1
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Yu F. Origins of the unphysical noncovalent interaction energy curves obtained with the 2011 and 2012 Minnesota density functionals. J Chem Phys 2024; 160:214120. [PMID: 38836783 DOI: 10.1063/5.0212534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024] Open
Abstract
With the noncovalent interaction energy curves of the methane dimer [(CH4)2], we have clarified two different origins of the unphysical noncovalent interaction energy curves obtained with the Minnesota density functionals of M11-L, MN12-L, and MN12-SX. For the M11-L functional, the unphysical inflection point on the (CH4)2 interaction energy curve originates from the inclusion of the long-range exchange. As to the MN12-L and MN12-SX functionals, the lack of smoothness restraints results in unphysical inflection points on the corresponding (CH4)2 interaction energy curves. As a result, exchange functionals are as important as dispersion corrections for density functionals to map noncovalent interaction energy surfaces reasonably. Moreover, very highly parameterized functionals with smoothness restraints are suggested for investigating noncovalent interaction energy surfaces.
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Affiliation(s)
- Feng Yu
- Department of Physics, School of Freshmen, Xi'an Technological University, No. 4 Jinhua North Road, Xi'an, Shaanxi 710032, China
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2
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Montejo-López W, Sampieri-Cabrera R, Nicolás-Vázquez MI, Aceves-Hernández JM, Razo-Hernández RS. Analysing the effect caused by increasing the molecular volume in M1-AChR receptor agonists and antagonists: a structural and computational study. RSC Adv 2024; 14:8615-8640. [PMID: 38495977 PMCID: PMC10938299 DOI: 10.1039/d3ra07380g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
M1 muscarinic acetylcholine receptor (M1-AChR), a member of the G protein-coupled receptors (GPCR) family, plays a crucial role in learning and memory, making it an important drug target for Alzheimer's disease (AD) and schizophrenia. M1-AChR activation and deactivation have shown modifying effects in AD and PD preclinical models, respectively. However, understanding the pharmacology associated with M1-AChR activation or deactivation is complex, because of the low selectivity among muscarinic subtypes, hampering their therapeutic applications. In this regard, we constructed two quantitative structure-activity relationship (QSAR) models, one for M1-AChR agonists (total and partial), and the other for the antagonists. The binding mode of 59 structurally different compounds, including agonists and antagonists with experimental binding affinity values (pKi), were analyzed employing computational molecular docking over different structures of M1-AChR. Furthermore, we considered the interaction energy (Einter), the number of rotatable bonds (NRB), and lipophilicity (ilogP) for the construction of the QSAR model for agonists (R2 = 89.64, QLMO2 = 78, and Qext2 = 79.1). For the QSAR model of antagonists (R2 = 88.44, QLMO2 = 82, and Qext2 = 78.1) we considered the Einter, the fraction of sp3 carbons fCsp3, and lipophilicity (MlogP). Our results suggest that the ligand volume is a determinant to establish its biological activity (agonist or antagonist), causing changes in binding energy, and determining the affinity for M1-AChR.
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Affiliation(s)
- Wilber Montejo-López
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México Avenida 1o de Mayo s/n, Colonia Santa María las Torres Cuautitlán Izcalli Estado de Mexico 54740 Mexico
| | - Raúl Sampieri-Cabrera
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Centro de Ciencias de Complejidad, Universidad Nacional Autónoma de México Mexico
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México Avenida 1o de Mayo s/n, Colonia Santa María las Torres Cuautitlán Izcalli Estado de Mexico 54740 Mexico
| | - Juan Manuel Aceves-Hernández
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México Cuautitlán Izcalli Estado de Mexico 54714 Mexico
| | - Rodrigo Said Razo-Hernández
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos Av. Universidad 1001 Cuernavaca 62209 Mexico
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3
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Xiao Y, Woods RJ. Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation. J Chem Theory Comput 2023; 19:5503-5515. [PMID: 37493980 PMCID: PMC10448718 DOI: 10.1021/acs.jctc.3c00300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 07/27/2023]
Abstract
Here, we develop an empirical energy function based on quantum mechanical data for the interaction between methane and benzene that captures the contribution from CH-π interactions. Such interactions are frequently observed in protein-ligand crystal structures, particularly for carbohydrate ligands, but have been hard to quantify due to the absence of a model for CH-π interactions in typical molecular mechanical force fields or docking scoring functions. The CH-π term was added to the AutoDock Vina (AD VINA) scoring function enabling its performance to be evaluated against a cohort of more than 1600 occurrences in 496 experimental structures of protein-ligand complexes. By employing a conformational grid search algorithm, inclusion of the CH-π term was shown to improve the prediction of the preferred orientation of flexible ligands in protein-binding sites and to enhance the detection of carbohydrate-binding sites that display CH-π interactions. Last but not least, this term was also shown to improve docking performance for the CASF-2016 benchmark set and a carbohydrate set.
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Affiliation(s)
- Yao Xiao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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4
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Kleine Büning JB, Grimme S. Computation of CCSD(T)-Quality NMR Chemical Shifts via Δ-Machine Learning from DFT. J Chem Theory Comput 2023. [PMID: 37262324 DOI: 10.1021/acs.jctc.3c00165] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
NMR spectroscopy undoubtedly plays a central role in determining molecular structures across different chemical disciplines, and the accurate computational prediction of NMR parameters is highly desirable. In this work, a new Δ-machine learning approach is presented to correct DFT-computed NMR chemical shifts using input features from the calculation and in addition highly accurate reference data at the CCSD(T)/pcSseg-2 level of theory with a basis set extrapolation scheme. The model is trained on a data set containing 1000 optimized and geometrically distorted structures of small organic molecules comprising most elements of the first three periods and containing data for 7090 1H and 4230 13C NMR chemical shifts. Applied to the PBE0/pcSseg-2 method, the mean absolute deviation (MAD) on the internal NMR shift test set is reduced by 81% for 1H and 92% for 13C at virtually no additional computational cost. For 12 different DFT functional and basis set combinations, the MAD of the ML-corrected NMR shifts ranges from 0.021 to 0.039 ppm (1H) and from 0.38 to 1.07 ppm (13C). Importantly, the new method consistently outperforms the simple and widely used linear regression correction technique. This behavior is reproduced on three different external benchmark sets, confirming the generality and robustness of the correction scheme, which can easily be applied in DFT-based spectral simulations.
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Affiliation(s)
- Julius B Kleine Büning
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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5
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Ng SC, Biswas A, Huyton T, Schünemann J, Reber S, Görlich D. Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length. Nat Commun 2023; 14:747. [PMID: 36765044 PMCID: PMC9918544 DOI: 10.1038/s41467-023-36331-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Nup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We show that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier - all consistent with a sieve-like phase. Phase separation tolerates mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remains preserved. NTR-entry, however, is sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we observed that arginines promote FG-phase-entry apparently also by hydrophobic interactions/ hydrogen-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displays remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations make the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxes this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
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Affiliation(s)
- Sheung Chun Ng
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Abin Biswas
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Biological Optomechanics, Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Simone Reber
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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6
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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7
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Strom A, Shah R, Dolot R, Rogers MS, Tong CL, Wang D, Xia Y, Lipscomb JD, Wagner CR. Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and Activators of Antiviral ProTides. Biochemistry 2022; 61:2648-2661. [PMID: 36398895 PMCID: PMC9854251 DOI: 10.1021/acs.biochem.2c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human histidine triad nucleotide-binding (hHINT) proteins catalyze nucleotide phosphoramidase and acyl-phosphatase reactions that are essential for the activation of antiviral proTides, such as Sofosbuvir and Remdesivir. hHINT1 and hHINT2 are highly homologous but exhibit disparate roles as regulators of opioid tolerance (hHINT1) and mitochondrial activity (hHINT2). NMR studies of hHINT1 reveal a pair of dynamic surface residues (Q62, E100), which gate a conserved water channel leading to the active site 13 Å away. hHINT2 crystal structures identify analogous residues (R99, D137) and water channel. hHINT1 Q62 variants significantly alter the steady-state kcat and Km for turnover of the fluorescent substrate (TpAd), while stopped-flow kinetics indicate that KD also changes. hHINT2, like hHINT1, exhibits a burst phase of adenylation, monitored by fluorescent tryptamine release, prior to rate-limiting hydrolysis and nucleotide release. hHINT2 exhibits a much smaller burst-phase amplitude than hHINT1, which is further diminished in hHINT2 R99Q. Kinetic simulations suggest that amplitude variations can be accounted for by a variable fluorescent yield of the E·S complex from changes in the environment of bound TpAd. Isothermal titration calorimetry measurements of inhibitor binding show that these hHINT variants also alter the thermodynamic binding profile. We propose that these altered surface residues engender long-range dynamic changes that affect the orientation of bound ligands, altering the thermodynamic and kinetic characteristics of hHINT active site function. Thus, studies of the cellular roles and proTide activation potential by hHINTs should consider the importance of long-range interactions and possible protein binding surfaces far from the active site.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rachit Shah
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rafal Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Cher-Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David Wang
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Youlin Xia
- Department of Structural Biology, St. Jude’s Research Hospital, Memphis, Tennessee 38105, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Carston R. Wagner
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States,Address correspondence to: Carston R. Wagner, University of Minnesota, Department of Medicinal Chemistry, 2231 6th Street S.E., Cancer & Cardiovascular Research Building, Minneapolis, Minnesota 55455, USA,
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8
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Xie C, Kim J, Mai BK, Cao S, Ye R, Wang XY, Liu P, Kwon O. Enantioselective Synthesis of Quaternary Oxindoles: Desymmetrizing Staudinger-Aza-Wittig Reaction Enabled by a Bespoke HypPhos Oxide Catalyst. J Am Chem Soc 2022; 144:21318-21327. [PMID: 36375169 PMCID: PMC10746329 DOI: 10.1021/jacs.2c09421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper describes a catalytic asymmetric Staudinger-aza-Wittig reaction of (o-azidoaryl)malonates, allowing access to chiral quaternary oxindoles through phosphine oxide catalysis. We designed a novel HypPhos oxide catalyst to enable the desymmetrizing Staudinger-aza-Wittig reaction through the PIII/PV═O redox cycle in the presence of a silane reductant and an IrI-based Lewis acid. The reaction occurs under mild conditions, with good functional group tolerance, a wide substrate scope, and excellent enantioselectivity. Density functional theory revealed that the enantioselectivity in the desymmetrizing reaction arose from the cooperative effects of the IrI species and the HypPhos catalyst. The utility of this methodology is demonstrated by the (formal) syntheses of seven alkaloid targets: (-)-gliocladin C, (-)-coerulescine, (-)-horsfiline, (+)-deoxyeseroline, (+)-esermethole, (+)-physostigmine, and (+)-physovenine.
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Affiliation(s)
- Changmin Xie
- Department of Chemistry and Biochemistry, University of California─Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, California 90095-1569, United States
| | - Jacob Kim
- Department of Chemistry and Biochemistry, University of California─Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, California 90095-1569, United States
| | - Binh Khanh Mai
- Department of Chemistry and Biochemistry, University of California─Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, California 90095-1569, United States
| | - Shixuan Cao
- Department of Chemistry and Biochemistry, University of California─Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, California 90095-1569, United States
| | - Rong Ye
- Department of Chemistry and Biochemistry, University of California─Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, California 90095-1569, United States
| | - Xin-Yi Wang
- Department of Chemistry and Biochemistry, University of California─Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, California 90095-1569, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ohyun Kwon
- Department of Chemistry and Biochemistry, University of California─Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, California 90095-1569, United States
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9
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Benzene, an Unexpected Binding Unit in Anion–π Recognition: The Critical Role of CH/π Interactions. SCI 2022. [DOI: 10.3390/sci4030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We report high-level ab initio calculations (CCSD(T)(full)/CBS//SCS-RI-MP2(full)/aug-cc-pwCVTZ) that demonstrate the importance of cooperativity effects when Anion–π and CH/π interactions are simultaneously established with benzene as the π-system. In fact, most of the complexes exhibit high cooperativity energies that range from 17% to 25.3% of the total interaction energy, which is indicative of the strong influence of the CH/π on the Anion–π interaction and vice versa. Moreover, the symmetry-adapted perturbation theory (SAPT) partition scheme was used to study the different energy contributions to the interaction energies and to investigate the physical nature of the interplay between both interactions. Furthermore, the Atoms in Molecules (AIM) theory and the Non-Covalent Interaction (NCI) approach were used to analyze the two interactions further. Finally, a few examples from the Protein Data Bank (PDB) are shown. All results stress that the concurrent formation of both interactions may play an important role in biological systems due to the ubiquity of CH bonds, phenyl rings, and anions in biomolecules.
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10
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Bel Haj Salah S, Hermi S, Alotaibi AA, Alotaibi KM, Lefebvre F, Kaminsky W, Ben Nasr C, Mrad MH. Stabilization of hexachloride net with mixed Sn(IV) metal complex and 2,3-dimethylanilinium organic cation: elaboration, optical, spectroscopic, computational studies and thermal analysis. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-021-01974-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Sánchez-González Á, Castro TG, Melle-Franco M, Gil A. From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA. Phys Chem Chem Phys 2021; 23:26680-26695. [PMID: 34825685 DOI: 10.1039/d1cp04529f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]2+ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)2 DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.
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Affiliation(s)
- Ángel Sánchez-González
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Adrià Gil
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal. .,CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia - San Sebastian, Euskadi, Spain
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12
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Abstract
At the heart of drug design is the discovery of molecules that bind with high affinity to their drug targets. Biotin forms the strongest known noncovalent ligand-protein interactions with avidin and streptavidin, achieving femtomolar and picomolar affinities, respectively. This is made even more exceptional because biotin achieves this with a meagre molecular weight of 240 Da. Surprisingly, the approaches by which biotin achieves this are not in the standard repertoire of current medicinal chemistry practice. Biotin's biggest lesson is the importance of nonclassical H-bonds in protein-ligand complexes. Most of biotin's affinity stems from its flexible valeric acid side chain that forms CH-π, CH-O, and classical H-bonds with the lipophilic region of the binding pocket. Biotin also utilizes an oxyanion hole, a sulfur-centered H-bond, and water solvation in the bound state to achieve its potency. The facets and advantages of biotin's approach to binding should be more widely adopted in drug design.
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Affiliation(s)
- Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
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13
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Sparrow ZM, Ernst BG, Joo PT, Lao KU, DiStasio RA. NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts. J Chem Phys 2021; 155:184303. [PMID: 34773949 DOI: 10.1063/5.0068862] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (Eint) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The Eint values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) Eint value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the Eint values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive Eint values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Paul T Joo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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14
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Jaworski A, Hedin N. Local energy decomposition analysis and molecular properties of encapsulated methane in fullerene (CH 4@C 60). Phys Chem Chem Phys 2021; 23:21554-21567. [PMID: 34550137 DOI: 10.1039/d1cp02333k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methane has been successfully encapsulated within cages of C60 fullerene, which is an appropriate model system to study confinement effects. Its chemistry and physics are also relevant for theoretical model descriptions. Here we provide insights into intermolecular interactions and predicted spectroscopic responses of the CH4@C60 complex and compared them with results from other methods and with data from the literature. Local energy decomposition analysis (LED) within the domain-based local pair natural orbital coupled cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) framework was used, and an efficient protocol for studies of endohedral complexes of fullerenes is proposed. This approach allowed us to assess energies in relation to electronic and geometric preparation, electrostatics, exchange, and London dispersion for the CH4@C60 endohedral complex. The calculated stabilization energy of CH4 inside the C60 fullerene was -13.5 kcal mol-1 and its magnitude was significantly larger than the latent heat of evaporation of CH4. Evaluation of vibrational frequencies and polarizabilities of the CH4@C60 complex revealed that the infrared (IR) and Raman bands of the endohedral CH4 were essentially "silent" due to the dielectric screening effect of C60, which acted as a molecular Faraday cage. Absorption spectra in the UV-vis domain and ionization potentials of C60 and CH4@C60 were predicted. They were almost identical. The calculated 1H/13C NMR shifts and spin-spin coupling constants were in very good agreement with experimental data. In addition, reference DLPNO-CCSD(T) interaction energies for complexes with noble gases (Ng@C60; Ng = He, Ne, Ar, Kr) were calculated. The values were compared with those derived from supramolecular MP2/SCS-MP2 calculations and estimates with London-type formulas by Pyykkö and coworkers [Phys. Chem. Chem. Phys., 2010, 12, 6187-6203], and with values derived from DFT-based symmetry-adapted perturbation theory (DFT-SAPT) by Hesselmann & Korona [Phys. Chem. Chem. Phys., 2011, 13, 732-743]. Selected points at the potential energy surface of the endohedral He2@C60 trimer were considered. In contrast to previous theoretical attempts with the DFT/MP2/SCS-MP2/DFT-SAPT methods, our calculations at the DLPNO-CCSD(T) level of theory predicted the He2@C60 trimer to be thermodynamically stable, which is in agreement with experimental observations.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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15
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Ojeda-López R, Ramos-Sánchez G, García-Mendoza C, C. S. Azevedo D, Guzmán-Vargas A, Felipe C. Effect of Calcination Temperature and Chemical Composition of PAN-Derived Carbon Microfibers on N 2, CO 2, and CH 4 Adsorption. MATERIALS 2021; 14:ma14143914. [PMID: 34300825 PMCID: PMC8305112 DOI: 10.3390/ma14143914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 02/05/2023]
Abstract
This work investigates the interplay of carbonization temperature and the chemical composition of carbon microfibers (CMFs), and their impact on the equilibration time and adsorption of three molecules (N2, CO2, and CH4). PAN derived CMFs were synthesized by electrospinning and calcined at three distinct temperatures (600, 700 and 800 °C), which led to samples with different textural and chemical properties assessed by FTIR, TGA/DTA, XRD, Raman, TEM, XPS, and N2 adsorption. We examine why samples calcined at low/moderate temperatures (600 and 700 °C) show an open hysteresis loop in nitrogen adsorption/desorption isotherms at -196.15 °C. The equilibrium time in adsorption measurements is nearly the same for these samples, despite their distinct chemical compositions. Increasing the equilibrium time did not allow for the closure of the hysteresis loop, but by rising the analysis temperature this was achieved. By means of the isosteric enthalpy of adsorption measurements and ab initio calculations, adsorbent/adsorbate interactions for CO2, CH4 and N2 were found to be inversely proportional to the temperature of carbonization of the samples (CMF-600 > CMF-700 > CMF-800). The enhancement of adsorbent/adsorbate interaction at lower carbonization temperatures is directly related to the presence of nitrogen and oxygen functional groups on the surface of CMFs. Nonetheless, a higher concentration of heteroatoms also causes: (i) a reduction in the adsorption capacity of CO2 and CH4 and (ii) open hysteresis loops in N2 adsorption at cryogenic temperatures. Therefore, the calcination of PAN derived microfibers at temperatures above 800 °C is recommended, which results in materials with suitable micropore volume and a low content of surface heteroatoms, leading to high CO2 uptake while keeping acceptable selectivity with regards to CH4 and moderate adsorption enthalpies.
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Affiliation(s)
- Reyna Ojeda-López
- Laboratório de Pesquisa em Adsorção e Captura de CO2 (LPACO2), Departamento de Engenharia Química, Universidade Federal do Ceará (UFC), Fortaleza 60455-760, CE, Brazil;
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), 09340 Mexico City, Mexico;
- Correspondence: (R.O.-L.); (C.F.)
| | - Guadalupe Ramos-Sánchez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), 09340 Mexico City, Mexico;
- CONACYT, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), 09340 Mexico City, Mexico
| | - Cinthia García-Mendoza
- Laboratorio de Nanotecnología, Centro de Investigación de Ciencia y Tecnología Avanzada de Tabasco (CICTAT), División Académica de Ingeniería y Arquitectura, Universidad Juárez Autónoma de Tabasco (UJAT), 86690 Tabasco, Mexico;
| | - Diana C. S. Azevedo
- Laboratório de Pesquisa em Adsorção e Captura de CO2 (LPACO2), Departamento de Engenharia Química, Universidade Federal do Ceará (UFC), Fortaleza 60455-760, CE, Brazil;
| | - Ariel Guzmán-Vargas
- Laboratorio de Investigación en Materiales Porosos, Catálisis Ambiental y Química Fina, ESIQIE, Instituto Politécnico Nacional (IPN), 07738 Mexico City, Mexico;
| | - Carlos Felipe
- Departamento de Biociencias e Ingeniería, Centro Interdisciplinario de Investigaciones y Estudios sobre Medio Ambiente y Desarrollo (CIIEMAD), Instituto Politécnico Nacional (IPN), 07340 Mexico City, Mexico
- Correspondence: (R.O.-L.); (C.F.)
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16
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Wang H, Chen J, Duan C, Xu X, Zheng Y, Grabow JU, Gou Q, Caminati W. Switching Aromatic Character by Complexation: π to π* Change Seen in Molecular Rotation Spectra. J Phys Chem Lett 2021; 12:5150-5155. [PMID: 34032447 DOI: 10.1021/acs.jpclett.1c01318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A dominating F···π*aromatic interaction is found to govern the benzaldehyde···tetrafluoromethane complex, as revealed by this rotational spectroscopic investigation. Secondary F···π*-C=O- and C σ*CF4···πaromatic interactions also contribute to the stability of the observed isomer. Narrow splittings have been observed in the rotational spectrum originating from a 3-fold internal rotation of CF4 above the aromatic moiety, and a corresponding V3 barrier was determined to be 1.572(14) kJ mol-1. This is the first rotational spectroscopic evidence in the literature implying that the aromatic π* antibonding orbital can be activated not only by electron-withdrawing substituents but also by complexation partners containing atoms with high electronegativity, like CF4. The results emphasize the partner molecules' role to modulate the π electron structure and show a change in the orbital character (π or π*) when participating in the formation of noncovalent interactions.
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Affiliation(s)
- Hao Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Junhua Chen
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Chunguo Duan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Xuefang Xu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie & Elektrochemie Leibniz, Universität Hannover, 30167 Hannover, Germany
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Shapingba, Chongqing 401331, China
| | - Walther Caminati
- Dipartimento di Chimica "G. Ciamician", Università; di Bologna, I-40126 Bologna, Italy
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17
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Taherinia D, Mahmoodi MM, Fattahi A. Theoretical investigation of the effect of hydrogen bonding on the stereoselectivity of the Diels–Alder reaction. NEW J CHEM 2021. [DOI: 10.1039/d1nj01373d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we report the computational prediction of high exo selectivities in a series of Diels–Alder reactions with H-bonding interaction.
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Affiliation(s)
- Davood Taherinia
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
| | - M. Mohsen Mahmoodi
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
| | - Alireza Fattahi
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
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18
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DFT study on binding of single and double methane with aromatic hydrocarbons and graphene: stabilizing CH…HC interactions between two methane molecules. Struct Chem 2020. [DOI: 10.1007/s11224-020-01657-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Halter DP, Klein RA, Boreen MA, Trump BA, Brown CM, Long JR. Self-adjusting binding pockets enhance H 2 and CH 4 adsorption in a uranium-based metal-organic framework. Chem Sci 2020; 11:6709-6716. [PMID: 32953032 PMCID: PMC7473405 DOI: 10.1039/d0sc02394a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/27/2020] [Indexed: 11/21/2022] Open
Abstract
A new, air-stable, permanently porous uranium(iv) metal-organic framework U(bdc)2 (1, bdc2- = 1,4-benzenedicarboxylate) was synthesized and its H2 and CH4 adsorption properties were investigated. Low temperature adsorption isotherms confirm strong adsorption of both gases in the framework at low pressures. In situ gas-dosed neutron diffraction experiments with different D2 loadings revealed a rare example of cooperative framework contraction (ΔV = -7.8%), triggered by D2 adsorption at low pressures. This deformation creates two optimized binding pockets for hydrogen (Q st = -8.6 kJ mol-1) per pore, in agreement with H2 adsorption data. Analogous experiments with CD4 (Q st = -24.8 kJ mol-1) and N,N-dimethylformamide as guests revealed that the binding pockets in 1 adjust by selective framework contractions that are unique for each adsorbent, augmenting individual host-guest interactions. Our results suggest that the strategic combination of binding pockets and structural flexibility in metal-organic frameworks holds great potential for the development of new adsorbents with an enhanced substrate affinity.
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Affiliation(s)
- Dominik P Halter
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
- Materials Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
| | - Ryan A Klein
- Chemistry and Nanoscience Department , National Renewable Energy Laboratory , Golden , CO 80401 , USA
- Center for Neutron Research , National Institute of Standards and Technology , Gaithersburg , MD 20899 , USA
| | - Michael A Boreen
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
| | - Benjamin A Trump
- Center for Neutron Research , National Institute of Standards and Technology , Gaithersburg , MD 20899 , USA
| | - Craig M Brown
- Center for Neutron Research , National Institute of Standards and Technology , Gaithersburg , MD 20899 , USA
- Department of Chemical Engineering , University of Delaware , Newark , DE 19716 , USA
| | - Jeffrey R Long
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
- Materials Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
- Department of Chemical and Biomolecular Engineering , University of California , Berkeley , CA 94720 , USA
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20
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Escalante CH, Martínez-Mora EI, Espinoza-Hicks C, Camacho-Dávila AA, Ramos-Morales FR, Delgado F, Tamariz J. Highly selective Diels-Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole. Beilstein J Org Chem 2020; 16:1320-1334. [PMID: 32595780 PMCID: PMC7308616 DOI: 10.3762/bjoc.16.113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 05/28/2020] [Indexed: 01/01/2023] Open
Abstract
A highly regio-, chemo- and stereoselective divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles is herein described, starting from 2-formylpyrrole and employing Diels-Alder and Heck arylation reactions. 3-(N-Benzyl-2-pyrrolyl)acrylates and 4-(pyrrol-2-yl)butenones underwent a highly endo-Diels-Alder cycloaddition with maleimides to furnish octahydropyrrolo[3,4-e]indoles, which served as precursors in the regioselective synthesis of aza-polycyclic skeletons via an intramolecular Heck arylation reaction. Through the latter reaction, the 3-(N-benzyl-2-pyrrolyl)acrylates give rise to 3-(pyrrolo[2,1-a]isoindol-3-yl)acrylates. A further oxidative aromatization of the polycyclic intermediates provides the corresponding polycyclic pyrrolo-isoindoles and isoindolo-pyrrolo-indoles. A theoretical study on the stereoselective Diels-Alder reactions, carried out by calculating the endo/exo transition states, revealed the assistance of non-covalent interactions in governing the endo stereocontrol.
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Affiliation(s)
- Carlos H Escalante
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, 11340 Mexico City, Mexico
| | - Eder I Martínez-Mora
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, 11340 Mexico City, Mexico
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Blvd. Venustiano Carranza e Ing. J. Cárdenas S/N, 25280 Saltillo, Coah., Mexico
| | - Carlos Espinoza-Hicks
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, 31125 Chihuahua, Chih., Mexico
| | - Alejandro A Camacho-Dávila
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, 31125 Chihuahua, Chih., Mexico
| | - Fernando R Ramos-Morales
- Unidad de Servicios de Apoyo en Resolución Analítica, Universidad Veracruzana, Luis Castelazo Ayala S/N, 91190 Xalapa, Ver., Mexico
| | - Francisco Delgado
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, 11340 Mexico City, Mexico
| | - Joaquín Tamariz
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, 11340 Mexico City, Mexico
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21
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Tian Y, Wang L, Fu G, Zhang C, Lu R, Dong X. Theoretical investigation on the substituent effects of the C–H/π interaction. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02595-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Phan A, Striolo A. Evidence of Facilitated Transport in Crowded Nanopores. J Phys Chem Lett 2020; 11:1814-1821. [PMID: 31976670 PMCID: PMC7145346 DOI: 10.1021/acs.jpclett.9b03751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Fluid transport in nature often occurs through crowded nanopores, where a number of phenomena can affect it, because of fluid-fluid and fluid-solid interactions, as well as the presence of organic compounds filling the pores and their structural fluctuations. Employing molecular dynamics, we probe here the transport of fluid mixtures (CO2-CH4 and H2S-CH4) through silica nanopores filled with benzene. Both CO2 and H2S are strongly adsorbed within the organic-filled pore, partially displacing benzene. Unexpectedly, CO2/H2S adsorption facilitates CH4 transport. Analysis of the trajectories suggests that both CO2 and H2S act as vehicle-like carriers and might swell benzene, generating preferential transport pathways within the crowded pore. The results are useful for identifying unexpected transport mechanisms and for developing engineering approaches that could lead to storage of CO2 in caprocks.
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Affiliation(s)
- Anh Phan
- Department
of Chemical Engineering, University College
London, London WC1E 7JE, U.K.
| | - Alberto Striolo
- Department
of Chemical Engineering, University College
London, London WC1E 7JE, U.K.
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23
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Li P, Vik EC, Maier JM, Karki I, Strickland SMS, Umana JM, Smith MD, Pellechia PJ, Shimizu KD. Electrostatically Driven CO−π Aromatic Interactions. J Am Chem Soc 2019; 141:12513-12517. [DOI: 10.1021/jacs.9b06363] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ping Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Erik C. Vik
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Josef M. Maier
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ishwor Karki
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sharon M. S. Strickland
- Department of Biology, Chemistry, and Physics, Converse College, Spartanburg, South Carolina 29302, United States
| | - Jessica M. Umana
- Department of Biology, Chemistry, and Physics, Converse College, Spartanburg, South Carolina 29302, United States
| | - Mark D. Smith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D. Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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24
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Wang J, Liu Z, Li J, Song Z, Hu C, Su Z. exo/endo Selectivity Control in Diels-Alder Reactions of Geminal Bis(silyl) Dienes: Theoretical and Experimental Studies. J Org Chem 2019; 84:3940-3952. [PMID: 30865446 DOI: 10.1021/acs.joc.8b03090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The factors controlling the reactivity and exo/ endo selectivity of Diels-Alder reactions of geminal bis(silyl) dienes catalyzed by AlEt2Cl are studied at the B3LYP-D3(BJ)(SMD,CH2Cl2)/6-31++G**//B3LYP-D3(BJ)(SMD,CH2Cl2)/6-31+G* theoretical level. The reaction proceeds via a two-stage one-step mechanism, and the AlEt2Cl as a Lewis acid catalyst enhances the electrophilicity of the carbonyl compound by coordination, consequently accelerating a cycloaddition reaction with a low energy barrier. A geminal bis(silyl) group of the diene and an α-substituent in α,β-unsaturated carbonyl compounds adjust the interaction energy (Δ Eint) as well as the deformation energy (Δ Estrain) of the diene and dienophile, affecting the barrier height and the diastereochemical outcome accordingly. The steric repulsion between the geminal bis(silyl) group and Al(III) catalyst increases the Pauli repulsion energy (Δ EPauli) and strain energy of dienophile fragment (Δ Estrain(dienophile-LA)) in the endo pathway, ensuring the exo selectivity. The introduction of a halogen atom (Cl or Br) or methyl group at the α-position of α,β-unsaturated carbonyl compounds increases the deformation energy of the diene fragment. Meanwhile, the noncovalent interactions (that is, dispersion and electrostatic interaction) stabilize the endo transition state, leading to predominant endo products. The theoretical predictions of the exo/ endo selectivity for Diels-Alder reactions of the substituted α,β-unsaturated carbonyl compound with Cl or Br atoms by the DFT method are also well confirmed by experiment.
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Affiliation(s)
- Junming Wang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610041 , People's Republic of China
| | - Zengjin Liu
- Key Laboratory of Drug Targeting and Drug Delivery System, Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy , Sichuan University , Chengdu 610041 , People's Republic of China
| | - Jing Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610041 , People's Republic of China
| | - Zhenlei Song
- Key Laboratory of Drug Targeting and Drug Delivery System, Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy , Sichuan University , Chengdu 610041 , People's Republic of China.,State Key Laboratory of Biotherapy, West China Hospital , Sichuan University , Chengdu 610041 , People's Republic of China
| | - Changwei Hu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610041 , People's Republic of China
| | - Zhishan Su
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610041 , People's Republic of China
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25
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Makuvaza JT, Kokkin DL, Loman JL, Reid SA. C-H/π and C-H-O Interactions in Concert: A Study of the Anisole-Methane Complex using Resonant Ionization and Velocity Mapped Ion Imaging. J Phys Chem A 2019; 123:2874-2880. [PMID: 30860841 DOI: 10.1021/acs.jpca.9b01020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Noncovalent forces such as hydrogen bonding, halogen bonding, π-π stacking, and C-H/π and C-H/O interactions hold the key to such chemical processes as protein folding, molecular self-assembly, and drug-substrate interactions. Invaluable insight into the nature and strength of these forces continues to come from the study of isolated molecular clusters. In this work, we report on a study of the isolated anisole-methane complex, where both C-H/π and C-H/O interactions are possible, using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity mapped ion imaging (VMI). Using 2CAP and VMI, we derive the binding energies of the complex in ground, excited, and cation radical states. The experimental values from the two methods are in excellent agreement, and they are compared with selected theoretical values calculated using density functional theory and ab initio methods. The optimized ground-state cluster geometry, which is consistent with the experimental observations, shows methane sitting above the ring, interacting with anisole via both C-H/π and C-H/O interactions, and this dual mode of interaction is reflected in a larger ground-state binding energy as compared with the prototypical benzene-methane system.
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Affiliation(s)
- James T Makuvaza
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Damian L Kokkin
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - John L Loman
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Scott A Reid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
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26
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Huang CJ, Li EY. Molecular design principles towards exo-exclusive Diels–Alder reactions. RSC Adv 2019; 9:7246-7250. [PMID: 35519943 PMCID: PMC9061082 DOI: 10.1039/c8ra10438g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/24/2019] [Indexed: 11/21/2022] Open
Abstract
The exo selective Diels–Alder reactions, reported as special cases, usually involve catalytic reaction conditions and specific cyclic structural motifs on the diene and/or the dienophile. Here we report a systematic computational investigation on the substituent effect for simple, linear dienes and dienophiles towards exo control in Diels–Alder reactions under thermal conditions. Through detailed characterization of reaction pathways for Diels–Alder cycloadditions between linear dienes and dienophiles with various substituents, we summarize a set of design principles aiming for an optimal and nearly-exclusive exo selectivity. These results shall lead to valuable guidelines and more versatile strategies in organic synthesis that are in accordance with the principles of green chemistry. Exo-exclusive stereoselectivity for simple, terminal-substituted dienes and dienophiles may be achieved under thermal conditions through a delicate control of substituent identities.![]()
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Affiliation(s)
- Ci-Jhang Huang
- Department of Chemistry
- National Taiwan Normal University
- Taipei
- Taiwan
| | - Elise Y. Li
- Department of Chemistry
- National Taiwan Normal University
- Taipei
- Taiwan
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27
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Cai XO, Sun M, Shao YJ, Liu F, Liu QL, Zhu YY, Sun ZG, Dong DP, Li J. Two Highly Stable Luminescent Lead Phosphonates Based on Mixed Ligands: Highly Selective and Sensitive Sensing for Thymine Molecule and VO 3 - Anion. ACS OMEGA 2018; 3:16443-16452. [PMID: 31458280 PMCID: PMC6643760 DOI: 10.1021/acsomega.8b02030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/20/2018] [Indexed: 06/10/2023]
Abstract
Two luminescent lead phosphonates with two-dimensional (2D) layer and three-dimensional (3D) framework structure, namely, Pb3[(L1)2(Hssc)(H2O)2] (1) and [Pb2(L2)0.5(bts)(H2O)2]·H2O (2) (H2L1 = O(CH2CH2)2NCH2PO3H2, H4L2 = H2PO3CH2NH(C2H4)2NHCH2PO3H2, H3ssc = 5-sulfosalicylic acid, NaH2bts = 5-sulfoisophthalic acid sodium) have been prepared via hydrothermal techniques. The two compounds not only show excellent thermal stability but also remain intact in aqueous solution within an extensive pH range. Moreover, the atomic absorption spectroscopy analysis experiment indicates that there does not exist the leaching of Pb2+ ions from the lead phosphonates, which show they are nontoxic in aqueous solution. In compound 1, the Pb(1)O4, Pb(2)O7, Pb(3)O4, and CPO3 polyhedra are interlinked into a one-dimensional chain, which is further connected to adjacent chain by sharing the Hssc2- to form a 2D layer. Interestingly, compound 1 as a highly selective and sensitive luminescent material can be used to detect the thymine molecule with a very low detection limit of 8.26 × 10-7 M. In compound 2, the Pb(1)O6 and Pb(2)O5 polyhedra are interlinked into a dimer via edge sharing, which is further connected to adjacent dimer to form a tetramer via corner sharing, and such a tetramer is then interlinked into a 2D layer through bts3- ligands; the adjacent 2D layers are finally constructed to a 3D structure by sharing the L2 4- ligand. Compound 2 can be applied as an excellent luminescent sensor for sensing of VO3 - anion. Furthermore, the probable fluorescent quenching mechanisms of the two compounds have also been studied.
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Affiliation(s)
- Xiao-Ou Cai
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
| | - Meng Sun
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
| | - Yu-Jing Shao
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
| | - Fang Liu
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
| | - Qun-Li Liu
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
| | - Yan-Yu Zhu
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
| | - Zhen-Gang Sun
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
| | - Da-Peng Dong
- School
of Physics and Materials Engineering, Dalian
Nationalities University, Dalian 116600, P. R. China
| | - Jing Li
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, P. R. China
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28
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Abstract
Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C-H⋯O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings.
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29
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Malakar S, Shree Sowndarya SV, Sunoj RB. A quantification scheme for non-covalent interactions in the enantio-controlling transition states in asymmetric catalysis. Org Biomol Chem 2018; 16:5643-5652. [PMID: 30039152 DOI: 10.1039/c8ob01158c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The origin of enantioselectivity in asymmetric catalysis is attributed to the energy difference between lower and higher energy diastereomeric transition states, which are respectively responsible for the formation of major and minor enantiomers. Although the increase in the number of transition state models emphasizes the role of weak non-covalent interactions in asymmetric induction, the strength of such interactions is seldom quantified. Through this article, we propose a simple and effective method of quantifying the total non-covalent interaction in stereocontrolling transition states belonging to a group of three representative asymmetric catalytic reactions involving chiral phosphoric acids. Our method relies on rational partitioning of a given transition state into two (or three) sub-units, such that the complex network of intramolecular interactions can be ameliorated to a set of intermolecular interactions between two sub-units. The computed strength of interaction obtained using the counterpoise (CP) method on suitably partitioned transition states provides improved estimates of non-covalent interactions, which are also devoid of basis set superposition error (BSSE). It has been noted that catalysts decorated with larger aromatic arms provide cumulative non-covalent interactions (C-Hπ, N-Hπ and ππ) to the tune of 10 to 15 kcal mol-1. Fine-tuning of the magnitude and nature of these interactions can provide valuable avenues in the design of asymmetric catalysts.
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Affiliation(s)
- Santanu Malakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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30
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Huber R, Passera A, Gubler E, Mezzetti A. P-Stereogenic PN(H)P Iron(II) Catalysts for the Asymmetric Hydrogenation of Ketones: The Importance of Non-Covalent Interactions in Rational Ligand Design by Computation. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800433] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Raffael Huber
- Dept. of Chemistry and Applied Biosciences; ETH Zürich; Switzerland
| | | | - Erik Gubler
- Dept. of Chemistry and Applied Biosciences; ETH Zürich; Switzerland
| | - Antonio Mezzetti
- Dept. of Chemistry and Applied Biosciences; ETH Zürich; Switzerland
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31
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Mishra BK, Venkatnarayan R. Substituents’ influence on the C–H···π interaction in the T-shaped benzene dimer. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2249-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Østrøm I, Ortolan AO, Schneider FSS, Caramori GF, Parreira RLT. Quest for Insight into Ultrashort C–H···π Proximities in Molecular “Iron Maidens”. J Org Chem 2018; 83:5114-5122. [DOI: 10.1021/acs.joc.8b00461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ina Østrøm
- Departamento de Química, Universidade Federal de Santa Catarina, Campus Universitário Trindade, CP 476, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Alexandre O. Ortolan
- Departamento de Química, Universidade Federal de Santa Catarina, Campus Universitário Trindade, CP 476, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Felipe S. S. Schneider
- Departamento de Química, Universidade Federal de Santa Catarina, Campus Universitário Trindade, CP 476, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Giovanni F. Caramori
- Departamento de Química, Universidade Federal de Santa Catarina, Campus Universitário Trindade, CP 476, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Renato L. T. Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, 14404-600 Franca, São Paulo, Brazil
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33
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Ang SJ, Mak AM, Sullivan MB, Wong MW. Site specificity of halogen bonding involving aromatic acceptors. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp08343b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Based on Cambridge structural database survey and quantum chemical studies, aromatic halogen bond (XB) acceptors are found to have unique pattern of XB binding sites and rim specificity.
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Affiliation(s)
- Shi Jun Ang
- NUS Graduate School for Integrative Sciences and Engineering
- Centre for Life Sciences
- Singapore 117456
- Singapore
- Institute of High Performance Computing
| | - Adrian M. Mak
- Institute of High Performance Computing
- Singapore 138632
- Singapore
| | - Michael B. Sullivan
- Institute of High Performance Computing
- Singapore 138632
- Singapore
- Department of Chemistry
- National University of Singapore
| | - Ming Wah Wong
- NUS Graduate School for Integrative Sciences and Engineering
- Centre for Life Sciences
- Singapore 117456
- Singapore
- Department of Chemistry
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34
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Zuo Y, Su Z, Wang J, Hu C. Theoretical study on the mechanism and selectivity of asymmetric cycloaddition reactions of 3-vinylindole catalyzed by chiral N,N'-dioxide-Ni(II) complex. Catal Today 2017. [DOI: 10.1016/j.cattod.2017.05.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Lin Y, Currie SL, Rosen MK. Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs. J Biol Chem 2017; 292:19110-19120. [PMID: 28924037 PMCID: PMC5704491 DOI: 10.1074/jbc.m117.800466] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 09/12/2017] [Indexed: 01/04/2023] Open
Abstract
Liquid–liquid phase separation (LLPS) is thought to contribute to the establishment of many biomolecular condensates, eukaryotic cell structures that concentrate diverse macromolecules but lack a bounding membrane. RNA granules control RNA metabolism and comprise a large class of condensates that are enriched in RNA-binding proteins and RNA molecules. Many RNA granule proteins are composed of both modular domains and intrinsically disordered regions (IDRs) having low amino acid sequence complexity. Phase separation of these molecules likely plays an important role in the generation and stability of RNA granules. To understand how folded domains and IDRs can cooperate to modulate LLPS, we generated a series of engineered proteins. These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline–rich-motif (polyPRM) ligand. We found that the wild-type IDR promotes LLPS of the polySH3–polyPRM system, decreasing the phase separation threshold concentration by 8-fold. Systematic mutation of tyrosine residues in Gly/Ser-Tyr-Gly/Ser motifs of the IDR reduced this effect, depending on the number but not on the position of these substitutions. Mutating all tyrosines to non-aromatic residues or phosphorylating the IDR raised the phase separation threshold above that of the unmodified polySH3–polyPRM pair. These results show that low-complexity IDRs can modulate LLPS both positively and negatively, depending on the degree of aromaticity and phosphorylation status. Our findings provide plausible mechanisms by which these sequences could alter RNA granule properties on evolutionary and cellular timescales.
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Affiliation(s)
- Yuan Lin
- From the Department of Biophysics, University of Texas Southwestern Medical Center and.,the Howard Hughes Medical Institute, Dallas, Texas 75390
| | - Simon L Currie
- From the Department of Biophysics, University of Texas Southwestern Medical Center and.,the Howard Hughes Medical Institute, Dallas, Texas 75390
| | - Michael K Rosen
- From the Department of Biophysics, University of Texas Southwestern Medical Center and .,the Howard Hughes Medical Institute, Dallas, Texas 75390
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36
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Chen T, Yang S, Chai J, Song Y, Fan J, Rao B, Sheng H, Yu H, Zhu M. Crystallization-induced emission enhancement: A novel fluorescent Au-Ag bimetallic nanocluster with precise atomic structure. SCIENCE ADVANCES 2017; 3:e1700956. [PMID: 28835926 PMCID: PMC5562423 DOI: 10.1126/sciadv.1700956] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/13/2017] [Indexed: 05/22/2023]
Abstract
We report the first noble metal nanocluster with a formula of Au4Ag13(DPPM)3(SR)9 exhibiting crystallization-induced emission enhancement (CIEE), where DPPM denotes bis(diphenylphosphino)methane and HSR denotes 2,5-dimethylbenzenethiol. The precise atomic structure is determined by x-ray crystallography. The crystalline state of Au4Ag13 shows strong luminescence at 695 nm, in striking contrast to the weak emission of the amorphous state and hardly any emission in solution phase. The structural analysis and the density functional theory calculations imply that the compact C-H⋯π interactions significantly restrict the intramolecular rotations and vibrations and thus considerably enhance the radiative transitions in the crystalline state. Because the noncovalent interactions can be easily modulated via varying the chemical environments, the CIEE phenomenon might represent a general strategy to amplify the fluorescence from weakly (or even non-) emissive nanoclusters.
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Affiliation(s)
- Tao Chen
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Sha Yang
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Jinsong Chai
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Yongbo Song
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Jiqiang Fan
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Bo Rao
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Hongting Sheng
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Haizhu Yu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Manzhou Zhu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui University, Hefei, Anhui 230601, P. R. China
- AnHui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui 230601, P. R. China
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37
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Li P, Maier JM, Vik EC, Yehl CJ, Dial BE, Rickher AE, Smith MD, Pellechia PJ, Shimizu KD. Stabilizing Fluorine–π Interactions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702950] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Ping Li
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Josef M. Maier
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Erik C. Vik
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Christopher J. Yehl
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Brent E. Dial
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Amanda E. Rickher
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Mark D. Smith
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Perry J. Pellechia
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Ken D. Shimizu
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
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38
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Li P, Maier JM, Vik EC, Yehl CJ, Dial BE, Rickher AE, Smith MD, Pellechia PJ, Shimizu KD. Stabilizing Fluorine–π Interactions. Angew Chem Int Ed Engl 2017; 56:7209-7212. [DOI: 10.1002/anie.201702950] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Ping Li
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Josef M. Maier
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Erik C. Vik
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Christopher J. Yehl
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Brent E. Dial
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Amanda E. Rickher
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Mark D. Smith
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Perry J. Pellechia
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
| | - Ken D. Shimizu
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC 29208 USA
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39
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Maxwell PI, Popelier PLA. Accurate prediction of the energetics of weakly bound complexes using the machine learning method kriging. Struct Chem 2017. [DOI: 10.1007/s11224-017-0928-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Yepes D, Pérez P, Jaque P, Fernández I. Effect of Lewis acid bulkiness on the stereoselectivity of Diels–Alder reactions between acyclic dienes and α,β-enals. Org Chem Front 2017. [DOI: 10.1039/c7qo00154a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The influence of Lewis acid bulkiness on the stereoselectivity of Diels–Alder reactions is analysed computationally in detail.
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Affiliation(s)
- Diana Yepes
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Patricia Pérez
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Pablo Jaque
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Israel Fernández
- Departamento de Química Orgánica I
- Facultad de Ciencias Químicas
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Universidad Complutense de Madrid
- 28040-Madrid
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41
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Vujović M, Zlatar M, Milčić M, Gruden M. in/out Isomerism of cyclophanes: a theoretical account of 2,6,15-trithia-[34,10][7]metacyclophane and [34,10][7]metacyclophane as well as their halogen substituted analogues. Phys Chem Chem Phys 2017; 19:9500-9508. [DOI: 10.1039/c7cp00557a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
What are the effects responsible for cyclophane isomer stability?
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Affiliation(s)
- Milena Vujović
- Center for Computational Chemistry and Bioinformatics
- Faculty of Chemistry
- University of Belgrade
- 11001 Belgrade
- Serbia
| | - Matija Zlatar
- Department of Chemistry
- Institute of Chemistry
- Technology and Metallurgy
- University of Belgrade
- Belgrade
| | - Miloš Milčić
- Center for Computational Chemistry and Bioinformatics
- Faculty of Chemistry
- University of Belgrade
- 11001 Belgrade
- Serbia
| | - Maja Gruden
- Center for Computational Chemistry and Bioinformatics
- Faculty of Chemistry
- University of Belgrade
- 11001 Belgrade
- Serbia
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42
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Fernández I, Bickelhaupt FM. Deeper Insight into the Diels-Alder Reaction through the Activation Strain Model. Chem Asian J 2016; 11:3297-3304. [DOI: 10.1002/asia.201601203] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Israel Fernández
- Departamento de Química Orgánica I; Universidad Complutense de Madrid; Ciudad Universitaria 28040- Madrid Spain
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute of Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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43
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Driver RW, Claridge TDW, Scheiner S, Smith MD. Torsional and Electronic Factors Control the C-H⋅⋅⋅O Interaction. Chemistry 2016; 22:16513-16521. [PMID: 27709689 PMCID: PMC5113693 DOI: 10.1002/chem.201602905] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 01/07/2023]
Abstract
The precise role of non‐conventional hydrogen bonds such as the C−H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β‐turn mimetics using X‐ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C−H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one. Within a small molecule that is designed to resemble the complexity of the environment within peptides and proteins, the interplay of different steric burdens, hydrogen‐acceptor/‐donor properties and rotational profiles illustrate why unambiguous conclusions based solely on NMR chemical shift data are extremely challenging to rationalize.
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Affiliation(s)
- Russell W Driver
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA.
| | - Martin D Smith
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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44
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Bian C, Wang S, Liu Y, Su K, Jing X. Role of Nonbond Interactions in the Glass Transition of Novolac-Type Phenolic Resin: A Molecular Dynamics Study. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b02136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Kehe Su
- Key
Laboratory of Space Applied Physics and Chemistry of the Ministry
of Education, School of Natural and Applied Sciences, Northwestern Polytechnical University, Xi’an 710072, China
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45
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García-Rodeja Y, Fernández I. Factors Controlling the Reactivity and Selectivity of the Diels–Alder Reactions Involving 1,2-Azaborines. J Org Chem 2016; 81:6554-62. [DOI: 10.1021/acs.joc.6b01182] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yago García-Rodeja
- Departamento de Química
Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Israel Fernández
- Departamento de Química
Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
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46
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Gómez-Tamayo JC, Cordomí A, Olivella M, Mayol E, Fourmy D, Pardo L. Analysis of the interactions of sulfur-containing amino acids in membrane proteins. Protein Sci 2016; 25:1517-24. [PMID: 27240306 DOI: 10.1002/pro.2955] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 01/17/2023]
Abstract
The interactions of Met and Cys with other amino acid side chains have received little attention, in contrast to aromatic-aromatic, aromatic-aliphatic or/and aliphatic-aliphatic interactions. Precisely, these are the only amino acids that contain a sulfur atom, which is highly polarizable and, thus, likely to participate in strong Van der Waals interactions. Analysis of the interactions present in membrane protein crystal structures, together with the characterization of their strength in small-molecule model systems at the ab-initio level, predicts that Met-Met interactions are stronger than Met-Cys ≈ Met-Phe ≈ Cys-Phe interactions, stronger than Phe-Phe ≈ Phe-Leu interactions, stronger than the Met-Leu interaction, and stronger than Leu-Leu ≈ Cys-Leu interactions. These results show that sulfur-containing amino acids form stronger interactions than aromatic or aliphatic amino acids. Thus, these amino acids may provide additional driving forces for maintaining the 3D structure of membrane proteins and may provide functional specificity.
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Affiliation(s)
- José C Gómez-Tamayo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, E-08193, Bellaterra, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, E-08193, Bellaterra, Spain
| | - Mireia Olivella
- Departament de Biologia de Sistemes, Universitat de Vic, Vic, 08500, Spain
| | - Eduardo Mayol
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, E-08193, Bellaterra, Spain
| | - Daniel Fourmy
- Laboratoire de Physique et Chimie des Nano-Objets University of Toulouse, CNRS, INSA, INSERM, Toulouse, France
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, E-08193, Bellaterra, Spain
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47
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Henley A, Bound M, Besley E. Effective Binding of Methane Using a Weak Hydrogen Bond. J Phys Chem A 2016; 120:3701-9. [DOI: 10.1021/acs.jpca.6b03331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alice Henley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Michelle Bound
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Elena Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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48
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Bakr BW, Sherrill CD. Analysis of transition state stabilization by non-covalent interactions in the Houk-List model of organocatalyzed intermolecular Aldol additions using functional-group symmetry-adapted perturbation theory. Phys Chem Chem Phys 2016; 18:10297-308. [PMID: 27020417 DOI: 10.1039/c5cp07281f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rational design of catalysts would be aided by a better understanding of how non-covalent interactions stabilize transition states. Here, we apply the newly-developed Functional-Group Symmetry-Adapted Perturbation Theory (F-SAPT) to quantify non-covalent interactions in transition states of the proline-catalyzed intermolecular aldol reaction between benzaldehyde and cyclohexanone, according to the Houk-List mechanism [Bahmanyar et al., J. Am. Chem. Soc., 2003, 125, 2475]. A recent re-examination of this organocatalytic reaction by Rzepa and co-workers [Armstrong et al., Chem. Sci., 2014, 5, 2057] used electron density analysis to identify three key non-covalent interactions thought to influence stereoselectivity: (1) a favorable electrostatic interaction (originally identified by Houk and List) between the NCH(δ+) group of the enamine intermediate and the (δ-)O[double bond, length as m-dash]C of benzaldehyde; (2) a C-H/π interaction between the cyclohexene group of the enamine intermediate and the benzaldehyde phenyl ring; (3) a stabilizing contact between an ortho-hydrogen of the phenyl and an oxygen of the carboxylic acid group of the enamine. These three interactions have been directly computed using F-SAPT, which confirms the stabilizing interaction between an ortho-hydrogen and the carboxylic acid in the (S,S) and (R,S) transition state stereoisomers. F-SAPT analysis also finds stabilizing dispersion and electrostatic interactions due to a C-H/π interaction between the cyclohexene and phenyl groups in the (S,S) and (R,R) transition states. However, unfavorable exchange-repulsion cancels the attractive terms that favor these stereoisomers. Surprisingly, the interaction thought to be most important for stereoselectivity, the NCH(δ+)(δ-)O[double bond, length as m-dash]C interaction, is actually found to be repulsive due to the negative charge on the nitrogen. Hence, our results indicate that geometric analysis and/or density-based analysis does not necessarily produce a reliable picture of non-covalent stabilization. As confirmed by high-level coupled-cluster computations, intermolecular interaction energies are strongest for the (R,R) transition states, which are not the experimentally favored products. This suggests that at least for this reaction, stereoselectivity is also strongly dependent on the energy required to distort the reacting molecules into the transition state geometry.
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Affiliation(s)
- Brandon W Bakr
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
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49
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Wagner FF, Lundh M, Kaya T, McCarren P, Zhang YL, Chattopadhyay S, Gale JP, Galbo T, Fisher SL, Meier BC, Vetere A, Richardson S, Morgan NG, Christensen DP, Gilbert TJ, Hooker JM, Leroy M, Walpita D, Mandrup-Poulsen T, Wagner BK, Holson EB. An Isochemogenic Set of Inhibitors To Define the Therapeutic Potential of Histone Deacetylases in β-Cell Protection. ACS Chem Biol 2016; 11:363-74. [PMID: 26640968 DOI: 10.1021/acschembio.5b00640] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Modulation of histone deacetylase (HDAC) activity has been implicated as a potential therapeutic strategy for multiple diseases. However, it has been difficult to dissect the role of individual HDACs due to a lack of selective small-molecule inhibitors. Here, we report the synthesis of a series of highly potent and isoform-selective class I HDAC inhibitors, rationally designed by exploiting minimal structural changes to the clinically experienced HDAC inhibitor CI-994. We used this toolkit of isochemogenic or chemically matched inhibitors to probe the role of class I HDACs in β-cell pathobiology and demonstrate for the first time that selective inhibition of an individual HDAC isoform retains beneficial biological activity and mitigates mechanism-based toxicities. The highly selective HDAC3 inhibitor BRD3308 suppressed pancreatic β-cell apoptosis induced by inflammatory cytokines, as expected, or now glucolipotoxic stress, and increased functional insulin release. In addition, BRD3308 had no effect on human megakaryocyte differentiation, while inhibitors of HDAC1 and 2 were toxic. Our findings demonstrate that the selective inhibition of HDAC3 represents a potential path forward as a therapy to protect pancreatic β-cells from inflammatory cytokines and nutrient overload in diabetes.
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Affiliation(s)
- Florence F. Wagner
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Morten Lundh
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department
of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Taner Kaya
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Patrick McCarren
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Yan-Ling Zhang
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Shrikanta Chattopadhyay
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Jennifer P. Gale
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Thomas Galbo
- Department
of Internal Medicine, Yale University, New Haven, Connecticut 06520, United States
| | - Stewart L. Fisher
- SL Fisher Consulting, LLC, PO Box 3052, Framingham, Massachusetts 01701, United States
| | - Bennett C. Meier
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Amedeo Vetere
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Sarah Richardson
- University of Exeter Medical School, RD&E Hospital, Wonford EX2 5DW, U.K
| | - Noel G. Morgan
- University of Exeter Medical School, RD&E Hospital, Wonford EX2 5DW, U.K
| | - Dan Ploug Christensen
- Department
of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Tamara J. Gilbert
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Jacob M. Hooker
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Athinoula
A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital,
Department of Radiology, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Mélanie Leroy
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Deepika Walpita
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Thomas Mandrup-Poulsen
- Department
of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Bridget K. Wagner
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Edward B. Holson
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
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50
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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