On Analysis of Temperature Based Topological Indices of Some Covid-19 Drugs

A variety of graphical invariants have been described and tested, offering lots of applications in the fields of nanochemistry, computational networks and in different scientific research areas. One commonly studied group of invariants is the topological index, which allows to research the chemical, biological, and physical properties of a chemical structure. Topological indexes are numerical quantities that can be used to describe the properties of the molecular graph. In this article, we draw from the analytically closed formulas of certain molecular structures of coronavirus such as Ribavirin, Sofosbuvir and Oseltamivir by calculating temperature based topological indices.

Structural and Computational Studies of Cobalt(II) and Copper(II) Complexes with Aromatic Heterocyclic Ligand

Two coordination complexes, a cobalt(II) complex tris(1,10-phenanthroline)-cobalt perchlorate hydrate, [Co(phen)3]·(ClO4)2·H2O(1), and a copper(II) complex tris(1,10-phenanthroline)-copper perchlorate 4-bromo-2-{[(naphthalene-1-yl)imino]methyl}phenol hydrate, [Cu(phen)3]·(ClO4)2·HL·[O] (2), [where, phen = 1,10-phenathroline as aromatic heterocyclic ligand, HL = 4-bromo-2-((Z)-(naphthalene-4-ylimino) methyl) phenol] have been synthesized and structurally characterized. Single crystal X-ray analysis of both complexes has revealed the presence of a distorted octahedral geometry around cobalt(II) and copper(II) ions. density functional theory (DFT)-based quantum chemical calculations were performed on the cationic complex [Co(phen)3]2+ and copper(II) complex [Cu(phen)3]2+ to get the structure property relationship. Hirshfeld surface and 2-D fingerprint plots have been explored in the crystal structure of both the metal complexes. To find potential SARS-CoV-2 drug candidates, both the complexes were subjected to molecular docking calculations with SARS-CoV-2 virus (PDB ID: 7BQY and 7C2Q). We have found stable docked structures where docked metal chelates could readily bound to the SARS-CoV-2 Mpro. The molecular docking calculations of the complex (1) into the 7C2Q-main protease of SARS-CoV-2 virus revealed the binding energy of −9.4 kcal/mol with a good inhibition constant of 1.834 µM, while complex (2) exhibited the binding energy of −9.0 kcal/mol, and the inhibition constant of 1.365 µM at the inhibition binding site of receptor protein. Overall, our in silico studies explored the potential role of cobalt(II) complex (1), and copper(II) complex (2) complex as the viable and alternative therapeutic solution for SARS-CoV-2.

Synthesis, Characterization and Molecular Docking of New Nucleosides and Schiff Bases Derived from Ampyrone as Antiviral Agents to Contain the COVID-19 Virus

A new series of nucleoside derivatives was prepared from the reaction of 4-aminoantipyrene with different sugar moieties. In addition, ampyrone's reaction with different aromatic aldehydes gave the corresponding Schiff base derivatives, which were also synthesized. Both molecular docking and in vitro antiviral activities at different concentrations of different synthesized compounds against SARS-CoV-2 were screened. All newly synthesized compounds were characterized on the basis of IR, 1H NMR and 13C NMR spectral data and physical data. The compounds were screened for potential cytotoxic activities. The molecular docking analysis showed that compounds 6b, 6e, 6c, 6f and 6d exhibited relatively higher binding energies (−8.1, −8.1, −8.3, −8.4 and −8.7 kcal/mol, respectively) compared to all the other compounds. However, the different compounds did not show any promising in vitro antiviral activities against SARS-CoV-2.

Computational Investigations for Identification of Bioactive Molecules from Baccaurea ramiflora and Bergenia ciliata as Inhibitors of SARS-CoV-2 Mpro

In this study, a hybrid compound library of 72 phytocompounds from two antiviral medicinal plants (Baccaurea ramiflora and Bergenia ciliata) was computationally investigated for their inhibitory potential against SARS-CoV-2 Mpro. Molecular docking showed that 6-O-vanilloylicariside B5, 6-O-vanilloylisotachioside, leucoanthocyanidin 4-(2-galloyl), and p-hydroxybenzoyl bergenin has good binding affinity for Mpro. However, p-hydroxybenzoyl bergenin did not bind at the catalytic cavity. The RMSD and RMSF data obtained from 100 ns MD simulations revealed stable protein–ligand complexes for 6-O-vanilloylicariside B5, 6-O-vanilloylisotachioside, leucoanthocyanidin 4-(2-galloyl). Ligand trajectory study found 6-O-vanilloylisotachioside and leucoanthocyanidin 4-(2-galloyl) to be stable. Studies on ligand interaction profile and timeline interaction profile showed that 6-O-vanilloylisotachioside and leucoanthocyanidin 4-(2-galloyl) interacted with HIS41–CYS145 dyad and other crucial amino acids of the catalytic site cavity during the entire 100 ns MD simulations. Molecular mechanics generalized born solvent accessibility binding free energy calculations, density functional theory analysis, quantitative structure–property relationship studies, and ADMET profiling of 6-O-vanilloylisotachioside and leucoanthocyanidin 4-(2-galloyl) supported the results generated by molecular docking and MD simulations studies. Based on the current computational investigations, we conclude that that 6-O-vanilloylisotachioside of B. ramiflora and leucoanthocyanidin 4-(2-galloyl) of B. ciliata are two potential inhibitors of SARS-CoV-2 Mpro that are worthy of further investigations.

Crystal Growth, Structural, Vibrational, Effects of Hydrogen Bonding(C-H…O and C-H…N), Chemical Reactivity, Antimicrobial Activity, Inhibitory Effects and Molecular Dynamic Simulation of 4-Methoxy-N-(Nitrobenzylidene)-Aniline

The present study aims to provide deeper knowledge about the structural, vibrational, chemical, antimicrobial activity, molecular dynamic simulation and drug likeness of synthesized compound 4-Methoxy-N-(nitrobenzylidene)-aniline. The FT-IR and FT-Raman spectra of 4-Methoxy-N-(nitrobenzylidene)-aniline have been recorded in the powder form in the region 4000–500 cm−1 and 3500–50 cm−1. The vibrational analysis were carried out with the help of normal coordinate analysis (NCA). The molecular geometry, hydrogen bonding interaction and vibrational frequencies have been calculated using the density functional method (DFT/B3LYP) with 6-311 G (D) basis set. The natural bond orbital (NBO), atoms in molecule (AIM), and Hirshfeld surface analysis and RDG were applied to evaluate the relative strength of hydrogen bond interactions and represent their effect on the stabilities of molecular arrangements. Related molecules were compared by computation in order to understand the effect of non-bonded interactions (i.e. intermolecular and intramolecular hydrogen bonding). The HOMO and LUMO analysis was used to determine the charge transfer within the molecule. Furthermore, the in vitro antimicrobial study was carried out for the title compound against Aspergillus niger and Staphylococcus aureus. The antimicrobial activity was confirmed on the compounds with molecular docking (A.niger, S.aureus, Homosapians, Sars-Cov-19 and anticancer) studies and molecular dynamic simulation. The non-linear optical (NLO) properties were also analyzed for the molecules.

Synthesis, DFT and In Silico Anti-COVID Evaluation of Novel Tetrazole Analogues

A new series of 3-aryl/heteroaryl-2-(1H-tetrazol-5-yl) acrylamides have been synthesized through catalyst-free, one-pot cascade reactions, utilizing click chemistry approach and evaluated for their anti-COVID activities against two proteins in silico. The structural properties of the synthesized molecules were evaluated based on DFT calculations. Total energy of the synthesized tetrazole compounds were obtained through computational analysis which indicate the high stability of the synthesized compounds. The Frontier Molecular Orbitals (FMO) and associated energies and molecular electrostatic potential (MEP) surfaces were generated for the compounds. Spectral analysis by DFT gave additional evidence to the structural properties of the synthesized molecules. All tetrazole analogues come under good ADMET data as they followed the standard value for ADMET parameters. Docking studies offered evidence of the molecules displaying excellent biological properties as an anti-Covid drug. Compound 4 g exhibited excellent anti-COVID-19 properties with four hydrogen binding interactions with amino acids GLN 2.486 Å, GLN 2.436 Å, THR 2.186 Å and HSD 2.468 Å with good full-fitness score (–1189.12) and DeltaG (–7.19). Similarly, compound 4d shown potent activity against anti-COVID-19 mutant protein (PDB: 3K7H) with three hydrogen binding interactions, i.e., SER 2.274 Å, GLU 1.758 Å and GLU 1.853 Å with full-fitness score of –786.60) and DeltaG (–6.85). The result of these studies revealed that the compounds have the potential to become lead molecules in the drug discovery process.

SARS‐CoV‐2 spike protein capture by peptide functionalized networks

Coronavirus disease 2019 (COVID‐19) has significantly impacted human health, the global economy, and society. Viruses residing on common surfaces represent a potential source of contamination for the general population. Spike binding peptide 1, SBP1 is a 23 amino acid peptide, which has micromolar binding affinity (1.3 μM) towards the spike protein receptor‐binding domain. We hypothesize that if we can covalently immobilize this SBP1 peptide in a covalent crosslinked network system, we can develop a surface that would preferentially bind spike protein and, therefore, which could limit viral spread. A series of covalently crosslinked networks of hydroxy ethyl acrylate (HEA) with different primary chain lengths and crosslinker density was prepared. Later, this network system was functionalized using 2% SBP1 peptide. Our study found that with a shorter chain length and lower crosslinker density, the HEA network system alone could capture almost 80% of the spike protein. We reported that the efficiency could be enhanced almost by 17% with higher crosslinker density.

Activities Carried Out in the Basic Organic Chemistry Virtual Course for First-Year Agronomic Engineering Students: Quick Question/Answer Games Using Available Applications

The COVID-19 pandemic has changed education. In these circumstances, technology aided learning by providing new ways of teaching and communicating with students. In this work, we report the online activities carried out in the Basic Organic Chemistry virtual course of the Chemistry Department at UNS (Argentina) for first-year students of the Agronomic Engineering career. In particular, we present the use and results obtained from quick question/answer games using available applications to reinforce theoretical concepts. These activities helped to review and emphasize essential concepts of the course. It is noteworthy that the proposed activities also supported learning during the return to face-to-face classes.

Approaches to Promoting Student Engagement in Organic Chemistry Before, During, and After the COVID-19 Pandemic: Insights and Reflections

Active engagement is critical to student success in Organic Chemistry. In this paper, I trace the trajectory of student engagement in an introductory organic chemistry lecture series over the course of the COVID-19 pandemic. I detail my approach to cultivating student engagement in an online environment, evaluate the success of these approaches and discuss modifications, and recount our efforts to combat the "learned disengagement” that students exhibited upon returning to an in-person class format. Although engagement gradually dwindled over the course of online instruction, multiple interventions succeeded in maintaining a sense of classroom community in students and encouraging active participation. By building opportunities for engagement into the course structure and rewarding students who partake in class activities, I hope to once again enjoy the level of engagement that we had prior to the pandemic. © 2022 American Chemical Society and Division of Chemical Education, Inc.

Applying Reuse and Reduce in an Undergraduate Organic Laboratory: Sustainable Practices

In this section of Resonance, we invite readers to pose questions likely to be raised in a classroom situation. We may suggest strategies for dealing with them, or invite responses, or both. "Classroom " is equally a forum for raising broader issues and sharing personal experiences and viewpoints on matters related to teaching and learning science.Amidst the Covid-19 pandemic, we have planned a strategy for our institution which aims towards reuse and reduce principles of Green Chemistry. Organic preparations in the undergraduate curriculum can be utilized for other sister laboratory experiments such as recrystallization, determination of physical constants (m.pt) and detection of extra elements, detection of functional group and in qualitative analysis. The product of preparation can also be subjected to a second synthesis. This approach will reduce the amount of chemicals needed for carrying out experiments other than organic preparations. This paper illustrates a few organic preparations which can be reused for other companion laboratory exercises. This approach may set a model towards sustainability for other undergraduate laboratories.

Synthesis, E-pharmacophore, Molecular Docking Studies with SARS-CoV-2 Protease, Their Biological Properties and DFT Calculation of Some New Indolo[3,2-c]Isoquinoiline Hybrids

A series of novel indolo[3,2-c]isoquinoline hybrids derivatives were synthesized. On the basis of spectroscopic and analytical data, the structures of newly synthesized compounds were determined. They were further evaluated for their in vitro antimicrobial, antioxidant anticancer and anti-TB activities. Results reveal that compounds 4a and 5a displayed better potency against all bacterial strains and compound 3b showed significant antifungal action against all fungi tested. Compound 4b display excellent antioxidant capability. Compounds 3a, 4a, and 5a bearing chloro on indolo[3,2-c]isoquinoline ring were found have higher potency against all cancer cell lines. Compound 5b displayed potent antitubercular activity against Mycobacterium tuberculosis H37Rv strain with MIC 0.12 μg/mL. Consequently, a five-point e-pharmacophore model (AADDR) was built. Docking studies displayed that compounds 2a, 2b, 3a, 4b, and 4c exhibited stronger interactions and higher binding affinity toward Glu166, Gln189, and His41, which are critical amino acid residues that play a significant role in PDB: 7D1M (SARS-CoV-2 Mpro) through hydrogen bonding, hydrophobic and π-π interactions. Further, frontier molecular orbitals studies were executed to understand their orbital energies and HOMO-LUMO lowest energy gap is 8.39 eV shown by compound 5a.

Approaches to Promoting Student Engagement in Organic Chemistry Before, During, and After the COVID-19 Pandemic: Insights and Reflections

Active engagement is critical to student success in Organic Chemistry. In this paper, I trace the trajectory of student engagement in an introductory organic chemistry lecture series over the course of the COVID-19 pandemic. I detail my approach to cultivating student engagement in an online environment, evaluate the success of these approaches and discuss modifications, and recount our efforts to combat the "learned disengagement" that students exhibited upon returning to an in-person class format. Although engagement gradually dwindled over the course of online instruction, multiple interventions succeeded in maintaining a sense of classroom community in students and encouraging active participation. By building opportunities for engagement into the course structure and rewarding students who partake in class activities, I hope to once again enjoy the level of engagement that we had prior to the pandemic.

Activities Carried Out in the Basic Organic Chemistry Virtual Course for First-Year Agronomic Engineering Students: Quick Question/ Answer Games Using Available Applications

The COVID-19 pandemic has changed education. In these circumstances, technology aided learning by providing new ways of teaching and communicating with students. In this work, we report the online activities carried out in the Basic Organic Chemistry virtual course of the Chemistry Department at UNS (Argentina) for first-year students of the Agronomic Engineering career. In particular, we present the use and results obtained from quick question/answer games using available applications to reinforce theoretical concepts. These activities helped to review and emphasize essential concepts of the course. It is noteworthy that the proposed activities also supported learning during the return to face-to-face classes.

The effect of COVID-19 restrictions on atmospheric new particle formation in Beijing

During the COVID-19 lockdown, the dramatic reduction of anthropogenic emissions provided a unique opportunity to investigate the effects of reduced anthropogenic activity and primary emissions on atmospheric chemical processes and the consequent formation of secondary pollutants. Here, we utilize comprehensive observations to examine the response of atmospheric new particle formation (NPF) to the changes in the atmospheric chemical cocktail. We find that the main clustering process was unaffected by the drastically reduced traffic emissions, and the formation rate of 1.5 nm particles remained unaltered. However, particle survival probability was enhanced due to an increased particle growth rate (GR) during the lockdown period, explaining the enhanced NPF activity in earlier studies. For GR at 1.5–3 nm, sulfuric acid (SA) was the main contributor at high temperatures, whilst there were unaccounted contributing vapors at low temperatures. For GR at 3–7 and 7–15 nm, oxygenated organic molecules (OOMs) played a major role. Surprisingly, OOM composition and volatility were insensitive to the large change of atmospheric NOx concentration;instead the associated high particle growth rates and high OOM concentration during the lockdown period were mostly caused by the enhanced atmospheric oxidative capacity. Overall, our findings suggest a limited role of traffic emissions in NPF.

A Research Presentation as a Flexible Alternative to a Practical Lab Exam in Organic Chemistry

Covid-19 public health measures have forced educators to adapt their courses to an online or hybrid presentation format with laboratory components facing particular challenges. We surmised that having introductory organic chemistry students orally present selected faculty literature publications would provide a flexible alternative to our final laboratory assessment held at the end of term, and this exercise exceeded our expectations. Using video conferencing software, students presented the research findings of a faculty publication and showed how second-year organic chemistry laboratory techniques were being similarly used by research groups on campus. Apart from improving scientific literacy and oral communication skills, this task provided students with perspective and context for the materials taught in undergraduate-level chemistry and demonstrated how even introductory lab skills are used at the highest levels of research. This presentation can be delivered online or in-person, is scalable in length and scope, and can be used in various second-year or higher-level courses. The presentation material is self-refreshing since newly published faculty papers can be provided for students to read every year. Lastly, reviewing the work of local professors has the potential to increase the sense of community and foster connections between teaching and research. Due to positive feedback from students and instructors, the research presentation has been permanently incorporated into our laboratory curriculum.

STR120: A Web-Based Board Game for Aiding Students in Review of the Structural Theory of Organic Compounds

This paper provides information about a multi-lingual (Portuguese, English, Spanish, Italian, and French) virtual card game for computers and smartphones. Facing the disruption caused by the Covid-19 pandemic, this game allows students to play remotely or face-to-face with friends in a fun and cooperative environment and review the topics related to the structural theory of organic compounds simultaneously. Brazilian and Italian undergraduate students played and evaluated the game positively. Also, learning assessments revealed that the game promotes learning equivalent to the traditional solving-problem classes. Therefore, the game is a playfu l alternative method to the conventional educational strategies for reviewing the content related to the structural theory of org a n i c compounds in a fun way in a collaborative environment in which the students discuss the answer to each question.

Labapalooza: What Happens When Students Return to In-Person Laboratories After Taking Laboratories Online for a Year?

Due to the COVID-19 pandemic, in-person undergraduate chemistry laboratories at North Carolina State University were not available to students during the 2020-2021 academic year and were replaced with online laboratories. With the return to in-person laboratories in the fall semester of 2021, there was widespread concern among the faculty that chemistry majors might struggle with the application of concepts and techniques that they learned online in the in-person lab environment. An event to bring students back to campus for a day was designed by the faculty in charge of teaching organic and analytical chemistry laboratories with extensive input from students. Participants were asked to choose the lab techniques that they wanted to review, were given agency to choose the day and time of the gathering, and were encouraged to suggest a name for the event. In this paper we describe the outcomes regarding student choices, participation, and self-assessed efficacy before and after testing in person the lab techniques that had been learned online.

Synthesis of Immucillins BCX‐1777and BCX‐4430 from a Common Precursor

A convergent route for the synthesis of BCX‐1777 and BCX‐4430 from a Boc‐protected 2‐pyrrolidinone, derived from 2,3,5‐tri‐O‐benzyl‐d‐ribonolactone, and a dihalogenated pyrrolopyrimidine as the key starting materials is reported. A chemoselective cross‐coupling was achieved from the two key starting materials in 79 % yield. Luche reduction and mesylation resulted in the stereoselective formation of an advanced intermediate in 77 % yield over two steps, which served as a precursor for synthesizing BCX‐1777 and BCX‐4430 in 38 % (over 10 steps) and 32 % (over 11 steps) overall yields, respectively, from 2,3,5‐tri‐O‐benzyl‐d‐ribonolactone.Dedicated to the students in my lab for their perseverance during the COVID-19 pandemic

Teaching organic nomenclature for pharmacy students: Adapting a course to online mode during COVID-19

Introduction: Due to the confinement of the COVID-19 pandemic, educational centres have remained closed, transferring the teaching process to online mode, thus adapting infrastructure, methodologies, and the university community. Objectives: This work aims to evaluate the effectiveness of strategies in learning organic nomenclature and seek student opinions about committing fraud in organic chemistry course assessments in the online mode in the pharmaceutical career. Methods: The methodologies used allowed the students to understand and apply the organic nomenclature rules, using online collaborative guides and crosswords worked in synchronous classes, previous reading, and the collaborative asynchronous creation of informative files for the recognition of heterocyclic compounds and formative assessment. All assessments were applied in three-people groups in the synchronous classes. Finally, an anonymous survey was administered to know the student perception of the possibility of fraud during the course. Results: A substantial improvement (from 47.7% to 80.5%) was observed in the application of IUPAC rules for organic compounds. Of the students who responded to the anonymous survey, 81% reported that the methodology used decreased the opportunity to commit fraud during assessments.

Reassessing Undergraduate Polymer Chemistry LaboratoryExperiments for Virtual Learning Environments br

Chemistry laboratory experiments are invaluable tostudents'acquisition of necessary synthetic, analytical, andinstrumental skills during their undergraduate studies. However,the COVID-19 pandemic rendered face-to-face (f2f), in-personteaching laboratory experiences impossible from late 2019-2020and forced educators to rapidly develop new solutions to deliverchemistry laboratory education remotely. Unfortunately, achievinglearning and teaching objectives to the same caliber of in-personexperiments is very difficult through distance learning. Toovercome these hurdles, educators have generated many virtual and remote learning options for not only foundational chemistrycourses but also laboratory experiments. Although the pandemic challenged high-level chemistry education, it has also created anopportunity for both students and educators to be more cognizant of virtual learning opportunities and their potential benefits withinchemistry curriculum. Irrespective of COVID-19, virtual learning techniques, especially virtual lab experiments, can complement f2flaboratories and offer a cost-efficient, safe, and environmentally sustainable alternative to their in-person counterparts.Implementation of virtual and distance learning techniques???including kitchen chemistry and at-home laboratories, prerecordedvideos, live-stream video conferencing, digital lab environment, virtual and augmented reality, and others???can provide a wide-ranging venue to teach chemistry laboratories effectively and encourage diversity and inclusivity in thefield. Despite their relevanceto real-world applications and potential to expand upon fundamental chemical principles, polymer lab experiments areunderrepresented in the virtual platform. Polymer chemistry education can help prepare students for industrial and academicpositions. The impacts of polymers in our daily life can also promote students'interests in science and scientific research. Hence, thetranslation of polymer lab experiments into virtual settings improves the accessibility of polymer chemistry education. Herein, weassess polymer experiments in the emergence of virtual learning environments and provide suggestions for further incorporation ofeffective polymer teaching and learning techniques into virtual settings