WORKSHOP ON THE USE OF THE MOLVIEW APPLICATION IN CHEMISTRY EDUCATION AT SMA NEGERI 5 PALANGKA RAYA

The purpose of implementing the Workshop on the Use of the MolView Application in Chemistry Education at SMA Negeri 5 Palangka Raya is to enable partner teachers (chemistry subject teachers) to facilitate students in visualizing molecular structures using the MolView application. The benefits of this activity include increasing insights and providing skills in developing teaching modules assisted by the MolView application in chemistry education. The stages of the workshop include 1) preparation stages, including field surveys, planning, administrative preparation, and providing support facilities; 2) training stages, including confirming attendance, Phase I training, Phase II training; 3) mentoring stages, including evaluation and participant support. The results of this activity can be reviewed based on participant satisfaction. This is evident from the questionnaire results filled out by the participants. In the workshop material aspect, the average score is 93.33%. The Team workshop aspect has an average score of 96.00%, the atmosphere aspect has an average score of 96.00%, and the media usage aspect has an average score of 93.78%. Furthermore, the overall satisfaction level of the workshop averages 94.78% with a "Very Satisfied" category. Therefore, it can be concluded that this training is highly significant and beneficial, and it is expected to continue for the benefit of other teachers in the future

Using Augmented Reality as a Tool for Distance Learning of VSEPR Theory

Distance learning poses challenges in most academic settings, especially at the undergraduate laboratory level. Improving this mode of learning diminishes the impact of current events on young scientists’ development of foundational laboratory concepts. Our work explores the use of augmented reality (AR) in a laboratory setting. We developed a completely virtual valence shell electron pair repulsion (VSEPR) theory lab activity consistent with the goals of Keck Science Department’s Introduction to Chemistry course’s in-person VSEPR lab activity. We were able to maintain a hands-on learning experience for students while using a tool many students already own: an iPhone as an alternative to model kits typically used for this lesson. Evaluating the efficacy of the AR lab activity was done in the Fall 2020 semester with Keck Science Department’s CHEM14 class. I used a series of post-lab surveys, for instructors and students, to determine the efficacy of our approach and gauge students’ experience with the technology. Ultimately, instructors and students found the lab activity helpful and felt AR was the most helpful in mastering VSEPR theory

Development of Guided Inquiry based E-Learning Teaching Material on the Intermolecular Forces Enriched with Molview

The intermolecular force is one of the chemistry topics covered in the high school curriculum in Indonesia. As the characteristics of chemistry concepts in general, intermolecular forces concepts can be presented in the three levels of chemical representations (microscopic, symbolic, and macroscopic).  Currently, chemistry teaching materials are available in Indonesian schools mostly have limited support for helping students to visualize the molecular aspect of intermolecular forces concepts mainly in the form of three-dimensional space (3D). This study aimed to produce an E-Learning teaching material enriched with 3D Molecular Visualization. The product (teaching material) in this study is presented by considering the syntax of guided inquiry-based learning. The product was developed with the procedure adopted from Lee and Owens, including assessment/analysis, need assessment, front-end analysis, design, and development. The product is valid and suitable to be applied in online chemistry teaching. However, further study to investigate the effectiveness of this product empirically need to be explored in the future

The electronic spectra of protonated PANH molecules

Aims. This study was designed to examine the viability of protonated nitrogen-substituted polycyclic aromatic hydrocarbons (H+PANHs) as candidates for the carriers of the diffuse interstellar bands (DIBs). Methods. We obtained the electronic spectra of two protonated PANH cations, protonated acridine and phenanthridine, using parent ion photo-fragment spectroscopy and generated theoretical electronic spectra using ab initio calculations. Results. We show that the spectra of the two species studied here do not correspond to known DIBs. However, based on the general properties derived from the spectra of these small protonated nitrogen-substituted PAHs, we propose that larger H+PANH cations represent good candidates for DIB carriers due to the expected positions of their electronic transitions in the UV-visible and their narrow spectral bands.Comment: 7 pages, 2 figures, accepted for publication in A&

New approaches to protein docking

In the first part of this work, we propose new methods for protein docking. First, we present two approaches to protein docking with flexible side chains. The first approach is a fast greedy heuristic, while the second is a branch -&-cut algorithm that yields optimal solutions. For a test set of protease-inhibitor complexes, both approaches correctly predict the true complex structure. Another problem in protein docking is the prediction of the binding free energy, which is the the final step of many protein docking algorithms. Therefore, we propose a new approach that avoids the expensive and difficult calculation of the binding free energy and, instead, employs a scoring function that is based on the similarity of the proton nuclear magnetic resonance spectra of the tentative complexes with the experimental spectrum. Using this method, we could even predict the structure of a very difficult protein-peptide complex that could not be solved using any energy-based scoring functions. The second part of this work presents BALL (Biochemical ALgorithms Library), a framework for Rapid Application Development in the field of Molecular Modeling. BALL provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility, which results from an object-oriented and generic programming approach, distinguishes it from other software packages.Der erste Teil dieser Arbeit beschäftigt sich mit neuen Ansätzen zum Proteindocking. Zunächst stellen wir zwei Ansätze zum Proteindocking mit flexiblen Seitenketten vor. Der erste Ansatz beruht auf einer schnellen, gierigen Heuristik, während der zweite Ansatz auf branch-&-cut-Techniken beruht und das Problem optimal lösen kann. Beide Ansätze sind in der Lage die korrekte Komplexstruktur für einen Satz von Testbeispielen (bestehend aus Protease-Inhibitor-Komplexen) vorherzusagen. Ein weiteres, grösstenteils ungelöstes, Problem ist der letzte Schritt vieler Protein-Docking-Algorithmen, die Vorhersage der freien Bindungsenthalpie. Daher schlagen wir eine neue Methode vor, die die schwierige und aufwändige Berechnung der freien Bindungsenthalpie vermeidet. Statt dessen wird eine Bewertungsfunktion eingesetzt, die auf der Ähnlichkeit der Protonen-Kernresonanzspektren der potentiellen Komplexstrukturen mit dem experimentellen Spektrum beruht. Mit dieser Methode konnten wir sogar die korrekte Struktur eines Protein-Peptid-Komplexes vorhersagen, an dessen Vorhersage energiebasierte Bewertungsfunktionen scheitern. Der zweite Teil der Arbeit stellt BALL (Biochemical ALgorithms Library) vor, ein Rahmenwerk zur schnellen Anwendungsentwicklung im Bereich MolecularModeling. BALL stellt eine Vielzahl von Datenstrukturen und Algorithmen für die FelderMolekülmechanik,Vergleich und Analyse von Proteinstrukturen, Datei-Import und -Export, NMR-Shiftvorhersage und Visualisierung zur Verfügung. Beim Entwurf von BALL wurde auf Robustheit, einfache Benutzbarkeit und Erweiterbarkeit Wert gelegt. Von existierenden Software-Paketen hebt es sich vor allem durch seine Erweiterbarkeit ab, die auf der konsequenten Anwendung von objektorientierter und generischer Programmierung beruht

A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond.

Drug similarity studies are driven by the hypothesis that similar drugs should display similar therapeutic actions and thus can potentially treat a similar constellation of diseases. Drug-drug similarity has been derived by variety of direct and indirect sources of evidence and frequently shown high predictive power in discovering validated repositioning candidates as well as other in-silico drug development applications. Yet, existing resources either have limited coverage or rely on an individual source of evidence, overlooking the wealth and diversity of drug-related data sources. Hence, there has been an unmet need for a comprehensive resource integrating diverse drug-related information to derive multi-evidenced drug-drug similarities. We addressed this resource gap by compiling heterogenous information for an exhaustive set of small-molecule drugs (total of 10 367 in the current version) and systematically integrated multiple sources of evidence to derive a multi-modal drug-drug similarity network. The resulting database, 'DrugSimDB' currently includes 238 635 drug pairs with significant aggregated similarity, complemented with an interactive user-friendly web interface (http://vafaeelab.com/drugSimDB.html), which not only enables database ease of access, search, filtration and export, but also provides a variety of complementary information on queried drugs and interactions. The integration approach can flexibly incorporate further drug information into the similarity network, providing an easily extendable platform. The database compilation and construction source-code has been well-documented and semi-automated for any-time upgrade to account for new drugs and up-to-date drug information

Utilização didática de ferramentas virtuais gratuitas no ensino superior de química

Selecionou-se e avaliou-se três programas gratuitos acerca de suas aplicações didáticas, a saber, a simulação em HTML Molecule Shapes, a ferramenta online MolView e o software Avogadro. Propôs-se exemplos de tais utilizações, após se discutir as características de cada programa. Concluiu-se que a aplicação das ferramentas requer diferentes abordagens e interferências do docente, de acordo com suas funcionalidades, e que somente uma ferramenta desenvolvida com o intuito didático pode atingir um aproveitamento máximo de suas capacidades