Article
Chemistry, Physical
Marti Gimferrer, Abdulrahman Aldossary, Pedro Salvador, Martin Head-Gordon
Summary: This study introduces a new method called oxidation state localized orbitals (OSLO) for assigning oxidation states in molecules and evaluating the fragment orbital localization index (FOLI) using an algorithm. The OSLO approach produces satisfactory results in challenging cases and provides new evidence for the emergence of covalent interactions between fragments.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Yoichi Yamada, Ryohei Tsuruta, Yuho Yamamoto, Yutaro Ono, Tomohiro Nobeyama, Masato Iwasawa, Masahiro Sasaki, Rahul Suresh, Artem Kuklin, Hans Agren
Summary: We show that field emission from a single molecule at the apex of a metallic tip exhibits a well-defined angular distribution pattern with a spherical harmonics shape, regardless of the molecule species. By carefully controlling simultaneous measurements of the emission pattern, current, and energy, we deduced the formation mechanism of these patterns, in which electrons from the metallic tip resonantly tunnel into vacuum via a molecule-induced state at the tip's Fermi level. The characteristic patterns were consistent with the Fourier transform of superatom molecular orbitals (SAMOs), making this method unique for real-time imaging of SAMOs or low-lying Rydberg states of single molecules.
Article
Mathematics
Aiman Arshad, Aqsa Sattar, Muhammad Javaid, Mamo Abebe Ashebo
Summary: Graph theory is widely used in cheminformatics to develop physicochemical, chemical structure, and property models. By employing numerical structure invariants, chemical graph details can be manipulated and studied. This article focuses on the study of topological indices based on connection numbers, such as the Zagreb index and modified Zagreb index. The results of these indices are obtained through the analysis of Cartesian product and numerical calculations.
JOURNAL OF MATHEMATICS
(2023)
Article
Mathematics
Kamel Jebreen, Muhammad Haroon Aftab, M. I. Sowaity, B. Sharada, A. M. Naji, M. Pavithra
Summary: This article investigates the eccentric harmonic index of Cartesian product graphs and obtains the formulas for the Hamming and Hypercube graphs. These formulas have significant applications in QSAR and QSPR studies in mathematical chemistry.
JOURNAL OF MATHEMATICS
(2022)
Article
Chemistry, Physical
Giovanni Macetti, Erna K. Wieduwilt, Alessandro Genoni
Summary: The article introduces a novel multiscale embedding strategy, QM/ELMO, which has been widely applied in ground and excited state calculations, as well as successful applications in crystallography. By combining quantum mechanics with extremely localized molecular orbitals, the QM/ELMO scheme can replicate the results of fully quantum mechanical calculations at a lower computational cost. Future applications of this strategy in various chemical problems are expected, along with potential advancements in algorithmic improvements and methodological developments.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Mathematics
Maryam Atapour, Akbar Jahanbani, Rana Khoeilar
Summary: This paper investigates the Randic index, obtaining lower and upper bounds in terms of graph size, maximum degree, and minimum degree. Additionally, a general lower and upper bound for the Randic index is derived.
JOURNAL OF MATHEMATICS
(2021)
Article
Chemistry, Physical
Sarai Dery Folkestad, Regina Matveeva, Ida-Marie Hoyvik, Henrik Koch
Summary: We present a trust-region optimization of the Edmiston-Ruedenberg orbital localization function, which can be used to localize both occupied and virtual orbitals. This is the first demonstration of general virtual orbital localization using the Edmiston-Ruedenberg localization function. In the optimization process, the sum of orbital self-repulsion energies is maximized to obtain the localized orbitals.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Sarai Dery Folkestad, Regina Matveeva, Ida-Marie Hoyvik, Henrik Koch
Summary: In this study, a trust-region optimization of the Edmiston-Ruedenberg orbital localization function is presented. The approach successfully localizes both the occupied and the virtual orbitals, making it the first demonstration of general virtual orbital localization using the Edmiston-Ruedenberg localization function. The optimization is performed in the molecular orbital basis, and the Cholesky decomposition is used to reduce the cost. The results show that the cost of virtual orbital localization is higher and the resulting orbital spreads are larger compared to other, less expensive localization functions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Marjory C. Clement, Xiao Wang, Edward F. Valeev
Summary: The study presents a robust method for determining PM Wannier functions using the Broyden-Fletcher-Goldfarb-Shanno method, which shows faster convergence compared to other methods (such as steepest ascent and conjugate gradient) and performs well in solids of different dimensions, including supercells with thousands of atoms. Additionally, a simple definition of atomic charges and an automated method for generating initial guesses for the WFs contribute significantly to the robustness of the solver.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Zhenling Wang, Abdulrahman Aldossary, Martin Head-Gordon
Summary: In this paper, the sparsity of the electron repulsion integral (ERI) tensor in second-order Moller-Plesset theory (MP2) is explored. Different approaches to achieving sparsity are compared, and it is found that the orthogonal valence virtual-hard virtual set of virtual orbitals gives the sparsest ERI tensor. The low-rank pair natural orbital (PNO) representation achieves significant rank reduction but requires more memory, while the occupied-specific virtual (OSV) approach has similar memory usage but greater algorithmic complexity.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Mathematics
Suha Wazzan, Nurten Urlu Ozalan
Summary: This paper presents a new approach that explores the application of graph energy variants in chemistry, specifically in the development of platinum anticancer drugs. The study focuses on investigating the correlation between topological indices and energies of these drugs, as well as the possibility of utilizing these energies as structural descriptors. The research showcases promising results and suggests potential improvements in the manufacturing of anticancer drugs.
JOURNAL OF MATHEMATICS
(2023)
Article
Mathematics
Durbar Maji, Ganesh Ghorai, Muhammad Khalid Mahmood, Md. Ashraful Alam
Summary: The study focuses on the inverse problem based on topological indices, specifically on the Y-index, Gourava indices, second hyper-Zagreb index, reformulated first Zagreb index, and reformulated F-index.
JOURNAL OF MATHEMATICS
(2021)
Article
Chemistry, Multidisciplinary
Raksha Poojary, Arathi K. Bhat, Manjunatha Prasad Karantha, S. Arumugam, Ivan Gutman
Summary: This paper presents a unified approach to characterize the multiplicity of the eigenvalue zero in the spectrum of a graph G of order n. It is shown that all known results on trees, unicyclic graphs, bicyclic graphs, graphs with minimum degree 1, and r-partite graphs with the multiplicity of the eigenvalue zero being n-4 are corollaries of a theorem by Chang, Huang, and Yeh.
MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Muhammad Javaid, Saira Javed, Abdulaziz Mohammed Alanazi, Majdah R. Alotaibi
Summary: This study explores the relationship between the chemical properties of chemical compounds and drugs and their molecular structures, using graph-theoretic techniques to analyze the physicochemical and structural properties of molecular graphs. The computation of Zagreb indices of generalized sum graphs based on factor graphs was conducted, with specific graph classes used for illustration and analysis to identify efficient subclasses with dominant indices.
JOURNAL OF CHEMISTRY
(2021)
Article
Crystallography
Erna K. Wieduwilt, Giovanni Macetti, Rebecca Scatena, Piero Macchi, Alessandro Genoni
Summary: In this paper, the use of ELMO transferability to quickly obtain wavefunctions, electron densities, and electrostatic potentials of three-dimensional coordination polymers such as metal organic frameworks (MOFs) is investigated. A protocol is proposed to properly describe the secondary building units of MOFs using the novel QM/ELMO approach. Benchmark tests on HKUST-1 metal organic framework show promising results for further improvements and applications of this strategy.
Article
Chemistry, Physical
Shivesh Pathak, Ignacio Ema Lopez, Alex J. Lee, William P. Bricker, Rafael Lopez Fernandez, Susi Lehtola, Joshua A. Rackers
Summary: The HF theorem allows efficient force calculations for large systems using ML models for the electron density. However, the well-known Pulay force has hindered the general acceptance of the HF approach for atom-centered basis sets due to its significant error. This work demonstrates that by using an augmented Gaussian basis set for density functional calculations, the Pulay force can be suppressed and HF forces can be computed as accurately as analytical forces, enabling reliable geometry optimization and molecular dynamics simulations. These results provide a clear path for accurate and efficient simulation of large systems using ML densities and the HF theorem.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Soroush Rash, Elvar Orn Jonsson, Hannes Jonsson, Jorg Meyer
Summary: This study calculates and analyzes the anomalous volume isotope effect of ice Ih, taking into account nuclear quantum effects in the Helmholtz free energy. The results show that the MB-pol potential function yields better agreement with experimental measurements than DFT calculations. The short-range three-body terms in the MB-pol function are found to have a significant influence on the results. A decomposition of vibrational modes and the use of benchmark values from Raman spectroscopy reveal the delicate competition between different modes as the reason for the volume isotope effect.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Jan Kloppenburg, Livia B. Partay, Hannes Jonsson, Miguel A. Caro
Summary: A Gaussian approximation machine learning interatomic potential for platinum is developed based on density-functional theory (DFT) data. The potential exhibits excellent transferability and agreement with DFT in various properties such as bulk elasticity, surface energetics, and nanoparticle stability. It provides state-of-the-art accuracy at a low computational cost. Two examples are presented to demonstrate the potential's capability in modeling Pt systems: the pressure-temperature phase diagram of Pt calculated using nested sampling and a study of the spontaneous crystallization of a large Pt nanoparticle based on classical dynamics simulations over several nanoseconds.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Susi Lehtola
Summary: Density functional calculations on atoms are used to determine accurate initial guesses and generate various types of pseudopotential approximations and efficient atomic-orbital basis sets. This study describes the implementation of the spherical symmetric densities for density functional approximations (DFAs) and discusses the importance of density thresholding. The results show that all the functionals studied in this work yield total energies converged to 0.1 mu Eh when densities smaller than 10-11a0-3 are screened out.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yorick L. A. Schmerwitz, Gianluca Levi, Hannes Jonsson
Summary: Excited electronic states are calculated by finding saddle points on the energy surface. This method has advantages in density functional calculations as it avoids collapse to the ground state and allows for variationally optimized orbitals. A mode following method is presented to find higher-order saddle points, allowing for calculations even at avoided crossings. Results are presented for charge transfer excitations and a diplatinum-silver complex, demonstrating the applicability of the method to larger molecules.
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
Susi Lehtola
Summary: This study re-examines the determination of the regularized nuclear potential and finds errors in the original tabulations. Using a simple radial quadrature scheme, higher accuracy and normalization condition satisfaction can be achieved. Furthermore, the study shows that the regularized potential can accurately reproduce orbital energies and shapes even with small parameter values and can converge to sub-meV precision in specific cases.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Susi Lehtola
Summary: This article describes the implementation of atomic electronic structure calculations using numerical radial basis functions within the finite element method. The stability of the calculation method at small r is discussed, as well as the choice of shape functions. The performance of different shape functions is compared, and it is found that first-order Hermite interpolating polynomials perform well even with large numbers of nodes and nonuniform element grids. The implications of Hermite interpolating polynomials on calculations with meta-GGA functionals are also discussed, and issues with Minnesota functionals are identified.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Susi Lehtola, Miguel A. L. Marques
Summary: Density functional theory is a fundamental method in chemistry and materials science. However, the lack of reliable reference data has resulted in verification problems for novel density functional approximations (DFAs). This work aims to ensure the reproducibility of DFAs and proposes a common framework for verification and testing.
JOURNAL OF CHEMICAL PHYSICS
(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
Materials Science, Multidisciplinary
M. N. Potkina, I. S. Lobanov, H. Jonsson, V. M. Uzdin
Summary: The lifetime of a magnetic skyrmion in a two-dimensional lattice is investigated and found to increase with the size of the skyrmion. This is due to the decrease in entropy of the transition state compared to the skyrmion state, resulting in a significant increase in the pre-exponential factor, and the activation energy reaching an upper bound. The largest skyrmions studied include over 20,000,000 spins.
Article
Chemistry, Physical
Sander o. Hanslin, Hannes Jonsson, Jaakko Akola
Summary: Transition metal dichalcogenides (TMDs) are inexpensive and abundant alternatives to precious metals as catalyst materials. Experimental measurements show that MoS2 has significant electrocatalytic activity for the hydrogen evolution reaction (HER). However, the activity varies depending on the preparation method. To understand the mechanism and active sites for HER, calculations were performed on transition metal doped basal plane of MoS2 under electrochemical conditions, taking into account electrode potential and solvent effects.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Materials Science, Multidisciplinary
Moritz Sallermann, Hannes Jonsson, Stefan Bluegel
Summary: Magnetic hopfions are three-dimensional, string-like topological solitons with a Hopf number. They serve as a fundamental prototype for magnetic quasiparticles and have potential applications in spintronics. While their existence has been predicted in certain magnets, the physical realization of freely moving hopfions in bulk magnets has been challenging.
Article
Chemistry, Physical
Alec E. Sigurdarson, Yorick L. A. Schmerwitz, Dagrun K. V. Tveiten, Gianluca Levi, Hannes Jonsson
Summary: In this study, density functional calculations were performed on several molecules to investigate their Rydberg excited states up to high energy. The results show that the generalized gradient approximation (GGA) functional of Perdew, Burke, and Ernzerhof (PBE) can accurately predict the excitation energy when combined with self-interaction correction and complex-valued orbitals. The results from the Tao, Perdew, Staroverov, and Scuseria (TPSS) and r2SCAN meta-GGA functionals did not provide a systematic improvement over the uncorrected PBE functional.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Sander O. Hanslin, Hannes Jonsson, Jaakko Akola
Summary: This study employs a grand-canonical approach to calculate the kinetics of the hydrogen evolution reaction on intrinsic sites of MoS2. The results reveal that certain edge configurations, particularly S-deficient edges on the Mo-termination, exhibit significantly higher activity. The findings suggest that catalyst design for transition metal dichalcogenides should focus on modifying the metal sites rather than activating the chalcogen sites.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)