Integrating Computational Molecular Modeling into the Undergraduate Organic Chemistry Curriculum

Clauss, Allen D.; Nelsen, Stephen F.

doi:10.1021/ed086p955

Cited by 51 publications

(53 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We are currently investigating this effect on small organic molecules. 64 one is unhybridized type (mostly pure p z ), n O () and the other one is hybridized -type, n O () (s-rich) ( Figure 6). compared to all the other lone pairs (green diamond in Figure 6).…”

Section: Methodsmentioning

confidence: 99%

SynvsAntiCarboxylic Acids in Hybrid Peptides: Experimental and Theoretical Charge Density and Chemical Bonding Analysis

et al. 2018

View full text Add to dashboard Cite

A comparative study of syn vs anti carboxylic acids in hybrid peptides based on experimental electron density studies and theoretical calculations shows that, in the anti form, all three bond angles surrounding C of the -COOH group are close to ∼120°, as expected for a C-sp atom, whereas in the syn form, the ∠C-C(O)-O angle is significantly smaller by 5-10°. The oxygen atom in the carboxyl group is more electronegative in the anti form, so the polarity of the acidic O-H bond is higher in the anti form compared to the syn form, as observed within the limitations of H atom treatment in X-ray diffraction. Consequently, the investigated anti carboxylic acid forms the strongest O-H···O hydrogen bond among all model compounds. Furthermore, according to natural bond orbital analysis, the oxygen lone pairs are clearly nonequivalent, as opposed to the general notion of hybridization of equivalent sp and sp lone pairs on carbonyl or hydroxyl oxygen atoms. The hybridization of the lone pairs is directly related to the directionality and strength of hydrogen bonds.

show abstract

Section: Methodsmentioning

confidence: 99%

SynvsAntiCarboxylic Acids in Hybrid Peptides: Experimental and Theoretical Charge Density and Chemical Bonding Analysis

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The offline media used is the Spartan Student V6 software and ChemAxon reactor software as shown in Figure 1 The Spartan Student V6 software is included in an interface that makes 3D structures for organic, inorganic and organometallic compounds. Student Spartan V6 media also has the ability to display 2D sketches for organic molecules, polypeptides, polynucleotides, and has procedures for guessing transition states [13]. As with the ChemAxon Reactor application, it provides a practical way to process virtual reactions quickly, resulting in compounds that have been registered; In addition, reactions that contain rules defined in chemical terms can provide products that are synthetically feasible [11].…”

Section: Methodsmentioning

confidence: 99%

“…In addition, we can use ChemAxon reactor in learning media that can develop ability of students in predicting reactions. In addition to knowing molecular integrity, students can use the Spartan Student v6 software media in the learning of synthetic organic chemistry [11][12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

How are studentsr ability and perception in using media through synthesis organic chemistry learning?

Amsad¹,

Liliasari²,

Kadarohman³

et al. 2018

Proceedings of the Seminar Nasional Kimia - National Seminar on Chemistry (SNK 2018)

View full text Add to dashboard Cite

Lecturer usually uses media in order to help students' understanding about organic chemistry. In this research, the aim is to find out the ability and perception of students in learning by using media in the form of online and offline. The offline media we used was namely Spartan Student V6, and ChemAxon Reactor software, while the online media used is Reaction Predictor. Participants from this study were 16 students from one of the state universities in Papua. This research is a descriptive research by using the percentage of data and from questionnaire results. It shows the ability of students' in using media.. Based on the results of this study, it was found that the ability of students in using mediathrough the learning of organic synthesis was still low, around 10-40%. The media that highest used is Reaction Predictor onlinemedia and the lowest used is Spartan Student V6 offline media. It was also known that the results of students' responses for using media in learning synthetic organic chemistry are positive.

show abstract

“…1,2 In the pharmaceutical industry, computer-aided molecular design methods are now an integral part of drug discovery projects. 3,4 Incorporation of molecular modeling into the organic, 5−7 inorganic, 8 and physical chemistry 9 curriculums have all been discussed.…”

mentioning

confidence: 99%

An Integrated Visualization and Basic Molecular Modeling Laboratory for First-Year Undergraduate Medicinal Chemistry

Hayes

2014

J. Chem. Educ.

View full text Add to dashboard Cite

A 3D model visualization and basic molecular modeling laboratory suitable for first-year undergraduates studying introductory medicinal chemistry is presented. The 2 h practical is embedded within a series of lectures on drug design, target−drug interactions, enzymes, receptors, nucleic acids, and basic pharmacokinetics. Serving as a teaching aid to the lecture material, 3D models of biological macromolecules exploiting Schrodinger software and the Maestro graphical user interface (GUI) is explored to enhance student learning. A considerably positive response was received from the participants. Background and details of the laboratory are outlined, while the student handout with answers is included as Supporting Information.

show abstract

Integrating Computational Molecular Modeling into the Undergraduate Organic Chemistry Curriculum

Cited by 51 publications

References 3 publications

SynvsAntiCarboxylic Acids in Hybrid Peptides: Experimental and Theoretical Charge Density and Chemical Bonding Analysis

SynvsAntiCarboxylic Acids in Hybrid Peptides: Experimental and Theoretical Charge Density and Chemical Bonding Analysis

How are studentsr ability and perception in using media through synthesis organic chemistry learning?

An Integrated Visualization and Basic Molecular Modeling Laboratory for First-Year Undergraduate Medicinal Chemistry

Contact Info

Product

Resources

About