The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties

Jensen, Jan H.; Kromann, Jimmy C.

doi:10.1021/ed400164n

Cited by 39 publications

(33 citation statements)

References 7 publications

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“…Thus, it is widely used for visualization in multiple websites for displaying structures retrieved from databases [48], as well as for calculations and for extracting information from files with molecular data in web applications such as protein sequences from PDB files ( Figure 3C,D) [16]. Also, JSmol is often used for building molecules and submitting them to servers for calculations through third-party programs, as in the MolCalc [49] web app for fast quantum mechanics-based estimation of molecular properties using GAMESS [50], whose results are displayed back through JSmol-a very interesting tool for education, outreach, and simple research questions. Further interesting resources built from JSmol are a Crystal Symmetry Explorer, including a tool to create files for 3D printing directly from JSmol [51], web interfaces that connect structures to spectral data display with JSpecView described above, and a powerful molecular editor dubbed "Hack-a-mol", described next.…”

Section: Javascript Molecular Viewers Editors and Calculators Frommentioning

confidence: 99%

Web Apps Come of Age for Molecular Sciences

Abriata

2017

Informatics

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Whereas server-side programs are essential to maintain databases and run data analysis pipelines and simulations, client-side web-based computing tools are also important as they allow users to access, visualize and analyze the content delivered to their devices on-the-fly and interactively. This article reviews the best-established tools for in-browser plugin-less programming, including JavaScript as used in HTML5 as well as related web technologies. Through examples based on JavaScript libraries, web applets, and even full web apps, either alone or coupled to each other, the article puts on the spotlight the potential of these technologies for carrying out numerical calculations, text processing and mining, retrieval and analysis of data through queries to online databases and web services, effective visualization of data including 3D visualization and even virtual and augmented reality; all of them in the browser at relatively low programming effort, with applications in cheminformatics, structural biology, biophysics, and genomics, among other molecular sciences.

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Section: Javascript Molecular Viewers Editors and Calculators Frommentioning

confidence: 99%

Web Apps Come of Age for Molecular Sciences

Abriata

2017

Informatics

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“…Recent development in the field of high-performance computing (HPC) and cloud computing has led to many online computing platforms. For instance, MatCloud [1], rescale [2], WebMO [3], and MolCalc [4], provide web services for materials and chemistry calculation. These web-based tools provide remotely controlling computing resources, and their accessibility and compatibility make them extremely popular.…”

Section: Introductionmentioning

confidence: 99%

3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal

et al. 2020

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Background: The increasing number of organic and inorganic structures promotes the development of the "Big Data" in chemistry and material science, and raises the need for cross-platform and web-based methods to search, view and edit structures. Many web-based three-dimensional (3D) structure tools have been developed for displaying existing models, building new models, and preparing initial input files for external calculations. But few of these tools can deal with crystal structures. Results: We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. Four displayed styles, namely "Primitive cell", "Original", "In-cell" and "Packing" can be used to visualize a unit cell. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen. Conclusions: 3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT opensource license and is available on: https ://matge n.nscc-gz.cn/Tools .html.

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Section: Introductionunclassified

“…El impacto de los laboratorios virtuales, y la disyuntiva entre experimentos tradicionales y virtuales, han sido objeto de un considerable interés por parte de la comunidad educativa en los últimos años en diferentes áreas de conocimiento: Física (Deutsch, 2014;Finkelstein, 2005;Franco, 2013;Wieman, 2008), Química (Bortnik, 2017;Climent-Bellido, 2003; García Armada, 2016;Jensen, 2013;Moore, 2014; Tatli, 2010), Biología y Ciencias de la Vida (Lewis, 2014;Sanz, 2005;Stuckey-Mickell, 2007) e Ingeniería (Chan, 2009;Heradio, 2016;Ma, 2006;Potkonjak, 2016).…”

Section: Introductionunclassified

“…Su uso presenta muchas ventajas (Bortnik, 2017;Chan, 2009;Climent-Bellido, 2003;Cobb, 2009;De Jong, 2013;Franco, 2013; García Armada, 2016;Heradio, 2016;Jensen, 2013): fomentan el trabajo en equipo, son motivantes, implican menos costes que los laboratorios tradicionales, fomentan la creatividad y un aprendizaje más autónomo, se pueden repetir las experiencias tantas veces como sea necesario, disminuyen el miedo al error y al fracaso por parte del discente, facilitan la visualización de procesos y conceptos abstractos, y permiten al docente llevar a cabo actividades de laboratorio sin tener que cambiar de aula. Además, ofrecen alternativas para la enseñanza híbrida y a distancia.El impacto de los laboratorios virtuales, y la disyuntiva entre experimentos tradicionales y virtuales, han sido objeto de un considerable interés por parte de la comunidad educativa en los últimos años en diferentes áreas de conocimiento: Física (Deutsch, 2014;Finkelstein, 2005;Franco, 2013;Wieman, 2008), Química (Bortnik, 2017;Climent-Bellido, 2003; García Armada, 2016;Jensen, 2013;Moore, 2014; Tatli, 2010), Biología y Ciencias de la Vida (Lewis, 2014;Sanz, 2005;Stuckey-Mickell, 2007) e Ingeniería (Chan, 2009;Heradio, 2016;Ma, 2006;Potkonjak, 2016).En general, diferentes estudios, tanto de Ciencias Experimentales como de Ciencias de la Salud, muestran niveles similares de éxito con ambos enfoques en cuanto a calificaciones, adquisición de contenidos y/o valoración (Cobb, 2009;Darrah, 2014;De Jong, 2013;Hawkins, 2013;Klar, 2007;Lewis, 2014;Makransky, 2016;Pyatt, 2012; Spernjak, 2017;Triona, 2003;Tsihouridis, 2013;Winkelmann, 2014;…”

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Valoración del alumnado de los experimentos virtuales frente a los experimentos tradicionales

Pérez

García

Cortés

et al. 2018

Libro De Actas IN-RED 2018: IV Congreso Nacional De Innovación Educativa Y Docencia en Red

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Traditional laboratory experiments are critical to the learning process across all areas and levels of study in science subjects. However, along with hands-on experiments, virtual labs have received considerable attention over the past several years due to the popularisation of ICT tools in Education, which may help teachers consider multiple learning styles to pursue meaningful learning. In this regard, studies concerning pupils' experiences with both approaches are needed. The main aim of this study is to analyse the impact of the use of both virtual and hands-on labs in basic science subjects (BSS) in Health Sciences university degrees. For this reason, we have analysed different variables: general assessment, level of satisfaction, increase in motivation and increase in academic performance concerning BSS, as well as gender differences in the perception of both methodologies.A total of 129 undergraduate students from one Spanish university (degree in Dentistry) participated in the study. The results point out to statistically significant differences in favour of traditional labs in all the considered parameters.In conclusion, the results point out the importance of carrying out hands-on experiments to boost students' motivation and performance. Keywords: laboratory, ICT, simulation, interactivity, active learning. Resumen Las prácticas de laboratorio tradicionales juegan un papel protagonista en la enseñanza de las ciencias en todas las áreas y niveles. Sin embargo, en los últimos años la popularidad de los laboratorios virtuales ha aumentado significativamente, debido a que la aplicación de las herramientas TIC en educación permite atender adecuadamente a la diversidad del alumnado y fomentar el aprendizaje activo. En este sentido, resulta necesario estudiar las experiencias del alumnado con ambos enfoques. 270 Valoración del alumnado de los experimentos virtuales frente a los experimentos tradicionales 2018, Universitat Politècnica de ValènciaCongreso IN-RED (2018) IntroducciónEn la enseñanza del siglo XXI, las TIC (Tecnologías de la Información y Comunicación) aplicadas a la educación (es decir, las TAC, Tecnologías del Aprendizaje y del Conocimiento) ocupan un lugar protagonista. Con su uso, se pretende fomentar una mayor implicación por parte del alumnado, lo cual constituye la base del constructivismo (Coll, 2007;Hyslop-Margison, 2007;Phillips, 1995;Pozo, 2006;Spencer, 1999), que fomenta el aprendizaje activo y significativo (Freeman, 2014;Michael, 2006;Pinto, 2008;Prince, 2004). Esta corriente es especialmente importante en las orientaciones metodológicas que los expertos proponen a los docentes de las asignaturas de Ciencias (Pinto, 2008;Pozo, 2006;Rocard, 2007; Sanmartí, 2009), fomentando la comprensión frente a la mera memorización, esto es, desarrollando habilidades cognitivas de orden superior, de acuerdo con la taxonomía de Bloom de los objetivos didácticos (Cook, 2013;Krathwohl, 2002).Con el auge de Internet y las TIC (Livingstone, 2012), no sólo la enseñanza presencial tradicional...

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The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties

Cited by 39 publications

References 7 publications

Web Apps Come of Age for Molecular Sciences

Web Apps Come of Age for Molecular Sciences

3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal

Valoración del alumnado de los experimentos virtuales frente a los experimentos tradicionales

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