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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:e202100541. [PMID: 34957691 DOI: 10.1002/cplu.202100541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Invited for this month's cover are collaborators from the TheoCheM group of the Vrije Universiteit Amsterdam and the University of Perugia. The cover picture shows a σ-electron traveling through a hydrogen-bonded squaramide linear chain. The charge transfer within the σ-electronic system is the cause for the cooperativity in the investigated urea, deltamide, and squaramide polymers. More information can be found in the Full Paper by Célia Fonseca Guerra, and co-workers.
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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, 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, 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
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Zaccaria F, van der Lubbe SCC, Nieuwland C, Hamlin TA, Fonseca Guerra C. How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes. Chemphyschem 2021; 22:2265-2266. [PMID: 34791760 DOI: 10.1002/cphc.202100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The front cover artwork is provided by the TheoCheM group of the Vrije Universiteit Amsterdam. The image shows that guanine quadruplexes have a stronger binding affinity for divalent cations than monovalent cations. Read the full text of the Article at 10.1002/cphc.202100529.
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Affiliation(s)
- Francesco Zaccaria
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Celine Nieuwland
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, 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
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Zaccaria F, van der Lubbe SCC, Nieuwland C, Hamlin TA, Fonseca Guerra C. How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes. Chemphyschem 2021; 22:2286-2296. [PMID: 34435425 PMCID: PMC9293024 DOI: 10.1002/cphc.202100529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/24/2021] [Indexed: 11/06/2022]
Abstract
The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+, Ca2+, Sr2+, and Ba2+), and (post‐)transition metal (Zn2+, Cd2+, Hg2+, and Pb2+) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+). Importantly, we establish the nature of the cation‐GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.
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Affiliation(s)
- Francesco Zaccaria
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Celine Nieuwland
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, 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
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5
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Chen J, Wang J, van der Lubbe SCC, Cheng M, Qiu D, Monchaud D, Mergny JL, Guerra CF, Ju H, Zhou J. A Push–Pull Mechanism Helps Design Highly Competent G-Quadruplex-DNA Catalysts. CCS Chem 2021. [DOI: 10.31635/ccschem.020.202000473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Stephanie C. C. van der Lubbe
- Theoretical Chemistry, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, Amsterdam 1081 HV
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS, Université de Bourgogne Franche-Comté, Dijon 21078
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Célia Fonseca Guerra
- Theoretical Chemistry, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, Amsterdam 1081 HV
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden 2333 CD
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
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de Azevedo Santos L, van der Lubbe SCC, Hamlin TA, Ramalho TC, Matthias Bickelhaupt F. A Quantitative Molecular Orbital Perspective of the Chalcogen Bond. ChemistryOpen 2021; 10:390. [PMID: 33793082 DOI: 10.1002/open.202100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Invited for this month's cover are the groups of Prof. Dr. Teodorico C. Ramalho (Federal University of Lavras and University Hradec Kralove) and Prof. Dr. F. Matthias Bickelhaupt (Vrije Universiteit Amsterdam and Radboud University). The cover picture shows the key message of their work, that is, the covalency of the chalcogen bonds, in an elegantly simple and attractive manner. To that end, the chalcogen bonds are represented by schematic 3D structures of the bond donor D2 Ch and the bond acceptor A- , and their attractive interaction in green. Then, a colorful molecular orbital (MO) diagram where the HOMO-LUMO mixing is represented by the mixing of red (HOMO) and blue (LUMO) into purple (MO) is presented. Read the full text of their Full Paper at 10.1002/open.202000323.
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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.,Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, CEP 37200-900, Lavras-MG, Brazil
| | - 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
| | - Trevor A Hamlin
- 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
| | - Teodorico C Ramalho
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, CEP 37200-900, Lavras-MG, Brazil.,Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| | - F Matthias Bickelhaupt
- 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.,Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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de Azevedo Santos L, van der Lubbe SCC, Hamlin TA, Ramalho TC, Matthias Bickelhaupt F. A Quantitative Molecular Orbital Perspective of the Chalcogen Bond. ChemistryOpen 2021; 10:391-401. [PMID: 33594829 PMCID: PMC8015733 DOI: 10.1002/open.202000323] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO-LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A- to D2 Ch.
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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 AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
| | - 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 AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Teodorico C. Ramalho
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute for Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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van der Lubbe SCC, Vermeeren P, Fonseca Guerra C, Bickelhaupt FM. The Nature of Nonclassical Carbonyl Ligands Explained by Kohn-Sham Molecular Orbital Theory. Chemistry 2020; 26:15690-15699. [PMID: 33045113 PMCID: PMC7756819 DOI: 10.1002/chem.202003768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Indexed: 12/02/2022]
Abstract
When carbonyl ligands coordinate to transition metals, their bond distance either increases (classical) or decreases (nonclassical) with respect to the bond length in the isolated CO molecule. C−O expansion can easily be understood by π‐back‐donation, which results in a population of the CO's π*‐antibonding orbital and hence a weakening of its bond. Nonclassical carbonyl ligands are less straightforward to explain, and their nature is still subject of an ongoing debate. In this work, we studied five isoelectronic octahedral complexes, namely Fe(CO)62+, Mn(CO)6+, Cr(CO)6, V(CO)6− and Ti(CO)62−, at the ZORA‐BLYP/TZ2P level of theory to explain this nonclassical behavior in the framework of Kohn–Sham molecular orbital theory. We show that there are two competing forces that affect the C−O bond length, namely electrostatic interactions (favoring C−O contraction) and π‐back‐donation (favoring C−O expansion). It is a balance between those two terms that determines whether the carbonyl is classical or nonclassical. By further decomposing the electrostatic interaction ΔVelstat into four fundamental terms, we are able to rationalize why ΔVelstat gives rise to the nonclassical behavior, leading to new insights into the driving forces behind C−O contraction.
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Affiliation(s)
- Stephanie C C van der Lubbe
- Department of Theoretical Chemistry, Amsterdam Institute of, Molecular and Life Sciences (AIMMS), Amsterdam Center of, Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of, Molecular and Life Sciences (AIMMS), Amsterdam Center of, 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 of, 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, CD, Leiden, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of, Molecular and Life Sciences (AIMMS), Amsterdam Center of, Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
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Margiotta E, van der Lubbe SCC, de Azevedo Santos L, Paragi G, Moro S, Bickelhaupt FM, Fonseca Guerra C. Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design. J Chem Inf Model 2020; 60:1317-1328. [PMID: 32003997 PMCID: PMC7093837 DOI: 10.1021/acs.jcim.9b00946] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Halogen bonds are highly important
in medicinal chemistry as halogenation
of drugs, generally, improves both selectivity and efficacy toward
protein active sites. However, accurate modeling of halogen bond interactions
remains a challenge, since a thorough theoretical investigation of
the bonding mechanism, focusing on the realistic complexity of drug–receptor
systems, is lacking. Our systematic quantum-chemical study on ligand/peptide-like
systems reveals that halogen bonding is driven by the same bonding
interactions as hydrogen bonding. Besides the electrostatic and the
dispersion interactions, our bonding analyses, based on quantitative
Kohn–Sham molecular orbital theory together with energy decomposition
analysis, reveal that donor–acceptor interactions and steric
repulsion between the occupied orbitals of the halogenated ligand
and the protein need to be considered more carefully within the drug
design process.
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Affiliation(s)
- Enrico Margiotta
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lucas de Azevedo Santos
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Gabor Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,MTA-SZTE Biomimetic Systems Research Group, Dom ter 8, 6720 Szeged, Hungary.,Institute of Physics, University of Pecs, Ifjusag utja 6, 7624 Pecs, Hungary
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Institute of Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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10
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van der Lubbe SCC, Zaccaria F, Sun X, Guerra CF. Secondary Electrostatic Interaction Model Revised: Prediction Comes Mainly from Measuring Charge Accumulation in Hydrogen-Bonded Monomers. J Am Chem Soc 2019; 141:4878-4885. [PMID: 30799606 PMCID: PMC6439436 DOI: 10.1021/jacs.8b13358] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The
secondary electrostatic interaction (SEI) model is often used
to predict and explain relative hydrogen bond strengths of self-assembled
systems. The SEI model oversimplifies the hydrogen-bonding mechanisms
by viewing them as interacting point charges, but nevertheless experimental
binding strengths are often in line with the model’s predictions.
To understand how this rudimentary model can be predictive, we computationally
studied two tautomeric quadruple hydrogen-bonded systems, DDAA-AADD
and DADA-ADAD. Our results reveal that when the proton donors D (which
are electron-donating) and the proton acceptors A (which are electron-withdrawing)
are grouped together as in DDAA, there is a larger accumulation of
charge around the frontier atoms than when the proton donor and acceptor
groups are alternating as in DADA. This accumulation of charge makes
the proton donors more positive and the proton acceptors more negative,
which enhances both the electrostatic and covalent interactions in
the DDAA dimer. The SEI model is thus predictive because it provides
a measure for the charge accumulation in hydrogen-bonded monomers.
Our findings can be understood from simple physical organic chemistry
principles and provide supramolecular chemists with meaningful understanding
for tuning hydrogen bond strengths and thus for controlling the properties
of self-assembled systems.
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Affiliation(s)
- Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Francesco Zaccaria
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Xiaobo Sun
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling , 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
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11
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Grosch AA, van der Lubbe SCC, Fonseca Guerra C. Nature of Intramolecular Resonance Assisted Hydrogen Bonding in Malonaldehyde and Its Saturated Analogue. J Phys Chem A 2018; 122:1813-1820. [PMID: 29357252 PMCID: PMC5817623 DOI: 10.1021/acs.jpca.7b12635] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The nature of resonance-assisted
hydrogen bonds (RAHB) is still
subject of an ongoing debate. We therefore analyzed the σ and
π charge redistributions associated with the formation of intramolecular
hydrogen bonds in malonaldehyde (MA) and its saturated analogue 3-hydroxypropanal
(3-OH) and addressed the question whether there is a resonance assistance
phenomenon in the sense of a synergistic interplay between the σ
and π electron systems. Our quantum chemical calculations at
the BP86/TZ2P level of theory show that the π charge flow is
indeed in line with the Lewis structure as proposed by the RAHB model.
This typical rearrangement of charge is only present in the unsaturated
system, and not in its saturated analogue. Resonance in the π
electron system assists the intramolecular hydrogen bond by reducing
the hydrogen bond distance, and by providing an additional stabilizing
component to the net bonding energy. The σ orbital interaction
plays an important role in the enhanced hydrogen bond strength in
MA as well. However, there is no resonance assistance in the sense
of an interplay between σ charge transfer and π polarization;
σ and π contribute independently from each other.
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Affiliation(s)
- Alice A Grosch
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University , 2333 CC Leiden, The Netherlands
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van der Lubbe SCC, Fonseca Guerra C. Hydrogen-Bond Strength of CC and GG Pairs Determined by Steric Repulsion: Electrostatics and Charge Transfer Overruled. Chemistry 2017; 23:10249-10253. [PMID: 28485530 PMCID: PMC6563699 DOI: 10.1002/chem.201701821] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Indexed: 02/03/2023]
Abstract
Theoretical and experimental studies have elucidated the bonding mechanism in hydrogen bonds as an electrostatic interaction, which also exhibits considerable stabilization by charge transfer, polarization, and dispersion interactions. Therefore, these components have been used to rationalize the differences in strength of hydrogen‐bonded systems. A completely new viewpoint is presented, in which the Pauli (steric) repulsion controls the mechanism of hydrogen bonding. Quantum chemical computations on the mismatched DNA base pairs CC and GG (C=cytosine, G=guanine) show that the enhanced stabilization and shorter distance of GG is determined entirely by the difference in the Pauli repulsion, which is significantly less repulsive for GG than for CC. This is the first time that evidence is presented for the Pauli repulsion as decisive factor in relative hydrogen‐bond strengths and lengths.
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Affiliation(s)
- Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, The Netherlands
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