1
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Lončarević A, Malbaša Z, Kovačić M, Ostojić K, Angaïts A, Skoko Ž, Szpunar J, Urlić I, Gallego Ferrer G, Rogina A. Copper-zinc/chitosan complex hydrogels: Rheological, degradation and biological properties. Int J Biol Macromol 2023; 251:126373. [PMID: 37595698 DOI: 10.1016/j.ijbiomac.2023.126373] [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: 04/28/2023] [Revised: 07/05/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Polymer hydrogels crosslinked by therapeutic metal ions have attracted increased interest in recent years due to their unique and versatile properties. Chitosan hydrogels are widely investigated for various biomedical applications such as tissue engineering and drug delivery. Copper and zinc ions are considered as therapeutic metal ions, that have important roles in bone regeneration. The aim of this study was to investigate the physicochemical and biological properties of bimetallic-chitosan complex hydrogels with different cupric and zinc ions content. Scanning electron microscopy (SEM) revealed changes in the morphology from the microstructure with larger, tubular pores for aerogels with higher Zn content, to the sheets-like structure with long pores for samples with higher Cu content. FTIR analysis indicated the formation of bimetallic-chitosan aerogels. The obtained X-ray diffraction patterns showed a broadening of chitosan's characteristic diffraction maximum, while characterization of physical properties showed decreased swelling ability and increased shear modulus with higher Cu content. ICP-MS results showed a negligible amount of copper and zinc ions released under physiological conditions during 24 h indicating a strong physical crosslink between metal ions and chitosan chains. Furthermore, accelerated in vitro degradation showed that hydrogels maintained good stability during four weeks of lysozyme activity. The MTT assay indicated that the cytotoxicity of Cu2+-Zn2+/chitosan complexes could be adjusted by the amount of cupric ions. All results imply that Cu2+ and Zn2+ ions act as physical crosslinkers of the polymer network. Also, results are in agreement with the prediction of density functional theory (DFT) which indicated stronger chitosan-Cu tetrahedral aqua complex interactions in comparison to the chitosan-[Zn(H2O)4]2+ interactions.
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Affiliation(s)
- Andrea Lončarević
- University of Zagreb, Faculty of Chemical Engineering and Technology, Trg Marka Marulića 19, HR-10000 Zagreb, Croatia.
| | - Zoran Malbaša
- University of Zagreb, Faculty of Chemical Engineering and Technology, Trg Marka Marulića 19, HR-10000 Zagreb, Croatia.
| | - Marin Kovačić
- University of Zagreb, Faculty of Chemical Engineering and Technology, Trg Marka Marulića 19, HR-10000 Zagreb, Croatia.
| | - Karla Ostojić
- University of Zagreb, Faculty of Science, Department of Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia.
| | - Ange Angaïts
- Institute of Analytical and Physical Chemistry for the Environment and Materials (IPREM), UMR5254 CNRS-University of Pau, Hélioparc, 2, Av. Pr. Angot, 64053 Pau, France.
| | - Željko Skoko
- University of Zagreb, Faculty of Science, Department of Physics, Bijenička c. 32, HR-10000 Zagreb, Croatia.
| | - Joanna Szpunar
- Institute of Analytical and Physical Chemistry for the Environment and Materials (IPREM), UMR5254 CNRS-University of Pau, Hélioparc, 2, Av. Pr. Angot, 64053 Pau, France.
| | - Inga Urlić
- University of Zagreb, Faculty of Science, Department of Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia.
| | - Gloria Gallego Ferrer
- Centre for Biomaterial and Tissue Engineering, Universitat Politècnica de València, Valencia, Spain; Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Valencia, Spain.
| | - Anamarija Rogina
- University of Zagreb, Faculty of Chemical Engineering and Technology, Trg Marka Marulića 19, HR-10000 Zagreb, Croatia.
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2
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Harle J, Slater C, Cafiero M. Investigating Paracetamol's Role as a Potential Treatment for Parkinson's Disease: Ab Initio Analysis of Dopamine, l-DOPA, Paracetamol, and NAPQI Interactions with Enzymes Involved in Dopamine Metabolism. ACS OMEGA 2023; 8:38053-38063. [PMID: 37867718 PMCID: PMC10586264 DOI: 10.1021/acsomega.3c03888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Recently, it was found that paracetamol can extend the therapeutic window of l-DOPA treatment for Parkinson's disease [Golding (2019) BJPharm, 4(2), Article 619]. It has been posited that the effect could be due to paracetamol and its metabolite, NAPQI, inhibiting pain signals in the spinal column. In this work, we examine the possibility that the therapeutic effect of the paracetamol for the Parkinson's disease patient may be due to an inhibition of the enzymes that metabolize dopamine and/or l-DOPA, thus effectively extending the lifetime of the l-DOPA treatment. In this work, we use the M062X/6-311+G* level of theory to calculate the electronic binding energies (including explicit desolvation) of several ligands (paracetamol, NAPQI, dopamine, and l-DOPA) with a series of enzymes important to the production and metabolism of dopamine and compare them to calculated binding energy values for the natural substrates for those enzymes in order to predict possible inhibition. Benchmark interaction energies for a subset of the systems studied are calculated using the more accurate second-order Møller-Plesset perturbation (MP2) method in order to calibrate the accuracy of the M062X method. If we assume that the interaction energies calculated here can serve as a proxy for in vivo inhibition, then we can predict that paracetamol and NAPQI should not inhibit the natural production of dopamine and may in fact inhibit the metabolism of l-DOPA and dopamine, thus extending the length of l-DOPA treatments.
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Affiliation(s)
- Joshua Harle
- School
of Chemistry Food and Pharmacy, University
of Reading, Reading RG6 6AD, U.K.
| | - Catherine Slater
- School
of Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, U.K.
| | - Mauricio Cafiero
- School
of Chemistry Food and Pharmacy, University
of Reading, Reading RG6 6AD, U.K.
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3
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Jalali Sarvestani MR, Doroudi Z, Ahmadi R. Picric Acid Adsorption on the Surface of Pristine and Al-doped Boron Nitride Nanocluster: a Comprehensive Theoretical Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793122010286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Juraskova V, Celerse F, Laplaza R, Corminboeuf C. Assessing the persistence of chalcogen bonds in solution with neural network potentials. J Chem Phys 2022; 156:154112. [DOI: 10.1063/5.0085153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what are the most prevalent non-covalent interactions occurring in a solute-Cl$^-$-THF mixture. The simulations in explicit solvent highlight competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.
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5
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Nieuwland C, Hamlin TA, Fonseca Guerra C, Barone G, Bickelhaupt FM. B-DNA Structure and Stability: The Role of Nucleotide Composition and Order. ChemistryOpen 2022; 11:e202100231. [PMID: 35083880 PMCID: PMC8805170 DOI: 10.1002/open.202100231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/10/2021] [Indexed: 11/08/2022] Open
Abstract
We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.
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Affiliation(s)
- Celine Nieuwland
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
| | - Célia Fonseca Guerra
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
- Leiden Institute of ChemistryGorlaeus LaboratoriesLeiden UniversityEinsteinweg 552300 CCLeiden (TheNetherlands
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e FarmaceuticheUniversità degli Studi di PalermoViale delle Scienze, Edificio 1790128PalermoItaly
| | - F. Matthias Bickelhaupt
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
- Institute of Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
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6
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Mechanistic Insights into the Inhibition of SARS-CoV-2 Main Protease by Clovamide and Its Derivatives: In Silico Studies. BIOPHYSICA 2021. [DOI: 10.3390/biophysica1040028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The novel coronavirus SARS-CoV-2 Main Protease (Mpro) is an internally encoded enzyme that hydrolyzes the translated polyproteins at designated sites. The protease directly mediates viral replication processes; hence, a promising target for drug design. Plant-based natural products, especially polyphenols and phenolic compounds, provide the scaffold for many effective antiviral medications, and have recently been shown to be able to inhibit Mpro of SARS-CoV-2. Specifically, polyphenolic compounds found in cacao and chocolate products have been shown by recent experimental studies to have strong inhibitory effects against Mpro activities. This work aims to uncover the inhibition processes of Mpro by a natural phenolic compound found in cacao and chocolate products, clovamide. Clovamide (caffeoyl-DOPA) is a naturally occurring caffeoyl conjugate that is found in the phenolic fraction of Theobroma Cacao L. and a potent radical-scavenging antioxidant as suggested by previous studies of our group. Here, we propose inhibitory mechanisms by which clovamide may act as a Mpro inhibitor as it becomes oxidized by scavenging reactive oxygen species (ROS) in the body, or becomes oxidized as a result of enzymatic browning. We use molecular docking, annealing-based molecular dynamics, and Density Functional Theory (DFT) calculations to study the interactions between clovamide with its derivatives and Mpro catalytic and allosteric sites. Our molecular modelling studies provide mechanistic insights of clovamide inhibition of Mpro, and indicate that clovamide may be a promising candidate as a drug lead molecule for COVID-19 treatments.
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7
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Vymětal J, Jakubec D, Galgonek J, Vondrášek J. Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. Nucleic Acids Res 2021; 49:W15-W20. [PMID: 34019656 PMCID: PMC8262704 DOI: 10.1093/nar/gkab377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/10/2021] [Accepted: 04/27/2021] [Indexed: 12/29/2022] Open
Abstract
Interactions among amino acid residues are the principal contributor to the stability of the three-dimensional structure of a protein. The Amino Acid Interactions (INTAA) web server (https://bioinfo.uochb.cas.cz/INTAA/) has established itself as a unique computational resource, which enables users to calculate the contribution of individual residues in a biomolecular structure to its total energy using a molecular mechanical scoring function. In this update, we describe major additions to the web server which help solidify its position as a robust, comprehensive resource for biomolecular structure analysis. Importantly, a new continuum solvation model was introduced, allowing more accurate representation of electrostatic interactions in aqueous media. In addition, a low-overhead pipeline for the estimation of evolutionary conservation in protein chains has been added. New visualization options were introduced as well, allowing users to easily switch between and interrelate the energetic and evolutionary views of the investigated structures.
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Affiliation(s)
- Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic.,Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Praha 1, 118 00, Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic
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8
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Millan J, Lesarri A, Fernández JA, Martínez R. Exploring Epigenetic Marks by Analysis of Noncovalent Interactions. Chembiochem 2020; 22:408-415. [PMID: 32815664 DOI: 10.1002/cbic.202000380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/19/2020] [Indexed: 01/28/2023]
Abstract
Epigenetic marks are modest chemical modifications on DNA and histone proteins that regulate the activation or silencing of genes through modulation of the intermolecular interactions between the DNA strands and the protein machinery. The process is complex and not always well understood. One of the systems studied in greater detail is the epigenetic mark on H3K9: lysine 9 of histone 3. The degree of methylation or acetylation of this histone is linked to silencing or activation of the corresponding gene, but it is not clear which effect each mark has in gene expression. We shed light on this particular methylation process by using density functional theory (DFT) calculations. First, we built a model consisting of a DNA double strand containing three base pairs and a sequence of three amino acids of the histone's tail. Then, we computed the modulation introduced into the intermolecular interactions by each epigenetic modification: from mono- to trimethylation and acetylation. The calculations show that whereas acetylation and trimethylation result in a reduction of the DNA-peptide interaction; non-, mono-, and dimethylation increase the intermolecular interactions. Such observations compare well with the findings reported in the literature, and highlight the correlation between the balance of intermolecular forces and biological properties, simultaneously advancing quantum-mechanical studies of large biochemical systems at molecular level through the use of DFT methods.
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Affiliation(s)
- Judith Millan
- Departamento de Química, Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios, 53, Logroño, 26006, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, I.U. CINQUIMA, Universidad de Valladolid, Valladolid, 47011, Spain
| | - José A Fernández
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco-UPV/EHU, Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Rodrigo Martínez
- Departamento de Química, Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios, 53, Logroño, 26006, Spain
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9
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Athmani AS, Madi F, Laafifi I, Cheriet M, Issaoui N, Nouar L, Merdes R. DFT Investigation of a Charge-Transfer Complex Formation Between p-Phenylenediamine and 3,5-Dinitrosalicylic Acid. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476619120060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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10
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Long J, Youli Q, Yu L. Effect analysis of quantum chemical descriptors and substituent characteristics on Henry's law constants of polybrominated diphenyl ethers at different temperatures. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 145:176-183. [PMID: 28734220 DOI: 10.1016/j.ecoenv.2017.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 06/07/2023]
Abstract
Twelve substituent descriptors, 17 quantum chemical descriptors and 1/T were selected to establish a quantitative structure-property relationship (QSPR) model of Henry's law constants for 7 polybrominated diphenyl ethers (PBDEs) at five different temperatures. Then, the lgH of 202 congeners at different temperatures were predicted. The variation rule and regulating mechanism of lgH was studied from the perspectives of both quantum chemical descriptors and substituent characteristics. The R2 for modeling and testing sets of the final QSPR model are 0.977 and 0.979, respectively, thus indicating good fitness and predictive ability for Henry' law constants of PBDEs at different temperatures. The favorable hydrogen binding sites are the 5,5',6,6'-positions for high substituent congeners and the O atom of the ether bond for low substituent congeners, which affects the interaction between PBDEs and water molecules. lgH is negatively and linearly correlated with 1/T, and the variation trends of lgH with temperature are primarily regulated by individual substituent characteristics, wherein: the more substituents involved, the smaller the lgH. The significant sequence for the main effect of substituent positions is para>meta>ortho, where the ortho-positions are mainly involved in second-order interaction effect (64.01%). Having two substituents in the same ring also provides a significant effect, with 81.36% of second-order interaction effects, particularly where there is an adjacent distribution (55.02%).
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Affiliation(s)
- Jiang Long
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China; North China Electric Power Research Institute Co Ltd., Beijing 100045, China
| | - Qiu Youli
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Li Yu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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11
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Aguiló E, Moro AJ, Gavara R, Alfonso I, Pérez Y, Zaccaria F, Guerra CF, Malfois M, Baucells C, Ferrer M, Lima JC, Rodríguez L. Reversible Self-Assembly of Water-Soluble Gold(I) Complexes. Inorg Chem 2017; 57:1017-1028. [DOI: 10.1021/acs.inorgchem.7b02343] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elisabet Aguiló
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Inorgànica, Universitat de Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
| | - Artur J. Moro
- LAQV-REQUIMTE,
Departamento de Química, CQFB, Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal
| | - Raquel Gavara
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Inorgànica, Universitat de Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
| | | | | | - Francesco Zaccaria
- Department
of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, 1081 HV Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department
of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, 1081 HV Amsterdam, The Netherlands
- Leiden
Institute
of Chemistry, Gorlaeus Laboratories, Leiden University, 2311 EZ Leiden, The Netherlands
| | - Marc Malfois
- ALBA Synchrotron Light Laboratory (CELLS), Carrer de la Llum 2−26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Clara Baucells
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Inorgànica, Universitat de Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
| | - Montserrat Ferrer
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Inorgànica, Universitat de Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
| | - João Carlos Lima
- LAQV-REQUIMTE,
Departamento de Química, CQFB, Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal
| | - Laura Rodríguez
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Inorgànica, Universitat de Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
- Institut
de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
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12
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Cabria I, López MJ, Alonso JA. Searching for DFT-based methods that include dispersion interactions to calculate the physisorption of H2 on benzene and graphene. J Chem Phys 2017; 146:214104. [DOI: 10.1063/1.4984106] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- I. Cabria
- Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid, Spain
| | - M. J. López
- Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid, Spain
| | - J. A. Alonso
- Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid, Spain
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13
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Paragi G, Fonseca Guerra C. Cooperativity in the Self-Assembly of the Guanine Nucleobase into Quartet and Ribbon Structures on Surfaces. Chemistry 2017; 23:3042-3050. [DOI: 10.1002/chem.201604830] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Gábor Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- MTA-SZTE; Supramolecular and Nanostructured Materials Research Group; Dóm tér 8 Szeged Hungary
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
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14
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Astani EK, Heshmati E, Chen CJ, Hadipour NL. A theoretical study on the characteristics of the intermolecular interactions in the active site of human androsterone sulphotransferase: DFT calculations of NQR and NMR parameters and QTAIM analysis. J Mol Graph Model 2016; 68:14-22. [PMID: 27337388 DOI: 10.1016/j.jmgm.2016.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 05/29/2016] [Accepted: 06/07/2016] [Indexed: 11/29/2022]
Abstract
A theoretical study at the level of density functional theory (DFT) was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond interactions, in the active site of enzyme human androsterone sulphotransferase (SULT2A1/ADT). Geometry optimization, interaction energy, (2)H, (14)N, and (17)O electric field gradient (EFG) tensors, (1)H, (13)C, (17)O, and (15)N chemical shielding (CS) tensors, Natural Bonding Orbital (NBO) analysis, and quantum theory of atoms in molecules (QTAIM) analysis of this active site were investigated. It was found that androsterone (ADT) is able to form hydrogen bonds with residues Ser80, Ile82, and His99 of the active site. The interaction energy calculations and NBO analysis revealed that the ADT molecule forms the strongest hydrogen bond with Ser80. Results revealed that ADT interacts with the other residues through electrostatic and Van der Waals interactions. Results showed that these hydrogen bonds influence on the calculated (2)H, (14)N, and (17)O quadrupole coupling constants (QCCs), as well as (1)H, (13)C, (17)O, and (15)N CS tensors. The magnitude of the QCC and CS changes at each nucleus depends directly on its amount of contribution to the hydrogen bond interaction.
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Affiliation(s)
- Elahe K Astani
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, 14115-175, Iran
| | - Emran Heshmati
- Department of Biology, Faculty of Science, Zanjan University, Zanjan, Iran
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Taiwan
| | - Nasser L Hadipour
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, 14115-175, Iran.
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15
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Jambrec D, Haddad R, Lauks A, Gebala M, Schuhmann W, Kokoschka M. DNA Intercalators for Detection of DNA Hybridisation: SCS(MI)-MP2 Calculations and Electrochemical Impedance Spectroscopy. Chempluschem 2016; 81:604-612. [DOI: 10.1002/cplu.201600173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Daliborka Jambrec
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Raoudha Haddad
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Anna Lauks
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Magdalena Gebala
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
- Department of Biochemistry; Stanford University; Stanford CA 94305 USA
| | - Wolfgang Schuhmann
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Malte Kokoschka
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
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16
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Astani E, Heshmati E, Chen CJ, Hadipour NL, Shekarsaraei S. Noncovalent intermolecular interactions between dehydroepiandrosterone and the active site of human dehydroepiandrosterone sulphotransferase: A density functional theory based treatment. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Hatstat AK, Morris M, Peterson LW, Cafiero M. Ab initio study of electronic interaction energies and desolvation energies for dopaminergic ligands in the catechol-O-methyltransferase active site. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J. Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures. J Chem Theory Comput 2015; 5:982-92. [PMID: 26609607 DOI: 10.1021/ct800508v] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Interactions between amino acid side chains play a crucial role both within a folded protein and between the interacting protein molecules. Here we have selected a representative set of 24 of the 400 (20 × 20) possible interacting side chain pairs based on data from Atlas of Protein Side-Chain Interactions. For each pair, we obtained its most favorable interaction geometry from the structural data and computed the interaction energy in the gas phase using several different, commonly used, ab initio and force field methods, namely Møller-Plesset perturbation theory (MP2), density functional theory combined with symmetry-adapted perturbation theory (DFT-SAPT), density functional theory empirically augmented with an empirical dispersion term (DFT-D), and empirical potentials using the OPLS-AA/L and Amber03 force fields. All the methods were compared against a reference method taken to be the CCSD(T) level of theory extrapolated to the complete basis set limit. We found a high degree of agreement between the different methods, even though the range of binding energies obtained was extremely large. The most computationally intensive methods yielded the best results. Among the less computationally time-consuming methods, the DFT-D method as well as parm03 force field provided consistently good results when compared to the reference values. We also tested how representative the chosen geometries of the side chains were and investigated the effect on the binding energies of the dielectric constant of the surrounding medium.
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Affiliation(s)
- Karel Berka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Roman Laskowski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Kevin E Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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19
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Wolters LP, Koekkoek R, Bickelhaupt FM. Role of Steric Attraction and Bite-Angle Flexibility in Metal-Mediated C–H Bond Activation. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01354] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lando P. Wolters
- Department
of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Rick Koekkoek
- Department
of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - F. Matthias Bickelhaupt
- Department
of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
- Institute
for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg
135, NL-6525 AJ
Nijmegen, The Netherlands
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20
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Interplay of micro- and macroscopic solvation in spectral responses of PACO in 1,4-dioxane–water mixtures: A combined experimental and quantum chemical analysis. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2015.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Bigler DJ, Peterson LW, Cafiero M. Effects of implicit solvent and relaxed amino acid side chains on the MP2 and DFT calculations of ligand–protein structure and electronic interaction energies of dopaminergic ligands in the SULT1A3 enzyme active site. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Yurenko YP, Novotný J, Mitoraj MP, Sklenář V, Michalak A, Marek R. Nucleic Acid Quadruplexes Based on 8-Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex Stems. J Chem Theory Comput 2014; 10:5353-65. [DOI: 10.1021/ct5007554] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yevgen P. Yurenko
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
| | - Jan Novotný
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mariusz P. Mitoraj
- Department
of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Krakow PL-30060, Poland
| | - Vladimir Sklenář
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00 Brno, Czech Republic
| | - Artur Michalak
- Department
of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Krakow PL-30060, Poland
| | - Radek Marek
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00 Brno, Czech Republic
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23
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Carter DJ, Rohl AL. van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface. J Comput Chem 2014. [DOI: 10.1002/jcc.23745] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Damien J. Carter
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
| | - Andrew L. Rohl
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
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24
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Gao D, Lang D, Robinson T. Computational study of the thermodynamic stabilities of hydrogen-bonded complexes in solution. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1577-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Carter DJ, Rohl AL. Benchmarking Calculated Lattice Parameters and Energies of Molecular Crystals Using van der Waals Density Functionals. J Chem Theory Comput 2014; 10:3423-37. [DOI: 10.1021/ct500335b] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Damien J. Carter
- Nanochemistry
Research Institute
and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
| | - Andrew L. Rohl
- Nanochemistry
Research Institute
and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
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26
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Fromm A, van Wüllen C, Hackenberger D, Gooßen LJ. Mechanism of Cu/Pd-Catalyzed Decarboxylative Cross-Couplings: A DFT Investigation. J Am Chem Soc 2014; 136:10007-23. [DOI: 10.1021/ja503295x] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Andreas Fromm
- Fachbereich Chemie and Forschungszentrum
OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany
| | - Christoph van Wüllen
- Fachbereich Chemie and Forschungszentrum
OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany
| | - Dagmar Hackenberger
- Fachbereich Chemie and Forschungszentrum
OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany
| | - Lukas J. Gooßen
- Fachbereich Chemie and Forschungszentrum
OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany
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27
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Kabanda MM, Ebenso EE. MP2, DFT and DFT-D study of the dimers of diazanaphthalenes: a comparative study of their structures, stabilisation and binding energies. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.852191] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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KABANDA MWADHAMM, EBENSO ENOE. DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.
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Affiliation(s)
- MWADHAM M. KABANDA
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
| | - ENO E. EBENSO
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
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29
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Barone G, Fonseca Guerra C, Bickelhaupt FM. B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands. ChemistryOpen 2013; 2:186-93. [PMID: 24551565 PMCID: PMC3892189 DOI: 10.1002/open.201300019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Indexed: 11/16/2022] Open
Abstract
We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)2 <d(CpA)2 <d(ApT)2 <d(ApA)2 <d(GpT)2 <d(GpA)2 <d(ApG)2 <d(CpG)2 <d(GpG)2 <d(GpC)2, where the energy differences between the last four dimers, d(ApG)2, d(CpG)2, d(GpG)2 and d(GpC)2, is within 4.0 kcal mol−1, and the energy between the most and the least stable isomers is 13.4 kcal mol−1. This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5’- to the 3’-end.
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Affiliation(s)
- Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università di Palermo Viale delle Scienze, Edificio 17, 90128, Palermo (Italy) E-mail:
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands) E-mail:
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands) E-mail: ; Institute for Molecules and Materials, Radboud University Nijmegen Heyendaalseweg 135, 6525 AJ Nijmegen (The Netherlands)
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30
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MP2//DFT calculations of interaction energies between acetaminophen and acetaminophen analogues and the aryl sulfotransferase active site. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Schmidt S, Abkai G, Rosendahl T, Rominger F, Hofmann P. Inter- and Intramolecular Interactions in Triptycene-Derived Bisphosphite Hydroformylation Catalysts: Structures, Energies, and Caveats for DFT-Assisted Ligand Design. Organometallics 2013. [DOI: 10.1021/om301027x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Schmidt
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld
270, D-69120 Heidelberg, Germany
| | - Golnar Abkai
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld
270, D-69120 Heidelberg, Germany
| | - Tobias Rosendahl
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld
270, D-69120 Heidelberg, Germany
- Catalysis Research Laboratory
(CaRLa), Universität Heidelberg,
Im Neuenheimer Feld 584, D-69120 Heidelberg, Germany
| | - Frank Rominger
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld
270, D-69120 Heidelberg, Germany
| | - Peter Hofmann
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld
270, D-69120 Heidelberg, Germany
- Catalysis Research Laboratory
(CaRLa), Universität Heidelberg,
Im Neuenheimer Feld 584, D-69120 Heidelberg, Germany
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32
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Yang Q, Xing H, Su B, Bao Z, Wang J, Yang Y, Ren Q. The essential role of hydrogen-bonding interaction in the extractive separation of phenolic compounds by ionic liquid. AIChE J 2012. [DOI: 10.1002/aic.13939] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qiwei Yang
- Key Laboratory of Biomass Chemical Engineering; Ministry of Education; Dept. of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Huabin Xing
- Key Laboratory of Biomass Chemical Engineering; Ministry of Education; Dept. of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Baogen Su
- Key Laboratory of Biomass Chemical Engineering; Ministry of Education; Dept. of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Zongbi Bao
- Key Laboratory of Biomass Chemical Engineering; Ministry of Education; Dept. of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Jun Wang
- Key Laboratory of Biomass Chemical Engineering; Ministry of Education; Dept. of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Yiwen Yang
- Key Laboratory of Biomass Chemical Engineering; Ministry of Education; Dept. of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
| | - Qilong Ren
- Key Laboratory of Biomass Chemical Engineering; Ministry of Education; Dept. of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 China
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33
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Extensive theoretical investigation: influence of the electrostatic environment on the I3 −···I3 − anion–anion interaction. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1281-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Meliá C, Ferrer S, Moliner V, Tuñón I, Bertrán J. Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution. J Comput Chem 2012; 33:1948-59. [DOI: 10.1002/jcc.23030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 04/10/2012] [Accepted: 04/13/2012] [Indexed: 11/10/2022]
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35
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Cerón-Carrasco JP, Requena A, Jacquemin D. Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1188-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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36
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Carter DJ, Rohl AL. Noncovalent Interactions in SIESTA Using the vdW-DF Functional: S22 Benchmark and Macrocyclic Structures. J Chem Theory Comput 2011; 8:281-9. [DOI: 10.1021/ct200679b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Damien J. Carter
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, 26 Dick Perry Avenue, Technology Park, Kensington, WA, Australia 6151
| | - Andrew L. Rohl
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, 26 Dick Perry Avenue, Technology Park, Kensington, WA, Australia 6151
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37
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Fonseca Guerra C, Zijlstra H, Paragi G, Bickelhaupt FM. Telomere Structure and Stability: Covalency in Hydrogen Bonds, Not Resonance Assistance, Causes Cooperativity in Guanine Quartets. Chemistry 2011; 17:12612-22. [DOI: 10.1002/chem.201102234] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Indexed: 11/06/2022]
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38
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Araque JC, Panagiotopoulos AZ, Robert MA. Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics. J Chem Phys 2011; 134:165103. [PMID: 21528982 DOI: 10.1063/1.3568145] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A coarse-grained lattice model of DNA oligonucleotides is proposed to investigate the general mechanisms by which single-stranded oligonucleotides hybridize to their complementary strands in solution. The model, based on a high-coordination cubic lattice, is simple enough to allow the direct simulation of DNA solutions, yet capturing how the fundamental thermodynamic processes are microscopically encoded in the nucleobase sequences. Physically relevant interactions are considered explicitly, such as interchain excluded volume, anisotropic base-pairing and base-stacking, and single-stranded bending rigidity. The model is studied in detail by a specially adapted Monte Carlo simulation method, based on parallel tempering and biased trials, which is designed to overcome the entropic and enthalpic barriers associated with the sampling of hybridization events of multiple single-stranded chains in solution. This methodology addresses both the configurational complexity of bringing together two complementary strands in a favorable orientation (entropic barrier) and the energetic penalty of breaking apart multiple associated bases in a double-stranded state (enthalpic barrier). For strands with sequences restricted to nonstaggering association and homogeneous pairing and stacking energies, base-pairing is found to dominate the hybridization over the translational and conformational entropy. For strands with sequence-dependent pairing corresponding to that of DNA, the complex dependence of the model's thermal stability on concentration, sequence, and degree of complementarity is shown to be qualitatively and quantitatively consistent both with experiment and with the predictions of statistical mechanical models.
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Affiliation(s)
- Juan C Araque
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
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39
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Ababneh-Khasawneh M, Fortier-McGill BE, Occhionorelli ME, Bain AD. Solvent Effects on Chemical Exchange in a Push–Pull Ethylene as Studied by NMR and Electronic Structure Calculations. J Phys Chem A 2011; 115:7531-7. [PMID: 21627168 DOI: 10.1021/jp201885q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Blythe E. Fortier-McGill
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada L8S 4M1
| | - Marzia E. Occhionorelli
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada L8S 4M1
| | - Alex D. Bain
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada L8S 4M1
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π-π interaction of quinacridone derivatives. J Comput Chem 2011; 32:2055-63. [DOI: 10.1002/jcc.21782] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 01/05/2011] [Accepted: 02/09/2011] [Indexed: 11/07/2022]
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Riley KE, Hobza P. Noncovalent interactions in biochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin E. Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
- Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
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Mahadevi AS, Neela YI, Sastry GN. A theoretical study on structural, spectroscopic and energetic properties of acetamide clusters [CH3CONH2] (n = 1–15). Phys Chem Chem Phys 2011; 13:15211-20. [DOI: 10.1039/c1cp21346f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Utkov H, Livengood M, Cafiero M. Using Density Functional Theory Methods for Modeling Induction and Dispersion Interactions in Ligand–Protein Complexes. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2010. [DOI: 10.1016/s1574-1400(10)06007-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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van der Wijst T, Lippert B, Swart M, Guerra CF, Bickelhaupt FM. Differential stabilization of adenine quartets by anions and cations. J Biol Inorg Chem 2009; 15:387-97. [PMID: 19943071 PMCID: PMC2830606 DOI: 10.1007/s00775-009-0611-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 10/26/2009] [Indexed: 11/29/2022]
Abstract
We have investigated the structures and stabilities of four different adenine quartets with alkali and halide ions in the gas phase and in water, using dispersion-corrected density functional theory at the BLYP-D/TZ2P level. First, we examine the empty quartets and how they interact with alkali cations and halide anions with formation of adenine quartet–ion complexes. Second, we examine the interaction in a stack, in which a planar adenine quartet interacts with a cation or anion in the periphery as well as in the center of the quartet. Interestingly, for the latter situation, we find that both cations and anions can stabilize a planar adenine quartet in a stack.
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Affiliation(s)
- Tushar van der Wijst
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
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Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0634-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Peverati R, Baldridge KK. Implementation and Optimization of DFT-D/COSab with Respect to Basis Set and Functional: Application to Polar Processes of Furfural Derivatives in Solution. J Chem Theory Comput 2009; 5:2772-86. [DOI: 10.1021/ct900363n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Roberto Peverati
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Kim K. Baldridge
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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de Hoog P, Robertazzi A, Mutikainen I, Turpeinen U, Gamez P, Reedijk J. An Electron-Poor Host Receptor for Electron-Rich Guests Involving Anion-π and Lone-Pair-π Interactions. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900183] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Berka K, Hobza P, Vondrášek J. Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin. Chemphyschem 2009; 10:543-8. [DOI: 10.1002/cphc.200800401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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