1
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Complex investigation of H-bond in Water-N-methylacetamide system: Volumetric properties, DFT, IR, MD analysis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2
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Jian C, Wang Y, Liu H, Yin Z. A biotin-modified and H 2O 2-activatable theranostic nanoplatform for enhanced photothermal and chemical combination cancer therapy. Eur J Pharm Biopharm 2022; 177:24-38. [PMID: 35667614 DOI: 10.1016/j.ejpb.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022]
Abstract
Although synergistic effects of photothermal therapy (PTT) and chemotherapy for cancer have been extensively investigated in previous studies, more potential strategies need to be exploited to alleviate severe adverse effects. In this study, a biotin-modified and activatable nanotheranostic system is developed. This system (BPSP/DOX-CyBA) composed of H2O2-sensitive thioketal (TK) linker, hydrophilic biotin-decorated polyethylene glycol (PEG) segment, hydrophobic polycaprolactone (PCL) segment, could self-assemble into (99±1.3) nm nanoparticles and co-deliver H2O2-triggered photosensitizer CyBA and cytotoxic drugs DOX to tumor site. In vitro, DOX and CyBA could release rapidly from nanoparticles, CyBA accumulation in the mitochondria causes mitochondrial damage, leading to mitochondrial dysfunctions,while rising the level of ROS in B16F10 cells, and further to promote the micells to trigger release. CyBA could be activated into CyOH and the photothermal therapy was turn "off" into "on". In BPSP/DOX-CyBA group, the local temperature within tumor reached 50℃ and cell apoptosis rate reached 68.6% under Laser irradiation(650 nm, 1W/cm2). Fluorescence microscopy and flow cytometry analysis further demonstrated the better uptake efficiency on B16F10 cells with biotin decoration. In a mice B16F10 tumor model, the group with co-delivery CyBA and DOX had the best tumor retention effect, the maximal local temperature increasement and the minimum tumor growth with negligible side effects, suggesting the potential of BPSP/DOX-CyBA nanopalteform that synergistic photothermal therapy and chemotherapy and mitochondria damage as an effective melanoma treatment strategy.
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Affiliation(s)
- Chuanjiang Jian
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ying Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Huijun Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Zongning Yin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
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3
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M, Cabezas C, León I, Alonso JL. Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group. Phys Chem Chem Phys 2021; 22:20284-20294. [PMID: 32966425 DOI: 10.1039/d0cp03136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.
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Affiliation(s)
- Gildas Goldsztejn
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - José Luis Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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4
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Panuszko A, Stangret J, Nowosielski B, Bruździak P. Interactions between hydration spheres of two different solutes in solution: The least squares fitting with constraints as a tool to determine water properties in ternary systems. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Brenner V, Gloaguen E, Mons M. Rationalizing the diversity of amide-amide H-bonding in peptides using the natural bond orbital method. Phys Chem Chem Phys 2019; 21:24601-24619. [PMID: 31670335 DOI: 10.1039/c9cp03825f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural bond orbital (NBO) analysis of electron delocalization in a series of capped isolated peptides is used to diagnose amide-amide H-bonding and backbone-induced hyperconjugative interactions, and to rationalize their spectral effects. The sum of the stabilization energies corresponding to the interactions between NBOs that are involved in the H-bonding is demonstrated as an insightful indicator for the H-bond strength. It is then used to decouple the effect of the H-bond distance from that, intrinsic, of the donor/acceptor relative orientation, i.e., the geometrical approach. The diversity of the approaches given by the series of peptides studied enables us to illustrate the crucial importance of the approach when the acceptor is a carbonyl group, and emphasizes that efficient approaches can be achieved despite not matching the usual picture of a proton donor directly facing a lone pair of the proton acceptor, i.e., that encountered in intermolecular H-bonds. The study also illustrates the role of backbone flexibility, partly controlled by backbone-amide hyperconjugative interactions, in influencing the equilibrium structures, in particular by frustrating or enhancing the HB for a given geometrical approach. Finally, the presently used NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor amide NH stretching mode, but this simple picture is blurred by ubiquitous hyperconjugative effects between the backbone and amide groups, whose magnitude can be comparable to that of the weakest H-bonds.
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Affiliation(s)
- Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
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6
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Kotov N, Raus V, Dybal J. Intermolecular Interactions in N, N-Dimethylacetamide without and with LiCl Studied by Infrared Spectroscopy and Quantum Chemical Model Calculations. J Phys Chem B 2018; 122:8921-8930. [PMID: 30179487 DOI: 10.1021/acs.jpcb.8b05569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mixture of LiCl and N, N-dimethylacetamide (DMAc) is an important laboratory-scale solvent for cellulose. However, the mechanism of cellulose dissolution in DMAc/LiCl could not be fully established due to the limited knowledge about the interactions between DMAc and LiCl. To address this issue, we studied neat DMAc and DMAc/LiCl mixtures by ATR FTIR spectroscopy and quantum chemical model calculations. On the basis of the calculations, we newly assigned the bands at 1660 and 1642 cm-1 in the ν(C═O) region of the spectra to DMAc monomeric and dimeric structures. The latter are presumably stabilized by the C-H···O═C weak hydrogen bonds that prevail in both neat DMAc and DMAc/LiCl mixtures. The analysis of the concentrated (7.9 wt % of LiCl) DMAc/LiCl mixture revealed that only about half of DMAc molecules interact directly with LiCl. The resulting average stoichiometry of about 2.8:1 (DMAc:LiCl), indicating the predominance of [(DMAc)2-LiCl] and [(DMAc)3-LiCl] complexes, was found to be temperature independent. Conversely, the stoichiometry was considerably temperature sensitive for the diluted DMAc/LiCl mixture (2.6 wt % of LiCl), indicating that further DMAc molecules can be incorporated into the primary solvation shell of LiCl at higher temperatures. These results highlight the dynamic character of the DMAc/LiCl system that needs to be considered when studying the cellulose dissolution mechanism.
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Affiliation(s)
- Nikolay Kotov
- Institute of Macromolecular Chemistry , Academy of Sciences of the Czech Republic , Heyrovsky Sq. 2 , 162 06 Prague 6 , Czech Republic
| | - Vladimír Raus
- Institute of Macromolecular Chemistry , Academy of Sciences of the Czech Republic , Heyrovsky Sq. 2 , 162 06 Prague 6 , Czech Republic
| | - Jiří Dybal
- Institute of Macromolecular Chemistry , Academy of Sciences of the Czech Republic , Heyrovsky Sq. 2 , 162 06 Prague 6 , Czech Republic
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7
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Magnetic Nanoparticles Conjugated with Peptides Derived from Monocyte Chemoattractant Protein-1 as a Tool for Targeting Atherosclerosis. Pharmaceutics 2018; 10:pharmaceutics10020062. [PMID: 29795012 PMCID: PMC6027309 DOI: 10.3390/pharmaceutics10020062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/21/2018] [Accepted: 05/21/2018] [Indexed: 12/26/2022] Open
Abstract
Atherosclerosis is a multifactorial inflammatory disease that may progress silently for long period, and it is also widely accepted as the main cause of cardiovascular diseases. To prevent atherosclerotic plaques from generating, imaging early molecular markers and quantifying the extent of disease progression are desired. During inflammation, circulating monocytes leave the bloodstream and migrate into incipient lipid accumulation in the artery wall, following conditioning by local growth factors and proinflammatory cytokines; therefore, monocyte accumulation in the arterial wall can be observed in fatty streaks, rupture-prone plaques, and experimental atherosclerosis. In this work, we synthesized monocyte-targeting iron oxide magnetic nanoparticles (MNPs), which were incorporated with the peptides derived from the chemokine receptor C-C chemokine receptor type 2 (CCR2)-binding motif of monocytes chemoattractant protein-1 (MCP-1) as a diagnostic tool for potential atherosclerosis. MCP-1-motif MNPs co-localized with monocytes in in vitro fluorescence imaging. In addition, with MNPs injection in ApoE knockout mice (ApoE KO mice), the well-characterized animal model of atherosclerosis, MNPs were found in specific organs or regions which had monocytes accumulation, especially the aorta of atherosclerosis model mice, through in vivo imaging system (IVIS) imaging and magnetic resonance imaging (MRI). We also performed Oil Red O staining and Prussian Blue staining to confirm the co-localization of MCP-1-motif MNPs and atherosclerosis. The results showed the promising potential of MCP-1-motif MNPs as a diagnostic agent of atherosclerosis.
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8
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Diaferia C, Sibillano T, Altamura D, Roviello V, Vitagliano L, Giannini C, Morelli G, Accardo A. Structural Characterization of PEGylated Hexaphenylalanine Nanostructures Exhibiting Green Photoluminescence Emission. Chemistry 2017; 23:14039-14048. [PMID: 28782843 DOI: 10.1002/chem.201703055] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Indexed: 12/31/2022]
Abstract
Peptides containing aromatic residues are known to exhibit spontaneous phenomena of supramolecular organization into ordered nanostructures (NSs). In this work we studied the structural behavior and optoelectronic properties of new biocompatible materials obtained by the self-assembly of a series of hexaphenylalanines (F6) modified at the N terminus by a PEG chain of different lengths. PEG12 -F6, PEG18 -F6, and PEG24 -F6 peptides were synthesized by coupling sequentially two, three, or four units of amino-carboxy-PEG6 blocks, each one containing six oxyethylene repetitions. Changes in the length and composition of the PEG chain were found to modulate the structural organization of the phenylalanine-based nanostructures. An increase in the self-aggregation tendency was observed with longer PEG chains, whereas, independently of the PEG length, the peptide NSs display cross-β-like secondary structures with an antiparallel β-strand arrangement. WAXS/GIWAXS diffraction patterns indicate a progressive decrease in fiber order along the series. All the PEG-F6 derivatives present blue photoluminescent (PL) emission at 460 nm, with the adduct with the longest PEG chain (PEG24 -F6) showing an additional green emission at 530 nm.
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Affiliation(s)
- Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Davide Altamura
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and Centro Servizi Metrologici Avanzati, University of Naples "Federico II", Corso Nicolangelo Protopisani, 80146, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
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9
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Abstract
The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group. Mixing of these orbitals releases energy, resulting in an attractive interaction. Hints of such interactions were evident in small-molecule crystal structures as early as the 1970s, but not until 2001 was the role of such interactions articulated clearly. These non-covalent interactions were first discovered during investigations into the thermostability of the proline-rich protein collagen, which achieves a robust structure despite a relatively low potential for hydrogen bonding. It was found that by modulating the distance between two carbonyl groups in the peptide backbone, one could alter the conformational preferences of a peptide bond to proline. Specifically, only the trans conformation of a peptide bond to proline allows for an attractive interaction with an adjacent carbonyl group, so when one increases the proximity of the two carbonyl groups, one enhances their interaction and promotes the trans conformation of the peptide bond, which increases the thermostability of collagen. More recently, attention has been paid to the nature of these interactions. Some have argued that rather than resulting from electron donation, carbonyl interactions are a particular example of dipolar interactions that are well-approximated by classical mechanics. However, experimental evidence has demonstrated otherwise. Numerous examples now exist where an increase in the dipole moment of a carbonyl group decreases the strength of its interactions with other carbonyl groups, demonstrating unequivocally that a dipolar mechanism is insufficient to describe these interactions. Rather, these interactions have important quantum-mechanical character that can be evaluated through careful experimental analysis and judicious use of computation. Although individual n→π* interactions are relatively weak (∼0.3-0.7 kcal/mol), the ubiquity of carbonyl groups across chemistry and biology gives the n→π* interaction broad impact. In particular, the n→π* interaction is likely to play an important role in dictating protein structure. Indeed, bioinformatics analysis suggests that approximately one-third of residues in folded proteins satisfy the geometric requirements to engage in an n→π* interaction, which is likely to be of particular importance for the α-helix. Other carbonyl-dense polymeric materials like polyesters and peptoids are also influenced by n→π* interactions, as are a variety of small molecules, some with particular medicinal importance. Research will continue to identify molecules whose conformation and activity are affected by the n→π* interaction and will clarify their specific contributions to the structures of biomacromolecules.
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Affiliation(s)
- Robert W. Newberry
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
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10
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Zeng ZY, Wang YS, Chao SD. Hydrogen bonded dimers of small alkyl substituted amides: Structures, energetics, and spectral analyses based on density functional theory calculations. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Forsting T, Gottschalk HC, Hartwig B, Mons M, Suhm MA. Correcting the record: the dimers and trimers of trans-N-methylacetamide. Phys Chem Chem Phys 2017; 19:10727-10737. [DOI: 10.1039/c6cp07989j] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman jet spectroscopy reveals three N-methylacetamide molecules organizing into a ring structure, previously overlooked in computations.
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Affiliation(s)
- Thomas Forsting
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | | | - Beppo Hartwig
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Michel Mons
- LIDYL; CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
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12
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Zierkiewicz W, Fanfrlík J, Hobza P, Michalska D, Zeegers-Huyskens T. Ab initio and DFT studies of the interaction between carbonyl and thiocarbonyl groups: the role of S···O chalcogen bonds. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1972-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Yuan C, Wu H, Jia M, Su P, Luo Z, Yao J. A theoretical study of weak interactions in phenylenediamine homodimer clusters. Phys Chem Chem Phys 2016; 18:29249-29257. [DOI: 10.1039/c6cp04922b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.
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Affiliation(s)
- Chengqian Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Haiming Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Meiye Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Peifeng Su
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Zhixun Luo
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Jiannian Yao
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
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14
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Dissection of the Factors Affecting Formation of a CH∙∙∙O H-Bond. A Case Study. CRYSTALS 2015. [DOI: 10.3390/cryst5030327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Esquivel RO, Molina-Espíritu M, López-Rosa S, Soriano-Correa C, Barrientos-Salcedo C, Kohout M, Dehesa JS. Predominant information quality scheme for the essential amino acids: an information-theoretical analysis. Chemphyschem 2015; 16:2571-81. [PMID: 26175003 DOI: 10.1002/cphc.201500282] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/11/2015] [Indexed: 11/05/2022]
Abstract
In this work we undertake a pioneer information-theoretical analysis of 18 selected amino acids extracted from a natural protein, bacteriorhodopsin (1C3W). The conformational structures of each amino acid are analyzed by use of various quantum chemistry methodologies at high levels of theory: HF, M062X and CISD(Full). The Shannon entropy, Fisher information and disequilibrium are determined to grasp the spatial spreading features of delocalizability, order and uniformity of the optimized structures. These three entropic measures uniquely characterize all amino acids through a predominant information-theoretic quality scheme (PIQS), which gathers all chemical families by means of three major spreading features: delocalization, narrowness and uniformity. This scheme recognizes four major chemical families: aliphatic (delocalized), aromatic (delocalized), electro-attractive (narrowed) and tiny (uniform). All chemical families recognized by the existing energy-based classifications are embraced by this entropic scheme. Finally, novel chemical patterns are shown in the information planes associated with the PIQS entropic measures.
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Affiliation(s)
- Rodolfo O Esquivel
- Departamento de Química, Universidad Autónoma Metropolitana, 09340-México, D.F. (México). .,Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, 18071-Granada (Spain).
| | | | - Sheila López-Rosa
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, 18071-Granada (Spain).,Departamento de Física Aplicada II, Universidad de Sevilla, 41012-Sevilla (Spain)
| | - Catalina Soriano-Correa
- Laboratorio de Química Computacional, FES-Zaragoza, Universidad Nacional Autónoma de México, 09230-Iztapalapa, México, D.F. (México)
| | - Carolina Barrientos-Salcedo
- Facultad de Bioanálisis-Veracruz, Universidad Veracruzana, Laboratorio de Química Médica y Quimiogenómica, 91700-Veracruz (México)
| | - Miroslav Kohout
- Max Planck Institute for Chemical Physics of Solids, Noethnitzer Str. 40, 01187-Dresden (Germany)
| | - Jesús S Dehesa
- Departamento de Física Atómica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain)
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16
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Importance of asparagine on the conformational stability and chemical reactivity of selected anti-inflammatory peptides. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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17
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Crespo-Otero R, Mardykov A, Sanchez-Garcia E, Sander W, Barbatti M. Photo-stability of peptide-bond aggregates: N-methylformamide dimers. Phys Chem Chem Phys 2015; 16:18877-87. [PMID: 25081138 DOI: 10.1039/c4cp02518k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The formation of weakly-bound dimers of N-methylformamide (NMF) and the photochemistry of these dimers after irradiation at 248 nm were explored using matrix-isolation spectroscopy. Calculations were used to characterize the diverse isomers and assign their IR spectra; non-adiabatic dynamics was simulated to understand their photo-deactivation mechanism. The most stable dimers, and , were obtained by trans-trans aggregation (N-HO[double bond, length as m-dash]C interactions) and could be identified in the matrix. The main products formed after irradiation are the trans-cis dimers ( and ), also stabilized by N-HO[double bond, length as m-dash]C interactions. In contrast to the photochemistry of the monomers, no dissociative products were observed after 248 nm irradiation of the dimers. The absence of dissociative products can be explained by a proton-transfer mechanism in the excited state that is faster than the photo-dissociative mechanism. The fact that hydrogen bonding has such a significant effect on the photochemical stability of NMF has important implications to understand the stability of peptide-bonded systems to UV irradiation.
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Affiliation(s)
- Rachel Crespo-Otero
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilheim-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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18
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Azofra LM. Towards an understanding of the CO2-philicity in glycine: Deepening into the CO2:Aminoacid interactions. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Adhikari U, Scheiner S. Effects of Charge and Substituent on the S···N Chalcogen Bond. J Phys Chem A 2014; 118:3183-92. [DOI: 10.1021/jp501449v] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Upendra Adhikari
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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20
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Azofra LM, Scheiner S. Complexes containing CO2and SO2. Mixed dimers, trimers and tetramers. Phys Chem Chem Phys 2014; 16:5142-9. [DOI: 10.1039/c3cp55489a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two stable minima for the 1 : 1 heterodimer of CO2 : SO2, both bound by about 2 kcal mol−1. Binding is dominated by charge transfer from O lone pairs of SO2to CO π* antibonding orbitals.
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Affiliation(s)
- Luis Miguel Azofra
- Instituto de Química Médica
- CSIC
- Juan de la Cierva
- Madrid, Spain
- Department of Chemistry and Biochemistry
| | - Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan, USA
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21
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Esrafili MD, Yourdkhani S, Bahrami A. Characteristics and nature of the halogen-bonding interactions between CCl3F and ozone: a supermolecular and SAPT study. Mol Phys 2013. [DOI: 10.1080/00268976.2013.788740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Hauchecorne D, Herrebout WA. Experimental Characterization of C–X···Y–C (X = Br, I; Y = F, Cl) Halogen–Halogen Bonds. J Phys Chem A 2013; 117:11548-57. [DOI: 10.1021/jp4077323] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dieter Hauchecorne
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Wouter A. Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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23
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Horowitz S, Dirk LMA, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. J Am Chem Soc 2013; 135:15536-48. [PMID: 24093804 DOI: 10.1021/ja407140k] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon-oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.
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Affiliation(s)
- Scott Horowitz
- Howard Hughes Medical Institute , Ann Arbor, Michigan 48109, United States
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Witts RN, Hopson EC, Koballa DE, Van Boening TA, Hopkins NH, Patterson EV, Nagan MC. Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure. J Phys Chem B 2013; 117:7489-97. [PMID: 23742318 DOI: 10.1021/jp400084p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transfer RNA (tRNA) anticodons adopt a highly ordered 3'-stack without significant base overlap. Density functional theory at the M06-2X/6-31+G(d,p) level in combination with natural bond orbital analysis was utilized to calculate the intramolecular interactions within the tRNA anticodon that are responsible for stabilizing the stair-stepped conformation. Ten tRNA X-ray crystal structures were obtained from the PDB databank and were trimmed to include only the anticodon bases. Hydrogenic positions were added and optimized for the structures in the stair-stepped conformation. The sugar-phosphate backbone has been retained for these calculations, revealing the role it plays in RNA structural stability. It was found that electrostatic interactions between the sugar-phosphate backbone and the base provide the most stability, rather than the traditionally studied interbase stacking. Base-stacking interactions, though present, were weak and inconsistent. Aqueous solvation was found to have little effect on the intramolecular interactions.
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Affiliation(s)
- Rachel N Witts
- Department of Chemistry, Truman State University, 100 East Normal, Kirksville, Missouri 63501, USA
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