Publisher Summary This chapter deals with the recent developments regarding the description and nature of the conformation of proteins and polypeptides with special reference to the stereochemical aspects of the problem. This chapter considers the parameters that are required for an adequate description of a polypeptide chain. This chapter focuses the attention on what may be called “internal parameters”—that is, those which can be defined in terms of the relationships among atoms or units that form the building blocks of the polypeptide chains. This chapter also provides an account of the mathematical method of utilizing these parameters for calculating the coordinates of all the atoms in a suitable frame of reference, so that all the interatomic distances, and bond angles, can be calculated and their consequences worked out. This chapter observes conformations in amino acids, peptides, polypeptides, and proteins.

Conformation of Polypeptides and Proteins

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Synthetic molecular motors and mechanical machines.

The widespread use of molecular machines in biology has long suggested that great rewards could come from bridging the gap between synthetic molecular systems and the machines of the macroscopic world. In the last two decades, it has proved possible to design synthetic molecular systems with architectures where triggered large amplitude positional changes of submolecular components occur. Perhaps the best way to appreciate the technological potential of controlled molecular-level motion is to recognize that nanomotors and molecular-level machines lie at the heart of every significant biological process. Over billions of years of evolution, nature has not repeatedly chosen this solution for performing complex tasks without good reason. When mankind learns how to build artificial structures that can control and exploit molecular level motion and interface their effects directly with other molecular-level substructures and the outside world, it will potentially impact on every aspect of functional molecule and materials design. An improved understanding of physics and biology will surely follow.

The first steps on the long path to the invention of artificial molecular machines were arguably taken in 1827 when the Scottish botanist Robert Brown observed the haphazard motion of tiny particles under his microscope.1,2 The explanation for Brownian motion, that it is caused by bombardment of the particles by molecules as a consequence of the kinetic theory of matter, was later provided by Einstein, followed by experimental verification by Perrin.3,4 The random thermal motion of molecules and its implications for the laws of thermodynamics in turn inspired Gedankenexperiments (“thought experiments”) that explored the interplay (and apparent paradoxes) of Brownian motion and the Second Law of Thermodynamics. Richard Feynman’s famous 1959 lecture “There’s plenty of room at the bottom” outlined some of the promise that manmade molecular machines might hold.5,6 However, Feynman’s talk came at a time before chemists had the necessary synthetic and analytical tools to make molecular machines. While interest among synthetic chemists began to grow in the 1970s and 1980s, progress accelerated in the 1990s, particularly with the invention of methods to make mechanically interlocked molecular systems (catenanes and rotaxanes) and control and switch the relative positions of their components.7−24

Here, we review triggered large-amplitude motions in molecular structures and the changes in properties these can produce. We concentrate on conformational and configurational changes in wholly covalently bonded molecules and on catenanes and rotaxanes in which switching is brought about by various stimuli (light, electrochemistry, pH, heat, solvent polarity, cation or anion binding, allosteric effects, temperature, reversible covalent bond formation, etc.). Finally, we discuss the latest generations of sophisticated synthetic molecular machine systems in which the controlled motion of subcomponents is used to perform complex tasks, paving the way to applications and the realization of a new era of “molecular nanotechnology”.

1.1. The Language Used To Describe Molecular Machines
Terminology needs to be properly and appropriately defined and these meanings used consistently to effectively convey scientific concepts. Nowhere is the need for accurate scientific language more apparent than in the field of molecular machines. Much of the terminology used to describe molecular-level machines has its origins in observations made by biologists and physicists, and their findings and descriptions have often been misinterpreted and misunderstood by chemists. In 2007 we formalized definitions of some common terms used in the field (e.g., “machine”, “switch”, “motor”, “ratchet”, etc.) so that chemists could use them in a manner consistent with the meanings understood by biologists and physicists who study molecular-level machines.14

The word “machine” implies a mechanical movement that accomplishes a useful task. This Review concentrates on systems where a stimulus triggers the controlled, relatively large amplitude (or directional) motion of one molecular or submolecular component relative to another that can potentially result in a net task being performed. Molecular machines can be further categorized into various classes such as “motors” and “switches” whose behavior differs significantly.14 For example, in a rotaxane-based “switch”, the change in position of a macrocycle on the thread of the rotaxane influences the system only as a function of state. Returning the components of a molecular switch to their original position undoes any work done, and so a switch cannot be used repetitively and progressively to do work. A “motor”, on the other hand, influences a system as a function of trajectory, meaning that when the components of a molecular motor return to their original positions, for example, after a 360° directional rotation, any work that has been done is not undone unless the motor is subsequently rotated by 360° in the reverse direction. This difference in behavior is significant; no “switch-based” molecular machine can be used to progressively perform work in the way that biological motors can, such as those from the kinesin, myosin, and dynein superfamilies, unless the switch is part of a larger ratchet mechanism.14

Artificial Molecular Machines

This review focuses on key aspects of the thermal decomposition of multinary or mixed hydride materials, with a particular emphasis on the rational control and chemical tuning of the strategically important thermal decomposition temperature of such hydrides, Tdec. An attempt is also made to predict the thermal stability of as-yet unknown, elusive or even unknown hydrides. The future of a particularly promising class of materials for hydrogen storage, namely the catalytically enhanced complex metal hydrides, is discussed. The predictions are supported by thermodynamics considerations, calculations derived from molecular orbital (MO) theory and backed up by simple chemical insights and intuition.

Thermal decomposition of the non-interstitial hydrides for the storage and production of hydrogen.

The general conformations of a system of three linked peptide units are studied, and it is found that there are three types of conformations which contain NH…O hydrogen bonding between the first and the third units. One of them is part of a 310-helix, while the other two arc nonhelical. The two nonhelical conformations are very similar, and in both the cases the peptide chain turns around, reversing the direction of progress. Such a conformation can therefore occur in the region where a polypeptide chain folds back on itself, as in the cross-β structure. The method of representing these interesting tripeptide conformations in a (ϕ,ψ) map is described. Examples of such hydrogen-bonded, nonhelical conformations which occur in peptides and proteins are discussed—e.g., in cyclohexaglyeyl, an open tetrapeptide Gly-L-Pro-L-Leu-Gly, and in parts of the lysozyme chain.

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Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units.

Strukturuntersuchungen von trifluorsulfuryl(iv), (sf3)(+)-salzen einschliesslich der kristallstruktur von (sf3)(+)(bf4)(-)

Conformational analysis in multisulfur heterocycles part 8, 3,3/6,6-bis(tetramethylene)-s-tetrathiane and 3,3/6,6-bis(pentamethylene)-s-tetrathiane, slow s-tetrathiane chair-to-twist, chair-to-chair, and twist-to-twist interconversion

Donnees cristallographiques pour les quatre composes et spectres IR et RMN pour les composes du zirconium, du thorium et de l'uranium. Coordination tetraedrique des atomes metalliques dans tous les cas

Allan Zalkin

Papers

Strukturuntersuchungen von trifluorsulfuryl(iv), (sf3)(+)-salzen einschliesslich der kristallstruktur von (sf3)(+)(bf4)(-)

Conformational analysis in multisulfur heterocycles part 8, 3,3/6,6-bis(tetramethylene)-s-tetrathiane and 3,3/6,6-bis(pentamethylene)-s-tetrathiane, slow s-tetrathiane chair-to-twist, chair-to-chair, and twist-to-twist interconversion

Syntheses and crystal structures of the tetrakis(methyltrihydroborato) compounds of zirconium(iv), thorium(iv), uranium(iv), and neptunium(iv)