Article
Chemistry, Physical
Jonas Amsler, Philipp N. Plessow, Felix Studt, Tomas Bucko
Summary: In this paper, a new method for calculating anharmonic contributions to free energy barriers, called constrained thermodynamic lambda-path integration (lambda-TI), is introduced as an alternative to the established Blue Moon ensemble method (xi-TI). The lambda-TI method is benchmarked against the xi-TI method for several reactions and shows good agreement in all cases. An advantage of lambda-TI is its ability to use any reference state to compute anharmonic contributions, which is particularly useful for catalysis. Additionally, the combination of the Bennett acceptance ratio method with lambda-TI is demonstrated to improve computational efficiency.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Thermodynamics
Stephen J. Klippenstein, Raghu Sivaramakrishnan, Ultan Burke, Kieran P. Somers, Henry J. Curran, Liming Cai, Heinz Pitsch, Matteo Pelucchi, Tiziano Faravelli, Peter Glarborg
Summary: The H O center dot 2 + H O center dot 2 reaction is important in combustion under low temperatures and high pressures. Previous theoretical and experimental studies have shown discrepancies. This study uses high-level electronic structure theory, sophisticated transition state theory, and master equation analyses to predict the thermal kinetics on the H2O4 surface and discovers a new reaction channel.
COMBUSTION AND FLAME
(2022)
Article
Chemistry, Physical
Juncheng Harry Zhang, Timothy C. Ricard, Cody Haycraft, Srinivasan S. Iyengar
Summary: The weighted-graph approach presented in this paper offers an adaptive method to calculate contributions from many-body approximations in highly fluxional chemical systems for post-Hartree-Fock ab initio molecular dynamics. By dynamically combining graphs and considering a range of neighboring graphical representations during dynamics, the approach improves dynamic trajectories using lower-order many-body interaction terms. This method outperforms traditional approaches in terms of accuracy and cost-effectiveness when computing dynamical properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Paul L. Houston, Chen Qu, Apurba Nandi, Riccardo Conte, Qi Yu, Joel M. Bowman
Summary: Researchers have recently made further improvements to permutationally invariant polynomial (PIP) regression, including compacting purified basis and speeding up gradient evaluation using reverse differentiation method. They found that PIP computation time for energy and force evaluation is significantly faster than other machine-learning methods, and have introduced a new PIP potential energy surface (PES) for ethanol.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Kerstin Andersson
Summary: The aim of this study is to calculate precise values of molecular properties of tetracyanoquinodimethane (TCNQ) and anions using complete active space self-consistent field and complete active space second-order perturbation theory methods. The accuracy of the calculations has been evaluated using various basis sets and active spaces. The calculated properties have been confirmed by experimental data in many cases, such as the ionization potential and electron affinity of TCNQ, as well as the transition energies to excited singlet states and electron attachment energies of TCNQ.
THEORETICAL CHEMISTRY ACCOUNTS
(2023)
Article
Chemistry, Physical
Yuzhe Zhang, Xi Xu, Nan Yang, Zehua Chen, Yang Yang
Summary: Proton transfer plays a crucial role in chemical and biological processes. However, accurately and efficiently describing proton transfer is still a challenge due to nuclear quantum effects. In this study, the authors applied constrained nuclear-electronic orbital density functional theory (CNEO-DFT) and constrained nuclear-electronic orbital molecular dynamics (CNEO-MD) to investigate proton transfer in three prototypical shared proton systems. They found that CNEO-DFT and CNEO-MD achieved a good description of the geometries and vibrational spectra of the shared proton systems, in contrast to traditional DFT and DFT-based ab initio molecular dynamics. CNEO-MD, as an efficient method based on classical simulations, shows promise for future investigations of larger and more complex proton transfer systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Martin Tschoepe, Benjamin Schroeder, Sebastian Erfort, Guntram Rauhut
Summary: Ketenimine, a complex organic molecule in astrochemistry, is likely a building block for biologically relevant molecules. Despite experimental data limitations, accurate quantum chemical calculations provide insight into its rovibrational spectrum and reveal strong Fermi resonances. The comparison between theoretical calculations and experimental data validates the results and uncovers new insights about the system, highlighting significant Coriolis coupling effects.
FRONTIERS IN CHEMISTRY
(2021)
Article
Materials Science, Multidisciplinary
Zhongyu Wan, Wenjun Xu, Tianyi Yang, Ruiqin Zhang
Summary: In this study, crystal structure search algorithms were used to explore the possibility of forming unique electrides in the As-Li system. It was found that under appropriate pressure, AsLi7 can exhibit superionic and plastic states, showing higher superconductivity and unusual physical phenomena compared to classical electrides. These findings contribute to the expansion of the research field on electrides.
Article
Chemistry, Inorganic & Nuclear
Jia-Jun Lai, Ze-Yu Ruan, Guo-Zhang Huang, Jun-Liang Liu, Ming-Liang Tong
Summary: In this study, a {Zn2Dy} single-ion magnet with octahedral coordination geometry (O-h) was synthesized and characterized. Magnetic susceptibility measurements revealed magnetic blocking below 4.1 K. Combining experimental data and ab initio calculations, the dynamic relaxation characteristics of this complex were detailed.
INORGANIC CHEMISTRY COMMUNICATIONS
(2021)
Article
Computer Science, Software Engineering
Alberto De Marchi, Xiaoxi Jia, Christian Kanzow, Patrick Mehlitz
Summary: This paper investigates finite-dimensional constrained structured optimization problems with composite objective functions and set-membership constraints. The problem class provides a modeling framework for various applications with an expressive yet simple language. The study focuses on stationarity and regularity concepts and proposes a flexible augmented Lagrangian scheme. The algorithm is theoretically characterized and its convergence results for fully nonconvex problems are derived. Additionally, a matrix-free implementation of the algorithm is described and numerically tested, showing the versatility of constrained composite programs as a modeling tool and the challenges arising in this problem class.
MATHEMATICAL PROGRAMMING
(2023)
Article
Chemistry, Physical
Juan J. J. Aucar, Alejandro F. F. Maldonado, Juan I. I. Melo
Summary: In this work, relativistic corrections to the electric field gradient (EFG) are presented, including spin-dependent corrections for the first time. The results show that these new corrections significantly improve the performance of the existing method and are in close agreement with calculations at the four-component Dirac-Hartree-Fock (4c-DHF) level. The accuracy of the EFG values obtained with this new method allows for the analysis of the electronic origin of relativistic effects using well-known nonrelativistic operators.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Automation & Control Systems
Michael R. Metel, Akiko Takeda
Summary: This paper focuses on stochastic proximal gradient methods for optimizing a smooth non-convex loss function with a non-smooth non-convex regularizer and convex constraints. The authors present the first non-asymptotic convergence bounds for this class of problem and compare their algorithms with the current state-of-the-art deterministic algorithm, finding superior convergence in a numerical experiment.
JOURNAL OF MACHINE LEARNING RESEARCH
(2021)
Article
Automation & Control Systems
Changxin Liu, Yang Shi, Huiping Li, Wenli Du
Summary: In this article, decentralized convex constrained optimization problems in networks are studied. Two new decentralized dual averaging (DDA) algorithms are proposed, which achieve faster convergence compared to existing methods. The first algorithm uses a second-order dynamic average consensus protocol to estimate the global dual variable accurately. The second algorithm utilizes extrapolation technique and achieves fast convergence without relying on the spectrum of the mixing matrix.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2023)
Article
Chemistry, Physical
Mukesh Singh, Alok Shukla, Brahmananda Chakraborty
Summary: In this study, the hydrogen-storage properties of Zr-decorated g-graphyne monolayer were investigated using Density Functional Theory (DFT). The results predict that each Zr atom can adsorb up to seven H2 molecules with a hydrogen gravimetric density of 7.95 wt% and a desorption temperature of 574 K, making it suitable for fuel-cell applications. The strong attachment between decorated Zr atom and graphyne sheet is due to charge transfer, while hydrogen molecules adsorb on Zr decorated graphyne through Kubas type of interactions. The stability of Zr+g-graphyne was confirmed through ab-initio molecular dynamics simulations. Overall, these findings suggest that Zr functionalized on g-graphyne could be a promising solid-state hydrogen storage material.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2023)
Article
Chemistry, Physical
Domonkos A. Tasi, Gabor Czako
Summary: This article describes a dynamical characterization of the polyatom-polyatom reaction between NH2- and CH3I, including the development of a global potential energy surface and the discovery of novel retention pathways.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Marcus Johansson, Valera Veryazov
JOURNAL OF CHEMINFORMATICS
(2017)
Article
Chemistry, Multidisciplinary
Oskar Weser, Valera Veryazov
FRONTIERS IN CHEMISTRY
(2017)
Article
Chemistry, Physical
Per-Olof Widmark, J. Patrick Zobel, Victor P. Vysotskiy, Takashi Tsuchiya, Valera Veryazov
JOURNAL OF CHEMICAL PHYSICS
(2018)
Article
Chemistry, Physical
Ignacio Fdez Galvan, Morgane Vacher, Ali Alavi, Celestino Angeli, Francesco Aquilante, Jochen Autschbach, Jie J. Bao, Sergey I. Bokarev, Nikolay A. Bogdanov, Rebecca K. Carlson, Liviu F. Chibotaru, Joel Creutzberg, Nike Dattani, Mickael G. Delcey, Sijia S. Dong, Andreas Dreuw, Leon Freitag, Luis Manuel Frutos, Laura Gagliardi, Frederic Gendron, Angelo Giussani, Leticia Gonzalez, Gilbert Grell, Meiyuan Guo, Chad E. Hoyer, Marcus Johansson, Sebastian Keller, Stefan Knecht, Goran Kovacevic, Erik Kallman, Giovanni Li Manni, Marcus Lundberg, Yingjin Ma, Sebastian Mai, Joao Pedro Malhado, Per Ake Malmqvist, Philipp Marquetand, Stefanie A. Mewes, Jesper Norell, Massimo Olivucci, Markus Oppel, Quan Manh Phung, Kristine Pierloot, Felix Plasser, Markus Reiher, Andrew M. Sand, Igor Schapiro, Prachi Sharma, Christopher J. Stein, Lasse Kragh Sorensen, Donald G. Truhlar, Mihkel Ugandi, Liviu Ungur, Alessio Valentini, Steven Vancoillie, Valera Veryazov, Oskar Weser, Tomasz A. Wesolowski, Per-Olof Widmark, Sebastian Wouters, Alexander Zech, J. Patrick Zobel, Roland Lindh
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2019)
Article
Chemistry, Physical
J. Patrick Zobel, Per-Olof Widmark, Valera Veryazov
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Chemistry, Physical
E. D. Larsson, J. P. Zobel, V. Veryazov
Summary: The selection of basis sets is crucial for multiconfigurational wave function calculation, and the ANO-R basis set is suggested as a replacement for the ANO-RCC basis set for scalar-relativistic correlated calculations. This study evaluates the performance of the ANO-R basis set on various atoms and compounds, including those with open shells. The results show that the ANO-R basis set performs similarly to the ANO-RCC basis set in multiconfigurational calculations, but has some deficiencies in certain properties. Additionally, the ANO-R basis sets are more compact and have smaller computational costs.
ELECTRONIC STRUCTURE
(2022)
Article
Chemistry, Physical
Ernst D. Larsson, Marek Kros, Valera Veryazov
Summary: This article introduces a new program, SCEPIC, for generating ab initio model potentials and evaluates its applicability for three simple ionic solids. The results demonstrate good agreement with periodic density functional theory calculations, feasibility of geometry optimizations, and accurate computation of band gaps and ligand-field splittings.
Article
Chemistry, Multidisciplinary
Ernst D. Larsson, Valera Veryazov
Summary: Embedded-cluster models are important for accurate wave function methods in solids. The ab-initio model potential method, dividing the crystal into three fragments, has been successful in describing electronic structure in ionic solids. In this study, the convergence of electronic structure properties with respect to cluster size was analyzed using MgO crystal and Ni:MgO. It was demonstrated that larger cluster sizes result in similar electron density to the periodic model, making embedded-clusters a good alternative.
FRONTIERS IN CHEMISTRY
(2022)
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
Ernst D. Larsson, Valera Veryazov
Summary: Multiconfigurational theory combined with the embedded cluster approach is a precise and ab initio method for describing the electronic structure of solids. In this study, the spectrum of a Ce(III) dopant in YVO4 was investigated using complete active space perturbation theory of the second order (CASPT2), with the host material represented as a set of ab initio model potentials and point-charges. The comparison between the computational model and experimental results demonstrates the robustness and accuracy of the embedding approach in modeling the spectrum of low-concentration dopants in complex host materials.
JOURNAL OF CHEMICAL PHYSICS
(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)
Article
Chemistry, Inorganic & Nuclear
Ernst D. Larsson, Geng Dong, Valera Veryazov, Ulf Ryde, Erik D. Hedegard
DALTON TRANSACTIONS
(2020)
Article
Biochemistry & Molecular Biology
Igor Schapiro, Moussa Gueye, Marco Paolino, Stefania Fusi, Gabriel Marchand, Stefan Haacke, M. Elena Martin, Mark Huntress, Victor P. Vysotskiy, Valera Veryazov, Jeremie Leonard, Massimo Olivucci
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2019)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Alexei I. Abrikosov, Goran Kovacevic, Valera Veryazov
INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2018 (ICCMSE-2018)
(2018)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Fereshteh Naderi, Valera Veryazov
PROCEEDINGS OF THE INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2017 (ICCMSE-2017)
(2017)
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)