Using Molecular Modeling in the Organic Chemistry Course for Majors

Molecular modeling provides a way to correlate theoretical concepts with experimental data; therefore, we have introduced organic chemistry students to molecular modeling early in the first semester. This approach provides students with additional skills for clarifying chemical and theoretical concepts by means of demonstrations in the classroom and hands-on tutorial modules. In this manner the impact of the active-learning process is increased. In addition, this tool allows us to further enhance laboratory experiments already developed using a guided-inquiry approach and to design new experiments. Chemical concepts such as conformational analysis, stereochemistry, IR spectra, molecular and electronic properties, molecular orbitals, and chemical reactivity are emphasized through this approach.     

Photoelectron spectra,reactions and structures of some acyclic 2-azadiene systems

A series of substituted 2-azadiene systems has been prepared and characterized by reactivity, structure, and photoelectron-spectroscopic studies. An attempt has been made to employ photo-electron spectroscopy as a tool for predicting sites of chemical reactivity for these azadiene systems. Although such correlations can be tenuous, they seem to be useful in this limited study.     

A reactivity pattern for discrimination of ER agonism and antagonism based on 3-D molecular attributes

Various models have been developed to predict the relative binding affinity (RBA) of chemicals to estrogen receptors (ER). These models can be used to prioritize chemicals for further tiered biological testing to assess the potential for endocrine disruption. One shortcoming of models predicting RBA has been the inability to distinguish potential receptor antagonism from agonism, and hence in vivo response. It has been suggested that steroid receptor antagonists are less compact than agonists; thus, ER binding of antagonists may prohibit proper alignment of receptor protein helices preventing subsequent transactivation. The current study tests the theory of chemical bulk as a defining parameter of antagonism by employing a 3-D structural approach for development of reactivity patterns for ER antagonists and agonists. Using a dataset of 23 potent ER ligands (16 agonists, 7 antagonists), molecular parameters previously found to be associated with ER binding affinity, namely global (E(HOMO)) and local (donor delocalizabilities and charges) electron donating ability of electronegative sites and steric distances between those sites, were found insufficient to discriminate ER antagonists from agonists. However, parameters related to molecular bulk, including solvent accessible surface and negatively charged Van der Waal's surface, provided reactivity patterns that were 100% successful in discriminating antagonists from agonists in the limited data set tested. The model also shows potential to discriminate pure antagonists from partial agonist/antagonist structures. Using this exploratory model it is possible to predict additional chemicals for their ability to bind but inactivate the ER, providing a further tool for hypothesis testing to elucidate chemical structural characteristics associated with estrogenicity and anti-estrogenicity.     

A reactivity pattern for discrimination of ER agonism and antagonism based on 3-D molecular attributes

Various models have been developed to predict the relative binding affinity (RBA) of chemicals to estrogen receptors (ER). These models can be used to prioritize chemicals for further tiered biological testing to assess the potential for endocrine disruption. One shortcoming of models predicting RBA has been the inability to distinguish potential receptor antagonism from agonism, and hence in vivo response. It has been suggested that steroid receptor antagonists are less compact than agonists; thus, ER binding of antagonists may prohibit proper alignment of receptor protein helices preventing subsequent transactivation. The current study tests the theory of chemical bulk as a defining parameter of antagonism by employing a 3-D structural approach for development of reactivity patterns for ER antagonists and agonists. Using a dataset of 23 potent ER ligands (16 agonists, 7 antagonists), molecular parameters previously found to be associated with ER binding affinity, namely global ( E HOMO ) and local (donor delocalizabilities and charges) electron donating ability of electronegative sites and steric distances between those sites, were found insufficient to discriminate ER antagonists from agonists. However, parameters related to molecular bulk, including solvent accessible surface and negatively charged Van der Waal's surface, provided reactivity patterns that were 100% successful in discriminating antagonists from agonists in the limited data set tested. The model also shows potential to discriminate pure antagonists from partial agonist/antagonist structures. Using this exploratory model it is possible to predict additional chemicals for their ability to bind but inactivate the ER, providing a further tool for hypothesis testing to elucidate chemical structural characteristics associated with estrogenicity and anti-estrogenicity.     

A General Chemistry Experiment to Predict and Measure Functional-Group Stretching Frequencies

An experiment suitable for first-year students is reported. In this activity, students use a molecular modeling program to compute infrared spectra for a series of molecules. From the data obtained, students generate a group frequency chart and use it to identify unknowns. This provides students with an introduction to vibrational spectroscopy and the use of molecular modeling.     

Reaction of bromine with 4,5-dimethyl-1,4-cyclohexadiene-1,2-dicarboxylic acid: a green chemistry puzzle for organic chemistry students

Abstract

Bromination of an alkene is a typical addition reaction covered in an introductory organic chemistry course and laboratory. In this undergraduate organic chemistry laboratory exercise, students studied the bromination of a 4,5-dimethyl-1,4-cyclohexadiene-1,2-dicarboxylic acid. The reaction has an unexpected outcome as bromination yields the aromatic product, 4,5-dimethylphthalic acid. Green chemistry modification involves application of a “bromide/peroxide reaction” with NaBr/H₂O₂ in an acidic medium as an in situ source of bromine. The experiment was carried out as a two-day exercise and the students integrated molecular modeling, interpretation of mass spectra, knowledge of stability of organic compounds, and knowledge of the reaction mechanisms of addition and elimination to explain the experimental outcome.     

Measurement of the kinetics of photo-oxidation of self-assembled monolayers using friction force microscopy

The advancement of molecular nanotechnology requires new tools for the characterization of surface chemical reactivity with nanometer spatial resolution. While spectroscopy on sub-100 nm length scales remains challenging, friction force microscopy (FFM) is a promising tool for the characterization of molecular materials, although to date it has been little used in studies of surface reactivity. Here we report the use of FFM to measure the kinetics of photo-oxidation of self-assembled monolayers (SAMs) of alkanethiols adsorbed on gold surfaces. Two alternative approaches (analysis of friction-load plots and the use of line sections through images of patterned materials) are compared and found to yield data in very good agreement, with rate constants being found to be in good agreement despite being carried out on different microscopes. The use of line-section analysis provides a convenient method for the quantification of the extent of reaction in nanometer-scale patterns created in SAMs by the novel approach of scanning near-field photolithography.     

Local and nonlocal density functional calculations of the molecular structure of isomeric thiadiazoles

The chemistry of thiadiazoles and their derivatives is of considerable interest in chemistry owing to their pharmacological and potential industrial applications. In this context, a detailed study of isomeric thiadiazole molecules has been done using local (SVWN; Slater, and Vosko, Wilk and Nusair) and nonlocal (BLYP; Becke, and Lee, Yang and Parr) density functionals and optimizing the molecular geometries by means of the gradient technique. A charge sensitivity analysis of the studied molecule has been performed by resorting to density functional theory, obtaining several sensitivity coefficients such as the molecular energy, net atomic charges, global and local hardness, global and local softness and Fukui functions. With these results and the analysis of the dipole moments, the molecular electrostatic potentials and the total electron density maps, several conclusions have been inferred about the preferred sites of chemical reaction of the studied compounds. The condensed Fukui functions are shown to be one of the best criteria for predicting chemical reactivity.     

Integrating Molecular Modeling with Semiempirical Quantum Mechanical Calculations into the Upper-Level Inorganic Chemistry Course

The analysis of chemical bonding and reactivity from the perspective of molecular orbital theory is challenging for students at the undergraduate level. In an attempt to improve the instruction of this material in my upper-level inorganic chemistry course I developed a series of computational experiments using a molecular modeling program that can perform semiempirical quantum mechanical calculations. These exercises explore the chemistry of molecular systems through an analysis of the variation in the attractive and repulsive forces in the system as a function of structure or composition. The exercises challenge the analysis skills of the students by requiring them to consider how two or more factors contribute to the properties of the system. Examples of exercises that demonstrate different types of computational experiments are given. These sample exercises examine the structure of simple molecules, the reactivity of Lewis acids, and the bonding in transition metal complexes.     

Efficient chemical kinetic modeling through neural network maps

An approach to modeling nonlinear chemical kinetics using neural networks is introduced. It is found that neural networks based on a simple multivariate polynomial architecture are useful in approximating a wide variety of chemical kinetic systems. The accuracy and efficiency of these ridge polynomial networks (RPNs) are demonstrated by modeling the kinetics of H(2) bromination, formaldehyde oxidation, and H(2)+O(2) combustion. RPN kinetic modeling has a broad range of applications, including kinetic parameter inversion, simulation of reactor dynamics, and atmospheric modeling.     

Modeling drug-induced anorexia by molecular topology

Molecular topology (MT) has demonstrated to be a very good technique for describing molecular structures and to predict physical, chemical, and biological properties of compounds. In this paper, a topological-mathematical model based on MT has been developed for identifying drug compounds showing anorexia as a side effect. An external validation (test set) has been carried out, yielding over an 80% correct classification in the active and inactive compounds. These results reinforce the role of MT as a potential useful tool for predicting drug side effects.     

Synthesis and reactivity of new l-(1-adamantyl)pyrazoles

Using 1-adamantylhydrazine as starting material, a series of 1-(1-adamantyl)pyrazoles has been prepared. Electrophilic reactivity (bromination and nitration) and nucleophilic reactivity (quaternarization) have been studied. Proton nuclear magnetic resonance spectra of all the new compounds are recorded.     

Reactivity for boryl(phosphino)carbenyl carbene analogues with group 14 elements (C, Si, Ge, Sb, and Pb) as a heteroatom: a theoretical study

The potential energy surfaces for the chemical reactions of group 14 carbenes have been studied using density functional theory (B3LYP/LANL2DZ). Five boryl(phosphino)-based carbene (B-?-P) species, where ? = C, Si, Ge, Sn, and Pb, have been chosen as model reactants in this work. Also, four kinds of chemical reactions; intramolecular 1,2-migration, water insertion, alkene cycloaddition, and intermolecular dimerization, have been used to study the chemical reactivities of these group 14 carbenes. The present theoretical investigations suggest that the relative carbenic reactivity decreases in the order C > Si > Ge > Sn > Pb. That is, the heavier the group 14 atom (E), the more stable is the boryl(phosphino)-based B-?-P species towards chemical reactions. Our theoretical findings thus demonstrate that all boryl(phosphino)-based carbenes are isolable at room temperature because they are quite inert to chemical reactions, except that they are also moisture-sensitive molecules. Furthermore, the singlet-triplet energy splitting of the B-?-P, as described in the configuration mixing model attributed to the work of Pross and Shaik, can serve as a diagnostic tool for a better understanding and predicting of their chemical reactivities, kinetically and thermodynamically. The results obtained allow a number of predictions to be made.     

Calculating physical properties of organic compounds for environmental modeling from molecular structure

Mathematical models for predicting the transport and fate of pollutants in the environment require reactivity parameter values – that is the value of the physical and chemical constants that govern reactivity. Although empirical structure–activity relationships have been developed that allow estimation of some constants, such relationships are generally valid only within limited families of chemicals. The computer program, SPARC, uses computational algorithms based on fundamental chemical structure theory to estimate a large number of chemical reactivity parameters and physical properties for a wide range of organic molecules strictly from molecular structure. Resonance models were developed and calibrated using measured light absorption spectra, whereas electrostatic interaction models were developed using measured ionization pK_as in water. Solvation models (i.e., dispersion, induction, H-bonding, etc.) have been developed using various measured physical properties data. At the present time, SPARC’s physical property models can predict vapor pressure and heat of vaporization (as a function of temperature), boiling point (as a function of pressure), diffusion coefficient (as a function of pressure and temperature), activity coefficient, solubility, partition coefficient and chromatographic retention time as a function of solvent and temperature. This prediction capability crosses chemical family boundaries to cover a broad range of organic compounds.     

Vanadium-catalyzed oxidative bromination promoted by Brønsted acid or Lewis acid

The oxidative bromination of arenes was induced by a vanadium catalyst in the presence of a bromide salt and a Brønsted acid or a Lewis acid under molecular oxygen, which provides an eco-friendly bromination method as compared with a conventional bromination one with bromine. This catalytic reaction could be applied to the bromination of alkenes and alkynes to give the corresponding vic-bromides. Use of aluminum halide as a Lewis acid in place of a Brønsted acid was demonstrated to provide a more practical protocol for the oxidative bromination. From ketones, α-bromination products were obtained. AlBr₃ was found to serve as both a bromide source and a Lewis acid to induce the bromination smoothly. ⁵¹V NMR experiment showed that this catalytic bromination is likely to depend on the redox cycle of a vanadium catalyst under molecular oxygen.     

Regioselective reactivity of some 5,7-dimethoxyindoles

The reactivity of some 5,7-dimethoxyindoles with respect to electrophiles has been investigated. The favoured sites for reaction are C3 and C4 and regioselectivity can be controlled by the judicious arrangement of electron-withdrawing substituents. Results of formylation, acylation, the Mannich reaction, bromination and nitration are described.     

Trainable structure–activity relationship model for virtual screening of CYP3A4 inhibition

A new structure–activity relationship model predicting the probability for a compound to inhibit human cytochrome P450 3A4 has been developed using data for >800 compounds from various literature sources and tested on PubChem screening data. Novel GALAS (Global, Adjusted Locally According to Similarity) modeling methodology has been used, which is a combination of baseline global QSAR model and local similarity based corrections. GALAS modeling method allows forecasting the reliability of prediction thus defining the model applicability domain. For compounds within this domain the statistical results of the final model approach the data consistency between experimental data from literature and PubChem datasets with the overall accuracy of 89%. However, the original model is applicable only for less than a half of PubChem database. Since the similarity correction procedure of GALAS modeling method allows straightforward model training, the possibility to expand the applicability domain has been investigated. Experimental data from PubChem dataset served as an example of in-house high-throughput screening data. The model successfully adapted itself to both data classified using the same and different IC₅₀ threshold compared with the training set. In addition, adjustment of the CYP3A4 inhibition model to compounds with a novel chemical scaffold has been demonstrated. The reported GALAS model is proposed as a useful tool for virtual screening of compounds for possible drug-drug interactions even prior to the actual synthesis.