Article
Chemistry, Multidisciplinary
Junzi Liu, Lan Cheng
Summary: The article reviews the development of relativistic coupled-cluster and equation-of-motion coupled-cluster methods, focusing on recent efforts to improve computational efficiency and extend the methods to molecules containing heavy elements. Future directions for the development of these methods are also discussed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2021)
Article
Chemistry, Physical
Artur Nowak, Ors Legeza, Katharina Boguslawski
Summary: Wave functions based on electron-pair states provide reliable models for describing quantum many-body problems with strongly correlated electrons, especially when broken-pair states are corrected appropriately. The study analyzes the performance of electron-pair methods in predicting orbital-based correlation spectra, focusing on the pCCD-LCC ansatz. It is found that pCCD-LCC accurately reproduces orbital-pair correlation patterns in weak correlation limits and for molecules close to their equilibrium structure.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Spectroscopy
Yuliya Osika, Maksim Shundalau
Summary: The potential energy curves of the ground and five low-lying excited terms of the RaF molecule were calculated using the Fock-space relativistic coupled theory. Various spectroscopic constants were predicted and a scheme for direct laser cooling was proposed. The study suggests that the A(2)Pi(1/2) -> X-2 Sigma(+) channel in the RaF molecule is an almost ideal case for direct laser cooling.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Physical
Somesh Chamoli, Kshitijkumar Surjuse, Bhavnesh Jangid, Malaya K. Nayak, Achintya Kumar Dutta
Summary: This study presents a reduced cost four-component relativistic coupled cluster method based on frozen natural spinors, and provides benchmark results to demonstrate its efficiency and accuracy. The method converges faster and can be controlled by adjusting a single threshold.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Optics
Ravi Kumar, S. Chattopadhyay, D. Angom, B. K. Mani
Summary: A new all-particle Fock-space relativistic coupled-cluster method was developed and successfully applied to calculate clock properties in Al+, yielding results in excellent agreement with experimental values, demonstrating the accuracy and effectiveness of the method.
Article
Engineering, Multidisciplinary
Yizhong Sun, Weiwei Sun, Haibiao Zheng
Summary: In this paper, a parallel domain decomposition method is proposed for solving the fully-mixed Stokes-Darcy coupled problem with the Beavers-Joseph-Saffman interface conditions. The method decouples the original problem into two independent subproblems with newly constructed Robin-type boundary conditions and modified weak formulation. Convergence analysis and numerical examples demonstrate the effectiveness of the proposed method.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2021)
Article
Optics
Fang Li, Hong Ma, Yong-Bo Tang
Summary: The hyperfine-structure constants A and B of 24 low-lying states of La2+ are calculated using the singles and doubles approximated relativistic coupled-cluster method. The results show reasonable agreement with experimental values for certain states, but significant deviations for others. The role of electron correlation effects is further investigated using lower-order many-body perturbation theory and coupled-cluster methods.
JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS
(2021)
Article
Chemistry, Physical
Daniil A. Fedotov, Sonia Coriani, Christof Haettig
Summary: The study presents an implementation of a complex solver for computing the complex response functions of damped response theory. The solver uses a partitioned formulation to avoid storing double excitation amplitudes, making it widely applicable in the context of the resolution-of-identity (RI) coupled cluster singles and approximate doubles (CC2) method.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Optics
Fei-Chen Li, Hao-Xue Qiao, Yong-Bo Tang, Ting-Yun Shi
Summary: The study calculates multiple transition properties of Th 3+ using the coupled-cluster method, with good agreement compared to experimental data. Many results are reported for the first time, and it is of great significance for future spectral analysis and precision experiments.
JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER
(2022)
Article
Mathematics, Applied
Leonardo Boledi, Fabian Key, Benjamin Terschanski, Stefanie Elgeti, Julia Kowalski
Summary: We present a numerical workflow for modeling and simulating transient close-contact melting processes using the space-time finite element method. Our contribution is to derive a model for the transient melting process of a planar heat source and update the melting velocity based on the heat flux in the vicinity of the heat source.
COMPUTERS & MATHEMATICS WITH APPLICATIONS
(2023)
Article
Computer Science, Interdisciplinary Applications
Gabriel Stankiewicz, Chaitanya Dev, Paul Steinmann
Summary: In this work, density-based topology optimization and node-based shape optimization are combined into a single optimization problem using an embedding domain discretization technique. The use of a variable pseudo-density field allows for the design of fine-tuned structures without predefined topological features. Through this approach, the advantages of both topology and shape optimization methods are brought together to provide an efficient way to generate production-ready designs.
STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION
(2021)
Article
Spectroscopy
Yi-Wei Fan, Huai-Qian Wang, Hui-Fang Li
Summary: The study on hydrated clusters Co(H2O)(n)(-) in gas phase using DFT coupled with stochastic kicking method reveals that the global minimum structure of Co(H2O)(n)(-) exhibits a low-symmetry pattern. The Co- ion tends to be located at the vertex site of the water molecular clusters to reduce repulsion with O atom. These results demonstrate that the formation of these low-lying isomers is determined by the delicate balance between ion-water and water-water interactions.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Physics, Atomic, Molecular & Chemical
Mary Marshall, Zhaoguo Zhu, Junzi Liu, Kit H. Bowen, Lan Cheng
Summary: A study on the photoelectron spectroscopy of the uranyl dichloride anion showed good agreement between experimental and theoretical data, providing valuable information on the uranium 5f orbital energies.
JOURNAL OF MOLECULAR SPECTROSCOPY
(2021)
Review
Biochemistry & Molecular Biology
Ketan D. Patel, Monica R. MacDonald, Syed Fardin Ahmed, Jitendra Singh, Andrew M. Gulick
Summary: Nonribosomal peptide synthetases (NRPSs) are enzymes that catalyze the biosynthesis of important peptide natural products. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and growing peptides. While conserved conformational states have been identified within a single module, interactions between modules are more dynamic. This article describes the structures of NRPS protein domains and modules and discusses their implications for future natural product discovery.
NATURAL PRODUCT REPORTS
(2023)
Article
Mathematics, Applied
Meiling Yue, Fei Xu, Hongkun Ma
Summary: This study introduces a new framework for solving coupled semilinear elliptic equations by constructing a set of nested finite element spaces and using domain decomposition method to solve decoupled linear elliptic equations in each level space. The proposed algorithm is highly flexible and has very low requirements for the smoothness of nonlinear terms, which improves efficiency compared to traditional domain decomposition methods.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Article
Chemistry, Physical
Gergely Barcza, Viktor Ivady, Tibor Szilvasi, Marton Voros, Libor Veis, Adam Gali, Ors Legeza
Summary: This study analyzes the numerical aspects of the inherent multireference density matrix renormalization group (DMRG) calculations on top of the periodic Kohn-Sham density functional theory using the complete active space approach. Results show excellent consistency of the DMRG energy spectrum in terms of sample size, basis size, and active space selection protocol, with good agreement with results obtained from standard quantum chemical calculations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Jiri Brabec, Jan Brandejs, Karol Kowalski, Sotiris Xantheas, Ors Legeza, Libor Veis
Summary: This study represents the first attempt to use a super-computer platform for QC-DMRG calculations, showing the scalability of the parallel approach up to approximately 2000 CPU cores in the largest calculation, with testing on three different molecules.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Ana Sanchez-Grande, Jose Urgel, Libor Veis, Shayan Edalatmanesh, Jose Santos, Koen Lauwaet, Pingo Mutombo, Jose M. Gallego, Jiri Brabec, Pavel Beran, Dana Nachtigallova, Rodolfo Miranda, Nazario Martin, Pavel Jelinek, David Ecija
Summary: Polycyclic aromatic hydrocarbons (PAHs) are organic compounds with multiple fused aromatic rings, some of which exhibit open-shell magnetic ground states. Recent research has focused on the synthesis and study of acene and fused acene (periacene) families, with experimental evidence of a magnetic ground state reported for isolated peripentacene molecules. This discovery contributes to a better understanding of organic compounds with magnetic properties, particularly in the development of carbon-based spintronic devices.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Jie Su, Wei Fan, Pingo Mutombo, Xinnan Peng, Shaotang Song, Martin Ondracek, Pavlo Golub, Jiri Brabec, Libor Veis, Mykola Telychko, Pavel Jelinek, Jishan Wu, Jiong Lu
Summary: This study reports the synthesis of an open-shell [7]triangulene quantum ring molecule on Au(111) through surface-assisted cyclodehydrogenation of a rationally designed kekulene derivative. Bond-resolved scanning tunneling microscopy (BR-STM) and dI/dV mapping revealed the molecular structure and edge-localized electronic states of [7]TQR, confirming its retention of an open-shell septuple ground state on Au(111). This work demonstrates a new approach for designing high-spin graphene quantum rings for future quantum devices.
Article
Quantum Science & Technology
P. Bauman Nicholas, Jaroslav Chladek, Libor Veis, Jiri Pittner, Kowalski Karol
Summary: This paper discusses the utilization of VQE and GUCC formalism for diagonalization of Hamiltonians in active spaces, considering effective Hamiltonians defined by downfolding virtual orbitals and freezing core orbitals. Various solvers are considered to identify solutions of the GUCC equations, with benchmark systems N-2, H2O, and C2H4 illustrating the performance of the combined framework.
QUANTUM SCIENCE AND TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Benjamin Mallada, Bruno de la Torre, Jesus Mendieta-Moreno, Dana Nachtigallova, Adam Matej, Mikulas Matousek, Pingo Mutombo, Jiri Brabec, Libor Veis, Timothee Cadart, Martin Kotora, Pavel Jelinek
Summary: This study presents a novel route using on-surface chemistry to synthesize nonalternant polycyclic aromatic hydrocarbons containing up to four distinct kinds of non-benzenoid rings. The surface-induced mechanical constraints and peculiar ring current play a decisive role in forming the energetically unfavorable products. The research offers a new approach for synthesizing novel hydrocarbons with internal stress driven by the surface, not achievable by traditional organic chemistry methods in solution.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Pavlo Golub, Andrej Antalik, Libor Veis, Jiri Brabec
Summary: The article proposes a neural network-based approach for automatic selection of active spaces, focusing on transition metal systems. The machine learning models show reasonable accuracy in predicting active space orbitals and demonstrate transferability onto out-of-the-model systems. Additionally, the correctness of automatically selected active spaces is validated on a Fe(II)-porphyrin model.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Carlos Mejuto-Zaera, Demeter Tzeli, David Williams-Young, Norm M. Tubman, Mikulas Matousek, Jiri Brabec, Libor Veis, Sotiris S. Xantheas, Wibe A. de Jong
Summary: Iron-sulfur clusters are important functional motifs in biological catalytic centers, capable of performing important chemical transformations at ambient conditions. The electronic structure of these clusters is complex and sensitive to geometric changes, requiring large active space calculations to reveal their properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Daria Drwal, Pavel Beran, Micha Hapka, Marcin Modrzejewski, Adam Sokol, Libor Veis, Katarzyna Pernal
Summary: In this work, a new approach based on adiabatic connection is proposed to accurately describe the electronic structure, especially for systems with strong electron correlation. It is more efficient than existing ab initio multireference dynamic correlation methods.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Editorial Material
Chemistry, Multidisciplinary
Libor Veis
Summary: This article discusses recent progress in numerically studying the performance of ASP on strongly correlated molecules and presents several approaches to improve the quality of prepared ground state wave functions.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Chemistry, Physical
Mikulas Matousek, Michal Hapka, Libor Veis, Katarzyna Pernal
Summary: A multiconfigurational adiabatic connection (AC) formalism is an attractive approach to compute the dynamic correlation within DMRG models. The study investigates the effect of removing the fixed-RDM approximation in AC and finds that lifting this approximation is a viable way toward improving the accuracy of existing AC approximations.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Pavel Beran, Katarzyna Pernal, Fabijan Pavosevic, Libor Veis
Summary: The density matrix renormalization group (DMRG) method is an efficient and accurate computational method for treating strong correlation in large active spaces. However, its application on larger molecules is limited by computational scaling and the treatment of missing dynamical electron correlation. In this work, we present a first step towards combining DMRG with density functional theory (DFT) through projection-based wave function (WF)-in-DFT embedding. On proof-of-concept molecular examples, we demonstrate that the developed DMRG-in-DFT approach accurately describes molecules with strongly correlated fragments.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Daria Drwal, Mikulas Matousek, Pavlo Golub, Aleksandra Tucholska, Michal Hapka, Jiri Brabec, Libor Veis, Katarzyna Pernal
Summary: The new generation of proposed light-emitting molecules for OLEDs with a negative ST gap has attracted research interest. Spin polarization plays a role in the inversion mechanism of the ST gap. A descriptor for screening candidate molecules with negative ST gaps is proposed. Numerical results show that the effect of spin polarization decreases linearly with increasing HOMO-LUMO exchange integral.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Materials Science, Multidisciplinary
C. Krumnow, L. Veis, J. Eisert, Oe. Legeza
Summary: The study explores the use of matrix-product states in two-dimensional fermionic models, showing significantly higher accuracy levels compared to direct embeddings into one-dimensional systems. By utilizing fermionic mode transformations and overcoming the prejudice of local embeddings in one dimension, the method captures the natural correlation structure more accurately.
