Why Urea Eliminates Ammonia Rather than Hydrolyzes in Aqueous Solution

Alexandrova, Anastassia N.; Jorgensen, William L.

doi:10.1021/jp066478s

Cited by 97 publications

(82 citation statements)

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“…As such, it has been studied by many authors at various levels of theory, [37][38][39][40][41][42][43][44] including ab initio metadynamics calculations, [39] and elucidation of the role of the general base (H 2 O, NH 3 , histidine) in the catalytic action of serine proteases. [37] Despite its simplicity, it is still a matter of ongoing debates and therefore we consider it as an appropriate model for benchmarking the methods used further in this study.…”

Section: Resultsmentioning

confidence: 99%

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Navrátil

Klusák

Rulı́s̆ek

2013

Chemistry A European J

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Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the absence of metal ions (represented by formamide and Ala-Ala) and the hydrolysis in the presence of one and two zinc(II) ions, mimicking the active sites of mono- and dizinc metallopeptidases, respectively (by using thermolysin and glutamate carboxypeptidase II as the model catalytic systems and formamide as the model substrate). The results obtained using CCSD(T)/def2-TZVP and CCSD(T)/aug-cc-pVTZ calculations were used as the benchmark values to which the set of cheaper methods, such as (RI-)DFT, (RI-)MP2, and SCS-MP2, were referenced. It was shown that deviations of 3-5 kcal mol(-1) (translating to 2-3 orders in reaction constants) with respect to the reference CCSD(T) barriers are frequently encountered for many correlated methods and most of studied DFT functionals. It has been concluded that from the set of wave-function methods, both MP2 and SCS-MP2 methods can be recommended for smaller models (measured by the mean absolute deviation of the activation barriers over the four systems studied), whereas among the popular DFT functionals, B3LYP and especially M06-2X are likely to be reasonable choices for calculating the activation barriers of zinc metallopeptidases. Finally, with the model of glutamate carboxypeptidase II, issues related to the convergence of the calculated barriers with the size of the model system used as the representative of the enzyme active site were addressed. The intricacies related to system truncation are demonstrated, and suggest that the correlated wave-function methods may suffer from problems, such as intramolecular BSSE, which make their usage for the larger system questionable. Altogether, the presented data should contribute to efforts to understand enzymatic catalysis more deeply and to gain control of the accuracy and deficiencies of the available theoretical methods and computational approaches.

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Section: Resultsmentioning

confidence: 99%

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Navrátil

Klusák

Rulı́s̆ek

2013

Chemistry A European J

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“…Foi dada preferência ao monitoramento Esquema 1. Formação do carbamato de etila a partir da uréia [5][6][7][8][9][10][11] …”

Section: Formação De Carbamato De Etilaunclassified

“…Foi dada preferência ao monitoramento Esquema 1. Formação do carbamato de etila a partir da uréia [5][6][7][8][9][10][11] do íon m/z = 62 ([M-C 2 H 3 ]) com respeito ao íon m/z = 44, apesar deste último sinal ser o mais abundante nos espectros de massas de substancias orgânicas, quando se utiliza ionização por impacto eletrônico. Assim, este sinal estaria, em tese, mais suscetível a interferências.…”

Section: Formação De Carbamato De Etilaunclassified

“…Em presença de água a uréia decompõe-se termicamente em amônia (NH 3 ), dióxido de carbono (CO 2 ), ácidos ciânico (HOCN) e isociânico (HNCO). O ácido ciânico converte-se em ácido isociânico [5][6][7][8][9][10][11] e este último reagiria com o etanol levando à formação de CE (Esquema 1, reação II e Esquema 2). Procurando contribuir para o conhecimento da formação de CE em aguardentes, descreve-se o decaimento da concentração do íon cianato (OCN) -em soluções aquo-etanólicas.…”

Section: Introductionunclassified

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Decaimento de íons cianato e a formação de carbamato de etila

Silva¹,

Ohe²,

Franco³

2013

Quím. Nova

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Recebido em 12/11/12; aceito em 3/5/13; publicado na web em 1/7/13 CYANATE ION DECAY AND ETHYL CARBAMATE FORMATION. Cyanate ion stability was studied in aqueous/ethanolic solutions, pH = 4.5 (CH 3 COOH/NaCH 3 COO), at different temperatures. Following the decay [(OCN) -] versus time, in the presence of excess C 2 H 5 OH, the rate constant for this reaction (k 1 ) was calculated as (2.5 ± 0. Uma das rotas propostas para a formação do carbamato de etila envolve a reação de decomposição de uréia (H 2 NCONH 2 ) em meio ácido entre 60 o C e 100 o C, na presença de etanol (Esquema 1, reação I). Em presença de água a uréia decompõe-se termicamente em amônia (NH 3 ), dióxido de carbono (CO 2 ), ácidos ciânico (HOCN) e isociânico (HNCO). O ácido ciânico converte-se em ácido isociânico 5-11 e este último reagiria com o etanol levando à formação de CE (Esquema 1, reação II e Esquema 2). Procurando contribuir para o conhecimento da formação de CE em aguardentes, descreve-se o decaimento da concentração do íon cianato (OCN) -em soluções aquo-etanólicas. PARTE EXPERIMENTAL ReagentesOs reagentes e solventes utilizados, sempre de grau analítico ou cromatográfico, foram adquiridos das seguintes companhias: Sigma-Aldrich (Steinheim, Germany), Mallinckrodt Baker (Paris, United States of America), Fluka (Buchs, Switzerland), Carlo Erba (Milano, Italy) e Tedia (Phillipsburg, United States of America). A água utilizada foi previamente destilada e a seguir deionizada por um sistema Milli-Q da Millipore (Bedford, United States of America).As soluções aquo/etanólicas foram tamponadas a pH = 4,5, valor este que corresponde ao valor mediano de pH apresentado pelas aguardentes, utilizando o sistema tampão ácido acético e acetato de sódio. Estas soluções foram fortificadas com alíquotas de solução estoque de cianato de potássio, recém-preparada. As soluções resultantes foram transferidas para frascos de vidro (vials) de 28 mL, lacrados com septos de borracha e alumínio e então acondicionados em banho termostático. Alíquotas destas soluções foram retiradas de tempos em tempos para o acompanhamento do decaimento do íon cianato. . A partir destas soluções, acompanhou-se o decaimento da concentração do íon (OCN) -em função do tempo, utilizando-se a metodologia baseada na reação de ciclização do ácido 2-aminobenzóico. ) seguindo-se seu aquecimento a 65 ± 0,5 o C (banho seco) por 10 minutos. A benzoiluréia assim obtida foi resfriada à temperatura ambiente e a absorbância da solução determinada a 310 nm (ε = 412 L mol -1 cm -1 ) 6 utilizando espectrofotômetro UV-visível Hitachi modelo U-3501(Tokio, Japan). A solução de ácido 2-aminobenzóico foi sempre preparada no mesmo dia do seu uso e antes da realização dos experimentos, sendo sempre mantida ao abrigo da luz. Formação de carbamato de etilaA formação de carbamato de etila foi acompanhada utilizando--se cromatógrafo para fase gasosa Shimadzu GC-17A acoplado a espectrômetro de massas GCMS-QP5050 operando no modo SIM (monitoramento de íon seletivo com razão m/z = 62) usando impacto eletrônico de ...

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“…In this system, urea was used as the precipitant to gradually release hydroxyl ions at the appropriate reaction temperature. It is well known that decomposition of urea affords ammonia and carbon dioxide [24][25][26][27], followed by the release of OH − ions by hydrolysis of the ammonia solution. Simultaneously, the oxidation of a portion of Mn 2+ to Mn 3+ took place due to oxygen in the air, and the color of the solution changed from colorless to red-brown.…”

Section: Introductionmentioning

confidence: 99%

Shape-controlled synthesis of Mn3O4 nanocrystals and their catalysis of the degradation of methylene blue

et al. 2010

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Various sizes and shapes of Mn 3 O 4 nanocrystals have been prepared in a one-pot synthesis in extremely dilute solution by soft template self-assembly. To better control size and shape, the effects of varying the growth time, reaction temperature, surfactant, and manganese source were examined. The average size of octahedral Mn 3 O 4 crystallites was found to be related to the reaction time, while higher reaction temperature (150 °C ) and the use of a cetyltrimethylammonium bromide/poly(vinylpyrrolidone) (CTAB/PVP) mixture allowed construction of a better-defined octahedral morphologies. When PVP or poly(ethylene oxide)-poly(propylene oxide) (P123) was used as template, large-scale agglomeration resulting in loss of the octahedral morphology occurred and crystallites with a quasi-spherical shape were obtained. The nano-octahedral crystallites were shown to be an efficient catalyst for the oxidation of methylene blue.

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Why Urea Eliminates Ammonia Rather than Hydrolyzes in Aqueous Solution

Cited by 97 publications

References 78 publications

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Decaimento de íons cianato e a formação de carbamato de etila

Shape-controlled synthesis of Mn3O4 nanocrystals and their catalysis of the degradation of methylene blue

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