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Ahmed Y, Elkhodary KI, Youssef M. Molecular assessment of drug-phospholipid interactions consequent to cancer treatment: a study of anthracycline-induced cardiotoxicity. Sci Rep 2023; 13:22155. [PMID: 38092839 PMCID: PMC10719326 DOI: 10.1038/s41598-023-48184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Cardiotoxicity limits the use of anthracyclines as potent chemotherapeutics. We employ classical molecular dynamics to explore anthracycline interactions with a realistic myocardial membrane and compare to an ideal membrane widely used in literature. The interaction of these two membranes with four anthracyclines; doxorubicin, epirubicin, daunorubicin, and idarubicin are studied. Careful analysis was conducted on three forms of each drug; pristine, primary metabolite, and cationic salt. By examining the molecular residence time near the membrane's surface, the average number of molecule/membrane hydrogen bonds, the immobilization of the molecules near the membrane, and the location of those molecules relative to the mid-plane of the membrane we found out that salt forms exhibit the highest cardiotoxic probability, followed by the metabolites and pristine forms. Additionally, all forms have more affinity to the upper layer of the realistic myocardial membrane. Meanwhile, an ideal membrane consisting of a single type of phospholipids is not capable of capturing the specific interactions of each drug form. These findings confirm that cardiotoxic mechanisms are membrane-layer and drug-form dependent.
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Affiliation(s)
- Yara Ahmed
- Nanotechnology Program, The American University in Cairo, AUC Avenue, P.O. Box 74, New Cairo, 11835, Egypt
| | - Khalil I Elkhodary
- Department of Mechanical Engineering, The American University in Cairo, AUC Avenue, P.O. Box 74, New Cairo, 11835, Egypt
| | - Mostafa Youssef
- Department of Mechanical Engineering, The American University in Cairo, AUC Avenue, P.O. Box 74, New Cairo, 11835, Egypt.
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2
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Erba A, Desmarais JK, Casassa S, Civalleri B, Donà L, Bush IJ, Searle B, Maschio L, Edith-Daga L, Cossard A, Ribaldone C, Ascrizzi E, Marana NL, Flament JP, Kirtman B. CRYSTAL23: A Program for Computational Solid State Physics and Chemistry. J Chem Theory Comput 2023; 19:6891-6932. [PMID: 36502394 PMCID: PMC10601489 DOI: 10.1021/acs.jctc.2c00958] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 12/14/2022]
Abstract
The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.
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Affiliation(s)
- Alessandro Erba
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jacques K. Desmarais
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Silvia Casassa
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Bartolomeo Civalleri
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Lorenzo Donà
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Ian J. Bush
- STFC
Rutherford Appleton Laboratory, Chilton Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Barry Searle
- SFTC
Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, United Kingdom
| | - Lorenzo Maschio
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Loredana Edith-Daga
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Alessandro Cossard
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Chiara Ribaldone
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Eleonora Ascrizzi
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Naiara L. Marana
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jean-Pierre Flament
- Université
de Lille, CNRS, UMR 8523 — PhLAM — Physique des Lasers, Atomes et Molécules, 59000 Lille, France
| | - Bernard Kirtman
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
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3
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Effect of cation configuration and solvation on the band positions of zinc ferrite (100). Photochem Photobiol Sci 2022; 21:1091-1100. [PMID: 35355230 DOI: 10.1007/s43630-022-00201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
Abstract
Zinc ferrite ZnFe[Formula: see text]O[Formula: see text] belongs to the spinel-type ferrites that have been proposed as photocatalysts for water splitting. The electronic band gap and the band edge positions are of utmost importance for the efficiency of the photocatalytic processes. We, therefore, calculated the absolute band energies of the most stable surface of ZnFe[Formula: see text]O[Formula: see text], the Zn-terminated (100) surface at self-consistent hybrid density functional theory level. The effect of Fe- and Zn-rich environments, cation exchange as antisite defects and implicit solvation on the band positions is investigated. Calculated flat band potentials of the pristine surface model ranges from [Formula: see text] to [Formula: see text] V against SHE in vacuum. For Zn-rich (Fe-rich) models this changes 0.3-0.9 (0.0-0.7) V against SHE. Fe-rich models are closest to the experimental range of reported flat band potentials. Solvent effects lower the calculated flat band potentials by up to 1.8 eV. The calculated band gaps range from 1.5 to 2.9 eV in agreement with previous theoretical work and experiment. Overall, our calculations confirm the experimentally observed low activity of ZnFe[Formula: see text]O[Formula: see text] and its dependence on preparation conditions.
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4
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Živković A, Sheehama J, Warwick MEA, Jones DR, Mitchel C, Likius D, Uahengo V, Dzade NY, Meenakshisundaram S, Dunnill CW, de Leeuw NH. Structural and electronic properties of Cu 4O 3 (paramelaconite): the role of native impurities. PURE APPL CHEM 2021. [DOI: 10.1515/pac-2021-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Hybrid density functional theory has been used to study the phase stability and formation of native point defects in Cu4O3. This intermediate copper oxide compound, also known as paramelaconite, was observed to be difficult to synthesize due to stabilization issues between mixed-valence Cu1+ and Cu2+ ions. The stability range of Cu4O3 was investigated and shown to be realized in an extremely narrow region of phase space, with Cu2O and CuO forming readily as competing impurity phases. The origin of p-type conductivity is confirmed to arise from specific intrinsic copper vacancies occurring on the 1+ site. Away from the outlined stability region, the dominant charge carriers become oxygen interstitials, impairing the conductivity by creating deep acceptor states in the electronic band gap region and driving the formation of alternative phases. This study further demonstrates the inadequacy of native defects as a source of n-type conductivity and complements existing experimental findings.
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Affiliation(s)
- Aleksandar Živković
- School of Chemistry , Cardiff University , Main Building Park Place , Cardiff CF10 3AT , UK
- Department of Earth Sciences , Utrecht University , Princetonlaan 8a , 3548CB Utrecht , The Netherlands
| | - Jacobina Sheehama
- Department of Chemistry and Biochemistry , University of Namibia , 340 Mandume Ndemufayo Avenue , Windhoek 9000 , Namibia
| | - Michael E. A. Warwick
- Energy Safety Research Institute , Swansea University , Bay Campus, Fabian Way , Swansea SA1 8EN , UK
| | - Daniel R. Jones
- Energy Safety Research Institute , Swansea University , Bay Campus, Fabian Way , Swansea SA1 8EN , UK
| | - Claire Mitchel
- School of Chemistry , Cardiff University , Main Building Park Place , Cardiff CF10 3AT , UK
| | - Daniel Likius
- Department of Chemistry and Biochemistry , University of Namibia , 340 Mandume Ndemufayo Avenue , Windhoek 9000 , Namibia
| | - Veikko Uahengo
- Department of Chemistry and Biochemistry , University of Namibia , 340 Mandume Ndemufayo Avenue , Windhoek 9000 , Namibia
| | - Nelson Y. Dzade
- School of Chemistry , Cardiff University , Main Building Park Place , Cardiff CF10 3AT , UK
| | | | - Charles W. Dunnill
- Energy Safety Research Institute , Swansea University , Bay Campus, Fabian Way , Swansea SA1 8EN , UK
| | - Nora H. de Leeuw
- School of Chemistry , Cardiff University , Main Building Park Place , Cardiff CF10 3AT , UK
- Department of Earth Sciences , Utrecht University , Princetonlaan 8a , 3548CB Utrecht , The Netherlands
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
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5
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Ulpe AC, Bauerfeind KC, Granone LI, Arimi A, Megatif L, Dillert R, Warfsmann S, Taffa DH, Wark M, Bahnemann DW, Bredow T. Photoelectrochemistry of Ferrites: Theoretical Predictions vs. Experimental Results. Z PHYS CHEM 2019. [DOI: 10.1515/zpch-2019-1449] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
This paper gives an overview about recent theoretical and experimental work on electronic and optical properties of spinel ferrites MFe2O4. These compounds have come into focus of research due to their possible application as photocatalyst material for photoelectrochemical water splitting. The theoretical background of state-of-the-art quantum-chemical approaches applied for predicting electronic and optical band gaps, absolute band positions, optical absorption spectra, dielectric functions and Raman spectra, is briefly reviewed. Recent applications of first-principles methods on magnetic and electronic properties of ferrites with M = Mg and the first row of subgroup elements Sc to Zn are presented, where it is shown that the fundamental band gap is strongly dependent on the spin state and the degree of inversion of the spinel structure. The observed variation of electronic properties may serve as an explanation for the large scattering of experimental results. The exchange of M and Fe cations has also a pronounced effect on the Raman spectra of ferrites, which is analyzed at atomic scale from first principles. Calculated optical absorption spectra of ferrites are compared to experimental spectra. The electronic nature of the first excitations and the role of oxygen vacancies are discussed. For the calculation of absolute band positions, which have a significant impact on the photoelectrochemical activity of the ferrites, models of the most stable ferrite surfaces are developed that take into account their polar nature and the interaction with the solvent. Theoretically predicted valence and conduction band edges are compared to results from electrochemical measurements. The role of cation exchange on the surface electronic structure is investigated both theoretically and experimentally.
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Affiliation(s)
- Anna C. Ulpe
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn , Beringstraße 4-6, D-53115 Bonn , Germany
| | - Katharina C.L. Bauerfeind
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn , Beringstraße 4-6, D-53115 Bonn , Germany
| | - Luis I. Granone
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover , Callinstraße 3, D-30167 Hannover , Germany
| | - Arsou Arimi
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover , Callinstraße 3, D-30167 Hannover , Germany
| | - Lena Megatif
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover , Callinstraße 3, D-30167 Hannover , Germany
| | - Ralf Dillert
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover , Callinstraße 3, D-30167 Hannover , Germany
- Laboratorium für Nano- und Quantenengineering, Gottfried Wilhelm Leibniz Universität Hannover , Schneiderberg 39, D-30167 Hannover , Germany
| | - Sven Warfsmann
- Institute of Chemistry , Chemical Technology 1, Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg , Germany
| | - Dereje H. Taffa
- Institute of Chemistry , Chemical Technology 1, Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg , Germany
| | - Michael Wark
- Institute of Chemistry , Chemical Technology 1, Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg , Germany
| | - Detlef W. Bahnemann
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover , Callinstraße 3, D-30167 Hannover , Germany
- Laboratory ’Photoactive Nanocomposite Materials’, Saint-Petersburg State University , Ulyanovskaya Str. 1 , Peterhof, Saint-Petersburg , 198504 Russia
| | - Thomas Bredow
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn , Beringstraße 4-6, D-53115 Bonn , Germany
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6
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Stahl B, Bredow T. Critical Assessment of the DFT + U Approach for the Prediction of Vanadium Dioxide Properties. J Comput Chem 2019; 41:258-265. [DOI: 10.1002/jcc.26096] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/25/2019] [Accepted: 10/10/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Berenike Stahl
- Mulliken Center for Theoretical ChemistryInstitute for Physical and Theoretical Chemistry, University of Bonn Beringstr. 4, Bonn Germany
- MPI for Chemical Energy Conversion Stiftstrasse 34‐36, Mülheim an der Ruhr Germany
| | - Thomas Bredow
- Mulliken Center for Theoretical ChemistryInstitute for Physical and Theoretical Chemistry, University of Bonn Beringstr. 4, Bonn Germany
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7
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Synthesis and Doping Strategies to Improve the Photoelectrochemical Water Oxidation Activity of BiVO4 Photoanodes. Z PHYS CHEM 2019. [DOI: 10.1515/zpch-2019-1476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
BiVO4 is one of the most investigated and most promising metal oxide based photoanode materials for photoelectrochemical (PEC) water oxidation. Although it has several advantages (suitable band gap around 2.4 eV, suitable valence-band position for water oxidation, low toxicity, high abundance), it suffers from slow charge-carrier transport properties, high surface recombination, and limited water-oxidation activity. In the present work, we review the synthesis and doping strategies that we developed in the last years to improve the PEC performance of BiVO4 photoanodes. Strategies ranging from single anion doping or cation doping to anion and cation co-doping will be presented for fluoride and molybdenum as anion and cation dopants, respectively. One major result is that co-doping allows combining the most important PEC specific benefits of each type of dopant, i.e. an increased charge-injection efficiency in case of fluoride as well as an increased charge-separation efficiency in case of molybdenum.
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8
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Desmarais JK, Flament JP, Erba A. Fundamental Role of Fock Exchange in Relativistic Density Functional Theory. J Phys Chem Lett 2019; 10:3580-3585. [PMID: 31188603 DOI: 10.1021/acs.jpclett.9b01401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We perform a formal analysis of relativistic density functional theory for the treatment of spin-orbit coupling (SOC), noncollinear magnetization (NCM), and orbital current density (OCD). We identify specific components of the spinors (namely, those mapped onto imaginary diagonal spin-blocks of the density matrix) that arise from the SOC operator and define the OCD. We show that these pieces of the spinors only enter in the bielectronic part of the potential through the exact Fock exchange (FE) operator. The lack of FE therefore leads to a correspondingly incorrect physical description of SOC, NCM, and OCD. This analysis is complemented with an illustrative example, where we show that, while in the absence of FE, the theory fails even at reproducing the expected right-hand relationship between the NCM and OCD, its inclusion provides results that match those from a reference SOC configuration-interaction calculation.
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Affiliation(s)
- Jacques K Desmarais
- Dipartimento di Chimica , Università di Torino , via Giuria 5 , 10125 Torino , Italy
- Department of Geological Sciences , University of Saskatchewan , Saskatoon , SK S7N 5E2 , Canada
- Department of Physics and Engineering Physics , University of Saskatchewan , Saskatoon , SK S7N 5E2 , Canada
| | - Jean-Pierre Flament
- Laboratoire de Physique des Lasers et des Molecules , UFR de Physique, Batiment P5, Universite de Lille, 59655 Villeneuve D'Ascq Cedex, France
| | - Alessandro Erba
- Dipartimento di Chimica , Università di Torino , via Giuria 5 , 10125 Torino , Italy
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9
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Ulpe AC, Bauerfeind KCL, Bredow T. Influence of Spin State and Cation Distribution on Stability and Electronic Properties of Ternary Transition-Metal Oxides. ACS OMEGA 2019; 4:4138-4146. [PMID: 31459622 PMCID: PMC6648862 DOI: 10.1021/acsomega.8b03254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/18/2019] [Indexed: 06/10/2023]
Abstract
This work is a systematic ab initio study of the influence of spin state and cation distribution on the stability, dielectric constant, electronic band gap, and density of states of ternary transition-metal oxides. As an example, the chemical family of spinel ferrites MFe2O4, with M = Mg, Sc-Zn is chosen. Dielectric constant and band gap are calculated for various spin states and cation configurations via dielectric-dependent self-consistent hybrid functionals and compared to available experimental data. When choosing the most stable spin state and cation configuration, the calculated electronic properties are in reasonable agreement with measured values. The nature of the excitation is investigated through projected density of states. A pronounced dependence of band gap energy and dielectric constant on the spin state and cation configuration is observed, which is a possible explanation for the large variation of the experimental results, in particular, if several states are energetically close.
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Affiliation(s)
| | | | - Thomas Bredow
- E-mail: . Phone: +49 (0)228 733839. Fax: +49 (0)228 739064
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10
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Kuklin MS, Karttunen AJ. Crystal Structure Prediction of Magnetic Transition-Metal Oxides by Using Evolutionary Algorithm and Hybrid DFT Methods. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:24949-24957. [PMID: 30416641 PMCID: PMC6221369 DOI: 10.1021/acs.jpcc.8b08238] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/10/2018] [Indexed: 06/09/2023]
Abstract
Although numerous crystal structures have been successfully predicted by using currently available computational techniques, prediction of strongly correlated systems such as transition-metal oxides remains a challenge. To overcome this problem, we have interfaced evolutionary algorithm-based USPEX method with the CRYSTAL code, enabling the use of Gaussian-type localized atomic basis sets and hybrid density functional (DFT) methods for the prediction of crystal structures. We report successful crystal structure predictions of several transition-metal oxides (NiO, CoO, α-Fe2O3, V2O3, and CuO) with correct atomic magnetic moments, spin configurations, and structures by using the USPEX method in combination with the CRYSTAL code and Perdew-Burke-Ernzerhof (PBE0) hybrid functional. Our benchmarking results demonstrate that USPEX + hybrid DFT is a suitable combination to reliably predict the magnetic structures of strongly correlated materials.
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Affiliation(s)
- Mikhail S. Kuklin
- Department of Chemistry and
Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Antti J. Karttunen
- Department of Chemistry and
Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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11
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Gerosa M. Special issue on self-interaction corrected functionals for solids and surfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:230301. [PMID: 29708501 DOI: 10.1088/1361-648x/aac150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Matteo Gerosa
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, United States of America
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12
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Dovesi R, Erba A, Orlando R, Zicovich‐Wilson CM, Civalleri B, Maschio L, Rérat M, Casassa S, Baima J, Salustro S, Kirtman B. Quantum‐mechanical condensed matter simulations with CRYSTAL. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1360] [Citation(s) in RCA: 834] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | | | | | | | | | | | - Michel Rérat
- Equipe de Chimie Physique, IPREM UMR5254Université de Pau et des Pays de l’AdourPauFrance
| | | | - Jacopo Baima
- Dipartimento di ChimicaUniversità di TorinoTorinoItaly
| | | | - Bernard Kirtman
- Department of Chemistry and BiochemistryUniversity of CaliforniaSanta Barbara, California
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