1
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Hancock AC, Giudici E, Goerigk L. How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models. J Comput Chem 2024; 45:1667-1681. [PMID: 38553847 DOI: 10.1002/jcc.27351] [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: 01/25/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 06/04/2024]
Abstract
Time-dependent double hybrids with spin-component or spin-opposite scaling to their second-order perturbative correlation correction have demonstrated competitive robustness in the computation of electronic excitation energies. Some of the most robust are those recently published by our group (M. Casanova-Páez, L. Goerigk, J. Chem. Theory Comput. 2021, 20, 5165). So far, the implementation of these functionals has not allowed correctly calculating their ground-state total energies. Herein, we define their correct spin-scaled ground-state energy expressions which enables us to test our methods on the noncovalent excited-state interaction energies of four aromatic excimers. A range of 22 double hybrids with and without spin scaling are compared to the reasonably accurate wavefunction reference from our previous work (A. C. Hancock, L. Goerigk, RSC Adv. 2023, 13, 35964). The impact of spin scaling is highly dependent on the underlying functional expression, however, the smallest overall errors belong to spin-scaled functionals with range separation: SCS- and SOS- ω PBEPP86, and SCS-RSX-QIDH. We additionally determine parameters for DFT-D3(BJ)/D4 ground-state dispersion corrections of these functionals, which reduce errors in most cases. We highlight the necessity of dispersion corrections for even the most robust TD-DFT methods but also point out that ground-state based corrections are insufficient to completely capture dispersion effects for excited-state interaction energies.
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Affiliation(s)
- Amy C Hancock
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
| | - Erica Giudici
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
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2
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Hancock AC, Goerigk L. Noncovalently bound excited-state dimers: a perspective on current time-dependent density functional theory approaches applied to aromatic excimer models. RSC Adv 2023; 13:35964-35984. [PMID: 38090083 PMCID: PMC10712016 DOI: 10.1039/d3ra07381e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 05/12/2024] Open
Abstract
Excimers are supramolecular systems whose binding strength is influenced by many factors that are ongoing challenges for computational methods, such as charge transfer, exciton coupling, and London dispersion interactions. Treating the various intricacies of excimer binding at an adequate level is expected to be particularly challenging for time-dependent Density Functional Theory (TD-DFT) methods. In addition to well-known limitations for some TD-DFT methods in the description of charge transfer or exciton coupling, the inherent London dispersion problem from ground-state DFT translates to TD-DFT. While techniques to appropriately treat dispersion in DFT are well-developed for electronic ground states, these dispersion corrections remain largely untested for excited states. Herein, we aim to shed light on current TD-DFT methods, including some of the newest developments. The binding of four model excimers is studied across nine density functionals with and without the application of additive dispersion corrections against a wave function reference of SCS-CC2/CBS(3,4) quality, which approximates select CCSDR(3)/CBS data adequately. To our knowledge, this is the first study that presents single-reference wave function dissociation curves at the complete basis set level for the assessed model systems. It is also the first time range-separated double-hybrid density functionals are applied to excimers. In fact, those functionals turn out to be the most promising for the description of excimer binding followed by global double hybrids. Range-separated and global hybrids-particularly with large fractions of Fock exchange-are outperformed by double hybrids and yield worse dissociation energies and inter-molecular equilibrium distances. The deviation between each assessed functional and reference increases with system size, most likely due to missing dispersion interactions. Additive dispersion corrections of the DFT-D3(BJ) and DFT-D4 types reduce the average errors for TD-DFT methods but do so inconsistently and therefore do not offer a black-box solution in their ground-state parametrised form. The lack of appropriate description of dispersion effects for TD-DFT methods is likely hindering the practical application of the herein identified more efficient methods. Dispersion corrections parametrised for excited states appear to be an important next step to improve the applicability of TD-DFT methods and we hope that our work assists with the future development of such corrections.
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Affiliation(s)
- Amy C Hancock
- School of Chemistry, The University of Melbourne Parkville Australia +61-(0)3-8344 6784
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne Parkville Australia +61-(0)3-8344 6784
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3
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Adjal C, Timón V, Guechtouli N, Boussassi R, Hammoutène D, Senent ML. The Role of Water in the Adsorption of Nitro-Organic Pollutants on Activated Carbon. J Phys Chem A 2023; 127:8146-8158. [PMID: 37748125 PMCID: PMC10561263 DOI: 10.1021/acs.jpca.3c03877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/04/2023] [Indexed: 09/27/2023]
Abstract
The density functional theory (DFT) is applied to theoretically study the capture and storage of three different nitro polycyclic aromatic hydrocarbons, 4-nitrophenol, 2-nitrophenol, and 9-nitroanthracene by activated carbon, with and without the presence of water. These species are pollutants derived from vehicle and industry emissions. The modeling of adsorption is carried out at the molecular level using a high-level density functional theory with the B3LYP-GD(BJ)/6-31+G(d,p) level of theory. The adsorption energies of polluting gases considered isolated and in a humid environment are compared to better understand the role of water. The calculations reveal different possible pathways involving the formation of chemical bonds between adsorbent and adsorbate on the formation of intermolecular van der Waals interactions. The negative adsorption energy on AC for the three species is obtained when they are treated individually and in mixture with H2O. The basis-set superposition error, estimated using the counterpoise correction, varies the adsorption energies by 2-13%. Dispersion effects were also taken into account. The adsorption energy ranges from -10 to -414 kJ/mol suggesting a diversity of pathways. The resulting analysis suggests three preferred pathways for capture. The main pathway is physical interaction due to π-π stacking. Other means are capture due to the formation of hydrogen bonds resulting from water adsorbed on the surface and the simultaneous adsorption of pollutant and water where water can act as a link that promotes adsorption. The thermodynamic properties give a clue to the most eco-friendly approaches for molecular adsorption.
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Affiliation(s)
- Celia Adjal
- Laboratory
of Thermodynamics and Molecular Modeling, Faculty of Chemistry, USTHB, BP32, El Alia, Bab Ezzouar,Algiers 16111, Algeria
- Instituto
de Estructura de la Materia, CSIC, Serrano 121, Madrid 28006, Spain
| | - Vicente Timón
- Instituto
de Estructura de la Materia, CSIC, Serrano 121, Madrid 28006, Spain
| | - Nabila Guechtouli
- Laboratory
of Thermodynamics and Molecular Modeling, Faculty of Chemistry, USTHB, BP32, El Alia, Bab Ezzouar,Algiers 16111, Algeria
- Faculty
of Sciences, Department of Chemistry, Mouloud
Mammeri University of Tizi Ouzou, UMMTO, Tizi Ouzou 15000, Algeria
| | - Rahma Boussassi
- Laboratory
of Thermodynamics and Molecular Modeling, Faculty of Chemistry, USTHB, BP32, El Alia, Bab Ezzouar,Algiers 16111, Algeria
| | - Dalila Hammoutène
- Laboratory
of Thermodynamics and Molecular Modeling, Faculty of Chemistry, USTHB, BP32, El Alia, Bab Ezzouar,Algiers 16111, Algeria
| | - María Luisa Senent
- Instituto
de Estructura de la Materia, CSIC, Serrano 121, Madrid 28006, Spain
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4
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Boden P, Strebert PH, Meta M, Dietrich F, Riehn C, Gerhards M. Chromone-methanol clusters in the electronic ground and lowest triplet state: a delicate interplay of non-covalent interactions. Phys Chem Chem Phys 2022; 24:15208-15216. [PMID: 35579075 DOI: 10.1039/d2cp01341j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chromone offers two energetically almost equivalent docking sites for alcohol molecules, in which the hydroxyl group is hydrogen bonded to one of the free electron pairs of the carbonyl O atom. Here, the delicate balance between these two competing arrangements is studied by combining IR/R2PI and UV/IR/UV spectroscopy in a molecular beam supported by quantum-chemical calculations. Most interestingly, chromone undergoes an efficient intersystem crossing into the triplet manifold upon electronic excitation, so that the studies on aromatic molecule-solvent complexes are for the first time extended to such a cluster in a triplet state. As the lowest triplet state (T1) is of ground state character, powerful energy decomposition approaches such as symmetry-adapted perturbation theory (SAPT) and local energy decomposition using the domain-based local pair natural orbital coupled-cluster method (DLPNO-CCSD(T)/LED) are applied. From the theoretical analysis we infer for the T1 state a loss of planarity (puckering) of the 4-pyrone ring of the chromone unit, which considerably affects the interplay between different types of non-covalent interactions at the two possible binding sites.
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Affiliation(s)
- Pol Boden
- Fachbereich Chemie & State Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Patrick H Strebert
- Fachbereich Chemie & State Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Marcel Meta
- Fachbereich Chemie & State Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Fabian Dietrich
- Fachbereich Chemie & State Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany.,Núcleo Milenio MultiMat & Departamento de Ciencias Físicas, Universidad de La Frontera, Temuco, Chile.
| | - Christoph Riehn
- Fachbereich Chemie & State Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- Fachbereich Chemie & State Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
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5
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Czernek J, Brus J, Czerneková V. A computational inspection of the dissociation energy of mid-sized organic dimers. J Chem Phys 2022; 156:204303. [DOI: 10.1063/5.0093557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The gas-phase value of the dissociation energy ( D0) is a key parameter employed in both experimental and theoretical descriptions of noncovalent complexes. The D0 data were obtained for a set of mid-sized organic dimers in their global minima which was located using geometry optimizations that applied ample basis sets together with either the conventional second-order Møller–Plesset (MP2) method or several dispersion-corrected density-functional theory (DFT-D) schemes. The harmonic vibrational zero-point (VZP) and deformation energies from the MP2 calculations were combined with electronic energies from the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit to estimate D0 with the aim of inspecting values that were most recently measured, and an analogous comparison was performed using the DFT-D data. In at least one case (namely, for the aniline⋯methane cluster), the D0 estimate that employed the CCSD(T)/CBS energies differed from experiment in the way that could not be explained by a possible deficiency in the VZP contribution. Curiously, one of the DFT-D schemes (namely, the B3LYP-D3/def2-QZVPPD) was able to reproduce all measured D0 values to within 1.0 kJ/mol from experimental error bars. These findings show the need for further measurements and computations of some of the complexes. In order to facilitate such studies, the physical nature of intermolecular interactions in the investigated dimers was analyzed by means of the DFT-based symmetry-adapted perturbation theory.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 06 Praha 6, The Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 162 06 Praha 6, The Czech Republic
| | - Vladimíra Czerneková
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, The Czech Republic
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6
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Hancock AC, Goerigk L. Noncovalently bound excited-state dimers: a perspective on current time-dependent density functional theory approaches applied to aromatic excimer models. RSC Adv 2022; 12:13014-13034. [PMID: 35520129 PMCID: PMC9062889 DOI: 10.1039/d2ra01703b] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023] Open
Abstract
Excimers are supramolecular systems whose binding strength is influenced by many factors that are ongoing challenges for computational methods, such as charge transfer, exciton coupling, and London dispersion interactions. Treating the various intricacies of excimer binding at an adequate level is expected to be particularly challenging for Time-Dependent Density Functional Theory (TD-DFT) methods. In addition to well-known limitations for some TD-DFT methods in the description of charge transfer or exciton coupling, the inherent London dispersion problem from ground-state DFT translates to TD-DFT. While techniques to appropriately treat dispersion in DFT are well-developed for electronic ground states, these dispersion corrections remain largely untested for excited states. Herein, we aim to shed light on current TD-DFT methods, including some of the newest developments. The binding of four model excimers is studied across nine density functionals with and without the application of additive dispersion corrections against a wave function reference of SCS-CC2/CBS(3,4) quality, which approximates select CCSDR(3)/CBS data adequately. To our knowledge, this is the first study that presents single-reference wave function dissociation curves at the complete basis set level for the assessed model systems. It is also the first time range-separated double-hybrid density functionals are applied to excimers. In fact, those functionals turn out to be the most promising for the description of excimer binding followed by global double hybrids. Range-separated and global hybrids-particularly with large fractions of Fock exchange-are outperformed by double hybrids and yield worse dissociation energies and inter-molecular equilibrium distances. The deviation between each assessed functional and reference increases with system size, most likely due to missing dispersion interactions. Additive dispersion corrections of the DFT-D3(BJ) and DFT-D4 types reduce the average errors for TD-DFT methods but do so inconsistently and therefore do not offer a black-box solution in their ground-state parametrised form. The lack of appropriate description of dispersion effects for TD-DFT methods is likely hindering the practical application of the herein identified more efficient methods. Dispersion corrections parametrised for excited states appear to be an important next step to improve the applicability of TD-DFT methods and we hope that our work assists with the future development of such corrections.
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Affiliation(s)
- Amy C Hancock
- School of Chemistry, The University of Melbourne Parkville Australia +61-3-8344-6784
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne Parkville Australia +61-3-8344-6784
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7
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Loman JL, Makuvaza JT, Kokkin DL, Reid SA. Unraveling a trifecta of weak non-covalent interactions: The dissociation energy of the anisole-ammonia 1:1 complex. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Radkowska I, Bragiel P, Belka R, Ficek P. Non-linear optical properties of polystyrene and polyvinyl alcohol composites with 4-methoxy-1-naphthol. Z PHYS CHEM 2020. [DOI: 10.1515/zpch-2019-1594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The analysis of the NLO properties of 4-methoxy-1-naphthol (4M1N) reveals that this molecule has the value of polarizability tensor, α, more than 340% greater than that obtained, at the same level of theory, for urea molecule. This improvement grows to 500% when the second-order hyperpolarizability is considered. Calculations performed within LR-PCM-B3LYP/6-311+G(3d,2p) model proved that embedding of 4M1N in the polymer matrix significantly improved these results suggesting applications of 4M1N as the cheap and effective NLO material. The molecule was also studied, both theoretically and experimentally, to determine its full vibrational characterisation and structural description. Calculations were performed with HF, MP2, SVWN and B3LYP methods, in two, varying in size, basis sets, to find optimized structures, conformational isomers and UV–VIS, IR and Raman spectra. The accordance of simulated oscillation and absorption spectra with experimental ones is very good; IR values are slightly red-shifted. NBO charge distribution analysis was made to generate frontier orbitals and find most reactive parts of the molecule.
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Affiliation(s)
- Ilona Radkowska
- Department of Science and Technology , Jan Dlugosz University , Czestochowa , Poland
| | - Piotr Bragiel
- Department of Science and Technology , Jan Dlugosz University , Czestochowa , Poland
| | - Radosław Belka
- Faculty of Electrical Engineering, Automatical Control and Computer Science , Kielce University of Technology , Kielce , Poland
| | - Pawel Ficek
- Department of Science and Technology , Jan Dlugosz University , Czestochowa , Poland
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9
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Reiter S, Roos MK, Vivie‐Riedle R. Excited State Conformations of Bridged and Unbridged Pyrene Excimers. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sebastian Reiter
- Department of ChemistryLudwig Maximilian University of Munich Butenandtstr. 11 81377 Munich Germany
| | - Matthias K. Roos
- Department of ChemistryLudwig Maximilian University of Munich Butenandtstr. 11 81377 Munich Germany
| | - Regina Vivie‐Riedle
- Department of ChemistryLudwig Maximilian University of Munich Butenandtstr. 11 81377 Munich Germany
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10
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Fabrizio A, Corminboeuf C. How do London Dispersion Interactions Impact the Photochemical Processes of Molecular Switches? J Phys Chem Lett 2018; 9:464-470. [PMID: 29320636 DOI: 10.1021/acs.jpclett.7b03316] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In the last two decades, linear-response time-dependent density functional theory (LR-TDDFT) has become one of the most widely used approaches for the computation of the excited-state properties of atoms and molecules. Despite its success in describing the photochemistry and the photophysics of a vast majority of molecular systems, its domain of applicability has been limited by several substantial drawbacks. Commonly identified problems of LR-TDDFT include the correct description of Rydberg states, charge-transfer excited states, doubly excited states, and nearly degenerate states. In addition to these widely recognized shortcomings, the approximate functionals used in LR-TDDFT are unable to fully describe London dispersion interactions. In this work, we aim at understanding the impact of van der Waals interactions on the properties of chemical systems beyond their electronic ground state. For this purpose, we compare the results of excited-state energy profiles and dynamic trajectories for the prototypical cis-stilbene molecule with its 3-3',5-5'-tetra-tert-butyl derivative. While the explicit treatment of London dispersion interactions results in negligible changes for the cis-stilbene, we show that these attractive forces have a substantial influence on the energetics and structural evolution of the substituted derivative. In the latter case, intramolecular dispersion interactions impact the outcome of the simulation qualitatively, leading to an increased preference for the photocyclization pathway. The methodological consequences of this work are not uniquely applicable to the illustrative stilbene case. In fact, this molecule is representative of a whole class of chemical situations, where dispersion forces dominate the interactions between the unexcited substituents of a photoexcited chromophore. This is, for instance, a common situation in organic photovoltaics where donor molecules are usually functionalized with long alkyl side chains to improve solubility and assembly.
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Affiliation(s)
- Alberto Fabrizio
- Laboratory for Computational Molecular Design and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne, Switzerland
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne, Switzerland
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne, Switzerland
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11
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Biczysko M, Krupa J, Wierzejewska M. Theoretical studies of atmospheric molecular complexes interacting with NIR to UV light. Faraday Discuss 2018; 212:421-441. [DOI: 10.1039/c8fd00094h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical structural and spectroscopic data for weakly bonded atmospheric complexes of formaldehyde interacting with Earth’s electromagnetic spectrum.
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Affiliation(s)
- Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures
- Department of Physics
- College of Sciences
- Shanghai University
- Shanghai
| | - Justyna Krupa
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
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12
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Schwabe T, Goerigk L. Time-Dependent Double-Hybrid Density Functionals with Spin-Component and Spin-Opposite Scaling. J Chem Theory Comput 2017; 13:4307-4323. [PMID: 28763220 DOI: 10.1021/acs.jctc.7b00386] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
For the first time, we combine time-dependent double-hybrid density functional approximations (TD-DHDFAs) for the calculation of electronic excitation energies with the concepts of spin-component and spin-opposite scaling (SCS/SOS) of electron-pair contributions to their nonlocal correlation components. Different flavors of this idea, ranging from standard SCS parameters to fully fitted parameter sets, are presented and tested on six different parent DHDFAs. For cross-validation, we assess those methods on three benchmark sets that cover small- to medium-sized chromophores (up to 78 atoms) and different excitation types. For this purpose, we also introduce new CC3 reference values for the popular Gordon benchmark set that we recommend using in future studies. Our results confirm that already the (unscaled) parent TD-DHDFAs are accurate and outperform some wave function methods. Further introduction of SCS/SOS eliminates extreme outliers, reduces deviation spans from reference values by up to 0.5 eV, aligns the performance of the Tamm-Dancoff approximation (TDA) to that of full TD calculations, and also enables a more balanced description of different excitation types. The best-performing TD-based methods in our cross validation have mean absolute deviations as low as 0.14 eV compared to the time- and resource-intensive CC3 approach. A very important finding is that we also obtained SOS variants with excellent performance, contrary to wave function based methods. This opens a future pathway to highly efficient methods for the optimization of excited-state geometries, particularly when paired with computing strategies such as the Laplace transform. We recommend our SCS- and SOS-based variants for further testing and subsequent applications.
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Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and Physical Chemistry Institute, University of Hamburg , Bundesstraße 43, D-20146 Hamburg, Germany
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne , Parkville, Victoria 3010, Australia
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13
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Brückner C, Stolte M, Würthner F, Pflaum J, Engels B. QM/MM calculations combined with the dimer approach on the static disorder at organic-organic interfaces of thin-film organic solar cells composed of small molecules. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Charlotte Brückner
- Institut für Theoretische Chemie, Universität Würzburg; Würzburg Germany
| | - Matthias Stolte
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry; Würzburg Germany
| | - Frank Würthner
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry; Würzburg Germany
| | - Jens Pflaum
- Experimentelle Physik VI; Universität Würzburg; Würzburg Germany
- Bayerisches Zentrum für Angewandte Energieforschung (ZAE Bayern e.V.); Würzburg Germany
| | - Bernd Engels
- Institut für Theoretische Chemie, Universität Würzburg; Würzburg Germany
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14
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Lage-Estebanez I, Del Olmo L, López R, García de la Vega JM. The role of errors related to DFT methods in calculations involving ion pairs of ionic liquids. J Comput Chem 2017; 38:530-540. [PMID: 28133839 DOI: 10.1002/jcc.24707] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 01/17/2023]
Abstract
Ionic liquids (ILs) play a key role in many chemical applications. As regards the theoretical approach, ILs show added difficulties in calculations due to the composition of the ion pair and to the fact that they are liquids. Although density functional theory (DFT) can treat this kind of systems to predict physico-chemical properties, common versions of these methods fail to perform accurate predictions of geometries, interaction energies, dipole moments, and other properties related to the molecular structure. In these cases, dispersion and self-interaction error (SIE) corrections need to be introduced to improve DFT calculations involving ILs. We show that the inclusion of dispersion is needed to obtain good geometries and accurate interaction energies. SIE needs to be corrected to describe the charges and dipoles in the ion pair correctly. The use of range-separated functionals allows us to obtain interaction energies close to the CCSD(T) level. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Isabel Lage-Estebanez
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
| | - Lourdes Del Olmo
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
| | - Rafael López
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
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15
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Ryazantsev SV, Tarroni R, Feldman VI, Khriachtchev L. Effect of Noncovalent Interactions on Vibronic Transitions: An Experimental and Theoretical Study of the C2
H⋅⋅⋅CO2
Complex. Chemphyschem 2017; 18:949-958. [DOI: 10.1002/cphc.201601441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/20/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Sergey V. Ryazantsev
- Department of Chemistry; University of Helsinki; P. O. Box 55 FI-00014 Helsinki Finland
- Department of Chemistry; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Riccardo Tarroni
- Dipartimento di Chimica Industriale “Toso Montanari”; Università di Bologna, Viale; Risorgimento 4 40136 Bologna Italy
| | - Vladimir I. Feldman
- Department of Chemistry; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Leonid Khriachtchev
- Department of Chemistry; University of Helsinki; P. O. Box 55 FI-00014 Helsinki Finland
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16
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Penocchio E, Mendolicchio M, Tasinato N, Barone V. Structural features of the carbon-sulfur chemical bond: a semi-experimental perspective. CAN J CHEM 2016; 94:1065-1076. [PMID: 28912608 PMCID: PMC5595238 DOI: 10.1139/cjc-2016-0282] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this work semi-experimental and theoretical equilibrium geometries of 10 sulfur-containing organic molecules, as well as 4 oxygenated ones, are determined by means of a computational protocol based on density functional theory. The results collected in the present paper further enhance our online database of accurate semi-experimental equilibrium molecular geometries, adding 13 new molecules containing up to 8 atoms, for 12 of which the first semi-experimental equilibrium structure is reported, to the best of our knowledge. We focus in particular on sulfur-containing compounds, aiming both to provide new accurate data on some rather important chemical moieties, only marginally represented in the literature of the field, and to examine the structural features of carbon-sulfur bonds in the light of the previously presented linear regression approach. The structural changes issuing from substitution of oxygen by sulfur are discussed to get deeper insights on how modifications in electronic structure and nuclear potential can affect equilibrium geometries. With respect to our previous works, we perform non-linear constrained optimizations of equilibrium SE structures with a new general and user-friendly software under development in our group with updated definition of useful statistical indicators.
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Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem Rev 2016; 116:5105-54. [DOI: 10.1021/acs.chemrev.5b00533] [Citation(s) in RCA: 799] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | | | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
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18
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Fornaro T, Biczysko M, Bloino J, Barone V. Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases. Phys Chem Chem Phys 2016; 18:8479-90. [PMID: 26940362 PMCID: PMC5612391 DOI: 10.1039/c5cp07386c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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20
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Penocchio E, Piccardo M, Barone V. Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route. J Chem Theory Comput 2015; 11:4689-707. [PMID: 26574259 DOI: 10.1021/acs.jctc.5b00622] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.
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21
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Fornaro T, Burini D, Biczysko M, Barone V. Hydrogen-Bonding Effects on Infrared Spectra from Anharmonic Computations: Uracil–Water Complexes and Uracil Dimers. J Phys Chem A 2015; 119:4224-36. [DOI: 10.1021/acs.jpca.5b01561] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Diletta Burini
- Dipartimento
di Matematica e Informatica, Università di Perugia, INFN Sezione
Perugia Via Vanvitelli, I-106123 Perugia, Italy
| | - Malgorzata Biczysko
- Physics
Department, and International Centre for Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai, 200444 China
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici
(ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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22
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Piccardo M, Penocchio E, Puzzarini C, Biczysko M, Barone V. Semi-Experimental Equilibrium Structure Determinations by Employing B3LYP/SNSD Anharmonic Force Fields: Validation and Application to Semirigid Organic Molecules. J Phys Chem A 2015; 119:2058-82. [DOI: 10.1021/jp511432m] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Matteo Piccardo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Emanuele Penocchio
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle Ricerche, Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca CNR,
UOS di Pisa, Via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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23
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Fornaro T, Carnimeo I, Biczysko M. Toward Feasible and Comprehensive Computational Protocol for Simulation of the Spectroscopic Properties of Large Molecular Systems: The Anharmonic Infrared Spectrum of Uracil in the Solid State by the Reduced Dimensionality/Hybrid VPT2 Approach. J Phys Chem A 2014; 119:5313-26. [DOI: 10.1021/jp510101y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy
| | - Malgorzata Biczysko
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della
Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
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24
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Mączka M, Kadłubański P, Freire PTC, Macalik B, Paraguassu W, Hermanowicz K, Hanuza J. Temperature- and pressure-induced phase transitions in the metal formate framework of [ND₄][Zn(DCOO)₃] and [NH₄][Zn(HCOO)₃]. Inorg Chem 2014; 53:9615-24. [PMID: 25147972 DOI: 10.1021/ic501074x] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Vibrational properties and the temperature-induced phase transition mechanism have been studied in [NH4][Zn(HCOO)3] and [ND4][Zn(DCOO)3] metal organic frameworks by variable-temperature dielectric, IR, and Raman measurements. DFT calculations allowed proposing the detailed assignment of vibrational modes to respective motions of atoms in the unit cell. Temperature-dependent studies reveal a very weak isotopic effect on the phase transition temperature and confirm that ordering of ammonium cations plays a major role in the mechanism of the phase transition. We also present high-pressure Raman scattering studies on [ND4][Zn(DCOO)3]. The results indicate the rigidity of the formate ions and strong compressibility of the ZnO6 octahedra. They also reveal the onset of a pressure-induced phase transition at about 1.1 GPa. This transition has strong first-order character, and it is associated with a large distortion of the metal formate framework. Our data indicate the presence of at least two nonequivalent formate ions in the high-pressure structure with very different C-D bonds. The decompression experiment shows that the transition is reversible.
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Affiliation(s)
- Mirosław Mączka
- Institute of Low Temperature and Structure Research , Polish Academy of Sciences, Box 1410, 50-950 Wrocław 2, Poland
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25
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Latour RA. Perspectives on the simulation of protein-surface interactions using empirical force field methods. Colloids Surf B Biointerfaces 2014; 124:25-37. [PMID: 25028242 DOI: 10.1016/j.colsurfb.2014.06.050] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/21/2014] [Accepted: 06/23/2014] [Indexed: 12/25/2022]
Abstract
Protein-surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein-surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation.
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Affiliation(s)
- Robert A Latour
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA.
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26
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Fornaro T, Biczysko M, Monti S, Barone V. Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers. Phys Chem Chem Phys 2014; 16:10112-28. [PMID: 24531740 PMCID: PMC4612423 DOI: 10.1039/c3cp54724h] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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27
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Foi A, Corrêa RS, Ellena J, Doctorovich F, Di Salvo F. Halogen⋯halogen contacts for the stabilization of a new polymorph of 9,10-dichloroanthracene. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.11.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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29
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Maranzana A, Giordana A, Indarto A, Tonachini G, Barone V, Causà M, Pavone M. Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes. J Chem Phys 2013; 139:244306. [DOI: 10.1063/1.4846295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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30
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Liao MS, Huang MJ, Watts JD. Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study. J Phys Chem B 2013; 117:10103-14. [PMID: 23926882 PMCID: PMC3810174 DOI: 10.1021/jp403998u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron-histidine (Fe-His) binding. The Heme-AB (AB = O2, NO) and Fe-His binding energies in iron porphyrin FeP(His)(AB), myoglobin Mb(AB), H-NOX(AB), and Tyr140 → Phe mutated H-NOX[Y140F(AB)] were determined for comparison. The calculated stabilization of bound O2 is even higher in H-NOX than that in a myoglobin (Mb), consistent with the observation that the H-NOX domain of T. tengcongensis has a very high affinity for its oxygen molecule. Among the two different X-ray crystal structures for the Tt H-NOX protein, the calculated results for both AB = O2 and NO appear to support the crystal structure with the PDB code 1XBN , where the Trp9 and Asn74 residues do not form a hydrogen-bonding network with Tyr140. A hydrogen bond interaction from the polar residue does not have obvious effects on the Fe-His binding strength, but a dispersion contribution to Ebind(Fe-His) may be significant, depending on the crystal structure used. We speculate that the Fe-His binding strength in the deoxy form of a native protein could be an important factor in determining whether the bond of His to Fe is broken or maintained upon binding of NO to Fe.
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Affiliation(s)
- Meng-Sheng Liao
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - Ming-Ju Huang
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - John D. Watts
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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31
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Liao MS, Huang MJ, Watts JD. Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies. J Mol Model 2013; 19:3307-23. [PMID: 23661270 PMCID: PMC3726265 DOI: 10.1007/s00894-013-1864-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 04/18/2013] [Indexed: 10/26/2022]
Abstract
The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.
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Affiliation(s)
- Meng-Sheng Liao
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - Ming-Ju Huang
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - John D. Watts
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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32
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Chandar NB, Ganguly B. A first principles investigation of aging processes in soman conjugated AChE. Chem Biol Interact 2013; 204:185-90. [DOI: 10.1016/j.cbi.2013.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 05/10/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
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33
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On the Relevance of Considering the Intermolecular Interactions on the Prediction of the Vibrational Spectra of Isopropylamine. J CHEM-NY 2013. [DOI: 10.1155/2013/682514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effects of implicitly considering the effects of hydrogen bonding on the molecular properties, such as vibrational frequencies, were inferred on the basis of DFT calculations. Several clusters of isopropylamine were assembled and theoretically characterized. The results showed that maximum H-bond cooperativity is achieved when the amine group acts simultaneously as donor and acceptor. The effect of H-bond cooperativity manifests itself in the relative cluster stability and on the structural and vibrational frequency predictions. Referring to the vibrational frequencies it was found that theNH2stretching and torsion vibrational modes are the most affected by the amine involvement in hydrogen bonding. Both stretching modes were found to be significantly redshifted relative to the monomer. TheNH2torsional mode, on the other hand, was found to be blueshifted up to 350 cm-1. Finally, the comparative study between the theory levels performed allows to conclude that the small 6-31G* basis set is able to stabilize weakC–H⋯Ninteractions as long as the new dispersion corrected DFT methods are considered. The impairments observed with conventional DFT methods for describing weak interactions may be overcome with the improvement of basis set, but the associated increase of computational costs may turn the calculations unfeasible.
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Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study. J Inorg Biochem 2012; 118:28-38. [PMID: 23123336 DOI: 10.1016/j.jinorgbio.2012.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 11/21/2022]
Abstract
DFT and dispersion-corrected DFT calculations were carried out to probe the factors that distort the heme structure in Heme-Nitric oxide/OXygen-binding (H-NOX) protein domains. Various model systems that include heme, heme+surrounding residues, and heme+surrounding residues+additional protein environment were examined; the latter system was calculated with a quantum mechanics/molecular mechanics (QM/MM) method. The computations were extended to a myoglobin (Mb) protein, in which the heme structure is quite planar, in contrast to that in H-NOX. The natural tendency of the heme is to be planar. The strong structural distortion in H-NOX is mainly brought about by the intermolecular interactions between the whole heme molecule (heme ring plus its peripheral substituents) and the surrounding residues, among which the polar residues (Tyr140, Pro115, Mse98) play major roles in distorting the heme structure. The two peripheral propionate substituents that are oriented on the same side of the heme plane can also make the molecule distort, but the distortion caused by this factor is not significant. In Mb, the surrounding residues considered are all nonpolar and do not cause a structural distortion. The different structural features of the heme macrocycle in the different proteins (H-NOX and Mb) are reproduced by the calculations. The dispersion correction is necessary, since it improves the calculated structures. The effects of the distortion on the binding affinity of the axial ligand to the heme were also examined.
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35
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In search of OH–π interactions between 1-methylimidazole and water using a combined computational quantum chemistry and ATR-FTIR spectroscopy approach. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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36
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Ikabata Y, Nakai H. Extension of local response dispersion method to excited-state calculation based on time-dependent density functional theory. J Chem Phys 2012; 137:124106. [DOI: 10.1063/1.4754508] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Liao MS, Huang MJ, Watts JD. Assessment of dispersion corrections in DFT calculations on large biological systems. Mol Phys 2012. [DOI: 10.1080/00268976.2012.695811] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Rönnholm P, Gräfenstein J, Norrby PO, Hilmersson G, Nilsson Lill SO. A computational study of the enantioselective addition of n-BuLi to benzaldehyde in the presence of a chiral lithium N,P amide. Org Biomol Chem 2012; 10:2807-14. [DOI: 10.1039/c2ob06910e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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On the potential application of DFT methods in predicting the interaction-induced electric properties of molecular complexes. Molecular H-bonded chains as a case of study. J Mol Model 2011; 18:3073-86. [PMID: 22179307 PMCID: PMC3382286 DOI: 10.1007/s00894-011-1312-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 11/14/2011] [Indexed: 10/26/2022]
Abstract
A detailed analysis of the selected DFT functionals for the calculations of interaction-induced dipole moment, polarizability and first-order hyperpolarizability has been carried out. The hydrogen-bonded model chains consisting of HF, H(2)CO and H(3)N molecules have been chosen as a case study. The calculations of the components of the static electric properties using the diffuse Dunning's basis set (aug-cc-pVDZ) have been performed employing different types of density functionals (B3LYP, LC-BLYP, PBE0, M06-2X and CAM-B3LYP). Obtained results have been compared with those gained at the CCSD(T) level of theory. The counterpoise correction scheme, namely site-site function counterpoise, has been applied in order to eliminate basis set superposition error. The performed tests allow to conclude that the DFT functionals can provide a useful tool for prediction of the interaction-induced electric properties, however a caution has to be urged to their decomposition to the two- and many-body terms.
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40
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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41
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1165] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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Pietraperzia G, Pasquini M, Mazzoni F, Piani G, Becucci M, Biczysko M, Michalski D, Bloino J, Barone V. Noncovalent Interactions in the Gas Phase: The Anisole–Phenol Complex. J Phys Chem A 2011; 115:9603-11. [DOI: 10.1021/jp200444a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giangaetano Pietraperzia
- LENS, Polo Scientifico e Tecnologico dell’Università di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
- Dipartimento di Chimica, Polo Scientifico e Tecnologico dell’Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Massimiliano Pasquini
- LENS, Polo Scientifico e Tecnologico dell’Università di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
- Dipartimento di Chimica, Polo Scientifico e Tecnologico dell’Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Federico Mazzoni
- LENS, Polo Scientifico e Tecnologico dell’Università di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
- Dipartimento di Chimica, Polo Scientifico e Tecnologico dell’Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Giovanni Piani
- LENS, Polo Scientifico e Tecnologico dell’Università di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
| | - Maurizio Becucci
- LENS, Polo Scientifico e Tecnologico dell’Università di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
- Dipartimento di Chimica, Polo Scientifico e Tecnologico dell’Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Malgorzata Biczysko
- Scuola Normale Superiore di Pisa and INFN Sezione di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Department of Chemistry “P. Corradini”, Università di Napoli “Federico II” and INSTM “M3-Village”, Complesso Universitario Monte Sant’Angelo, Via Cintia, 80126 Naples, Italy
| | - Daniel Michalski
- Department of Chemistry “P. Corradini”, Università di Napoli “Federico II” and INSTM “M3-Village”, Complesso Universitario Monte Sant’Angelo, Via Cintia, 80126 Naples, Italy
| | - Julien Bloino
- Scuola Normale Superiore di Pisa and INFN Sezione di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Department of Chemistry “P. Corradini”, Università di Napoli “Federico II” and INSTM “M3-Village”, Complesso Universitario Monte Sant’Angelo, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa and INFN Sezione di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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Gautier R, Audebrand N, Furet E, Gautier R, Fur EL. VOPO4·H2O: A Stacking Faults Structure Studied by X-ray Powder Diffraction and DFT-D Calculations. Inorg Chem 2011; 50:4378-83. [DOI: 10.1021/ic102473s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Romain Gautier
- Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes 1-Ecole Nationale Supérieure de Chimie de Rennes, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
| | - Nathalie Audebrand
- Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes 1-Ecole Nationale Supérieure de Chimie de Rennes, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
| | - Eric Furet
- Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes 1-Ecole Nationale Supérieure de Chimie de Rennes, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
| | - Régis Gautier
- Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes 1-Ecole Nationale Supérieure de Chimie de Rennes, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
| | - Eric Le Fur
- Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes 1-Ecole Nationale Supérieure de Chimie de Rennes, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
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Green JR, Dunbar RC. When Do Molecular Bowls Encapsulate Metal Cations? J Phys Chem A 2011; 115:4968-75. [DOI: 10.1021/jp111843r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jason R. Green
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Robert C. Dunbar
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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Nilsson Lill SO. On the dimerization of chlorophyll in photosystem II. Phys Chem Chem Phys 2011; 13:16022-7. [DOI: 10.1039/c1cp21390c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Larkin JD, Fossey JS, James TD, Brooks BR, Bock CW. A computational investigation of the nitrogen-boron interaction in o-(N,N-dialkylaminomethyl)arylboronate systems. J Phys Chem A 2010; 114:12531-9. [PMID: 21050022 DOI: 10.1021/jp1087674] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
o-(N,N-Dialkylaminomethyl)arylboronate systems are an important class of compounds in diol-sensor development. We report results from a computational investigation of fourteen o-(N,N-dialkylaminomethyl)arylboronates using second-order Møller-Plesset (MP2) perturbation theory. Geometry optimizations were performed at the MP2/cc-pVDZ level and followed by single-point calculations at the MP2/aug-cc-pVDZ(cc-pVTZ) levels. These results are compared to those from density functional theory (DFT) at the PBE1PBE(PBE1PBE-D)/6-311++G(d,p)(aug-cc-pVDZ) levels, as well as to experiment. Results from continuum PCM and CPCM solvation models were employed to assess the effects of a bulk aqueous environment. Although the behavior of o-(N,N-dialkylaminomethyl) free acid and ester proved to be complicated, we were able to extract some important trends from our calculations: (1) for the free acids the intramolecular hydrogen-bonded B-O-H···N seven-membered ring conformers 12 and 16 are found to be slightly lower in energy than the dative-bonded N→B five-membered ring conformers 10 and 14 while conformers 13 and 17, with no direct boron-nitrogen interaction, are significantly higher in energy than 12 and 16; (2) for the esters where no intramolecular B-O-H···N bonded form is possible, the N→B conformers 18 and 21 are significantly lower in energy than the no-interaction forms 20 and 23; (3) H(2)O insertion reactions into the N→B structures 10, 14, 18, and 21 leading to the seven-membered intermolecular hydrogen-bonded B···OH(2)···N ring structures 11, 15, 19, and 22 are all energetically favorable.
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Affiliation(s)
- Joseph D Larkin
- National Heart, Lung, and Blood Institute, The National Institutes of Health, Building 50, Bethesda, Maryland 20851, USA
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Pedone A, Biczysko M, Barone V. Environmental effects in computational spectroscopy: accuracy and interpretation. Chemphyschem 2010; 11:1812-32. [PMID: 20358575 DOI: 10.1002/cphc.200900976] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical-chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.
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Affiliation(s)
- Alfonso Pedone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, Italy
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Bretherick NH, van Mourik T. π Interactions Studied with Electronic Structure Methods: The Ethyne Methyl Isocyanide Complex and Thioanisole. J Chem Theory Comput 2010; 6:2687-700. [DOI: 10.1021/ct100295f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Natalie H. Bretherick
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| | - Tanja van Mourik
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
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Biswal HS, Shirhatti PR, Wategaonkar S. O−H···O versus O−H···S Hydrogen Bonding. 2. Alcohols and Thiols as Hydrogen Bond Acceptors. J Phys Chem A 2010; 114:6944-55. [DOI: 10.1021/jp102346n] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Himansu S. Biswal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
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Xiong R, Keffer DJ, Fuentes-Cabrera M, Nicholson DM, Michalkova A, Petrova T, Leszczynski J, Odbadrakh K, Doss BL, Lewis JP. Effect of charge distribution on RDX adsorption in IRMOF-10. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:5942-5950. [PMID: 20205416 DOI: 10.1021/la9039013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Quantum mechanical (QM) calculations, classical grand canonical Monte Carlo (GCMC) simulations, and classical molecular dynamics (MD) simulations are performed to test the effect of charge distribution on hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) adsorption and diffusion in IRMOF-10. Several different methods for mapping QM electron distributions onto atomic point charges are explored, including the electrostatic potential (ESP) method, Mulliken population analysis, Lowdin population analysis, and natural bond orbital analysis. Classical GCMC and MD simulations of RDX in IRMOF-10 are performed using 15 combinations of charge sources of RDX and IRMOF-10. As the charge distributions vary, interaction potential energies, the adsorption loading, and the self-diffusivities are significantly different. None of the 15 combinations are able to quantitatively capture the dependence of the energy of adsorption on local configuration of RDX as observed in the QM calculations. We observe changes in the charge distributions of RDX and IRMOF-10 with the introduction of an RDX molecule into the cage. We also observe a large dispersion contribution to the interaction energy from QM calculations that is not reproduced in the classical simulations, indicating that the source of discrepancy may not lie exclusively with the assignment of charges.
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Affiliation(s)
- Ruichang Xiong
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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