1
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Villegas-Escobar N. Insights into the variations of kinetic and potential energies in a multi-bond reaction: the reaction electronic flux perspective. J Mol Model 2024; 30:262. [PMID: 38990414 DOI: 10.1007/s00894-024-06024-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
CONTEXT The debate over whether kinetic energy (KE) or potential energy (PE) are the fundamental energy components that contribute to forming covalent bonds has been enduring and stimulating over time. However, the supremacy of these energy components in reactions where multiple bonds are simultaneously formed or broken has yet to be explored. In this study, we use the reaction electronic flux (REF), an effective tool for investigating changes in driving electronic activity when bond formation or dissociation occurs in a chemical reaction, to examine the fluctuations in the KE and PE in a multi-bond reaction. To that end, the activation of CO2 by low-valent group 14 catalysts through a concerted σ -bond metathesis mechanism is analyzed. The findings of this preliminary study suggest that the REF can be utilized as a tool to rationalize alterations in the KE and PE in a multi-bond reaction. Specifically, analyses across the reaction coordinate reveal that changes in the KE and PE precede activation in the REF, stimulating the electronic activity where bond formation or dissociation processes dominate. METHODS The activation of CO2 by the low-valent LEH catalysts (L = N,N'-bis(2,6-diisopropyl phenyl)- β -diketiminate; E = Si, Ge, Sn, and Pb) was studied along the reaction coordinate at the M06-2X/6-31 G(d,p)-LANL2DZ(E) level of theory. The respective minimum energy path calculations were obtained using the intrinsic reaction coordinate (IRC) procedure. The reaction electronic flux (REF) was calculated through the computation of the electronic chemical potential using the frontier molecular orbital approximation. Mayer bond orders along the reaction coordinate have been determined using the NBO 3.1 program in Gaussian16. Most of the reaction coordinate quantities reported in this study (REF, KE, PE, among others) have been determined using the Kudi program and custom Python scripts.
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Affiliation(s)
- Nery Villegas-Escobar
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, 4070139, Chile.
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2
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Cooper DL, Penotti FE, Karadakov PB. Reassessing the Composition of Hybrid Orbitals in Contemporary VB Calculations. J Phys Chem A 2023. [PMID: 37257152 DOI: 10.1021/acs.jpca.3c01857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Large variations in the ratios between the p and s components of individual hybrid orbitals that have been observed in contemporary ab initio VB calculations are reassessed, and links are established to specific energy terms that drive bond formation. It is demonstrated that the ratios between the p and s components for individual hybrid orbitals are not indicative of the overall hybridization status of the relevant atom, which exhibits only relatively small variations with the level of theory, irrespective of whether or not non-dynamical and dynamical electron correlation effects are accounted for. An alternative orbital representation that turns out to be far more consistent with the overall hybridization of the relevant atom is examined. The chosen test cases, which can be compared with the classical sp3, sp2, and sp hybridization models for a central carbon atom, are CH4 (Td), trigonal CH3 (D3h), and triplet CH2 distorted from its ground state geometry so as to be linear (D∞h).
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Affiliation(s)
- David L Cooper
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K
| | - Fabio E Penotti
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Via Golgi 19, I-20133 Milano (MI), Italy
| | - Peter B Karadakov
- Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
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3
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Zhao J, Chi CX, Meng LY, Jiang XL, Grunenberg J, HU HS, Zhou M, Li J, Schwarz W. Cis- and Trans-Binding Influences in [NUO · (N2)n]+ . J Chem Phys 2022; 157:054301. [DOI: 10.1063/5.0098068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Uranium nitride-oxide cations [NUO]+ and their complexes with equatorial N2 ligands, [NUO·(N2) n]+ ( n=1-7), were synthesized in the gas phase. Mass-selected infrared photo-dissociation spectroscopy and quantum-chemical calculations confirm [NUO·(N2)5]+ as the sterically fully coordinated cation, with electronic singlet ground state of 1A1, linear [NUO]+ core, and C5v structure. The short N-U bond distances and high stretching modes, with slightly elongated U-O bond distances and lowered stretching modes, are rationalized as due to cooperative covalent and dative [ǀN≡U≡Oǀ]+ triple bonds. The mutual trans-interaction through the flexible electronic U-5f6d7sp valence shell, and the linearly increasing perturbation by an increasing number of equatorial dative N2 ligands are rationalized. It highlights the bonding and distinctiveness of uranium chemistry.
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Affiliation(s)
| | | | - Lu-Yan Meng
- East China University of Technology, Nanchang, China
| | - Xue-Lian Jiang
- Southern University of Science and Technology, Shenzhen, China
| | | | | | | | - Jun Li
- Tsinghua University, China
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4
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Depastas T, Androutsopoulos A, Tzeli D. Analysis of chemical bonding of the ground and low-lying states of Mo 2 and of Mo 2Cl x complexes, x = 2 - 10. J Chem Phys 2022; 157:054302. [DOI: 10.1063/5.0091907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In the present study, we perform accurate calculations via multireference configuration interaction and coupled cluster methodologies on the dimolybdenum molecule in conjunction with complete series of correlation and weighted core correlation consistent basis sets up to quintuple size. The bonding, dissociation energies, and spectroscopic parameters of the seven states that correlate to the ground state products are calculated. The ground state has a sextuple chemical bond and each of the calculated excited state has one less bond than the previous one. The calculated values for the ground(X1Σg+ ) state of Mo2 have been extrapolated to the complete basis set limits. Our final values, re=1.9324 Å and De(D0)=4.502{plus minus}0.007(4.471{plus minus}0.009) eV, are in excellent agreement with the experimental values of re=1.929, 1.938(9) Å and D0=4.476(10) eV. The Mo2 in 13Σg+ state is a weakly bound dimer, forming 5s...5pz bonds, with De=0.120 eV at re=3.53 Å. All calculated excited states (except 13Σg+) have a highly multireference character (C0=0.25-0.55). The ordering of the molecular bonding orbitals changes as the spin is increased from quintet to septet state. The quite low bond dissociation energy of the ground state is due to the splitting of the molecular bonding orbitals in two groups differing in energy by ~3 eV. Finally, the bond breaking of Mo2, as the multiplicity of spin is increased, is analyzed in parallel with the Mo-Mo bond breaking in a series of Mo2Clx complexes when x is increased. Physical insight into the nature of the sextuple bond and its low dissociation energy is provided.
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Affiliation(s)
| | | | - Demeter Tzeli
- Department of Chemistry, National and Kapodistrian University of Athens Department of Chemistry, Greece
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5
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Zhao L, Pan S, Frenking G. The Nature of the Polar Covalent Bond . J Chem Phys 2022; 157:034105. [DOI: 10.1063/5.0097304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quantum chemical calculations using density functional theory are reported for the diatomic molecules LiF, BeO, and BN. The nature of the interatomic interactions is analyzed with the EDA-NOCV method, and the results are critically discussed and compared with data from QTAIM, NBO and Mayer approaches. Polar bonds, like nonpolar bonds, are caused by the interference of wave functions, which lead to an accumulation of electronic charge in the bonding region. Polar bonds generally have a larger percentage of electrostatic bonding to the total attraction, but nonpolar bonds may also possess large contributions from Coulombic interaction. The term "ionic contribution" refers to VB structures and is misleading because it refers to separate fragments with negligible overlap that occur only in the solid state and in solution, not in a molecule. The EDA-NOCV method gives detailed information about the individual orbital contributions, which can nicely be identified by visual inspection of the associated deformation densities. It is very important, particularly for polar bonds to distinguish between the interatomic interactions of the final dissociation products after bond rupture and the interactions between the fragments in the eventually formed bond.
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Affiliation(s)
- Lili Zhao
- Nanjing Tech University College of Chemistry and Molecular Engineering, China
| | | | - Gernot Frenking
- Fachbereich Chemie, Philipps-Universität Marburg Fachbereich 15, Germany
- Nanjing Tech University College of Chemistry and Molecular Engineering
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6
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Martín Pendás Á, Francisco E. The role of references and the elusive nature of the chemical bond. Nat Commun 2022; 13:3327. [PMID: 35680893 PMCID: PMC9184482 DOI: 10.1038/s41467-022-31036-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chemical bonding theory is of utmost importance to chemistry, and a standard paradigm in which quantum mechanical interference drives the kinetic energy lowering of two approaching fragments has emerged. Here we report that both internal and external reference biases remain in this model, leaving plenty of unexplored territory. We show how the former biases affect the notion of wavefunction interference, which is purportedly recognized as the most basic bonding mechanism. The latter influence how bonding models are chosen. We demonstrate that the use of real space analyses are as reference-less as possible, advocating for their use. Delocalisation emerges as the reference-less equivalent to interference and the ultimate root of bonding. Atoms (or fragments) in molecules should be understood as a statistical mixture of components differing in electron number, spin, etc. The theory of chemical bonding relies on arbitrary references. Here the authors report a fundamental study on the chemical bond showing that considering the binding fragments as objects in real space enables to eliminate inherent biases.
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Affiliation(s)
- Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006, Oviedo, Spain.
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006, Oviedo, Spain
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7
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Abstract
According to Ruedenberg's classic treatise on the theory of chemical bonding [K. Ruedenberg, Rev. Mod. Phys. 34, 326-376 (1962)], orbital contraction is an integral consequence of covalent bonding. While the concept is clear, its quantification by quantum chemical calculations is not straightforward, except for the simplest of molecules, such as H2 + and H2. This paper proposes a new, yet simple, approach to the problem, utilizing the modified atomic orbital (MAO) method of Ehrhardt and Ahlrichs [Theor. Chim. Acta 68, 231 (1985)]. Through the use of MAOs, which are an atom-centered minimal basis formed from the molecular and atomic density operators, the wave functions of the species of interest are re-expanded, allowing the computation of the kinetic energy (and any other expectation value) of free and bonded fragments. Thus, it is possible to quantify the intra- and interfragment changes in kinetic energy, i.e., the effects of contraction. Computations are reported for a number of diatomic molecules H2, Li2, B2, C2, N2, O2, F2, CO, P2, and Cl2 and the polyatomics CH3-CH3, CH3-SiH3, CH3-OH, and C2H5-C2H5 (where the single bonds between the heavy atoms are studied) as well as dimers of He, Ne, Ar, and the archetypal ionic molecule NaCl. In all cases, it is found that the formation of a covalent bond is accompanied by an increase in the intra-fragment kinetic energy, an indication of orbital contraction and/or deformation.
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Affiliation(s)
- George B Bacskay
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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8
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Chen K, Li WL, Schwarz WHE. d- and s-orbital populations in the d block: unbound atoms in physical vacuum versus chemical elements in condensed matter. A Dronskowski-population analysis. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2021. [DOI: 10.1515/znb-2021-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The electron configurations of Ca, Zn and the nine transition elements M in between (and their heavier homologs) are reviewed on the basis of density functional theory and experimental facts. The d-s orbital energy and population patterns are systematically diverse. (i) The dominant valence electron configuration of most free neutral atoms M0 of groups g = 2–12 is 3d
g−2
4s
2
(textbook rule), or 3d
g−14s
1. (ii) Formal M
q+
cations in chemical compounds have the dominant configuration 3d
g−q
4s
0
(basic concept of transition metal chemistry). (iii) M0 atoms in metallic phases [M∞] of hcp, ccp(fcc) and bcc structures have intermediate populations near 3d
g−1
4s
1
(lower d populations for Ca (ca. ½) and Zn (ca. 10)). Including the 4p valence orbitals, the dominant metallic configuration is 3d
g−δ
4(sp)
δ
with δ ≈ 1.4 (±0.2) throughout (except for Zn). (iv) The 3d,4s population of atomic clusters M
m
varies for increasing m smoothly from single-atomic 3d
g−24s
2 toward metallic 3d
g−14s
1. – The textbook rule for the one-electron energies, i.e., ns < (n−1)d, holds ‘in a broader sense’ for the s block, but in general not for the d block, and never for the p block. It is more important to teach realistic atomic orbital (AO) populations such as the ones given above.
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Affiliation(s)
- Kaixuan Chen
- Chair of Solid-State and Quantum Chemistry , Institute of Inorganic Chemistry, RWTH Aachen University , 52056 Aachen , Germany
| | - Wan-Lu Li
- Department of Chemistry and Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education , Tsinghua University , Beijing 100084 , P. R. China
| | - W. H. Eugen Schwarz
- Tsinghua University, Theoretical Chemistry Center , Beijing 100084 , P. R. China
- University at Siegen, Physical and Theoretical Chemistry Group , 57068 Siegen , Germany
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9
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Fernández I, Holzmann N, Frenking G. The Valence Orbitals of the Alkaline-Earth Atoms. Chemistry 2020; 26:14194-14210. [PMID: 32666598 PMCID: PMC7702052 DOI: 10.1002/chem.202002986] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Indexed: 11/24/2022]
Abstract
Quantum chemical calculations of the alkaline-earth oxides, imides and dihydrides of the alkaline-earth atoms (Ae=Be, Mg, Ca, Sr, Ba) and the calcium cluster Ca6 H9 [N(SiMe3 )2 ]3 (pmdta)3 (pmdta=N,N,N',N'',N''-pentamethyldiethylenetriamine) have been carried out by using density functional theory. Analysis of the electronic structures by charge and energy partitioning methods suggests that the valence orbitals of the lighter atoms Be and Mg are the (n)s and (n)p orbitals. In contrast, the valence orbitals of the heavier atoms Ca, Sr and Ba comprise the (n)s and (n-1)d orbitals. The alkaline-earth metals Be and Mg build covalent bonds like typical main-group elements, whereas Ca, Sr and Ba covalently bind like transition metals. The results not only shed new light on the covalent bonds of the heavier alkaline-earth metals, but are also very important for understanding and designing experimental studies.
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Affiliation(s)
- Israel Fernández
- Departamento de Química Orgánica ICentro de Innovación en, Química Avanzada (ORFEO-CINQA)Facultad de Ciencias QuímicasUniversidad Complutense de Madrid28040MadridSpain
| | - Nicole Holzmann
- Research Center for Computer-Aided Drug DiscoveryShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Gernot Frenking
- Fachbereich ChemiePhilipps-Universität MarburgHans-Meerwein-Strasse 435032MarburgGermany
- Institute of Advanced SynthesisSchool of Chemistry and Molecular EngineeringJiangsu National Synergetic Innovation Center for, Advanced MaterialsNanjing Tech UniversityNanjing211816China
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10
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Clarifying the quantum mechanical origin of the covalent chemical bond. Nat Commun 2020; 11:4893. [PMID: 32994392 PMCID: PMC7524788 DOI: 10.1038/s41467-020-18670-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/28/2020] [Indexed: 11/08/2022] Open
Abstract
Lowering of the electron kinetic energy (KE) upon initial encounter of radical fragments has long been cited as the primary origin of the covalent chemical bond based on Ruedenberg's pioneering analysis of H[Formula: see text] and H2 and presumed generalization to other bonds. This work reports KE changes during the initial encounter corresponding to bond formation for a range of different bonds; the results demand a re-evaluation of the role of the KE. Bonds between heavier elements, such as H3C-CH3, F-F, H3C-OH, H3C-SiH3, and F-SiF3 behave in the opposite way to H[Formula: see text] and H2, with KE often increasing on bringing radical fragments together (though the total energy change is substantially stabilizing). The origin of this difference is Pauli repulsion between the electrons forming the bond and core electrons. These results highlight the fundamental role of constructive quantum interference (or resonance) as the origin of chemical bonding. Differences between the interfering states distinguish one type of bond from another.
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11
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FT-IR and FT-Raman investigation, quantum chemical studies, molecular docking study and antimicrobial activity studies on novel bioactive drug of 1-(2,4-Dichlorobenzyl)-3-[2-(3-(4-chlorophenyl)-5-(4-(propan-2-yl)phenyl-4,5-dihydro-1H-pyrazol-1-yl]-4-oxo-4,5-dihydro-1,3-thiazol-5(4H)-ylidence]-2,3-dihydro-1H-indol-2-one. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128244] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Kruse H, Mrazikova K, D'Ascenzo L, Sponer J, Auffinger P. Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- National Centre for Biomolecular ResearchFaculty of ScienceMasaryk University Kamenice 5 62500 Brno Czech Republic
| | - Luigi D'Ascenzo
- Department of Integrative Structural and Computational BiologyThe Scripps Research Institute La Jolla CA 92037 USA
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and MaterialsFaculty of SciencePalacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pascal Auffinger
- Université de StrasbourgCNRS, Architecture et Réactivité de l'ARN, UPR9002 F-67000 Strasbourg France
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13
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Kruse H, Mrazikova K, D'Ascenzo L, Sponer J, Auffinger P. Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii. Angew Chem Int Ed Engl 2020; 59:16553-16560. [DOI: 10.1002/anie.202004201] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Luigi D'Ascenzo
- Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA 92037 USA
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pascal Auffinger
- Université de Strasbourg CNRS, Architecture et Réactivité de l'ARN, UPR9002 F-67000 Strasbourg France
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14
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Nordholm S, Bacskay GB. The Basics of Covalent Bonding in Terms of Energy and Dynamics. Molecules 2020; 25:E2667. [PMID: 32521828 PMCID: PMC7321125 DOI: 10.3390/molecules25112667] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/21/2022] Open
Abstract
We address the paradoxical fact that the concept of a covalent bond, a cornerstone of chemistry which is well resolved computationally by the methods of quantum chemistry, is still the subject of debate, disagreement, and ignorance with respect to its physical origin. Our aim here is to unify two seemingly different explanations: one in terms of energy, the other dynamics. We summarize the mechanistic bonding models and the debate over the last 100 years, with specific applications to the simplest molecules: H2+ and H2. In particular, we focus on the bonding analysis of Hellmann (1933) that was brought into modern form by Ruedenberg (from 1962 on). We and many others have helped verify the validity of the Hellmann-Ruedenberg proposal that a decrease in kinetic energy associated with interatomic delocalization of electron motion is the key to covalent bonding but contrary views, confusion or lack of understanding still abound. In order to resolve this impasse we show that quantum mechanics affords us a complementary dynamical perspective on the bonding mechanism, which agrees with that of Hellmann and Ruedenberg, while providing a direct and unifying view of atomic reactivity, molecule formation and the basic role of the kinetic energy, as well as the important but secondary role of electrostatics, in covalent bonding.
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Affiliation(s)
- Sture Nordholm
- Department of Chemistry and Molecular Biology, The University of Gothenburg, SE-412 96 Göteborg, Sweden
| | - George B. Bacskay
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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15
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Abraham CS, Muthu S, Prasana JC, Armaković S, Armaković SJ, Rizwana B F, Geoffrey B, David R HA. Computational evaluation of the reactivity and pharmaceutical potential of an organic amine: A DFT, molecular dynamics simulations and molecular docking approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 222:117188. [PMID: 31176999 PMCID: PMC7108230 DOI: 10.1016/j.saa.2019.117188] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 05/08/2023]
Abstract
2-[N-(carboxymethyl)anilino] acetic acid (PIDAA) molecule has been spectroscopically characterized and computationally investigated for its fundamental reactive properties by a combination of density functional theory (DFT) calculations, molecular dynamics (MD) simulations and molecular docking procedure. A comparison drawn between the simulated and experimentally attained spectra by FT-Raman and FT-IR showed concurrence. The natural bond orbital (NBO) analysis enabled in comprehending the stability and charge delocalization in the title molecule. The first hyperpolarizability which is an important parameter for future studies of nonlinear optics (NLO) was calculated to check the potential of the molecule to be an NLO material. Besides, frontier molecular orbitals (FMO), electron localization function (ELF) and localized orbital locator (LOL) analysis were performed. Energy gap (ΔE), electronegativity (χ), chemical potential (μ), global hardness (η), softness (S), Mulliken population analysis on atomic charges and thermodynamic properties of the title compound at different temperatures have been calculated. The local reactive properties of PIDAA have been addressed by MEP and ALIE surfaces, together with bond dissociation energy for hydrogen abstraction (H-BDE). MD simulations have been used in order to identify atoms with pronounced interactions with water molecules. The pharmaceutical potential of PIDAA has been considered by the analysis of drug likeness parameters and molecular docking procedure. The biological activity of the molecule in terms of molecular docking has been analyzed theoretically for the treatment of SARS and minimum binding energy calculated. The Ramachandran plot was used to check the stereochemistry of the protein structure. In addition, a comparison of the physiochemical parameters of PIDAA and commercially available drugs (Yu et al., 2004; Tan et al., 2004; Elshabrawy et al., 2014; Chu et al., 2004; Gopal Samy and Xavier, 2015) were carried out.
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Affiliation(s)
| | - S Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar 604407, Tamil Nadu, India.
| | | | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia
| | - Sanja J Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia
| | - Fathima Rizwana B
- Department of Physics, Madras Christian College, East Tambaram 600059, Tamil Nadu, India
| | - Ben Geoffrey
- Department of Physics, Madras Christian College, East Tambaram 600059, Tamil Nadu, India
| | - Host Antony David R
- Bioinformatics center of BITSnet, Madras Christian College, East Tambaram 600059, Tamil Nadu, India
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16
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Affiliation(s)
- Rebecca K. Carlson
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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17
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Zhao L, Pan S, Holzmann N, Schwerdtfeger P, Frenking G. Chemical Bonding and Bonding Models of Main-Group Compounds. Chem Rev 2019; 119:8781-8845. [DOI: 10.1021/acs.chemrev.8b00722] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lili Zhao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Sudip Pan
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Nicole Holzmann
- Scientific Computing Department, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Peter Schwerdtfeger
- The New Zealand Institute for Advanced Study, Massey University (Albany), 0632 Auckland, New Zealand
| | - Gernot Frenking
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
- Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
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Guttmann R, Hoja J, Lechner C, Maurer RJ, Sax AF. Adhesion, forces and the stability of interfaces. Beilstein J Org Chem 2019; 15:106-129. [PMID: 30680045 PMCID: PMC6334800 DOI: 10.3762/bjoc.15.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/12/2018] [Indexed: 11/23/2022] Open
Abstract
Weak molecular interactions (WMI) are responsible for processes such as physisorption; they are essential for the structure and stability of interfaces, and for bulk properties of liquids and molecular crystals. The dispersion interaction is one of the four basic interactions types – electrostatics, induction, dispersion and exchange repulsion – of which all WMIs are composed. The fact that each class of basic interactions covers a wide range explains the large variety of WMIs. To some of them, special names are assigned, such as hydrogen bonding or hydrophobic interactions. In chemistry, these WMIs are frequently used as if they were basic interaction types. For a long time, dispersion was largely ignored in chemistry, attractive intermolecular interactions were nearly exclusively attributed to electrostatic interactions. We discuss the importance of dispersion interactions for the stabilization in systems that are traditionally explained in terms of the “special interactions” mentioned above. System stabilization can be explained by using interaction energies, or by attractive forces between the interacting subsystems; in the case of stabilizing WMIs, one frequently speaks of adhesion energies and adhesive forces. We show that the description of system stability using maximum adhesive forces and the description using adhesion energies are not equivalent. The systems discussed are polyaromatic molecules adsorbed to graphene and carbon nanotubes; dimers of alcohols and amines; cellulose crystals; and alcohols adsorbed onto cellulose surfaces.
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Affiliation(s)
- Robin Guttmann
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Johannes Hoja
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria.,Present address: Physics and Materials Science Research Unit, University of Luxembourg, 1511 Luxembourg, Luxembourg
| | - Christoph Lechner
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Reinhard J Maurer
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Alexander F Sax
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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19
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Zhao L, Schwarz WHE, Frenking G. The Lewis electron-pair bonding model: the physical background, one century later. Nat Rev Chem 2019. [DOI: 10.1038/s41570-018-0052-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Abstract
A long-held view of the origin of covalent binding is based on the notion that electrostatic forces determine the stability of a system of charged particles and that, therefore, potential energy changes drive the stabilization of molecules. A key argument advanced for this conjecture is the rigorous validity of the virial theorem. Rigorous in-depth analyses have however shown that the energy lowering of covalent bonding is due to the wave mechanical drive of electrons to lower their kinetic energy through expansion. Since the virial theorem applies only to systems with Coulombic interaction potentials, its relevance as a foundation of the electrostatic view is tested here by calculations on analogues of the molecules H2+ and H2, where all 1/ r interaction potentials are replaced by Gaussian-type potentials that yield one-electron "atoms" with realistic stability ranges. The virial theorem does not hold in these systems, but covalent bonds are found to form nonetheless, and the wave mechanical bonding analysis yields analogous results as in the case of the Coulombic potentials. Notably, the key driving feature is again the electron delocalization that lowers the interatomic kinetic energy component. A detailed discussion of the role of the virial theorem in the context of covalent binding is given.
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Affiliation(s)
- George B Bacskay
- School of Chemistry , The University of Sydney , Sydney NSW 2006 , Australia
| | - Sture Nordholm
- Department of Chemistry and Molecular Biology , The University of Gothenburg , SE-412 96 Göteborg , Sweden
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory USDOE , Iowa State University , Ames , Iowa 50011 , United States
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21
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Frenking G. Covalent Bonding and Charge Shift Bonds: Comment on "The Carbon-Nitrogen Bonds in Ammonium Compounds Are Charge Shift Bonds". Chemistry 2017; 23:18320-18324. [PMID: 29240256 DOI: 10.1002/chem.201704244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Indexed: 11/10/2022]
Abstract
The paper by Gershoni-Poranne and Chen (R. Gershoni-Poranne, P. Chen, Chem. Eur. J. 2017, 23, 4659) gives an incorrect definition of covalent bonding. Furthermore, the assignment of so-called charge shift bonds in ammonium compounds has no physical foundation and is conceptually redundant.
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Affiliation(s)
- Gernot Frenking
- Institute of Advanced Synthesis, Nanjing Tech University, Nanjing, 211816, China.,Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Spain.,Fachbereich Chemie, Philipps-Universität Marburg, 35032, Marburg, Germany
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22
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Abstract
This work addresses the continuing disagreement between two schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, covalent bonding is a quantum mechanical phenomenon whereby lowering of the kinetic energy associated with electron sharing, i.e., delocalization, is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Following our study of H2+ we present an analogous detailed study of H2 where bonding involves an electron pair with repulsion and correlation playing a significant role in its properties. We use a range of different computational approaches to study and reveal the relevant contributions to bonding as seen in the electron density and corresponding kinetic and potential energy distributions. The energetics associated with the more complex electronic structure of H2, when examined in detail, clearly agrees with the analysis of Ruedenberg; i.e., covalent bonding is due to a decrease in the interatomic kinetic energy resulting from electronic delocalization. Our results support the view that covalent bonding is a quantum dynamical phenomenon requiring a properly quantized kinetic energy to be used in its description.
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Affiliation(s)
- George B Bacskay
- School of Chemistry, The University of Sydney , Sydney, NSW 2006, Australia
| | - Sture Nordholm
- Department of Chemistry and Molecular Biology, The University of Gothenburg , SE-412 96 Göteborg, Sweden
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23
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Zhao L, von Hopffgarten M, Andrada DM, Frenking G. Energy decomposition analysis. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1345] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lili Zhao
- Institute of Advanced Synthesis, School of Chemistry and Molecular EngineeringJiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University Nanjing China
| | | | | | - Gernot Frenking
- Institute of Advanced Synthesis, School of Chemistry and Molecular EngineeringJiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University Nanjing China
- Fachbereich ChemiePhilipps‐Universität Marburg Marburg Germany
- Donostia International Physics Center (DIPC) Donostia Spain
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24
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Sax AF. OVB analysis of symmetry allowed and symmetry forbidden chemical reactions. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Morgenstern A, Wilson TR, Eberhart ME. Predicting Chemical Reactivity from the Charge Density through Gradient Bundle Analysis: Moving beyond Fukui Functions. J Phys Chem A 2017; 121:4341-4351. [DOI: 10.1021/acs.jpca.7b00630] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda Morgenstern
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Timothy R. Wilson
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - M. E. Eberhart
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
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26
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Levine DS, Head-Gordon M. Quantifying the Role of Orbital Contraction in Chemical Bonding. J Phys Chem Lett 2017; 8:1967-1972. [PMID: 28414227 DOI: 10.1021/acs.jpclett.7b00766] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This work reports an approach to variationally quantify orbital contraction in chemical bonds by an extension of an energy decomposition analysis (EDA). The orbital contraction energy is defined as the energy lowering due to optimization of the isolated fragments (that combine to form the bond) with a specially constructed virtual set of contraction/expansion functions. This set contains one function per occupied orbital, obtained as the linear response to scaling the nuclear charges. EDA results for a variety of single bonds show substantial changes in the importance of orbital contraction; it plays a critical role for bonds to H but only a very minor role in the bonds between heavier elements. Additionally, energetic stabilization due to rehybridization is separated from inductive polarization by the fact that no mixing with virtual orbitals is involved and is shown to be significant in fragments such as NH2, OH, and F.
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Affiliation(s)
- Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California , Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California , Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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27
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28
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Fantuzzi F, Nascimento MAC. Description of Polar Chemical Bonds from the Quantum Mechanical Interference Perspective. J Chem Theory Comput 2015; 10:2322-32. [PMID: 26580752 DOI: 10.1021/ct500334f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Generalized Product Function Energy Partitioning (GPF-EP) method has been applied to a set of molecules, AH (A = Li, Be, B, C, N, O, F), CO and LiF with quite different dipole moments, in order to investigate the role played by the quantum interference effect in the formation of polar chemical bonds. The calculations were carried out with GPF wave functions treating all the core electrons as a single Hartree-Fock group and the bonding electrons at the Generalized Valence Bond Perfect-Pairing (GVB-PP) level, with the cc-pVTZ basis set. The results of the energy partitioning into interference and quasi-classical contributions along the respective Potential Energy Surfaces (PES) show that the main contribution to the depth of the potential wells comes from the interference term, which is an indication that all the molecules mentioned above form typical covalent bonds. In all cases, the stabilization promoted by the interference term comes from the kinetic contribution, in agreement with previous results. The analysis of the effect of quantum interference on the electron density reveals that while polarization effects (quasi-classical) tend to displace electronic density from the most polarizable atom toward the less polarizable one, interference (quantum effects) counteracts by displacing electronic density to the bond region, giving rise to the right electronic density and dipole moment.
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Affiliation(s)
- Felipe Fantuzzi
- Instituto de Química, Universidade Federal do Rio de Janeiro , Rio de Janeiro, RJ 21941-909, Brazil
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29
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Chemical bonding: the orthogonal valence-bond view. Int J Mol Sci 2015; 16:8896-933. [PMID: 25906476 PMCID: PMC4425115 DOI: 10.3390/ijms16048896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/17/2015] [Accepted: 03/31/2015] [Indexed: 01/05/2023] Open
Abstract
Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can be calculated, but the local information is hidden by the delocalized molecular orbitals (MO) used to construct the wave functions. The transformation of such wave functions into valence bond (VB) wave functions, which are based on localized orbitals, reveals the hidden information; this transformation is called a VB reading of MCSCF wave functions. The two-electron VB wave functions describing the Lewis electron pair that connects two atoms are frequently called covalent or neutral, suggesting that these wave functions describe an electronic situation where two electrons are never located at the same atom; such electronic situations and the wave functions describing them are called ionic. When the distance between two atoms decreases, however, every covalent VB wave function composed of non-orthogonal atomic orbitals changes its character from neutral to ionic. However, this change in the character of conventional VB wave functions is hidden by its mathematical form. Orthogonal VB wave functions composed of orthonormalized orbitals never change their character. When localized fragment orbitals are used instead of atomic orbitals, one can decide which local information is revealed and which remains hidden. In this paper, we analyze four chemical reactions by transforming the MCSCF wave functions into orthogonal VB wave functions; we show how the reactions are influenced by changing the atoms involved or by changing their local symmetry. Using orthogonal instead of non-orthogonal orbitals is not just a technical issue; it also changes the interpretation, revealing the properties of wave functions that remain otherwise undetected.
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31
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Schmidt MW, Ivanic J, Ruedenberg K. Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion. J Chem Phys 2014; 140:204104. [PMID: 24880263 PMCID: PMC4032414 DOI: 10.1063/1.4875735] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/29/2014] [Indexed: 12/16/2022] Open
Abstract
An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.
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Affiliation(s)
- Michael W Schmidt
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, USA
| | - Joseph Ivanic
- Advanced Biomedical Computing Center, Information Systems Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, USA
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32
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Jacobsen H. More on diphosphadithiatetrazocines and the importance of being bonded. Inorg Chem 2013; 52:11843-9. [PMID: 24083895 DOI: 10.1021/ic401383k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cross-ring sulfur-sulfur bond for seven R'RP(NSN)2PRR' molecules 1a (R = R' = Me), 1b (R = R' = Ph), 1c (R = R' = Et), 1d (R = Cl, R' = CCl3), 1e (R = R'= Cl), 1f (R = R' = F), and 1g (R = R' = H) has been scrutinized by a topology analysis for a bond descriptor based on the kinetic energy density, supported by a fragment-based bond energy analysis. Contrary to a regular disulfide bond, the cross-ring connection is only a secondary electron-sharing bond, about half as strong as a common S-S linkage. The regular disulfide bond itself is best described as a charge-shift bond. These analyses are based on results obtained from B3PW91/def2-TZVP density functional calculations.
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Affiliation(s)
- Heiko Jacobsen
- KemKom , 1215 Ursulines Avenue, New Orleans, Louisiana, 70116, United States
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33
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Schwarz WHE. 100th anniversary of Bohr's model of the atom. Angew Chem Int Ed Engl 2013; 52:12228-38. [PMID: 24123759 DOI: 10.1002/anie.201306024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Indexed: 11/11/2022]
Abstract
In the fall of 1913 Niels Bohr formulated his atomic models at the age of 27. This Essay traces Bohr's fundamental reasoning regarding atomic structure and spectra, the periodic table of the elements, and chemical bonding. His enduring insights and superseded suppositions are also discussed.
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Affiliation(s)
- W H Eugen Schwarz
- Department of Chemistry, University of Siegen, 57068 Siegen (Germany); Tsinghua University Beijing, Beijing 100084 (China).
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34
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35
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Jacobsen H. Bond descriptors based on kinetic energy densities reveal regions of slow electrons – Another look at aromaticity. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Bacskay GB, Nordholm S. Covalent Bonding: The Fundamental Role of the Kinetic Energy. J Phys Chem A 2013; 117:7946-58. [DOI: 10.1021/jp403284g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- George B Bacskay
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Sture Nordholm
- Department of Chemistry, The University of Gothenburg, SE-412 96 Göteborg,
Sweden
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37
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Vieira FS, Fantuzzi F, Cardozo TM, Nascimento MAC. Interference energy in C-H and C-C bonds of saturated hydrocarbons: dependence on the type of chain and relationship to bond dissociation energy. J Phys Chem A 2013; 117:4025-34. [PMID: 23574507 DOI: 10.1021/jp4005746] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interference energy for C-H and C-C bonds of a set of saturated hydrocarbons is calculated by the generalized product function energy partitioning (GPF-EP) method in order to investigate its sensitivity to the type of chain and also its contribution to the bond dissociation energy. All GPF groups corresponding to chemical bonds are calculated by use of GVB-PP wave functions to ensure the correct description of bond dissociation. The results show that the interference energies are practically the same for all the C-H bonds, presenting only small variations (0.5 kcal.mol(-1)) due to the structural changes in going from linear to branched and cyclic chains. A similar trend is verified for the C-C bonds, the sole exception being the cyclopropane molecule, for which only the C-C bond exhibits a more significant variation. On the other hand, although the interference energy is quantitatively the most important contribution to the bond dissociation energy (DE), one cannot predict DE only from the bond interference energy. Differences in the dissociation energies of C-C and C-H bonds due to structural changes in the saturated hydrocarbons can be mainly attributed to quasi-classical effects.
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Affiliation(s)
- Francisco Senna Vieira
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-590, Bazil
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38
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Jacobsen H. Topology maps of bond descriptors based on the kinetic energy density and the essence of chemical bonding. Phys Chem Chem Phys 2013; 15:5057-66. [DOI: 10.1039/c3cp44162h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Huang B, Zhuang L, Xiao L, Lu J. Bond-energy decoupling: principle and application to heterogeneous catalysis. Chem Sci 2013. [DOI: 10.1039/c2sc21232c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Schwarz WHE, Schmidbaur H. Observations and Descriptions versus Explanations-An Example: Does Nature, Does Theory Know About Steric Hindrance? Chemistry 2012; 18:4470-9. [DOI: 10.1002/chem.201102687] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 12/18/2011] [Indexed: 11/08/2022]
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41
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Nafziger J, Wu Q, Wasserman A. Molecular binding energies from partition density functional theory. J Chem Phys 2011; 135:234101. [DOI: 10.1063/1.3667198] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Affiliation(s)
- Yong-Hui Tian
- Department of Chemistry, Georgetown University, 37th & O Streets NW, Washington, D.C. 20057-1227, United States
| | - Miklos Kertesz
- Department of Chemistry, Georgetown University, 37th & O Streets NW, Washington, D.C. 20057-1227, United States
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43
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Gruden-Pavlović M, García-Fernández P, Andjelković L, Daul C, Zlatar M. Treatment of the Multimode Jahn–Teller Problem in Small Aromatic Radicals. J Phys Chem A 2011; 115:10801-13. [DOI: 10.1021/jp206083j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Pablo García-Fernández
- Ciencias de la Tierra y Física de la Materia Condensada, Universidad de Cantabria, Santander, Spain
| | | | - Claude Daul
- Department of Chemistry, University of Fribourg, Fribourg, Switzerland
| | - Matija Zlatar
- Center for Chemistry, IHTM, University of Belgrade, Belgrade, Serbia
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44
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Zeng T, Fedorov DG, Schmidt MW, Klobukowski M. Effects of Spin–Orbit Coupling on Covalent Bonding and the Jahn–Teller Effect Are Revealed with the Natural Language of Spinors. J Chem Theory Comput 2011; 7:2864-75. [DOI: 10.1021/ct200457q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tao Zeng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Michael W. Schmidt
- Department of Chemistry and Ames Laboratory USDOE, Iowa State University, Ames, Iowa 50011, United States
| | - Mariusz Klobukowski
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
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45
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Ruedenberg K, Schmidt MW. Physical understanding through variational reasoning: electron sharing and covalent bonding. J Phys Chem A 2010; 113:1954-68. [PMID: 19228050 DOI: 10.1021/jp807973x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Energy changes of stationary states resulting from geometric parameter changes in the Hamiltonian can be understood by variational reasoning in terms of the physical attributes of the kinetic and the potential energy functionals. In atoms as well as molecules, the energy minimization determines the ground state as the optimal compromise between the potential pull of the nuclear attractions and the localization-resisting kinetic pressure of the electron cloud. This variational competition is analyzed for the exact ab initio ground-state wave function of the hydrogen molecule ion to elucidate the formation of the bond. Its electronic wave function is shown to differ from the ground-state wave function of the hydrogen atom by polarization, sharing, and contraction, and the corresponding contributions to the binding energy are examined in detail. All told, the critical feature is that a molecular orbital, contracting (in the variational context) toward two nuclei simultaneously, can lower its potential energy while maintaining a certain degree of delocalization. As a consequence, its kinetic energy functional has a lower value than that of an orbital contracting toward a single nucleus equally closely. By contrast, the potential energy functional is lowered equally effectively whether the orbital contracts toward one nucleus or simultaneously toward two nuclei. Because of this weaker kinetic energy pressure, the electrostatic potential pull of the nuclei in the molecule is able to attach the orbital more tightly to each of the nuclei than the pull of the single nucleus in the atom is able to do. The role of the virial theorem is clarified. Generalizations to other molecules are discussed.
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Affiliation(s)
- Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, United States Department of Energy, Iowa State University, Ames, Iowa 50011, USA
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46
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Wang SG, Qiu YX, Schwarz W. Antibond Breaking-The Formation and Decomposition of He@Adamantane: Descriptions, Explanations, and Meaning of Concepts. Chemistry 2010; 16:9107-16. [DOI: 10.1002/chem.201000789] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Toward a physical understanding of electron-sharing two-center bonds. II. Pseudo-potential based analysis of diatomic molecules. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0758-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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48
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An Introduction to Relativistic Quantum Chemistry. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9975-5_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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49
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Jacobsen H. Kinetic energy density and covalent bonding – a complementary analysis at the border of bond and no bond. Dalton Trans 2010; 39:5426-8. [DOI: 10.1039/c0dt00083c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Shaik S, Chen Z, Wu W, Stanger A, Danovich D, Hiberty PC. An Excursion from Normal to Inverted CC Bonds Shows a Clear Demarcation between Covalent and Charge-Shift CC Bonds. Chemphyschem 2009; 10:2658-69. [DOI: 10.1002/cphc.200900633] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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