1
|
Rahali E, Noori Z, Arfaoui Y, Poater J. Chalcogen Noncovalent Interactions between Diazines and Sulfur Oxides in Supramolecular Circular Chains. Int J Mol Sci 2024; 25:7497. [PMID: 39000604 PMCID: PMC11242197 DOI: 10.3390/ijms25137497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/30/2024] [Accepted: 07/06/2024] [Indexed: 07/16/2024] Open
Abstract
The noncovalent chalcogen interaction between SO2/SO3 and diazines was studied through a dispersion-corrected DFT Kohn-Sham molecular orbital together with quantitative energy decomposition analyses. For this, supramolecular circular chains of up to 12 molecules were built with the aim of checking the capability of diazine molecules to detect SO2/SO3 compounds within the atmosphere. Trends in the interaction energies with the increasing number of molecules are mainly determined by the Pauli steric repulsion involved in these σ-hole/π-hole interactions. But more importantly, despite the assumed electrostatic nature of the involved interactions, the covalent component also plays a determinant role in its strength in the involved chalcogen bonds. Noticeably, π-hole interactions are supported by the charge transfer from diazines to SO2/SO3 molecules. Interaction energies in these supramolecular complexes are not only determined by the S···N bond lengths but attractive electrostatic and orbital interactions also determine the trends. These results should allow us to establish the fundamental characteristics of chalcogen bonding based on its strength and nature, which is of relevance for the capture of sulfur oxides.
Collapse
Affiliation(s)
- Emna Rahali
- Laboratory of Characterizations, Applications and Modeling of Materials (LR18ES08), Department of Chemistry, University of Tunis El Manar, Tunis 1068, Tunisia; (E.R.); (Y.A.)
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
| | - Zahra Noori
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
| | - Youssef Arfaoui
- Laboratory of Characterizations, Applications and Modeling of Materials (LR18ES08), Department of Chemistry, University of Tunis El Manar, Tunis 1068, Tunisia; (E.R.); (Y.A.)
| | - Jordi Poater
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
2
|
Szczygiel M, Derewenda U, Scheiner S, Minor W, Derewenda ZS. A structural role for tryptophan in proteins, and the ubiquitous Trp C δ1-H...O=C (backbone) hydrogen bond. Acta Crystallogr D Struct Biol 2024; 80:551-562. [PMID: 38941144 PMCID: PMC11220837 DOI: 10.1107/s2059798324005515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/09/2024] [Indexed: 06/29/2024] Open
Abstract
Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the Nϵ-H group, which is a potent donor in canonical hydrogen bonds, and a polarized Cδ1-H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C-H...O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C-H group. Consequently, Cα-H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the Cϵ1-H and Cδ2-H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cδ1-H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution (r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the Cδ1-H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5-3.0 kcal mol-1, depending on the specific stereochemistry.
Collapse
Affiliation(s)
- Michal Szczygiel
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
| | - Urszula Derewenda
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
| |
Collapse
|
3
|
de Azevedo Santos L, van der Voort S, Burema SR, Fonseca Guerra C, Bickelhaupt FM. Blueshift in Trifurcated Hydrogen Bonds: A Tradeoff between Tetrel Bonding and Steric Repulsion. Chemphyschem 2024; 25:e202300480. [PMID: 37864778 DOI: 10.1002/cphc.202300480] [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: 08/04/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
We have quantum chemically investigated the origin of the atypical blueshift of the H-C bond stretching frequency in the hydrogen-bonded complex X- •••H3 C-Y (X, Y=F, Cl, Br, I), as compared to the corresponding redshift occurring in Cl- •••H3 N and Cl- •••H3 C-H, using relativistic density functional theory (DFT) at ZORA-BLYP-D3(BJ)/QZ4P. Previously, this blueshift was attributed, among others, to the contraction of the H-C bonds as the H3 C moiety becomes less pyramidal. Herein, we provide quantitative evidence that, instead, the blueshift arises from a direct and strong X- •••C interaction of the HOMO of A- with the backside lobe on carbon of the low-lying C-Y antibonding σ* LUMO of the H3 C-Y fragment. This X- •••C bond, in essence a tetrel bond, pushes the H atoms towards a shorter H-C distance and makes the H3 C moiety more planar. The blueshift may, therefore, serve as a diagnostic for tetrel bonding.
Collapse
Affiliation(s)
- Lucas de Azevedo Santos
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Storm van der Voort
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Shiri R Burema
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg Auckland Park, Johannesburg, 2006, South Africa
| |
Collapse
|
4
|
Almacellas D, Fonseca Guerra C, Poater J. Strengthened cooperativity of DNA-based cyclic hydrogen-bonded rosettes by subtle functionalization. Org Biomol Chem 2023; 21:8403-8412. [PMID: 37830458 DOI: 10.1039/d3ob01391j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Cooperative effects cause extra stabilization of hydrogen-bonded supramolecular systems. In this work we have designed hydrogen-bonded rosettes derived from a guanine-cytosine Janus-type motif with the aim of finding a monomer that enhances the synergy of supramolecular systems. For this, relativistic dispersion-corrected density functional theory computations have been performed. Our proposal involves a monomer with three hydrogen-bonds pointing in the same direction, which translates into shorter bonds, stronger donor-acceptor interactions, and more attractive electrostatic interactions, thus giving rise to rosettes with strengthened cooperativity. This newly designed rosette has triple the cooperativity found for the naturally occurring guanine quadruplex.
Collapse
Affiliation(s)
- David Almacellas
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
5
|
Nieuwland C, Vermeeren P, Bickelhaupt FM, Fonseca Guerra C. Understanding chemistry with the symmetry-decomposed Voronoi deformation density charge analysis. J Comput Chem 2023; 44:2108-2119. [PMID: 37403918 DOI: 10.1002/jcc.27184] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
The symmetry-decomposed Voronoi deformation density (VDD) charge analysis is an insightful and robust computational tool to aid the understanding of chemical bonding throughout all fields of chemistry. This method quantifies the atomic charge flow associated with chemical-bond formation and enables decomposition of this charge flow into contributions of (1) orbital interaction types, that is, Pauli repulsive or bonding orbital interactions; (2) per irreducible representation (irrep) of any point-group symmetry of interacting closed-shell molecular fragments; and now also (3) interacting open-shell (i.e., radical) molecular fragments. The symmetry-decomposed VDD charge analysis augments the symmetry-decomposed energy decomposition analysis (EDA) so that the charge flow associated with Pauli repulsion and orbital interactions can be quantified both per atom and per irrep, for example, for σ, π, and δ electrons. This provides detailed insights into fundamental aspects of chemical bonding that are not accessible from EDA.
Collapse
Affiliation(s)
- Celine Nieuwland
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Pascal Vermeeren
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute of Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg, Johannesburg, South Africa
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
6
|
Nieuwland C, Fonseca Guerra C. How the Chalcogen Atom Size Dictates the Hydrogen‐Bond Donor Capability of Carboxamides, Thioamides, and Selenoamides. Chemistry 2022; 28:e202200755. [PMID: 35322485 PMCID: PMC9324920 DOI: 10.1002/chem.202200755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 12/21/2022]
Abstract
The amino groups of thio‐ and selenoamides can act as stronger hydrogen‐bond donors than of carboxamides, despite the lower electronegativity of S and Se. This phenomenon has been experimentally explored, particularly in organocatalysis, but a sound electronic explanation is lacking. Our quantum chemical investigations show that the NH2 groups in thio‐ and selenoamides are more positively charged than in carboxamides. This originates from the larger electronic density flow from the nitrogen lone pair of the NH2 group towards the lower‐lying π*C=S and π*C=Se orbitals than to the high‐lying π*C=O orbital. The relative energies of the π* orbitals result from the overlap between the chalcogen np and carbon 2p atomic orbitals, which is set by the carbon‐chalcogen equilibrium distance, a consequence of the Pauli repulsion between the two bonded atoms. Thus, neither the electronegativity nor the often‐suggested polarizability but the steric size of the chalcogen atom determines the amide's hydrogen‐bond donor capability.
Collapse
Affiliation(s)
- Celine Nieuwland
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Leiden Institute of Chemistry Gorlaeus Laboratories Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|
7
|
de Azevedo Santos L, Cesario D, Vermeeren P, van der Lubbe SCC, Nunzi F, Fonseca Guerra C. σ-Electrons Responsible for Cooperativity and Ring Equalization in Hydrogen-Bonded Supramolecular Polymers. Chempluschem 2021; 87:e202100436. [PMID: 34709769 DOI: 10.1002/cplu.202100436] [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: 09/29/2021] [Revised: 10/18/2021] [Indexed: 11/08/2022]
Abstract
We have quantum chemically analyzed the cooperative effects and structural deformations of hydrogen-bonded urea, deltamide, and squaramide linear chains using dispersion-corrected density functional theory at BLYP-D3(BJ)/TZ2P level of theory. Our purpose is twofold: (i) reveal the bonding mechanism of the studied systems that lead to their self-assembly in linear chains; and (ii) rationalize the C-C bond equalization in the ring moieties of deltamide and squaramide upon polymerization. Our energy decomposition and Kohn-Sham molecular orbital analyses reveal cooperativity in all studied systems, stemming from the charge separation within the σ-electronic system by charge transfer from the carbonyl oxygen lone pair donor orbital of one monomer towards the σ* N-H antibonding acceptor orbital of the neighboring monomer. This key orbital interaction causes the C=O bonds to elongate, which, in turn, results in the contraction of the adjacent C-C single bonds that, ultimately, makes the ring moieties of deltamide and squaramide to become more regular. Notably, the π-electron delocalization plays a much smaller role in the total interaction between the monomers in the chain.
Collapse
Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV Amsterdam, The Netherlands
| | - Diego Cesario
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV Amsterdam, The Netherlands
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, I-06123, Perugia, Italy
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV Amsterdam, The Netherlands
| | - Francesca Nunzi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, I-06123, Perugia, Italy
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (CNR-SCITEC), Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV Amsterdam, The Netherlands
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC Leiden, The Netherlands
| |
Collapse
|
8
|
Vermeeren P, Wolters LP, Paragi G, Fonseca Guerra C. Cooperative Self-Assembly in Linear Chains Based on Halogen Bonds. Chempluschem 2021; 86:812-819. [PMID: 33905182 PMCID: PMC8252609 DOI: 10.1002/cplu.202100093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/30/2021] [Indexed: 12/03/2022]
Abstract
Cooperative properties of halogen bonds were investigated with computational experiments based on dispersion-corrected relativistic density functional theory. The bonding mechanism in linear chains of cyanogen halide (X-CN), halocyanoacetylene (X-CC-CN), and 4-halobenzonitrile (X-C6 H4 -CN) were examined for X = H, Cl, Br, and I. Our energy decomposition and Kohn-Sham molecular-orbital analyses revealed the bonding mechanism of the studied systems. Cyanogen halide and halocyanoacetylene chains possess an extra stabilizing effect with increasing chain size, whereas the 4-halobenzonitrile chains do not. This cooperativity can be traced back to charge separation within the σ-electronic system by charge-transfer between the lone-pair orbital of the nitrogen (σHOMO ) on one unit and the acceptor orbital of the C-X (σ*LUMO ) on the adjacent unit. As such, the HOMO-LUMO gap in the σ-system decreases, and the cooperativity increases with chain length revealing the similarity in the bonding mechanisms of hydrogen and halogen bonds.
Collapse
Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Lando P. Wolters
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Gábor Paragi
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- MTA-SZTE Biomimetic Systems Research GroupEötvös Loránd Research Network (ELKH)Dóm tér 86720SzegedHungary
- Institute of PhysicsUniversity of PécsIfjúság útja 67624PécsHungary
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Leiden Institute of Chemistry, Gorlaeus LaboratoriesLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| |
Collapse
|