Article
Chemistry, Multidisciplinary
Markus Bursch, Jan-Michael Mewes, Andreas Hansen, Stefan Grimme
Summary: This work provides best-practice guidance on various methodological and technical aspects of DFT calculations, including how to choose computational protocols, functionals, basis sets, and achieve an optimal balance between accuracy, robustness, and efficiency through multi-level approaches.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Felipe Fantuzzi, Rubi Moral, Rian D. Dewhurst, Holger Braunschweig, Ashwini K. Phukan
Summary: Computational investigations have shown that certain base-stabilized borylenes can strongly bind to dinitrogen, but their isolation is challenging. This study suggests that novel boron-based compounds with potential for small-molecule activation can be designed by tuning the charge at the boron center.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Food Science & Technology
Tong Wang, Ning Wang, Minghao Wang, Liqi Wang, Yongge Shi, Jing Du, Dianyu Yu
Summary: Density functional theory (DFT) was used to simulate the degradation of A9-tetrahydrocannabinol (A9-THC) in hemp seed oil, and ultrasonic treatment was applied to degrade A9-THC. The results showed that the degradation of A9-THC to cannabinol (CBN) was a spontaneous exothermic reaction. Through electrostatic potential and molecular orbital analysis, it was found that A9-THC had stronger reactivity and required a certain amount of external energy to initiate the degradation process. Ultrasonic treatment effectively degraded A9-THC into CBN in both standard solution and hemp seed oil.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Chemistry, Physical
Kailai Lin, Patrick TomHon, Soren Lehmkuhl, Raul Laasner, Thomas Theis, Volker Blum
Summary: This study provides an in-depth theoretical analysis of key chemical equilibria in Signal Amplification by Reversible Exchange (SABRE) using density functional theory calculations and harmonic transition state theory. The research shows that under typical experimental conditions, the Gibbs free energies of the two key states involved in pyridine-hydrogen exchange are essentially the same, indicating optimality for SABRE. Additionally, a methanol-containing intermediate is proposed as a plausible transient species in the process.
Article
Chemistry, Organic
Abigail D. Richardson, Scott J. L'Heureux, Ava M. Henry, Elizabeth A. McDonough, Cameron J. Fleischer, Cameron C. McMullen, Trevor R. Reynafarje, Gisele P. Guerrero, Quinn E. Williams, Qingyang Zhou, David M. Malouf, Spencer E. Thurman, Julia E. Soeller, Jerry Y. Sheng, Erica A. Medhurst, Angel E. Canales, Ty B. Cecil, K. N. Houk, Philip J. Costanzo, Daniel A. Bercovici
Summary: Ylidenenorbornadienes (YNDs) prepared from fulvenes and acetylene carboxylates react with thiol nucleophiles to form a mixture of diastereomers that fragment via retro-[4 + 2] cycloaddition at varying rates. The rate constants of individual diastereomers were extrapolated using simulated kinetics and were found to correlate well with experimentally measured values. Density functional theory calculations supported an asynchronous retro-[4 + 2] cycloaddition mechanism for the fragmentation. The electron-rich aromatic rings attached to the ylidene bridge increased the fragmentation rate, while electron-deficient systems slowed the rate.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Carlos de la Cruz, Roberto Sanz, Anisley Suarez, Edgar Ventosa, Rebeca Marcilla, Andreas Mavrandonakis
Summary: This article utilizes density functional theory calculations to screen around 100 phenazine derivatives in aqueous media and identifies crucial positions for functionalization with multiple hydroxy groups to design new anolytes. The combination of experimental and computational methods guides the development of a new molecule with a record low reversible redox potential as a potential anolyte for aqueous redox flow batteries.
Article
Chemistry, Multidisciplinary
Yufang Yao, Nanxi Miao, Yutong Gong, Junjie Wang
Summary: The discovery of stable quaternary h-MAB phases through alloying offers new opportunities for material exploration, while selective removal of A components can be used to exfoliate h-MBenes from quaternary phases. Bi-metal combinations demonstrate advantages in the hydrogen evolution reaction (HER).
Article
Spectroscopy
Trevor J. Wolfe, Nicholas A. Kruse, Mohamed M. Radwan, Amira S. Wanas, Kalee N. Sigworth, Mahmoud A. Elsohly, Nathan I. Hammer
Summary: This study presents the Raman spectra of 11 cannabinoids and compares them to simulated spectra. The results show higher peak separation in the experimental spectra and deviations in the -OH stretching region, indicating that this region is a good indicator for decarboxylation reactions in these cannabinoids.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Review
Chemistry, Multidisciplinary
Nicholas A. Besley
Summary: The availability of X-ray light sources with increased resolution and intensity has provided a foundation for increasingly sophisticated experimental studies exploiting the spectroscopy of core electrons to probe fundamental chemical, physical, and biological processes. Quantum chemical calculations, particularly density functional theory (DFT) and time-dependent density functional theory (TDDFT), play a critical role in the analysis of experimental measurements. Current developments in applying DFT and TDDFT to study key X-ray spectroscopy techniques are presented, along with insights into the achievable accuracy and challenges in modeling core electron spectroscopy with DFT.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Ferran Planas, Stefanie V. Kohlhepp, Genping Huang, Abraham Mendoza, Fahmi Himo
Summary: The dynamic equilibria of organomagnesium reagents are studied using DFT calculations and kinetic experiments to investigate the Pummerer coupling between sulfoxides and turbo-organomagnesium amides. Heterometallic open cubane structures are shown to play a key role as reactive intermediates in turbo-organomagnesium amide mixtures through a concerted anion-anion coupling/S-O cleavage step. This research introduces a new reaction pathway and sheds light on the importance of open cubane organometallics in these mixtures.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Andrew S. Rosen, Victor Fung, Patrick Huck, Cody T. O'Donnell, Matthew K. Horton, Donald G. Truhlar, Kristin A. Persson, Justin M. Notestein, Randall Q. Snurr
Summary: In this study, a dataset of predicted electronic structure properties for metal-organic frameworks (MOFs) is presented, aiming to accelerate the design and discovery of MOFs for electronic, optoelectronic, and energy storage applications. The widely used PBE generalized gradient approximation (GGA) functional is found to severely underpredict MOF band gaps, especially for semiconductors and insulators without magnetic character. Different density functional approximations yield similar predictions for partial atomic charges, but significant differences arise when comparing different charge partitioning schemes. Machine-learning models are trained using the computed MOF properties dataset, enabling rapid prediction of MOF band gaps for multiple density functional approximations.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Chemistry, Physical
Irina Osadchuk, Riina Aav, Victor Borovkov, Eric Clot
Summary: In this study, the influence of various controlling factors on electronic circular dichroism (ECD) spectra was investigated by modeling sixteen different zinc porphyrins using DFT and TD-DFT approaches. The factors mainly affected the excitation energy of electronic transitions and their intensity.
Review
Chemistry, Multidisciplinary
Evgeni S. Penev, Nicola Marzari, Boris Yakobson
Summary: Predictive modeling of two-dimensional (2D) materials lies at the intersection of two rapidly growing interests: the exploration of 2D materials in experimental labs and the development of theoretical-computational models for materials. This field encompasses modeling methods, philosophical assessments, and practical examples related to the structures, properties, functionalities, and synthetic routes of 2D materials.
Article
Chemistry, Multidisciplinary
Thomas Fransson, Mickael G. Delcey, Iulia Emilia Brumboiu, Manuel Hodecker, Xin Li, Zilvinas Rinkevicius, Andreas Dreuw, Young Min Rhee, Patrick Norman
Summary: The eChem project has published an e-book as a web page, which contains Jupyter notebooks for explaining and exploring computational chemistry theory in an interactive way and demonstrating the workflows for simulating complex molecular systems. The eChem book is suitable for self-directed learning and can also be used for workshops targeting specific needs and interests. The project has received positive feedback for its interactive nature and has also developed open-source software for quantum molecular modeling.
JOURNAL OF CHEMICAL EDUCATION
(2023)
Article
Biochemistry & Molecular Biology
Mikhail S. Kuklin, Kim Eklund, Jarno Linnera, Artturi Ropponen, Nikolas Tolvanen, Antti J. Karttunen
Summary: In this study, the structural properties, magnetic ground states, and fundamental electronic properties of 100 binary d-metal oxides were systematically investigated using hybrid density functional methods and localized basis sets. The PBE0 hybrid functional method was found to accurately describe the structural properties of most d-metal oxides, except for molecular oxides with weak intermolecular forces. A database of optimized geometries and magnetic ground states was provided for future studies on the more complex properties of binary d-metal oxides.
Review
Chemistry, Multidisciplinary
Alberto Baiardi, Stephanie A. Grimmel, Miguel Steiner, Paul L. Turtscher, Jan P. Unsleber, Thomas Weymuth, Markus Reiher
Summary: Quantum mechanical methods are crucial for elucidating reaction paths and molecular dynamics. Recent developments cover strategies ranging from heuristic rules based on quantum mechanics, external biases to enforce reactive events, manual steering facilitated by interactive quantum mechanics, to new approaches for transition-state optimization. These explorative approaches are likely to lead to surprising discoveries in computational chemistry by reducing human effort and covering more extensive regions of configuration space.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Katja-Sophia Csizi, Lina Eckert, Christoph Brunken, Thomas B. Hofstetter, Markus Reiher
Summary: In this study, the role of the substrate in the O2 activation process of Rieske dioxygenase was investigated theoretically. The results showed that the presence of substrate did not affect the reaction energies and structural effects at the non-heme FeII center, but played a role in regulating the reactivity of Rieske dioxygenase.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
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
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
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
Thomas Weymuth, Markus Reiher
Summary: Every practical method to solve the Schrodinger equation for interacting many-particle systems introduces approximations and systematic errors. The traditional way of benchmarking data to assess error has uncertainties regarding the transferability to specific molecular systems. This study demonstrates the uncertainty of error estimates and advocates a rolling and system-focused approach for quantifying the uncertainty of quantum chemical results.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Ruben Laplaza, Jan-Grimo Sobez, Matthew D. Wodrich, Markus Reiher, Clemence Corminboeuf
Summary: This article introduces a multi-level computational pipeline using graph-based methods to study the mechanism of chemical reactions. By constructing an ensemble of molecular catalysts and considering multiple conformations, reaction selectivity can be accurately predicted. The effectiveness of this approach is demonstrated through the study of a Rh(iii) catalyzed reaction.
