1
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Tognetti V, Joubert L. Exchange-correlation effects in interatomic energies for pure density functionals and their application to the molecular energy prediction. J Comput Chem 2024; 45:2270-2283. [PMID: 38847367 DOI: 10.1002/jcc.27431] [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: 11/28/2023] [Revised: 04/02/2024] [Accepted: 04/28/2024] [Indexed: 08/15/2024]
Abstract
In this proof-of-concept paper, we show how exchange-correlation effects can be simply recovered for interatomic energies within the interacting quantum atoms decomposition when local, gradient generalized, or meta-gradient generalized approximations are used in density functional theory (DFT) calculations. We also demonstrate how inhomogeneity and non-local effects can be introduced even from a pure local scheme, without resorting to any orbital information. Finally, we provide numerical evidence on a database of selected energetic molecules that this decomposition scheme can be efficiently used to build accurate models for the prediction of molecular energies from an initial "cheap" DFT calculation.
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Affiliation(s)
- Vincent Tognetti
- University of Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie University, Rouen, France
| | - Laurent Joubert
- University of Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie University, Rouen, France
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2
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Gray NAG, Vargas-Baca I, Emslie DJH. A Synthetic, Structural, Spectroscopic, and Computational Study of Alkali Metal-Thioether, -Selenoether, and -Telluroether Interactions. Inorg Chem 2023; 62:16974-16985. [PMID: 37782565 DOI: 10.1021/acs.inorgchem.3c02719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The rigid thioether- and selenoether-containing pro-ligands, 4,5-bis(phenylsulfido)-2,7,9,9-tetramethylacridan (H[AS2Ph2] (1)) and 4,5-bis(phenylselenido)-2,7,9,9-tetramethylacridan (H[ASe2Ph2] (2)), were deprotonated with one equiv of nBuLi to afford dimeric lithium complexes [Li(AE2Ph2)]2 (E = S (3), Se (4)) or with one equiv of KCH2Ph to afford the previously reported potassium complexes [K(AS2Ph2)(dme)]x (5) and [K(ASe2Ph2)(dme)2] (6). Attempts to prepare a direct telluroether analogue of compounds 1-2 were unsuccessful. However, the bulky selenoether- and telluroether-containing pro-ligands 4,5-bis(2,4,6-triisopropylphenylselenido)-2,7,9,9-tetramethylacridan (H[ASe2Tripp2] (7)) and 4,5-bis(2,4,6-triisopropylphenyltellurido)-2,7,9,9-tetramethylacridan (H[ATe2Tripp2] (8)) were accessed via the reaction of 4,5-dibromo-2,7,9,9-tetramethylacridan with three equiv of nBuLi, followed by the addition of two equiv of the corresponding diaryl dichalcogenide and quenching with dilute HCl(aq). The new selenoether- and telluroether-containing pro-ligands were subsequently deprotonated using KCH2Ph to afford [K(AE2Tripp2)(dme)2] (E = Se (9), Te (10)). Compounds 1-10 were characterized by 1H, 13C{1H}, 77Se{1H}, 125Te{1H}, and 7Li NMR spectroscopy, where applicable, and single-crystal X-ray structures were obtained for all lithium and potassium complexes (3-6 and 9-10). DFT calculations were also performed to assess the nature of bonding between the hard group 1 cations and the soft chalcogenoethers.
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Affiliation(s)
- Novan A G Gray
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Ignacio Vargas-Baca
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - David J H Emslie
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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3
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Verma P, Srivastava A, Tandon P, Shimpi MR. Insights into structural, spectroscopic, and hydrogen bonding interaction patterns of nicotinamide-oxalic acid (form I) salt by using experimental and theoretical approaches. Front Chem 2023; 11:1203278. [PMID: 37476653 PMCID: PMC10354448 DOI: 10.3389/fchem.2023.1203278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
In the present work, nicotinamide-oxalic acid (NIC-OXA, form I) salt was crystallized by slow evaporation of an aqueous solution. To understand the molecular structure and spectroscopic properties of NIC after co-crystallization with OXA, experimental infrared (IR), Raman spectroscopic signatures, X-ray powder diffraction (XRPD), and differential scanning calorimetry (DSC) techniques were used to characterize and validate the salt. The density functional theory (DFT) methodology was adopted to perform all theoretical calculations by using the B3LYP/6-311++G (d, p) functional/basis set. The experimental geometrical parameters were matched in good correlation with the theoretical parameters of the dimer than the monomer, due to the fact of covering the nearest hydrogen bonding interactions present in the crystal structure of the salt. The IR and Raman spectra of the dimer showed the red (downward) shifting and broadening of bands among (N15-H16), (N38-H39), and (C13=O14) bonds of NIC and (C26=O24), (C3=O1), and (C26=O25) groups of OXA, hence involved in the formation of NIC-OXA salt. The atoms in molecules (AIM) analysis revealed that (N8-H9···O24) is the strongest (conventional) intermolecular hydrogen bonding interaction in the dimer model of salt with the maximum value of interaction energy -12.1 kcal mol-1. Furthermore, the natural bond orbital (NBO) analysis of the Fock matrix showed that in the dimer model, the (N8-H9···O24) bond is responsible for the stabilization of the salt with an energy value of 13.44 kcal mol-1. The frontier molecular orbitals (FMOs) analysis showed that NIC-OXA (form I) salt is more reactive and less stable than NIC, as the energy gap of NIC-OXA (form I) salt is less than that of NIC. The global and local reactivity descriptor parameters were calculated for the monomer and dimer models of the salt. The electrophilic, nucleophilic, and neutral reactive sites of NIC, OXA, monomer, and dimer models of salt were visualized by plotting the molecular electrostatic potential (MESP) surface. The study provides valuable insights into combining both experimental and theoretical results that could define the physicochemical properties of molecules.
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Affiliation(s)
- Priya Verma
- Department of Physics, University of Lucknow, Lucknow, India
| | | | - Poonam Tandon
- Department of Physics, University of Lucknow, Lucknow, India
| | - Manishkumar R. Shimpi
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
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4
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Gimferrer M, Salvador P. Exact decompositions of the total KS-DFT exchange-correlation energy into one- and two-center terms. J Chem Phys 2023; 158:234105. [PMID: 37326158 DOI: 10.1063/5.0142778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
In the so-called Interacting Quantum Atoms (IQA) approach, the molecular energy is numerically decomposed as a sum of atomic and diatomic contributions. While proper formulations have been put forward for both Hartree-Fock and post-Hartree-Fock wavefunctions, this is not the case for the Kohn-Sham density functional theory (KS-DFT). In this work, we critically analyze the performance of two fully additive approaches for the IQA decomposition of the KS-DFT energy, namely, the one from Francisco et al., which uses atomic scaling factors, and that from Salvador and Mayer based upon the bond order density (SM-IQA). Atomic and diatomic exchange-correlation (xc) energy components are obtained for a molecular test set comprising different bond types and multiplicities and along the reaction coordinate of a Diels-Alder reaction. Both methodologies behave similarly for all systems considered. In general, the SM-IQA diatomic xc components are less negative than the Hartree-Fock ones, which is in good agreement with the known effect of electron correlation upon (most) covalent bonds. In addition, a new general scheme to minimize the numerical error of the sum of two-electron energy contributions (i.e., Coulomb and exact exchange) in the framework of overlapping atoms is described in detail.
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Affiliation(s)
- Martí Gimferrer
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Pedro Salvador
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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5
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Lomas JS, Rosenberg RE. Cooperativity and intermolecular hydrogen bonding in donor‐acceptor complexes of phenol and polyhydroxybenzenes. J PHYS ORG CHEM 2023. [DOI: 10.1002/poc.4506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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6
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Khaoua O, Benbellat N, Zeroual S, Mouffouk S, Golhen S, Gouasmia A, Chermette H, Haba H. Combined experimental, computational studies (synthesis, crystal structural, DFT calculations, spectral analysis) and biological evaluation of the new homonuclear complex Di-µ-benzoato-bis [benzoatodipyridine-cobalt (II)]. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Espitia Cogollo E, Echeverría GA, Piro OE, Jios JL, Ulic SE. Perhalomethyl Chromones: Spectroscopic, X‐Ray Diffraction, Hirshfeld Surface, and Density Functional Theory Studies of the Noncovalent Interactions. CRYSTAL RESEARCH AND TECHNOLOGY 2022. [DOI: 10.1002/crat.202200085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Edeimis Espitia Cogollo
- CEQUINOR (CONICET‐UNLP) Facultad de Ciencias Exactas Universidad Nacional de La Plata Bv. 120 N° 1465 La Plata 1900 Argentina
| | - Gustavo A. Echeverría
- Departamento de Física Facultad de Ciencias Exactas Universidad Nacional de La Plata e IFLP (CONICET, CCT‐La Plata) C. C. 67 La Plata 1900 Argentina
| | - Oscar E. Piro
- Departamento de Física Facultad de Ciencias Exactas Universidad Nacional de La Plata e IFLP (CONICET, CCT‐La Plata) C. C. 67 La Plata 1900 Argentina
| | - Jorge L. Jios
- Laboratorio UPL (UNLP‐CIC) Campus Tecnológico Gonnet (CIC‐BA) Cno. Centenario e/505 y 508 Gonnet (1897) Argentina
- Departamento de Química Facultad de Ciencias Exactas Universidad Nacional de La Plata 47 esq. 115 La Plata (1900) Argentina
| | - Sonia E. Ulic
- CEQUINOR (CONICET‐UNLP) Facultad de Ciencias Exactas Universidad Nacional de La Plata Bv. 120 N° 1465 La Plata 1900 Argentina
- Departamento de Ciencias Básicas Universidad Nacional de Luján Rutas 5 y 7 Luján Buenos Aires 6700 Argentina
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8
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Zhu L, Wang D. Deciphering the cooperative effect of base and N-substituents on the origin of enantioselectivity switching for Mannich reactions of glycinate by carbonyl catalysts. J Catal 2022. [DOI: 10.1016/j.jcat.2022.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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9
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Yu YD, Price JS, Romero PE, Emslie DJH. Homoleptic 1-norbornyl complexes of group 4 and manganese: synthesis, structures, volatility, and thermal stability. CAN J CHEM 2022. [DOI: 10.1139/cjc-2022-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Detailed syntheses are reported for the previously reported homoleptic 1-norbornyl complexes [M(norb)4] {M = Ti (1), Zr (3), Hf (4), and Mn (5)}. These compounds were characterized by combustion elemental analysis, NMR spectroscopy, single crystal X-ray diffraction (for 1 and 3), and SQUID magnetometry (for 5). The reaction by-product [{(norb)3Ti}2(μ-O)] (2) was also spectroscopically and structurally characterized. To assess the potential viability of 1 and 3–5 as precursors for thin film deposition by CVD or ALD, their volatility and thermal stability were evaluated by sublimation, thermogravimetric analysis, and in the case of 4, bulk thermolysis.
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Affiliation(s)
- Ya-Dong Yu
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
| | - Jeffrey S. Price
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
| | - Patricio E. Romero
- Intel Corporation, Components Research, 2511 NW 229th Ave., Hillsboro, OR 97124, USA
| | - David J. H. Emslie
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
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10
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Brémond É, Tognetti V, Chermette H, Sancho-García JC, Joubert L, Adamo C. Electronic Energy and Local Property Errors at QTAIM Critical Points while Climbing Perdew's Ladder of Density-Functional Approximations. J Chem Theory Comput 2021; 18:293-308. [PMID: 34958205 DOI: 10.1021/acs.jctc.1c00981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the relationships between electron-density and electronic-energy errors produced by modern exchange-correlation density-functional approximations belonging to all of the rungs of Perdew's ladder. To this aim, a panel of relevant (semi)local properties evaluated at critical points of the electron-density field (as defined within the framework of Bader's atoms-in-molecules theory) are computed on a large selection of molecular systems involved in thermodynamic, kinetic, and noncovalent interaction chemical databases using density functionals developed in a nonempirical and minimally and highly parametrized fashion. The comparison of their density- and energy-based performance, also discussed in terms of density-driven errors, casts light on the strengths and weaknesses of the most recent and efficient density-functional approximations.
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Affiliation(s)
- Éric Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Vincent Tognetti
- Normandy University, COBRA UMR 6014 and FR 3038, Université de Rouen INSA Rouen, CNRS, F-76821 Mont St Aignan, France
| | - Henry Chermette
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, 5 rue de la Doua, F-69100 Villeurbanne, France
| | | | - Laurent Joubert
- Normandy University, COBRA UMR 6014 and FR 3038, Université de Rouen INSA Rouen, CNRS, F-76821 Mont St Aignan, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), UMR 8060, F-75005 Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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11
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Wöhner K, Wulf T, Vankova N, Heine T. Strong Binding of Noble Gases to [B 12X 11] -: A Theoretical Study. J Phys Chem A 2021; 125:4760-4765. [PMID: 34036781 DOI: 10.1021/acs.jpca.1c01909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We systematically explore the stability and properties of [B12X11NG]- adducts resulting from the binding of noble gas atoms to anionic [B12X11]- clusters in the gas phase of mass spectrometers. [B12X11]- can be obtained by stripping one X- off the icosahedral closo-dodecaborate dianion [B12X12]2-. We study the binding of the noble gas atoms He, Ne, Ar, Kr, and Xe to [B12X11]- with substituents X = F, Cl, Br, I, and CN. While He cannot be captured by these clusters and Ne only binds at low temperatures, the complexes with the heavier noble gas atoms Ar, Kr, and Xe show appreciable complexation energies and exceed 1 eV at room temperature in the case of [B12(CN)11Xe]-. The predicted B-NG equilibrium distance in the complexes with Ar, Kr, and Xe is only 0.10-0.25 Å longer than the sum of the covalent radii of the two corresponding atoms, and a significant charge transfer from the noble gas atom to the icosahedral B12 cage is observed.
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Affiliation(s)
- Kevin Wöhner
- Institute of Resource Ecology, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, TU Dresden, 01062 Dresden, Germany.,Wilhelm Ostwald Institute of Physical and Theoretical Chemistry, Faculty for Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany
| | - Toshiki Wulf
- Institute of Resource Ecology, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany.,Wilhelm Ostwald Institute of Physical and Theoretical Chemistry, Faculty for Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany
| | - Nina Vankova
- Faculty of Chemistry and Food Chemistry, School of Science, TU Dresden, 01062 Dresden, Germany
| | - Thomas Heine
- Institute of Resource Ecology, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, TU Dresden, 01062 Dresden, Germany.,Department of Chemistry, Yonsei University, Seodaemun-gu, Seoul 120-749, Republic of Korea
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12
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Mounssef Jr B, de Alcântara Morais SF, de Lima Batista AP, de Lima LW, Braga AAC. DFT study of H 2 adsorption at a Cu-SSZ-13 zeolite: a cluster approach. Phys Chem Chem Phys 2021; 23:9980-9990. [PMID: 33870397 DOI: 10.1039/d1cp00422k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work the H2 adsorption at a Cu(i)-SSZ-13 exchanged zeolite was theoretically investigated. A systematic cluster approach was used and different density functionals (B3LYP, B3LYP-D3(BJ), M06L, PBE, PBE-D3(BJ) and ωB97XD) and a def2-SVP basis set were benchmarked. In order to select the best approach to the H2 adsorption over a Cu(i)-SSZ-13 cluster with 78 atoms (16 T-sites), two main tasks were performed: (1) a comparison between theoretical and experimental structures and (2) a comparison between theoretical and experimental adsorption enthalpies. By employing the most suitable functional - the ωB97X-D - the H2 interaction with the zeolite structure was studied by means of NBO, NCI, AIM and DLPNO-CCSD(T)/LED analyses.
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Affiliation(s)
- Bassim Mounssef Jr
- GQCA - Grupo de Química Computacional Aplicada, Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil.
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13
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Qiu Y, Yuan H, Zhang X, Zhang J. Insights into the Chiral Phosphoric Acid-Catalyzed Dynamic Kinetic Asymmetric Hydroamination of Racemic Allenes: An Allyl Carbocation/Phosphate Pair Mechanism. J Org Chem 2021; 86:4121-4130. [PMID: 33617248 DOI: 10.1021/acs.joc.0c02956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Computational studies of chiral phosphoric acid (CPA)-catalyzed dynamic kinetic asymmetric hydroamination (DyKAH) of racemic allenes show that the reaction proceeds through a catalytic asymmetric model involving a highly reactive π-allylic carbocationic intermediate, generated from a racemic allene through an intermolecular proton transfer mediated by CPA, which also results in a high E/Z selectivity. Moreover, the distortion-interaction, atom in molecule, and electrostatic interaction analyses and space-filling models are employed on the basis of the DyKAH catalyzed by (S)-A5 (reaction 1) or (R)-A2 (reaction 2) to explain the high enantioselectivity and the controlling effects of SPINOL scaffolds on the signs of enantioselectivity. Our calculations indicate that the enantioselectivity of reactions 1 and 2 can be mainly ascribed to the favorable noncovalent interactions within the stronger chiral electrostatic environment created by the phosphoric acid in the preferential transition states. Finally, the effect of (S/R)-SPINOL-based CPAs on the signs of enantioselectivity can be explained by the different combination modes of substrates into the chiral binding pocket of the catalyst controlled by the chirality of SPINOL backbones. Overall, the new insights into the reaction rationalize the outcome and these key factors that affect the product enantioselectivity are important to guide the DyKAHs.
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Affiliation(s)
- Yuting Qiu
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Haiyan Yuan
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Xiaoying Zhang
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Jingping Zhang
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
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14
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Zhu LH, Yuan HY, Zhang JP. Enantioselective synthesis of chiral tetrasubstituted allenes: harnessing electrostatic and noncovalent interactions in a bifunctional activation model for N-triflylphosphoramide catalysis. Org Chem Front 2021. [DOI: 10.1039/d0qo01250e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DFT calculation reveals that the oxygen activation model is preferred than the nitrogen activation model due to the preferred chiral electrostatic environment.
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Affiliation(s)
- Li-Han Zhu
- Faculty of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Hai-Yan Yuan
- Faculty of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Jing-Ping Zhang
- Faculty of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
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15
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Lomas JS, Rosenberg RE, Brémond E. Cooperativity in a cycloalkane-1,2/1,3-polyol corona: Topological hydrogen bonding in 1,2-diol motifs. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:957-968. [PMID: 32529717 DOI: 10.1002/mrc.5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/06/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
A corona, consisting of 18 carbon atoms bearing 12 hydroxy groups in a continuous hydrogen-bonded chain, is built up by alternating degenerate conformations of alternating alkane-1,2-diol and 1,3-diol motifs. Geometries, proton nuclear magnetic resonance shifts and interaction energies for the dodecahydroxycyclo-octadecane and selected fragments are determined by density functional calculations at the B3LYP/6-311+G(d,p) level. Cooperative effects of O-H⋯O-H bonding are evident from the simple juxtaposition of these two motifs with a common OH group in butane-1,2,4-triol conformers. Bracketing a 1,2-diol motif with two 1,3-diol motifs in hexane-1,3,4,6-tetrol leads to a structure in which the 1,2-diol motif displays a bond critical point for hydrogen bonding. This is associated with enhancement of the shift of the hydrogen-bonded OH proton and of the corresponding H⋯O interaction energy. The full corona has a complete outer ring of O-H⋯O-H bond paths, and an inner ring of bond paths, due to C-H⋯H-C hydrogen-hydrogen bonding, which result in a central ring critical point. The topological O-H⋯O-H hydrogen bond, never seen in simple alkane-1,2-diols, is associated with cooperative enhancement of the H⋯O interaction energy, but this is not a necessary condition for a bond path: values for topological C-H⋯H-C hydrogen-hydrogen bonds can be as low as -0.4 kcal mol-1 .
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Affiliation(s)
- John S Lomas
- ITODYS, CNRS, Université de Paris, Paris, France
| | | | - Eric Brémond
- ITODYS, CNRS, Université de Paris, Paris, France
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16
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Anisimov AA, Ananyev IV. Interatomic exchange-correlation interaction energy from a measure of quantum theory of atoms in molecules topological bonding: A diatomic case. J Comput Chem 2020; 41:2213-2222. [PMID: 32731310 DOI: 10.1002/jcc.26390] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 01/01/2023]
Abstract
The potential relations between the measure of topological interatomic bonding-integrals of electron density with respect to internuclear axis over the corresponding quantum theory of atoms in molecules (QTAIM)-defined interatomic surface (IAS)-and interatomic exchange-correlation contributions from the interacting quantum atoms approach are discussed. The quantum chemical computations of 38 equilibrium diatomic systems at different levels of theory (HF, MP2, MP4SDQ, and CCSD) are invoked to support abstract considerations. Parameters of excellent correlations between IAS integrals and interatomic exchange-correlation energy are found by the optimization. The performance of these trends depends on the accuracy of the electronic correlation treatment. The resulting trends are a unique feature of equilibrium states, whereas more complicated dependencies are explored for several systems at non-equilibrium conditions. The relations of established trends with other IAS-based estimations of strength of bonding interactions between topological atoms and issues explored for multiatomic systems are briefly discussed.
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Affiliation(s)
- Aleksei A Anisimov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, Moscow, 119991, GSP-1, Russia
| | - Ivan V Ananyev
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, Moscow, 119991, GSP-1, Russia.,National Research University Higher School of Economics, Miasnitskaya Str. 20, Moscow, 101000, Russia
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17
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Lomas JS. Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H … OH and C─H … OH bonding interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:666-684. [PMID: 32201981 DOI: 10.1002/mrc.5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Université de Paris, Paris, France
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18
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Viegas LSP, Jensen F. Reactivity of α,ω-Dihydrofluoropolyethers toward OH Predicted by Multiconformer Transition State Theory and the Interacting Quantum Atoms Approach. J Phys Chem A 2020; 124:3460-3470. [PMID: 32242667 DOI: 10.1021/acs.jpca.0c02911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report rate constants for the tropospheric reaction between the OH radical and α,ω-dihydrofluoropolyethers, which represent a specific class of the hydrofluoropolyethers family with the formula HF2C(OCF2CF2)p(OCF2)qOCF2H. Four cases were considered: p0q2, p0q3, p1q0, and p1q1 (pxqy denoting p = x and q = y) with the calculations performed by a cost-effective protocol developed for bimolecular hydrogen-abstraction reactions. This protocol is based on multiconformer transition state theory and relies on computationally accessible M08-HX/apcseg-2//M08-HX/pcseg-1 calculations. Within the protocol's approximations, the results show that (1) the calculated rate constants are within a factor of five of the experimental results (p1q0 and p1q1) and (2) the chain length and composition have a negligible effect on the rate constants, which is consistent with the experimental work. The interacting quantum atoms energy decomposition scheme is used to analyze the observed trends and extract chemical information related to the imaginary frequencies and barrier heights that are key parameters controlling the reactivity of the reaction. The intramolecular exchange-correlation contributions in the reactants and transition states were found to be the dominating factor.
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Affiliation(s)
- Luı S P Viegas
- Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, Buildings 1630-1632, Aarhus 8000, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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19
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The effect of CF3 functional group substituent on bifunctional activation model and enantioselectivity for BINOL N-triflylphosphoramides catalyzed rearrangement reaction. J Catal 2020. [DOI: 10.1016/j.jcat.2020.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Carpio‐Martínez P, Barquera‐Lozada JE, Pendás AM, Cortés‐Guzmán F. Laplacian of the Hamiltonian Kinetic Energy Density as an Indicator of Binding and Weak Interactions. Chemphyschem 2019; 21:194-203. [DOI: 10.1002/cphc.201900769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/06/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Pablo Carpio‐Martínez
- Instituto de QuímicaUnversidad Nacional Autónoma de México México DF 04510 Mexico
- Department of ChemistryUniversity of Alberta, Edmonton Alberta AB T6G 2G2 Canada
| | | | - Angel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de QuímicaUniversidad de Oviedo E-33006- Oviedo Spain
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21
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Zhu L, Yuan H, Zhang J. Chiral Phosphoric Acid-Catalyzed Enantioselective Direct Arylation of Iminoquinones: A Case Study of the Model Selectivity. J Org Chem 2019; 84:13473-13482. [PMID: 31536352 DOI: 10.1021/acs.joc.9b01714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chiral phosphoric acid (CPA)-catalyzed enantioselective arylation reactions have attracted immense attention recently. However, the preferential activation model in the stereodetermining step is controversial, and hence, the origin of enantioselectivity is still far from being understood. Two stereochemical models are provided on the basis of the asymmetric arylations of iminoquinones with naphthylamines (reaction 1) or naphthols (reaction 2) catalyzed by (R/S)-TRIP to explain the high enantioselectivity and the effect of CPAs scaffolds. Unexpectedly, our calculations reveal that substrate naphthylamines or naphthols prefer enantioselective aminal formation model II or 1,4-addition model I, respectively, which is the reverse of Tan's and Xu's model. The different noncovalent and steric interactions between catalysts and substrates are responsible for the observed model preference. Moreover, the enantioselectivity arises from distortion (reaction 1) and noncovalent interactions (reaction 2) that discriminate between the diastereomeric transition states. We further investigated the effect of SPINOL-based CPAs on the enantioselectivity and found that the more rigid skeleton and a smaller binding pocket lead to lower enantioselectivity as compared with that of BINOL-based CPA. The new insights into the reaction activation model rationalize the stereoselectivity outcome of direct asymmetric arylation reactions, and our general model can be extended to related transformations.
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Affiliation(s)
- Lihan Zhu
- Faculty of Chemistry , Northeast Normal University , Changchun 130024 , China
| | - Haiyan Yuan
- Faculty of Chemistry , Northeast Normal University , Changchun 130024 , China
| | - Jingping Zhang
- Faculty of Chemistry , Northeast Normal University , Changchun 130024 , China
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22
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23
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García-Ruiz KM, Marmolejo-Valencia AF, González-Navejas A, Dominguez L, Amador-Bedolla C. Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases. J Mol Model 2019; 25:110. [DOI: 10.1007/s00894-019-3984-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 03/13/2019] [Indexed: 02/03/2023]
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24
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Jabłoński M. On the Uselessness of Bond Paths Linking Distant Atoms and on the Violation of the Concept of Privileged Exchange Channels. ChemistryOpen 2019; 8:497-507. [PMID: 31019875 PMCID: PMC6470636 DOI: 10.1002/open.201900109] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Indexed: 11/09/2022] Open
Abstract
We refer to frequently used determinants suggesting dominant interactions between distant atoms in various dimers. First of all, we show, against the still-prevailling opinion, that, in general, bond paths have nothing in common with dominant intermolecular interactions and therefore they are useless in such cases. Quite the contrary, reliable information about dominant intermolecular interactions can be obtained by means of electrostatic potential maps, which very convincingly explain mutual orientation of molecules in a dimer. For the first time, numerous examples of interactions that violate both the concept of privileged exchange channels proposed by Pendás and his collaborators as well as inequalities obtained by Tognetti and Joubert for the β parameter related to secondary interactions are presented. The possible cause of this violation is suggested. We also show that the so-called counterintuitive bond paths result from quite natural behavior of the electron density gradient vector, i. e. searching for those areas of space that are characterized by large values of electron density or the most expanded its distributions.
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of ChemistryNicolaus Copernicus University in Toruń7-Gagarina St.87-100ToruńPoland
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25
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Bignon E, Rizza S, Filomeni G, Papaleo E. Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase. Comput Struct Biotechnol J 2019; 17:415-429. [PMID: 30996821 PMCID: PMC6451115 DOI: 10.1016/j.csbj.2019.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular processes. It is endogenously synthesized by NO synthase (NOS) as the product of L-arginine oxidation to L-citrulline, requiring NADPH, molecular oxygen, and a pterin cofactor. Two NOS isoforms are constitutively present in cells, nNOS and eNOS, and a third is inducible (iNOS). Despite their biological relevance, the details of their complex structural features and reactivity mechanisms are still unclear. In this review, we summarized the contribution of computational biochemistry to research on NOS molecular mechanisms. We described in detail its use in studying aspects of structure, dynamics and reactivity. We also focus on the numerous outstanding questions in the field that could benefit from more extensive computational investigations.
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Affiliation(s)
- Emmanuelle Bignon
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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26
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Muessig JH, Thaler M, Dewhurst RD, Paprocki V, Seufert J, Mattock JD, Vargas A, Braunschweig H. Phosphanstabilisierte Diioddiborene: Isolierbare Diborene mit sechs labilen Bindungen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814230] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jonas H. Muessig
- Institut für Anorganische ChemieJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
- Institut für nachhaltige Chemie & Katalyse mit BorJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
| | - Melanie Thaler
- Institut für Anorganische ChemieJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
- Institut für nachhaltige Chemie & Katalyse mit BorJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
| | - Rian D. Dewhurst
- Institut für Anorganische ChemieJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
- Institut für nachhaltige Chemie & Katalyse mit BorJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
| | - Valerie Paprocki
- Institut für Anorganische ChemieJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
- Institut für nachhaltige Chemie & Katalyse mit BorJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
| | - Jens Seufert
- Institut für Anorganische ChemieJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
- Institut für nachhaltige Chemie & Katalyse mit BorJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
| | - James D. Mattock
- Department of ChemistrySchool of Life SciencesUniversity of Sussex Brighton BN1 9QJ Sussex UK
| | - Alfredo Vargas
- Department of ChemistrySchool of Life SciencesUniversity of Sussex Brighton BN1 9QJ Sussex UK
| | - Holger Braunschweig
- Institut für Anorganische ChemieJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
- Institut für nachhaltige Chemie & Katalyse mit BorJulius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Deutschland
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27
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Maji R, Ugale H, Wheeler SE. Understanding the Reactivity and Selectivity of Fluxional Chiral DMAP-Catalyzed Kinetic Resolutions of Axially Chiral Biaryls. Chemistry 2019; 25:4452-4459. [PMID: 30657217 DOI: 10.1002/chem.201806068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/17/2019] [Indexed: 12/17/2022]
Abstract
Fluxional chiral DMAP-catalyzed kinetic resolutions of axially chiral biaryls were examined using density functional theory. Computational analyses lead to a revised understanding of this reaction in which the interplay of numerous non-covalent interactions control the conformation and flexibility of the active catalyst, the preferred mechanism, and the stereoselectivity. Notably, while the DMAP catalyst itself is confirmed to be highly fluxional, electrostatically driven π⋅⋅⋅π+ interactions render the active, acylated form of the catalyst highly rigid, explaining its pronounced stereoselectivity.
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Affiliation(s)
- Rajat Maji
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - Heena Ugale
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - Steven E Wheeler
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.,Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
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28
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Muessig JH, Thaler M, Dewhurst RD, Paprocki V, Seufert J, Mattock JD, Vargas A, Braunschweig H. Phosphine-Stabilized Diiododiborenes: Isolable Diborenes with Six Labile Bonds. Angew Chem Int Ed Engl 2019; 58:4405-4409. [PMID: 30719809 DOI: 10.1002/anie.201814230] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Indexed: 01/22/2023]
Abstract
The lability of B=B, B-P, and B-halide bonds is combined in the syntheses of the first diiododiborenes. In a series of reactivity tests, these diiododiborenes undergo cleavage of all six of their central bonds in different ways, leading to products of B=B hydrogenation and dihalogenation as well as halide exchange.
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Affiliation(s)
- Jonas H Muessig
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Melanie Thaler
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Rian D Dewhurst
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Valerie Paprocki
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Jens Seufert
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - James D Mattock
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton, BN1 9QJ, Sussex, UK
| | - Alfredo Vargas
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton, BN1 9QJ, Sussex, UK
| | - Holger Braunschweig
- Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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29
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Varadwaj A, Marques HM, Varadwaj PR. Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions? Molecules 2019; 24:E379. [PMID: 30678158 PMCID: PMC6384640 DOI: 10.3390/molecules24030379] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/23/2022] Open
Abstract
Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
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30
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Zhu L, Mohamed H, Yuan H, Zhang J. The control effects of different scaffolds in chiral phosphoric acids: a case study of enantioselective asymmetric arylation. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01420a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DFT calculations disclosed that the sign of enantioselectivity in chiral-phosphoric-acid catalyzed reactions can be tuned by BINOL- or SPINOL-derived backbones.
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Affiliation(s)
- Lihan Zhu
- Faculty of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Hend Mohamed
- Faculty of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Haiyan Yuan
- Faculty of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Jingping Zhang
- Faculty of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
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31
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Jara-Cortés J, Landeros-Rivera B, Hernández-Trujillo J. Unveiling the role of intra and interatomic interactions in the energetics of reaction schemes: a quantum chemical topology analysis. Phys Chem Chem Phys 2018; 20:27558-27570. [PMID: 30371704 DOI: 10.1039/c8cp03775b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work we present a detailed analysis of selected reaction schemes in terms of the atomic components of the electronic energy defined by the quantum theory of atoms in molecules and the interacting quantum atoms method. The aim is to provide an interpretation tool for the energy change involved in a chemical reaction by means of the atomic and interaction contributions to the energies of the molecules involved. Ring strain in cyclic alkanes, the resonance energy of aromatic and antiaromatic molecules, local aromaticity in polycyclic aromatic hydrocarbons, intermolecular bonding in hydrogen fluoride clusters, and hydration of d-block metal dications were selected for the study. It was found that in addition to the changes in the strong C-C interactions in the carbon skeleton of the organic molecular rings, other contributions not usually considered to be important such as those between C and H atoms (either bonded or not) need to be considered in order to account for the net energy changes. The analysis unveils the role of the ionic and covalent contributions to the hydrogen bonding in HF clusters and the energetic origin and extent of cooperative effects involved. Moreover, the "double-hump" behavior observed for the hydration energy trend of [M(H2O)6]2+ complexes is explained in terms of the deformation energy of the metal cation and the increasingly covalent metal-water interactions. In addition, proper comparisons with the description provided by other methodologies are briefly discussed. The topological approach proposed in this contribution proves to be useful for the description of energy changes of apposite reaction schemes in chemically meaningful terms.
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Affiliation(s)
- Jesús Jara-Cortés
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, México City, 04510, Mexico.
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32
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Jabłoński M. Bond paths between distant atoms do not necessarily indicate dominant interactions. J Comput Chem 2018; 39:2183-2195. [PMID: 30298926 DOI: 10.1002/jcc.25532] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 12/16/2022]
Abstract
The goal of the article is to revive discussion on the interpretation of bond paths linking distant atoms, particularly tracing weak interactions in dimers. According to the Pendás' concept of privileged exchange channel, a bond path is formed between this pair of competing atoms, which is associated with larger value of the exchange energy. We point out that, due to the short-range nature of the exchange energy, bond paths linking distant atoms clearly become doubtful indicators of dominant intermolecular interactions, particularly if some other characteristics (geometric, spectroscopic, based on electrostatic parameters, etc.) indicate other intermolecular interactions as dominant. Several such cases are thoroughly investigated. We show that electrostatic parameters are much more reliable indicators of dominant intermolecular interactions than bond paths. Then, we pay attention that the presence of ("unexpected", i.e., not necessarily indicating dominant intermolecular interactions) bond paths between pairs of atoms featuring highly expanded charge distributions can be easily explained by visual exploration of isodensity contour plots. As always pointing in the direction of the steepest increase, the gradient vector of the electron density favors areas of its high values gaining higher exchange energy, yet being blind to highly electron deficient areas nearby, which, however, can quite often be involved in dominant intermolecular interactions as strongly suggested by many other bonding analysis. We also suggest that an interatomic component of Hellmann-Feynman force would most likely be the most reliable indicator of attractive or repulsive character of individual interatomic interaction. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7-Gagarina Street, 87-100, Toruń, Poland
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33
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Hoffmann G, Tognetti V, Joubert L. Can molecular and atomic descriptors predict the electrophilicity of Michael acceptors? J Mol Model 2018; 24:281. [DOI: 10.1007/s00894-018-3802-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/16/2018] [Indexed: 12/21/2022]
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34
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Tognetti V, Silva AF, Vincent MA, Joubert L, Popelier PLA. Decomposition of Møller–Plesset Energies within the Quantum Theory of Atoms-in-Molecules. J Phys Chem A 2018; 122:7748-7756. [DOI: 10.1021/acs.jpca.8b05357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Vincent Tognetti
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821 Mont St Aignan, Cedex, France
| | - Arnaldo F. Silva
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| | - Mark A. Vincent
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| | - Laurent Joubert
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821 Mont St Aignan, Cedex, France
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
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35
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Petković M, Nakarada Đ, Etinski M. When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms. J Comput Chem 2018; 39:1868-1877. [PMID: 29799128 DOI: 10.1002/jcc.25359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/16/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Abstract
Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11 158, Serbia
| | - Đura Nakarada
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11 158, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11 158, Serbia
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36
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Cs+–π interactions and the design of macrocycles for the capture of environmental radiocesium (Cs-137): DFT, QTAIM, and CSD studies. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2298-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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37
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Das SK, Bhanja P, Kundu SK, Mondal S, Bhaumik A. Role of Surface Phenolic-OH Groups in N-Rich Porous Organic Polymers for Enhancing the CO 2 Uptake and CO 2/N 2 Selectivity: Experimental and Computational Studies. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23813-23824. [PMID: 29956910 DOI: 10.1021/acsami.8b05849] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Design and successful synthesis of phenolic-OH and amine-functionalized porous organic polymers as adsorbent for postcombustion CO2 uptake from flue gas mixtures along with high CO2/N2 selectivity is a very demanding research area in the context of developing a suitable adsorbent to mitigate greenhouse gases. Herein, we report three triazine-based porous organic polymers TrzPOP-1, -2, and -3 through the polycondensation of two triazine rings containing tetraamine and three dialdehydes. These porous organic polymers possess high Brunauer-Emmett-Teller (BET) surface areas of 995, 868, and 772 m2 g-1, respectively. Out of the three materials, TrzPOP-2 and TrzPOP-3 contain additional phenolic-OH groups along with triazine moiety and secondary amine linkages. At 273 K, TrzPOP-1, -2, and -3 displayed CO2 uptake capacities of 6.19, 7.51, and 8.54 mmol g-1, respectively, up to 1 bar pressure, which are considerably high among all porous polymers reported till date. Despite the lower BET surface area, TrzPOP-2 and TrzPOP-3 containing phenolic-OH groups showed higher CO2 uptakes. To understand the CO2 adsorption mechanism, we have further performed the quantum chemical studies to analyze noncovalent interactions between CO2 molecules and different polar functionalities present in these porous polymers. TrzPOP-1, -2, and -3 have the capability of selective CO2 uptake over that of N2 at 273 K with the selectivity of 61:1, 117:1, and 142:1 by using the initial slope comparing method, along with 108.4, 140.6, and 167.4 by using ideal adsorbed solution theory (IAST) method, respectively. On the other hand, at 298 K, the calculated CO2/N2 selectivities in the initial slope comparing method for TrzPOP-1, -2, and -3 are 27:1, 72:1, and 96:1, whereas those using IAST method are 42.1, 75.7, and 94.5, respectively. Cost effective and scalable synthesis of these porous polymeric materials reported herein for selective CO2 capture has a very promising future for environmental clean-up.
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Affiliation(s)
| | | | - Sudipta K Kundu
- Department of Organic Chemistry, Rajabazar Science College , University of Calcutta , 92 A. P. C. Road , Kolkata 700009 , India
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies. Chemphyschem 2018; 19:1486-1499. [PMID: 29569853 DOI: 10.1002/cphc.201800023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 01/13/2023]
Abstract
We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
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39
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Rodríguez-Mayorga M, Via-Nadal M, Solà M, Ugalde JM, Lopez X, Matito E. Electron-Pair Distribution in Chemical Bond Formation. J Phys Chem A 2018; 122:1916-1923. [PMID: 29381071 DOI: 10.1021/acs.jpca.7b12556] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical formation process has been studied from relaxation holes, Δh(u), resulting from the difference between the radial intracule density and the nonrelaxed counterpart, which is obtained from atomic radial intracule densities and the pair density constructed from the overlap of the atomic densities. Δh(u) plots show that the internal reorganization of electron pairs prior to bond formation and the covalent bond formation from electrons in separate atoms are completely recognizable processes from the shape of the relaxation hole, Δh(u). The magnitude of Δh(u), the shape of Δh(u) ∀ u < Req, and the distance between the minimum and the maximum in Δh(u) provide further information about the nature of the chemical bond formed. A computational affordable approach to calculate the radial intracule density from approximate pair densities has been also suggested, paving the way to study electron-pair distributions in larger systems.
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Affiliation(s)
- M Rodríguez-Mayorga
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, and Donostia International Physics Center (DIPC). P.K. 1072 , 20080 Donostia, Euskadi, Spain.,Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, University of Girona , C/ Maria Aurèlia Capmany, 69, 17003 Girona, Catalonia, Spain
| | - M Via-Nadal
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, and Donostia International Physics Center (DIPC). P.K. 1072 , 20080 Donostia, Euskadi, Spain
| | - M Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, University of Girona , C/ Maria Aurèlia Capmany, 69, 17003 Girona, Catalonia, Spain
| | - J M Ugalde
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, and Donostia International Physics Center (DIPC). P.K. 1072 , 20080 Donostia, Euskadi, Spain
| | - X Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, and Donostia International Physics Center (DIPC). P.K. 1072 , 20080 Donostia, Euskadi, Spain
| | - E Matito
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, and Donostia International Physics Center (DIPC). P.K. 1072 , 20080 Donostia, Euskadi, Spain.,IKERBASQUE, Basque Foundation for Science , 48013 Bilbao, Euskadi, Spain
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40
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Maxwell P, Pendás ÁM, Popelier PLA. Extension of the interacting quantum atoms (IQA) approach to B3LYP level density functional theory (DFT). Phys Chem Chem Phys 2018; 18:20986-1000. [PMID: 26804126 DOI: 10.1039/c5cp07021j] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
An interaction between two atoms, bonded or non-bonded, consists of interatomic contributions: electrostatic energy, exchange energy and electronic correlation energy. Together with the intra-atomic energy of an atom, these contributions are the basic components of the Interacting Quantum Atom (IQA) energy decomposition scheme. Here, we investigate IQA's proper use in conjunction with an explicit implementation of the B3LYP functional. The recovery of the total molecular energy from the IQA components is emphasised, for the first time. A systematic study of three model systems of biological relevance, N-methylacetamide (NMA), the doubly capped tripeptide GlyGlyGly and an alloxan dimer, shows the stabilization effect of B3LYP on most of the interatomic exchange energies (V) compared to their Hartree-Fock values. Diagrams of exchange energies versus interatomic distance show the clustering of interactions, one cluster for each 1,n (n = 1 to 6 where the atoms are separated by n - 1 bonds). The positioning of some V values outside their expected cluster marks interesting interactions.
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Affiliation(s)
- Peter Maxwell
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, UK. and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ángel Martín Pendás
- Departamento de Quimica Fisica y Analitica, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, UK. and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
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41
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Geboes Y, De Vos E, Herrebout WA. S⋯S and S⋯P chalcogen bonding in solution: a cryospectroscopic study of the complexes of 2,2,4,4-tetrafluoro-1,3-dithietane with dimethyl sulfide and trimethylphosphine. NEW J CHEM 2018. [DOI: 10.1039/c8nj01648h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental evidence on the formation of S⋯S and P⋯S chalcogen bonded complexes between 2,2,4,4-tetrafluoro-1,3-dithiethane and the Lewis bases dimethyl sulfide and trimethylphosphine is obtained using infrared spectroscopy of solutions in liquid krypton.
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Affiliation(s)
- Yannick Geboes
- Department of Chemistry
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - Elias De Vos
- Department of Chemistry
- University of Antwerp
- 2020 Antwerp
- Belgium
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42
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Tokar А, Synchuk E, Chigvintseva O. The quantum-chemical modelling of structure and spectral characteristics for molecular complexes in pentaplast-terlon system. CHEMISTRY & CHEMICAL TECHNOLOGY 2017. [DOI: 10.23939/chcht11.04.405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Maxwell PI, Popelier PLA. Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective. J Comput Chem 2017; 38:2459-2474. [PMID: 28841241 PMCID: PMC5659141 DOI: 10.1002/jcc.24904] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 01/06/2023]
Abstract
Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (Oi-1 , Ci , Ni , Ni+1 ) and some sidechain hydrogen atoms (Hγ ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the Oi-1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Peter I. Maxwell
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain and School of Chemistry, University of Manchester, Oxford RoadManchesterGreat BritainM13 9PL
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain and School of Chemistry, University of Manchester, Oxford RoadManchesterGreat BritainM13 9PL
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44
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Jara-Cortés J, Hernández-Trujillo J. Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method. J Comput Chem 2017; 39:1103-1111. [PMID: 29076165 DOI: 10.1002/jcc.25089] [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: 05/27/2017] [Revised: 09/04/2017] [Accepted: 10/06/2017] [Indexed: 01/21/2023]
Abstract
A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Jesús Jara-Cortés
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, México City, 04510, México
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45
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Lomas JS, Joubert L. On the importance of intramolecular hydrogen bond cooperativity in d-glucose - an NMR and QTAIM approach. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:893-901. [PMID: 28432857 DOI: 10.1002/mrc.4599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/15/2017] [Accepted: 04/18/2017] [Indexed: 05/16/2023]
Abstract
The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge-including atomic orbital calculations on the known conformers of the α and β anomers of d-glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom-atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules. Association of OH1 in the counterclockwise conformers with a strong acceptor, pyridine, is accompanied by cooperative participation from OH2, but there is no significant change in the bonding of the two following 1,2-diol motifs. The OH6... O5 (G-g+/cc/t and G+g-/cc/t conformers) or OH6... O4 (Tg+/cc/t conformer) distance is reduced, and the OH6 proton is slightly deshielded. In the latter case, this shortening and the associated increase in the OH6-O4 interaction energy may be interpreted as a small cooperative effect, but intermolecular interaction energies are practically the same for all three conformers. In most of the pyridine complexes, one ortho proton interacts with the endocyclic oxygen O5. Analogous results are obtained when the clockwise conformer, G-g+/cl/g-, detected for the α anomer, and a hypothetical conformer, Tt/cl/g-, are complexed with pyridine through OH6. Generally, the cooperative effect does not go beyond the first two OH groups of a chain. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Univ Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, F-76821, Mont St Aignan Cedex, France
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46
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Mignot M, Schammé B, Tognetti V, Joubert L, Cardinael P, Peulon-Agasse V. Anthracenyl polar embedded stationary phases with enhanced aromatic selectivity. Part II: A density functional theory study. J Chromatogr A 2017; 1519:91-99. [DOI: 10.1016/j.chroma.2017.08.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 12/28/2022]
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47
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Maji R, Champagne PA, Houk KN, Wheeler SE. Activation Mode and Origin of Selectivity in Chiral Phosphoric Acid-Catalyzed Oxacycle Formation by Intramolecular Oxetane Desymmetrizations. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02993] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rajat Maji
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Pier Alexandre Champagne
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
- Center
for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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48
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Maji R, Wheeler SE. Importance of Electrostatic Effects in the Stereoselectivity of NHC-Catalyzed Kinetic Resolutions. J Am Chem Soc 2017; 139:12441-12449. [DOI: 10.1021/jacs.7b01796] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Rajat Maji
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Center
for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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49
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Tognetti V, Joubert L. On Atoms‐in‐Molecules Energies from Kohn–Sham Calculations. Chemphyschem 2017; 18:2675-2687. [DOI: 10.1002/cphc.201700637] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/01/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Vincent Tognetti
- Normandy Univ. COBRA UMR 6014 & FR 3038Université de Rouen, INSA Rouen, CNRS 1 rue Tesniére 76821 Mont St Aignan, Cedex France
| | - Laurent Joubert
- Normandy Univ. COBRA UMR 6014 & FR 3038Université de Rouen, INSA Rouen, CNRS 1 rue Tesniére 76821 Mont St Aignan, Cedex France
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50
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Sreekumar SS, Mohan N, Kurup MRP. Water-Encapsulated Ni(II) Salphen-Type Host Complexes: Experimental and Theoretical Analysis of Potentially Bioactive Quasi-Isostructural Polymorphs. ChemistrySelect 2017. [DOI: 10.1002/slct.201701229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sreejith S. Sreekumar
- Department of Applied chemistry; Cochin University of Science and Technology; Kochi Kerala-682022 India
| | - Nithya Mohan
- Department of Applied chemistry; Cochin University of Science and Technology; Kochi Kerala-682022 India
| | - Maliyeckal R. Prathapachandra Kurup
- Department of Applied chemistry; Cochin University of Science and Technology; Kochi Kerala-682022 India
- Department of chemistry, School of Physical Sciences; Central University of Kerala, Riverside Transit campus; Neeleshwar Kerala-671314 India
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