nunes Cabral Tenorio, Donald G. Truhlar, Liviu Ungur, Morgane Vacher, Valera Veryazov, Torben Arne Voss, Oskar Weser, Dihua Wu, Xuchun Yang, David Yarkony, Chen Zhou, J. Patrick Zobel, Roland Lindh
Summary: This article describes the developments of the open-source OpenMolcas chemistry software environment since spring 2020, focusing on the novel functionalities in the stable branch and interfaces with other packages. These developments cover a wide range of topics in computational chemistry and provide an overview of the chemical phenomena and processes that OpenMolcas can address.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Moritz Bensberg, Markus Reiher
Summary: This study demonstrates how active orbital spaces can be consistently selected along reaction coordinates in a fully automated way. The approach combines the Direct Orbital Selection orbital mapping ansatz with the fully automated active space selection algorithm AUTOCAS, without the need for structure interpolation between reactants and products. The algorithm is demonstrated for the potential energy profile of the homolytic carbon-carbon bond dissociation and rotation around the double bond of 1-pentene in the electronic ground state, but it also applies to electronically excited Born-Oppenheimer surfaces.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Robin Feldmann, Alberto Baiardi, Markus Reiher
Summary: In this paper, a symmetry projection technique is presented for enforcing rotational and parity symmetries in nuclear-electronic Hartree-Fock wave functions. A trial wave function with the correct symmetry properties is generated by projecting the wave function onto representations of the three-dimensional rotation group. The efficiency of the technique is demonstrated by calculating the energies of low-lying rotational states of H-2 and H-3(+) molecules.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Enric Petrus, Diego Garay-Ruiz, Markus Reiher, Carles Bo
Summary: In this study, a unique computational approach was used to successfully simulate the self-assembly processes of metal-oxide nanoclusters. By estimating activation energies and correcting pK (a) values, multi-time-scale kinetic simulations were conducted, reproducing reactions ranging from tens of femtoseconds to months of reaction time. Analysis of the kinetic data and reaction network topology revealed the details of the main reaction mechanisms, explaining the origin of kinetic and thermodynamic control. Simulations at alkaline pH fully reproduced experimental evidence as clusters did not form under those conditions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Robin Feldmann, Alberto Baiardi, Markus Reiher
Summary: We propose a symmetry projection technique for enforcing rotational and parity symmetries in nuclear-electronic Hartree-Fock wave functions, which treats electrons and nuclei equally. By projecting the wave function onto representations of the three-dimensional rotation group, the technique generates a trial wave function with the correct symmetry properties and makes the wave function an eigenfunction of the angular momentum operator.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Giovanni Li Manni, Ignacio Fdez. Galvan, Ali Alavi, Flavia Aleotti, Francesco Aquilante, Jochen Autschbach, Davide Avagliano, Alberto Baiardi, Jie J. Bao, Stefano Battaglia, Letitia Birnoschi, Alejandro Blanco-Gonzalez, Sergey I. Bokarev, Ria Broer, Roberto Cacciari, Paul B. Calio, Rebecca K. Carlson, Rafael Carvalho Couto, Luis Cerdan, Liviu F. Chibotaru, Nicholas F. Chilton, Jonathan Richard Church, Irene Conti, Sonia Coriani, Juliana Cuellar-Zuquin, Razan E. Daoud, Nike Dattani, Piero Decleva, Coen de Graaf, Mickael G. Delcey, Luca De Vico, Werner Dobrautz, Sijia S. Dong, Rulin Feng, Nicolas Ferre, Michael Filatov(Gulak), Laura Gagliardi, Marco Garavelli, Leticia Gonzalez, Yafu Guan, Meiyuan Guo, Matthew R. Hennefarth, Matthew R. Hermes, Chad E. Hoyer, Miquel Huix-Rotllant, Vishal Kumar Jaiswal, Andy Kaiser, Danil S. Kaliakin, Marjan Khamesian, Daniel S. King, Vladislav Kochetov, Marek Krosnicki, Arpit Arun Kumaar, Ernst D. Larsson, Susi Lehtola, Marie-Bernadette Lepetit, Hans Lischka, Pablo Lopez Rios, Marcus Lundberg, Dongxia Ma, Sebastian Mai, Philipp Marquetand, Isabella C. D. Merritt, Francesco Montorsi, Maximilian Morchen, Artur Nenov, Vu Ha Anh Nguyen, Yoshio Nishimoto, Meagan S. Oakley, Massimo Olivucci, Markus Oppel, Daniele Padula, Riddhish Pandharkar, Quan Manh Phung, Felix Plasser, Gerardo Raggi, Elisa Rebolini, Markus Reiher, Ivan Rivalta, Daniel Roca-Sanjuan, Thies Romig, Arta Anushirwan Safari, Aitor Sanchez-Mansilla, Andrew M. Sand, Igor Schapiro, Thais R. Scott, Javier Segarra-Marti, Francesco Segatta, Dumitru-Claudiu Sergentu, Prachi Sharma, Ron Shepard, Yinan Shu, Jakob K. Staab, Tjerk P. Straatsma, Lasse Kragh Sorensen, Bruno Nunes Cabral Tenorio, Donald G. Truhlar, Liviu Ungur, Morgane Vacher, Valera Veryazov, Torben Arne Voss, Oskar Weser, Dihua Wu, Xuchun Yang, David Yarkony, Chen Zhou, J. Patrick Zobel, Roland Lindh
Summary: This article describes the recent developments in the open-source chemistry software environment, OpenMolcas, since spring 2020. It focuses on the new functionalities and interfaces with other packages. The article presents various topics in computational chemistry, including electronic structure theory, electronic spectroscopy simulations, molecular structure optimizations, ab initio molecular dynamics, and other new features. Overall, it highlights the capabilities of OpenMolcas in addressing chemical phenomena and processes, making it an attractive platform for advanced atomistic computer simulations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
