Artificial neural network modeling studies to predict the yield of enzymatic synthesis of betulinic acid ester

3\u3b2-O-phthalic ester of betulinic acid was synthesized from reaction of betulinic acid and phthalic anhydride using lipase as biocatalyst. This ester has clinical potential as an anticancer agent. In this study, artificial neural network (ANN) analysis of Candida antarctica lipase (Novozym 435) -catalyzed esterification of betulinic acid with phthalic anhydride was carried out. A multilayer feed-forward neural network trained with an error back-propagation algorithm was incorporated for developing a predictive model. The input parameters of the model are reaction time, reaction temperature, enzyme amount and substrate molar ratio while the percentage isolated yield of ester is the output. Four different training algorithms, belonging to two classes, namely gradient descent and Levenberg-Marquardt (LM), were used to train ANN. The paper makes a robust comparison of the performances of the above four algorithms employing standard statistical indices. The results showed that the quick propagation algorithm (QP) with 4-9-1 arrangement gave the best performances. The root mean squared error (RMSE), coefficient of determination (R2) and absolute average deviation (AAD) between the actual and predicted yields were determined as 0.0335, 0.9999 and 0.0647 for training set, 0.6279, 0.9961 and 1.4478 for testing set and 0.6626, 0.9488 and 1.0205 for validation set using quick propagation algorithm (QP)

Funktion und Mechanismus der Ethylbenzol Dehydrogenase

Typische Initialreaktionen anaerober Kohlenwasserstoffabbauwege sind die Hydroxylierung von Ethylbenzol und die Addition von Fumarat an Toluol oder Alkane. Die Hydroxylierung von Ethylbenzol zu (S)-Phenylethanol leitet den anaeroben Abbau von Ethylbenzol in denitrifizierenden Bakterien wie Aromatoleum aromaticum ein. Diese sauerstoffunabhängige und stereospezifische Reaktion wird katalysiert durch die Ethylbenzol Dehydrogenase (EbDH), ein Molybdän/Eisen-Schwefel/Häm-Enzym aus der DMSO Reduktase Familie. Der anaerobe Abbau von Toluol in denitrifizierenden Bakterien wie Thauera aromatica und der anaerobe Abbau von Alkanen in den meisten sulfatreduzierenden Bakterien wird dagegen durch die Addition von Fumarat an die Methylgruppe von Toluol bzw. an das C2 Atom der Alkane eingeleitet. Ziel dieser Arbeit war es den Reaktionsmechanismus der Ethylbenzol Dehydrogenase weiter aufzuklären sowie Untersuchungen zum Anwendungspotential des Enzyms durchzuführen. Außerdem wurden die ersten Untersuchungen zur Identifizierung eines neuartigen anaeroben Alkanabbauweges in dem sulfatreduzierenden Bakterium Desulfococcus oleovorans durchgeführt. Anhand der Kinetik von Substraten und chemoinformatischen Berechnungen wurde ein Reaktionsmechanismus für die EbDH vorgeschlagen. In der vorliegenden Dissertation wurden enzymkinetische Untersuchungen mit alternativen Substraten und Inhibitoren durchgeführt, mit denen weitere Daten zur Bestätigung des postulierten Reaktionsmechanismus erhalten wurden. Das spezifische Verhalten bzw. die Kinetik der Substrate und Inhibitoren sowie die Natur der Hydroxylierungsprodukte der Substrate geben einen starken Hinweis auf die Existenz der vermuteten Radikal- und Carbokation-Intermediate im katalytischen Mechanismus des Enzyms. So wurde festgestellt, dass die Natur und Position bestimmter Substituenten am benzylischen Ring der Substrate die Reaktivität mit der EbDH positiv und negativ beeinflussen können, indem sie die vermuteten Radikal- und/oder Carbokation-Intermediate stabilisieren oder destabilisieren. Im Gegensatz dazu können mit den EbDH Inhibitoren die Energiebarrieren zur Bildung der Radikal- und/oder Carbokation-Intermediate nicht überwunden werden. Zudem konnte in dieser Arbeit eine neuartige Klasse von Inhibitoren in Form von BN-CC Isosteren von Ethylbenzol identifiziert werden (Azaborine). Diese Untersuchungen zeigen zum ersten Mal, dass künstliche Azaborin-Derivate von organischen Verbindungen biologische Aktivität aufweisen und erbringen daher den Nachweis des Konzepts das BN-CC Isosterie zu neuartigen Verbindungen mit neuartigen Eigenschaften führen kann. Eine weitere Untersuchung in dieser Arbeit war die Bestimmung der Enantioselektivität der Wasserstoffabspaltung vom C1 Atom des Ethylsubstituenten von Ethylbenzol als initialem Schritt des Reaktionsmechanismus. Dazu wurden spezifisch deuterierte Ethylbenzolderivate synthetisiert die am C1 Atom des Ethylsubstituenten jeweils ein Deuteriumatom an Stelle eines Wasserstoffatoms in (S)- oder (R)-Konfiguration tragen. Mit enzymkinetischen Untersuchungen wurden kinetische Isotopeneffekte gemessen werden, die darauf hinweisen, dass wie für den initialen Schritt des Reaktionsmechanismus postuliert, der pro(S) Wasserstoff abgespalten wird. Zur Bestimmung des kinetischen Modells des Reaktionsmechanismus der EbDH wurden enzymkinetische Untersuchungen mit zwei ausgewählten Substraten und zwei ausgewählten artifiziellen Elektronenakzeptoren durchgeführt. Die Auswertung der Daten ergab, dass das Enzym höchstwahrscheinlich einem Ping-Pong Mechanismus folgt. Das sulfatreduzierende Bakterium Desulfococcus oleovorans verwendet für den anaeroben Alkanabbau keine Fumarat-Additionsreaktion wie andere bekannte alkanabbauende Mikroorganismen, sondern eine unbekannte Initialreaktion. Zur Identifizierung dieser Initialreaktion wurde D. oleovorans in der vorliegenden Dissertation mit Alkanen bzw. Fettsäuren als Kohlenstoff- und Elektronenquelle anaerob kultiviert und mit dem Zellextrakt der Kulturen proteomische Analysen durchgeführt. Dabei wurde festgestellt, dass drei Proteine ausschließlich in den Kulturen die auf Alkanen gewachsen waren, induziert sind. Eine massenspektrometrische Analyse dieser induzierten Proteinbanden ergab, dass es sich dabei um die drei Untereinheiten eines Ethylbenzol Dehydrogenase-ähnlichen Enzyms handelt. Die Aminosäuresequenz dieses Enzyms zeigt eine hohe Sequenzidentität zur Ethylbenzol Dehydrogenase. Aus diesem Grund wird postuliert, dass der Alkanabbau in D. oleovorans durch eine sauerstoffunabhängige Hydroxylierung der Alkane initiiert wird

A Machine Learning Based Approach to Accelerate Catalyst Discovery

Computational catalysis, in contrast to experimental catalysis, uses approximations such as density functional theory (DFT) to compute properties of reaction intermediates. But DFT calculations for a large number of surface species on variety of active site models are resource intensive. In this work, we are building a machine learning based predictive framework for adsorption energies of intermediate species, which can reduce the computational overhead significantly. Our work includes the study and development of appropriate machine learning models and effective fingerprints or descriptors to predict energies accurately for different scenarios. Furthermore, Bayesian inverse problem, that integrates experimental catalysis with its computational counterpart, uses Markov chain Monte Carlo (MCMC) methods to refine the uncertainties on the quantities-of-interest such as turnover frequency. However, large number of forward simulations required by MCMC can become a bottleneck, especially in computational catalysis, where the evaluation of likelihood functions involves finding the solution to microkinetic models. A novel and faster MCMC method is proposed to reduce the number of expensive target evaluations and to shorten the burn-in period by emulating the target along with using a better informed proposal distribution

Biomimetic Based Applications

The interaction between cells, tissues and biomaterial surfaces are the highlights of the book "Biomimetic Based Applications". In this regard the effect of nanostructures and nanotopographies and their effect on the development of a new generation of biomaterials including advanced multifunctional scaffolds for tissue engineering are discussed. The 2 volumes contain articles that cover a wide spectrum of subject matter such as different aspects of the development of scaffolds and coatings with enhanced performance and bioactivity, including investigations of material surface-cell interactions

Aplicación computacional de un nuevo algoritmo híbrido (ANN-AGDC) en cinética química

[ES] Un Algoritmo Híbrido (AH) es aquel que combina dos o más algoritmos distintos con el fin de resolver el mismo problema matemático. En el campo de la Química Física se han utilizado Algoritmos Híbridos (AH) para resolver diversos problemas, estos AH utilizan metodologías basadas en Redes Neuronales Artificiales junto con Algoritmos Genéticos. Uno de los objetivos alcanzados en este trabajo ha sido el desarrollo y diseño de un nuevo y robusto Algoritmo Híbrido para su aplicación en Cinética Química isotérmica y no isotérmica. Este algoritmo está constituido por una combinación de dos algoritmos: el método de Redes Neuronales Artificiales (ANN) y el Algoritmo General de Descenso Controlado (AGDC). La metodología ANN ha sido ampliamente utilizada en Química en áreas muy diversas. En la mayoría de los casos se utiliza la metodología ANN para obtener conclusiones de tipo cualitativo, siendo pocos los casos en los que se utiliza para obtener resultados de tipo cuantitativo. En este trabajo se planteo como otro de los objetivos fundamentales la aplicación de la metodología ANN para realizar la determinación cuantitativa de parámetros cinéticos y termodinámicos. Por otro lado el algoritmo AGDC ha sido diseñado y aplicado con éxito en el tratamiento de muchos sistemas en el campo de la Química Física, y en especial en Cinética Química. Por tanto, un algoritmo formado por la combinación de las dos metodologías, ANN y AGDC, permite la determinación cuantitativa de parámetros cinéticos y Termodinámicos de Activación con mayor grado de fiabilidad y precisión en los resultados. Además puede ser de gran ayuda en la investigación cinética de modelos y mecanismos de reacciones complejas, permitiendo identificar las etapas de un proceso cinético (modelización). Por tanto, el objetivo principal consiste en el desarrollo de un Algoritmo Híbrido capaz de determinar Parámetros Termodinámicos de Activación y las constantes individuales de velocidad de diversos mecanismos de reacción. El AH propuesto está formado por la combinación de la metodología que utiliza Redes Neuronales Artificiales y el algoritmo de Optimización Matemática AGDC. En una primera etapa se utiliza la metodología ANN para determinar los valores de los parámetros y posteriormente se ha aplicado el algoritmo AGDC para mejorar los valores de dichos parámetros

Book of abstracts of the 10th International Chemical and Biological Engineering Conference: CHEMPOR 2008

This book contains the extended abstracts presented at the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008, held in Braga, Portugal, over 3 days, from the 4th to the 6th of September, 2008. Previous editions took place in Lisboa (1975, 1889, 1998), Braga (1978), Póvoa de Varzim (1981), Coimbra (1985, 2005), Porto (1993), and Aveiro (2001). The conference was jointly organized by the University of Minho, “Ordem dos Engenheiros”, and the IBB - Institute for Biotechnology and Bioengineering with the usual support of the “Sociedade Portuguesa de Química” and, by the first time, of the “Sociedade Portuguesa de Biotecnologia”. Thirty years elapsed since CHEMPOR was held at the University of Minho, organized by T.R. Bott, D. Allen, A. Bridgwater, J.J.B. Romero, L.J.S. Soares and J.D.R.S. Pinheiro. We are fortunate to have Profs. Bott, Soares and Pinheiro in the Honor Committee of this 10th edition, under the high Patronage of his Excellency the President of the Portuguese Republic, Prof. Aníbal Cavaco Silva. The opening ceremony will confer Prof. Bott with a “Long Term Achievement” award acknowledging the important contribution Prof. Bott brought along more than 30 years to the development of the Chemical Engineering science, to the launch of CHEMPOR series and specially to the University of Minho. Prof. Bott’s inaugural lecture will address the importance of effective energy management in processing operations, particularly in the effectiveness of heat recovery and the associated reduction in greenhouse gas emission from combustion processes. The CHEMPOR series traditionally brings together both young and established researchers and end users to discuss recent developments in different areas of Chemical Engineering. The scope of this edition is broadening out by including the Biological Engineering research. One of the major core areas of the conference program is life quality, due to the importance that Chemical and Biological Engineering plays in this area. “Integration of Life Sciences & Engineering” and “Sustainable Process-Product Development through Green Chemistry” are two of the leading themes with papers addressing such important issues. This is complemented with additional leading themes including “Advancing the Chemical and Biological Engineering Fundamentals”, “Multi-Scale and/or Multi-Disciplinary Approach to Process-Product Innovation”, “Systematic Methods and Tools for Managing the Complexity”, and “Educating Chemical and Biological Engineers for Coming Challenges” which define the extended abstracts arrangements along this book. A total of 516 extended abstracts are included in the book, consisting of 7 invited lecturers, 15 keynote, 105 short oral presentations given in 5 parallel sessions, along with 6 slots for viewing 389 poster presentations. Full papers are jointly included in the companion Proceedings in CD-ROM. All papers have been reviewed and we are grateful to the members of scientific and organizing committees for their evaluations. It was an intensive task since 610 submitted abstracts from 45 countries were received. It has been an honor for us to contribute to setting up CHEMPOR 2008 during almost two years. We wish to thank the authors who have contributed to yield a high scientific standard to the program. We are thankful to the sponsors who have contributed decisively to this event. We also extend our gratefulness to all those who, through their dedicated efforts, have assisted us in this task. On behalf of the Scientific and Organizing Committees we wish you that together with an interesting reading, the scientific program and the social moments organized will be memorable for all.Fundação para a Ciência e a Tecnologia (FCT

Non-covalent interactions in organotin(IV) derivatives of 5,7-ditertbutyl- and 5,7-diphenyl-1,2,4-triazolo[1,5-a]pyrimidine as recognition motifs in crystalline self- assembly and their in vitro antistaphylococcal activity

Non-covalent interactions are known to play a key role in biological compounds due to their stabilization of the tertiary and quaternary structure of proteins [1]. Ligands similar to purine rings, such as triazolo pyrimidine ones, are very versatile in their interactions with metals and can act as model systems for natural bio-inorganic compounds [2]. A considerable series (twelve novel compounds are reported) of 5,7-ditertbutyl-1,2,4-triazolo[1,5-a]pyrimidine (dbtp) and 5,7-diphenyl- 1,2,4-triazolo[1,5-a]pyrimidine (dptp) were synthesized and investigated by FT-IR and 119Sn M\uf6ssbauer in the solid state and by 1H and 13C NMR spectroscopy, in solution [3]. The X-ray crystal and molecular structures of Et2SnCl2(dbtp)2 and Ph2SnCl2(EtOH)2(dptp)2 were described, in this latter pyrimidine molecules are not directly bound to the metal center but strictly H-bonded, through N(3), to the -OH group of the ethanol moieties. The network of hydrogen bonding and aromatic interactions involving pyrimidine and phenyl rings in both complexes drives their self-assembly. Noncovalent interactions involving aromatic rings are key processes in both chemical and biological recognition, contributing to overall complex stability and forming recognition motifs. It is noteworthy that in Ph2SnCl2(EtOH)2(dptp)2 \u3c0\u2013\u3c0 stacking interactions between pairs of antiparallel triazolopyrimidine rings mimick basepair interactions physiologically occurring in DNA (Fig.1). M\uf6ssbauer spectra suggest for Et2SnCl2(dbtp)2 a distorted octahedral structure, with C-Sn-C bond angles lower than 180\ub0. The estimated angle for Et2SnCl2(dbtp)2 is virtually identical to that determined by X-ray diffraction. Ph2SnCl2(EtOH)2(dptp)2 is characterized by an essentially linear C-Sn-C fragment according to the X-ray all-trans structure. The compounds were screened for their in vitro antibacterial activity on a group of reference staphylococcal strains susceptible or resistant to methicillin and against two reference Gramnegative pathogens [4] . We tested the biological activity of all the specimen against a group of staphylococcal reference strains (S. aureus ATCC 25923, S. aureus ATCC 29213, methicillin resistant S. aureus 43866 and S. epidermidis RP62A) along with Gram-negative pathogens (P. aeruginosa ATCC9027 and E. coli ATCC25922). Ph2SnCl2(EtOH)2(dptp)2 showed good antibacterial activity with a MIC value of 5 \u3bcg mL-1 against S. aureus ATCC29213 and also resulted active against methicillin resistant S. epidermidis RP62A

Proceedings of the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008

This volume contains full papers presented at the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008, held in Braga, Portugal, between September 4th and 6th, 2008.FC

Incorporating standardised drift-tube ion mobility to enhance non-targeted assessment of the wine metabolome (LC×IM-MS)

Liquid chromatography with drift-tube ion mobility spectrometry-mass spectrometry (LCxIM-MS) is emerging as a powerful addition to existing LC-MS workflows for addressing a diverse range of metabolomics-related questions [1,2]. Importantly, excellent precision under repeatability and reproducibility conditions of drift-tube IM separations [3] supports the development of non-targeted approaches for complex metabolome assessment such as wine characterisation [4]. In this work, fundamentals of this new analytical metabolomics approach are introduced and application to the analysis of 90 authentic red and white wine samples originating from Macedonia is presented. Following measurements, intersample alignment of metabolites using non-targeted extraction and three-dimensional alignment of molecular features (retention time, collision cross section, and high-resolution mass spectra) provides confidence for metabolite identity confirmation. Applying a fingerprinting metabolomics workflow allows statistical assessment of the influence of geographic region, variety, and age. This approach is a state-of-the-art tool to assess wine chemodiversity and is particularly beneficial for the discovery of wine biomarkers and establishing product authenticity based on development of fingerprint libraries