Theresa Julia Zielinski

Quantum-Mechanical Prediction of Tautomeric Equilibria

Publisher Summary This chapter illustrates the scope and limitations of quantum-mechanical methods and several aspects of the tautomeric equilibria of heterocyclic compounds are discussed. Quantum-mechanical studies on the tautomerism of heterocyclic compounds generally involve two aspects. The first deals with the prediction of physicochemical properties of defined tautomeric forms, such as ultraviolet spectra, dipole moments, and ionization potentials. Using any semi-empirical or non-empirical quantum-mechanical computational method, depending on approximations involved in the method, the properties that more or less, agree with experimental values can be calculated. Calculations of this type do not contribute to a direct estimation of the relative stability of the tautomers. However, they are particularly important for cases in which a tautomeric form of a compound is so rare that it is not possible to measure it directly. The second covers the prediction of the relative stability of tautomers in vapor phase and the estimation of the tautomeric constant in this phase, prediction of the influence of substituents, such as methyl group, halogen atom on the shift of tautomeric equilibrium (the relative change of tautomeric constant caused by substituents), and even the estimation of the stability of defined tautomers in solution. The difficulties connected with an attempt to apply quantum chemistry in this case are also discussed in the chapter.

Computer graphics presentations and analysis of hydrogen bonds from molecular dynamics simulation

To obtain better insights into the dynamic nature of hydrogen bonding, computer graphics representations were introduced as an aid for the analysis of molecular dynamics trajectories. A schematic representation of hydrogen bonding patterns is generated to reflect the frequency and the type of hydrogen bonding occurring during the simulation period. Various trajectory plots for monitoring geometrical parameters and for analyzing three-center hydrogen bonding were also generated. The methods proposed are applicable to a variety of biopolymers. In this study, hydrogen bonding in the d(G)6.d(C)6 system was examined. For the nucleic acid fragments examined, three-center hydrogen bonds can be classified as in-plane and major or minor groove types. The in-plane three-center hydrogen bond represents a stable state in which both bonds simultaneously satisfy the relaxed hydrogen bonding criteria for a measurable period. On the other hand, groove three-center hydrogen bonds behave as a transient intermediate state in a flip-flop hydrogen bonding system.

High propeller twist and unusual hydrogen bonding patterns from the MD simulation of (dG)6 · (dC)6

A molecular dynamics (MD) study of (dG)6 · (dC)6 including counter ions and 292 water molecules was made. The hydrogen bonding pattern and propeller twist angles for the mini‐helix are reported as averages for times spanning 21–30, 31–40, 41–50, and 51–60 ps. The propeller twist angles range from 18° to 38°. Bifurcated and interstrand neighboring base (twisted) hydrogen bonding patterns were found.

What Chemists (or Chemistry Students) Need to Know about Computing

During the on-line conference, “Applications of Technology in Teaching Chemistry,” June 14-August 20, 1993, the topic “What Chemists (or Chemistry Students) Need to Know About Computing” generated considerable discussion. In this paper some of the key points of the discussion are collected and integrated with information from the literature. The key points developed here include: the computer as a tool for learning study, research, and communication; hardware, software, computing concepts and other teaching concerns; and the appropriate place for chemistry computer usage instruction. Some suggestions for access, implementation, and extent of implementation of useful skills for the chemist and chemistry student are given in the paper. The papers, graphics, discussion streams, and related materials from the on-line conference have been archived. Information on retrieving these documents and the documents themselves can be obtained through anonymous ftp: inform.umd.edu, Path: /Educational Resources/Faculty Resources and Support/Chemistry Conference (CHEMCONF).

JCE QBank:: Physical Chemistry Question Database for Quantum Chemistry

This technology report describes a collection of nearly 1000 closed-response questions for learning and assessment in undergraduate quantum chemistry. Formats include multiple-choice and multiple-response questions, plus a few fill-in-the-blank and matching questions; the questions in the collection have been tested in varied settings, accruing positive student feedback and achieving measurable learning gains. The complete JCE QBank collection, including answers, is available online for instructors.

Demystifying Some Advanced Undergraduate Chemical Computations

Introduces four symbolic mathematics worksheets for learners of physical chemistry and quantitative/instrumental analysis. The templates are designed to use Symbolic Mathematics Engine software in the service of more efficient and effective instruction.

JCE LrnComOnline: Mission Statement

A new feature column, JCE LrnComOnline, aims to promote creation, dissemination, and utilization of well-crafted online instructional modules that span the chemistry curriculum. This brief mission statement outlines the goals and parameters for the column and includes instructions for submissions.

Learning that Prepares for More Learning: Symbolic Mathematics in Physical Chemistry.

Five Mathcad templates focus student learning on pressure-volume work, the Boltzmann distribution, the Gibbs free energy function, intermolecular potentials and the second virial coefficient, and quantum mechanical tunneling.

Making physical chemistry relevant with modern chemical dynamics

Three Mathcad documents that respond to the call for relevance in physical chemistry. The focus of this column is chemical dynamics applied to atmospheric chemistry and oscillating reactions.