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Genoni A, Martín Pendás Á. Critical assessment of the x-ray restrained wave function approach: Advantages, drawbacks, and perspectives for density functional theory and periodic ab initio calculations. J Chem Phys 2024; 160:234108. [PMID: 38899684 DOI: 10.1063/5.0213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
The x-ray restrained wave function (XRW) method is a quantum crystallographic technique to extract wave functions compatible with experimental x-ray diffraction data. The approach looks for wave functions that minimize the energies of the investigated systems and also reproduce sets of x-ray structure factors. Given the strict relationship between x-ray structure factors and electron distributions, the strategy practically allows determining wave functions that correspond to given (usually experimental) electron densities. In this work, the capabilities of the XRW approach were further tested. The aim was to evaluate whether the XRW technique could serve as a tool for suggesting new exchange-correlation functionals for density functional theory or refining existing ones. Additionally, the ability of the method to address the influences of the crystalline environment was also assessed. The outcomes of XRW computations were thus compared to those of traditional gas-phase, embedding quantum mechanics/molecular mechanics, and fully periodic calculations. The results revealed that, irrespective of the initial conditions, the XRW computations practically yield a consensus electron density, in contrast to the currently employed density functional approximations (DFAs), which tend to give a too large range of electron distributions. This is encouraging in view of exploiting the XRW technique to develop improved functionals. Conversely, the calculations also emphasized that the XRW method is limited in its ability to effectively address the influences of the crystalline environment. This underscores the need for a periodic XRW technique, which would allow further untangling the shortcomings of DFAs from those inherent to the XRW approach.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Avenida Julian Clavería 8, 33006 Oviedo, Spain
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2
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Skogh M, Dobrautz W, Lolur P, Warren C, Biznárová J, Osman A, Tancredi G, Bylander J, Rahm M. The electron density: a fidelity witness for quantum computation. Chem Sci 2024; 15:2257-2265. [PMID: 38332826 PMCID: PMC10848700 DOI: 10.1039/d3sc05269a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/19/2023] [Indexed: 02/10/2024] Open
Abstract
There is currently no combination of quantum hardware and algorithms that can provide an advantage over conventional calculations of molecules or materials. However, if or when such a point is reached, new strategies will be needed to verify predictions made using quantum devices. We propose that the electron density, obtained through experimental or computational means, can serve as a robust benchmark for validating the accuracy of quantum computation of chemistry. An initial exploration into topological features of electron densities, facilitated by quantum computation, is presented here as a proof of concept. Additionally, we examine the effects of constraining and symmetrizing measured one-particle reduced density matrices on noise-driven errors in the electron density distribution. We emphasize the potential benefits and future need for high-quality electron densities derived from diffraction experiments for validating classically intractable quantum computations of materials.
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Affiliation(s)
- Mårten Skogh
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
- Data Science & Modelling, Pharmaceutical Science, R&D, AstraZeneca Gothenburg Sweden
| | - Werner Dobrautz
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
| | - Phalgun Lolur
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
| | - Christopher Warren
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Janka Biznárová
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Amr Osman
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Giovanna Tancredi
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Jonas Bylander
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Martin Rahm
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
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3
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Genoni A. Elucidating the nature of chemical bonds in a coordination compound through quantum crystallographic techniques. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:253-254. [PMID: 37561073 DOI: 10.1107/s2052520623006364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023]
Abstract
Investigations simultaneously involving multiple techniques of quantum crystallography could be very useful to prove the consistency of obtained results or to highlight different facets of the same scientific phenomenon or problem. Pinto et al. [Acta Cryst. (2023), B79, 282-296] exploit three different quantum crystallographic techniques (Hansen & Coppens multipole model refinement, QTAIM analysis of the electron density, and Hirshfeld atom refinement) to characterize the nature of chemical bonds and of intra/intermolecular interactions in an organometallic compound.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57070, France
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4
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Wieduwilt EK, Boto RA, Macetti G, Laplaza R, Contreras-García J, Genoni A. Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J Chem Theory Comput 2023; 19:1063-1079. [PMID: 36656682 DOI: 10.1021/acs.jctc.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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5
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Landeros-Rivera B, Ramírez-Palma D, Cortés-Guzmán F, Dominiak PM, Contreras-García J. How do density functionals affect the Hirshfeld atom refinement? Phys Chem Chem Phys 2023; 25:12702-12711. [PMID: 36644944 DOI: 10.1039/d2cp04098k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this work, the effect of mixing different amounts of Hartree-Fock (HF) exchange with hybrid density functionals applied to the Hirshfeld atom refinement (HAR) of urea and oxalic acid dihydrate is explored. Together, the influence of using different basis sets, methods (including MP2 and HF) and cluster sizes (to model bulk effects) is studied. The results show that changing the amount of HF exchange, no matter the level of theory, has an impact almost exclusively on the H atom refinement parameters. Contrary to pure quantum mechanical calculations where good geometries are obtained with intermediate HF exchange mixtures, in the HAR the best match with neutron diffraction reference values is not necessarily found for these admixtures. While the non-hydrogen covalent bond lengths are insensitive to the combination of method or basis set employed, the X-H bond lengths always increase proportionally to the HF exchange for the analysed systems. This outcome is opposite to what is normally observed from geometry optimisations, i.e., shorter bonds are obtained with greater HF exchange. Additionally, the thermal ellipsoids tend to shrink with larger HF exchange, especially for the H atoms involved in strong hydrogen bonding. Thus, it may be the case that the development of density functionals or basis sets suitable for quantum crystallography should take a different path than those fitted for quantum chemistry calculations.
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Affiliation(s)
| | - David Ramírez-Palma
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV), Avenida IPN 2508, Col. San Pedro Zacatenco, Ciudad de México, 07360, Mexico
| | - Fernando Cortés-Guzmán
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México, 04510, Mexico
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Poland
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6
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Macetti G, Genoni A. Introduction of a weighting scheme for the X-ray restrained wavefunction approach: advantages and drawbacks. Acta Crystallogr A Found Adv 2023; 79:25-40. [PMID: 36601761 DOI: 10.1107/s2053273322010221] [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: 07/04/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022] Open
Abstract
In a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136-146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λJ for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
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7
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Genoni A. On the termination of the X-ray constrained wavefunction procedure: reformulation of the method for an unequivocal determination of λ. Acta Crystallogr A Found Adv 2022; 78:302-308. [DOI: 10.1107/s2053273322003746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/05/2022] [Indexed: 11/10/2022] Open
Abstract
The X-ray constrained/restrained wavefunction (XCW/XRW) approach of quantum crystallography is revisited by introducing the stationary condition of the Jayatilaka functional with respect to the Lagrange multiplier λ. The theoretical derivation has unequivocally shown that the right value of λ is a maximum stationary point of the functional to optimize, thus enabling the solution of the longstanding problem of establishing the point at which to halt the XCW/XRW procedure. Based on the new finding, a reformulation of the X-ray constrained wavefunction algorithm is proposed and its implementation is envisaged. In addition to relying on more solid mathematical grounds, the new variant of the method will be intrinsically more physically meaningful, allowing a straightforward evaluation of the highest level of confidence with which the experimental X-ray diffraction data can be possibly reproduced.
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Abstract
Aromaticity, a very important term in organic chemistry, has never been defined unambiguously. Various ways to describe it come from different phenomena that have been experimentally observed. The most important examples related to some theoretical concepts are presented here.
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Bürgi HB. Crystal structures. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:283-289. [PMID: 35695099 DOI: 10.1107/s205252062200292x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
A personal view is offered on various solved and open problems related to crystal structures: the present state of reconstructing the crystal electron density from X-ray diffraction data; characterization of atomic and molecular motion from a combination of atomic displacement parameters and quantum chemical calculations; Bragg diffraction and diffuse scattering: twins, but different; models of real (as opposed to ideal) crystal structures from diffuse scattering; exploiting unexplored neighbourhoods of crystallography to mathematics, physics and chemistry.
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Affiliation(s)
- Hans Beat Bürgi
- Department of Chemistry, Biochemistry and Pharmacy, University of Berne, Freiestrasse 12, Bern, CH-3012, Switzerland
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10
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Davidson ML, Grabowsky S, Jayatilaka D. X-ray constrained wavefunctions based on Hirshfeld atoms. I. Method and review. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:312-332. [PMID: 35695105 DOI: 10.1107/s2052520622004097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
The X-ray constrained wavefunction (XCW) procedure for obtaining an experimentally reconstructed wavefunction from X-ray diffraction data is reviewed. The two-center probability distribution model used to perform nuclear-position averaging in the original paper [Grimwood & Jayatilaka (2001). Acta Cryst. A57, 87-100] is carefully distinguished from the newer one-center probability distribution model. In the one-center model, Hirshfeld atoms are used, and the Hirshfeld atom based X-ray constrained wavefunction (HA-XCW) procedure is described for the first time, as well as its efficient implementation. In this context, the definition of the related X-ray wavefunction refinement (XWR) method is refined. The key halting problem for the XCW method - the procedure by which one determines when overfitting has occurred - is named and work on it reviewed.
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Affiliation(s)
- Max L Davidson
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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11
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Ziemniak M, Pawlędzio S, Zawadzka-Kaźmierczuk A, Dominiak PM, Trzybiński D, Koźmiński W, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B. X-ray wavefunction refinement and comprehensive structural studies on bromo-substituted analogues of 2-deoxy-d-glucose in solid state and solution. RSC Adv 2022; 12:8345-8360. [PMID: 35424802 PMCID: PMC8985090 DOI: 10.1039/d1ra08312k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/01/2022] [Accepted: 03/05/2022] [Indexed: 11/21/2022] Open
Abstract
The structural studies on two bromo-substituted derivatives of 2-deoxy-d-glucose (2-DG), namely 2-deoxy-2-bromo-d-glucose (2-BG) and 2-deoxy-2-bromo-d-mannose (2-BM) are described. 2-DG itself is an inhibitor of hexokinase, the first enzyme in the glycolysis process, playing a vital role in both cancer cell metabolism and viral replication in host cells. Because of that, 2-DG derivatives are considered as potential anti-cancer and anti-viral drugs. An X-ray quantum crystallography approach allowed us to obtain more accurate positions of hydrogen atoms by applying Hirshfeld atom refinement, providing a better description of hydrogen bonding even in the case of data from routine X-ray experiments. Obtained structures showed that the introduction of bromine at the C2 position in the pyranose ring has a minor influence on its conformation but still, it has a noticeable effect on the crystal structure. Bromine imposes the formation of a layered supramolecular landscape containing hydrogen bonds, which involves the bromine atom. Periodic DFT calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings and highlighted energetic changes upon bromine substitution. Based on molecular wavefunction from the refinement, we calculated the electrostatic potential, Laplacian, and ELI-D, and applied them to charge-density studies, which confirmed the geometry of hydrogen bonding and involvement of the bromine atom with these intermolecular interactions. NMR studies in the solution show that both compounds do not display significant differences in their anomeric equilibria compared to 2-DG, and the pyranose ring puckering is similar in both aqueous and solid state.
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Affiliation(s)
- Marcin Ziemniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Anna Zawadzka-Kaźmierczuk
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Rafał Zieliński
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Izabela Fokt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Waldemar Priebe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology Kozielska 4 01-163 Warsaw Poland
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12
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Jiang XM, Deng S, Whangbo MH, Guo GC. Material research from the viewpoint of functional motifs. Natl Sci Rev 2022; 9:nwac017. [PMID: 35983369 PMCID: PMC9379984 DOI: 10.1093/nsr/nwac017] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
As early as 2001, the need for the ‘functional motif theory’ was pointed out to assist the rational design of functional materials. The properties of materials are determined by their functional motifs and by how they are arranged in the materials. Uncovering the functional motifs and their arrangements is crucial in understanding the properties of materials and rationally designing new materials of desired properties. The functional motifs of materials are the critical microstructural units (e.g. constituent components and building blocks) that play a decisive role in generating certain material functions, and could not be replaced with other structural units without losing or significantly suppressing the relevant functions. The role of functional motifs and their arrangements in materials with representative examples was presented. These examples could be classified into six types of material microscopic structures on a length scale smaller than ∼10 nm with maximum subatomic resolution, i.e. the crystal, magnetic, aperiodic, defect, local, and electronic structures. The method of functional motif analysis could be employed in the function-oriented design of materials, as elucidated by taking infrared nonlinear optical materials as an example. Machine learning is more efficient in predicting material properties and screening materials with high efficiency than high-throughput experimentation and high-throughput calculations. In extracting the functional motifs and finding their quantitative relationships, developing sufficiently reliable databases for material structures and properties is imperative.
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Affiliation(s)
- Xiao-Ming Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
| | - Shuiquan Deng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
| | - Myung-Hwan Whangbo
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
- Department of Chemistry, North Carolina State University, Raleigh, NC27695-8204, USA
| | - Guo-Cong Guo
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
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13
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Landeros-Rivera B, Hernández-Trujillo J. Control of Molecular Conformation and Crystal Packing of Biphenyl Derivatives. Chempluschem 2022; 87:e202100492. [PMID: 34984848 DOI: 10.1002/cplu.202100492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/15/2021] [Indexed: 11/10/2022]
Abstract
This Review presents a discussion of the conformation of biphenyl derivatives in different chemical environments. The interplay between aromatic stabilization and steric repulsion, normally considered to explain the conformation of the molecule, is contrasted with the interpretation provided by models not based on molecular orbitals. The electronic control of conformation by means of appropriate hydrogen substitution is discussed by examples taken from chemistry and molecular electronics. Supramolecular synthons involving biphenyl are critically analyzed in terms of the molecular conformation, crystal packing and intermolecular forces. Some directions for future research on the control of the conformation of biphenyls are also presented.
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Affiliation(s)
- Bruno Landeros-Rivera
- Sorbonne Université & CNRS, Laboratoire de Chimie Théorique, UMR CNRS 7616, 4 Place Jussieu, 75005, Paris, France
| | - Jesús Hernández-Trujillo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Escolar Ciudad Universitaria, Mexico City, 04510, Mexico
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14
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Wenger JS, Wang X, Johnstone TC. H-Atom Assignment and Sb-O Bonding of [Mes 3SbOH][O 3SPh] Confirmed by Neutron Diffraction, Multipole Modeling, and Hirshfeld Atom Refinement. Inorg Chem 2021; 60:16048-16052. [PMID: 34661394 DOI: 10.1021/acs.inorgchem.1c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neutron wavelength-resolved Laue diffraction experiments permit accurate refinement of the H-atom positions and anisotropic displacement parameters of [Mes3SbOH][O3SPh]. A multipole-based charge density refinement and a topological analysis of the refined electron density were also performed. Hirshfeld atom refinement (HAR) recovers the neutron-determined H-atom parameters, and the quantum-mechanical electron density used in HAR recovers the electron density topology from the refined multipole model. These results confirm that [Mes3SbOH][O3SPh] does indeed feature a hydroxystibonium cation with a nominal Sb-O single bond and not a stibine oxide with an Sb=O/Sb+-O- bond.
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Affiliation(s)
- John S Wenger
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Xiaoping Wang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy C Johnstone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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15
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Midgley L, Bourhis LJ, Dolomanov OV, Grabowsky S, Kleemiss F, Puschmann H, Peyerimhoff N. Vanishing of the atomic form factor derivatives in non-spherical structural refinement - a key approximation scrutinized in the case of Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:519-533. [PMID: 34726630 DOI: 10.1107/s2053273321009086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/02/2021] [Indexed: 11/10/2022]
Abstract
When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.
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Affiliation(s)
- Laura Midgley
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, United Kingdom
| | - Luc J Bourhis
- Bruker, 4 Allée Lorentz, Champs-sur-Marne, 77447 Marne-la-Vallée cedex 2, France
| | - Oleg V Dolomanov
- OlexSys Ltd, Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florian Kleemiss
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Horst Puschmann
- OlexSys Ltd, Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Norbert Peyerimhoff
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, United Kingdom
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16
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Macetti G, Genoni A. Initial Maximum Overlap Method for Large Systems by the Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Technique. J Chem Theory Comput 2021; 17:4169-4182. [PMID: 34196174 DOI: 10.1021/acs.jctc.1c00388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum chemistry offers a large variety of methods to treat excited states. Many of them are based on a multireference wave function ansatz and are therefore characterized by an intrinsic complexity and high computational costs. To overcome these drawbacks and also some limitations of simpler single-reference approaches (e.g., configuration interaction singles and time-dependent density functional theory), the single-determinant Δself-consistent field-initial maximum overlap method (ΔSCF-IMOM) has been proposed. This strategy substitutes the aufbau principle with a criterion that occupies molecular orbitals at successive SCF iterations on the basis of their maximum overlap with a proper set of guess orbitals for the target excited state. In this way, it prevents the SCF process to collapse to the ground state wave function and provides excited state single Slater determinant solutions to the SCF equations. Here, we propose to extend the applicability of the IMOM to the treatment of localized excited states of large systems. To accomplish this task, we coupled it with the QM/ELMO (quantum mechanics/extremely localized molecular orbitals) strategy, a quantum mechanical embedding method in which the most chemically relevant part of the system is treated with traditional quantum chemical approaches, while the rest is described by extremely localized molecular orbitals transferred from recently constructed libraries or proper model molecules. After presenting the theoretical foundations of the new IMOM/ELMO technique, in this paper, we will show and discuss the results of preliminary test calculations carried out on both model systems (i.e., decanoic acid, decene, decapentaene, and solvated acrolein) and a system of biological interest (flavin mononucleotide in the flavodoxin protein). We observed that, for localized excited states, the new IMOM/ELMO method provides reliable results, and it reproduces the outcomes of fully IMOM calculations within the chemical accuracy threshold (i.e., 0.043 eV) by including only a limited number of atoms in the QM region. Furthermore, the first application of our embedding technique to a larger biological system gave completely plausible results in line with those obtained through more traditional quantum mechanical methods, thus opening the possibility of using the new approach in future investigations of photobiology problems.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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17
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Milašinović V, Molčanov K, Krawczuk A, Bogdanov NE, Zakharov BA, Boldyreva EV, Jelsch C, Kojić-Prodić B. Charge density studies of multicentre two-electron bonding of an anion radical at non-ambient temperature and pressure. IUCRJ 2021; 8:644-654. [PMID: 34258012 PMCID: PMC8256703 DOI: 10.1107/s2052252521005273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The variation of charge density of two-electron multicentre bonding (pancake bonding) between semi-quinone radicals with pressure and temperature was studied on a salt of 5,6-di-chloro-2,3-di-cyano-semi-quinone radical anion (DDQ) with 4-cyano-N-methyl-pyridinium cation (4-CN) using the Transferable Aspheric Atom Model (TAAM) refinement. The pancake-bonded radical dimers are stacked by non-bonding π-interactions. With rising pressure, the covalent character of interactions between radicals increases, and above 2.55 GPa, the electron density indicates multicentric covalent interactions throughout the stack. The experimental charge densities were verified and corroborated by periodic DFT computations. The TAAM approach has been tested and validated for atomic resolution data measured at ambient pressure; this work shows this approach can also be applied to diffraction data obtained at pressures up to several gigapascals.
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Affiliation(s)
- Valentina Milašinović
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Krešimir Molčanov
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Anna Krawczuk
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, Göttingen 37077, Germany
- Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, Krakow 30-387, Poland
| | - Nikita E. Bogdanov
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Boris A. Zakharov
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Elena V. Boldyreva
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Christian Jelsch
- CRM2, CNRS, UMR 7036, Université de Lorraine, BP 70239 Nancy, France
| | - Biserka Kojić-Prodić
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
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18
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Macetti G, Genoni A. Three-Layer Multiscale Approach Based on Extremely Localized Molecular Orbitals to Investigate Enzyme Reactions. J Phys Chem A 2021; 125:6013-6027. [PMID: 34190569 DOI: 10.1021/acs.jpca.1c05040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) calculations are widely used embedding techniques to computationally investigate enzyme reactions. In most QM/MM computations, the quantum mechanical region is treated through density functional theory (DFT), which offers the best compromise between chemical accuracy and computational cost. Nevertheless, to obtain more accurate results, one should resort to wave function-based methods, which however lead to a much larger computational cost already for relatively small QM subsystems. To overcome this drawback, we propose the coupling of our QM/ELMO (quantum mechanics/extremely localized molecular orbital) approach with molecular mechanics, thus introducing the three-layer QM/ELMO/MM technique. The QM/ELMO strategy is an embedding method in which the chemically relevant part of the system is treated at the quantum mechanical level, while the rest is described through frozen ELMOs. Since the QM/ELMO method reproduces results of fully QM computations within chemical accuracy and with a much lower computational effort, it can be considered a suitable strategy to extend the range of applicability and accuracy of the QM/MM scheme. In this paper, other than briefly presenting the theoretical bases of the QM/ELMO/MM technique, we will also discuss its validation on the well-tested deprotonation of acetyl coenzyme A by aspartate in citrate synthase.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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19
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Malaspina LA, Genoni A, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Grabowsky S. The advanced treatment of hydrogen bonding in quantum crystallography. J Appl Crystallogr 2021; 54:718-729. [PMID: 34188611 PMCID: PMC8202034 DOI: 10.1107/s1600576721001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/31/2021] [Indexed: 11/16/2022] Open
Abstract
Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.
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Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Dylan Jayatilaka
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Michael J. Turner
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute/Diffraction and Scattering Division, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eiji Nishibori
- Department of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
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Macetti G, Wieduwilt EK, Genoni A. QM/ELMO: A Multi-Purpose Fully Quantum Mechanical Embedding Scheme Based on Extremely Localized Molecular Orbitals. J Phys Chem A 2021; 125:2709-2726. [DOI: 10.1021/acs.jpca.0c11450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Erna K. Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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21
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Wieduwilt EK, Macetti G, Genoni A. Climbing Jacob's Ladder of Structural Refinement: Introduction of a Localized Molecular Orbital-Based Embedding for Accurate X-ray Determinations of Hydrogen Atom Positions. J Phys Chem Lett 2021; 12:463-471. [PMID: 33369421 DOI: 10.1021/acs.jpclett.0c03421] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The positions of hydrogen atoms in molecules are fundamental in many aspects of chemistry. Nevertheless, most molecular structures are obtained from refinements of X-ray data exploiting the independent atom model (IAM), which uses spherical atomic densities and provides bond lengths involving hydrogen atoms that are too short compared to the neutron reference values. To overcome the IAM shortcomings, the wave function-based Hirshfeld atom refinement (HAR) method has been recently proposed, emerging as a promising strategy able to give element-hydrogen bond distances in excellent agreement with the neutron ones in terms of accuracy and precision. In this Letter, we propose a significant improvement of HAR based on the idea of describing the crystal environment explicitly in the underlying wave function calculation through a quantum mechanical embedding strategy that exploits extremely localized molecular orbitals. Test-bed refinements on a crystal structure characterized by strong intermolecular interactions are also discussed.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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22
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Wieduwilt EK, Boisson JC, Terraneo G, Hénon E, Genoni A. A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. J Chem Inf Model 2021; 61:795-809. [PMID: 33444021 DOI: 10.1021/acs.jcim.0c01188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Jean-Charles Boisson
- CReSTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milan I-20131, Italy
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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23
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Quantum mechanics/extremely localized molecular orbital embedding technique: Theoretical foundations and further validation. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Macetti G, Genoni A. Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Strategy for Excited States: Coupling to Time-Dependent Density Functional Theory and Equation-of-Motion Coupled Cluster. J Chem Theory Comput 2020; 16:7490-7506. [PMID: 33241930 DOI: 10.1021/acs.jctc.0c00956] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The QM/ELMO (quantum mechanics/extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under examination is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited states, and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT) and Equation-of-Motion Coupled Cluster with single and double substitutions (EOM-CCSD). The proposed TDDFT/ELMO and EOM-CCSD/ELMO strategies underwent a series of preliminary tests that were already considered for the validation of other embedding methods for excited states. The obtained results showed that the novel techniques allow the accurate description of localized excitations in large systems by only including a relatively small number of atoms in the region treated at fully quantum chemical level. Furthermore, for TDDFT/ELMO, it was also observed that (i) the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations, even using functionals that do not take into account long-range corrections, and (ii) the novel approach can be also successfully exploited to investigate local electronic transitions in quite large systems (e.g., reduced model of the Green Fluorescent Protein), and the accuracy of the results can be improved by including a sufficient number of chemically crucial fragments/residues in the quantum mechanical region. Finally, concerning EOM-CCSD/ELMO, it was also seen that, despite the quite crude approximation of an embedding potential given by frozen extremely localized molecular orbitals, the new strategy is able to satisfactorily account for the effects of the environment. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical strategies for excited states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multireferences methods.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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