Article
Chemistry, Physical
Christopher J. N. Coveney, David P. P. Tew
Summary: We propose a scalable single-particle framework for treating electronic correlation in molecules and materials based on Green's function theory. By introducing the Goldstone self-energy, we derive a size-extensive Brillouin-Wigner perturbation theory from the single-particle Green's function. This new ground state correlation energy, named Quasi-Particle MP2 theory (QPMP2), avoids the characteristic divergences in strongly correlated systems present in second-order Moller-Plesset perturbation theory and Coupled Cluster Singles and Doubles methods, and demonstrates excellent performance in reproducing exact ground state energy and properties of the Hubbard dimer as well as larger Hubbard models.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jeppe Olsen, Andreas Erbs Hillers-Bendtsen, Frederik Orsted Kjeldal, Nicolai Machholdt Hoyer, Kurt V. Mikkelsen, Poul Jorgensen
Summary: The convergence of cluster perturbation expansions is analyzed to develop mathematical tools for describing these expansions and identify the factors affecting their convergence rate. The rate of convergence and critical states are determined for small molecules and a model is proposed to describe the convergence pattern at lower orders. The behavior of perturbation corrections is rationalized based on the critical points.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Naoki Negishi, Daisuke Yokogawa
Summary: In this study, the second-order Moller-Plesset perturbation theory combined with the reference interaction site model was successfully used to predict the activation free energies of a Diels-Alder reaction, with results within 2 kcal/mol of experimental data.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Peter J. Knowles
Summary: This paper introduces a new general approach for defining the optimum zero-order Hamiltonian in Rayleigh-Schrodinger perturbation theory. Instead of directly deriving the operator from a model problem, it is constructed to be the best fit to the exact Hamiltonian in any desired functional form. When applied to many-body perturbation theory for electrons, significantly improved convergence is observed in cases where the conventional Fock Hamiltonian leads to divergence or slow convergence.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
L. Urban, T. H. Thompson, C. Ochsenfeld
Summary: An empirically scaled version of the MP2-F12 method is introduced, which requires a basis set dependent scaling factor determined by fitting a set of test molecules, and accurately describes a wide range of systems. The new method not only shows remarkably good performance on the S22 and L7 test sets, but also exhibits distinct speedups compared to the unscaled F12 correction for all considered systems.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Applied
Jongmin Park, Jiyeong Cho, Myung-June Park, Won Bo Lee
Summary: In this study, computational chemistry and microkinetic modeling methods were used to analyze the reaction pathways of DME synthesis by methanol dehydration over a H-zeolite catalyst. The dissociative pathway was identified as the dominant pathway, with the reaction CH3OHCH3-Z -> CH3OCH3-H-Z being the rate-determining step. The developed model was also used to investigate the effects of temperature on the site fractions over the catalyst.
Article
Chemistry, Physical
Carmelo Naim, Pau Besalu-Sala, Robert Zalesny, Josep M. Luis, Frederic Castet, Eduard Matito
Summary: The design and optimization of organic-based electro-optic devices are difficult due to their nonlinear optical responses, which are challenging to model. Computational chemistry provides tools to investigate a large number of molecules in search of target compounds. Density functional approximations (DFAs) are commonly used for calculating static nonlinear optical properties (SNLOPs), but their accuracy depends on the amount of exact exchange and electron correlation included, making it unreliable for many molecular systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Tingting Zhao, Megan Simons, Devin A. Matthews
Summary: In this study, we extend the least-squares tensor hypercontraction (LS-THC) method to open-shell systems by employing diagrammatic techniques and explicit spin summation. The resulting LS-THC-MP2 and LS-THC-MP3 methods exhibit high accuracy and robustness in studying the reactivity of open-shell species, while significantly reducing computational complexity and costs.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Kevin Carter-Fenk, Martin Head-Gordon
Summary: In this work, the authors propose an alternative partitioning of the Hamiltonian that leads to a regular Brillouin-Wigner perturbation series, which is size-extensive and size-consistent through the second order. This approach offers improvements relative to MP2 for various chemical applications and can describe the exact dissociation limit of H-2 in a minimal basis set.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Inorganic & Nuclear
Kai Wang, Shao-Zheng Fang, Zheng Fan, Hong-Yuan Zhao, Lin Miao, Guang-Jia Yin, Ramiro Moro, Lei Ma
Summary: The electric polarizability of the aluminum atom has been an important benchmark in polarizability measurements. Previous values had a large discrepancy with experimental measurements, but this study presents a more accurate computation using various ab initio methods. The recommended value reconciles the theoretical and experimental values, reaffirming its reliability for future experiments.
JOURNAL OF CLUSTER SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Thomas Bondo Pedersen, Susi Lehtola, Ignacio Fdez Galvan, Roland Lindh
Summary: This review provides an overview of the RI/DF and CD methods in electronic structure calculations, highlighting the close relationship between these two approaches. It traces the evolution and current state of the CD method, which offers not only a numerical procedure for handling ERIs, but also highly accurate approaches for generating auxiliary basis sets for the RI/DF approximation.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Physical
Chenchen Song, Todd J. Martinez, Jeffrey B. Neaton
Summary: The new diagrammatic approach allows for automatic derivation of analytical nuclear gradients for THC methods, ensuring performance comparable to energy calculations with roughly three times the cost. Its application to THC-MP2 and multi-reference perturbation theory leads to more efficient computations and developments in analytical nuclear gradients.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Hans-Joachim Werner, Andreas Hansen
Summary: An overview of the approximations in explicitly correlated local coupled cluster methods PNO-LCCSD(T)-F12 and DLPNO-CCSD(T)(F12) is provided. The selection options for projected atomic orbitals (PAOs), pair natural orbitals (PNOs), and triples natural orbitals (TNOs) in both Molpro and ORCA programs are described and compared. The PNO-LCCSD(T)-F12 method is applied to compute new reference energies for benchmark sets, showing promising accuracy and computational efficiency.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Michael Glasbrenner, Daniel Graf, Christian Ochsenfeld
Summary: A method for computing NMR shieldings using direct RPA is presented, with accuracy depending on the DFT reference orbitals and amount of Hartree-Fock exchange. Results show that shieldings with Hartree-Fock reference are more accurate than MP2 and comparable to CCSD shieldings. At least triple-zeta basis sets are required for reliable results in basis set convergence analysis.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
J. Grant Hill, Robert A. Shaw
Summary: New correlation consistent basis sets have been developed for group 11 and 12 elements, specifically for use in F12 calculations, leading to improved convergence of properties. Compared to conventional methods, the accuracy and convergence patterns of the basis sets have been significantly enhanced.
JOURNAL OF CHEMICAL PHYSICS
(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
Lukas Bucinsky, Marian Gall, Jan Matuska, Michal Pitonak, Marek Steklac
Summary: This study presents three different machine learning approaches (TensorFlow, XGBoost, and SchNetPack) for predicting docking scores. AutoDock Vina is used to evaluate the inhibitory potential of ZINC15 compounds against SARS-CoV-2 main protease. The training and evaluation sets are divided into in-vivo and in-vitro-only compounds, and the prediction capability of the trained ML models is analyzed. Factors such as compound charge, number of atoms, and docking score are considered in the analysis of prediction error contributions. Weighting the ML input based on the desired property (low docking score) shows promise in improving ML performance. The proposed models help reduce the number of compounds that require further investigation.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Physical
David Vrska, Pavel Neogrady, Vladimir Kello, Miroslav Urban, Michal Pitonak
Summary: We use CASPT2 calculations to determine the vertical excitation energies for low-lying singlet and triplet states of auroderivatives of acetylene and ethylene, as well as supplementing the data with CCSD(T) results for triplet states. Our findings show a significant decrease in the low-lying excitation energies of these aurocarbons compared to their parent molecules. The singlet and triplet excitation energies of diauroacetylene decrease by 57% and 48%, respectively, and for tetraauroethylene, the decreases are 68% and 56%. Additionally, the singlet-triplet energy gap is further reduced. We emphasize the importance of incorporating dynamical correlation in CASPT2 calculations and discuss the challenges in selecting the appropriate active space for aurocarbons.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Physical
Benedicte Sverdrup Ofstad, Hakon Emil Kristiansen, Einar Aurbakken, Oyvind Sigmundson Schoyen, Simen Kvaal, Thomas Bondo Pedersen
Summary: Real-time simulations of laser-driven electron dynamics allow for the extraction of molecular optical properties through all orders in response theory. However, accuracy deteriorates for higher-order responses due to nonadiabatic effects caused by the finite-time ramping of the external laser field. Three different approaches for extracting electrical properties from real-time electronic-structure simulations are investigated. Quadratic ramping is found to yield highly accurate results at approximately half the computational cost for polarizabilities, hyperpolarizabilities, and a measure of reliability.
JOURNAL OF CHEMICAL PHYSICS
(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
Andy Kaiser, Razan E. Daoud, Francesco Aquilante, Oliver Kuhn, Luca De Vico, Sergey I. Bokarev
Summary: We implemented the Frenkel exciton model into the OpenMolcas program package to calculate collective electronic excited states of molecular aggregates. Our protocol does not rely on diabatization schemes or supermolecule calculations, and the use of Cholesky decomposition for pair interactions improves computational efficiency. We applied our method to two test systems and compared it with the dipole approximation.
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)
Review
Chemistry, Multidisciplinary
Benedicte Sverdrup Ofstad, Einar Aurbakken, Oyvind Sigmundson Schoyen, Hakon Emil Kristiansen, Simen Kvaal, Thomas Bondo Pedersen
Summary: In recent years, there has been growing interest in time-dependent coupled-cluster (TDCC) theory for simulating laser-driven electronic dynamics in atoms and molecules, as well as molecular vibrational dynamics. This review covers different types of single-reference TDCC theory based on orthonormal static, orthonormal time-dependent, or biorthonormal time-dependent spin orbitals. The time-dependent extension of equation-of-motion coupled-cluster theory and various applications of TDCC methods are also discussed, including the calculation of linear absorption spectra, response functions, high harmonic generation spectra, and ionization dynamics. Additionally, the role of TDCC theory in finite-temperature many-body quantum mechanics and other application areas is briefly described.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Physical
Juliana Cuellar-Zuquin, Ana Julieta Pepino, Ignacio Fdez Galvan, Ivan Rivalta, Francesco Aquilante, Marco Garavelli, Roland Lindh, Javier Segarra-Marti
Summary: We characterized the photochemically relevant conical intersections between different DNA/RNA nucleobases using CASSCF algorithms. Our results show that the size of the active space significantly affects the conical intersection topographies, while the basis set size seems to have a minor effect. We ruled out structural changes as a key factor and highlighted the importance of accurately describing the electronic states involved in these intersections.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Eirill Hauge, Hakon Emil Kristiansen, Lukas Konecny, Marius Kadek, Michal Repisky, Thomas Bondo Pedersen
Summary: We propose a novel function fitting method for approximating the propagation of the time-dependent electric dipole moment from real-time electronic structure calculations. The method achieves arbitrary spectral resolution through extrapolation by fitting shorter dipole trajectories. Numerical testing demonstrates that this fitting method can reproduce high-resolution spectra using short dipole trajectories.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Hannes Kneiding, Ruslan Lukin, Lucas Lang, Simen Reine, Thomas Bondo Pedersen, Riccardo De Bin, David Balcells
Summary: This paper introduces a method for studying transition metal complexes (TMCs) using deep graph learning, which utilizes electronic structure data from natural bond orbital (NBO) analysis and develops a representation called natural quantum graph (NatQG). With this method, the quantum properties of TMCs can be predicted, and the performance is better compared to traditional descriptor-based methods.
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, Multidisciplinary
Scott Wilcox, Daniel Sethio, Jas S. Ward, Antonio Frontera, Roland Lindh, Kari Rissanen, Mate Erdelyi
Summary: The interaction between a [bis(pyridine)iodine(i)](+) cation and a [bis(pyridine)silver(i)](+) cation, where an iodonium ion acts as a nucleophile by transferring electron density to the silver(i) cation, is reinvestigated in this study. No measurable interaction is observed between the cationic species in solution using NMR. DFT calculations suggest that any attractive interaction between these complexes in solution is primarily due to the pi-pi interaction of pyridines.
CHEMICAL COMMUNICATIONS
(2022)