Advances in Physical Organic Chemistry

Ian Williams, Nick Williams

• Publisher: Academic Press
• Year: 2016
• Print ISBN: 9780128047163
• eBook ISBN: 9780128050811
• Topic: Physical Sciences
• Subtopic: Organic Chemistry

Advances in Physical Organic Chemistry series is the definitive resource for authoritative reviews of work in physical organic chemistry. It aims to provide a valuable source of information not only for physical organic chemists applying their expertise to both novel and traditional problems, but also for non-specialists across diverse areas who identify a physical organic component in their approach to research. Its hallmark is a quantitative, molecular level understanding of phenomena across a diverse range of disciplines.- Reviews the application of quantitative and mathematical methods to help readers understand chemical problems- Provides the chemical community with authoritative and critical assessments of the many aspects of physical organic chemistry- Covers organic, organometallic, bioorganic, enzymes, and materials topics- Presents the only regularly published resource for reviews in physical organic chemistry- Written by authoritative experts who cover a wide range of topics that require a quantitative, molecular-level understanding of phenomena across a diverse range of disciplines

Chapter One

Equilibrium Effective Molarity As a Key Concept in Ring-Chain Equilibria, Dynamic Combinatorial Chemistry, Cooperativity and Self-assembly

S. Di Stefano^∗,1 and G. Ercolani^{§,1 ∗}Sapienza Università di Roma, Roma, Italy ^§Università di Roma Tor Vergata, Roma, Italy
¹ Corresponding authors: E-mail: [email protected]; [email protected]

Abstract

The growing interest towards cyclizations under thermodynamic control is witnessed by the large number of papers dedicated to ring-chain equilibria, dynamic combinatorial chemistry, cooperativity and self-assembly. No doubt, in all these topics, cyclic or polycyclic molecular entities play a dominant role. In this chapter, the concept of equilibrium effective molarity (EM), which gives a quantification of the ease of formation of a cyclic compound, is presented as a fil rouge that allows a quantitative analysis of the phenomenology related to the title matters. Initially, the physicochemical bases on which the concept of EM is founded are described together with connections to the Jacobson–Stockmayer theory on intramolecular reactions in linear systems. Distributions of the species in ring-chain and ring–ring systems in terms of the EM, and conditions to obtain a selected macrocycle (self-assembly macrocyclization) are discussed. The EM concept is further applied to dynamic combinatorial libraries based on a single monomer, and two different monomers. The case of a templated dynamic library is also considered. Finally, after a due discussion of the methods for the evaluation of statistical factors, the phenomenon of cooperativity in binding processes is analysed by dissecting it into three contributions, namely, allosteric, chelate and interannular cooperativity. It is shown that the chelate effect, as measured by the EM, plays a key role for the quantifications of the latter two contributions, which are crucial for the assessment of multivalency, and the stability of molecular assemblies.

Keywords

Cooperativity; Critical concentration; Dynamic combinatorial chemistry; Effective molarity; Jacobson–Stockmayer theory; Macrocyclization equilibria; Multivalency; Ring-chain equilibria; Self-Assembly

1. Introduction

A cyclization or, more generally, the formation of any covalent or noncovalent intramolecular bond always occurs in competition with the corresponding intermolecular process. Thus, a measure of the propensity for cyclization must take into account the relative driving force of the two processes. This is customarily done by considering the ratio of the corresponding rate constants for kinetically controlled reactions (Fig. 1A and Eq. [1]), or the ratio of the corresponding equilibrium constants for reactions occurring under thermodynamic control (Fig. 1B and Eq. [2]):

EMk=kintrak

[1]

EMe=KintraK

[2]

If the concentration is expressed in mol L⁻¹, the two ratios have units of molarity and correspond to the definition of kinetic effective molarity (EM_k) and equilibrium effective molarity (EM_e), respectively. The term effective concentration, which is synonymous with effective molarity, is also in use, especially among polymer chemists. Kinetic effective molarity ...

Table of contents

• Cover image
• Title page
• Table of Contents
• Advisory Board
• Copyright
• Contributors
• Preface
• Chapter One. Equilibrium Effective Molarity As a Key Concept in Ring-Chain Equilibria, Dynamic Combinatorial Chemistry, Cooperativity and Self-assembly
• Chapter Two. Thermodynamic Effective Molarities for Supramolecular Complexes
• Chapter Three. Reactivity of Nucleic Acid Radicals
• Chapter Four. Computational Studies of Environmental Effects and Their Interplay With Experiment
• Subject Index
• Author Index
• Cumulative Index of Titles
• Cumulative Index of Authors