1
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Budny-Godlewski K, Piekarski DG, Justyniak I, Leszczyński MK, Nawrocki J, Kubas A, Lewiński J. Uncovering Factors Controlling Reactivity of Metal-TEMPO Reaction Systems in the Solid State and Solution. Chemistry 2024; 30:e202401968. [PMID: 38801170 DOI: 10.1002/chem.202401968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
Nitroxides find application in various areas of chemistry, and a more in-depth understanding of factors controlling their reactivity with metal complexes is warranted to promote further developments. Here, we report on the effect of the metal centre Lewis acidity on both the distribution of the O- and N-centered spin density in 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO) and turning TEMPO from the O- to N-radical mode scavenger in metal-TEMPO systems. We use Et(Cl)Zn/TEMPO model reaction system with tuneable reactivity in the solid state and solution. Among various products, a unique Lewis acid-base adduct of Cl2Zn with the N-ethylated TEMPO was isolated and structurally characterised, and the so-called solid-state 'slow chemistry' reaction led to a higher yield of the N-alkylated product. The revealed structure-activity/selectivity correlations are exceptional yet are entirely rationalised by the mechanistic underpinning supported by theoretical calculations of studied model systems. This work lays a foundation and mechanistic blueprint for future metal/nitroxide systems exploration.
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Affiliation(s)
- Krzysztof Budny-Godlewski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Dariusz G Piekarski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Iwona Justyniak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Michał K Leszczyński
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Jan Nawrocki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Janusz Lewiński
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
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2
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Voss J. Machine learning for accuracy in density functional approximations. J Comput Chem 2024; 45:1829-1845. [PMID: 38668453 DOI: 10.1002/jcc.27366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/16/2024] [Accepted: 03/25/2024] [Indexed: 07/21/2024]
Abstract
Machine learning techniques have found their way into computational chemistry as indispensable tools to accelerate atomistic simulations and materials design. In addition, machine learning approaches hold the potential to boost the predictive power of computationally efficient electronic structure methods, such as density functional theory, to chemical accuracy and to correct for fundamental errors in density functional approaches. Here, recent progress in applying machine learning to improve the accuracy of density functional and related approximations is reviewed. Promises and challenges in devising machine learning models transferable between different chemistries and materials classes are discussed with the help of examples applying promising models to systems far outside their training sets.
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Affiliation(s)
- Johannes Voss
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California, USA
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3
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Achevski B, Pejov L. Molecular Hydrogen Acts as a Hydrogen Bond Proton Acceptor: From Protonated Betaine Tagging to the Weakest Hydrogen Bond. J Phys Chem A 2024; 128:3968-3981. [PMID: 38720275 DOI: 10.1021/acs.jpca.4c01331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
In an attempt to gain further insights into the intermolecular interactions implied by Rizzo's group's cautionary tale related to molecular tagging in infrared multiple photon dissociation (IRMPD) spectroscopy with molecular messengers [Masson, A. . J. Chem. Phys. 2015, 143, 104313], in the present study, we provide an in-depth analysis of the noncovalent interaction between the molecular hydrogen and protonated betaine molecule in the gas phase. We aim to shed some new light on the fundamental issues concerning the wide diapason of hydrogen-bonding-type intermolecular interactions, with a wide variety of proton acceptors. We demonstrate that in the course of tagging the protonated betaine with molecular hydrogen from the OH group side, it is the σ bond of molecular hydrogen that plays the role of hydrogen-bonding proton acceptor. The tagging thus induces a small yet significant red shift of the protonated betaine O-H stretching mode. We investigate the performance of a wide range of density functional theory (DFT) functionals for the calculation of anharmonic vibrational frequency shifts of the studied system, which are essential for the correct interpretation of the experimental IRMPD data. For an accurate prediction of the OH stretching frequency shifts, specifically designed functionals such as Handy's group HCTH/407 should be applied. The empirical dispersion correction enhances the systematic overestimation of the anharmonic frequency shift, characteristic of the most widely used DFT functionals. Combining the full-wave function approach with the charge field perturbation and natural bond orbital (NBO) deletion analyses, we demonstrate that the frequency shift in the OH-tagged structure is governed by the σHH → σ*OH intermolecular charge transfer. This interaction stabilizes the OH-tagged dimer as well, in contrast to the dipole-quadrupole electrostatic interaction energy term. Topological analysis of the electron density reveals the presence of an intermolecular bond critical point with a positive value of the density Laplacian very close to the lower limit for hydrogen bonds. NCI analyses demonstrate that the OH···H2 interaction is weaker than the intramolecular CH···O one within the protonated betaine molecule, with the through of reduced density gradient appearing at less negative sign(λ2)·ρ values. Analyzing the O-H stretching vibrational potential with the second-generation absolutely localized molecular orbitals energy decomposition analysis (ALMO-EDA 2) revealed that in the case of betaineH(+) tagged from the OH group side, the permanent electrostatics (ΔEelec), polarization (ΔEpol), and charge-transfer (ΔEct) contributions to the total intermolecular interaction energy contribute favorably to the weak hydrogen bond formation and to the red shift of the fundamental O-H stretching frequency, the ΔEct contribution being the most significant in the last context. The Pauli repulsion term, on the other hand, favors an O-H stretching frequency blue shift as a consequence of the vibrational confinement effects.
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Affiliation(s)
- Blagoj Achevski
- Institute of Chemistry, Faculty of Natural Sciences and Mathematics, SS Cyril and Methodius University, PO Box 162, 1000 Skopje, Republic of North Macedonia
- Faculty of Pharmacy, SS Cyril and Methodius University, 1000 Skopje, Republic of North Macedonia
| | - Ljupcho Pejov
- Institute of Chemistry, Faculty of Natural Sciences and Mathematics, SS Cyril and Methodius University, PO Box 162, 1000 Skopje, Republic of North Macedonia
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Mailbox 8600, 4036 Stavanger, Norway
- The Polytechnic School, Ira A. Fulton Schools of Engineering, Arizona State University, 6049 S Backus Mall Mesa, Arizona 85212, United States
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4
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Avcı D, Cömert HE, Sönmez F, Dege N, Tamer Ö, Atalay Y. Comparative assessment of structure-property relationships of new Cu(II) complex in selected density functionals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123489. [PMID: 37844450 DOI: 10.1016/j.saa.2023.123489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/14/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023]
Abstract
In order to evaluate the structure-property relationships of Cu(II) complex by using DFT methods, the structure of the newly synthesized Cu(II) complex, [Cu(6-Brpic)2(bpy)], was investigated by XRD, FTIR, UV-Vis, and fluorescence spectroscopic methods. In addition, Hirshfeld surface and NBO analyses were fulfilled to identify possible interactions in the intermolecular and coordination environment. The five different DFT methods (HCTH, M06L, TPSSTPSS, B3LYP, and CAM-B3LYP levels), having four different functionalities (the GGA, meta-GGA, hybrid-GGA, and range-separated hybrid), were carried out so as to investigate the structure-property relationship, considering the geometric parameters (bond lengths and angles), vibrational frequencies, electronic absorption wavelengths, electronic transitions, and linear and nonlinear optical parameters. The R2 for structural and vibrational parameters, as well as MPD%, MAD, an optimal scaling factor (λ) and overall root mean square (RMS) deviation, were considered only at vibration frequencies. While it was determined that M06-L and TPSSTPSS levels gave the best results for the bond lengths and angles of the Cu(II) complex, the best results for vibrational frequencies were obtained in the HCTH method along with these methods. In NLO parameters, the static and dynamic first-order hyperpolarizability (<β(0;0,0)> and β(-ω;ω,0)/<β(-2ω;ω,ω)>) values, the largest values were obtained in the HCTH method (38.817 × 10-30 and 437.86 × 10-30/201.55 × 10-30 esu), whereas the smallest values were found to be in the CAM-B3LYP/TPSSTPSS levels (6.118 × 10-30 esu, 8.270 × 10-30/11.730 × 10-30 esu). By regarding the static γ (<γ(0;0,0,0)>) and dynamic (<γ(-ω;ω,0,0)> parameters, the largest values were calculated in the M06L (232.101 × 10-36) and HCTH (1711.52 × 10-36) methods and the smallest values were obtained in the CAM-B3LYP (43.281 × 10-36 and 60.844 × 10-36) method. In fact, it is obviously seen that the β and γ values obtained by the aforementioned DFT levels are many times higher than that of the standard molecule of urea. These results indicate that the Cu(II) complex may be used as a potential NLO material to evolve optoelectronic devices.
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Affiliation(s)
- Davut Avcı
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey.
| | - Hatice Esra Cömert
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey
| | - Fatih Sönmez
- Sakarya University of Applied Sciences, Pamukova Vocational High School, 54055 Sakarya, Turkey
| | - Necmi Dege
- Ondokuz Mayıs University, Faculty of Science, Department of Physics, 55139 Samsun, Turkey
| | - Ömer Tamer
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey
| | - Yusuf Atalay
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey
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5
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Franco LR, Marchiori C, Araujo CM. Unveiling the impact of exchange-correlation functionals on the description of key electronic properties of non-fullerene acceptors in organic photovoltaics. J Chem Phys 2023; 159:204110. [PMID: 38018752 DOI: 10.1063/5.0163180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Non-fullerene electron acceptors have emerged as promising alternatives to traditional electron-acceptors in the active layers of organic photovoltaics. This is due to their tunable energy levels, optical response in the visible light spectrum, high electron mobility, and photochemical stability. In this study, the electronic properties of two representative non-fullerene acceptors, ITIC and Y5, have been calculated within the framework of density functional theory using a range of hybrid and non-hybrid density functionals. Screened range-separated hybrid (SRSH) approaches were also tested. The results are analyzed in light of the previously reported experimental outcomes. Specifically, we have calculated the oxidation and reduction potentials, fundamental and optical gaps, the highest occupied molecular orbital and lowest unoccupied molecular orbital energies, and exciton binding energies. Additionally, we have investigated the effects of the medium dielectric constant on these properties employing a universal implicit solvent model. It was found that hybrid functionals generally perform poorly in predicting oxidation potentials, while non-hybrid functionals tend to overestimate reduction potentials. The inclusion of a large Hartree-Fock contribution to the global or long range was identified as the source of inaccuracy for many hybrid functionals in predicting both redox potentials and the fundamental and optical gaps. Corroborating with the available literature, ∼50% of all tested functionals predicted very small exciton binding energies, within the range of ±0.1 eV, that become even smaller by increasing the dielectric constant of the material. Finally, the OHSE2PBE and tHCTHhyb functionals and the optimal tuning SRSH approach emerged as the best-performing methods, with good accuracy in the description of the electronic properties of interest.
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Affiliation(s)
- Leandro R Franco
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden
| | - Cleber Marchiori
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden
| | - C Moyses Araujo
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden
- Materials Theory Division, Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
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6
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Le PQ, Nguyen NQ, Nguyen TT. DFT approach towards accurate prediction of 1H/ 13C NMR chemical shifts for dipterocarpol oxime. RSC Adv 2023; 13:31811-31819. [PMID: 37908664 PMCID: PMC10613955 DOI: 10.1039/d3ra04688e] [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: 07/13/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
A computational NMR approach for accurate predicting the 1H/13C chemical shifts of triterpenoid oximes featuring the screening of 144 DFT methods was demonstrated. Efficiently synthesized dipterocarpol oxime was employed as a model compound. The six highest accurate methods from the screening generated root-mean-square-error (RMSE) values in the range of 0.84 ppm (0.55%) to 1.14 ppm (0.75%) for calculated 13C shifts. For 1H results, simple, economical 6-31G basis set unexpectedly outperformed other more expensive basic sets; and the couple of it with selected functionals provided high accuracy shifts (0.0617 ppm (1.49%) ≤ RMSE ≤ 0.0870 ppm (2.04%)). These computational results strongly supported the proton and carbon assignments of the oxime including the difficult ones of diastereotopic methyl groups, the methyl groups attached to an internal olefin, and diastereotopic α-protons.
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Affiliation(s)
- Phong Q Le
- School of Biotechnology, International University, VNU HCM Quarter 6, Linh Trung Ward, Thu Duc City Ho Chi Minh City Vietnam
| | - Nhu Q Nguyen
- School of Biotechnology, International University, VNU HCM Quarter 6, Linh Trung Ward, Thu Duc City Ho Chi Minh City Vietnam
| | - Thien T Nguyen
- Faculty of Pharmacy, College of Medicine and Pharmacy, Duy Tan University Da Nang 550000 Vietnam
- Institute of Research and Development, Duy Tan University Da Nang 550000 Vietnam
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7
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Lehtola S, Marques MAL. Reproducibility of density functional approximations: How new functionals should be reported. J Chem Phys 2023; 159:114116. [PMID: 37725491 DOI: 10.1063/5.0167763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
Density functional theory is the workhorse of chemistry and materials science, and novel density functional approximations are published every year. To become available in program packages, the novel density functional approximations (DFAs) need to be (re)implemented. However, according to our experience as developers of Libxc [Lehtola et al., SoftwareX 7, 1 (2018)], a constant problem in this task is verification due to the lack of reliable reference data. As we discuss in this work, this lack has led to several non-equivalent implementations of functionals such as Becke-Perdew 1986, Perdew-Wang 1991, Perdew-Burke-Ernzerhof, and Becke's three-parameter hybrid functional with Lee-Yang-Parr correlation across various program packages, yielding different total energies. Through careful verification, we have also found many issues with incorrect functional forms in recent DFAs. The goal of this work is to ensure the reproducibility of DFAs. DFAs must be verifiable in order to prevent the reappearance of the above-mentioned errors and incompatibilities. A common framework for verification and testing is, therefore, needed. We suggest several ways in which reference energies can be produced with free and open source software, either with non-self-consistent calculations with tabulated atomic densities or via self-consistent calculations with various program packages. The employed numerical parameters-especially the quadrature grid-need to be converged to guarantee a ≲0.1 μEh precision in the total energy, which is nowadays routinely achievable in fully numerical calculations. Moreover, as such sub-μEh level agreement can only be achieved when fully equivalent implementations of the DFA are used, the source code of the reference implementation should also be made available in any publication describing a new DFA.
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Affiliation(s)
- Susi Lehtola
- Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Miguel A L Marques
- Research Center Future Energy Materials and Systems of the University Alliance Ruhr, Faculty of Mechanical Engineering, Ruhr University Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
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8
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Morgante P, Peverati R. Comparison of the Performance of Density Functional Methods for the Description of Spin States and Binding Energies of Porphyrins. Molecules 2023; 28:molecules28083487. [PMID: 37110720 PMCID: PMC10146789 DOI: 10.3390/molecules28083487] [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: 03/28/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
This work analyzes the performance of 250 electronic structure theory methods (including 240 density functional approximations) for the description of spin states and the binding properties of iron, manganese, and cobalt porphyrins. The assessment employs the Por21 database of high-level computational data (CASPT2 reference energies taken from the literature). Results show that current approximations fail to achieve the "chemical accuracy" target of 1.0 kcal/mol by a long margin. The best-performing methods achieve a mean unsigned error (MUE) <15.0 kcal/mol, but the errors are at least twice as large for most methods. Semilocal functionals and global hybrid functionals with a low percentage of exact exchange are found to be the least problematic for spin states and binding energies, in agreement with the general knowledge in transition metal computational chemistry. Approximations with high percentages of exact exchange (including range-separated and double-hybrid functionals) can lead to catastrophic failures. More modern approximations usually perform better than older functionals. An accurate statistical analysis of the results also casts doubts on some of the reference energies calculated using multireference methods. Suggestions and general guidelines for users are provided in the conclusions. These results hopefully stimulate advances for both the wave function and the density functional side of electronic structure calculations.
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Affiliation(s)
- Pierpaolo Morgante
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Roberto Peverati
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
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9
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Cohen RD, Wood JS, Lam YH, Buevich AV, Sherer EC, Reibarkh M, Williamson RT, Martin GE. DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking. Molecules 2023; 28:molecules28062449. [PMID: 36985422 PMCID: PMC10051451 DOI: 10.3390/molecules28062449] [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: 01/25/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Density functional theory (DFT) benchmark studies of 1H and 13C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured 1H and 13C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for 1H and 13C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Maximum deviations were less than 0.5 and 6.5 ppm for 1H and 13C, respectively.
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Affiliation(s)
- Ryan D Cohen
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Jared S Wood
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
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10
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Miranda W, Frazão N, Moreira E, Azevedo D. Penta-belt: A new carbon nanobelt. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Liu R, Zhang C, Liang X, Liu J, Wu X, Chen M. Structural and Dynamic Properties of Solvated Hydroxide and Hydronium Ions in Water from Ab Initio Modeling. J Chem Phys 2022; 157:024503. [DOI: 10.1063/5.0094944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water has been a challenging task from ab initio molecular dynamics (AIMD). The difficulty mainly comes from a lack of accurate and efficient exchange-correlation functional in elucidating the amphiphilic nature and the ubiquitous proton transfer behaviors of the two ions. By adopting the strongly-constrained and appropriately normed (SCAN) meta-GGA functional in AIMD simulations, we systematically examine the amphiphilic properties, the solvation structures, the electronic structures, and the dynamic properties of the two water ions. In particular, we compare these results to those predicted by the PBE0-TS functional, which is an accurate yet computationally more expensive exchange-correlation functional. We demonstrate that the general-purpose SCAN functional provides a reliable choice in describing the two water ions. Specifically, in the SCAN picture of water ions, the appearance of the fourth and fifth hydrogen bonds near hydroxide stabilizes the pot-like shape solvation structure and suppresses the structural diffusion, while the hydronium stably donates three hydrogen bonds to its neighbors. We apply a detailed analysis of the proton transfer mechanism of the two ions and find the two ions exhibit substantially different proton transfer patterns. Our AIMD simulations indicate hydroxide diffuses slower than hydronium in water, which is consistent with the experiments.
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Affiliation(s)
| | | | | | | | - Xifan Wu
- Physics, Temple University, United States of America
| | - Mohan Chen
- College of Engineering, Peking University, China
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12
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Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantum chemical methods for the calculation of indirect NMR spin–spin coupling constants and chemical shifts are always in progress. They never stay the same due to permanently developing computational facilities, which open new perspectives and create new challenges every now and then. This review starts from the fundamentals of the nonrelativistic and relativistic theory of nuclear magnetic resonance parameters, and gradually moves towards the discussion of the most popular common and newly developed methodologies for quantum chemical modeling of NMR spectra.
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13
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Ivanova G, Bozova N, Petkov N, An C, Hu B, Mutovska M, Konstantinov K, Zagranyarski Y, Videva V, Yordanova A, Baumgarten M, Ivanova A. Benchmarking of Density Functionals for the Description of Optical Properties of Newly Synthesized π-Conjugated TADF Blue Emitters. Chemistry 2022; 28:e202104411. [PMID: 35107870 DOI: 10.1002/chem.202104411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Indexed: 11/10/2022]
Abstract
Computational modeling of the optical characteristics of organic molecules with potential for thermally activated delayed fluorescence (TADF) may assist markedly the development of more efficient emitting materials for organic light-emitting diodes. Recent theoretical studies in this area employ mostly methods from density functional theory (DFT). In order to obtain accurate predictions within this approach, the choice of a proper functional is crucial. In the current study, we focus on testing the performance of a set of DFT functionals for estimation of the excitation and emission energy and the excited singlet-triplet energy gap of three newly synthesized compounds with capacity for TADF. The emitters are designed specifically to enable charge transfer by π-electron conjugation, at the same time possessing high-energy excited triplet states. The functionals chosen for testing are from various groups ranging from gradient-corrected through global hybrids to range-separated ones. The results show that the monitored optical properties are especially sensitive to how the long-range part of the exchange energy is treated within the functional. The accurate functional should also be able to provide well balanced distribution of the π-electrons among the molecular fragments. Global hybrids with moderate (less than 0.4) share of exact exchange (B3LYP, PBE0) and the meta-GGA HSE06 are outlined as the best performing methods for the systems under study. They can predict all important optical parameters correctly, both qualitatively and quantitatively.
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Affiliation(s)
- Georgia Ivanova
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
| | - Nadezhda Bozova
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
| | - Nikolay Petkov
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
| | - Cunbin An
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Benlin Hu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Monika Mutovska
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
| | - Konstantin Konstantinov
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
| | - Yulian Zagranyarski
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
| | - Vladimira Videva
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria.,Institute of Optical Materials and Technologies, Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria
| | - Adelina Yordanova
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
| | - Martin Baumgarten
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Anela Ivanova
- Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier blvd., 1164, Sofia, Bulgaria
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14
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Benassi E. An inexpensive density functional theory-based protocol to predict accurate 19 F-NMR chemical shifts. J Comput Chem 2022; 43:170-183. [PMID: 34757623 DOI: 10.1002/jcc.26780] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 01/31/2023]
Abstract
Thanks to its advantages, 19 F-NMR is an increasingly popular technique for the structural characterization of F-containing molecules, among which polymers, materials, fluorophores, pharmaceuticals, and so forth. However, the computational calculation of the 19 F-NMR chemical shifts, both for prediction and interpretation of experimental spectra, remains a challenge. In this work a density functional theory (DFT) based protocol for the calculation of the chemical shifts is established within the framework of the gauge-independent atomic orbital method, upon verifying the performance of Hartree-Fock and 60 DFT functionals coupled with seven different basis sets. The benchmark is conducted using two sets of molecules, namely one used for testing methods and another used for probing; the former set consists of 134 molecules, the latter 50, yet both of them with F in different chemical environments. Following Bally-Rablen-Tantillo strategy, the scaling parameters and other statistical quantities were computed for each method upon least squares linear regression between experimental and computed chemical shifts. The designed computational workflow is computationally inexpensive and represents a significant improvement with respect to the current state of the art.
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Affiliation(s)
- Enrico Benassi
- Faculty of Chemistry, Novosibirsk State University, Novosibirsk, Russia
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15
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Ferrández-Gómez B, Sánchez A, Jordá JD, Fonfría ES, Bordehore C, Cerdán M. Effectiveness of Oxygen-Saturated Seawater Injections and Air Sparging Technologies in Remediation of Coastal Marine Sediments from Sludge. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:4975-4986. [PMID: 33966170 DOI: 10.1007/s10653-021-00952-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
The occurrence of hypoxic muddy sediments on shallow beaches and other sheltered areas is a well-known environmental problem, which negatively affects coastal areas, tourism potential, the public use of beaches and sediment biodiversity. The usual solution is limited to dredging and removal of sludge to a landfill site. In this study, a laboratory-scale experiment was performed to determine the effectiveness of two technologies: a modification of air sparging and a new approach based on injecting oxygen-saturated seawater in hypoxic muddy sediments (oxygen-saturated seawater injections method), for remediating sludge in coastal sediments, minimizing environmental impact respect to dredging. Our results showed that both technologies significantly increased dissolved oxygen content in pore water, facilitating the oxidation of more than 90% of the organic matter, and other reduced inorganic compounds such as sulphide, with the consequent increase in sulphate concentration from 0.3 to 3.0 g·L-1. Moreover, a rise of redox potential from - 258 mV to above 200 mV, and a dramatic drop in chemical oxygen demand were also indicators that oxic conditions had been restored. After 65 days, soft, black, muddy and hypoxic sediment with high organic matter content and a characteristic foul odour was transformed into well-oxygenated sediment, which had a low organic matter content and had lost its initial shiny black colour and odour. The main difference between both technologies was the depth influenced by sediment remediation; oxygen-saturated seawater injections affected deeper areas than clean pressurized air injections.
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Affiliation(s)
- Borja Ferrández-Gómez
- Instituto Universitario de Materiales de Alicante, Universidad de Alicante, Campus San Vicente del Raspeig, 03690, Alicante, Spain
| | - Antonio Sánchez
- Departamento de Agroquímica y Bioquímica. Facultad de Ciencias, Universidad de Alicante. Campus de San Vicente del Raspeig, 03690, Alicante, Spain
| | - Juana D Jordá
- Departamento de Agroquímica y Bioquímica. Facultad de Ciencias, Universidad de Alicante. Campus de San Vicente del Raspeig, 03690, Alicante, Spain
- Instituto Multidisciplinar Para El Estudio del Medio "Ramón Margalef", Universidad de Alicante, Campus San Vicente del Raspeig, 03690, Alicante, Spain
| | - Eva S Fonfría
- Instituto Multidisciplinar Para El Estudio del Medio "Ramón Margalef", Universidad de Alicante, Campus San Vicente del Raspeig, 03690, Alicante, Spain
| | - César Bordehore
- Instituto Multidisciplinar Para El Estudio del Medio "Ramón Margalef", Universidad de Alicante, Campus San Vicente del Raspeig, 03690, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Campus San Vicente del Raspeig, 03690, Alicante, Spain
| | - Mar Cerdán
- Departamento de Agroquímica y Bioquímica. Facultad de Ciencias, Universidad de Alicante. Campus de San Vicente del Raspeig, 03690, Alicante, Spain.
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16
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Combinations of density functionals for accurate molecular properties of Be/W/H compounds. NUCLEAR MATERIALS AND ENERGY 2021. [DOI: 10.1016/j.nme.2021.101026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Zahn SLV, Hammerich O, Hansen PE, Sauer SPA. The best density functional theory functional for the prediction of 1 H and 13 C chemical shifts of protonated alkylpyrroles. J Comput Chem 2021; 42:1248-1262. [PMID: 33931893 DOI: 10.1002/jcc.26540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/20/2023]
Abstract
The prediction of 13 C chemical shifts can be challenging with density functional theory (DFT). In this study 39 different functionals and three different basis sets were tested on three neutral alkylpyrroles and their corresponding protonated species. The calculated shielding constants were compared to experimental data and results from previous calculations at the MP2. We find that the meta-hybrid functional TPSSh with either the Pople style basis set 6-311++G(2d,p) or the polarization consistent basis set pcSseg-1 gives the best results for the 13 C chemical shifts, whereas for the 1 H chemical shifts it is the TPSSh functional with either the 6-311++G(2d,p) or pcSseg-2 basis set. Including an explicit solvent molecule hydrogen bonded to NH in the alkylpyrroles improves the results slightly for the 13 C chemical shifts. On the other hand, for 1 H chemical shifts the opposite is true. Compared to calculations at the MP2 level none of the DFT functionals can compete with MP2 for the 13 C chemical shifts but for the 1 H chemical shifts the investigated DFT functionals are shown to give better agreement with experiment than MP2 calculations.
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Affiliation(s)
- Sarah L V Zahn
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Ole Hammerich
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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18
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Bella G, Santoro A, Nicolò F, Bruno G, Cordaro M. Do Secondary Electrostatic Interactions Influence Multiple Dihydrogen Bonds? AA-DD Array on an Amine-Borane Aza-Coronand: Theoretical Studies and Synthesis. Chemphyschem 2021; 22:593-605. [PMID: 33432782 DOI: 10.1002/cphc.202000906] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/09/2021] [Indexed: 11/06/2022]
Abstract
Hydrogen bond plays a key role in a wide range of inorganic, organic, as well as biological systems. The understanding on how the chemical environment can affect this kind of interaction is crucial to predict its binding strength and consequently the robustness and the dynamic properties of many supramolecular systems. In this paper a new donor-acceptor complex was synthesized and characterized by SCXRD, showing for the first time in an organic system an AA-DD pattern of a particular hydrogen interaction, called dihydrogen bond. Over 250 functionals were computationally evaluated to select the best method to reproduce the binding interaction geometry of this new pattern. Moreover, a new vector force model was used to split the contribution of primary and secondary electrostatic interactions (SEIs), in order to evaluate how the latter one can modify the binding strength of this unusual hydrogen-hydrogen interaction.
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Affiliation(s)
- Giovanni Bella
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Antonio Santoro
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Francesco Nicolò
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Giuseppe Bruno
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Massimiliano Cordaro
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
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19
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Nemykin VN, Nevonen DE, Ferch LS, Shepit M, Herbert DE, van Lierop J. Accurate Prediction of Mössbauer Hyperfine Parameters in Bis-Axially Coordinated Iron(II) Phthalocyanines Using Density Functional Theory Calculations: A Story of a Single Orbital Revealed by Natural Bond Orbital Analysis. Inorg Chem 2021; 60:3690-3706. [PMID: 33651595 DOI: 10.1021/acs.inorgchem.0c03373] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Density Functional Theory (DFT) calculations coupled with several exchange-correlation functionals were used for the prediction of Mössbauer hyperfine parameters of 36 bis-axially coordinated iron(II) phthalocyanine complexes with the general formulas PcFeL2, PcFeL'L″, and [PcFeX2]2-, including four new compounds. Both gas-phase and PCM calculations using BPW91 and MN12L exchange-correlation functionals were found to accurately predict both Mössbauer quadrupole splittings and the correct trends in experimentally observed isomer shifts. In comparison, hybrid exchange-correlation functionals underestimated quadrupole splittings, while still accurately predicted isomer shifts. Out of ∼40 exchange-correlation functionals tested, only MN12L was found to correctly reproduce quadrupole splitting trends in the PcFeL2 complexes coordinated with phosphorus-donor axial ligands (i.e., P(OnBu)3 ≈ P(OEt)3 < PMe3 < P[(CH2O)2CH2]-p-C6H4NO2 < PEt3 ≈ PnBu3). Natural Bond Orbital (NBO) analysis was successfully used to explain the general trends in the observed quadrupole splitting for all compounds of interest. In particular, the general trends in the quadrupole splitting correlate well with the axial ligand dependent, NBO-predicted population of the 3dz2 orbital of the Fe ion and are reflective of the hypothesis proposed by Ohya and co-workers ( Inorg. Chem., 1984, 23, 1303) on the adaptability of the phthalocyanine's π-system toward Fe-Lax interactions. The first X-ray crystal structure of a PcFeL2 complex with axial phosphine ligands is also reported.
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Affiliation(s)
- Victor N Nemykin
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dustin E Nevonen
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Laura S Ferch
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Michael Shepit
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - David E Herbert
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Johan van Lierop
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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20
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Mendes RA, Haiduke RLA, Bartlett RJ. The Devil's Triangle of Kohn-Sham density functional theory and excited states. J Chem Phys 2021; 154:074106. [PMID: 33607901 DOI: 10.1063/5.0035446] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Exchange-correlation (XC) functionals from Density Functional Theory (DFT) developed under the rigorous arguments of Correlated Orbital Theory (COT) address the Devil's Triangle of prominent errors in Kohn-Sham (KS) DFT. At the foundation of this triangle lie the incorrect one-particle spectrum, the lack of integer discontinuity, and the self-interaction error. At the top level, these failures manifest themselves in incorrect charge transfer and Rydberg excitation energies, along with poor activation barriers. Accordingly, the Quantum Theory Project (QTP) XC functionals have been created to address several of the long-term issues encountered in KS theory and its Time Dependent DFT (TDDFT) variant for electronic excitations. Recognizing that COT starts with a correct one-particle spectrum, a condition imposed on the QTP functionals by means of minimum parameterization, the question that arises is how does this affect the electronically excited states? Among up to 28 XC functionals considered, the QTP family provides one of the smallest mean absolute deviations for charge-transfer excitations while also showing excellent results for Rydberg states. However, there is some room for improvement in the case of excitation energies to valence states, which are systematically underestimated by all functionals investigated. An alternative path for better treatment of excitation energies, mainly for valence states, is offered by using orbital energies from QTP functionals, especially by CAM-QTP-02 and LC-QTP. In this case, the deviations from the reference data can be reduced approximately by half.
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Affiliation(s)
- Rodrigo A Mendes
- Departamento de Química e Física Molecular, Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, 13560-970 São Carlos, SP, Brazil
| | - Roberto L A Haiduke
- Departamento de Química e Física Molecular, Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, 13560-970 São Carlos, SP, Brazil
| | - Rodney J Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
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21
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Lehtola S, Marques MAL. Meta-Local Density Functionals: A New Rung on Jacob's Ladder. J Chem Theory Comput 2021; 17:943-948. [PMID: 33502183 PMCID: PMC8023657 DOI: 10.1021/acs.jctc.0c01147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The homogeneous electron gas (HEG) is a key ingredient in the construction of most exchange-correlation functionals of density-functional theory. Often, the energy of the HEG is parameterized as a function of its spin density nσ, leading to the local density approximation (LDA) for inhomogeneous systems. However, the connection between the electron density and kinetic energy density of the HEG can be used to generalize the LDA by evaluating it on a geometric average nσavg(r) = nσ1-x(r)ñσx(r) of the local spin density nσ(r) and the spin density ñσ(r) of a HEG that has the local kinetic energy density τσ(r) of the inhomogeneous system. This leads to a new family of functionals that we term meta-local density approximations (meta-LDAs), which are still exact for the HEG, which are derived only from properties of the HEG and which form a new rung of Jacob's ladder of density functionals [ AIP Conf. Proc. 2001, 577, 1]. The first functional of this ladder, the local τ approximation (LTA) of Ernzerhof and Scuseria [ J. Chem. Phys. 1999, 111, 911] that corresponds to x = 1 is unfortunately not stable enough to be used in self-consistent field calculations because it leads to divergent potentials, as we show in this work. However, a geometric averaging of the LDA and LTA densities with smaller values of x not only leads to numerical stability of the resulting functional but also yields more accurate exchange energies in atomic calculations than the LDA, the LTA, or the tLDA functional (x = 1/4) of Eich and Hellgren [ J. Chem. Phys. 2014, 141, 224107]. We choose x = 0.50, as it gives the best total energy in self-consistent exchange-only calculations for the argon atom. Atomization energy benchmarks confirm that the choice x = 0.50 also yields improved energetics in combination with correlation functionals in molecules, almost eliminating the well-known overbinding of the LDA and reducing its error by two thirds.
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Affiliation(s)
- Susi Lehtola
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FI-00014 University of Helsinki, Finland
| | - Miguel A L Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle, Saale, Germany
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22
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Nguyen TT, Le PQ, Helminen J, Sipilä J. The 1H and 13C chemical shifts of 5–5 lignin model dimers: An evaluation of DFT functionals. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Liang C, Yang J, Luo G, Luo Y. Benchmark study of density functionals for the insertions of olefin and polar monomers catalyzed by α–diimine palladium complexes. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Moltved KA, Kepp KP. Using electronegativity and hardness to test density functionals. J Chem Phys 2020; 152:244113. [PMID: 32610960 DOI: 10.1063/5.0006189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Density functional theory (DFT) is used in thousands of papers each year, yet lack of universality reduces DFT's predictive capacity, and functionals may produce energy-density imbalances. The absolute electronegativity (χ) and hardness (η) directly reflect the energy-density relationship via the chemical potential ∂E/∂N and we thus hypothesized that they probe universality. We studied χ and η for atoms Z = 1-36 using 50 diverse functionals covering all major classes. Very few functionals describe both χ and η well. η benefits from error cancellation, whereas χ is marred by error propagation from IP and EA; thus, almost all standard GGA and hybrid functionals display a plateau in the MAE at ∼0.2 eV-0.3 eV for η. In contrast, variable performance for χ indicates problems in describing the chemical potential by DFT. The accuracy and precision of a functional is far from linearly related, yet for a universal functional, we expect linearity. Popular functionals such as B3LYP, PBE, and revPBE perform poorly for both properties. Density sensitivity calculations indicate large density-derived errors as occupation of degenerate p- and d-orbitals causes "non-universality" and large dependency on exact exchange. Thus, we argue that performance for χ for the same systems is a hallmark of an important aspect of universality by probing ∂E/∂N. With this metric, B98, B97-1, PW6B95D3, MN-15, rev-TPSS, HSE06, and APFD are the most "universal" among the tested functionals. B98 and B97-1 are accurate for very diverse metal-ligand bonds, supporting that a balanced description of ∂E/∂N and ∂E2/∂N2, via χ and η, is probably a first simple probe of universality.
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Affiliation(s)
- Klaus A Moltved
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
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25
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Blumberger J, Gaigeot MP, Sulpizi M, Vuilleumier R. Frontiers in molecular simulation of solvated ions, molecules and interfaces. Phys Chem Chem Phys 2020; 22:10393-10396. [PMID: 32352136 DOI: 10.1039/d0cp90091e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This themed collection is a collection of articles on frontiers in molecular simulation of solvated ions, molecules and interfaces.
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Affiliation(s)
- J Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, UK.
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26
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Hu Y, Vasiliu M, Thanthiriwatte KS, Jackson VE, Chaka AM, Dixon DA. Thermodynamics of Metal Carbonates and Bicarbonates and Their Hydrates for Mg, Ca, Fe, and Cd Relevant to Mineral Energetics. J Phys Chem A 2020; 124:1829-1840. [DOI: 10.1021/acs.jpca.9b11741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yiqin Hu
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Monica Vasiliu
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - K. Sahan Thanthiriwatte
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Virgil E. Jackson
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Anne M. Chaka
- Pacific Northwest National Laboratory, P.O. Box 999, MS K8-96, Richland, Washington 99352, United States
| | - David A. Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
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27
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Structure, Properties, and Reactivity of Porphyrins on Surfaces and Nanostructures with Periodic DFT Calculations. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10030740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Porphyrins are fascinating molecules with applications spanning various scientific fields. In this review we present the use of periodic density functional theory (PDFT) calculations to study the structure, electronic properties, and reactivity of porphyrins on ordered two dimensional surfaces and in the formation of nanostructures. The focus of the review is to describe the application of PDFT calculations for bridging the gaps in experimental studies on porphyrin nanostructures and self-assembly on 2D surfaces. A survey of different DFT functionals used to study the porphyrin-based system as well as their advantages and disadvantages in studying these systems is presented.
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28
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Performance of DFT functionals for properties of small molecules containing beryllium, tungsten and hydrogen. NUCLEAR MATERIALS AND ENERGY 2020. [DOI: 10.1016/j.nme.2020.100731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Synthesis, structural characterization, and computational study of (E)-N′-(3,4-dimethoxybenzylidene)furan-2-carbohydrazide. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2018.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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30
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Sakti AW, Nishimura Y, Nakai H. Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aditya W. Sakti
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
| | - Hiromi Nakai
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering Waseda University Tokyo Japan
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31
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Rana B, Herbert JM. Role of hemibonding in the structure and ultraviolet spectroscopy of the aqueous hydroxyl radical. Phys Chem Chem Phys 2020; 22:27829-27844. [DOI: 10.1039/d0cp05216g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of a two-center, three-electron hemibond in the solvation structure of the aqueous hydroxl radical has long been debated, as its appearance can be sensitive to self-interaction error in density functional theory.
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Affiliation(s)
- Bhaskar Rana
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
| | - John M. Herbert
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
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32
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Kim MJ, Kang YK. Predicting Potential Inversion Behavior of Ru–aqua Complexes via Using Cost Effective DFT Calculations. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Moon Ju Kim
- Department of ChemistrySangmyung University Seoul 03016 Korea
| | - Youn K. Kang
- Department of ChemistrySangmyung University Seoul 03016 Korea
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33
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Borlido P, Aull T, Huran AW, Tran F, Marques MAL, Botti S. Large-Scale Benchmark of Exchange-Correlation Functionals for the Determination of Electronic Band Gaps of Solids. J Chem Theory Comput 2019; 15:5069-5079. [PMID: 31306006 PMCID: PMC6739738 DOI: 10.1021/acs.jctc.9b00322] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We
compile a large data set designed for the efficient benchmarking
of exchange–correlation functionals for the calculation of
electronic band gaps. The data set comprises information on the experimental
structure and band gap of 472 nonmagnetic materials and includes a
diverse group of covalent-, ionic-, and van der Waals-bonded solids.
We used it to benchmark 12 functionals, ranging from standard local
and semilocal functionals, passing through meta-generalized-gradient
approximations, and several hybrids. We included both general purpose
functionals, like the Perdew–Burke–Ernzerhof approximation,
and functionals specifically crafted for the determination of band
gaps. The comparison of experimental and theoretical band gaps shows
that the modified Becke–Johnson is at the moment the best available
density functional, closely followed by the Heyd–Scuseria–Ernzerhof
screened hybrid from 2006 and the high-local-exchange generalized-gradient
approximation.
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Affiliation(s)
- Pedro Borlido
- Institut für Festkörpertheorie und -optik , Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility , Max-Wien-Platz 1 , 07743 Jena , Germany
| | - Thorsten Aull
- Institut für Physik , Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle , Germany
| | - Ahmad W Huran
- Institut für Physik , Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle , Germany
| | - Fabien Tran
- Institute of Materials Chemistry , Vienna University of Technology , Getreidemarkt 9/165-TC , A-1060 Vienna , Austria
| | - Miguel A L Marques
- Institut für Physik , Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle , Germany
| | - Silvana Botti
- Institut für Festkörpertheorie und -optik , Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility , Max-Wien-Platz 1 , 07743 Jena , Germany
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34
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Arunachalam V, Tummanapelli AK, Vasudevan S. The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations. Phys Chem Chem Phys 2019; 21:9212-9217. [PMID: 30993274 DOI: 10.1039/c9cp00761j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The hexapeptide glutathione disulfide (GSSG) has six ionizable groups with six associated dissociation constants. The experimentally measured pH-titration curve, however, does not exhibit the six corresponding equivalence points and bears little resemblance to standard textbook examples of acid-base pH-titration curves. The curve highlights the difficulties in determining multiple pKa values of polyprotic acids - typically proteins and peptides - from experiment. The six pKa values of GSSG can, however, be estimated using Car-Parrinello molecular dynamics (CPMD) simulations in conjunction with metadynamics sampling of the underlying free energy landscape of the dissociation reactions. Ab initio MD simulations were performed on a GSSG molecule solvated by 200 water molecules. Using the estimated pKa values the theoretical titration curve was calculated and found to be in good agreement with experiment. The results clearly highlight how dissociation constants estimated from ab initio MD simulations can facilitate the interpretation of the pH-titration curves of complex chemical and biological systems.
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35
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Poovathingal SJ, Minton TK, Szilagyi RK. Evaluating Density Functionals by Examining Molecular Structures, Chemical Bonding, and Relative Energies of Mononuclear Ru-Cl-H-PR 3 Isomers. J Phys Chem A 2019; 123:343-358. [PMID: 30540469 DOI: 10.1021/acs.jpca.8b03216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to define a robust level of theory using density functionals for investigating the reactivity of ruthenium complexes, we used benchmark wave function theory, with saturated basis sets to validate generalized gradient approximation (GGA), meta-GGA, and hyper-GGA functionals in the presence and absence of empirical dispersion and range-separated corrections. We first selected potentially suitable functionals that gave accurate predictions of the relative energetics of coordination isomers. These functionals were further evaluated for the chemical accuracy of their predicted geometric and electronic structures. For the latter, both the ionic and covalent interactions were considered. The reference level of theory for comparison was coupled-cluster perturbation theory using full treatment of singles and doubles (CCSD) with a saturated triple-ζ quality basis set (TZVP) and corresponding small-core, effective core potentials for ruthenium. Several population analysis methods were evaluated to predict the ionic interactions. We found that the atomic charges obtained from fitting the electrostatic potential provided the most reasonable estimates for the ruthenium complexes. The covalent interactions were quantified by considering the atomic compositions of Ru 4d x2- y2- and 4d z2-based frontier unoccupied orbitals. Comparison of more than two dozen functionals with reference data from high-level wave function calculations revealed trends that allowed for the formulation of an optimal hybrid density functional: PBE exchange and correlation functionals with 50% HF exchange component. This level of theory was found to reproduce the experimental structure of Ru(II) complexes. These complexes were used to investigate chemical speciation in a simplified model for an ionic liquid environment.
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Affiliation(s)
- Savio J Poovathingal
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Timothy K Minton
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Robert K Szilagyi
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
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36
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Morgante P, Peverati R. Statistically representative databases for density functional theory via data science. Phys Chem Chem Phys 2019; 21:19092-19103. [DOI: 10.1039/c9cp03211h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cluster analysis applied to quantum chemistry: a new broad database of chemical properties with a reasonable computational cost.
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37
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Perlt E, Ray P, Hansen A, Malberg F, Grimme S, Kirchner B. Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies. J Chem Phys 2018; 148:193835. [PMID: 30307237 DOI: 10.1063/1.5013122] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.
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Affiliation(s)
- Eva Perlt
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Promit Ray
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Friedrich Malberg
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, D-53115 Bonn, Germany
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38
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Schattenberg CJ, Maier TM, Kaupp M. Lessons from the Spin-Polarization/Spin-Contamination Dilemma of Transition-Metal Hyperfine Couplings for the Construction of Exchange-Correlation Functionals. J Chem Theory Comput 2018; 14:5653-5672. [DOI: 10.1021/acs.jctc.8b00597] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caspar J. Schattenberg
- Institut für Chemie, Technische Universität Berlin, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Toni M. Maier
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
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39
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Shibl MF, Moncho S, Brothers EN. What Happens Without Nickel? Cyclization Reactions of Ethylene with Ethanedithial and Related Molecules. J Comput Chem 2018; 39:1158-1167. [PMID: 29271503 DOI: 10.1002/jcc.25142] [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: 07/22/2017] [Revised: 11/01/2017] [Accepted: 11/18/2017] [Indexed: 11/06/2022]
Abstract
We present a computational study of the mechanism of the formation of 6-member heterocycles through the binding of ethylene to oxaldehyde, ethanedithial, and 2-thioxoacetaldehyde. This process is related to the olefin separation technology by metal dithiolenes and dioxolenes, being the formation of those heterocycles the main decomposition route. We also present a benchmark of 26 density functionals (spanning hybrid, double-hybrid, range-separated, semilocal, and local functionals) related to CCSD(T)/CBS reference values. Both the cyclization reaction and the isomerization of the cyclic product are included in the benchmark. The best functional among those tested for these reactions is ωB97XD, and the effect of the basis set is also investigated for it. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mohamed F Shibl
- Department of Chemistry, College of Engineering, Qatar University, Doha, Qatar
| | - Salvador Moncho
- Department of Chemistry, Texas A&M University at Qatar, Education City, Doha, Qatar
| | - Edward N Brothers
- Department of Chemistry, Texas A&M University at Qatar, Education City, Doha, Qatar
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40
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Brémond E, Savarese M, Adamo C, Jacquemin D. Accuracy of TD-DFT Geometries: A Fresh Look. J Chem Theory Comput 2018; 14:3715-3727. [DOI: 10.1021/acs.jctc.8b00311] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Eric Brémond
- Sorbonne Paris Cité, ITODYS, UMR CNRS 7086, Université Paris Diderot, 15 rue Jean-Antoine de Baı̈f, F-75013 Paris, France
| | - Marika Savarese
- D3 Compunet, Istituto Italiano di Tecnologia via Morego, 30 16163 Genova, Italy
| | - Carlo Adamo
- Chimie ParisTech, CNRS, Institut de Recherche de Chimie Paris, PSL Research University, 11 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Denis Jacquemin
- Laboratoire CEISAM, UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP 92208, 44322 Cedex 3 Nantes, France
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41
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Kraus P, Frank I. Density Functional Theory for Microwave Spectroscopy of Noncovalent Complexes: A Benchmark Study. J Phys Chem A 2018; 122:4894-4901. [PMID: 29750513 DOI: 10.1021/acs.jpca.8b03345] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we compare the results obtained with 89 computational methods for predicting noncovalent bond lengths in weakly bound complexes. Evaluations for the performance in noncovalent interaction energies and covalent bond lengths obtained from five other data sets are included. The overall best performing density functional is the ωB97M-V method, achieving balanced results across all three categories. For noncovalent geometries, the best methods include B97M-V, B3LYP-D3(BJ) and DSD-PBEPBE-D3(BJ). The effects of systematic improvement of the density functional approximation and of dispersion corrections are also discussed.
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Affiliation(s)
- P Kraus
- Institut für Physikalische Chemie und Elektrochemie , Leibniz Universität Hannover , Callinstraße 3A , 30167 Hannover , Germany
| | - I Frank
- Institut für Physikalische Chemie und Elektrochemie , Leibniz Universität Hannover , Callinstraße 3A , 30167 Hannover , Germany
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42
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Hait D, Head-Gordon M. How Accurate Is Density Functional Theory at Predicting Dipole Moments? An Assessment Using a New Database of 200 Benchmark Values. J Chem Theory Comput 2018; 14:1969-1981. [DOI: 10.1021/acs.jctc.7b01252] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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43
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Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer. Nat Chem 2018. [DOI: 10.1038/s41557-018-0010-2] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Brandenburg JG, Bannwarth C, Hansen A, Grimme S. B97-3c: A revised low-cost variant of the B97-D density functional method. J Chem Phys 2018; 148:064104. [DOI: 10.1063/1.5012601] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Jan Gerit Brandenburg
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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45
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Assessment of ten density functionals through the use of local hyper–softness to get insights about the catalytic activity. J Mol Model 2018; 24:42. [DOI: 10.1007/s00894-017-3576-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/25/2017] [Indexed: 10/18/2022]
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46
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Eizig Bar-On Z, Iron MA, Kasdan HL, Amir D, Afrimzon E, Zurgil N, Moshkov S, Deutsch M. The cationic dye basic orange 21 (BO21) as a potential fluorescent sensor. Photochem Photobiol Sci 2018; 17:1417-1428. [DOI: 10.1039/c7pp00455a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cationic dye BO21's unique fluorescence properties in aqueous glycerol solution – a potential sensor for white blood cells and heparin.
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Affiliation(s)
- Zehavit Eizig Bar-On
- The Biophysical Interdisciplinary Schottenstein Center for the Research and Technology of the Cellome
- Physics Department
- Bar Ilan University
- Ramat-Gan
- 5290002 Israel
| | - Mark A. Iron
- Computational Chemistry Unit
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot
- Israel 7610001
| | | | - Dan Amir
- The Goodman Faculty of Life Sciences
- Bar Ilan University
- Ramat Gan
- 5290002 Israel
| | - Elena Afrimzon
- The Biophysical Interdisciplinary Schottenstein Center for the Research and Technology of the Cellome
- Physics Department
- Bar Ilan University
- Ramat-Gan
- 5290002 Israel
| | - Naomi Zurgil
- The Biophysical Interdisciplinary Schottenstein Center for the Research and Technology of the Cellome
- Physics Department
- Bar Ilan University
- Ramat-Gan
- 5290002 Israel
| | - Sergei Moshkov
- The Biophysical Interdisciplinary Schottenstein Center for the Research and Technology of the Cellome
- Physics Department
- Bar Ilan University
- Ramat-Gan
- 5290002 Israel
| | - Mordechai Deutsch
- The Biophysical Interdisciplinary Schottenstein Center for the Research and Technology of the Cellome
- Physics Department
- Bar Ilan University
- Ramat-Gan
- 5290002 Israel
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47
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Kinzhalov MA, Buldakov AV, Petrov AV, Mahmudov KT, Ivanov AY, Suslonov VV. Low-temperature equilibriums in solutions of isocyanide-phosphine complexes of palladium(II) chloride. RUSS J GEN CHEM+ 2017. [DOI: 10.1134/s1070363217110159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Minenkov Y, Cavallo L. Ground-State Gas-Phase Structures of Inorganic Molecules Predicted by Density Functional Theory Methods. ACS OMEGA 2017; 2:8373-8387. [PMID: 31457376 PMCID: PMC6645218 DOI: 10.1021/acsomega.7b01203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/01/2017] [Indexed: 06/10/2023]
Abstract
We tested a battery of density functional theory (DFT) methods ranging from generalized gradient approximation (GGA) via meta-GGA to hybrid meta-GGA schemes as well as Møller-Plesset perturbation theory of the second order and a single and double excitation coupled-cluster (CCSD) theory for their ability to reproduce accurate gas-phase structures of di- and triatomic molecules derived from microwave spectroscopy. We obtained the most accurate molecular structures using the hybrid and hybrid meta-GGA approximations with B3PW91, APF, TPSSh, mPW1PW91, PBE0, mPW1PBE, B972, and B98 functionals, resulting in lowest errors. We recommend using these methods to predict accurate three-dimensional structures of inorganic molecules when intramolecular dispersion interactions play an insignificant role. The structures that the CCSD method predicts are of similar quality although at considerably larger computational cost. The structures that GGA and meta-GGA schemes predict are less accurate with the largest absolute errors detected with BLYP and M11-L, suggesting that these methods should not be used if accurate three-dimensional molecular structures are required. Because of numerical problems related to the integration of the exchange-correlation part of the functional and large scattering of errors, most of the Minnesota models tested, particularly MN12-L, M11, M06-L, SOGGA11, and VSXC, are also not recommended for geometry optimization. When maintaining a low computational budget is essential, the nonseparable gradient functional N12 might work within an acceptable range of error. As expected, the DFT-D3 dispersion correction had a negligible effect on the internuclear distances when combined with the functionals tested on nonweakly bonded di- and triatomic inorganic molecules. By contrast, the dispersion correction for the APF-D functional has been found to shorten the bonds significantly, up to 0.064 Å (AgI), in Ag halides, BaO, BaS, BaF, BaCl, Cu halides, and Li and Na halides and hydrides. These results do not agree well with very accurate structures derived from microwave spectroscopy; we therefore believe that the dispersion correction in the APF-D method should be reconsidered. Finally, we found that inaccurate structures can easily lead to errors of few kcal/mol in single-point energies.
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Affiliation(s)
- Yury Minenkov
- Physical Science and Engineering Division
(PSE), KAUST Catalysis Center (KCC), King
Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Luigi Cavallo
- Physical Science and Engineering Division
(PSE), KAUST Catalysis Center (KCC), King
Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
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49
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Iron MA. Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions using Density Functional Theory-The Advantage of Long-Range Corrected Functionals. J Chem Theory Comput 2017; 13:5798-5819. [PMID: 29016125 DOI: 10.1021/acs.jctc.7b00772] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The various factors influencing the accuracy of 13C NMR calculations using density functional theory (DFT), including the basis set, exchange-correlation (XC) functional, and isotropic shielding calculation method, are evaluated. A wide selection of XC functionals (over 70) were considered, and it was found that long-range corrected functionals offer a significant improvement over the other classes of functionals. Based on a thorough study, it is recommended that for calculating NMR chemical shifts (δ) one should use the CSGT method, the COSMO solvation model, and the LC-TPSSTPSS exchange-correlation functional in conjunction with the cc-pVTZ basis set. A selection of problems in natural product identification are considered in light of the newly recommended level of theory.
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Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 7610001, Israel
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50
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Barroso daSilva FL, Dias LG. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophys Rev 2017; 9:699-728. [PMID: 28921104 PMCID: PMC5662048 DOI: 10.1007/s12551-017-0311-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022] Open
Abstract
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.
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Affiliation(s)
- Fernando Luís Barroso daSilva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do café, s/no. - Universidade de São Paulo, BR-14040-903, Ribeirão Preto, SP, Brazil.
- UCD School of Physics, UCD Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland.
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Luis Gustavo Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900 - Universidade de São Paulo, BR-14040-901, Ribeirão Preto, SP, Brazil
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