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1.
ACS Catal ; 14(13): 10295-10316, 2024 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-38988649

RESUMO

Fe(II) carboxylates react with dioxygen and carboxylic acid to form Fe6(µ-OH)2(µ3-O)2(µ-X)12(HX)2 (X = acetate or pivalate), which is an active oxidant for Rh-catalyzed arene alkenylation. Heating (150-200 °C) the catalyst precursor [(η2-C2H4)2Rh(µ-OAc)]2 with ethylene, benzene, Fe(II) carboxylate, and dioxygen yields styrene >30-fold faster than the reaction with dioxygen in the absence of the Fe(II) carboxylate additive. It is also demonstrated that Fe6(µ-OH)2(µ3-O)2(µ-X)12(HX)2 is an active oxidant under anaerobic conditions, and the reduced material can be reoxidized to Fe6(µ-OH)2(µ3-O)2(µ-X)12(HX)2 by dioxygen. At optimized conditions, a turnover frequency of ∼0.2 s-1 is achieved. Unlike analogous reactions with Cu(II) carboxylate oxidants, which undergo stoichiometric Cu(II)-mediated production of phenyl esters (e.g., phenyl acetate) as side products at temperatures ≥150 °C, no phenyl ester side product is observed when Fe carboxylate additives are used. Kinetic isotope effect experiments using C6H6 and C6D6 give k H/k D = 3.5(3), while the use of protio or monodeutero pivalic acid reveals a small KIE with k H/k D = 1.19(2). First-order dependencies on Fe(II) carboxylate and dioxygen concentration are observed in addition to complicated kinetic dependencies on the concentration of carboxylic acid and ethylene, both of which inhibit the reaction rate at a high concentration. Mechanistic studies are consistent with irreversible benzene C-H activation, ethylene insertion into the formed Rh-Ph bond, ß-hydride elimination, and reaction of Rh-H with Fe6(µ-OH)2(µ3-O)2(µ-X)12(HX)2 to regenerate a Rh-carboxylate complex.

2.
J Phys Chem Lett ; 15(17): 4568-4574, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38639377

RESUMO

Pauling and Corey expected that a racemic mixture would result in a rippled ß-sheet, however, it has been known from experiments that the racemic mixtures of triphenylalanine lead to a herringbone structure. Because of the theoretical limitations concerning crystal structures such as rippled ß-sheet, it is inevitable to understand how the interplay of the amino acids prefers a specific structural motif. In this paper we use molecular dynamics to understand the sequence- and enantiomer-dependent structures by comparisons between rippled ß-sheet and pleated ß-sheet, solvated and anhydrous rippled ß-sheet, and rippled ß-sheet and the herringbone structure, based on thermodynamics and structures at the atomic level. The tripeptides select the favored structure that can be stabilized through aromatic or hydrogen bonding interactions between tripeptides. Furthermore, the solubility is determined by the environment of space that is created around the side chains. Our findings provide comprehensive insight into the crystallized fibril motif of the polypeptide.

3.
Langmuir ; 40(15): 8067-8073, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38557046

RESUMO

Nanocomposites made of magnetite (Fe3O4) nanoparticles (NP)s with different surface chemistry and polyvinyl difluoride (PVDF) polymer were investigated using full atom molecular dynamics (MD) simulation. NPs with hydroxyl (OH), hexanoic, and oleic acid terminations were considered in this study. The effect of each surface chemistry was investigated in terms of the mechanical properties, the distribution of the internal energy around the NP, and the chain polarization gradient from the interface to the bulk. From this investigation, we find that oleic acid termination, although the most popular, is less favorable for interfacial interaction and local polarization. The OH-terminated NP results in the best configuration for the properties investigated. The hexanoic acid-grafted NP presents a good compromise. Hydrogen bonding governs the induced response of the nanocomposites. Although the hexanoic acid grafted NP presents less hydrogen bonding than the OH-terminated case, the conformation of the hexanoic acid acts as a mobility flow inhibitor, leading to a performance comparable to that of the OH-terminated NP composite. This work led to investigating routes to make nanocomposite materials with optimized properties. These results shed light on the multiple combinations offered by nanocomposites that go beyond the conventional effects of size.

4.
Proc Natl Acad Sci U S A ; 120(49): e2300919120, 2023 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-38015850

RESUMO

Smoothened (SMO) is an oncoprotein and signal transducer in the Hedgehog signaling pathway that regulates cellular differentiation and embryogenesis. As a member of the Frizzled (Class F) family of G protein-coupled receptors (GPCRs), SMO biochemically and functionally interacts with Gi family proteins. However, key molecular features of fully activated, G protein-coupled SMO remain elusive. We present the atomistic structure of activated human SMO complexed with the heterotrimeric Gi protein and two sterol ligands, equilibrated at 310 K in a full lipid bilayer at physiological salt concentration and pH. In contrast to previous experimental structures, our equilibrated SMO complex exhibits complete breaking of the pi-cation interaction between R4516.32 and W5357.55, a hallmark of Class F receptor activation. The Gi protein couples to SMO at seven strong anchor points similar to those in Class A GPCRs: intracellular loop 1, intracellular loop 2, transmembrane helix 6, and helix 8. On the path to full activation, we find that the extracellular cysteine-rich domain (CRD) undergoes a dramatic tilt, following a trajectory suggested by positions of the CRD in active and inactive experimental SMO structures. Strikingly, a sterol ligand bound to a shallow transmembrane domain (TMD) site in the initial structure migrates to a deep TMD pocket found exclusively in activator-bound SMO complexes. Thus, our results indicate that SMO interacts with Gi prior to full activation to break the molecular lock, form anchors with Gi subunits, tilt the CRD, and facilitate migration of a sterol ligand in the TMD to an activated position.


Assuntos
Proteínas Hedgehog , Esteróis , Humanos , Esteróis/metabolismo , Ligantes , Modelos Moleculares , Proteínas Hedgehog/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Receptor Smoothened/metabolismo
5.
Nat Commun ; 14(1): 1325, 2023 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-36899002

RESUMO

Understanding the roles of intermediate states in signaling is pivotal to unraveling the activation processes of G protein-coupled receptors (GPCRs). However, the field is still struggling to define these conformational states with sufficient resolution to study their individual functions. Here, we demonstrate the feasibility of enriching the populations of discrete states via conformation-biased mutants. These mutants adopt distinct distributions among five states that lie along the activation pathway of adenosine A2A receptor (A2AR), a class A GPCR. Our study reveals a structurally conserved cation-π lock between transmembrane helix VI (TM6) and Helix8 that regulates cytoplasmic cavity opening as a "gatekeeper" for G protein penetration. A GPCR activation process based on the well-discerned conformational states is thus proposed, allosterically micro-modulated by the cation-π lock and a previously well-defined ionic interaction between TM3 and TM6. Intermediate-state-trapped mutants will also provide useful information in relation to receptor-G protein signal transduction.


Assuntos
Receptores Acoplados a Proteínas G , Transdução de Sinais , Modelos Moleculares , Conformação Proteica , Receptores Acoplados a Proteínas G/metabolismo , Adenosina , Receptor A2A de Adenosina/metabolismo
6.
Nat Nanotechnol ; 18(2): 160-167, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-36536043

RESUMO

Electrochemistry can provide an efficient and sustainable way to treat environmental waters polluted by chlorinated organic compounds. However, the electrochemical valorization of 1,2-dichloroethane (DCA) is currently challenged by the lack of a catalyst that can selectively convert DCA in aqueous solutions into ethylene. Here we report a catalyst comprising cobalt phthalocyanine molecules assembled on multiwalled carbon nanotubes that can electrochemically decompose aqueous DCA with high current and energy efficiencies. Ethylene is produced at high rates with unprecedented ~100% Faradaic efficiency across wide electrode potential and reactant concentration ranges. Kinetic studies and density functional theory calculations reveal that the rate-determining step is the first C-Cl bond breaking, which does not involve protons-a key mechanistic feature that enables cobalt phthalocyanine/carbon nanotube to efficiently catalyse DCA dechlorination and suppress the hydrogen evolution reaction. The nanotubular structure of the catalyst enables us to shape it into a flow-through electrified membrane, which we have used to demonstrate >95% DCA removal from simulated water samples with environmentally relevant DCA and electrolyte concentrations.

7.
Proc Natl Acad Sci U S A ; 119(18): e2110085119, 2022 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-35452328

RESUMO

G protein­coupled receptors (GPCRs) activate cellular responses ranging from odorants to neurotransmitters. Binding an agonist leads to activation of a heterotrimeric G protein (GP) that stimulates external signaling. Unfortunately, the mechanism remains unknown. We show for 15 class A GPCRs, including opioids, adrenergics, adenosines, chemokines, muscarinics, cannabinoids, serotonins, and dopamines, that interaction of an inactive GP, including Gs, Gi, Go, G11, and Gq, to the inactive GPCR, containing the intracellular ionic lock between transmembrane (TM) helices 3 and 6, evolves exothermically to form a precoupled GPCR-GP complex with an opened TM3-TM6 and the GP-α5 helix partially inserted into the GPCR but not activated. We show that binding of agonist to this precoupled GPCR-GP complex causes the Gα protein to open into its active form, with the guanosine diphosphate exposed for signaling. This GP-first paradigm provides a strategy for developing selective agonists for GPCRs since it is the pharmacophore for the precoupled GPCR-GP complex that should be used to design drugs.


Assuntos
Receptores Acoplados a Proteínas G , Transdução de Sinais , Membrana Celular/metabolismo , Proteínas de Ligação ao GTP/metabolismo , Ligantes , Ligação Proteica , Receptores Acoplados a Proteínas G/metabolismo
8.
Biosens Bioelectron ; 209: 114222, 2022 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-35430407

RESUMO

The 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later cause a global pandemic, which paralyzes the world since then. We have designed novel immunosensors targeting conserved protein sequences of the N protein of SARS-CoV-2 based on lab-produced and purified anti-SARS-CoV-2 nucleocapsid antibodies that are densely grafted onto various surfaces (diamond/gold/glassy carbon). Titration of antibodies shows very strong reactions up to 1:72 900 dilution. Next, we showed the mechanism of interactions of our immunoassay with nucleocapsid N protein revealing molecular recognition by impedimetric measurements supported by hybrid modeling results with both density functional theory and molecular dynamics methods. Biosensors allowed for a fast (in less than 10 min) detection of SARS-CoV-2 virus with a limit of detection from 0.227 ng/ml through 0.334 ng/ml to 0.362 ng/ml for glassy carbon, boron-doped diamond, and gold surfaces, respectively. For all tested surfaces, we obtained a wide linear range of concentrations from 4.4 ng/ml to 4.4 pg/ml. Furthermore, our sensor leads to a highly specific response to SARS-CoV-2 clinical samples versus other upper respiratory tract viruses such as influenza, respiratory syncytial virus, or Epstein-Barr virus. All clinical samples were tested simultaneously on biosensors and real-time polymerase chain reactions.


Assuntos
Técnicas Biossensoriais , COVID-19 , Infecções por Vírus Epstein-Barr , Anticorpos Antivirais , Técnicas Biossensoriais/métodos , Boro , COVID-19/diagnóstico , Carbono , Diamante , Ouro , Herpesvirus Humano 4 , Humanos , Imunoensaio/métodos , Nucleocapsídeo , Proteínas do Nucleocapsídeo , SARS-CoV-2
9.
Nat Commun ; 13(1): 63, 2022 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-35039509

RESUMO

Direct implementation of metal-organic frameworks as the catalyst for CO2 electroreduction has been challenging due to issues such as poor conductivity, stability, and limited > 2e- products. In this study, Au nanoneedles are impregnated into a cupric porphyrin-based metal-organic framework by exploiting ligand carboxylates as the Au3+ -reducing agent, simultaneously cleaving the ligand-node linkage. Surprisingly, despite the lack of a coherent structure, the Au-inserted framework affords a superb ethylene selectivity up to 52.5% in Faradaic efficiency, ranking among the best for metal-organic frameworks reported in the literature. Through operando X-ray, infrared spectroscopies and density functional theory calculations, the enhanced ethylene selectivity is attributed to Au-activated nitrogen motifs in coordination with the Cu centers for C-C coupling at the metalloporphyrin sites. Furthermore, the Au-inserted catalyst demonstrates both improved structural and catalytic stability, ascribed to the altered charge conduction path that bypasses the incoherent framework. This study underlines the modulation of reticular metalloporphyrin structure by metal impregnation for steering the CO2 reduction reaction pathway.

10.
Proc Natl Acad Sci U S A ; 118(49)2021 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-34857633

RESUMO

G protein-coupled receptors display multifunctional signaling, offering the potential for agonist structures to promote conformational selectivity for biased outputs. For ß2-adrenergic receptors (ß2AR), unbiased agonists stabilize conformation(s) that evoke coupling to Gαs (cyclic adenosine monophosphate [cAMP] production/human airway smooth muscle [HASM] cell relaxation) and ß-arrestin engagement, the latter acting to quench Gαs signaling, contributing to receptor desensitization/tachyphylaxis. We screened a 40-million-compound scaffold ranking library, revealing unanticipated agonists with dihydroimidazolyl-butyl-cyclic urea scaffolds. The S-stereoisomer of compound C1 shows no detectable ß-arrestin engagement/signaling by four methods. However, C1-S retained Gαs signaling-a divergence of the outputs favorable for treating asthma. Functional studies with two models confirmed the biasing: ß2AR-mediated cAMP signaling underwent desensitization to the unbiased agonist albuterol but not to C1-S, and desensitization of HASM cell relaxation was observed with albuterol but not with C1-S These HASM results indicate biologically pertinent biasing of C1-S, in the context of the relevant physiologic response, in the human cell type of interest. Thus, C1-S was apparently strongly biased away from ß-arrestin, in contrast to albuterol and C5-S C1-S structural modeling and simulations revealed binding differences compared with unbiased epinephrine at transmembrane (TM) segments 3,5,6,7 and ECL2. C1-S (R2 = cyclohexane) was repositioned in the pocket such that it lost a TM6 interaction and gained a TM7 interaction compared with the analogous unbiased C5-S (R2 = benzene group), which appears to contribute to C1-S biasing away from ß-arrestin. Thus, an agnostic large chemical-space library identified agonists with receptor interactions that resulted in relevant signal splitting of ß2AR actions favorable for treating obstructive lung disease.


Assuntos
Agonistas de Receptores Adrenérgicos beta 2/farmacologia , Relaxamento Muscular/efeitos dos fármacos , Miócitos de Músculo Liso/efeitos dos fármacos , Agonistas de Receptores Adrenérgicos beta 2/química , Animais , Linhagem Celular , Simulação por Computador , Cricetinae , Descoberta de Drogas , Epinefrina/química , Epinefrina/farmacologia , Células HEK293 , Humanos , Modelos Moleculares , Estrutura Molecular , Músculo Liso/efeitos dos fármacos , Ligação Proteica , Conformação Proteica , Sistema Respiratório , Bibliotecas de Moléculas Pequenas
11.
Cell Mol Life Sci ; 79(1): 24, 2021 Dec 29.
Artigo em Inglês | MEDLINE | ID: mdl-34966948

RESUMO

Protecting neurons from death during oxidative and neuroexcitotoxic stress is key for preventing cognitive dysfunction. We uncovered a novel neuroprotective mechanism involving interaction between neurotrophic factor-α1 (NF-α1/carboxypeptidase E, CPE) and human 5-HTR1E, a G protein-coupled serotonin receptor with no previously known neurological function. Co-immunoprecipitation and pull-down assays confirmed interaction between NFα1/CPE and 5-HTR1E and 125I NF-α1/CPE-binding studies demonstrated saturable, high-affinity binding to 5-HTR1E in stably transfected HEK293 cells (Kd = 13.82 nM). Treatment of 5-HTR1E stable cells with NF-α1/CPE increased pERK 1/2 and pCREB levels which prevented a decrease in pro-survival protein, BCL2, during H2O2-induced oxidative stress. Cell survival assay in ß-arrestin Knockout HEK293 cells showed that the NF-α1/CPE-5-HTR1E-mediated protection against oxidative stress was ß-arrestin-dependent. Molecular dynamics studies revealed that NF-α1/CPE interacts with 5-HTR1E via 3 salt bridges, stabilized by several hydrogen bonds, independent of the serotonin pocket. Furthermore, after phosphorylating the C-terminal tail and intracellular loop 3 (ICL3) of NF-α1/CPE-5-HTR1E, it recruited ß-arrestin1 by forming numerous salt bridges and hydrogen bonds to ICL2 and ICL3, leading to activation of ß-arrestin1. Immunofluorescence studies showed 5-HTR1E and NF-α1/CPE are highly expressed and co-localized on cell surface of human hippocampal neurons. Importantly, knock-down of 5-HTR1E in human primary neurons diminished the NF-α1/CPE-mediated protection of these neurons against oxidative stress and glutamate neurotoxicity-induced cell death. Thus, NF-α1/CPE uniquely interacts with serotonin receptor 5-HTR1E to activate the ß-arrestin/ERK/CREB/BCL2 pathway to mediate stress-induced neuroprotection.


Assuntos
Carboxipeptidase H/metabolismo , Sistema de Sinalização das MAP Quinases , Fatores de Crescimento Neural/metabolismo , Neurônios/metabolismo , Neurotoxinas/toxicidade , Estresse Oxidativo , Receptores de Serotonina/metabolismo , beta-Arrestinas/metabolismo , Animais , Carboxipeptidase H/química , Sobrevivência Celular/efeitos dos fármacos , AMP Cíclico/metabolismo , Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/metabolismo , Regulação para Baixo/efeitos dos fármacos , Células HEK293 , Hipocampo/metabolismo , Humanos , Sistema de Sinalização das MAP Quinases/efeitos dos fármacos , Camundongos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Neurônios/efeitos dos fármacos , Neurônios/patologia , Fármacos Neuroprotetores/metabolismo , Fosforilação/efeitos dos fármacos , Ligação Proteica/efeitos dos fármacos , Domínios Proteicos , Receptores de Serotonina/química
12.
Angew Chem Int Ed Engl ; 60(30): 16448-16456, 2021 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-33973312

RESUMO

Motivated by in silico predictions that Co, Rh, and Ir dopants would lead to low overpotentials to improve OER activity of Ni-based hydroxides, we report here an experimental confirmation on the altered OER activities for a series of metals (Mo, W, Fe, Ru, Co, Rh, Ir) doped into γ-NiOOH. The in situ electrical conductivity for metal doped γ-NiOOH correlates well with the trend in enhanced OER activities. Density functional theory (DFT) calculations were used to rationalize the in situ conductivity of the key intermediate states of metal doped γ-NiOOH during OER. The simultaneous increase of OER activity with intermediate conductivity was later rationalized by their intrinsic connections to the double exchange (DE) interaction between adjacent metal ions with various d orbital occupancies, serving as an indicator for the key metal-oxo radical character, and an effective descriptor for the mechanistic evaluation and theoretical guidance in design and screening of efficient OER catalysts.

13.
PLoS One ; 16(2): e0246814, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33630857

RESUMO

During formation of the Hedgehog (Hh) signaling proteins, cooperative activities of the Hedgehog INTein (Hint) fold and Sterol Recognition Region (SRR) couple autoproteolysis to cholesterol ligation. The cholesteroylated Hh morphogens play essential roles in embryogenesis, tissue regeneration, and tumorigenesis. Despite the centrality of cholesterol in Hh function, the full structure of the Hint-SRR ("Hog") domain that attaches cholesterol to the last residue of the active Hh morphogen remains enigmatic. In this work, we combine molecular dynamics simulations, photoaffinity crosslinking, and mutagenesis assays to model cholesterolysis intermediates in the human Sonic Hedgehog (hSHH) protein. Our results provide evidence for a hydrophobic Hint-SRR interface that forms a dynamic, non-covalent cholesterol-Hog complex. Using these models, we suggest a unified mechanism by which Hh proteins can recruit, sequester, and orient cholesterol, and offer a molecular basis for the effects of disease-causing hSHH mutations.


Assuntos
Colesterol/química , Proteínas Hedgehog/química , Simulação de Dinâmica Molecular , Animais , Colesterol/genética , Colesterol/metabolismo , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster , Células HEK293 , Proteínas Hedgehog/genética , Proteínas Hedgehog/metabolismo , Humanos , Domínios Proteicos
14.
ACS Catal ; 11(16): 10208-10222, 2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-35186424

RESUMO

We present a series of experimental and computational mechanistic investigations of an unusually facile example of Ni-catalyzed C-O bond formation. Our method, originally reported in 2016, involves the formation of cyclic enol ethers from vinyl iodides bearing pendant alcohol groups. Our findings suggest that the observed reactivity arises from the coordination of the olefin in the vinyl iodide starting material and the enol ether product with Ni(0) intermediates. Density functional theory calculations reveal a plausible catalytic mechanism involving a Ni(II)/Ni(0) redox cycle featuring two-electron C-I oxidative addition and C-O reductive elimination steps. The direct formation of a η 2-enol ether Ni(0) complex from a key Ni(II) alkoxide intermediate dramatically alters the free energy (ΔG) for the vinyl C-O reductive elimination step relative to other examples of C-O reductive elimination at Ni(II). Furthermore, efficient σ-π mixing in the course of vinyl C-O reductive elimination leads to lower computed kinetic barriers (ΔG ‡) relative to those of aryl C-O reductive elimination. The conclusions drawn from these computational models are supported by synthetic organometallic experiments, whereby a vinyl-Ni(II) iodide intermediate was isolated, characterized, and proved to yield enol ether, following exposure to triethylamine. We conducted further experiments and computations, which indicated that the two-electron oxidative addition of vinyl iodides by Ni(0) depends on the formation of an η 2-vinyl iodide precomplex, based on the observation of one-electron activation of the same vinyl iodide in the presence of sterically encumbering ligands (e.g., tricyclohexylphosphine).

15.
J Phys Chem Lett ; 12(1): 73-79, 2021 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-33306392

RESUMO

Standard implementations of generalized gradient approximation (GGA)-based density functional theory (DFT) describe well strongly bound molecules and solids but fail to describe long-range London dispersion or van der Waals (vdW) attraction interactions that are important in molecular crystals and two-dimensional solids. To provide accurate values for the vdW distance and energies for the metals Cu, Ag, Au, Ni, Pd, and Pt, we determined empirical vdW corrections to Perdew, Burke, and Ernzerhof (PBE) DFT by fitting the experimental adsorption enthalpies measured by temperature-programmed desorption (TPD) from benzene monolayers by Campbell and co-workers ( J. Phys. Chem. C 2016, 120, 25161-25172). Benzene physisorbed to these metals without chemical reaction; therefore, we consider the bonding to be vdW. We use the low gradient form for the vdW corrections, EvdW-LG = -C6LG/[R6 + RvdwLG6] with just two parameters per atom (C6LG and RvdwLG). This LG form leads to negligible changes in bond distances and angles, so adjusting the parameters should not sacrifice accuracy for the bonding interactions. We demonstrate that the parameters fitted to benzene also describe well the physisorption enthalpies for other hydrocarbons (naphthalene, cyclohexane, methane, ethane, and propane) on Pt. We also report low gradient vdW correction parameters for the noble gases that fit the equilibrium lattice parameter and heat of vaporization of the crystals.

16.
Phys Chem Chem Phys ; 22(41): 24028-24040, 2020 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-33078174

RESUMO

In order to provide the means to predict from molecular dynamics (MD) simulations the structures of copolymer-based micelles in solution, we developed coarse grain force field (CGq FF) parameters for poly(ethylene glycol) (PEG) and for poly(ε-caprolactone) (PCL). A key advance here is the use of quantum mechanics to train the parameters describing the non-bonded (NB) interactions between the CG beads. The functional forms are the same as the MARTINI CG FF so standard MD codes can be used. Our CGq FF describes well the experimentally observed properties for the polymer-air and polymer-water interfaces, indicating the accuracy of the NB interactions. The structural properties (density, radius of gyration (Rg), and end-to-end distance (h)) match both experiment and all atom (AA) simulations. We illustrate the application of this CGq FF by following the formation of a spherical micelle from 250 chains of PEG23-b-PCL9 diblock copolymer, each block with molecular weight of 1000 Daltons (10 500 beads, corresponding to 123 250 atoms), in a water box with 119 139 water beads (426 553 water molecules).

17.
Nat Commun ; 11(1): 2256, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32382033

RESUMO

Experiments have shown that graphene-supported Ni-single atom catalysts (Ni-SACs) provide a promising strategy for the electrochemical reduction of CO2 to CO, but the nature of the Ni sites (Ni-N2C2, Ni-N3C1, Ni-N4) in Ni-SACs has not been determined experimentally. Here, we apply the recently developed grand canonical potential kinetics (GCP-K) formulation of quantum mechanics to predict the kinetics as a function of applied potential (U) to determine faradic efficiency, turn over frequency, and Tafel slope for CO and H2 production for all three sites. We predict an onset potential (at 10 mA cm-2) Uonset = -0.84 V (vs. RHE) for Ni-N2C2 site and Uonset = -0.92 V for Ni-N3C1 site in agreement with experiments, and Uonset = -1.03 V for Ni-N4. We predict that the highest current is for Ni-N4, leading to 700 mA cm-2 at U = -1.12 V. To help determine the actual sites in the experiments, we predict the XPS binding energy shift and CO vibrational frequency for each site.

18.
Phys Chem Chem Phys ; 20(41): 26098-26104, 2018 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-30283936

RESUMO

A detailed experimental analysis of the factors affecting cyclic durability of all-solid-state lithium batteries using poly(ethylene oxide)-based polymer electrolytes was published in EES by Nakayama et al. We use quantum mechanics to interpret these results, identifying processes involved in the degradation of rechargeable lithium batteries based on polyethylene oxide (PEO) polymer electrolyte with LiTFSI. We consider that ionization of the electrolyte near the cathode at the end of the recharge step is probably responsible for this degradation. We find that an electron is likely removed from PEO next to a TFSI anion, triggering a sequence of steps leading to neutralization of a TFSI anion and anchoring of another TFSI to the PEO. This decreases the polymer conductivity near the cathode, making it easier to ionize additional PEO and leading to complete degradation of the battery. We refer to this as the Cathode Overpotential Driven Ionization of the Solvent (CODIS) model. We suggest possible ways to confirm experimentally our interpretation and propose modifications to suppress or reduce electrolyte degradation.

19.
Cell ; 174(3): 672-687.e27, 2018 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-30053426

RESUMO

TCR-signaling strength generally correlates with peptide-MHC binding affinity; however, exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high frequency in the human T cell repertoire. Here, we studied human TCRs that are refractory to activation by pMHC ligands despite robust binding. Analysis of 3D affinity, 2D dwell time, and crystal structures of stimulatory versus non-stimulatory TCR-pMHC interactions failed to account for their different signaling outcomes. Using yeast pMHC display, we identified peptide agonists of a formerly non-responsive TCR. Single-molecule force measurements demonstrated the emergence of catch bonds in the activating TCR-pMHC interactions, correlating with exclusion of CD45 from the TCR-APC contact site. Molecular dynamics simulations of TCR-pMHC disengagement distinguished agonist from non-agonist ligands based on the acquisition of catch bonds within the TCR-pMHC interface. The isolation of catch bonds as a parameter mediating the coupling of TCR binding and signaling has important implications for TCR and antigen engineering for immunotherapy.


Assuntos
Antígenos de Histocompatibilidade Classe I/fisiologia , Ativação Linfocitária/fisiologia , Adulto , Feminino , Humanos , Cinética , Ligantes , Complexo Principal de Histocompatibilidade/fisiologia , Masculino , Pessoa de Meia-Idade , Simulação de Dinâmica Molecular , Oligopeptídeos , Peptídeos , Ligação Proteica/fisiologia , Receptores de Antígenos de Linfócitos T/metabolismo , Receptores de Antígenos de Linfócitos T/fisiologia , Transdução de Sinais , Imagem Individual de Molécula , Linfócitos T/fisiologia
20.
Nat Commun ; 9(1): 1809, 2018 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-29728558

RESUMO

Developing cost-effective electrocatalysts operated in the same electrolyte for water splitting, including oxygen and hydrogen evolution reactions, is important for clean energy technology and devices. Defects in electrocatalysts strongly influence their chemical properties and electronic structures, and can dramatically improve electrocatalytic performance. However, the development of defect-activated electrocatalyst with an efficient and stable water electrolysis activity in alkaline medium remains a challenge, and the understanding of catalytic origin is still limited. Here, we highlight defect-enriched bifunctional eletrocatalyst, namely, three-dimensional iron fluoride-oxide nanoporous films, fabricated by anodization/fluorination process. The heterogeneous films with high electrical conductivity possess embedded disorder phases in crystalline lattices, and contain numerous scattered defects, including interphase boundaries, stacking faults, oxygen vacancies, and dislocations on the surfaces/interface. The heterocatalysts efficiently catalyze water splitting in basic electrolyte with remarkable stability. Experimental studies and first-principle calculations suggest that the surface/edge defects contribute significantly to their high performance.

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