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Nieuwland C, Almacellas D, Veldhuizen MM, de Azevedo Santos L, Poater J, Fonseca Guerra C. Multiple hydrogen-bonded dimers: are only the frontier atoms relevant? Phys Chem Chem Phys 2024; 26:11306-11310. [PMID: 38054332 PMCID: PMC11022277 DOI: 10.1039/d3cp05244c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulation in the monomers.
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Affiliation(s)
- Celine Nieuwland
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
| | - David Almacellas
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Catalonia, Spain
| | - Mac M Veldhuizen
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
| | - Lucas de Azevedo Santos
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.
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2
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de Oliveira Martins E, Weber G. Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration. Biophys Chem 2024; 306:107156. [PMID: 38157701 DOI: 10.1016/j.bpc.2023.107156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/27/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
DNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and those available were obtained from a limited set of melting temperature at high sodium concentration. To our knowledge, there is currently no NN set of parameters for up to three mismatches covering all configurations at low sodium concentrations. Here, we are applying the NN model to a large set of 4096 published melting temperatures, covering all combinations of single, double and triple mismatches. Dealing with such a large set of temperature is challenging in several ways, bringing new methodological problems. Here, optimizing a large number of 252 independent parameters has required the development of a new method where we readjust the seed parameters using the definition of the Gibbs free energy. The new parameters predict the training set within 1.1 °C and the validation set to 2.7 °C.
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Affiliation(s)
- Erik de Oliveira Martins
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil; Escola Politécnica, Centro Universitário Católica do Leste de Minas Gerais, 35170-056 Coronel Fabriciano, MG, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.
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3
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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.
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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
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4
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Bali SD, Ahsan M, Revanasiddappa PD. Structural Insights into the Antiparallel G-Quadruplex in the Presence of K + and Mg 2+ Ions. J Phys Chem B 2023; 127:1499-1512. [PMID: 36757392 DOI: 10.1021/acs.jpcb.2c05128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
G-Quadruplex (GQ) is a secondary structural unit of DNA, formed at the telomere region of the chromosome with a high guanine content. It is reported that the GQs can hinder many biological processes. Thus, research thrives to explore the structural stability of GQs. Studies based on circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments established the vital role of cations such as K+ and Mg2+ in the stability of antiparallel G-quadruplexes (AGQs). However, there is a need to understand how stability in AGQ is attained in the presence of cations. Here, we employed molecular dynamics (MD) simulations, steered MD (SMD) simulations, and QM/MM calculations to understand the biophysical and electronic bases of the stability imparted to AGQs via cation binding. Our results showed that Mg2+ prefers to bind in the plane with the guanine tetrad, whereas K+ binds in between the AGQ tetrads. Thus, three Mg2+ cations or two K+ ions are needed to stabilize an AGQ molecule, where each and every tetrad binds to Mg2+ more robustly with a higher binding affinity. SMD revealed that the traversal of K+ through the AGQ central channel required less force than that of Mg2+, illustrating the presence of more strong interactions between Mg2+ and AGQ tetrads compared to K+. The stabilization in the AGQ tetrads due to cation binding is reassessed by employing ab initio simulations. Mixed QM/MM calculations confirmed that Mg2+ binds strongly to AGQ compared to K+, and it induces higher interactions between the guanine tetrads. However, K+ binding to AGQ induces a higher stabilization energy than Mg2+ binding to AGQ tetrads. Despite the higher binding energy, Mg2+ binding imparts lower stabilization to AGQ due to its unfavorable fermionic quantum energy.
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Affiliation(s)
- Sindhu D Bali
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru 572103, Karnataka, India
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, Riverside, California 92521-9800, United States
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Khan S, Zahoor M, Rahman MU, Gul Z. Cocrystals; basic concepts, properties and formation strategies. Z PHYS CHEM 2023. [DOI: 10.1515/zpch-2022-0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Abstract
Cocrystallization is an old technique and remains the focus of several research groups working in the field of Chemistry and Pharmacy. This technique is basically in field for improving physicochemical properties of material which can be active pharmaceutical ingredients (APIs) or other chemicals with poor profile. So this review article has been presented in order to combine various concepts for scientists working in the field of chemistry, pharmacy or crystal engineering, also it was attempt to elaborate concepts belonging to crystal designing, their structures and applications. A handsome efforts have been made to bring scientists together working in different fields and to make chemistry easier for a pharmacist and pharmacy for chemists pertaining to cocrystals. Various aspects of chemicals being used as co-formers have been explored which predict the formation of co-crystals or molecular salts and even inorganic cocrystals.
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Affiliation(s)
- Shahab Khan
- Department of Chemistry , University of Malakand , Dir Lower 18800 , Khyber Pakhtunkhwa , Pakistan
| | - Muhammad Zahoor
- Department of Biochemistry , University of Malakand , Dir Lower 18800 , Khyber Pakhtunkhwa , Pakistan
| | - Mudassir Ur Rahman
- Department of Chemistry , Government Degree College Lundkhwar , Mardan 23130 , Khyber Pakhtunkhwa , Pakistan
| | - Zarif Gul
- Department of Chemistry , University of Malakand , Dir Lower 18800 , Khyber Pakhtunkhwa , Pakistan
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6
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Storer MC, Hunter CA. Quantification of secondary electrostatic interactions in H-bonded complexes. Phys Chem Chem Phys 2022; 24:18124-18132. [PMID: 35852121 DOI: 10.1039/d2cp03004g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The H-bonding properties of compounds that contain multiple functional groups are difficult to predict, because there are through-bond polarisation effects and long-range secondary electrostatic interactions that have significant effects on the interactions with solvents and other molecules. Here we use experimental measurements of association constants for formation of 1 : 1 H-bonded complexes that contain a single well-defined H-bond and a single well-defined secondary electrostatic interaction to quantify the magnitude of this effect. The results were used to develop a computational method for calculating functional group H-bond parameters that accurately reproduce the magnitudes of both primary H-bonding interaction and secondary electrostatic interactions. The effects of secondary electrostatic interactions are observed in calculations of ab initio Molecular Electrostatic Potential (MEP) values, but at the van der Waals surface, the magnitude of the effect is highly overestimated. MEP values calculated on electron density isosurfaces that lie closer to the nuclei provide a more accurate description of the experimental observations. H-bond parameters calculated using this approach successfully account for the properties of arrays of multiple H-bond donor and acceptor groups in different configurations. The results provide insight into the factors that govern the interaction properties of molecules that contain multiple functional groups and provide an accurate method for prediction of solution phase complexation free energies based on gas phase calculations of individual molecules.
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Affiliation(s)
- Maria Chiara Storer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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7
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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.
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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
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8
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Highly-efficient PVDF adsorptive membrane filtration based on chitosan@CNTs-COOH simultaneous removal of anionic and cationic dyes. Carbohydr Polym 2021; 274:118664. [PMID: 34702483 DOI: 10.1016/j.carbpol.2021.118664] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/21/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022]
Abstract
An adsorptive membrane filtration based on polyvinylidene fluoride (PVDF) with chitosan (CS) and carboxylated carbon nanotubes (CNTs-COOH) is prepared by method of phase conversion, and the PVDF-CS@CNTs-COOH membranes can effectively separate anionic and cationic dye wastewater. Compared to pure PVDF membranes, PVDF-CS@CNTs-COOH increases pure water flux from 36.39 (L·m-2·h-1) to 85.25 (L·m-2·h-1), an increase of nearly 230%. The membrane exhibits excellent rejection performance in the filtration of six types of dye wastewater. The modified membranes also performed well in terms of rejection of mixed anionic and cationic dyes and also have a high performance in recycling, with a flux of over 94% for both anionic and cationic dyes. In addition, the adsorption curve fitting results showed that the adsorption process was more consistent with the pseudo-second-order adsorption kinetic model and Langmuir mode.
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9
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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] [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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10
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Chen L, Dang J, Du J, Wang C, Mo Y. Hydrogen and Halogen Bonding in Homogeneous External Electric Fields: Modulating the Bond Strengths. Chemistry 2021; 27:14042-14050. [PMID: 34319620 DOI: 10.1002/chem.202102284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/28/2022]
Abstract
Recent years have witnessed various fascinating phenomena arising from the interactions of noncovalent bonds with homogeneous external electric fields (EEFs). Here we performed a computational study to interpret the sensitivity of intrinsic bond strengths to EEFs in terms of steric effect and orbital interactions. The block-localized wavefunction (BLW) method, which combines the advantages of both ab initio valence bond (VB) theory and molecular orbital (MO) theory, and the subsequent energy decomposition (BLW-ED) approach were adopted. The sensitivity was monitored and analyzed using the induced energy term, which is the variation in each energy component along the EEF strength. Systems with single or multiple hydrogen (H) or halogen (X) bond(s) were also examined. It was found that the X-bond strength change to EEFs mainly stems from the covalency change, while generally the steric effect rules the response of H-bonds to EEFs. Furthermore, X-bonds are more sensitive to EEFs, with the key difference between H- and X-bonds lying in the charge transfer interaction. Since phenylboronic acid has been experimentally used as a smart linker in EEFs, switchable sensitivity was scrutinized with the example of the phenylboronic acid dimer, which exhibits two conformations with either antiparallel or parallel H-bonds, thereby, opposite or consistent responses to EEFs. Among the studied systems, the quadruple X-bonds in molecular capsules exhibit remarkable sensitivity, with its interaction energy increased by -95.2 kJ mol-1 at the EEF strength 0.005 a.u.
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Affiliation(s)
- Li Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Juan Du
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience & Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC 27401, USA
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11
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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.
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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
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12
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Larrañaga O, Arrieta A, Fonseca Guerra C, Bickelhaupt FM, de Cózar A. Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds. Chem Asian J 2021; 16:315-321. [PMID: 33372401 PMCID: PMC7898866 DOI: 10.1002/asia.202001201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/28/2020] [Indexed: 01/24/2023]
Abstract
We have quantum chemically studied the structure and nature of alkali- and coinage-metal bonds (M-bonds) versus that of hydrogen bonds between A-M and B- in archetypal [A-M⋅⋅⋅B]- model systems (A, B=F, Cl and M=H, Li, Na, Cu, Ag, Au), using relativistic density functional theory at ZORA-BP86-D3/TZ2P. We find that coinage-metal bonds are stronger than alkali-metal bonds which are stronger than the corresponding hydrogen bonds. Our main purpose is to understand how and why the structure, stability and nature of such bonds are affected if the monovalent central atom H of hydrogen bonds is replaced by an isoelectronic alkali- or coinage-metal atom. To this end, we have analyzed the bonds between A-M and B- using the activation strain model, quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analysis (EDA), and Voronoi deformation density (VDD) analysis of the charge distribution.
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Affiliation(s)
- Olatz Larrañaga
- Departamento de Química Orgánica I, Facultad de QuímicaUniversidad del País Vasco (UPV/EHU)Donostia International Physics Center (DIPC)P. K. 107220018San Sebastián-DonostiaSpain
| | - Ana Arrieta
- Departamento de Química Orgánica I, Facultad de QuímicaUniversidad del País Vasco (UPV/EHU)Donostia International Physics Center (DIPC)P. K. 107220018San Sebastián-DonostiaSpain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HV AmsterdamThe Netherlands
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HV AmsterdamThe Netherlands
- Institute of Molecules and MaterialsRadboud UniversityHeyendaalseweg 135NL-6525AJ NijmegenThe Netherlands
| | - Abel de Cózar
- Departamento de Química Orgánica I, Facultad de QuímicaUniversidad del País Vasco (UPV/EHU)Donostia International Physics Center (DIPC)P. K. 107220018San Sebastián-DonostiaSpain
- IKERBASQUE, Basque Foundation for SciencePlaza Euskadi 548009BilbaoSpain
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13
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Gao H, Hu L, Hu Y, Lv X, Wu YB, Lu G. Origins of Lewis acid acceleration in nickel-catalysed C–H, C–C and C–O bond cleavage. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00660f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The effects of charge transfer, Pauli repulsion and electrostatics/polarization are identified as dominant factors for Lewis acid accelerations in Ni-catalyzed C–X (X = H, C and O) bond cleavages.
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Affiliation(s)
- Han Gao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Lingfei Hu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Yanlei Hu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Xiangying Lv
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Yan-Bo Wu
- Key Lab for Materials of Energy Conversion and Storage of Shanxi Province and
- Key Lab of Chemical Biology and Molecular Engineering of Ministry of Education
- Institute of Molecular Science
- Shanxi University
- Taiyuan
| | - Gang Lu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
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14
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Li J, Lutz M, Klein Gebbink RJM. A Cp‐based Molybdenum Catalyst for the Deoxydehydration of Biomass‐derived Diols. ChemCatChem 2020. [DOI: 10.1002/cctc.202001115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jing Li
- Organic Chemistry and Catalysis Debye Institute for Nanomaterials Science Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Martin Lutz
- Crystal and Structural Chemistry Bijvoet Centre for Biomolecular Research Faculty of Science Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Robertus J. M. Klein Gebbink
- Organic Chemistry and Catalysis Debye Institute for Nanomaterials Science Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
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15
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Lu C, Wang C, Jimenez JC, Rheingold AL, Sauvé G. Large Non-planar Conjugated Molecule with Strong Intermolecular Interactions Achieved with Homoleptic Zn(II) Complex of Di(5-quinolylethynyl)-tetraphenylazadipyrromethene. ACS OMEGA 2020; 5:31467-31472. [PMID: 33324859 PMCID: PMC7726932 DOI: 10.1021/acsomega.0c05169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Zinc(II) complexes of tetraphenylazadipyrromethenes are potential non-planar n-type conjugated materials. To tune the properties, we installed 5-quinolylethynyl groups at the pyrrolic positions. Compared to the complex with 1-napthylethynyl, we found evidence for stronger intermolecular interactions in the new complex, including much higher overlap integrals in crystals. X-ray analysis revealed unconventional C-H···N hydrogen bonding between two quinolyls of neighboring molecules, pointing to a new strategy for the development of non-planar molecular semiconductors with stronger intermolecular interactions.
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Affiliation(s)
- Chenwei Lu
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44122, United States
| | - Chunlai Wang
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44122, United States
| | - Jayvic C. Jimenez
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44122, United States
| | - Arnold L. Rheingold
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla California, 92093, United States
| | - Genevieve Sauvé
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44122, United States
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16
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van der Lubbe SC, Haim A, van Heesch T, Fonseca Guerra C. Tuning the Binding Strength of Even and Uneven Hydrogen-Bonded Arrays with Remote Substituents. J Phys Chem A 2020; 124:9451-9463. [PMID: 33054218 PMCID: PMC7667637 DOI: 10.1021/acs.jpca.0c07815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/01/2020] [Indexed: 12/20/2022]
Abstract
We investigated the tunability of hydrogen bond strength by altering the charge accumulation around the frontier atoms with remote substituents. For pyridine···H2O with NH2 and CN substituted at different positions on pyridine, we find that the electron-withdrawing CN group decreases the negative charge accumulation around the frontier atom N, resulting in weakening of the hydrogen bond, whereas the electron-donating NH2 group increases the charge accumulation around N, resulting in strengthening of the hydrogen bond. By applying these design principles on DDAA-AADD, DADA-ADAD, DAA-ADD, and ADA-DAD hydrogen-bonded dimers, we find that the effect of the substituent is delocalized over the whole molecular system. As a consequence, systems with an equal number of hydrogen bond donor (D) and acceptor (A) atoms are not tunable in a predictable way because of cancellation of counteracting strengthening and weakening effects. Furthermore, we show that the position of the substituent and long-range electrostatics can play an important role as well. Overall, the design principles presented in this work are suitable for monomers with an unequal number of donor and acceptor atoms and can be exploited to tune the binding strength of supramolecular building blocks.
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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
| | - Anissa Haim
- 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
| | - Thor van Heesch
- 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
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17
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Cuyacot BJR, Durník I, Foroutan-Nejad C, Marek R. Anatomy of Base Pairing in DNA by Interacting Quantum Atoms. J Chem Inf Model 2020; 61:211-222. [PMID: 33112145 DOI: 10.1021/acs.jcim.0c00642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of purine and pyrimidine base pairs (BPs), which contributes to shaping of the canonical and noncanonical 3D structures of nucleic acids, is one the most investigated phenomena in chemistry and life sciences. In this contribution, the anatomy of the bond energy (BDE) of the base-pairing interaction in 39 different arrangements found experimentally or predicted for DNA structures containing the four common nucleobases (A, C, G, T) in their neutral or protonated forms is described in light of the theory of interacting quantum atoms within the context of the quantum theory of atoms in molecules. The interplay of individual energy components involved in the three stages of the bond formation process (structural deformation, electron-density promotion, and intermolecular interaction) is studied. We recognized that for the neutral BPs, variations in the kinetic and electrostatic contributions to the BDE are rather negligible, leaving the exchange-correlation energy as the main stabilizing component. It is shown that the contribution of the exchange-correlation term can be recovered by including atoms that are formally assumed to be hydrogen bonded (primary interaction). In contrast, to recover the electrostatic component of interaction, one must consider both the primary and secondary (formally nonbonded atoms) interatomic interactions. The results of our study were employed to design new types of BPs with altered bonding anatomy. We demonstrate that improving the electrostatic characteristics of the BPs does not necessarily result in greater interaction energies if weak secondary hydrogen bonding is destroyed. However, the main tuning factor for systems with conserved interacting faces (primary interactions) is the electrostatic component of the interaction energy resulting from the secondary atom-atom electrostatics.
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Affiliation(s)
- Ben Joseph R Cuyacot
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Ivo Durník
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia.,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia
| | - Radek Marek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
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18
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Oliveira LM, Long AS, Brown T, Fox KR, Weber G. Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches. Chem Sci 2020; 11:8273-8287. [PMID: 34094181 PMCID: PMC8163305 DOI: 10.1039/d0sc01700k] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bonding and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combinations of canonical base pairs in the same location under the same conditions. For a substantial number of single mismatch configurations, 15%, the measured melting temperatures were higher than the least stable AT base pair. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches. To highlight the applicability of our results, we discuss a number of practical situations such as enzyme binding affinities, thymine DNA glycosylase repair activity, and trinucleotide repeat expansions.
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Affiliation(s)
- Luciana M Oliveira
- Departamento de Física, Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil +55 31 3409 5600 +55 31 3409 6616
| | - Adam S Long
- School of Biological Sciences, University of Southampton Life Sciences Building 85 Southampton SO17 1BJ UK
| | - Tom Brown
- Department of Chemistry, University of Oxford Oxford UK
| | - Keith R Fox
- School of Biological Sciences, University of Southampton Life Sciences Building 85 Southampton SO17 1BJ UK
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil +55 31 3409 5600 +55 31 3409 6616
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19
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Karas LJ, Wu CH, Das R, Wu JIC. Hydrogen bond design principles. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020; 10. [PMID: 33936251 DOI: 10.1002/wcms.1477] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydrogen bonding principles are at the core of supramolecular design. This overview features a discussion relating molecular structure to hydrogen bond strengths, highlighting the following electronic effects on hydrogen bonding: electronegativity, steric effects, electrostatic effects, π-conjugation, and network cooperativity. Historical developments, along with experimental and computational efforts, leading up to the birth of the hydrogen bond concept, the discovery of nonclassical hydrogen bonds (C-H…O, O-H…π, dihydrogen bonding), and the proposal of hydrogen bond design principles (e.g., secondary electrostatic interactions, resonance-assisted hydrogen bonding, and aromaticity effects) are outlined. Applications of hydrogen bond design principles are presented.
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Affiliation(s)
- Lucas J Karas
- Department of Chemistry, University of Houston, Houston, TX
| | - Chia-Hua Wu
- Department of Chemistry, University of Houston, Houston, TX
| | - Ranjita Das
- Department of Chemistry, University of Houston, Houston, TX
| | - Judy I-Chia Wu
- Department of Chemistry, University of Houston, Houston, TX
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20
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C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3' Synonymous mRNA Codons. Int J Mol Sci 2020; 21:ijms21082882. [PMID: 32326096 PMCID: PMC7216251 DOI: 10.3390/ijms21082882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022] Open
Abstract
5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1–3 were assessed to be significantly lower compared to their 2-thio- and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called “new wobble base pair”, which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5′-NNG-3′ synonymous codons, unlike their 2-thio- and 2-oxo-precursors, which preferentially read the 5′-NNA-3′ codons. Thus, the interplay between the levels of U-, S2U- and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3′-A- and 3′-G-ending codons.
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21
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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] [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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22
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Understanding chemical reactivity using the activation strain model. Nat Protoc 2020; 15:649-667. [PMID: 31925400 DOI: 10.1038/s41596-019-0265-0] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022]
Abstract
Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.
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23
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van der Lubbe SCC, Fonseca Guerra C. The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths. Chem Asian J 2019; 14:2760-2769. [PMID: 31241855 PMCID: PMC6771679 DOI: 10.1002/asia.201900717] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 12/04/2022]
Abstract
Hydrogen bonds are a complex interplay between different energy components, and their nature is still subject of an ongoing debate. In this minireview, we therefore provide an overview of the different perspectives on hydrogen bonding. This will be done by discussing the following individual energy components: 1) electrostatic interactions, 2) charge-transfer interactions, 3) π-resonance assistance, 4) steric repulsion, 5) cooperative effects, 6) dispersion interactions and 7) secondary electrostatic interactions. We demonstrate how these energetic factors are essential in a correct description of the hydrogen bond, and discuss several examples of systems whose energetic and geometrical features are not captured by easy-to-use predictive models.
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Affiliation(s)
- Stephanie C. C. van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Leiden Institute of Chemistry, Gorlaeus LaboratoriesLeiden UniversityEinsteinweg 552333 CDLeidenThe Netherlands
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24
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Han X, Wang E, Cui Y, Lin Y, Chen H, An R, Liang X, Komiyama M. The staining efficiency of cyanine dyes for single-stranded DNA is enormously dependent on nucleotide composition. Electrophoresis 2019; 40:1708-1714. [PMID: 31004446 DOI: 10.1002/elps.201800445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/21/2019] [Accepted: 04/15/2019] [Indexed: 11/12/2022]
Abstract
The staining of nucleic acids with fluorescent dyes is one of the most fundamental technologies in relevant areas of science. For reliable and quantitative analysis, the staining efficiency of the dyes should not be very dependent on the sequences of the specimens. However, this assumption has not necessarily been confirmed by experimental results, especially in the staining of ssDNA (and RNA). In this study, we found that both SYBR Green II and SYBR Gold did not stain either homopyrimidines or ssDNA composed of only adenine (A) and cytosine (C). However, these two dyes emit strong fluorescence when the ssDNA contains both guanine (G) and C (and/or both A and thymine (T)) and form potential Watson-Crick base pairs. Interestingly, SYBR Gold, but not SYBR Green II, strongly stains ssDNA consisting of G and A (or G and T). Additionally, we found that the secondary structure of ssDNA may play an important role in DNA staining. To obtain reliable results for practical applications, sufficient care must be paid to the composition and sequence of ssDNA.
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Affiliation(s)
- Xutiange Han
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Erchi Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Yikai Lin
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
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25
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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: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [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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26
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Petelski AN, Fonseca Guerra C. Designing Self-Assembled Rosettes: Why Ammeline is a Superior Building Block to Melamine. ChemistryOpen 2019; 8:135-142. [PMID: 30740288 PMCID: PMC6356174 DOI: 10.1002/open.201800210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/25/2018] [Indexed: 01/16/2023] Open
Abstract
In supramolecular chemistry, the rational design of self-assembled systems remains a challenge. Herein, hydrogen-bonded rosettes of melamine and ammeline have been theoretically examined by using dispersion-corrected density functional theory (DFT-D). Our bonding analyses, based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA), show that ammeline is a much better building block than melamine for the fabrication of cyclic complexes based on hydrogen bonds. This superior capacity is explained by both stronger hydrogen bonding and the occurrence of a strong synergy.
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Affiliation(s)
- Andre Nicolai Petelski
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Departamento de Ingeniería QuímicaGrupo de Investigación en Química Teórica y Experimental (QuiTEx)Facultad Regional ResistenciaUniversidad Tecnológica NacionalFrench 414H3500CHJResistenciaChacoArgentina
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Leiden Institute of Chemistry, Gorlaeus LaboratoriesLeiden UniversityThe Netherlands
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27
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Zhang Y, Wu CH, Wu JIC. Why do A·T and G·C self-sort? Hückel aromaticity as a driving force for electronic complementarity in base pairing. Org Biomol Chem 2019; 17:1881-1885. [DOI: 10.1039/c8ob01669k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computations reveal that the potential for aromaticity gain and loss in nucleobases play key roles in modulating base pairing strengths.
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Affiliation(s)
- Yu Zhang
- Department of Chemistry
- University of Houston
- Houston
- USA
| | - Chia-Hua Wu
- Department of Chemistry
- University of Houston
- Houston
- USA
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28
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Yu S, de Bruijn HM, Svatunek D, Hamlin TA, Bickelhaupt FM. Factors Controlling the Diels-Alder Reactivity of Hetero-1,3-Butadienes. ChemistryOpen 2018; 7:995-1004. [PMID: 30524925 PMCID: PMC6276106 DOI: 10.1002/open.201800193] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Indexed: 12/29/2022] Open
Abstract
We have quantum chemically explored the Diels-Alder reactivities of a systematic series of hetero-1,3-butadienes with ethylene by using density functional theory at the BP86/TZ2P level. Activation strain analyses provided physical insight into the factors controlling the relative cycloaddition reactivity of aza- and oxa-1,3-butadienes. We find that dienes with a terminal heteroatom, such as 2-propen-1-imine (NCCC) or acrolein (OCCC), are less reactive than the archetypal 1,3-butadiene (CCCC), primarily owing to weaker orbital interactions between the more electronegative heteroatoms with ethylene. Thus, the addition of a second heteroatom at the other terminal position (NCCN and OCCO) further reduces the reactivity. However, the introduction of a nitrogen atom in the backbone (CNCC) leads to enhanced reactivity, owing to less Pauli repulsion resulting from polarization of the diene HOMO in CNCC towards the nitrogen atom and away from the terminal carbon atom. The Diels-Alder reactions of ethenyl-diazene (NNCC) and 1,3-diaza-butadiene (NCNC), which contain heteroatoms at both the terminal and backbone positions, are much more reactive due to less activation strain compared to CCCC.
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Affiliation(s)
- Song Yu
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Hans M de Bruijn
- Department of Theoretical Chemistry, 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 P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Dennis Svatunek
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institut für Angewandte Synthesechemie Technische Universität Wien (TU Wien) Getreidemarkt 9 1060 Vienna Austria
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM) Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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29
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Lin X, Jiang X, Wu W, Mo Y. Induction, Resonance, and Secondary Electrostatic Interaction on Hydrogen Bonding in the Association of Amides and Imides. J Org Chem 2018; 83:13446-13453. [DOI: 10.1021/acs.joc.8b02247] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuhui Lin
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiaoyu Jiang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350108, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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30
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Zarycz MNC, Fonseca Guerra C. NMR 1H-Shielding Constants of Hydrogen-Bond Donor Reflect Manifestation of the Pauli Principle. J Phys Chem Lett 2018; 9:3720-3724. [PMID: 29927254 PMCID: PMC6038099 DOI: 10.1021/acs.jpclett.8b01502] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 06/21/2018] [Indexed: 05/25/2023]
Abstract
NMR spectroscopy is one of the most useful methods for detection and characterization of hydrogen bond (H-bond) interactions in biological systems. For H bonds X-H···Y, where X and Y are O or N, it is generally believed that a decrease in 1H-shielding constants relates to a shortening of H-bond donor-acceptor distance. Here we investigated computationally the trend of 1H-shielding constants for hydrogen-bonded protons in a series of guanine C8-substituted GC pair model compounds as a function of the molecular structure. Furthermore, the electron density distribution around the hydrogen atom was analyzed with the Voronoi deformation density (VDD) method. Our findings demonstrate that 1H-shielding values of the hydrogen bond are determined by the depletion of charge around the hydrogen atom, which stems from the fact that electrons obey the Pauli exclusion principle.
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Affiliation(s)
- M. Natalia C. Zarycz
- Instituto de Investigaciones
en Físico-Química de Córdoba, (INFIQC), CONICET,
Facultad de Ciencias Químicas, Universidad
Nacional de Córdoba, Haya de la Torre esq. Medina Allende, X5000HUA Córdoba, Argentina
- CONICET-CCT Nordeste, Facultad de Ciencias
Exactas, Naturales y Agrimensura, Universidad
Nacional del Nordeste, Av. Libertad 5460, W3400AAS Corrientes, Argentina
| | - Célia Fonseca Guerra
- Department
of Chemistry and Pharmaceutical Sciences and 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, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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31
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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] [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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32
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Francese T, Ribas-Arino J, Novoa JJ, Havenith RW, Broer R, de Graaf C, Deumal M. The magnetic fingerprint of dithiazolyl-based molecule magnets. Phys Chem Chem Phys 2018; 20:20406-20416. [DOI: 10.1039/c8cp03173h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ferromagnetic fingerprint of dithiazolyl-based molecule materials is uncovered. Interestingly geometrical rather than electronic structure factors play the leading role.
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Affiliation(s)
- Tommaso Francese
- Dept. Ciència de Materials i Química Física
- Secció Química Física & IQTCUB
- Universitat de Barcelona
- Barcelona
- Spain
| | - Jordi Ribas-Arino
- Dept. Ciència de Materials i Química Física
- Secció Química Física & IQTCUB
- Universitat de Barcelona
- Barcelona
- Spain
| | - Juan J. Novoa
- Dept. Ciència de Materials i Química Física
- Secció Química Física & IQTCUB
- Universitat de Barcelona
- Barcelona
- Spain
| | - Remco W.A. Havenith
- Theoretical Chemistry
- Zernike Institute for Advance Materials
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Ria Broer
- Theoretical Chemistry
- Zernike Institute for Advance Materials
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Coen de Graaf
- Theoretical Chemistry
- Zernike Institute for Advance Materials
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Mercè Deumal
- Dept. Ciència de Materials i Química Física
- Secció Química Física & IQTCUB
- Universitat de Barcelona
- Barcelona
- Spain
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33
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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] [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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