1
|
Mortera-Carbonell AJ, Francisco E, Martín Pendás Á, Hernández-Trujillo J. The Ehrenfest force field: A perspective based on electron density functions. J Chem Phys 2023; 159:234110. [PMID: 38108480 DOI: 10.1063/5.0177631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023] Open
Abstract
The topology of the Ehrenfest force field (EhF) is investigated as a tool for describing local interactions in molecules and intermolecular complexes. The EhF is obtained by integrating the electronic force operator over the coordinates of all but one electron, which requires knowledge of both the electron density and the reduced pair density. For stationary states, the EhF can also be obtained as minus the divergence of the kinetic stress tensor, although this approach leads to well-documented erroneous asymptotic behavior at large distances from the nuclei. It is shown that these pathologies disappear using the electron density functions and that the EhF thus obtained displays the correct behavior in real space, with no spurious critical points or attractors. Therefore, its critical points can be unambiguously obtained and classified. Test cases, including strained molecules, isomerization reactions, and intermolecular interactions, were analyzed. Various chemically relevant facts are highlighted: for example, non-nuclear attractors are generally absent, potential hydrogen-hydrogen interactions are detected in crowded systems, and a bifurcation mechanism is observed in the isomerization of HCN. Moreover, the EhF atomic basins are less charged than those of the electron density. Although integration of the EhF over regions of real space can also be performed to yield the corresponding atomic forces, several numerical drawbacks still need to be solved if electron density functions are to be used for that purpose. Overall, the results obtained support the Ehrenfest force field as a reliable descriptor for the definition of atomic basins and molecular structure.
Collapse
Affiliation(s)
- Aldo J Mortera-Carbonell
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jesús Hernández-Trujillo
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| |
Collapse
|
2
|
Weinhold F. "Noncovalent Interaction": A Chemical Misnomer That Inhibits Proper Understanding of Hydrogen Bonding, Rotation Barriers, and Other Topics. Molecules 2023; 28:molecules28093776. [PMID: 37175185 PMCID: PMC10179974 DOI: 10.3390/molecules28093776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
We discuss the problematic terminology of "noncovalent interactions" as commonly applied to hydrogen bonds, rotation barriers, steric repulsions, and other stereoelectronic phenomena. Although categorization as "noncovalent" seems to justify classical-type pedagogical rationalizations, we show that these phenomena are irreducible corollaries of the same orbital-level conceptions of electronic covalency and resonance that govern all chemical bonding phenomena. Retention of such nomenclature is pedagogically misleading in supporting superficial dipole-dipole and related "simple, neat, and wrong" conceptions as well as perpetuating inappropriate bifurcation of the introductory chemistry curriculum into distinct "covalent" vs. "noncovalent" modules. If retained at all, the line of dichotomization between "covalent" and "noncovalent" interaction should be re-drawn beyond the range of quantal exchange effects (roughly, at the contact boundary of empirical van der Waals radii) to better unify the pedagogy of molecular and supramolecular bonding phenomena.
Collapse
Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
3
|
Scheiner S. On the reliability of atoms in molecules, noncovalent index, and natural bond orbital to identify and quantify noncovalent bonds. J Comput Chem 2022; 43:1814-1824. [DOI: 10.1002/jcc.26983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan Utah USA
| |
Collapse
|
4
|
Chernick ET, Abdollahi MF, Tabasi ZA, Junge MJ, Zhao Y. Study of a carbazole–bromobenzothiadiazole derived fluorescent molecular rotor: crystal structure, redox activity, and solvatofluorochromic effects. NEW J CHEM 2022. [DOI: 10.1039/d1nj04274b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A carbazole–benzothiadiazole based molecular rotor was systematically examined by experimental and modelling studies. The results disclosed interesting amphoteric redox activity and TICT emission that is sensitive to solvent polarity and viscosity.
Collapse
Affiliation(s)
- Erin T. Chernick
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Maryam F. Abdollahi
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, 1 6C1, Canada
| | - Zahra A. Tabasi
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, 1 6C1, Canada
| | - Marc J. Junge
- Institut für Organische Chemie, Universität Tübingen, 72076 Tübingen, Germany
| | - Yuming Zhao
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, 1 6C1, Canada
| |
Collapse
|
5
|
Riu MLY, Bistoni G, Cummins CC. Understanding the Nature and Properties of Hydrogen-Hydrogen Bonds: The Stability of a Bulky Phosphatetrahedrane as a Case Study. J Phys Chem A 2021; 125:6151-6157. [PMID: 34236879 DOI: 10.1021/acs.jpca.1c04046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recently, the first mixed C/P phosphatetrahedranes (tBuC)3P and (tBuCP)2 were reported. Unlike (tBuCP)2, (tBuC)3P exhibits remarkable thermal stability, which can be partially attributed to a network of nine hydrogen-hydrogen bonds (HHBs) localized between the tert-butyl substituents. The stabilizing contribution arising from this network of HHBs was obtained from local energy decomposition (LED) analysis calculated at the domain-based local pair natural orbital CCSD(T) (DLPNO-CCSD(T)) level of theory. These calculations suggest that each HHB contributes approximately -0.7 kcal/mol of stabilization; however, the net stabilization energy likely lies between -0.25 and -0.5 kcal/mol because of steric repulsion. Spatial analysis of the London dispersion energy via a dispersion interaction density (DID) plot reveals that the DID surface is localized at key C-H groups involved in HHBs, consistent with London dispersion interactions predominantly arising from HHBs. In addition, we present a computed mechanism that supports a phosphinidenoid species as a key reaction intermediate in the synthesis of (tBuC)3P.
Collapse
Affiliation(s)
- Martin-Louis Y Riu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
6
|
Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry and Department of Chemistry University of Wisconsin Madison Wisconsin 53706 USA
| |
Collapse
|
7
|
Bates TG, de Lange JH, Cukrowski I. The CH···HC interaction in biphenyl is a delocalized, molecular-wide and entirely non-classical interaction: Results from FALDI analysis. J Comput Chem 2021; 42:706-718. [PMID: 33565106 DOI: 10.1002/jcc.26491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/17/2021] [Accepted: 01/21/2021] [Indexed: 11/06/2022]
Abstract
In this study we aim to determine the origin of the electron density describing a CH···HC interaction in planar and twisted conformers of biphenyl. In order to achieve this, the fragment, atomic, localized, delocalized, intra- and inter-atomic (FALDI) decomposition scheme was utilized to decompose the density in the inter-nuclear region between the ortho-hydrogens in both conformers. Importantly, the structural integrity, hence also topological properties, were fully preserved as no 'artificial' partitioning of molecules was implemented. FALDI-based qualitative and quantitative analysis revealed that the majority of electron density arises from two, non-classical and non-local effects: strong overlap of ortho CH σ-bonds, and long-range electron delocalization between the phenyl rings and ortho carbons and hydrogens. These effects resulted in a delocalized electron channel, that is, a density bridge or a bond path in a QTAIM terminology, linking the H-atoms in the planar conformer. The same effects and phenomena are present in both conformers of biphenyl. We show that the CH···HC interaction is a molecular-wide event due to large and long-range electron delocalization, and caution against approaches that investigate CH···HC interactions without fully taking into account the remainder of the molecule.
Collapse
Affiliation(s)
- Thomas G Bates
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Jurgens H de Lange
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
8
|
Gupta R, Rezabal E, Hasrack G, Frison G. Comparison of Chemical and Interpretative Methods: the Carbon-Boron π-Bond as a Test Case*. Chemistry 2020; 26:17230-17241. [PMID: 32780465 DOI: 10.1002/chem.202001945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/05/2020] [Indexed: 12/16/2022]
Abstract
Quantum chemical calculations and NBO, ETS-NOCV, QTAIM and ELF interpretative approaches have been carried out on C-donor ligand-stabilized dihydrido borenium cations. Numerous descriptors of the C-B π-bond strength obtained from orbital localization, energy partitioning or topological methods as well as from structural and chemical parameters have been calculated for 39 C-donor ligands including N-heterocyclic carbenes and carbones. Comparison of the results allows the identification of relative and absolute descriptors of the π interaction. For both families of descriptors excellent correlations are obtained. This enables the establishment of a π-donation capability scale and shows that the interpretative methods, despite their conceptual differences, describe the same chemical properties. These results also reveal noticeable shortcomings in these popular methods, and some precautions that need to be taken to interpret their results adequately.
Collapse
Affiliation(s)
- Radhika Gupta
- LCM, CNRS, École polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Elixabete Rezabal
- LCM, CNRS, École polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.,Faculty of Chemistry, Donostia International Physics Center (DIPC), University of the Basque Country UPV/EHU, 20018, Donostia, Spain
| | - Golshid Hasrack
- LCM, CNRS, École polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Gilles Frison
- LCM, CNRS, École polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| |
Collapse
|
9
|
Cukrowski I, de Lange JH, van Niekerk DME, Bates TG. Molecular Orbitals Support Energy-Stabilizing "Bonding" Nature of Bader's Bond Paths. J Phys Chem A 2020; 124:5523-5533. [PMID: 32520541 DOI: 10.1021/acs.jpca.0c02234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Our MO-based findings proved a bonding nature of each density bridge (DB, or a bond path with an associated critical point, CP) on a Bader molecular graph. A DB pinpoints universal physical and net energy-lowering processes that might, but do not have to, lead to a chemical bond formation. Physical processes leading to electron density (ED) concentration in internuclear regions of three distinctively different homopolar H,H atom-pairs as well as classical C-C and C-H covalent bonds were found to be exactly the same. Notably, properties of individual MOs are internuclear-region specific as they (i) concentrate, deplete, or do not contribute to ED at a CP and (ii) delocalize electron-pairs through either in- (positive) or out-of-phase (negative) interference. Importantly, dominance of a net ED concentration and positive e--pairs delocalization made by a number of σ-bonding MOs is a common feature at a CP. This feature was found for the covalently bonded atoms as well as homopolar H,H atom-pairs investigated. The latter refer to a DB-free H,H atom-pair of the bay in the twisted biphenyl (Bph) and DB-linked H,H atom-pairs (i) in cubic Li4H4, where each H atom is involved in three highly repulsive interactions (over +80 kcal/mol), and (ii) in a weak attractive interaction when sterically clashing in the planar Bph.
Collapse
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Jurgens H de Lange
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Daniël M E van Niekerk
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Thomas G Bates
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| |
Collapse
|
10
|
Mitoraj MP, Sagan F, Szczepanik DW, de Lange JH, Ptaszek AL, van Niekerk DME, Cukrowski I. Origin of Hydrocarbons Stability from a Computational Perspective: A Case Study of Ortho-Xylene Isomers. Chemphyschem 2020; 21:494-502. [PMID: 31990431 DOI: 10.1002/cphc.202000066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Indexed: 01/12/2023]
Abstract
It is shown herein that intuitive and text-book steric-clash based interpretation of the higher energy "in-in" xylene isomer (as arising solely from the repulsive CH⋅⋅⋅HC contact) with respect to the corresponding global-minimum "out-out" configuration (where the clashing C-H bonds are tilted out) is misleading. It is demonstrated that the two hydrogen atoms engaged in the CH⋅⋅⋅HC contact in "in-in" are involved in attractive interaction so they cannot explain the lower stability of this isomer. We have proven, based on the arsenal of modern bonding descriptors (EDDB, HOMA, NICS, FALDI, ETS-NOCV, DAFH, FAMSEC, IQA), that in order to understand the relative stability of "in-in" versus "out-out" xylenes isomers one must consider the changes in the electronic structure encompassing the entire molecules as arising from the cooperative action of hyperconjugation, aromaticity and unintuitive London dispersion plus charge delocalization based intra-molecular CH⋅⋅⋅HC interactions.
Collapse
Affiliation(s)
- Mariusz P Mitoraj
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Filip Sagan
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Dariusz W Szczepanik
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Jurgens H de Lange
- Department of Chemistry Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Aleksandra L Ptaszek
- Department of Theoretical Chemistry Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-87, Krakow, Poland
| | - Daniel M E van Niekerk
- Department of Chemistry Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Ignacy Cukrowski
- Department of Chemistry Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| |
Collapse
|
11
|
Non-covalent interactions and spectroscopic study of chalcone derivative 1-(4-chlorophenyl)-3-(5-methylfuran-2-yl) prop-2-en-1-one. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
12
|
Zandiyeh Z, Ghiasi R, Jamaat PR. Computational Rationalization of the Interaction of Fe(CO)4 and Substituted Benzyne Ligands. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620020043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Grudova MV, Gil DM, Khrustalev VN, Nikitina EV, Sinelshchikova AA, Grigoriev MS, Kletskov AV, Frontera A, Zubkov FI. Synthesis, X-ray characterization and theoretical study of 3 a,6:7,9 a-diepoxybenzo[ de]isoquinoline derivatives: on the importance of F⋯O interactions. NEW J CHEM 2020. [DOI: 10.1039/d0nj04328a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This manuscript reports the synthesis, X-ray characterization and theoretical study of 3a,6:7,9a-diepoxybenzo[de]isoquinoline derivatives focusing on the importance of F···O interactions.
Collapse
Affiliation(s)
- Mariya V. Grudova
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
| | - Diego M. Gil
- INBIOFAL (CONICET – UNT), Instituto de Química Orgánica. Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán
- San Miguel de Tucumán
- Argentina
| | - Victor N. Khrustalev
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
- N. D. Zelinsky Institute of Organic Chemistry of RAS
- 119991 Moscow
| | - Eugeniya V. Nikitina
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
| | - Anna A. Sinelshchikova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences
- Moscow 119071
- Russian Federation
| | - Mikhail S. Grigoriev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences
- Moscow 119071
- Russian Federation
| | - Alexey V. Kletskov
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
| | - Fedor I. Zubkov
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
| |
Collapse
|
14
|
Lomas JS. Relationships between NMR shifts and interaction energies in biphenyls, alkanes, aza-alkanes, and oxa-alkanes with X─H … H─Y and X─H … Z (X, Y = C or N; Z = N or O) hydrogen bonding. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:1121-1135. [PMID: 31218728 DOI: 10.1002/mrc.4900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Hydrogen-hydrogen C─H… H─C bonding between the bay-area hydrogens in biphenyls, and more generally in congested alkanes, very strained polycyclic alkanes, and cis-2-butene, has been investigated by calculation of proton nuclear magnetic resonance (NMR) shifts and atom-atom interaction energies. Computed NMR shifts for all protons in the biphenyl derivatives correlate very well with experimental data, with zero intercept, unit slope, and a root mean square deviation of 0.06 ppm. For some congested alkanes, there is generally good agreement between computed values for a selected conformer and the experimental data, when it is available. In both cases, the shift of a given proton or pair of protons tends to increase with the corresponding interaction energy. Computed NMR shift differences for methylene protons in polycyclic alkanes, where one is involved in a very short contact ("in") and the other is not ("out"), show a rough correlation with the corresponding C─H… H─C exchange energies. The "in" and "in,in" isomers of selected aza- and diaza-cycloalkanes, respectively, are X─H… H─N hydrogen bonded, whereas the "out" and "in,out" isomers display X─H… N hydrogen bonds (X = C or N). Oxa-alkanes and the "in" isomers of aza-oxa-alkanes are X─H… O hydrogen bonded. There is a very good general correlation, including both N─H… H─Y (Y = C or N) and N─H… Z (Z = N or O) interactions, for NH proton shifts against the exchange energy. For "in" CH protons, the data for the different C─H… H─Y and C─H… Z interactions are much more dispersed and the overall shift/exchange energy correlation is less satisfactory.
Collapse
Affiliation(s)
- John S Lomas
- Interfaces, Traitements, Organisation et Dynamique des Systèmes (CNRS UMR-7086), Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
15
|
Yue X, Li L, Li P, Luo C, Pu M, Yang Z, Lei M. A Computational Study on Iridium‐Catalyzed Production of Acetic Acid from Ethanol and Water Solution. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xin Yue
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of ChemistryBeijing University of Chemical Technology Beijing 100029 China
| | - Longfei Li
- College of Pharmaceutical ScienceHebei University Baoding Hebei 071002 China
| | - Pengjie Li
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of ChemistryBeijing University of Chemical Technology Beijing 100029 China
| | - Chenguang Luo
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of ChemistryBeijing University of Chemical Technology Beijing 100029 China
| | - Min Pu
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of ChemistryBeijing University of Chemical Technology Beijing 100029 China
| | - Zuoyin Yang
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of ChemistryBeijing University of Chemical Technology Beijing 100029 China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of ChemistryBeijing University of Chemical Technology Beijing 100029 China
| |
Collapse
|
16
|
Carvalho LC, Bueno MA, de Oliveira BG. The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C 2H 2⋯HF and C 2H 4⋯HF small dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:438-455. [PMID: 30738351 DOI: 10.1016/j.saa.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C2H2⋯(HF), C2H2⋯2(HF), C2H2⋯4(HF), C2H4⋯(HF), C2H4⋯2(HF) and C2H4⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).
Collapse
|
17
|
Cukrowski I. Reliability of HF/IQA, B3LYP/IQA, and MP2/IQA data in interpreting the nature and strength of interactions. Phys Chem Chem Phys 2019; 21:10244-10260. [DOI: 10.1039/c9cp00243j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using CCSD/BBC1/IQA as a reference to describe interactions in glycol conformers, including O4⋯H6 and O3⋯O4 interactions, B3LYP/IQA data produced an exact qualitative picture and exceptionally reliable IQA energy changes, resulting in a perfectly comparable FAMSEC-based quantitative interpretation.
Collapse
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry
- Faculty of Natural and Agricultural Sciences
- University of Pretoria
- Pretoria
- South Africa
| |
Collapse
|
18
|
Poater J, Duran M, Solà M. Aromaticity Determines the Relative Stability of Kinked vs. Straight Topologies in Polycyclic Aromatic Hydrocarbons. Front Chem 2018; 6:561. [PMID: 30515378 PMCID: PMC6255896 DOI: 10.3389/fchem.2018.00561] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
It is well-known that kinked phenacenes are more stable than their isomeric linear acenes, the archetypal example being phenanthrene that is more stable than anthracene by about 4–8 kcal/mol. In previous studies, the origin of the higher stability of kinked polycyclic aromatic hydrocarbons (PAHs) was found to be better π-bonding interactions, i.e., larger aromaticity, in kinked as compared to linear PAHs. Some years ago, however, Dominikowska and Palusiak (2011) found that dicationic linear anthracene is more stable than the dicationic kinked phenanthrene. Therefore, these authors showed that, in some cases, the linear topology in PAHs can be preferred over the kinked one. Our results using energy decomposition analyses in combination with the turn-upside-down approach show that the origin of the higher stability of dicationic anthracene is the same as in the neutral species, i.e., better π-bonding interactions. A similar result is found for the kinked and straight pyrano-chromenes. We conclude that the aromaticity is the driving force that determines the relative stability of kinked vs. straight topologies in PAHs.
Collapse
Affiliation(s)
- Jordi Poater
- ICREA, Barcelona, Spain.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Barcelona, Spain
| | - Miquel Duran
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona, Spain
| |
Collapse
|
19
|
Mitoraj MP, Sagan F, Babashkina MG, Isaev AY, Chichigina YM, Safin DA. N
-Thiophosphorylthioureas RNHC(S)NHP(S)(Oi
Pr)2
as an Excellent Platform for Studying the Synergy between Hydrogen-Hydrogen Bonding and Other Families of Non-Covalent Interactions. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mariusz P. Mitoraj
- Department of Theoretical Chemistry; Faculty of Chemistry; Jagiellonian University; Gronostajowa 2 30-387 Cracow Poland
| | - Filip Sagan
- Department of Theoretical Chemistry; Faculty of Chemistry; Jagiellonian University; Gronostajowa 2 30-387 Cracow Poland
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; Place L. Pasteur 1 1348 Louvain-la-Neuve Belgium
| | - Alexey Y. Isaev
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
| | - Yana M. Chichigina
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
| | - Damir A. Safin
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; Place L. Pasteur 1 1348 Louvain-la-Neuve Belgium
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
| |
Collapse
|
20
|
Ghiasi R, Saraf SH, Pasdar H. Influences of the substituents on the Cr=C bond in [(OC)5Cr=C(OEt)-para-C6H4X] complexes: quantum Theory of Atoms in Molecules, Energy Decomposition Analysis, and Interacting Quantum Atoms. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2299-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
21
|
de Lange JH, van Niekerk DME, Cukrowski I. FALDI-based criterion for and the origin of an electron density bridge with an associated (3,-1) critical point on Bader's molecular graph. J Comput Chem 2018; 39:2283-2299. [PMID: 30318597 DOI: 10.1002/jcc.25548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/01/2018] [Accepted: 07/12/2018] [Indexed: 12/17/2022]
Abstract
The total electron density (ED) along the λ2 -eigenvector is decomposed into contributions which either facilitate or hinder the presence of an electron density bridge (DB, often called an atomic interaction line or a bond path). Our FALDI-based approach explains a DB presence as a result of a dominating rate of change of facilitating factors relative to the rate of change of hindering factors; a novel and universal criterion for a DB presence is, thus, proposed. Importantly, facilitating factors show, in absolute terms, a concentration of ED in the internuclear region as commonly observed for most chemical bonds, whereas hindering factors show a depletion of ED in the internuclear region. We test our approach on four intramolecular interactions, namely (i) an attractive classical H-bond, (ii) a repulsive O⋅⋅⋅O interaction, (iii) an attractive Cl⋅⋅⋅Cl interaction, and (iv) an attractive CH⋅⋅⋅HC interaction. (Dis)appearance of a DB is (i) shown to be due to a "small" change in molecular environment and (ii) qualitatively and quantitatively linked with specific atoms and atom-pairs. The protocol described is equally applicable (a) to any internuclear region, (b) regardless of what kind of interaction (attractive/repulsive) atoms are involved in, (c) at any level of theory used to compute the molecular structure and corresponding wavefunction, and (d) equilibrium or nonequilibrium structures. Finally, we argue for a paradigm shift in the description of chemical interactions, from the ED perspective, in favor of a multicenter rather than diatomic approach in interpreting ED distributions in internuclear regions. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Jurgens H de Lange
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Daniël M E van Niekerk
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| |
Collapse
|
22
|
Xu HL, Li QZ, Scheiner S. Effect of Magnesium Bond on the Competition Between Hydrogen and Halogen Bonds and the Induction of Proton and Halogen Transfer. Chemphyschem 2018; 19:1456-1464. [PMID: 29544030 DOI: 10.1002/cphc.201800102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Indexed: 01/18/2023]
Abstract
HOX (X=Cl, Br, I, and At) can engage in either a H-bond (HB) or halogen bond (XB) with a base-like HCN, NH3 , and imidazole. Although the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY2 forms a Mg-bond with the O atom of HOX, which grows stronger in the order X=Cl<Br<I<At and Y=F<Cl<Br. When all three molecules are combined, both the Mg and the H/X bonds are cooperatively strengthened to a large degree. Rather than causing a reversal in the HB/XB competition, the Mg-bond acts primarily to amplify the natural preference within the dimer. The Mg-bond induces a certain degree of transfer from O to N of the bridging atom in the H/X bond. Comparison is also made with the effects of a Be-bond.
Collapse
Affiliation(s)
- Hui-Li Xu
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qing-Zhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322-0300, USA
| |
Collapse
|
23
|
Singh A, Sahoo DK, Sethi SK, Jena S, Biswal HS. Nature and Strength of the Inner-Core H⋅⋅⋅H Interactions in Porphyrinoids. Chemphyschem 2017; 18:3625-3633. [DOI: 10.1002/cphc.201700742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ankit Singh
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Srikant Kumar Sethi
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| |
Collapse
|
24
|
Moore KB, Sadeghian K, Sherrill CD, Ochsenfeld C, Schaefer HF. C-H···O Hydrogen Bonding. The Prototypical Methane-Formaldehyde System: A Critical Assessment. J Chem Theory Comput 2017; 13:5379-5395. [PMID: 29039941 DOI: 10.1021/acs.jctc.7b00753] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Distinguishing the functionality of C-H···O hydrogen bonds (HBs) remains challenging, because their properties are difficult to quantify reliably. Herein, we present a study of the model methane-formaldehyde complex (MFC). Six stationary points on the MFC potential energy surface (PES) were obtained at the CCSD(T)/ANO2 level. The CCSDT(Q)/CBS interaction energies of the conformers range from only -1.12 kcal mol-1 to -0.33 kcal mol-1, denoting a very flat PES. Notably, only the lowest energy stationary point (MFC1) corresponds to a genuine minimum, whereas all other stationary points-including the previously studied ideal case of ae(C-H···O) = 180°-exhibit some degree of freedom that leads to MFC1. Despite the flat PES, we clearly see that the HB properties of MFC1 align with those of the prototypical water dimer O-H···O HB. Each HB property generally becomes less prominent in the higher-energy conformers. Only the MFC1 conformer prominently exhibits (1) elongated C-H donor bonds, (2) attractive C-H···O═C interactions, (3) n(O) → σ*(C-H) hyperconjugation, (4) critical points in the electron density from Bader's method and from the noncovalent interactions method, (5) positively charged donor hydrogen, and (6) downfield NMR chemical shifts and nonzero 2J(CM-HM···OF) coupling constants. Based on this research, some issues merit further study. The flat PES hinders reliable determinations of the HB-induced shifts of the C-H stretches; a similarly difficult challenge is observed for the experiment. The role of charge transfer in HBs remains an intriguing open question, although our BLW and NBO computations suggest that it is relevant to the C-H···O HB geometries. These issues notwithstanding, the prominence of the HB properties in MFC1 serves as clear evidence that the MFC is predominantly bound by a C-H···O HB.
Collapse
Affiliation(s)
- Kevin B Moore
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Keyarash Sadeghian
- Department of Chemistry, Ludwig-Maximilians University (LMU) , Munich D-81377, Germany
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig-Maximilians University (LMU) , Munich D-81377, Germany
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| |
Collapse
|
25
|
Yourdkhani S, Jabłoński M, Echeverría J. Attractive PHHP interactions revealed by state-of-the-art ab initio calculations. Phys Chem Chem Phys 2017; 19:28044-28055. [PMID: 28994835 DOI: 10.1039/c7cp04412g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report in this work a combined structural and state-of-the-art computational study of homopolar P-HH-P intermolecular contacts. Database surveys have shown the abundance of such surprisingly unexplored contacts, which are usually accompanied by other weak interactions in the solid state. By means of a detailed theoretical study utilizing SAPT(DFT), MP2, SCS-MP2, MP2C and CCSD(T) methods and both aug-cc-pVXZ and aug-cc-pCVXZ (X = D, T, Q, 5) basis sets as well as extrapolation to the CBS limit, we have shown that P-HH-P contacts are indeed attractive and considerably strong. SAPT(DFT) calculations have revealed the dispersive nature of the P-HH-P interaction with only minor contribution of the inductive term, whereas the first-order electrostatic term is clearly overbalanced by the first-order exchange energy. In general the computed interaction energies follow the trend: E ≈ E < E < E. Our results have also shown that the aug-cc-pVDZ (or aug-cc-pCVDZ) basis set is not yet well balanced and that the second-order dispersion energy term is the slowest converging among all SAPT(DFT) energy components. Compared to aug-cc-pVXZ basis sets, their core-correlation counterparts have a modest influence on all supermolecular interaction energies and a negligible influence on both the SAPT(DFT) interaction energy and its components.
Collapse
Affiliation(s)
- Sirous Yourdkhani
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | | | | |
Collapse
|
26
|
Pandey SK, Manogaran D, Manogaran S, Schaefer HF. Quantification of Hydrogen Bond Strength Based on Interaction Coordinates: A New Approach. J Phys Chem A 2017; 121:6090-6103. [DOI: 10.1021/acs.jpca.7b04752] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Dhivya Manogaran
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
| | - Sadasivam Manogaran
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
27
|
Conformations and interactions in pasiniazid: A spectroscopic and computational characterization. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
28
|
Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR. Molecules 2016; 21:molecules21111426. [PMID: 27801801 PMCID: PMC6274571 DOI: 10.3390/molecules21111426] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/30/2022] Open
Abstract
The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.
Collapse
|
29
|
Cukrowski I, Sagan F, Mitoraj MP. On the Stability of Cis- and Trans-2-Butene Isomers. An Insight Based on the FAMSEC, IQA, and ETS-NOCV Schemes. J Comput Chem 2016; 37:2783-2798. [PMID: 27730662 DOI: 10.1002/jcc.24504] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/08/2016] [Accepted: 09/10/2016] [Indexed: 01/19/2023]
Abstract
In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H-H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH-HC fragment (loc-FAMSEC = -3.6 kcal/mol) with most favourably changed intrafragment interactions on trans-eq→cis-eq. Moreover, lower stability of cis-eq vs. trans-eq is linked with the entire HCCH (ethylenic) fragment which destabilized cis-eq (mol-FAMSEC, +3.9 kcal/mol) the most. Although the H-H contact can be linked with smaller, relative to trans-, rotational energy barrier in cis-2-butene, we have proven that to rationalize this phenomenon one must account for changes in interactions between various fragments that constitute the entire molecule. Importantly, we discovered a number of comparable trends in fundamental properties of equivalent molecular fragments on a methyl group rotation; for example, interaction between BP-free H-atoms in trans-eq (involving CH bonds of the methyl and ethylenic units) and BP-linked H-atoms in cis-eq. Clearly, rotational energy barrier cannot be entirely (i) rationalized by the properties of or (ii) attributed to the H-H contact in cis-eq. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Mariusz Paweł Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| |
Collapse
|
30
|
|
31
|
Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3. CRYSTALS 2016. [DOI: 10.3390/cryst6030028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
32
|
Matczak P. Intramolecular C–H···H–C Contacts in Diheteroaryl Ketones and Thioketones: A Theoretical Analysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Piotr Matczak
- Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź
| |
Collapse
|
33
|
Matta CF, Sadjadi SA, Braden DA, Frenking G. The barrier to the methyl rotation inCis-2-butene and its isomerization energy toTrans-2-butene, revisited. J Comput Chem 2015; 37:143-54. [DOI: 10.1002/jcc.24223] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 08/02/2015] [Accepted: 09/06/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Chérif F. Matta
- Department of Chemistry and Physics; Mount Saint Vincent University; Halifax Nova Scotia B3M 2J6 Canada
- Department of Chemistry; Dalhousie University; Halifax Nova Scotia B3H 4J3 Canada
- Department of Chemistry; Saint Mary's University; Halifax Nova Scotia B3H 3C3 Canada
| | - Seyed Abdolreza Sadjadi
- Department of Physics, Faculty of Science, Space Astronomy Laboratory; The University of Hong Kong; Pokfulam Road Hong Kong SAR China
| | | | - Gernot Frenking
- Philipps-Universität Marburg Hans-Meerweinstr.; Marburg 4 D-35032 Germany
- Donostia International Physics Center (DIPC); P.K. 1072, 20080 Donostia Euskadi Spain
| |
Collapse
|
34
|
Safin DA, Babashkina MG, Robeyns K, Mitoraj MP, Kubisiak P, Garcia Y. Influence of the Homopolar Dihydrogen Bonding CH⋅⋅⋅HC on Coordination Geometry: Experimental and Theoretical Studies. Chemistry 2015; 21:16679-87. [DOI: 10.1002/chem.201501499] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Damir A. Safin
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
| | - Koen Robeyns
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
| | - Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30‐060 Krakow (Poland)
| | - Piotr Kubisiak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30‐060 Krakow (Poland)
| | - Yann Garcia
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
| |
Collapse
|
35
|
Scheiner S. Comparison of CH···O, SH···O, Chalcogen, and Tetrel Bonds Formed by Neutral and Cationic Sulfur-Containing Compounds. J Phys Chem A 2015; 119:9189-99. [DOI: 10.1021/acs.jpca.5b06831] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| |
Collapse
|
36
|
Cormanich RA, Bühl M, Rittner R. Understanding the conformational behaviour of Ac-Ala-NHMe in different media. A joint NMR and DFT study. Org Biomol Chem 2015. [PMID: 26219244 DOI: 10.1039/c5ob01296a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The conformational behaviour of Ac-Ala-NHMe was studied in the gas-phase and in solution by theoretical calculations (B3LYP-D3/aug-cc-pVDZ level) and experimental (1)H NMR. The conformational preferences of this compound were shown to result from a complex interplay between the strengths of possible intramolecular hydrogen bonds, steric interactions, hyperconjugation, entropy effects and the overall dipole moments. The Ac-Ala-N(Me)2 derivative was studied in addition, to design a system akin to Ac-Ala-NHMe, but with disrupted intramolecular hydrogen bonds involving the -NHMe group, mimicking the effect of polar protic solvents.
Collapse
Affiliation(s)
- Rodrigo A Cormanich
- Chemistry Institute, University of Campinas, Campinas, SP 13083-970, Brazil.
| | | | | |
Collapse
|
37
|
Dubis AT, Stasiewicz P, Pogorzelec-Glaser K, Łapiński A. Can 2-acylpyrroles form an intramolecular hydrogen bond? J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alina T. Dubis
- Institute of Chemistry; University of Bialystok; Hurtowa 1 15-399 Bialystok Poland
| | - Piotr Stasiewicz
- Institute of Chemistry; University of Bialystok; Hurtowa 1 15-399 Bialystok Poland
| | | | - Andrzej Łapiński
- Institute of Molecular Physics; Polish Academy of Sciences; ul. Smoluchowskiego 17 60-179 Poznan Poland
| |
Collapse
|
38
|
Hübner A, Kaese T, Diefenbach M, Endeward B, Bolte M, Lerner HW, Holthausen MC, Wagner M. A preorganized ditopic borane as highly efficient one- or two-electron trap. J Am Chem Soc 2015; 137:3705-14. [PMID: 25723124 DOI: 10.1021/jacs.5b01192] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Reduction of the bis(9-borafluorenyl)methane 1 with excess lithium furnishes the red dianion salt Li2[1]. The corresponding dark green monoanion radical Li[1] is accessible through the comproportionation reaction between 1 and Li2[1]. EPR spectroscopy on Li[1] reveals hyperfine coupling of the unpaired electron to two magnetically equivalent boron nuclei (a((11)B) = 5.1 ± 0.1 G, a((10)B) = 1.7 ± 0.2 G). Further coupling is observed to the unique B-CH-B bridgehead proton (a((1)H) = 7.2 ± 0.2 G) and to eight aromatic protons (a((1)H) = 1.4 ± 0.1 G). According to X-ray crystallography, the B···B distances continuously decrease along the sequence 1 → [1](•-) → [1](2-) with values of 2.534(2), 2.166(4), and 1.906(3) Å, respectively. Protonation of Li2[1] leads to the cyclic borohydride species Li[1H] featuring a B-H-B two-electron-three-center bond. This result strongly indicates a nucleophilic character of the boron atoms; the reaction can also be viewed as rare example of the protonation of an element-element σ bond. According to NMR spectroscopy, EPR spectroscopy, and quantum-chemical calculations, [1](2-) represents a closed-shell singlet without any spin contamination. Detailed wave function analyses of [1](•-) and [1](2-) reveal strongly localized interactions of the two boron pz-type orbitals, with small delocalized contributions of the 9-borafluorenyl π systems. Overall, our results provide evidence for a direct B-B one-electron and two-electron bonding interaction in [1](•-) and [1](2-), respectively.
Collapse
Affiliation(s)
- Alexander Hübner
- †Institut für Anorganische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Thomas Kaese
- †Institut für Anorganische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Martin Diefenbach
- †Institut für Anorganische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Burkhard Endeward
- ‡Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael Bolte
- †Institut für Anorganische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Hans-Wolfram Lerner
- †Institut für Anorganische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Max C Holthausen
- †Institut für Anorganische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Matthias Wagner
- †Institut für Anorganische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| |
Collapse
|
39
|
Della Porta P, Zanasi R, Monaco G. Hydrogen-hydrogen bonding: the current density perspective. J Comput Chem 2015; 36:707-16. [PMID: 25689556 DOI: 10.1002/jcc.23841] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 11/08/2022]
Abstract
Current density plots of closed-shell intermolecular H-H interactions characterized by a bond critical point (BCP) show two vortices separated by a saddle, a pattern which allows for a clear definition of a pair current strength. This H-H current strength turns out to be roughly related to the potential energy density at the BCP and then to the dissociation energy. The same pattern is also recognizable, at least for an azimuthal orientation of a field perpendicular to the H-H line, for the intramolecular interactions previously investigated to propose the H-H bonding. In the case of the H atoms of the bay region of polycyclic aromatic hydrocarbons, the current of the H-H delocalized diatropic vortex gives a quantitative indication of stabilization; however, on rotation of the field and the subsequent onset of a bay-delocalized paratropic vortex (a typical signature of antiaromaticity), the diatropic vortex can be reshaped or it can even disappear, consistently with its smallness, and thus showing the effect of other more relevant interactions.
Collapse
Affiliation(s)
- Paolo Della Porta
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, 84084 SA, Italy
| | | | | |
Collapse
|
40
|
Weinhold F, Klein RA. Improved General Understanding of the Hydrogen-Bonding Phenomena: A Reply. Angew Chem Int Ed Engl 2015; 54:2600-2. [DOI: 10.1002/anie.201500262] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 01/31/2023]
|
41
|
Weinhold F, Klein RA. Improved General Understanding of the Hydrogen-Bonding Phenomena: A Reply. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500262] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
42
|
Cukrowski I, de Lange JH, Adeyinka AS, Mangondo P. Evaluating common QTAIM and NCI interpretations of the electron density concentration through IQA interaction energies and 1D cross-sections of the electron and deformation density distributions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
43
|
Azofra LM, Scheiner S. Tetrel, chalcogen, and CH⋅⋅O hydrogen bonds in complexes pairing carbonyl-containing molecules with 1, 2, and 3 molecules of CO2. J Chem Phys 2015; 142:034307. [DOI: 10.1063/1.4905899] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luis M. Azofra
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
| |
Collapse
|
44
|
Craig NC, Demaison J, Groner P, Rudolph HD, Vogt N. Electron delocalization in polyenes: a semiexperimental equilibrium structure for (3E)-1,3,5-hexatriene and theoretical structures for (3Z,5Z)-, (3E,5E)-, and (3E,5Z)-1,3,5,7-octatetraene. J Phys Chem A 2015; 119:195-204. [PMID: 25465856 DOI: 10.1021/jp510237h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electronic structure theory reveals that π-electron delocalization increases with the chain length in polyenes. To analyze quantitatively this effect a semiexperimental equilibrium structure has been determined for trans-hexatriene by the mixed estimation method. For this fit rotational constants for a number of carbon and hydrogen isotopologues as well as a high-level ab initio structure have been used. The accuracy is 0.001 Å for bond lengths and 0.1° for bond angles. For the three isomers of octatetraene, high-level ab initio calculations have given a comparably accurate structure. These structures have been used in comparison with the structure of s-trans-butadiene to show that "C═C" bonds increase in length and "C-C" bonds decrease in length as the polyene chain lengthens. These structural effects of π-electron delocalization increase toward the center of polyenes. Most likely, π-π conjugation in the molecules studied plays a large part in their planarity that, in turn, forces the hydrogen atoms of cis fragments in bay regions to be in a close contact. Their distance is indeed shorter than the sum of their van der Waals radii, and they seem to participate in a six-membered ring.
Collapse
Affiliation(s)
- Norman C Craig
- Department of Chemistry and Biochemistry, Oberlin College , Oberlin, Ohio 44074, United States
| | | | | | | | | |
Collapse
|
45
|
Abstract
The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF3-C(O)-Gly-NHMe] and N-methyl[Ac-Gly-N(Me)2] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.
Collapse
Affiliation(s)
- R. A. Cormanich
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
- Chemistry Institute
| | - R. Rittner
- Chemistry Institute
- State University of Campinas
- Campinas
- Brazil
| | - M. Bühl
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
| |
Collapse
|
46
|
Lu F, Li X, Sun Z, Zeng Y, Meng L. Influences of the substituents on the M–M bonding in Cp4Al4 and Cp2M2X2 (M = B, Al, Ga; Cp = C5H5, X = halogen). Dalton Trans 2015; 44:14092-100. [DOI: 10.1039/c5dt01901j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The different stabilities of Cp*4Al4 and Cp4Al4 (Cp = C5H5) have been explained by theoretical methods.
Collapse
Affiliation(s)
- Feifei Lu
- College of Chemistry and Materials Science
- Hebei Normal University
- Shijiazhuang
- China
| | - Xiaoyan Li
- College of Chemistry and Materials Science
- Hebei Normal University
- Shijiazhuang
- China
| | - Zheng Sun
- College of Chemistry and Materials Science
- Hebei Normal University
- Shijiazhuang
- China
| | - Yanli Zeng
- College of Chemistry and Materials Science
- Hebei Normal University
- Shijiazhuang
- China
| | - Lingpeng Meng
- College of Chemistry and Materials Science
- Hebei Normal University
- Shijiazhuang
- China
| |
Collapse
|
47
|
Cormanich RA, Rittner R, O’Hagan D, Bühl M. Analysis of CF···FC Interactions on Cyclohexane and Naphthalene Frameworks. J Phys Chem A 2014; 118:7901-10. [DOI: 10.1021/jp504568c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodrigo A. Cormanich
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
- Chemistry
Institute, State University of Campinas, P.O. Box 6154, 13083-971 Campinas, SP, Brazil
| | - Roberto Rittner
- Chemistry
Institute, State University of Campinas, P.O. Box 6154, 13083-971 Campinas, SP, Brazil
| | - David O’Hagan
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Michael Bühl
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| |
Collapse
|
48
|
Eskandari K, Van Alsenoy C. Hydrogen-hydrogen interaction in planar biphenyl: A theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods. J Comput Chem 2014; 35:1883-9. [DOI: 10.1002/jcc.23698] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/08/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Kiamars Eskandari
- Department of Chemistry; Isfahan University of Technology; Isfahan 84156-83111 Iran
| | - Christian Van Alsenoy
- Department of Chemistry; University of Antwerp; Universiteitsplein 1 Antwerp 2610 Belgium
| |
Collapse
|