1
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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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Li C, Bhandary R, Marinow A, Bachmann S, Pöppler AC, Binder WH. Stability of Quadruple Hydrogen Bonds in an Ionic Liquid Environment. Macromol Rapid Commun 2024; 45:e2300464. [PMID: 37796474 DOI: 10.1002/marc.202300464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/02/2023] [Indexed: 10/06/2023]
Abstract
Hydrogen bonds (H-bonds) are highly sensitive to the surrounding environments owing to their dipolar nature, with polar solvents kown to significantly weaken H-bonds. Herein, the stability of the H-bonding motif ureidopyrimidinone (UPy) is investigated, embedded into a highly polar polymeric ionic liquid (PIL) consisting of pendant pyrrolidinium bis(trifluoromethylsulfonyl)imide (IL) moieties, to study the influence of such ionic environments on the UPy H-bonds. The content of the surrounding IL is changed by addition of an additional low molecular weight IL to further boost the IL content around the UPy moieties in molar ratios of UPy/IL ranging from 1/4 up to 1/113, thereby promoting the polar microenvironment around the UPy-H-bonds. Variable-temperature solid-state MAS NMR spectroscopy and FT-IR spectroscopy demonstrate that the UPy H-bonds are largely present as (UPy-) dimers, but sensitive to elevated temperatures (>70 °C). Subsequent rheology and DSC studies reveal that the ILs only solvate the polymeric chains but do not interfere with the UPy-dimer H-bonds, thus accounting for their high stability and applicability in many material systems.
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Affiliation(s)
- Chenming Li
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
| | - Rajesh Bhandary
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
| | - Anja Marinow
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
| | - Stephanie Bachmann
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ann-Christin Pöppler
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Wolfgang H Binder
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
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3
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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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4
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Jena NR. Rare Tautomers of Artificially Expanded Genetic Letters and their Effects on the Base pair Stabilities. Chemphyschem 2022; 23:e202100908. [PMID: 35029036 DOI: 10.1002/cphc.202100908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 11/11/2022]
Abstract
To expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently proposed second-generation artificially expanded genetic letters in producing stable duplex DNA. Here, a reliable dispersion-corrected density functional theory method is used to understand the electronic structures and properties of different rare tautomers of proposed expanded genetic letters and their effects on the base pair stabilities in the duplex DNA. It is found that the rare tautomers are not only stable in the aqueous medium but can also base pair with natural bases to produce stable mispairs. Except for J and V, all the artificial genetic letters are found to produce mispairs that are about 1-7 kcal/mol more stable than their complementary counterparts. They are also appreciably more stable than the naturally occurring G:C, A:T, and G:T pairs. The higher base pair stabilities are found to be mainly because of the polarity of monomers and attractive electrostatic interactions.
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Affiliation(s)
- N R Jena
- IIITDM Jabalpur, Discipline of Natural Sciences, Dumna Airport Road, Khamaria, India, 482005, Jabalpur, INDIA
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5
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Laplaza R, Peccati F, A. Boto R, Quan C, Carbone A, Piquemal J, Maday Y, Contreras‐García J. NCIPLOT
and the analysis of noncovalent interactions using the reduced density gradient. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1497] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rubén Laplaza
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Departamento de Química Física Universidad de Zaragoza Zaragoza Spain
| | - Francesca Peccati
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
| | - Roberto A. Boto
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Centro de Física de Materiales CFM‐MPC (CSIC‐UPV/EHU) Donostia Spain
| | - Chaoyu Quan
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
| | - Alessandra Carbone
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB) Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Jean‐Philip Piquemal
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Yvon Maday
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
- Institut Universitaire de France Paris France
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6
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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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7
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Zhou F, Wang J, Zhang Y, Wang Q, Guo C, Wang F, Zheng X, Zhang H. Theoretical studies on the bond strength and electron density characteristics in multiple hydrogen bonded arrays. J Mol Graph Model 2019; 93:107439. [DOI: 10.1016/j.jmgm.2019.107439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 11/28/2022]
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8
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Lin X, Wu W, Mo Y. How Resonance Modulates Multiple Hydrogen Bonding in Self-Assembled Systems. J Org Chem 2019; 84:14805-14815. [DOI: 10.1021/acs.joc.9b02381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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
| | - 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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9
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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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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: 45] [Impact Index Per Article: 9.0] [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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11
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Vallejo Narváez WE, Jiménez EI, Cantú-Reyes M, Yatsimirsky AK, Hernández-Rodríguez M, Rocha-Rinza T. Stability of doubly and triply H-bonded complexes governed by acidity-basicity relationships. Chem Commun (Camb) 2019; 55:1556-1559. [PMID: 30540294 DOI: 10.1039/c8cc06967k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used our recently proposed acidity-basicity interplay (ABI) model (Chem. Sci., 2018, 9, 4402) and the Jorgensen secondary interactions hypothesis (JSIH) to rationalise the experimentally observed trends in the formation constants of doubly and triply H-bonded systems with -NHO[double bond, length as m-dash]C- and -NHN- interactions. Unlike the JSIH, the ABI interpretation can explain the trends in the complexation of amide/imide homo- and heterodimers as well as ADA-DAD clusters. We found that the strongest H-bonds play a very important role, a condition which offers an alternative to the well established JSIH to modulate the stability of these relevant systems.
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Affiliation(s)
- Wilmer E Vallejo Narváez
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, 04510 Ciudad de México, Mexico.
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12
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Backhouse OJ, Thacker JCR, Popelier PLA. A Re-evaluation of Factors Controlling the Nature of Complementary Hydrogen-Bonded Networks. Chemphyschem 2019; 20:555-564. [DOI: 10.1002/cphc.201801180] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Oliver J. Backhouse
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN Great Britain
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL Great Britain
- Department of Physics; King's College London, Strand; London WC2R 2LS Great Britain
| | - Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN Great Britain
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL Great Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN Great Britain
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL Great Britain
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13
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Popelier PLA, Maxwell PI, Thacker JCR, Alkorta I. A relative energy gradient (REG) study of the planar and perpendicular torsional energy barriers in biphenyl. Theor Chem Acc 2018; 138:12. [PMID: 30872951 PMCID: PMC6383956 DOI: 10.1007/s00214-018-2383-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022]
Abstract
Biphenyl is a prototype molecule, the study of which is important for a proper understanding of stereo-electronic effects. In the gas phase it has an equilibrium central torsion angle of ~ 45° and shows both a planar (0°) and a perpendicular (90°) torsional energy barrier. The latter is analysed for the first time. We use the newly proposed REG method, which is an exhaustive procedure that automatically ranks atomic energy contributions according to their importance in explaining the energy profile of a total system. Here, the REG method operates on energy contributions computed by the interacting quantum atoms method. This method is minimal in architecture and provides a crisp picture of well-defined and well-separated electrostatic, steric and exchange (covalent) energies at atomistic level. It is shown that the bond critical point occurring between the ortho-hydrogens in the planar geometry has been wrongly interpreted as a sign of repulsive interaction. A convenient metaphor of analysing football matches is introduced to clarify the role of a REG analysis.
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Affiliation(s)
- Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN UK
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Peter I. Maxwell
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN UK
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN UK
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
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14
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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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15
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Thacker JCR, Vincent MA, Popelier PLA. Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV-1 Protease. Chemistry 2018; 24:11200-11210. [PMID: 29802794 PMCID: PMC6099506 DOI: 10.1002/chem.201802035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 11/10/2022]
Abstract
The reaction mechanism in an active site is of the utmost importance when trying to understand the role that an enzyme plays in biological processes. In a recently published paper [Theor. Chem. Acc. 2017, 136, 86], we formalised the Relative Energy Gradient (REG) method for automating an Interacting Quantum Atoms (IQA) analysis. Here, the REG method is utilised to determine the mechanism of peptide hydrolysis in the aspartic active site of the enzyme HIV-1 Protease. Using the REG method along with the IQA approach we determine the mechanism of peptide hydrolysis without employing any arbitrary parameters and with remarkable ease (albeit at large computational cost: the system contains 133 atoms, which means that there are 17 689 individual IQA terms to be calculated). When REG and IQA work together it is possible to determine a reaction mechanism at atomistic resolution from data directly derived from quantum calculations, without arbitrary parameters. Moreover, the mechanism determined by this novel method gives concrete insight into how the active site residues catalyse peptide hydrolysis.
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Affiliation(s)
- Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB)131 Princess StreetManchesterM1 7DNUK
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Mark A. Vincent
- Manchester Institute of Biotechnology (MIB)131 Princess StreetManchesterM1 7DNUK
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB)131 Princess StreetManchesterM1 7DNUK
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
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16
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Vallejo Narváez WE, Jiménez EI, Romero-Montalvo E, Sauza-de la Vega A, Quiroz-García B, Hernández-Rodríguez M, Rocha-Rinza T. Acidity and basicity interplay in amide and imide self-association. Chem Sci 2018; 9:4402-4413. [PMID: 29896381 PMCID: PMC5956980 DOI: 10.1039/c8sc01020j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/05/2018] [Indexed: 12/23/2022] Open
Abstract
Simple acid–base properties explain the differences in amide and imide dimerisation, and represent an alternative to the secondary interactions hypothesis.
Amides dimerise more strongly than imides despite their lower acidity. Such an unexpected result has been rationalised in terms of the Jorgensen Secondary Interactions Hypothesis (JSIH) that involves the spectator (C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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OS) and H-bonded (C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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OHB) carbonyl groups in imides. Notwithstanding the considerable body of experimental and theoretical evidence supporting the JSIH, there are some computational studies which suggest that there might be other relevant intermolecular interactions than those considered in this model. We conjectured that the spectator carbonyl moieties could disrupt the resonance-assisted hydrogen bonds in imide dimers, but our results showed that this was not the case. Intrigued by this phenomenon, we studied the self-association of a set of amides and imides via1H-NMR, 1H-DOSY experiments, DFT calculations, QTAIM topological analyses of the electron density and IQA partitions of the electronic energy. These analyses revealed that there are indeed repulsions of the type OS···OHB in accordance with the JSIH but our data also indicate that the C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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OS group has an overall attraction with the interacting molecule. Instead, we found correlations between self-association strength and simple Brønsted–Lowry acid/base properties, namely, N–H acidities and C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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O basicities. The results in CDCl3 and CCl4 indicate that imides dimerise less strongly than structurally related amides because of the lower basicity of their carbonyl fragments, a frequently overlooked aspect in the study of H-bonding. Overall, the model proposed herein could provide important insights in diverse areas of supramolecular chemistry such as the study of multiple hydrogen-bonded adducts which involve amide or imide functional groups.
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Affiliation(s)
- Wilmer E Vallejo Narváez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Eddy I Jiménez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Eduardo Romero-Montalvo
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Arturo Sauza-de la Vega
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Beatriz Quiroz-García
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Marcos Hernández-Rodríguez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Tomás Rocha-Rinza
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
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Wu CH, Zhang Y, van Rickley K, Wu JI. Aromaticity gain increases the inherent association strengths of multipoint hydrogen-bonded arrays. Chem Commun (Camb) 2018; 54:3512-3515. [DOI: 10.1039/c8cc00422f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Besides the textbook checklist for ways to control the association strengths of multipoint hydrogen-bonded arrays, “aromaticity” also makes the list!
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The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change. Theor Chem Acc 2017; 136:86. [PMID: 32025197 PMCID: PMC6979521 DOI: 10.1007/s00214-017-2113-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/16/2017] [Indexed: 12/15/2022]
Abstract
Much chemical insight ultimately comes down to finding out which fragment of a total system behaves like the total system, in terms of an energy profile. A simple example is that of the water dimer, where this system is regarded as held together by a hydrogen bond. The hydrogen bond consists of two atoms (H···O), which energetically behave similarly to the total system (H2O)2. However, from a quantum mechanical point of view, each atom in the total system interacts with any other atom. Thus, the view that the hydrogen bond by itself governs the energetic stability of the water dimer needs rigorous justification. In this work, we propose a method that provides such a justification, in general, but only illustrated on the water dimer here. This method is based on the topological energy partitioning method called interacting quantum atoms (IQA). The method is implemented in the program ANANKE, which calculates correlations between the energy profile of the total system and those of subsystems (or fragments). ANANKE acts on the IQA energy contributions obtained for a sequence of full-system geometries controlled by a coordinate of interest (e.g. the O···H distance in the water dimer). Although applied only for the water dimer in this work, the method is general and able to explain the gauche effect, the torsional barrier in biphenyl, the arrow-pushing scheme of an enzymatic reaction (peptide hydrolysis in the HIV-1 Protease active site), and halogen-alkane nucleophilic substitution (SN2) reactions. Those applications will appear elsewhere as separate and elaborated case studies; here we focus on the details of the ANANKE method and its justification, using the water dimer as a concrete case.
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Tiwari MK, Vanka K. Exploiting directional long range secondary forces for regulating electrostatics-dominated noncovalent interactions. Chem Sci 2017; 8:1378-1390. [PMID: 28451279 PMCID: PMC5361874 DOI: 10.1039/c6sc03642b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022] Open
Abstract
It has been well established that long range secondary electrostatic interactions (SEIs) have a significant effect on the stability of supramolecular complexes. However, general rules for exploiting SEIs in the rational design of diverse supramolecular complexes have been difficult to obtain. In this work, we outline a quantum chemical approach for understanding the strength of electrostatic interactions. This approach is seen to provide excellent correlation between the electrostatic force and the binding energy between two partners in hydrogen-bonded complexes, as well as that between two ions in ion-pair complexes. Furthermore, we illustrate how the understanding of the binding allows for the rational design of new complexes where the association constant between the two partners can be increased or decreased, as desired, by several orders of magnitude. Hence, the current work showcases a general, simple and powerful method of understanding and exploiting long range secondary electrostatic interactions.
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Affiliation(s)
- Mrityunjay K Tiwari
- Physical and Material Chemistry Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pashan , Pune-411008 , Maharashtra , India .
| | - Kumar Vanka
- Physical and Material Chemistry Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pashan , Pune-411008 , Maharashtra , India .
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22
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Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing. Molecules 2014; 19:11613-27. [PMID: 25100254 PMCID: PMC6271411 DOI: 10.3390/molecules190811613] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 01/19/2023] Open
Abstract
The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I) and 2'-deoxyribo-2,6-diaminopurine (D) as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.
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Tognetti V, Joubert L. Density functional theory and Bader's atoms-in-molecules theory: towards a vivid dialogue. Phys Chem Chem Phys 2014; 16:14539-50. [DOI: 10.1039/c3cp55526g] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Syzgantseva OA, Tognetti V, Joubert L. On the Physical Nature of Halogen Bonds: A QTAIM Study. J Phys Chem A 2013; 117:8969-80. [DOI: 10.1021/jp4059774] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Olga A. Syzgantseva
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
| | - Vincent Tognetti
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
| | - Laurent Joubert
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
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Tognetti V, Joubert L. On the physical role of exchange in the formation of an intramolecular bond path between two electronegative atoms. J Chem Phys 2013; 138:024102. [PMID: 23320663 DOI: 10.1063/1.4770495] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this paper, we present a detailed energetic decomposition of intramolecular O···X interactions (X being O, S, or a halogen atom) based on the interacting quantum atoms approach of Pendás and co-workers. The nature of these interactions (repulsive or attractive, more or less electrostatic) is discussed in the framework of Bader's atoms in molecules theory, a particular emphasis being put on delocalization (measured by delocalization indexes and in terms of the source function) and on the exchange contributions. Notably, the concept of exchange channels introduced by Pendás and collaborators provides means of rationalizing and predicting the presence of bond critical points, enhancing the physical meaning of bond paths.
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Affiliation(s)
- Vincent Tognetti
- Normandie Université, COBRA, UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821 Mont-Saint-Aignan Cedex, France.
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Deepa P, Kolandaivel P, Senthilkumar K. Hydrogen-bonding studies of amino acid side-chains with DNA base pairs. Mol Phys 2011. [DOI: 10.1080/00268976.2011.602649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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27
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An AAAA–DDDD quadruple hydrogen-bond array. Nat Chem 2011; 3:244-48. [PMID: 21336332 DOI: 10.1038/nchem.987] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 01/13/2011] [Indexed: 11/08/2022]
Abstract
Secondary electrostatic interactions between adjacent hydrogen bonds can have a significant effect on the stability of a supramolecular complex. In theory, the binding strength should be maximized if all the hydrogen-bond donors (D) are on one component and all the hydrogen-bond acceptors (A) are on the other. Here, we describe a readily accessible AAAA–DDDD quadruple hydrogen-bonding array that exhibits exceptionally strong binding for a small-molecule hydrogen-bonded complex in a range of different solvents (K(a) > 3 × 10(12) M(-1) in CH2Cl2, 1.5 × 10(6) M(-1) in CH3CN and 3.4 × 10(5) M(-1) in 10% v/v DMSO/CHCl3). The association constant in CH2Cl2 corresponds to a binding free energy (ΔG) in excess of –71 kJ mol(-1) (more than 20% of the thermodynamic stability of a carbon–carbon covalent bond), which is remarkable for a supramolecular complex held together by just four intercomponent hydrogen bonds.
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Blight BA, Camara-Campos A, Djurdjevic S, Kaller M, Leigh DA, McMillan FM, McNab H, Slawin AMZ. AAA-DDD triple hydrogen bond complexes. J Am Chem Soc 2009; 131:14116-22. [PMID: 19746984 DOI: 10.1021/ja906061v] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experiment and theory both suggest that the AAA-DDD pattern of hydrogen bond acceptors (A) and donors (D) is the arrangement of three contiguous hydrogen bonding centers that results in the strongest association between two species. Murray and Zimmerman prepared the first example of such a system (complex 3*2) and determined the lower limit of its association constant (K(a)) in CDCl(3) to be 10(5) M(-1) by (1)H NMR spectroscopy (Murray, T. J. and Zimmerman, S. C. J. Am. Chem. Soc. 1992, 114, 4010-4011). The first cationic AAA-DDD pair (3*4(+)) was described by Bell and Anslyn (Bell, D. A. and Anslyn, E. A. Tetrahedron 1995, 51, 7161-7172), with a K(a) > 5 x 10(5) M(-1) in CH(2)Cl(2) as determined by UV-vis spectroscopy. We were recently able to quantify the strength of a neutral AAA-DDD arrangement using a more chemically stable AAA-DDD system, 6*2, which has an association constant of 2 x 10(7) M(-1) in CH(2)Cl(2) (Djurdjevic, S., Leigh, D. A., McNab, H., Parsons, S., Teobaldi, G. and Zerbetto, F. J. Am. Chem. Soc. 2007, 129, 476-477). Here we report on further AA(A) and DDD partners, together with the first precise measurement of the association constant of a cationic AAA-DDD species. Complex 6*10(+)[B(3,5-(CF(3))(2)C(6)H(3))(4)(-)] has a K(a) = 3 x 10(10) M(-1) at RT in CH(2)Cl(2), by far the most strongly bound triple hydrogen bonded system measured to date. The X-ray crystal structure of 6*10(+) with a BPh(4)(-) counteranion shows a planar array of three short (NH...N distances 1.95-2.15 A), parallel (but staggered rather than strictly linear; N-H...N angles 165.4-168.8 degrees), primary hydrogen bonds. These are apparently reinforced, as theory predicts, by close electrostatic interactions (NH-*-N distances 2.78-3.29 A) between each proton and the acceptor atoms of the adjacent primary hydrogen bonds.
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Affiliation(s)
- Barry A Blight
- School of Chemistry, University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
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Osmialowski B. Systematic investigation of 2,7-dihydroxy-1,8-naphthyridine dimerization – secondary interactions and tautomeric preferences calculations. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Houjou H, Koga R. Explicit Representation of Anisotropic Force Constants for Simulating Intermolecular Vibrations of Multiply Hydrogen-Bonded Systems. J Phys Chem A 2008; 112:11256-62. [DOI: 10.1021/jp8057614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hirohiko Houjou
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Ryota Koga
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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31
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Xue C, Popelier PLA. Computational Study of Substituent Effects on the Interaction Energies of Hydrogen-Bonded Watson−Crick Cytosine:Guanine Base Pairs. J Phys Chem B 2008; 112:5257-64. [DOI: 10.1021/jp7108913] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chunxia Xue
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester, M1 7DN, Great Britain
| | - Paul L. A. Popelier
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester, M1 7DN, Great Britain
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32
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Newman SG, Taylor A, Boyd RJ. Factors controlling extremely strong AAA-DDD triply hydrogen-bonded complexes. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2007.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Joubert L, Adamo C. Static and dynamic descriptions of bond breaking/formation: A complementary view? J Chem Phys 2005; 123:211103. [PMID: 16356030 DOI: 10.1063/1.2133728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ab initio molecular-dynamic simulations using density-functional theory and the recent atom-centered density-matrix propagation (ADMP) method were used to study the bond breaking and formation for a case-study substitution nucleophilic bimolecular reaction, namely, the Walden inversion. Using the atoms-in-molecule approach, we have performed a detailed analysis to investigate intra- and intermolecular charge transfer along the ADMP trajectory. These results were compared to those obtained considering a static approach, such as the intrinsic reaction path. In particular, the topological properties computed along the dynamic trajectory well evidence a stronger electron exchange tending to spontaneously maximize the rising covalent interaction. Furthermore, their analysis suggests that the bond formation mechanism involves a reactive intermediate with a bonding interaction stronger than in the final product.
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Affiliation(s)
- Laurent Joubert
- Laboratoire d'Electrochimie et de Chimie Analytique, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7575, Ecole Nationale Supérieure de Chimie de Paris, Paris Cedex 05, France
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34
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Popelier PLA. Quantum Chemical Topology: on Bonds and Potentials. INTERMOLECULAR FORCES AND CLUSTERS I 2005. [DOI: 10.1007/b135617] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Stacking Interactions in Benzene and Cytosine Dimers: From Molecular Electron Density Perspective. Struct Chem 2005. [DOI: 10.1007/s11224-005-4455-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Liu WL, Chen GJ. Bending effect on the stabilities of quadruple hydrogen bonding systems: theoretical study of a series of self-constituted quadruple hydrogen bonded complexes (C9H9N5O2)2. Phys Chem Chem Phys 2005; 7:3943-7. [DOI: 10.1039/b511228a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Robertazzi A, Platts JA. Hydrogen Bonding and Covalent Effects in Binding of Cisplatin to Purine Bases: Ab Initio and Atoms in Molecules Studies. Inorg Chem 2004; 44:267-74. [PMID: 15651872 DOI: 10.1021/ic0489544] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio and density functional calculations are employed to investigate the role of hydrogen bonding in the binding of cisplatin to the purine bases guanine and adenine. Through the use of the theory of atoms in molecules (AIM), it is shown that hydrogen bonds are ubiquitous in such systems, with N-H...N and N-H...Cl interactions present in addition to the expected N-H...O. This in turn means that the known stability of cisplatin-guanine complexes cannot be ascribed solely to hydrogen bonding and allows decomposition of total binding energy into contributions from covalent and hydrogen bonds. To do so, a new method for predicting hydrogen bond energies from bond critical point properties is proposed, employing partial least-squares analysis to remove the family dependence of simple models. Still more hydrogen bond motifs are found in bifunctional complexes of the general type purine-[Pt(NH(3))(2)](2+)-purine, including purine...purine contacts, though again the energetics of these are insufficient to explain the observed trends in stability. Finally, the effect of platination on the pairing of guanine with cytosine is studied in a similar manner, revealing large redistributions of hydrogen bonding but surprisingly small overall changes in pairing energy.
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Affiliation(s)
- Arturo Robertazzi
- Department of Chemistry, Cardiff University, P.O. Box 912, Cardiff CF10 3TB, UK
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Parthasarathi R, Amutha R, Subramanian V, Nair BU, Ramasami T. Bader's and Reactivity Descriptors' Analysis of DNA Base Pairs. J Phys Chem A 2004. [DOI: 10.1021/jp031285f] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R. Parthasarathi
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - R. Amutha
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | | | - T. Ramasami
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
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Alvarez-Rua C, García-Granda S, Goswami S, Mukherjee R, Dey S, Claramunt RM, Santa María MD, Rozas I, Jagerovic N, Alkorta I, Elguero J. Multiple hydrogen bonds and tautomerism in naphthyridine derivatives. NEW J CHEM 2004. [DOI: 10.1039/b315692c] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Liem SY, Popelier PLA. High-rank quantum topological electrostatic potential: Molecular dynamics simulation of liquid hydrogen fluoride. J Chem Phys 2003. [DOI: 10.1063/1.1593012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Hydrogen bond cooperativity derived from neighboring hydrogen bond formation: case study in three iso-complexes of C8H9N5O2. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00116-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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42
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JOUBERT L, POPELIER PLA. Improved convergence of the ‘atoms in molecules’ multipole expansion of electrostatic interaction. Mol Phys 2002. [DOI: 10.1080/00268970210152773] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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