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Cukrowski I, Zaaiman S, Hussain S, de Lange JH. All-body concept and quantified limits of cooperativity and related effects in homodromic cyclic water clusters from a molecular-wide and electron density-based approach. J Comput Chem 2024. [PMID: 39189688 DOI: 10.1002/jcc.27489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/03/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024]
Abstract
We strongly advocate distinguishing cooperativity from cooperativity-induced effects. From the MOWeD-based approach, the origin of all-body cooperativity is synonymous with physics- and quantum-based processes of electron (e) delocalization throughout water clusters. To this effect, over 10 atom-pairs contribute to the total e-density at a BCP(H,O) between water molecules in a tetramer. Intermolecular all-body e-delocalization, that is, cooperativity, is an energy-minimizing process that fully explains non-additive increase in stability of a water molecule in clusters with an increase in their size. A non-linear change in cooperativity and cooperativity-induced effects, such as (i) structural (e.g., a change in d(O,O)) or topological intra- and intermolecular properties in water clusters (e.g., electron density or potential energy density at bond critical points) is theoretically reproduced by the proposed expression. It predicted the limiting value of delocalized electrons by a H2O molecule in homodromic cyclic clusters to be 1.58e. O-atoms provide the vast majority of electrons that "travel throughout a cluster predominantly on a privileged exchange quantum density highway" (⋅⋅⋅O-H⋅⋅⋅O-H⋅⋅⋅O-H⋅⋅⋅) using Bader's classical bond paths as density bridges linking water molecules. There are, however, additional electron exchange channels that are not seen on molecular graphs as bond paths. A 3D visual representation of the "privileged" and "additional" exchange channels as well as detailed intra- and inter-molecular patterns of e-sharing and (de)localizing is presented. The energy stabilizing contribution made by three O-atoms of neighboring water molecules was found to be large (-597 kcal/mol in cyclic hexamer) and 5 times more significant than that of a classical O-H⋅⋅⋅O intermolecular H-bond.
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Affiliation(s)
- Ignacy Cukrowski
- Faculty of Natural and Agricultural Sciences, Department of Chemistry, University of Pretoria, Hatfield, South Africa
| | - Stéfan Zaaiman
- Faculty of Natural and Agricultural Sciences, Department of Chemistry, University of Pretoria, Hatfield, South Africa
| | - Shahnawaz Hussain
- Faculty of Natural and Agricultural Sciences, Department of Chemistry, University of Pretoria, Hatfield, South Africa
- Department of Computer Science and Engineering, Indian Institute of Technology, Kharagpur, India
| | - Jurgens H de Lange
- Faculty of Natural and Agricultural Sciences, Department of Chemistry, University of Pretoria, Hatfield, South Africa
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Seuret-Hernández HY, Morera-Boado C. DFT Study of the Adsorption and SERS of Pyridine on M 10N 10 (M, N = Cu, Ag) Tetrahedral Clusters. J Phys Chem A 2023; 127:6697-6710. [PMID: 37535928 DOI: 10.1021/acs.jpca.3c02368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
This work presents a theoretical detailed analysis of the surface-enhanced Raman spectroscopy (SERS) of the pyridine-M10N10 (M, N = Ag, Cu) tetrahedral (Td) clusters considering two binding positions: vertex (V) and surface (S). In addition to the well-known monometallic Td structure, we added two different bimetallic Ag-Cu compositions, named Td1 and Td2 geometries. Density functional methodology with the use of BP86 and CAM-B3LYP exchange-correlation functionals (XCs) and LANL2DZ pseudopotential has been employed for analyzing the electronic structure and geometries, the chemical static (CHEM), and resonant Raman mechanisms (RR): charge transfer RR-CT and intracluster excitation RR-CR. The static CHEM mechanism shows an increase in the enhancement factors (EFs) of Py-V concerning Py-S positions, which can also be distinguished by the averaged adsorption energies and bond polarizabilities. The static SERS response for Cu-Py-V junction is from 5 to 10 times greater than Ag-Py-V EFs and up to 28 times greater than Py-S complexes. For the static Raman, we found that the analyses of ν8a and ν1 normal modes are related to the EF changes and allow us to distinguish V from S complexes. The TDDFT calculations show striking differences between BP86 and CAM-B3LYP XCs analyzed spectra, and CAM-B3LYP granted a clear distinction between V and S for the location of CT-type transitions. In addition, important differences were obtained from the analysis of the charge transfer excitations between both XCs. Resonant Raman calculations evidenced significant enhancements for RR-CT and RR-CR as compared to the static enhancements, and RR-CT can be distinguished from the RR-CR mechanism, while specific normal modes help to differentiate the vertex from the surface Py-junction. Bimetallic Ag-Cu nanostructures represent promising choices for SERS substrates, showing EFs higher than those of monometallic Ag.
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Affiliation(s)
- Halis Yenis Seuret-Hernández
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, 62209, Morelos, Mexico
| | - Cercis Morera-Boado
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, 62209, Morelos, Mexico
- Cátedra Conahcyt-Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, 62209, Morelos, Mexico
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Cukrowski I. A unified molecular‐wide and electron density based concept of chemical bonding. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences University of Pretoria Pretoria South Africa
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Tribedi S, Kitaura K, Nakajima T, Sunoj RB. On the question of steric repulsion versus noncovalent attractive interactions in chiral phosphoric acid catalyzed asymmetric reactions. Phys Chem Chem Phys 2021; 23:18936-18950. [PMID: 34612433 DOI: 10.1039/d1cp02499j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The origin of enantioselectivity in asymmetric catalysis is often built around the differential steric interaction in the enantiocontrolling transition states (TSs). A closer perusal of enantiocontrolling TSs in an increasingly diverse range of reactions has revealed that the cumulative effect of weak noncovalent interactions could even outweigh the steric effects. While enunciating this balance is conspicuously important, quantification of such intramolecular forces within a TS continues to remain scarce and challenging. Herein, we demonstrate the utility of the fragment molecular orbital method in establishing the relative contributions of various attractive and repulsive contributions in the total interaction energy between the suitably chosen fragments in enantiocontrolling TSs. Three types of reactions of high contemporary importance, namely, axially chiral phosphoric acid (CPA) catalyzed kinetic resolution of rac-α-methyl-γ-hydroxy ester (reaction I), asymmetric dearomative amination of β-naphthols by dimethyl azodicarboxylate (IIa and IIb), and intramolecular desymmetrization of β,β-disubstituted methyl oxetanes (IIIa) and hydroxyl oxetane (IIIb), bearing a tethered alcohol (-OCH2CH2OH or -(CH2)2CH2OH), are considered. In all the five reactions, the differences in the stabilizing contributions arising due to electrostatic, charge-transfer, and dispersion interactions between the catalyst and the reacting partners in the enantiocontrolling transition states are weighed against the destabilizing exchange interaction. The balancing interactions are found to be between dispersion and exchange repulsion in reaction I, a combination of charge transfer and dispersion energies offsets the repulsive energy in reaction IIb involving the electron rich anthryl groups in the catalyst, whereas the -(CF3)2C6H4 3,3'-substituent in the catalyst (reaction IIa) leads to a trade-off between dispersion and exchange energies. In reactions IIIa and IIIb, however, electrostatic and dispersion energies help compensate the repulsive interactions. These quantitative insights on the intramolecular interactions in the stereocontrolling TSs could help in the rational design of asymmetric catalysis.
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Affiliation(s)
- Soumi Tribedi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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5
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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.
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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
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de Beer S, Cukrowski I, de Lange JH. Characterization of bonding modes in metal complexes through electron density cross-sections. J Comput Chem 2020; 41:2695-2706. [PMID: 32956494 DOI: 10.1002/jcc.26423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 11/06/2022]
Abstract
Qualitative inspection of molecular orbitals (MOs) remains one of the most popular analysis tools used to describe the electronic structure and bonding properties of transition metal complexes. In symmetric coordination complexes, the use of group theory and the symmetry-adapted linear combination (SALC) of fragment orbitals allows for a very accurate and informative interpretation of MOs, but the same procedure cannot be performed for asymmetric complexes, such as Schrock and Fischer carbenes. In this work, we present a straight-forward approach for classifying and quantifying MO contributions to a particular metal-ligand interaction. Our approach utilizes the topology of MO density contributions to a cross-section of an inter-nuclear region, and is computationally inexpensive and applicable to symmetric and asymmetric complexes alike. We also apply the same approach with similar decompositions using Natural Bond Orbitals (NBO) and the recently developed Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) density decomposition scheme. In particular, FALDI analysis provides additional insights regarding the multi-centric nature of metal-carbene bonds without resorting to expensive multi-reference calculations.
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Affiliation(s)
- Shane de Beer
- 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
| | - Jurgens H de Lange
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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Abstract
AbstractTwo complementary methodologies for extracting useful insights into electronic structure and bonding from contemporary wavefunctions are compared. The first of these, known as the analysis of domain-averaged Fermi holes (DAFH), mostly provides visually appealing descriptions of the role and the extent of electron sharing in chemical bonding. The second one, known as the fragment, atom, localized, delocalized and interatomic (FALDI) charge density decomposition scheme, uses the partitioning of certain localization and delocalization indices to focus on highly visual contributions associated with individual domains and with pairs of domains, respectively. Four variants of a FALDI-like approach are investigated here in some detail, mostly to establish which of them are the most reliable and the most informative. In addition to ‘full’ calculations that use the correlated pair density, the consequences for the DAFH and FALDI-like procedures of using instead a popular one-electron approximation are explored. Additionally, the geometry dependence of the degree of acceptability of the errors that this introduces for delocalization indices is assessed for different formal bond multiplicities. The familiar molecular test systems employed for these various linked investigations are the breaking of the bonds in H2 and in N2, as well as the nature of the bonding in B2H6, as a simple example of multicenter bonding. One of the key outcomes of this study is a clear understanding of how DAFH analysis and a particular variant of FALDI-like analysis could be most profitably deployed to extract complementary insights into more complex and/or controversial bonding situations.
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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.
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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
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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.
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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
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de Lange JH, Cukrowski I. Exact and exclusive electron localization indices within QTAIM atomic basins. J Comput Chem 2018; 39:1517-1530. [DOI: 10.1002/jcc.25223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 11/06/2022]
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
| | - Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences; University of Pretoria, Lynnwood Road; Hatfield Pretoria 0002 South Africa
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de Lange JH, van Niekerk DME, Cukrowski I. FALDI-based decomposition of an atomic interaction line leads to 3D representation of the multicenter nature of interactions. J Comput Chem 2018; 39:973-985. [DOI: 10.1002/jcc.25175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/07/2017] [Accepted: 01/14/2018] [Indexed: 11/09/2022]
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
| | - 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
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Cukrowski I, van Niekerk DME, de Lange JH. Exploring fundamental differences between red- and blue-shifted intramolecular hydrogen bonds using FAMSEC, FALDI, IQA and QTAIM. Struct Chem 2017. [DOI: 10.1007/s11224-017-0956-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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