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Computational Chemistry Meets Experiments for Explaining the Geometry, Electronic Structure, and Optical Properties of Ca10V6O25
American Chemical Society (2018-11)In this paper, we present a combined experimental and theoretical study to disclose, for the first time, the structural, electronic, and optical properties of Ca10V6O25 crystals. The microwave-assisted hydrothermal (MAH) ... -
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases
The Royal Society of Chemistry (2022-03-15)While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics ... -
Computational design of biological catalysts
Royal Society of Chemistry (2008)The purpose of this tutorial review is to illustrate the way to design new and powerful catalysts. The first possibility to get a biological catalyst for a given chemical process is to use existing enzymes that catalyze ... -
Computational Modeling for the Ag Nanoparticle Coalescence Process: A Case of Surface Plasmon Resonance
American Chemical Society (2017-03)Motivated by recent transmission electron microscopy (TEM) experiments on α-Ag2WO4, the coalescence process of Ag nanoparticles (NPs) is investigated using molecular dynamics (MD) simulations. These Ag NPs are formed by ... -
Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformatión for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases
Royal Society of Chemistry (2009)Molecular dynamics simulations have been performed for non-covalent complexes of phenyl b-xylobioside with the retaining endo-b-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. ... -
Computational procedure to an accurate DFT simulation to solid state systems
Elsevier (2019-12)The density functional theory has become increasingly common as a methodology to explain the properties of crystalline materials because of the improvement in computational infrastructure and software development to perform ... -
Computational strategies for the design of new enzymatic functions
Elsevier (2015-09-15)In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels–Alder and Retro-Aldolase, ... -
Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point to Redesing New Diels-Alderases
American Chemical Society (2016-03)The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition due to its applications in organic synthesis and the ... -
Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides
American Chemical Society (2021-07-26)Environmentally friendly processes are nowadays a trending topic to get highly desired chemical compounds and, in this sense, the use of enzyme-catalyzed routes is becoming a promising alternative to traditional synthetic ... -
Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease
American Chemical Society (2017)Cysteine proteases of the papain family are involved in many diseases, making them attractive targets for developing drugs. In this paper, different catalytic mechanisms of cruzain cysteine protease have been studied on ... -
Computational study of the mechanism of half-reactions in class 1A dihydroorotate dehydrogenase from Trypanosoma cruzi
Royal Society of Chemistry (2013)Chagas' disease is considered to be a health problem affecting millions of people in Latin America. This disease is caused by the parasite Trypanosoma cruzi. Recently dihydroorotate dehydrogenase class 1A from Trypanosoma ... -
Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease
American Chemical Society (2018)Cruzain, a cysteine protease of the papain family, is essential in the development of the protozoan Trypanosoma cruzi, the etiologic agent of Chagas disease, making it an attractive target for developing new drugs. The ... -
Computational Study of the Phosphoryl Donor Activity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate
Wiley (2017-10)Adenosine triphosphate (ATP) is the main biological phosphoryl donor required in many enzymes including dihydroxyacetone kinases (DHAKs) that convert dihydroxyacetone (Dha) into dihydroxyacetone phosphate (Dha-P), a key ... -
Computational study on hydrolysis of Cefotaxime in gas phase and in aqueous solution
Wiley-Blackwell (2012)We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy ... -
Configuration interaction approach to Fermi liquid-Wigner crystal mixed phases in semiconductor nanodumbbells
American Institute of Physics (AIP) (2012)Full configuration interaction calculations demonstrate the existence of mixed correlation phases in truly three-dimensional elongated nanocrystals subject to inhomogeneous spatial confining potentials. In such phases, the ... -
Connecting morphology and photoluminescence emissions in β-Ag2MoO4 microcrystals
Elsevier (2021-10-23)This work elucidates the morphology-photoluminescence (PL) emission relationships, based on experimental and calculated results, on β-Ag2MoO4 samples synthesized by microwave-assisted hydrothermal method. It was shown that ... -
Connecting structural, optical, and electronic properties and photocatalytic activity of Ag3PO4:Mo complemented by DFT calculations
Elsevier (2018-12-15)The present join experimental and theoretical work provides in-depth understanding on the relationship among structural, optical, and electronic properties and photocatalytic activity of Ag3PO4:Mo microcrystals. We prepared ... -
Connecting the surface structure, morphology and photocatalytic activity of Ag2O: An in depth and unified theoretical investigation
Elsevier (2020-04-15)The surface morphology of the materials is known to have significant influence on the overall photocatalytic performance. Therefore, identifying the corresponding electronic structures associated with the surface redox ... -
Connecting Theory with Experiment to Understand the Sintering Processes of Ag Nanoparticles
American Chemical Society (2019-04)A complementary combination of long-time atomistic molecular dynamics simulations and real-time transmission electron microscopy (TEM) images has been utilized for unraveling, at an atomic resolution, the nature of the ... -
Convergence of Theory and Experiment on the Role of Preorganization, Quantum Tunneling, and Enzyme Motions into Flavoenzyme-Catalyzed Hydride Transfer
American Chemical Society (2017)Hydride transfer is one of the most common reactions catalyzed by enzymatic systems, and it has become an object of study because of possible significant quantum tunneling effects. In the present work, we provide a combination ...