1
|
Hayashi S, Kato T, Sugibayashi Y, Nakanishi W. Dynamic and Static Nature of XH-∗-π and YX-∗-π (X = F, Cl, Br, and I; Y = X and F) in the Distorted π-System of Corannulene Elucidated with QTAIM Dual Functional Analysis. Molecules 2023; 28:molecules28104219. [PMID: 37241959 DOI: 10.3390/molecules28104219] [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: 03/01/2023] [Revised: 04/28/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The dynamic and static nature of the XH-∗-π and YX-∗-π (X = F, Cl, Br, and I; Y = X and F) interactions in the distorted π-system of corannulene (π(C20H10)) is elucidated with a QTAIM dual functional analysis (QTAIM-DFA), where asterisks emphasize the presence of bond critical points (BCPs) on the interactions. The static and dynamic nature originates from the data of the fully optimized and perturbed structures, respectively, in QTAIM-DFA. On the convex side, H in F-H-∗-π(C20H10) and each X in Y-X-∗-π(C20H10) join to C of the central five-membered ring in π(C20H10) through a bond path (BP), while each H in X-H-∗-π(C20H10) does so to the midpoint of C=C in the central five-membered ring for X = Cl, Br, or I. On the concave side, each X in F-X-∗-π(C20H10) also joins to C of the central five-membered ring with a BP for X = H, Cl, Br, and I; however, the interactions in other adducts are more complex than those on the convex side. Both H and X in X-H-∗-π(C20H10) (X = Cl and Br) and both Fs in F-F-∗-π(C20H10) connect to the three C atoms in each central five-membered ring (with three BPs). Two, three, and five BPs were detected for the Cl-Cl, I-H, Br-Br, and I-I adducts, where some BPs do not stay on the central five-membered ring in π(C20H10). The interactions are predicted to have a vdW to CT-MC nature. The interactions on the concave side seem weaker than those on the convex side for X-H-∗-π(C20H10), whereas the inverse trend is observed for Y-X-∗-π(C20H10) as a whole. The nature of the interactions in the π(C20H10) adducts of the convex and concave sides is examined in more detail, employing the adducts with X-H and F-X placed on their molecular axis together with the π(C24H12) and π(C6H6) adducts.
Collapse
Affiliation(s)
- Satoko Hayashi
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Takahiro Kato
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yuji Sugibayashi
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Waro Nakanishi
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| |
Collapse
|
2
|
Hayashi S, Nishide T, Nakanishi W. Nature of intramolecular O-H⋯π interactions as elucidated by QTAIM dual functional analysis with QC calculations. RSC Adv 2019; 9:15521-15530. [PMID: 35514837 PMCID: PMC9064312 DOI: 10.1039/c9ra01788g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/09/2019] [Indexed: 11/21/2022] Open
Abstract
The intrinsic dynamic and static nature of intramolecular OH-*-π interactions is elucidated using a QTAIM dual functional analysis (QTAIM-DFA) after clarifying the structural features. Asterisks (*) are employed to emphasize the presence of bond critical points (BCPs) on the bond paths (BPs), which correspond to the interactions in question. Data from the fully optimized structures correspond to the static nature of the interactions. In our treatment, data from the perturbed structures, which are based around the fully optimized structure, are employed for the analysis in addition to those from the fully optimized structure, which represent the dynamic nature of the interaction. Seven intramolecular OH-*-C(π) interactions were detected in six-membered rings, with six BPs and BCPs for each, among the 72 conformers of the species examined here (1-15). The interactions are predicted to have a vdW or t-HBnc (typical hydrogen bonds with no covalency) nature, which appeared in the pure closed shell region. They appear to be stronger than the corresponding intermolecular interactions. Nine BPs with BCPs were also detected for the intramolecular O-*-X interactions (X = C(π) and H(π), joined to C(π)) in the 5-7-membered rings. The E(2) values of the interactions, as obtained by NBO, are discussed in relation to the stabilities of the conformers and the BPs with BCPs.
Collapse
Affiliation(s)
- Satoko Hayashi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| | - Taro Nishide
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| | - Waro Nakanishi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| |
Collapse
|
3
|
Nishide T, Hayashi S, Nakanishi W. Intrinsic Dynamic Nature of Neutral Hydrogen Bonds Elucidated with QTAIM Dual Functional Analysis: Role of the Compliance Force Constants and QTAIM-DFA Parameters in Stability. ChemistryOpen 2018; 7:565-575. [PMID: 30094124 PMCID: PMC6077874 DOI: 10.1002/open.201800051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Indexed: 12/24/2022] Open
Abstract
The dynamic and static nature of various neutral hydrogen bonds (nHBs) is elucidated with quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA). The perturbed structures generated by using the coordinates derived from the compliance force constants (Cij ) of internal vibrations are employed for QTAIM-DFA. The method is called CIV. The dynamic nature of CIV is described as the "intrinsic dynamic nature", as the coordinates are invariant to the choice of the coordinate system. nHBs are, for example, predicted to be van der Waals (H2Se-✶-HSeH; ✶=bond critical point), t-HBnc (typical-HBs with no covalency: HI-✶-HI), t-HBwc (t-HBs with covalency: H2C=O-✶-HI), CT-MC [molecular complex formation through charge transfer (CT): H2C=O-✶-HF], and CT-TBP (trigonal bipyramidal adduct formation through CT: H3N-✶-HI) in nature. The results with CIV were the same as those with POM in the calculation errors, for which the perturbed structures were generated by partial optimization, and the interaction distances in question were fixed suitably in POM. The highly excellent applicability of CIV for QTAIM-DFA was demonstrated for the various nHBs, as well as for the standard interactions previously reported. The stability of the HBs, evaluated by ΔE, is well correlated with Cij (ΔE×Cij =constant value of -165.64), and the QTAIM parameters, although a few deviations were detected.
Collapse
Affiliation(s)
- Taro Nishide
- Wakayama UniversityFaculty of Systems EngineeringWakayamaJapan
| | - Satoko Hayashi
- Wakayama UniversityFaculty of Systems EngineeringWakayamaJapan
| | - Waro Nakanishi
- Wakayama UniversityFaculty of Systems EngineeringWakayamaJapan
| |
Collapse
|
4
|
Hayashi S, Sugibayashi Y, Nakanishi W. Behaviour of the XH-*-π and YX-*-π interactions (X, Y = F, Cl, Br and I) in the coronene π-system, as elucidated by QTAIM dual functional analysis with QC calculations. RSC Adv 2018; 8:16349-16361. [PMID: 35542236 PMCID: PMC9080335 DOI: 10.1039/c8ra01862f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/24/2018] [Indexed: 11/24/2022] Open
Abstract
The dynamic and static nature of XH-*-π and YX-*-π in the coronene π-system (π(C24H12)) is elucidated by QTAIM dual functional analysis, where * emphasizes the presence of bond critical points (BCPs) in the interactions. The nature of the interactions is elucidated by analysing the plots of the total electron energy densities H b(r c) versus H b(r c) - V b(r c)/2 [=(ħ 2/8m)∇2 ρ b(r c)] for the interactions at BCPs, where V b(r c) are the potential energy densities at the BCPs. The data for the perturbed structures around the fully optimized structures are employed for the plots in addition to those of the fully optimized structures. The plots are analysed using the polar coordinate of (R, θ) for the data of the fully optimized structures, while those containing the perturbed structures are analysed using (θ p, κ p), where θ p corresponds to the tangent line of each plot and κ p is the curvature. Whereas (R, θ) show the static nature, (θ p, κ p) represent the dynamic nature of the interactions. All interactions in X-H-*-π(C24H12) (X = F, Cl, Br and I) and Y-X-*-π(C24H12) (Y-X = F-F, Cl-Cl, Br-Br, I-I, F-Cl, F-Br and F-I) are classified by pure CS (closed shell) interactions and are characterized as having the vdW nature, except for X-H = F-H and Y-X = F-Cl, F-Br and F-I, which show the typical-HB nature without covalency. The structural features of the complexes are also discussed.
Collapse
Affiliation(s)
- Satoko Hayashi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| | - Yuji Sugibayashi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| | - Waro Nakanishi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| |
Collapse
|
5
|
Tsubomoto Y, Hayashi S, Nakanishi W, Mapp LK, Coles SJ. High-resolution X-ray diffraction determination of the electron density of 1-(8-PhSC 10H 6)SS(C 10H 6SPh-8')-1' with the QTAIM approach: evidence for S 4 σ(4c-6e) at the naphthalene peri-positions. RSC Adv 2018; 8:9651-9660. [PMID: 35540809 PMCID: PMC9078645 DOI: 10.1039/c7ra13636f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 02/20/2018] [Indexed: 12/18/2022] Open
Abstract
An extended hypervalent S4 σ(4c-6e) system was confirmed for the linear BS-∗-AS-∗-AS-∗-BS interaction in 1-(8-PhBSC10H6)AS-AS(C10H6 BSPh-8')-1' (1) via high-resolution X-ray diffraction determination of electron densities. The presence of bond critical points (BCPs; ∗) on the bond paths confirms the nature and extent of this interaction. The recently developed QTAIM dual functional analysis (QTAIM-DFA) approach was also applied to elucidate the nature of the interaction. Total electron energy densities H b( r c) were plotted versus H b( r c) - V b( r c)/2 for the interaction at the BCPs, where V b( r c) represents the potential energy densities at the BCP. The results indicate that although the data for an interaction in the fully optimized structure corresponds to a static nature, the data obtained for the perturbed structures around it represent the dynamic nature of the interaction in QTAIM-DFA. The former classifies the interaction and the latter characterises it. Although AS-∗-AS in 1 is classified by a shared shell interaction and exhibits weak covalent character, AS-∗-BS is characterized as having typical hydrogen-bond nature with covalent properties in the region of the regular closed shell interactions. The experimental results are supported by matching theoretical calculations throughout, particularly for the extended hypervalent E4 σ(4c-6e) (E = S) interaction.
Collapse
Affiliation(s)
- Yutaka Tsubomoto
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| | - Satoko Hayashi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| | - Waro Nakanishi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan +81 73 457 8253 +81 73 457 8252
| | - Lucy K Mapp
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton Southampton SO17 1BJ UK +44 (0)2380596721
| | - Simon J Coles
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton Southampton SO17 1BJ UK +44 (0)2380596721
| |
Collapse
|
6
|
Behavior of the E-E' Bonds (E, E' = S and Se) in Glutathione Disulfide and Derivatives Elucidated by Quantum Chemical Calculations with the Quantum Theory of Atoms-in-Molecules Approach. Molecules 2018; 23:molecules23020443. [PMID: 29462964 PMCID: PMC6017556 DOI: 10.3390/molecules23020443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/10/2018] [Accepted: 02/14/2018] [Indexed: 11/25/2022] Open
Abstract
The nature of the E–E’ bonds (E, E’ = S and Se) in glutathione disulfide (1) and derivatives 2–3, respectively, was elucidated by applying quantum theory of atoms-in-molecules (QTAIM) dual functional analysis (QTAIM-DFA), to clarify the basic contribution of E–E’ in the biological redox process, such as the glutathione peroxidase process. Five most stable conformers a–e were obtained, after applying the Monte-Carlo method then structural optimizations. In QTAIM-DFA, total electron energy densities Hb(rc) are plotted versus Hb(rc) − Vb(rc)/2 at bond critical points (BCPs), where Vb(rc) are potential energy densities at BCPs. Data from the fully optimized structures correspond to the static nature. Those containing perturbed structures around the fully optimized one in the plot represent the dynamic nature of interactions. The behavior of E–E’ was examined carefully. Whereas E–E’ in 1a–3e were all predicted to have the weak covalent nature of the shared shell interactions, two different types of S–S were detected in 1, depending on the conformational properties. Contributions from the intramolecular non-covalent interactions to stabilize the conformers were evaluated. An inverse relationship was observed between the stability of a conformer and the strength of E–E’ in the conformer, of which reason was discussed.
Collapse
|
7
|
Masumoto Y, Miyamoto K, Iuchi T, Ochiai M, Hirano K, Saito T, Wang C, Uchiyama M. Mechanistic Study on Aryl-Exchange Reaction of Diaryl-λ 3-iodane with Aryl Iodide. J Org Chem 2018; 83:289-295. [PMID: 29183123 DOI: 10.1021/acs.joc.7b02701] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Because of its hyper-leaving ability, as well as its strong oxidizing ability, diaryl(triflato)-λ3-iodane transfers one of the aryl groups to iodoarenes simply upon gentle heating (>85 °C) in nonpolar solvents. We have performed an in-depth mechanistic study of this unusual aryl transfer reaction. A combination of experimental (product analysis, kinetic study, and substituent effects) and density functional theoretical approaches revealed that the reaction proceeds through a concerted bimolecular transition state, in which ipso-carbon binds loosely to both iodine centers. We also evaluated electronic effects on the thermodynamic stability of diaryl-λ3-iodanes.
Collapse
Affiliation(s)
- Yui Masumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan.,Elements Chemistry Laboratory, RIKEN, and Advanced Elements Chemistry Research Team, RIKEN Center for Sustainable Resource Science (CSRS) , Wako-shi, Saitama 351-0198, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takuto Iuchi
- Graduate School of Pharmaceutical Sciences, Tokushima University , 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Masahito Ochiai
- Graduate School of Pharmaceutical Sciences, Tokushima University , 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Keiichi Hirano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsuo Saito
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chao Wang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan.,Elements Chemistry Laboratory, RIKEN, and Advanced Elements Chemistry Research Team, RIKEN Center for Sustainable Resource Science (CSRS) , Wako-shi, Saitama 351-0198, Japan
| |
Collapse
|
8
|
Jouypazadeh H, Farrokhpour H, Solimannejad M. The effect of the hydrogen fluoride chain on the aromaticity of C6H6 in the C6H6···(HF)1–4 complexes. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1384578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
9
|
Hayashi S, Nagata K, Otsuki S, Nakanishi W. Linear Four-Chalcogen Interactions in Radical Cationic and Dicationic Dimers of 1,5-(Dichalcogena)canes: Nature of the Interactions Elucidated by QTAIM Dual Functional Analysis with QC Calculations. J Phys Chem A 2017; 121:2482-2496. [PMID: 28257204 DOI: 10.1021/acs.jpca.7b00667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamic and static nature of extended hypervalent interactions of the BE···AE···AE···BE type are elucidated for four center-seven electron interactions (4c-7e) in the radical cationic dimers (1·+) and 4c-6e in the dicationic dimers (12+) of 1,5-(dichalcogena)canes (2: AE(CH2CH2CH2)2BE: AE, BE = S, Se, Te, and O). The quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA) is applied for the analysis. Total electron energy densities Hb(rc) are plotted versus Hb(rc) - Vb(rc)/2 [= (ℏ2/8m)∇2ρb(rc)] at bond critical points (BCPs) of the interactions, where Vb(rc) values show potential energy densities at BCPs. Data from the fully optimized structures correspond to the static nature of the interactions. Those from the perturbed structures around the fully optimized ones are also plotted, in addition to those of the fully optimized ones, which represent the dynamic nature of interactions. The BE···AE-AE···BE interactions in 12+ are stronger than the corresponding ones in 1·+, respectively. On the one hand, for 12+ with AE, BE = S, Se, and Te, AE···AE are all classified by the shared shell interactions and predicted to have the weak covalent nature, except for those in 1a2+ (AE = BE = S) and 1d2+ (AE = BE = Se), which have the nature of regular closed shell (r-CS)/trigonal bipyramidal adduct formation through charge transfer (CT-TBP). On the other hand, AE···BE are predicted to have the nature of r-CS/molecular complex formation through charge transfer for 1a2+, 1b2+ (AE = Se; BE = S), and 1d2+ or r-CS/CT-TBP for 1c2+ (AE = Te; BE = S), 1e2+ (AE = Te; BE = Se), and 1f2+ (AE = BE = Te). The BE···AE-AE···BE interactions in 1·+ and 12+ are well-analyzed by applying QTAIM-DFA.
Collapse
Affiliation(s)
- Satoko Hayashi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University , 930 Sakaedani, Wakayama 640-8510, Japan
| | - Kengo Nagata
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University , 930 Sakaedani, Wakayama 640-8510, Japan
| | - Shota Otsuki
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University , 930 Sakaedani, Wakayama 640-8510, Japan
| | - Waro Nakanishi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University , 930 Sakaedani, Wakayama 640-8510, Japan
| |
Collapse
|
10
|
Tsubomoto Y, Hayashi S, Nakanishi W, Sasamori T, Tokitoh N. Nature ofE2X2σ(4c–6e) of theX---E—E---Xtype at naphthalene 1,8-positions and model, elucidated by X-ray crystallographic analysis and QC calculations with the QTAIM approach. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:265-275. [DOI: 10.1107/s205252061700364x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/07/2017] [Indexed: 11/10/2022]
Abstract
The nature ofE2X2σ(4c–6e) of theX-*-E-*-E-*-Xtype is elucidated for 1-(8-XC10H6)E–E(C10H6X-8′)-1′ [(1)E,X= S, Cl; (2) S, Br; (3) Se, Cl; (4) Se, Br] after structural determination of (1), (3) and (4), together with modelA[MeX---E(H)—E(H)---XMe (E= S and Se;X= Cl and Br)]. The quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA) is applied. The total electron energy densitiesHb(rc) are plottedversus Hb(rc) –Vb(rc)/2 for the interactions at the bond critical points (BCPs; *), whereVb(rc) show the potential energy densities at the BCPs. Data for the perturbed structures around the fully optimized structures are employed for the plots, in addition to those of the fully optimized structures. The plots were analysed using the polar coordinate (R, θ) representation of the data of the fully optimized structures. Data containing the perturbed structures were analysed by (θp, κp), where θpcorresponds to the tangent line of the plot and κpis the curvature. Whereas (R, θ) shows the static nature, (θp, κp) represents the dynamic nature of interactions.E-*-Eare all classified as shared shell (S) interactions for (1)–(4) and as weak covalent (Cov-w) in nature (S/Cov-w). The nature ofpureCS (closed shell)/typical-HB (hydrogen bond) with no covalency is predicted forE-*-Xin (1) and (3),regularCS/typical-HB nature with covalency is predicted for (4), and an intermediate nature is predicted for (2). The NBO energies evaluated forE-*-Xin (1)–(4) are substantially larger than those in modelAdue the shortened length at the naphthalene 1,8-positions. The nature ofE2X2of σ(4c–6e) is well elucidatedviaQTAIM-DFA.
Collapse
|
11
|
Matsuiwa K, Hayashi S, Nakanishi W. Dynamic and Static Behavior of Intramolecular π-π Interactions in [2.2]- and [3.3]Cyclophanes, Elucidated by QTAIM Dual Functional Analysis with QC Calculations. ChemistrySelect 2017. [DOI: 10.1002/slct.201602047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kohei Matsuiwa
- Department of Material Science and Chemistry; Faculty of Systems Engineering, Wakayama University; 930 Sakaedani Wakayama 640-8510 Japan
| | - Satoko Hayashi
- Department of Material Science and Chemistry; Faculty of Systems Engineering, Wakayama University; 930 Sakaedani Wakayama 640-8510 Japan
| | - Waro Nakanishi
- Department of Material Science and Chemistry; Faculty of Systems Engineering, Wakayama University; 930 Sakaedani Wakayama 640-8510 Japan
| |
Collapse
|
12
|
Matsuiwa K, Hayashi S, Nakanishi W. Intramolecular π-π Interactions in Diethanodihydronaphthalene and Derivatives: Dynamic and Static Behavior of the Interactions Elucidated by QTAIM Dual Functional Analysis. ChemistrySelect 2016. [DOI: 10.1002/slct.201600429] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kohei Matsuiwa
- Department of Material Science and Chemistry; Faculty of Systems Engineering; Wakayama University; 930 Sakaedani Wakayama 640-8510 Japan
| | - Satoko Hayashi
- Department of Material Science and Chemistry; Faculty of Systems Engineering; Wakayama University; 930 Sakaedani Wakayama 640-8510 Japan
| | - Waro Nakanishi
- Department of Material Science and Chemistry; Faculty of Systems Engineering; Wakayama University; 930 Sakaedani Wakayama 640-8510 Japan
| |
Collapse
|
13
|
Sugibayashi Y, Hayashi S, Nakanishi W. Behavior of Halogen Bonds of the Y-X⋅⋅⋅π Type (X, Y=F, Cl, Br, I) in the Benzene π System, Elucidated by Using a Quantum Theory of Atoms in Molecules Dual-Functional Analysis. Chemphyschem 2016; 17:2579-89. [PMID: 27124373 DOI: 10.1002/cphc.201600227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Indexed: 01/30/2023]
Abstract
The nature of halogen bonds of the Y-X-✶-π(C6 H6 ) type (X, Y=F, Cl, Br, and I) have been elucidated by using the quantum theory of atoms in molecules (QTAIM) dual-functional analysis (QTAIM-DFA), which we proposed recently. Asterisks (✶) emphasize the presence of bond-critical points (BCPs) in the interactions in question. Total electron energy densities, Hb (rc ), are plotted versus Hb (rc )-Vb (rc )/2 [=(ħ(2) /8m)∇(2) ρb (rc )] for the interactions in QTAIM-DFA, in which Vb (rc ) are potential energy densities at the BCPs. Data for perturbed structures around fully optimized structures were used for the plots, in addition to those of the fully optimized ones. The plots were analyzed by using the polar (R, θ) coordinate for the data of fully optimized structures with (θp , κp ) for those that contained the perturbed structures; θp corresponds to the tangent line of the plot and κp is the curvature. Whereas (R, θ) corresponds to the static nature, (θp , κp ) represents the dynamic nature of the interactions. All interactions in Y-X-✶-π(C6 H6 ) are classified by pure closed-shell interactions and characterized to have vdW nature, except for Y-I-✶-π(C6 H6 ) (Y=F, Cl, Br) and F-Br-✶-π(C6 H6 ), which have typical hydrogen-bond nature without covalency. I-I-✶-π(C6 H6 ) has a borderline nature between the two. Y-F-✶-π(C6 H6 ) (Y=Br, I) were optimized as bent forms, in which Y-✶-π interactions were detected. The Y-✶-π interactions in the bent forms are predicted to be substantially weaker than those in the linear F-Y-✶-π(C6 H6 ) forms.
Collapse
Affiliation(s)
- Yuji Sugibayashi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama, 640-8510, Japan
| | - Satoko Hayashi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama, 640-8510, Japan.
| | - Waro Nakanishi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama, 640-8510, Japan.
| |
Collapse
|
14
|
Holguín-Gallego FJ, Chávez-Calvillo R, García-Revilla M, Francisco E, Pendás ÁM, Rocha-Rinza T. Electron correlation in the interacting quantum atoms partition via coupled-cluster lagrangian densities. J Comput Chem 2016; 37:1753-65. [DOI: 10.1002/jcc.24372] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Fernando José Holguín-Gallego
- Institute of Chemistry; National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria; Delegación Coyoacán C.P. 04510 Mexico City Mexico
| | - Rodrigo Chávez-Calvillo
- School of Chemistry; National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria; Delegación Coyoacán C.P. 04510 Mexico City Mexico
| | - Marco García-Revilla
- Department of Chemistry; Division of Natural and Exact Sciences; University of Guanajuato; C.P. 36050, Guanajuato Guanajuato Mexico
| | - Evelio Francisco
- Department of Physical and Analytical Chemistry; University of Oviedo; Julián Clavería 8 Oviedo Spain
| | - Ángel Martín Pendás
- Department of Physical and Analytical Chemistry; University of Oviedo; Julián Clavería 8 Oviedo Spain
| | - Tomás Rocha-Rinza
- Institute of Chemistry; National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria; Delegación Coyoacán C.P. 04510 Mexico City Mexico
| |
Collapse
|
15
|
Hayashi S, Sugibayashi Y, Nakanishi W. Dynamic and static behavior of the H...π and E...π interactions in EH₂ adducts of benzene π-system (E = O, S, Se and Te), elucidated by QTAIM dual functional analysis. Phys Chem Chem Phys 2016; 18:9948-60. [PMID: 26818845 DOI: 10.1039/c5cp06062a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic and static behavior of the interactions in the EH2 adducts of a benzene π-system (E = O, S, Se and Te) is elucidated by applying QTAIM-DFA (QTAIM dual functional analysis). Two types of H-*-π and E-*-π interactions are detected in the adducts, where the asterisk (*) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Total electron energy densities Hb(rc) are plotted versus Hb(rc) -Vb(rc)/2 [=(ℏ(2)/8m)∇(2)ρb(rc)] at BCPs in QTAIM-DFA, where Vb(rc) are the potential energy densities at BCPs. Data from the fully optimized structures are analyzed by polar (R, θ) coordinate representation. Each plot for an interaction, containing data from the perturbed structures with those of the fully optimized one, shows a specific curve, which provides important information. The plot is expressed by (θp, κp): θp corresponds to the tangent line for the plot and κp is the curvature. θ and θp are measured from the y-axis and y-direction, respectively. Moreover, (R, θ) corresponds to the static nature, (θp, κp) represents the dynamic nature of interactions. While θ classifies the interaction in question, θp characterizes it. Both values are less than 90° for all H-*-π and E-*-π interactions examined in this study; therefore, they are all classified by the pure closed-shell interactions and predicted to have the character of vdW nature. However, it is suggested that E-*-π has the nature of the stronger interaction than the case of H-*-π for dynamic behavior in the same species evaluated at the MP2 and M06-2X levels. The nature of the interactions is well analyzed and specified by applying QTAIM-DFA.
Collapse
Affiliation(s)
- Satoko Hayashi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan.
| | | | | |
Collapse
|
16
|
Nakanishi W, Tsubomoto Y, Hayashi S. Nature of S2Se2 σ(4c–6e) at naphthalene 1,8-positions and models, elucidated by QTAIM dual functional analysis. RSC Adv 2016. [DOI: 10.1039/c6ra17767k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The nature of BE–*–AE–*–AE–*–BE σ(4c–6e) is primarily elucidated at naphthalene 1,8-positions: while the weak covalent nature is predicted for all AE–*–AE, the HB nature with covalency or the CT-MC (MC formation through CT) nature is for AE–*–BE.
Collapse
Affiliation(s)
- Waro Nakanishi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
| | - Yutaka Tsubomoto
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
| | - Satoko Hayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
| |
Collapse
|