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Kriebel MH, Tecmer P, Gałyńska M, Leszczyk A, Boguslawski K. Accelerating Pythonic Coupled-Cluster Implementations: A Comparison Between CPUs and GPUs. J Chem Theory Comput 2024; 20:1130-1142. [PMID: 38306601 PMCID: PMC10867805 DOI: 10.1021/acs.jctc.3c01110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 02/04/2024]
Abstract
In this work, we benchmark several Python routines for time and memory requirements to identify the optimal choice of the tensor contraction operations available. We scrutinize how to accelerate the bottleneck tensor operations of Pythonic coupled-cluster implementations in the Cholesky linear algebra domain, utilizing a NVIDIA Tesla V100S PCIe 32GB (rev 1a) graphics processing unit (GPU). The NVIDIA compute unified device architecture API interacts with CuPy, an open-source library for Python, designed as a NumPy drop-in replacement for GPUs. Due to the limitations of video memory, the GPU calculations must be performed batch-wise. Timing results of some contractions containing large tensors are presented. The CuPy implementation leads to a factor of 10-16 speed-up of the bottleneck tensor contractions compared to computations on 36 central processing unit (CPU) cores. Finally, we compare example CCSD and pCCD-LCCSD calculations performed solely on CPUs to their CPU-GPU hybrid implementation, which leads to a speed-up of a factor of 3-4 compared to the CPU-only variant.
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Affiliation(s)
- Maximilian H. Kriebel
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Marta Gałyńska
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Aleksandra Leszczyk
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
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2
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Tecmer P, Gałyńska M, Szczuczko L, Boguslawski K. Geminal-Based Strategies for Modeling Large Building Blocks of Organic Electronic Materials. J Phys Chem Lett 2023; 14:9909-9917. [PMID: 37903084 PMCID: PMC10641881 DOI: 10.1021/acs.jpclett.3c02434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/09/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
We elaborate on unconventional electronic structure methods based on geminals and their potential to advance the rapidly developing field of organic photovoltaics (OPVs). Specifically, we focus on the computational advantages of geminal-based methods over standard approaches and identify the critical aspects of OPV development. Examples are reliable and efficient computations of orbital energies, electronic spectra, and van der Waals interactions. Geminal-based models can also be combined with quantum embedding techniques and a quantum information analysis of orbital interactions to gain a fundamental understanding of the electronic structures and properties of realistic OPV building blocks. Furthermore, other organic components present in, for instance, dye-sensitized solar cells (DSSCs) represent another promising scope of application. Finally, we provide numerical examples predicting the properties of a small building block of OPV components and two carbazole-based dyes proposed as possible DSSC sensitizers.
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Affiliation(s)
- Paweł Tecmer
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Marta Gałyńska
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Lena Szczuczko
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics,
Astronomy, and Informatics, Nicolaus Copernicus
University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
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3
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Chakraborty R, Boguslawski K, Tecmer P. Static embedding with pair coupled cluster doubles based methods. Phys Chem Chem Phys 2023; 25:25377-25388. [PMID: 37705409 DOI: 10.1039/d3cp02502k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Quantum embedding methods have recently been significantly developed to model large molecular structures. This work proposes a novel wave function theory in a density functional theory (WTF-in-DFT) embedding scheme based on pair-coupled cluster doubles (pCCD)-type methods. While pCCD can reliably describe strongly-correlated systems with mean-field-like computational cost, the large extent of the dynamic correlation can be accounted for by (linearized) coupled-cluster corrections on top of the pCCD wave function. Here we focus on the linearized coupled-cluster singles and doubles (LCCSD) ansatz for electronic ground states and its extension to excited states within the equation of motion (EOM) formalism. We test our EOM-pCCD-LCCSD-in-DFT approach for the vertical excitation energies of the hydrogen-bonded water-ammonia complex, micro-solvated thymine, and uranyl tetrahalides (UO2X42-, X = F, Cl, Br). Furthermore, we assess the quality of the embedding potential using an orbital entanglement and correlation analysis. The approximate embedding models successfully capture changes in the excitation energies going from bare fragments to supramolecular structures and represent a promising computational method for excited states in large molecular systems.
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Affiliation(s)
- Rahul Chakraborty
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
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4
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Jahani S, Boguslawski K, Tecmer P. The relationship between structure and excited-state properties in polyanilines from geminal-based methods. RSC Adv 2023; 13:27898-27911. [PMID: 37736567 PMCID: PMC10509596 DOI: 10.1039/d3ra05621j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
We employ state-of-the-art quantum chemistry methods to study the structure-to-property relationship in polyanilines (PANIs) of different lengths and oxidation states. Specifically, we focus on leucoemeraldine, emeraldine, and pernigraniline in their tetramer and octamer forms. We scrutinize their structural properties, HOMO and LUMO energies, HOMO-LUMO gaps, and vibrational and electronic spectroscopy using various Density Functional Approximations (DFAs). Furthermore, the accuracy of DFAs is assessed by comparing them to experimental and wavefunction-based reference data. We perform large-scale orbital-optimized pair-Coupled Cluster Doubles (oo-pCCD) calculations for ground and electronically excited states and conventional Configuration Interaction Singles (CIS) calculations for electronically excited states in all investigated systems. The EOM-pCCD+S approach with pCCD-optimized orbitals allows us to unambiguously identify charge transfer and local transitions across the investigated PANI systems-an analysis not possible within a delocalized canonical molecular orbital basis obtained, for instance, by DFAs. We show that the low-lying part of the emeraldine and pernigraniline spectrum is dominated by charge transfer excitations and that polymer elongation changes the character of the leading transitions. Furthermore, we augment our study with a quantum informational analysis of orbital correlations in various forms of PANIs.
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Affiliation(s)
- Seyedehdelaram Jahani
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń Grudziadzka 5 87-100 Toruń Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń Grudziadzka 5 87-100 Toruń Poland
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń Grudziadzka 5 87-100 Toruń Poland
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5
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Mamache S, Gałyńska M, Boguslawski K. Benchmarking ionization potentials using the simple pCCD model. Phys Chem Chem Phys 2023. [PMID: 37378457 DOI: 10.1039/d3cp01963b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The electron-detachment energy is measured by the ionization potential (IP). As a result, it is a fundamental, observable and important molecular electronic signature in photoelectron spectroscopy. A precise theoretical prediction of electron-detachment energies or ionization potentials is essential for organic optoelectronic systems like transistors, solar cells, or light-emitting diodes. In this work, we benchmark the performance of the recently presented IP variant of the equation-of-motion pair coupled cluster doubles (IP-EOM-pCCD) model to determine IPs. Specifically, the predicted ionization energies are compared to experimental results and higher-order coupled cluster theories based on statistically assessing 201 electron-detached states of 41 organic molecules for three different molecular orbital basis sets and two sets of particle-hole operators. While IP-EOM-pCCD features a reasonable spread and skewness of ionization energies, its mean error and standard deviation differ by up to 1.5 eV from reference data. Our study, thus, highlights the importance of dynamical correlation to reliably predict IPs from a pCCD reference function in small organic molecules.
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Affiliation(s)
- Saddem Mamache
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Marta Gałyńska
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
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6
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Nowak A, Boguslawski K. A configuration interaction correction on top of pair coupled cluster doubles. Phys Chem Chem Phys 2023; 25:7289-7301. [PMID: 36810525 DOI: 10.1039/d2cp05171k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Numerous numerical studies have shown that geminal-based methods are a promising direction to model strongly correlated systems with low computational costs. Several strategies have been introduced to capture the missing dynamical correlation effects, which typically exploit a posteriori corrections to account for correlation effects associated with broken-pair states or inter-geminal correlations. In this article, we scrutinize the accuracy of the pair coupled cluster doubles (pCCD) method extended by configuration interaction (CI) theory. Specifically, we benchmark various CI models, including, at most double excitations against selected CC corrections as well as conventional single-reference CC methods. A simple Davidson correction is also tested. The accuracy of the proposed pCCD-CI approaches is assessed for challenging small model systems such as the N2 and F2 dimers and various di- and triatomic actinide-containing compounds. In general, the proposed CI methods considerably improve spectroscopic constants compared to the conventional CCSD approach, provided a Davidson correction is included in the theoretical model. At the same time, their accuracy lies between those of the linearized frozen pCCD and frozen pCCD variants.
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Affiliation(s)
- Artur Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
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7
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Tecmer P, Boguslawski K. Geminal-based electronic structure methods in quantum chemistry. Toward a geminal model chemistry. Phys Chem Chem Phys 2022; 24:23026-23048. [PMID: 36149376 DOI: 10.1039/d2cp02528k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this review, we discuss the recent progress in developing geminal-based theories for challenging problems in quantum chemistry. Specifically, we focus on the antisymmetrized geminal power, generalized valence bond, antisymmetrized product of strongly orthogonal geminals, singlet-type orthogonal geminals, the antisymmetric product of 1-reference orbital geminal, also known as the pair coupled cluster doubles ansatz, and geminals constructed from Richardson-Gaudin states. Furthermore, we review various corrections to account for the missing dynamical correlation effects in geminal models and possible extensions to target electronically excited states and open-shell species. Finally, we discuss some numerical examples and present-day challenges for geminal-based models, including a quantitative and qualitative analysis of wave functions, and software availability.
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Affiliation(s)
- Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
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8
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Leszczyk A, Dome T, Tecmer P, Kedziera D, Boguslawski K. Resolving the π-assisted U-N σ f-bond formation using quantum information theory. Phys Chem Chem Phys 2022; 24:21296-21307. [PMID: 36043327 DOI: 10.1039/d2cp03377a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We model the potential energy profiles of the UO2 (NCO)Cl2- → NUOCl2- + CO2 reaction pathway [Y. Gong, V. Vallet, M. del Carmen Michelini, D. Rios and J. K. Gibson, J. Phys. Chem. A, 2014, 118, 325-330] using different pair coupled-cluster doubles (pCCD) methods. Specifically, we focus on pCCD and pCCD-tailored coupled cluster models in predicting relative energies for the various intermediates and transition states along the reaction coordinate. Furthermore, we augment our study on energetics with an orbital-pair correlation analysis of the complete reaction pathway that features two distinct paths. Our analysis of orbital correlations sheds new light on the formation and breaking of respective bonds between the uranium, oxygen, and nitrogen atoms along the reaction coordinates where the "yl" bond is broken and a nitrido compound formed. Specifically, the strengthening of the U-N σf-bond is assisted by a π-type interaction that is delocalized over the C-N-U backbone of the UO2 (NCO)Cl2- complex.
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Affiliation(s)
- Aleksandra Leszczyk
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Tibor Dome
- Institute for Theoretical Physics, ETH Zürich, 8093 Zürich, Switzerland.,Institute of Astronomy, University of Cambridge, Madingley Road Cambridge, CB3 0HA, UK
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Dariusz Kedziera
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
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9
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Leszczyk A, Máté M, Legeza Ö, Boguslawski K. Assessing the Accuracy of Tailored Coupled Cluster Methods Corrected by Electronic Wave Functions of Polynomial Cost. J Chem Theory Comput 2021; 18:96-117. [PMID: 34965121 DOI: 10.1021/acs.jctc.1c00284] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tailored coupled cluster theory represents a computationally inexpensive way to describe static and dynamical electron correlation effects. In this work, we scrutinize the performance of various coupled cluster methods tailored by electronic wave functions of polynomial cost. Specifically, we focus on frozen-pair coupled cluster (fpCC) methods, which are tailored by pair-coupled cluster doubles (pCCD), and coupled cluster theory tailored by matrix product state wave functions optimized by the density matrix renormalization group (DMRG) algorithm. As test system, we selected a set of various small- and medium-sized molecules containing diatomics (N2, F2, C2, CN+, CO, BN, BO+, and Cr2) and molecules (ammonia, ethylene, cyclobutadiene, benzene, hydrogen chains, rings, and cuboids) for which the conventional single-reference coupled cluster singles and doubles (CCSD) method is not able to produce accurate results for spectroscopic constants, potential energy surfaces, and barrier heights. Most importantly, DMRG-tailored and pCCD-tailored approaches yield similar errors in spectroscopic constants and potential energy surfaces compared to accurate theoretical and/or experimental reference data. Although fpCC methods provide a reliable description for the dissociation pathway of molecules featuring single and quadruple bonds, they fail in the description of triple or hextuple bond-breaking processes or avoided crossing regions.
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Affiliation(s)
- Aleksandra Leszczyk
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudzia̧dzka 5, 87-100 Toruń, Poland
| | - Mihály Máté
- Strongly Correlated Systems "Lendület" Research Group, Wigner Research Center for Physics, H-1525 Budapest, Hungary.,Department of Physics of Complex Systems, Eötvös Loránd University, Pf. 32, H-1518 Budapest, Hungary
| | - Örs Legeza
- Strongly Correlated Systems "Lendület" Research Group, Wigner Research Center for Physics, H-1525 Budapest, Hungary.,Institute for Advanced Study, Technical University of Munich, 80333 Munich, Germany
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudzia̧dzka 5, 87-100 Toruń, Poland
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10
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Abstract
The pair coupled cluster doubles (pCCD) ansatz represents an inexpensive but accurate single-reference method to describe multi-reference problems. By construction, pCCD remains, however, applicable to closed-shell systems. For the first time, we present extensions to pCCD that allow us to target open-shell molecules with up to 4 unpaired electrons. Although requiring only modest computational cost, our methods approach chemical accuracy for some challenging cases, while their performance is comparable to more expensive models like DMRG or CCSD(T).
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Affiliation(s)
- Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudziądzka 5, 87-100 Toruń, Poland.
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11
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Nowak A, Legeza Ö, Boguslawski K. Orbital entanglement and correlation from pCCD-tailored coupled cluster wave functions. J Chem Phys 2021; 154:084111. [DOI: 10.1063/5.0038205] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Artur Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Torun, Poland
| | - Örs Legeza
- Strongly Correlated Systems “Lendület" Research Group, Wigner Research Center for Physics, H-1525 Budapest, Hungary
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Torun, Poland
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12
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Tecmer P, Schindler F, Leszczyk A, Boguslawski K. Mixed uranyl and neptunyl cation–cation interaction-driven clusters: structures, energetic stability, and nuclear quadrupole interactions. Phys Chem Chem Phys 2020; 22:10845-10852. [DOI: 10.1039/d0cp01068e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a quantum-chemical study of mixed CCI clusters, their structures, energetic stability, and nuclear quadrupole interactions.
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Affiliation(s)
- Paweł Tecmer
- Institute of Physics
- Faculty of Physics, Astronomy, and Informatics
- Nicolaus Copernicus University in Toruń, Grudziadzka 5
- 87-100 Torun
- Poland
| | - Frank Schindler
- Faculty of Physics
- University of Vienna
- Boltzmanngasse 5
- 1090 Vienna
- Austria
| | - Aleksandra Leszczyk
- Institute of Physics
- Faculty of Physics, Astronomy, and Informatics
- Nicolaus Copernicus University in Toruń, Grudziadzka 5
- 87-100 Torun
- Poland
| | - Katharina Boguslawski
- Institute of Physics
- Faculty of Physics, Astronomy, and Informatics
- Nicolaus Copernicus University in Toruń, Grudziadzka 5
- 87-100 Torun
- Poland
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13
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Brzęk F, Boguslawski K, Tecmer P, Żuchowski PS. Benchmarking the Accuracy of Seniority-Zero Wave Function Methods for Noncovalent Interactions. J Chem Theory Comput 2019; 15:4021-4035. [PMID: 31136703 DOI: 10.1021/acs.jctc.9b00189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filip Brzęk
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
| | - Piotr Szymon Żuchowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
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14
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Nowak A, Tecmer P, Boguslawski K. Assessing the accuracy of simplified coupled cluster methods for electronic excited states in f0 actinide compounds. Phys Chem Chem Phys 2019; 21:19039-19053. [DOI: 10.1039/c9cp03678d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We scrutinize the performance of different variants of equation of motion coupled cluster (EOM-CC) methods to predict electronic excitation energies and excited state potential energy surfaces in closed-shell actinide species.
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Affiliation(s)
- Artur Nowak
- Institute of Physics
- Faculty of Physics
- Astronomy, and Informatics
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
| | - Paweł Tecmer
- Institute of Physics
- Faculty of Physics
- Astronomy, and Informatics
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
| | - Katharina Boguslawski
- Institute of Physics
- Faculty of Physics
- Astronomy, and Informatics
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
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15
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Łachmańska A, Tecmer P, Legeza Ö, Boguslawski K. Elucidating cation–cation interactions in neptunyl dications using multi-reference ab initio theory. Phys Chem Chem Phys 2019; 21:744-759. [DOI: 10.1039/c8cp04267e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Understanding the binding mechanism in neptunyl clusters formed due to cation–cation interactions is of crucial importance in nuclear waste reprocessing and related areas of research.
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Affiliation(s)
- Aleksandra Łachmańska
- Institute of Physics
- Faculty of Physics
- Astronomy and Informatics
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
| | - Paweł Tecmer
- Institute of Physics
- Faculty of Physics
- Astronomy and Informatics
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
| | - Örs Legeza
- Strongly Correlated Systems “Lendület” Research Group
- Wigner Research Center for Physics
- H-1525 Budapest
- Hungary
| | - Katharina Boguslawski
- Institute of Physics
- Faculty of Physics
- Astronomy and Informatics
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
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16
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Boguslawski K. Targeting Doubly Excited States with Equation of Motion Coupled Cluster Theory Restricted to Double Excitations. J Chem Theory Comput 2018; 15:18-24. [DOI: 10.1021/acs.jctc.8b01053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
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17
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Boguslawski K, Réal F, Tecmer P, Duperrouzel C, Gomes ASP, Legeza Ö, Ayers PW, Vallet V. On the multi-reference nature of plutonium oxides: PuO 22+, PuO 2, PuO 3 and PuO 2(OH) 2. Phys Chem Chem Phys 2018; 19:4317-4329. [PMID: 28116368 DOI: 10.1039/c6cp05429c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Actinide-containing complexes present formidable challenges for electronic structure methods due to the large number of degenerate or quasi-degenerate electronic states arising from partially occupied 5f and 6d shells. Conventional multi-reference methods can treat active spaces that are often at the upper limit of what is required for a proper treatment of species with complex electronic structures, leaving no room for verifying their suitability. In this work we address the issue of properly defining the active spaces in such calculations, and introduce a protocol to determine optimal active spaces based on the use of the Density Matrix Renormalization Group algorithm and concepts of quantum information theory. We apply the protocol to elucidate the electronic structure and bonding mechanism of volatile plutonium oxides (PuO3 and PuO2(OH)2), species associated with nuclear safety issues for which little is known about the electronic structure and energetics. We show how, within a scalar relativistic framework, orbital-pair correlations can be used to guide the definition of optimal active spaces which provide an accurate description of static/non-dynamic electron correlation, as well as to analyse the chemical bonding beyond a simple orbital model. From this bonding analysis we are able to show that the addition of oxo- or hydroxo-groups to the plutonium dioxide species considerably changes the π-bonding mechanism with respect to the bare triatomics, resulting in bent structures with a considerable multi-reference character.
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Affiliation(s)
- Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland. and Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Florent Réal
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland.
| | - Corinne Duperrouzel
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France. and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, L8S 4M1, Canada
| | | | - Örs Legeza
- Strongly Correlated Systems "Lendület" Research Group, Wigner Research Center for Physics, H-1525 Budapest, Hungary
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, L8S 4M1, Canada
| | - Valérie Vallet
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France.
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18
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Boguslawski K. Erratum: “Targeting excited states in all-trans polyenes with electron-pair states” [J. Chem. Phys. 145, 234105 (2016)]. J Chem Phys 2017; 147:139901. [DOI: 10.1063/1.5006124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland and Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
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19
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Boguslawski K, Tecmer P. Benchmark of Dynamic Electron Correlation Models for Seniority-Zero Wave Functions and Their Application to Thermochemistry. J Chem Theory Comput 2017; 13:5966-5983. [DOI: 10.1021/acs.jctc.6b01134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katharina Boguslawski
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
- Faculty
of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Paweł Tecmer
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
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20
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Affiliation(s)
- Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland and Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
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21
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Abstract
A theoretical study of the CCIs between two bare uranyl units and their spectroscopic characterization.
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Affiliation(s)
- Paweł Tecmer
- Institute of Physics
- Faculty of Physics
- Astronomy and Informatics
- Nicolaus Copernicus University in Torun
- 87-100 Torun
| | - Sung W. Hong
- Melbourne Dental School
- University of Melbourne
- Parkville
- Australia
| | - Katharina Boguslawski
- Institute of Physics
- Faculty of Physics
- Astronomy and Informatics
- Nicolaus Copernicus University in Torun
- 87-100 Torun
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22
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Boguslawski K, Ayers PW. Linearized Coupled Cluster Correction on the Antisymmetric Product of 1-Reference Orbital Geminals. J Chem Theory Comput 2015; 11:5252-61. [DOI: 10.1021/acs.jctc.5b00776] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katharina Boguslawski
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - Paul W. Ayers
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, ON, L8S 4M1, Canada
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23
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Keller S, Boguslawski K, Janowski T, Reiher M, Pulay P. Selection of active spaces for multiconfigurational wavefunctions. J Chem Phys 2015; 142:244104. [DOI: 10.1063/1.4922352] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sebastian Keller
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Katharina Boguslawski
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Tomasz Janowski
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Pulay
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
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24
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Duperrouzel C, Tecmer P, Boguslawski K, Barcza G, Legeza Ö, Ayers PW. A quantum informational approach for dissecting chemical reactions. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Abstract
We present the first application of the variationally orbital optimized antisymmetric product of 1-reference orbital geminals (vOO-AP1roG) method to singlet-state actinide chemistry.
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Affiliation(s)
- Paweł Tecmer
- Department of Chemistry and Chemical Biology
- McMaster University
- Canada
| | | | - Paul W. Ayers
- Department of Chemistry and Chemical Biology
- McMaster University
- Canada
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26
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Stuart D, Tecmer P, Ayers PW, Boguslawski K. The effect of nitrido, azide, and nitrosyl ligands on magnetization densities and magnetic properties of iridium PNP pincer-type complexes. RSC Adv 2015. [DOI: 10.1039/c5ra17507k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The magnetisation density of different iridium PNP pincer-type complexes depends on the chosen quantum chemistry method.
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Affiliation(s)
- Daniel Stuart
- Department of Chemistry and Chemical Biology
- McMaster University
- Hamilton
- Canada
- Department of Chemistry and Biochemistry
| | - Paweł Tecmer
- Department of Chemistry and Chemical Biology
- McMaster University
- Hamilton
- Canada
- Institute of Physics, Faculty of Physics, Astronomy and Informatics
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology
- McMaster University
- Hamilton
- Canada
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics
- Nicolaus Copernicus University
- 87-100 Toruń
- Poland
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27
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Boguslawski K, Tecmer P, Bultinck P, De Baerdemacker S, Van Neck D, Ayers PW. Nonvariational Orbital Optimization Techniques for the AP1roG Wave Function. J Chem Theory Comput 2014; 10:4873-82. [DOI: 10.1021/ct500759q] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Katharina Boguslawski
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, L8S 4M1 Ontario, Canada
| | - Paweł Tecmer
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, L8S 4M1 Ontario, Canada
| | - Patrick Bultinck
- Department
of Inorganic and Physical Chemistry, Ghent University, Krijgslaan
281 (S3), 9000 Gent, East Flanders, Belgium
| | - Stijn De Baerdemacker
- Center
for Molecular Modelling, Ghent University, Technologiepark 903, 9052 Gent, East
Flanders, Belgium
| | - Dimitri Van Neck
- Center
for Molecular Modelling, Ghent University, Technologiepark 903, 9052 Gent, East
Flanders, Belgium
| | - Paul W. Ayers
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, L8S 4M1 Ontario, Canada
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28
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Boguslawski K, Tecmer P, Limacher PA, Johnson PA, Ayers PW, Bultinck P, De Baerdemacker S, Van Neck D. Projected seniority-two orbital optimization of the antisymmetric product of one-reference orbital geminal. J Chem Phys 2014; 140:214114. [PMID: 24907997 DOI: 10.1063/1.4880820] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Katharina Boguslawski
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, 1280 Main Street West, Ontario L8S 4M1, Canada
| | - Paweł Tecmer
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, 1280 Main Street West, Ontario L8S 4M1, Canada
| | - Peter A. Limacher
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, 1280 Main Street West, Ontario L8S 4M1, Canada
| | - Paul A. Johnson
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, 1280 Main Street West, Ontario L8S 4M1, Canada
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, 1280 Main Street West, Ontario L8S 4M1, Canada
| | - Patrick Bultinck
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S3), 9000 Gent, Belgium
| | - Stijn De Baerdemacker
- Center for Molecular Modelling, Ghent University, Technologiepark 903, 9052 Gent, Belgium
| | - Dimitri Van Neck
- Center for Molecular Modelling, Ghent University, Technologiepark 903, 9052 Gent, Belgium
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29
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Tecmer P, Boguslawski K, Johnson PA, Limacher PA, Chan M, Verstraelen T, Ayers PW. Assessing the Accuracy of New Geminal-Based Approaches. J Phys Chem A 2014; 118:9058-68. [PMID: 24745368 DOI: 10.1021/jp502127v] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Paweł Tecmer
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, L8S 4M1, Hamilton, Ontario, Canada
| | - Katharina Boguslawski
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, L8S 4M1, Hamilton, Ontario, Canada
| | - Paul A. Johnson
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, L8S 4M1, Hamilton, Ontario, Canada
| | - Peter A. Limacher
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, L8S 4M1, Hamilton, Ontario, Canada
| | - Matthew Chan
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, L8S 4M1, Hamilton, Ontario, Canada
| | - Toon Verstraelen
- Center
for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark
903, Zwijnaarde 9052, Belgium
| | - Paul W. Ayers
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, L8S 4M1, Hamilton, Ontario, Canada
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30
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Tecmer P, Boguslawski K, Legeza Ö, Reiher M. Unravelling the quantum-entanglement effect of noble gas coordination on the spin ground state of CUO. Phys Chem Chem Phys 2014; 16:719-27. [DOI: 10.1039/c3cp53975j] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Mottet M, Tecmer P, Boguslawski K, Legeza Ö, Reiher M. Quantum entanglement in carbon–carbon, carbon–phosphorus and silicon–silicon bonds. Phys Chem Chem Phys 2014; 16:8872-80. [DOI: 10.1039/c4cp00277f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present a quantum entanglement analysis to dissect the bond orders in polyatomic molecules.
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Affiliation(s)
- Matthieu Mottet
- ETH Zürich
- Laboratory of Physical Chemistry
- CH-8093 Zürich, Switzerland
| | - Paweł Tecmer
- ETH Zürich
- Laboratory of Physical Chemistry
- CH-8093 Zürich, Switzerland
| | | | - Örs Legeza
- Strongly Correlated Systems “Lendület” Research Group
- Wigner Research Center for Physics
- H-1525 Budapest, Hungary
| | - Markus Reiher
- ETH Zürich
- Laboratory of Physical Chemistry
- CH-8093 Zürich, Switzerland
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32
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Affiliation(s)
- Katharina Boguslawski
- ETH Zürich, Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
| | - Paweł Tecmer
- ETH Zürich, Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
| | - Gergely Barcza
- Strongly Correlated Systems ″Lendület″
Research Group, Wigner Research Center for Physics, H-1525 Budapest, Hungary
| | - Örs Legeza
- Strongly Correlated Systems ″Lendület″
Research Group, Wigner Research Center for Physics, H-1525 Budapest, Hungary
| | - Markus Reiher
- ETH Zürich, Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
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33
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Boguslawski K, Jacob CR, Reiher M. Optimized unrestricted Kohn–Sham potentials from ab initio spin densities. J Chem Phys 2013; 138:044111. [DOI: 10.1063/1.4788913] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Abstract
Electron correlation effects are essential for an accurate ab initio description of molecules. A quantitative a priori knowledge of the single- or multireference nature of electronic structures as well as of the dominant contributions to the correlation energy can facilitate the decision regarding the optimum quantum chemical method of choice. We propose concepts from quantum information theory as orbital entanglement measures that allow us to evaluate the single- and multireference character of any molecular structure in a given orbital basis set. By studying these measures we can detect possible artifacts of small active spaces.
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Affiliation(s)
- Katharina Boguslawski
- †ETH Zurich, Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland
| | - Pawel̷ Tecmer
- †ETH Zurich, Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland
| | - Örs Legeza
- ‡MTA-WRCP Strongly Correlated Systems "Lendület" Research Group, H-1525, Budapest, Hungary
| | - Markus Reiher
- †ETH Zurich, Laboratory of Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland
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35
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Abstract
We present an approach for the calculation of spin density
distributions
for molecules that require very large active spaces for a qualitatively
correct description of their electronic structure. Our approach is
based on the density-matrix renormalization group (DMRG) algorithm
to calculate the spin density matrix elements as a basic quantity
for the spatially resolved spin density distribution. The spin density
matrix elements are directly determined from the second-quantized
elementary operators optimized by the DMRG algorithm. As an analytic
convergence criterion for the spin density distribution, we employ
our recently developed sampling-reconstruction scheme [J.
Chem. Phys.2011, 134, 224101]
to build an accurate complete-active-space configuration-interaction
(CASCI) wave function from the optimized matrix product states. The
spin density matrix elements can then also be determined as an expectation
value employing the reconstructed wave function expansion. Furthermore,
the explicit reconstruction of a CASCI-type wave function provides
insight into chemically interesting features of the molecule under
study such as the distribution of α and β electrons in
terms of Slater determinants, CI coefficients, and natural orbitals.
The methodology is applied to an iron nitrosyl complex which we have
identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].
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36
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Boguslawski K, Jacob CR, Reiher M. Can DFT Accurately Predict Spin Densities? Analysis of Discrepancies in Iron Nitrosyl Complexes. J Chem Theory Comput 2011; 7:2740-52. [DOI: 10.1021/ct1006218] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Katharina Boguslawski
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Strasse 1a, 76131 Karlsruhe, Germany
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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38
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Allison JR, Boguslawski K, Fraternali F, van Gunsteren WF. A Refined, Efficient Mean Solvation Force Model that Includes the Interior Volume Contribution. J Phys Chem B 2011; 115:4547-57. [DOI: 10.1021/jp2017117] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jane R. Allison
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
| | - Katharina Boguslawski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
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39
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Bakheit MA, Schnittger L, Salih DA, Boguslawski K, Beyer D, Fadl M, Ahmed JS. Application of the recombinant Theileria annulata surface protein in an indirect ELISA for the diagnosis of tropical theileriosis. Parasitol Res 2004; 92:299-302. [PMID: 14722760 DOI: 10.1007/s00436-003-1055-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Accepted: 11/26/2003] [Indexed: 10/26/2022]
Abstract
The recombinant surface protein of Theileria annulata (TaSP) was used in the standardization and validation of an enzyme linked immunosorbent assay (ELISA) for the detection of circulating antibodies against tropical theileriosis. ELISA data were expressed as the percentage positivity (PP) of the reactivity of an internal positive control. A total of 50 sera samples from a disease-free area were used for the calculation of the cut-off value which served as a threshold between the positive and the negative sera samples. This was determined as the mean PP plus two standard deviations or the twice the mean PP of the results obtained with these negative samples. The obtained thresholds were 17.8% and 18.3%, respectively. Accordingly, the reactivity of 140 field sera samples collected at random from an area known to be endemic for tropical theileriosis in Sudan was determined as PP values which were then compared to the results obtained using the indirect fluorescence antibody test (IFAT) from the same samples. Both tests showed a high degree of correlation. The TaSP-ELISA had a sensitivity of 99.1% and specificity of 90.47% when taking the IFAT as a reference test. Our test has proved its suitability for the diagnosis of tropical theileriosis and could be used in serological surveys to map out the prevalence of the disease or to monitor vaccination efficiencies in disease-free populations.
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Affiliation(s)
- M A Bakheit
- Forschungszentrum Borstel, Parkallee 22, 23845 Borstel, Germany
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40
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Schnittger L, Hollmann C, Diemer U, Boguslawski K, Ahmed JS. Proliferation and cytokine profile of T. annulata-infected ovine, caprine, and bovine lymphoblastoid cells. Ann N Y Acad Sci 2001; 916:676-80. [PMID: 11193699 DOI: 10.1111/j.1749-6632.2000.tb05360.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
T. annulata, the causative agent of tropical theileriosis in cattle, can also infect ovine and caprine leukocytes in vitro. In vivo studies showed that this parasite causes a mild infection in both these animal species, and in sheep merozoite stage development seems to be inhibited. Since the nature of T. annulata infected caprine and ovine cells is not known, all three cell lines were karyotyped and phenotypically characterized by flow cytometry. They all express mRNA of cytokines IL-1 alpha, IL-1 beta, IL-8, and TNF-alpha, but not of IFN-gamma, IL-2, and IL-4. In contrast, IL-6 mRNA was expressed in the cattle cell line only, while mRNA of IL-10 was exclusively produced by the sheep cell line. The observed differences in cytokine mRNA expression may be responsible for the different pathogenesis of T. annulata infection in cattle and sheep.
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Affiliation(s)
- L Schnittger
- Forschungszentrum Borstel Parkallee 22, 23845 Borstel, Germany
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