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1.
Chem Rec ; 23(8): e202300075, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37166396

RESUMEN

A brief account is given of highlights of our computational efforts - often in collaboration with experimental groups - to understand spectroscopic and chemical properties of ionic liquids (ILs). Molecular dynamics, including their inhomogeneous character, responsible for key spectral features observed in dielectric absorption, infra-red (IR) and fluorescence correlation spectroscopy (FCS) measurements are elucidated. Mechanisms of chemical processes involving imidazolium-based ILs are illustrated for CO2 capture and related reactions, transesterification of cellulose, and Au nanocluster-catalyzed Suzuki cross-coupling reaction with attention paid to differing roles of IL ions. A comparison with experiments is also made.

2.
Biochemistry ; 61(7): 563-574, 2022 04 05.
Artículo en Inglés | MEDLINE | ID: mdl-35315646

RESUMEN

The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH2OH) is converted to nitric oxide (NO) and nitrous oxide (N2O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c'ß-Met, the cross-link is absent, and the cytochrome instead binds H2O2 forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt c'ß-Met─a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c'ß-Met is characterized by a large ß-sheet typical of P460 members; however, several localized structural differences render cyt c'ß-Met distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c'ß from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH2OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH2OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c'ß-Met to oxidize NH2OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions.


Asunto(s)
Amoníaco , Nitrosomonas europaea , Amoníaco/metabolismo , Citocromos/química , Peróxido de Hidrógeno , Oxidación-Reducción
3.
J Cell Physiol ; 237(8): 3381-3393, 2022 08.
Artículo en Inglés | MEDLINE | ID: mdl-35696529

RESUMEN

Cytoplasmic serine/threonine Pim kinases have emerged as important modulators of immune regulation and oncology. However, their regulatory roles in bone remodeling remain obscure. Here, we aimed to determine the roles of Pim kinases in periodontal disease (PD), focusing on the regulation of osteoclastogenesis and bone resorptive activity. We investigated Pim kinases expression in PD by analyzing data from the online Gene Expression Omnibus database and using ligature-induced periodontitis mouse model. The expression of Pim kinases during receptor activator of nuclear factor kB ligand (RANKL)-induced osteoclastogenesis was assessed in mouse bone marrow-derived macrophages (BMMs) using reverse transcription polymerase chain reaction. Osteoclast differentiation and bone resorption activity were respectively verified by tartrate-resistant acid phosphatase staining and dentin disc-based bone resorption assays. We silenced and overexpressed Pim-2 using small interfering RNA (siRNA) and retroviral vector, respectively, to investigate the molecular mechanisms underlying Pim-2 regulation in RANKL-induced osteoclastogenesis and bone resorption activity. Upregulated expression of Pim-2 was observed in both patients with PD and periodontitis-affected mouse gingival tissues. siRNA-mediated silencing of Pim-2 in BMMs diminished RANKL-induced resorptive activity without affecting osteoclastogenesis. Moreover, RANKL-triggered stimulation of a3 isoform, which is a subunit of vacuolar-type ATPase, was selectively attenuated in BMMs on silencing Pim-2. The overexpression of Pim-2 with a retroviral vector stimulated the a3 subunit, thus inducing bone resorption activity. Taken together, these results suggest that Pim-2 acts as a major modulator of osteoclastic activity by regulating a3 isoform expression in PD.


Asunto(s)
Resorción Ósea , Enfermedades Periodontales , Proteínas Serina-Treonina Quinasas , Proteínas Proto-Oncogénicas , ATPasas de Translocación de Protón Vacuolares , Animales , Resorción Ósea/genética , Resorción Ósea/metabolismo , Diferenciación Celular , Silenciador del Gen , Ratones , Osteoclastos/metabolismo , Enfermedades Periodontales/genética , Enfermedades Periodontales/metabolismo , Periodontitis/genética , Periodontitis/metabolismo , Isoformas de Proteínas/metabolismo , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas Proto-Oncogénicas/genética , Proteínas Proto-Oncogénicas/metabolismo , Ligando RANK/metabolismo , ARN Interferente Pequeño/genética , ATPasas de Translocación de Protón Vacuolares/metabolismo
4.
Biochemistry ; 59(5): 704-716, 2020 02 11.
Artículo en Inglés | MEDLINE | ID: mdl-31887031

RESUMEN

A defining characteristic of bacterial cytochromes (cyt's) in the P460 family is an unusual cross-link connecting the heme porphyrin to the side chain of a lysyl residue in the protein backbone. Here, via proteomics of the periplasmic fraction of the ammonia-oxidizing bacterium (AOB) Nitrosomonas europaea, we report the identification of a variant member of the P460 family that contains a methionyl residue in place of the cross-linking lysine. We formally designate this protein cytochrome "c'ß-Met" to distinguish it from other members bearing different residues at this position (e.g., cyt c'ß-Phe from the methane-oxidizing Methylococcus capsulatus Bath). As isolated, the monoheme cyt c'ß-Met is high-spin (S = 5/2). Optical spectroscopy suggests that a cross-link is absent. Hydroxylamine, the substrate for the cross-linked cyt P460 from N. europaea, did not appreciably alter the optical spectrum of cyt c'ß with up to 1000-fold excess at pH 7.5. Cyt c'ß-Met did however bind 1 equiv of H2O2, and with a slight excess, Mössbauer spectroscopy indicated the formation of a semistable ferryl (FeIV═O) Compound II-like species. The corresponding electron paramagnetic resonance showed a very low intensity signal indicative of a radical at g = 2.0. Furthermore, cyt c'ß-Met exhibited guaiacol-dependent peroxidase activity (kcat = 20.0 ± 1.2 s-1; KM = 2.6 ± 0.4 mM). Unlike cyt c'ß-Met, cyt P460 showed evidence of heme inactivation in the presence of 2 equiv of H2O2 with no appreciable guaiacol-dependent peroxidase activity. Mutagenesis of the cross-linking lysyl residue to an alanine in cyt P460, however, reversed this lack of activity.


Asunto(s)
Citocromos c/metabolismo , Hemo/metabolismo , Compuestos de Hierro/metabolismo , Lisina/metabolismo , Nitrosomonas/química , Peroxidasa/metabolismo , Citocromos c/química , Citocromos c/genética , Espectroscopía de Resonancia por Spin del Electrón , Hemo/química , Compuestos de Hierro/química , Lisina/química , Modelos Moleculares , Nitrosomonas/citología , Nitrosomonas/metabolismo , Peroxidasa/química , Proteómica , Espectroscopía de Mossbauer
5.
Ann Surg ; 269(1): 108-113, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-28742692

RESUMEN

OBJECTIVE: To determine the toxicity and oncologic outcome of neoadjuvant chemoradiotherapy (CRT) followed by curative total mesorectal excision (TME) in the elderly (≥70 yrs) and younger (<70 yrs) rectal cancer patients. BACKGROUND: Sufficient data for elderly rectal cancer patients who received definitive trimodality have not been accumulated yet. PATIENTS AND METHODS: A total of 1232 rectal cancer patients who received neoadjuvant CRT and TME were enrolled in this study. After propensity-score matching, 310 younger patients and 310 elderly patients were matched with 1:1 manner. Treatment response, toxicity, surgical outcome, recurrence, and survival were assessed and compared between the 2 groups of patients. RESULTS: The median age was 58 years for the younger patient group and 74 years for the elderly group. Pathologic complete response rates were not significantly different between the 2 groups (younger and elderly: 17.1% vs 14.8%, P = 0.443). The 5-year recurrence-free survival (younger and elderly: 67.7% vs 65.5%, P = 0.483) and overall survival (younger and elderly: 82.9% vs. 79.5%, P = 0.271) rates were not significantly different between the 2 groups either. Adjuvant chemotherapy after surgery was less frequently delivered to the elderly than that to younger patients (83.9% vs 69.0%). Grade 3 or higher acute hematologic toxicity was observed more frequently in the elderly than that in the younger group (9.0% vs 16.1%, P = 0.008). Late complication rate was higher in the elderly group compared with that in the younger group without statistical significance (2.6% vs 4.5%, P = 0.193). CONCLUSIONS: Although acute hematologic toxicity was observed more frequently in the elderly patients than that in the younger patients, elderly rectal cancer patients with good performance status who received preoperative CRT and TME showed favorable tumor response and recurrence-free survival similar to younger patients.


Asunto(s)
Adenocarcinoma/terapia , Antineoplásicos/uso terapéutico , Colectomía/métodos , Recurrencia Local de Neoplasia/epidemiología , Cuidados Preoperatorios/métodos , Puntaje de Propensión , Neoplasias del Recto/terapia , Adenocarcinoma/diagnóstico , Adenocarcinoma/mortalidad , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Casos y Controles , Quimioradioterapia Adyuvante , Supervivencia sin Enfermedad , Femenino , Estudios de Seguimiento , Humanos , Masculino , Persona de Mediana Edad , Morbilidad/tendencias , Terapia Neoadyuvante , Estadificación de Neoplasias , Pronóstico , Neoplasias del Recto/diagnóstico , Neoplasias del Recto/mortalidad , Recto/cirugía , República de Corea/epidemiología , Estudios Retrospectivos , Tasa de Supervivencia/tendencias
6.
Phys Chem Chem Phys ; 20(29): 19339-19349, 2018 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-29989138

RESUMEN

Reaction pathways for CS2 and COS in the ionic liquid, 1-ethyl-3-methylimidazolium (EMI+) acetate (OAc-), are studied using the ab initio self-consistent reaction field theory (SCRF) and molecular dynamics (MD) computer simulations. It is found that while CS2 converts to COS nearly at the 100% level through S/O exchange with acetate, both conversion and capture processes are kinetically possible for COS, yielding CO2/thioacetate and 1-ethyl-3-methylimidazole-2-thiocarboxylate (EMI-COS)/acetic acid as reaction products, respectively. These findings are in excellent agreement with recent experimental observations in the closely related 1-butyl-3-methylimidazolium acetate (BMI+OAc-) ionic liquid system. Constrained ab initio MD indicates that the capture reaction of COS (and CS2 if allowed) proceeds in a concerted fashion; viz., proton transfer from EMI+ to OAc- and carboxylation of EMI+ by COS (and CS2) occur concurrently, analogous to the concerted pathway proposed recently for CO2 capture in the imidazolium acetate ionic liquid family. As N-heterocyclic carbene (NHC) is not required, the concerted mechanism is fully consistent with the experimental fact that NHC has not been detected directly in this ionic liquid family. Computational analysis further predicts that if NHC would be present in the ionic liquid, it would react with CS2 and produce 1-ethyl-3-imidazole-2-dithiocarboxylate, prior to the conversion of CS2 to COS. Since such a dithiocarboxylate compound was not detected experimentally, the present analysis lends support to the view that NHC is not formed in the pure imidazolium acetate ionic liquid family.

7.
J Chem Phys ; 148(19): 193830, 2018 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-30307224

RESUMEN

Many ionic liquids show behavior similar to that of glassy systems, e.g., large and long-lasted deviations from Gaussian dynamics and clustering of "mobile" and "immobile" groups of ions. Herein a time-dependent four-point density correlation function-typically used to characterize glassy systems-is implemented for the ionic liquids, choline acetate, and 1-butyl-3-methylimidazolium acetate. Dynamic correlation beyond the first ionic solvation shell on the time scale of nanoseconds is found in the ionic liquids, revealing the cooperative nature of ion motions. The traditional solvent, acetonitrile, on the other hand, shows a much shorter length-scale that decays after a few picoseconds.

8.
J Biol Chem ; 291(33): 17417-26, 2016 08 12.
Artículo en Inglés | MEDLINE | ID: mdl-27317660

RESUMEN

The cellular transport of the cofactor heme and its biosynthetic intermediates such as protoporphyrin IX is a complex and highly coordinated process. To investigate the molecular details of this trafficking pathway, we created a synthetic lesion in the heme biosynthetic pathway by deleting the gene HEM15 encoding the enzyme ferrochelatase in S. cerevisiae and performed a genetic suppressor screen. Cells lacking Hem15 are respiratory-defective because of an inefficient heme delivery to the mitochondria. Thus, the biogenesis of mitochondrial cytochromes is negatively affected. The suppressor screen resulted in the isolation of respiratory-competent colonies containing two distinct missense mutations in Nce102, a protein that localizes to plasma membrane invaginations designated as eisosomes. The presence of the Nce102 mutant alleles enabled formation of the mitochondrial respiratory complexes and respiratory growth in hem15Δ cells cultured in supplemental hemin. Respiratory function in hem15Δ cells can also be restored by the presence of a heterologous plasma membrane heme permease (HRG-4), but the mode of suppression mediated by the Nce102 mutant is more efficient. Attenuation of the endocytic pathway through deletion of the gene END3 impaired the Nce102-mediated rescue, suggesting that the Nce102 mutants lead to suppression through the yeast endocytic pathway.


Asunto(s)
Endosomas/metabolismo , Hemo/metabolismo , Mitocondrias/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Transporte Biológico Activo/fisiología , Proteínas del Citoesqueleto/genética , Proteínas del Citoesqueleto/metabolismo , Endosomas/genética , Ferroquelatasa/genética , Ferroquelatasa/metabolismo , Hemo/genética , Mitocondrias/genética , Mutación Missense , Consumo de Oxígeno/fisiología , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética
9.
J Am Chem Soc ; 139(3): 1077-1080, 2017 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-28068082

RESUMEN

Electrocatalytic water splitting to produce hydrogen comprises the hydrogen and oxygen evolution half reactions (HER and OER), with the latter as the bottleneck process. Thus, enhancing the OER performance and understanding the mechanism are critically important. Herein, we report a strategy for OER enhancement by utilizing gold nanoclusters to form cluster/CoSe2 composites; the latter exhibit largely enhanced OER activity in alkaline solutions. The Au25/CoSe2 composite affords a current density of 10 mA cm-2 at small overpotential of ∼0.43 V (cf. CoSe2: ∼0.52 V). The ligand and gold cluster size can also tune the catalytic performance of the composites. Based upon XPS analysis and DFT simulations, we attribute the activity enhancement to electronic interactions between nanocluster and CoSe2, which favors the formation of the important intermediate (OOH) as well as the desorption of oxygen molecules over Aun/CoSe2 composites in the process of water oxidation. Such an atomic level understanding may provide some guidelines for design of OER catalysts.

10.
BJU Int ; 120(5): 682-688, 2017 11.
Artículo en Inglés | MEDLINE | ID: mdl-28632935

RESUMEN

OBJECTIVES: To assess the correlation of the resected and ischaemic volume (RAIV), which is a preoperatively calculated volume of nephron loss, with the amount of postoperative renal function (PRF) decline after minimally invasive partial nephrectomy (PN) in a multi-institutional dataset. PATIENTS AND METHODS: We identified 348 patients from March 2005 to December 2013 at six institutions. Data on all cases of laparoscopic (n = 85) and robot-assisted PN (n = 263) performed were retrospectively gathered. Univariable and multivariable linear regression analyses were used to identify the associations between various time points of PRF and the RAIV, as a continuous variable. RESULTS: The mean (sd) RAIV was 24.2 (29.2) cm3 . The mean preoperative estimated glomerular filtration rate (eGFR) and the eGFRs at postoperative day 1, 6 and 36 months after PN were 91.0 and 76.8, 80.2 and 87.7 mL/min/1.73 m2 , respectively. In multivariable linear regression analysis, the amount of decline in PRF at follow-up was significantly correlated with the RAIV (ß 0.261, 0.165, 0.260 at postoperative day 1, 6 and 36 months after PN, respectively). This study has the limitation of its retrospective nature. CONCLUSION: Preoperatively calculated RAIV significantly correlates with the amount of decline in PRF during long-term follow-up. The RAIV could lead our research to the level of prediction of the amount of PRF decline after PN and thus would be appropriate for assessing the technical advantages of emerging techniques.


Asunto(s)
Neoplasias Renales/cirugía , Riñón , Nefrectomía , Tratamientos Conservadores del Órgano , Cuidados Preoperatorios/métodos , Adulto , Anciano , Femenino , Tasa de Filtración Glomerular , Humanos , Riñón/fisiopatología , Riñón/cirugía , Neoplasias Renales/fisiopatología , Masculino , Persona de Mediana Edad , Nefrectomía/métodos , Nefrectomía/estadística & datos numéricos , Tratamientos Conservadores del Órgano/métodos , Tratamientos Conservadores del Órgano/estadística & datos numéricos , Estudios Retrospectivos
11.
Phys Chem Chem Phys ; 19(18): 11709, 2017 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-28418045

RESUMEN

Correction for 'A molecular dynamics study of the ionic liquid, choline acetate' by Jon A. L. Willcox et al., Phys. Chem. Chem. Phys., 2016, 18, 14850-14858.

12.
Phys Chem Chem Phys ; 19(2): 1361-1368, 2017 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-27976766

RESUMEN

Ionic liquids (ILs) provide a promising medium for CO2 capture. Recently, the family of ILs comprising imidazolium-based cations and acetate anions, such as 1-ethyl-3-methylimidazolium acetate (EMI+OAc-), has been found to react with CO2 and form carboxylate compounds. N-Heterocyclic carbene (NHC) is widely assumed to be responsible by directly reacting with CO2 though NHC has not been detected in these ILs. Herein, a computational analysis of CO2 capture in EMI+OAc- is presented. Quantum chemistry calculations predict that NHC is unstable in a polar environment, suggesting that NHC is not formed in EMI+OAc-. Ab initio molecular dynamics simulations indicate that an EMI+ ion "activated" by the approach of a CO2 molecule can donate its acidic proton to a neighboring OAc- anion and form a carboxylate compound with the CO2 molecule. Analysis of this termolecular process indicates that the EMI+-to-OAc- proton transfer and the formation of 1-ethyl-3-methylimidazolium-2-carboxylate occur essentially concurrently. Based on these findings, a novel concerted mechanism that does not involve NHC is proposed for CO2 capture.

13.
Phys Chem Chem Phys ; 18(9): 6754-62, 2016 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-26878460

RESUMEN

Interactions of a lithium bis(trifluoromethane sulfonyl)imide (Li(+)Tf2N(-)) ion pair with oligoethers are investigated via density functional theory (DFT). As a model for polymer electrolytes polyethyleneoxide (PEO) and perfluoropolyether (PFPE), CR3(OCR2CR2)n=1-5OCR3 (R = H or F) is considered. Topographical analysis of the molecular electrostatic potential (MESP) is performed to determine preferential binding sites of Li(+). Our study shows that the MESP value near the oxygen sites of the polymer backbone is more negative for PEO than for PFPE. This result indicates that substitution of hydrogen by fluorine in polyethers leads to reduction in Li(+)-polymer interactions, in concert with the experimental ionic conductivity results. S-O stretching vibrations of Tf2N(-) are calculated for the lithium salt in the presence and absence of electrolytes. The blue and red shifts predicted for S-O stretching are further explained by natural bond orbital analysis and molecular electron density topography. The S-O stretching vibrations can be used as a useful tool to understand the ion pair interactions and thus ion transport phenomena in polymer electrolytes.

14.
Phys Chem Chem Phys ; 18(22): 14850-8, 2016 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-27188287

RESUMEN

Structural and dynamic properties of the ionic liquid (IL) choline acetate are studied using molecular dynamics (MD) simulations. The hydroxyl group of choline shows significant hydrogen-bonding interactions with the oxygen atoms of acetate. Nearly all choline cations are found to form a hydrogen bond with acetate anions at 400 K, while about 67% of cations participate in hydrogen-bonding interactions at 600 K. At 400 K, subdiffusive and prominent non-Gaussian behavior persist for t > 10 ns. At 600 K, the usual diffusion regime is obtained after a few hundred ps of subdiffusive behavior. Analysis of reorientational motions of acetate ions, particularly those of their short axes, indicates a high degree of dynamic heterogeneity, in agreement with previous work on different IL systems.

15.
J Chem Phys ; 145(4): 044502, 2016 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-27475376

RESUMEN

Influence of the excitation energy of a probe solute molecule on its solvation dynamics and emission spectrum in 1-ethyl-3-methylimidazolium hexafluorophosphate (EMI(+)PF6 (-)) is studied via molecular dynamics simulations using a coarse-grained model description. By exciting the probe at different energies, each with an extremely narrow distribution, ensuing solvent relaxation and its dynamic variance are monitored using the isoconfigurational ensemble method. Resulting Stokes shift function, S(t), indicates that long-time solvent relaxation becomes slower with the decreasing excitation energy and approaches the equilibrium correlation function, C(t), of solvent fluctuations. This suggests that the system excited at the red-edge of the spectrum observes linear response better than that at the blue-edge. A detailed analysis of nonequilibrium trajectories shows that the effect of initial configurations on variance of relaxation dynamics is mainly confined to short times; it reaches a maximum around 0.1 ≲ t ≲ 1 ps and diminishes as time further increases. The influence of the initial velocity distribution, on the other hand, tends to grow with time and dominates the long-time variations of dynamics. The emission spectrum shows the red-edge effect in accord with previous studies.

16.
J Am Chem Soc ; 137(45): 14295-304, 2015 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-26498698

RESUMEN

The catalytic activity of Au25(SR)18 nanoclusters (R = C2H4Ph) for the aldehyde hydrogenation reaction in the presence of a base, e.g., ammonia or pyridine, and transition-metal ions M(z+), such as Cu(+), Cu(2+), Ni(2+) and Co(2+), as a Lewis acid is studied. The addition of a Lewis acid is found to significantly promote the catalytic activity of Au25(SR)18/CeO2 in the hydrogenation of benzaldehyde and a number of its derivatives. Matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry in conjunction with UV-vis spectroscopy confirm the generation of new species, Au25-n(SR)18-n (n = 1-4), in the presence of a Lewis acid. The pathways for the speciation of Au24(SR)17 from its parent Au25(SR)18 nanocluster as well as its structure are investigated via the density functional theory (DFT) method. The adsorption of M(z+) onto a thiolate ligand "-SR-" of Au25(SR)18, followed by a stepwise detachment of "-SR-" and a gold atom bonded to "-SR-" (thus an "Au-SR" unit) is found to be the most likely mechanism for the Au24(SR)17 generation. This in turn exposes the Au13-core of Au24(SR)17 to reactants, providing an active site for the catalytic hydrogenation. DFT calculations indicate that M(z+) is also capable of adsorbing onto the Au13-core surface, producing a possible active metal site of a different kind to catalyze the aldehyde hydrogenation reaction. This study suggests, for the first time, that species with an open metal site like adducts [nanoparticle-M]((z-1)+) or fragments Au25-n(SR)18-n function as the catalysts rather than the intact Au25(SR)18.

17.
Phys Chem Chem Phys ; 17(9): 6248-54, 2015 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-25649989

RESUMEN

The structural stability of isoreticular metal organic frameworks, IRMOF-1 and IRMOF-10, confining ionic liquids (ILs) inside their nano-porous cavities is studied via molecular dynamics (MD) simulations. Imidazolium- and pyridinium-based ILs, including BMI(+)PF6(-), BMI(+)Br(-), BMI(+)Tf2N(-), BMI(+)DCA(-), and BuPy(+)Tf2N(-) (BMI(+) = 1-butyl-3-methylimidazolium, PF6(-) = hexafluorophosphate, Br(-) = bromide, Tf2N(-) = bis(trifluoromethylsulfonyl)imide, DCA(-) = dicyanamide, and BuPy(+) = N-butylpyridinium), at different loadings are considered. It is found that both IRMOFs are structurally unstable and deform dramatically from their crystal structure in the presence of ILs. The interactions between the metallic parts of IRMOFs and IL anions play a major role in structural disruption and collapse of these MOFs. Thus elongated anions such as Tf2N(-) and DCA(-) that can interact with two different metal sites tend to lower IRMOF stability compared to spherical anions such as Br(-) and PF6(-). A further analysis via density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations lends support to the MD results regarding structural instability of IRMOFs in the presence of ILs.

18.
Biochim Biophys Acta ; 1827(5): 627-36, 2013 May.
Artículo en Inglés | MEDLINE | ID: mdl-23380393

RESUMEN

The Succinate Dehydrogenase (SDH) heterotetrameric complex catalyzes the oxidation of succinate to fumarate in the tricarboxylic acid (TCA) cycle and in the aerobic respiratory chains of eukaryotes and bacteria. Essential in this catalysis is the covalently-linked cofactor flavin adenine dinucleotide (FAD) in subunit1 (Sdh1) of the SDH enzyme complex. The mechanism of FAD insertion and covalent attachment to Sdh1 is unknown. Our working concept of this flavinylation process has relied mostly on foundational works from the 1990s and by applying the principles learned from other enzymes containing a similarly linked FAD. The discovery of the flavinylation factor Sdh5, however, has provided new insight into the possible mechanism associated with Sdh1 flavinylation. This review focuses on encapsulating prior and recent advances towards understanding the mechanism associated with flavinylation of Sdh1 and how this flavinylation process affects the overall assembly of SDH. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.


Asunto(s)
Complejo II de Transporte de Electrones/metabolismo , Flavina-Adenina Dinucleótido/metabolismo , Proteínas Mitocondriales/metabolismo , Succinato Deshidrogenasa/metabolismo , Complejo II de Transporte de Electrones/química , Humanos , Proteínas Mitocondriales/química , Modelos Moleculares , Unión Proteica , Estructura Terciaria de Proteína , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Succinato Deshidrogenasa/química
19.
J Phys Chem A ; 118(13): 2547-57, 2014 Apr 03.
Artículo en Inglés | MEDLINE | ID: mdl-24611825

RESUMEN

Electronic structure theory (density functional and Møller-Plesset perturbation theory) and vibrational spectroscopy (FT-IR and Raman) are employed to study molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Different conformers of a cation-anion pair based on their molecular interactions are simulated in the gas phase and in a dielectric continuum solvent environment. Although the ordering of conformers in energy varies with theoretical methods, their predictions for three lowest energy conformers in the gas phase are similar. Strong C-H---N interactions between the acidic hydrogen atom of the cation imidazole ring and the nitrogen atom of the anion are predicted for either the lowest or second lowest energy conformer. In a continuum solvent, different theoretical methods yield the same ion-pair conformation for the lowest energy state. In both phases, the density functional method predicts that the anion is in a trans conformation in the lowest energy ion pair state. The theoretical results are compared with experimental observations from Raman scattering and IR absorption spectroscopies and manifestations of the molecular interactions in the vibrational spectra are discussed. The directions of the frequency shifts of the characteristic vibrations relative to the free anion and cation are explained by calculating the difference electron density coupled with electron density topography.


Asunto(s)
Imidazoles/química , Imidas/química , Líquidos Iónicos/química , Estructura Molecular , Teoría Cuántica , Espectroscopía Infrarroja por Transformada de Fourier , Espectrometría Raman
20.
J Phys Chem B ; 128(25): 6134-6150, 2024 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-38874477

RESUMEN

Due to their many attractive physicochemical properties, ionic liquids (ILs) have received extensive attention with numerous applications proposed in various fields of science and technology. Despite this, the molecular origins of many of their properties, such as the moisture absorption capability, are still not well understood. For insight into this, we systematically synthesized 24 types of ILs by the combination of the dimethyl phosphate anion with various types of alkyl group-substituted cyclic cations─imidazolium, pyrazolium, 1,2,3-triazolium, and 1,2,4-triazolium cations─and performed a detailed analysis of the dehumidification properties of these ILs and their aqueous solutions. It was found that these IL systems have a high dehumidification capability (DC). Among the monocationic ILs, the best performance was obtained with 1-cyclohexylmethyl-4-methyl-1,2,4-triazolium dimethyl phosphate, whose DC (per mol) value is 14 times higher than that of popular solid desiccants like CaCl2 and silica gel. Dicationic ILs, such as 1,1'-(propane-1,3-diyl)bis(4-methyl-1,2,4-triazolium) bis(dimethyl phosphate), showed an even better moisture absorption, with a DC (per mol) value about 20 times higher than that of CaCl2. Small- and wide-angle X-ray scattering measurements of eight types of 1,2,4-triazolium dimethyl phosphate ILs were performed and revealed that the majority of these ILs form nanostructures. Such nanostructures, which vary with the identity of the IL and the water content, fall into three main categories: bicontinuous microemulsions, hexagonal cylinders, and micelle-like structures. Water in the solutions exists primarily in polar regions in the nanostructures; these spaces function as water pockets at relatively low water concentrations. Since the structure and stability of the aggregated forms of the ILs are mainly governed by the interactions of nonpolar groups, the alkyl side chains of the cations play an important role in the DC and temperature-dependent equilibrium water vapor pressure of the IL solutions. Our experimental findings and molecular dynamics simulation results shed light on the moisture absorption mechanism of the IL aqueous solutions from a molecular perspective.

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