bluuebunny/crossref_metadata_2025 huggingface dataset:
The MAD phasing method in macromolecular crystallography: general principles and the problem of the anisotropy of anomalous scattering
Authors: Fanchon E , Hendrickson W A
Published: November 2023

Several macromolecular structures have been solved with the Multiplewavelength Anomalous Diffraction (MAD) method in the recent years (Kahn et al. 1985, Korszun 1987, Krishna Murthy et al., 1988, Guss et al., 1988, Hendrickson et al. 1988, Hendrickson, Pahler et al. 1989, Graves et al., 1990). These successes have been made possible by the availability of tunable X-ray sources, the development of efficient area detectors and by advances in the methods for analysis of MAD data. Now the instrumentation is in place to make highly accurate measurements on macromolecular crystals so as to exploit the anomalous signal in direct phase determination. In this contribution we describe briefly the theoretical basis, experimental requirements and computational implementation of the MAD method (a more detailed review can be found in Fourme Hendrickson, 1990). In the last part we treat a problem specific to MAD, namely the effect of the anisotropy of anomalous scattering on the phase determination.
The phase problem in protein crystallography: integration of multiwavelength anomalous diffraction and direct methods
Authors: Krabbendam H
Published: November 2023

Direct methods have found a successful application in the solution of the phase problem in diffraction techniques, when applied to small-molecule structures. The method depends heavily on probability relations for three-phase structure invariants and, to a lesser extent, on relations for four-phase invariants. However, the probability relations break down if the number of atoms in the unit cell becomes large, as for macromolecular structures. Attempts to extend the range of classical direct methods to small protein structures have had some success (Woolfson & Yao Jia-xing [1988]); but for a systematic application to large-size structures a more fundamental revision of the methods, notably the maximum entropy methods (Bricogne [1984],[ 1988], Bricogne & Gilmore [1990], Gilmore, Bricogne & Bannister [1990]), seems to be called for.
Sayre’s equation and histogram methods for phase refinement and extension of protein structures
Authors: Cowtan K
Published: November 2023

The solution of crystal structures by x-ray diffraction methods has in recent years progressed along two independent paths. These paths have been dictated by the different data that has been available for the solution of different types of structures, and have led to quite distinct approaches to the solution of the phase problem.
A unified approach to crystallographic refinement and molecular replacement
Authors: Brünger A T
Published: November 2023

Computer simulations of macromolecules, such as energy minimization, molecular dynamics or Monte Carlo have a demonstrated utility in providing an atomic model that is in accord with the crystal diffraction information. This allows us to present here a unified view of crystallographic refinement and molecular replacement.
What are the alternatives?
Authors: Baggott Jim
Published: November 2023

So, where do we go from here? It is apparent from the last chapter that nature denies us the easy way out. We can rule out the idea of local hidden variables, one of the simpler solutions to the conceptual problems of quantum theory. Yet the Copenhagen interpretation is regarded by some to be no interpretation at all. Even those who adhere to the Copenhagen view tend to put aside or disregard the conceptual difficulties that it raises as they analyse the results from the latest particle accelerator experiment. This is not a very satisfactory situation.
Silicon based non-oxide ceramics
Authors: Trigg* M B , Murray M J
Published: November 2023

Silicon based non-oxide ceramics such as silicon carbide and silicon nitride are an emerging new class of engineering materials. At the present time, a major barrier to the widespread utilization of these materials is the high cost of both powders and products. Work currently under way within the CSIRO Division of Materials Science and Technology is aimed at identifying low cost routes for the production of both powders and product.
Organotin and organosilicon compounds in cross-coupling, aromatic nucleophilic substitution, and addition reactions
Authors: Beletskaya I P
Published: November 2023

Abstract

The reactions of organotin compounds with organic halides and acid halides catalysed by palladium complexes without phosphine ligands have been carried out under very mild conditions. These reactions afford biaryls, tolans, styrenes, dienes, and unsymmetrical ketones having various substituents. The synthesis of organotin compounds may be realized through the reactions of organic halides with hexaaryldistannanes catalysed by palladium and nickel complexes. The palladium-catalysed carbonylation of organic halides in the presence of organotin compounds of the series Alk SnNu (Nu= R, MeO, PhS, Et N, SnAik ) has proved to be a convenient method for the synthesis of ketones, derivatives of aromatic acids and o:-diketones.
Some features of tin solid state chemistry
Authors: Hagenmuller Paul
Published: November 2023

Three aspects of the solid state chemistry of tin are discussed. The first deals with the possibility of replacing 0 by F in Sn0 to give rise to low-mobility electrons in the conduction band. Electronic conductivity and IR reflectivity are enhanced without loss of transparency in the visible; applications to solar energy conversion are considered. The use of Sn Mossbauer spectroscopy is described in the second section to show that the technique is able to give quantitative information about bond covalency as well as the symmetry of the Sn(II) and Sn(IV) environments; mixed fluorides have been selected as a relevant example. The last section is devoted to F- conductivity of Sn(II) or Sn(IV) fluorides and a practical application to low-temperature oxygen pressure measurements is described.
Purification of GSH-S-transferase from Plutella xylostella larvae and its inhibition by organotin compounds
Authors: Balabaskaran S , Devi P Uma , Seow, S C , Das V G Kumar
Published: November 2023

Glutathione-S-transferases have been detected in the insecticide-resistant and susceptible strains of the larvae of Piute/la xylostella, a major pest of cruciferous vegetables. Although there was no significant difference in the enzyme-substrate affinities (Km) for glutathione (GSH) and 1-chloro- 2,4-dinitrobenzene (CDNB), the enzyme was present in almost five-fold excess in the resistant strain than in the susceptible strain. The enzyme in the crude supernatant suffered a marked loss in activity on standing; its activity, however, could be stabilized by thiol reagents such as 2-mercaptoethanol, cysteine or GSH, but not with metal ions.
Biological silicas, a study in organization
Authors: Perry Carole C
Published: November 2023

Silicas are found as biomineralized components of a variety of organisms (sponges, limpet teeth, stinging nettle hairs, diatoms). The biogenic silicas are composed of essentially monodisperse particles ranging from 2-15 nm in diameter depending on the structure. Such materials, however, show a range of extremely regular, sophisticated microscopic structures (fibrils, tubules, sheets). The extremely uniform particle sizes observed in these biogenic silicas, together with their complex but regular geometries, indicate a substantial degree of control over both polymerization and particle aggregation. This article provides information about microscopic and macroscopic structural order, aggregate surface chemistry, and addresses the question of the nature of the chemical and biological controls involved in precipitation. The direct result of our studies involving a wide range of structural, analytical, and biochemical techniques is the development of model systems for the investigation of silica particle formation from aqueous solutions, a situation found in both biological and industrial silica production.
Aromatic functionalized polyorganosiloxanes: synthesis, characterization, and application to gas separations
Authors: Reddy S R , Brisdon B J , Ashworth A J , England R , Zafar I
Published: November 2023

Membranes prepared from (co)polymers can be tailored to suit a given mass-separation task, and separations that are difficult using conventional procedures can be handled by employing membranes having selective side-chain functional groups. Although polydimethylsiloxane (PDMS) membranes have been found to be 10 times more permeable than commercially available polycelluloseacetate, their low selectivity for gas separations severely limits their commercial applications. ,2
Hydrolysis of polydimethylsiloxane monolayers on water surfaces
Authors: Rudoy V M
Published: November 2023

Studies of the chemical reactions of natural and synthetic polymers in surface layers are of considerable theoretical and applied interest. This is the case with polyorganosiloxanes which are often used as monolayers and thin films on liquid and solid surfaces. Although polydimethylsiloxane (PDMS) monolayers have been investigated by a number of workers, studies on the effect of the pH of the substrate on its properties have been limited only to oligomeric PDMS. The hydrolytic stability of the monolayers of high-molecular weight polydimethylsiloxanes has been studied in this present work.
Electrochemistry of triphenyltin acetate at a mercury-filmed glassy carbon electrode
Authors: Pascuat Cherrie Bunag , Vicente-Beckett Victoria A
Published: November 2023

The electrochemical behaviour of triphenyltin acetate was investigated by cyclicvoltammetry, differential pulse voltammetry, and controlled potential electrolysis at a mercury-filmed glassy carbon electrode. Effects on the electrochemical response of supporting electrolyte composition, pH, electrode rotation speed, and triphenyltin acetate concentration were determined.
Electrochemical recovery of tin from electroplating waste solutions
Authors: Abdel-Salam Omar E
Published: November 2023

Tin has been recovered from a simulated electroplating bath by using flow-through porous electrodes. The electrochemical recovery method is economically viable.
The origins of physical chemistry
Authors: Laidler Keith J
Published: November 2023

It is sometimes said that the year of birth of physical chemistry was 1887. In that year there were indeed several important events relating to the subject, one being the launching of the Zeitschrifi far physikalische Chemie,the first journal devoted exclusively to physical chemistry. That year also saw, in the first volume of the Zeitschnfi,Svante Arrhenius’s famous paper on electrolytic dissociation, and one of van’t Hoff’s more important papers on the thermodynamics of solutions, work that was later to win him the Nobel Prize for chemistry in the first year that the prizes were awarded. Towards the end of the nineteenth century there was certainly something of a change in attitude towards physical chemistry, which then began to be recognized as a distinct branch of chemistry. However, a good deal of physical chemistry had been done previously. For example, two centuries earlier Robert Boyle had been carrying out physicochemical investigations, and a good case can be made for regarding him as the first physical chemist. His approach to chemistry is well described by his own statement that he hoped ‘to beget a good understanding ‘twixt the chymists and the philosophers’.
Boltzmann’s Kinetic Equation
Authors: Mccourt Frederick R W , Beenakker Jan J M , Köhler Walter E , Kuščer Ivan
Published: November 2023

The state of a classical fluid of arbitrary density composed of N spherically symmetric atoms is characterized by a set of n -particle distribution functions fn(c1,,cn,r1,,rn,t), n = 1,× N, where r1, ×,rn and c1, × ,cn are the positions and velocities of the n particles. The lower the density, the smaller is the maximum number n required in order to describe the state of the gas with sufficient accuracy. We shall adopt the notational convention that no subscripts will be attached to the single-particle distribution function so that, accordingly, two-particle distribution functions will have the second particle labelled by a subscript ‘l ‘. For the so-called dilute gas regime, which in practice may extend over a pressure range from 10 to 10 Pa, a description of the state of the gas by means of the single-particle distribution f (c, r, t) is sufficient.
Field-Free Transport Properties
Authors: Mccourt Frederick R W , Beenakker Jan J M , Köhler Walter E , Kuščer Ivan
Published: November 2023

With the obvious exception of the volume viscosity, which is new, and the thermal conductivity, which involves the transport both of internal and trans lational energy, the transport properties of molecular gases behave much like those for monatomic gases as functions of temperature and, for mixtures, composition. The experimental techniques for their measurement are well known, and extensive critical surveys of most data exist. For these reasons, we shall restrict our detailed discussion to those phenomena for which the molecular character is an important feature: thus, we shall treat the thermal conductivity and the volume viscosity in greater detail than the shear viscosity, diffusion and the mixture cross effects. In any case, we shall present relevant formulae for all transport phenomena and comment upon their uses and interpretation.
Anomalous Field-Effects
Authors: Mccourt Frederick R W , Beenakker Jan J M , Köhler Walter E , Kuščer Ivan
Published: November 2023

The influence of either a magnetic or an electric field on transport properties of gases is based upon its effect upon the molecular angular momentum, which is no longer constant during free-flight motion between successive collisions; only its component along the field direction does not change. Previous chapters have been concerned essentially with rotational angular momentum alone (i.e. with diamagnetic molecules) and with linear Zeeman and Stark interactions. In the present chapter, we shall consider magnetic field-effects on the transport properties of gases of paramagnetic molecules possessing non-vanishing spin and/or electronic orbital angular momentum. In addition, we shall discuss anomalous behaviour of magnetic field-effects associated with molecules possessing a net nuclear spin angular momentum. Finally, we shall consider electric field-effects in gases of polar molecules which exhibit a transition from a quadratic Stark effect at low field strengths to a linear Stark effect at higher field strengths.
Observable Nonequilibrium Polarizations
Authors: Mccourt Frederick R W , Beenakker Jan J M , Köhler Walter E , Kuščer Ivan
Published: November 2023

In the two previous chapters, we have considered contributions of nonequilibrium polarizations to the transport properties. Such contributions may be thought of as indirect insofar as they constitute only a small portion of the total phenomenon. There are, however, also phenomena in which nonequilibrium polarizations can be observed directly. To do this, we must seek polarizations that give rise to macroscopically-observable alignment phenomena. From what we know about polarization contributions to transport phenomena, we may expect that such alignment phenomena will be rather weak.
Binary systems, partial miscibility in the liquid phase, and supercritical phenomena
Authors: Koningsveld R , Stockmayer W H , Nies E
Published: November 2023

So far, we have considered the components 1 and 2 to be completely miscible in all proportions in the liquid phase. The vapour phase was considered ideal in (69)—(81), but it was pointed out that the occurrence of a liquid/vapour critical point, as well as the curvatures of liquid/vapour equilibrium curves, show that those relations are not general.
Binary systems, solid solutions, and compounds
Authors: Koningsveld R , Stockmayer W H , Nies E
Published: November 2023

If a crystal lattice allows exchange of components, solid solutions will occur. In an extreme case, replacement is possible in any proportion and the solid solution might be close to ideal in the sense of (53). If ideal solutions obtain in both solid and liquid phases, the equilibrium relations are easily derived (Exercise 1). Examples of complete miscibility in the solid state exist, e.g., the systems Cu/Ni and Ge/Si.
The influence of pressure
Authors: Koningsveld R , Stockmayer W H , Nies E
Published: November 2023

Knowledge of the influence of pressure on phase relations in polymeric systems is needed in a number of practical instances. Polymerization processes in solution and in bulk applying elevated pressures are in technical use. We may mention the solution processes for the production of polyethylene, so-called linear low-density polyethylene (copolymers of ethylene and short-chain 1-alkenes such as 1-butene or 1-hexene), and elastomeric copolymers of ethylene and propylene, that take place in walkane mixtures, usually with the average composition of w-hexane. High pressures are applied in the production of low-density (long- and short-chain branched) polyethylene and copolymers like poly(ethylene-co-vinylacetate) in supercritical bulk ethylene.
(Quasi-)ternary polymer systems
Authors: Koningsveld R , Stockmayer W H , Nies E
Published: November 2023

By the term quasi-ternary polymer systemwe indicate mixtures containing three constituents, of which one, two, or all may be molecularly polydisperse polymers. The FHS free enthalpy of mixing for the strictly ternary case reads
Fractionation of polymers
Authors: Koningsveld R , Stockmayer W H , Nies E
Published: November 2023

Fractionations of polymers are carried out for two different purposes. One of these entails the analytical determination of the molar-mass distribution (MMD). The other refers to the preparation of fractions large enough in size to permit study of their properties. In analytical fractionations the amount of initial polymer is usually small; the fractions do not need to be separated and are often characterized on-line in automated fractional dissolution procedures. Some column techniques are in use that are based on thermodynamic equilibrium principles and may make use of either liquid/liquid or liquid/solid phase separations. In preparative polymer fractionation, scaling-up problems are the main issue, because the necessary amount of initial polymer increases considerably when purity requirements of the fractions are raised. It is usually necessary to resort to pilot-plant operations if relatively pure fractions of 100-gram size are required.
Many-Body Theory of Monolayers
Authors: Bruch L W , Cole Milton W , Zaremba Eugene
Published: November 2023

In this chapter we develop the theory of interacting monolayers, following a division into two classes: (1) those in which the substrate imposes such a strong lattice structure on the adsorbate that lattice gas approximations capture much of the essential physics and (2) those in which the continuous character of the configurations is dominant and for which an analogue of the theory of 3D rare gas solids is implemented. Section 5.1 treats the lattice gas models and results of the renormalization group theory of phase transitions (Domb and Green 1972, 1976). The concept of universality applies here and critical point exponents are expected to be insensitive to several parameters in the models. Section 5.2 treats the continuum systems, using methods applied to rare gas solids and liquids (Pollack 1964; Klein and Venables 1976, 1977). This is ‘nonuniversal theory’ and the goals are to account generically for the observations and to reach a quantitative understanding for a few systems. We emphasize the formulation of the theory and illustrate it with a few physical examples. Our aim is to highlight the considerations from which the theory begins and to show the relations among the different approximation methods. In Chapter 6 we give a more thorough account of a few series of adsorbates, covering the range from the initial monolayer condensation to the multilayer regime and contrasting the behavior to the 3D bulk phases of the adsorbate.
Residue-specific considerations
Authors: Jones John
Published: November 2023

Specific peptide bond formation with the α-amino group of lysine requires prior blockade of the ε-amino group. The necessary differentiation can be achieved by using the fact that the side-chain amino group is the more basic and nucleophilic because there is an electron-withdrawing group next to the α-amino group (Scheme 6.1), or by taking advantage of the fact that the two functionalities can engage in chelate formation (Scheme 6.2).
Solution peptide synthesis
Authors: Jones John
Published: November 2023

Hundreds of oligopeptides have been synthesized by the so-called ‘classical’ solution approach to peptide synthesis. The designation ‘classical’ is a little misleading, however. We deal here not with an elegant anachronism, but with a continuously evolving and lively art. That it operates to an increasing extent in the shadow of the solid phase approach has more to do with the expansion of the latter than with the contraction of the former. The flexibility of the solution approach makes it impossible to convey its full scope with a few examples, and we must content ourselves with four historically important and spectacular successes.
Combined approaches and semisynthesis
Authors: Jones John
Published: November 2023

It has been convenient to introduce the solution and solid phase approaches separately in the last two chapters. For the most part, they have been practised separately and exclusively too, but combined approaches are also possible, and we have yet to deal with partial or semisynthesis starting with fragments of biological origin, as opposed to the total synthesis of the conventional strategies.
Simple cyclopeptides
Authors: Jones John
Published: November 2023

Compounds in which a sequence of α-amino-acid residues is closed upon itself by peptide bond formation between the termini are produced by many organisms, especially bacteria and fungi. They are usually toxic to predatory or competing species.
More complex modified peptides
Authors: Jones John
Published: November 2023

Neither evolution nor Man has rested content with the relatively simple modifications to peptide structures by conjugation or cyclization which were the subjects of the last two chapters. A rich variety of more extensively modified peptides is found in natural sources.
Dehydration reactions
Authors: Mukaiyama Teruaki
Published: November 2023

Ureas and urethanes dissociate on heating into two components; isocyanates and amines, and isocyanates and alcohols, respectively (eqn (2.1)). Analysis of the rate of these thermal dissociation reactions allows us to conclude that ureas and urethanes dissociate via a ‘termolecular’ reaction mechanism.1 After all, ureas and urethanes can be viewed as addition products of isocyanates with amines and with alcohols, respectively. One of their analogues is a class of amides having an electron-withdrawing substituent at the a-carbon of their carbamoyl group. On heating, these amides are also expected to dissociate into their components in a manner similar to ureas and urethanes (eqn (2.2)).
Pyrolysis
Authors: Mukaiyama Teruaki
Published: November 2023

Dehydration of hydroxamic acid gives isocyanates by a rearrangement reaction. Although this process was well known as the Lassen rearrangement, it was often difficult to isolate the resultant isocyanates when common dehydrating agents were used. Among numerous such reagents, only phosgene, thionyl chloride, etc. allowed isolation of isocyanates from the reaction mixture. However, I still thought that it would be possible to isolate them by reaction with some of the dehydration agents noted in Chapter 2, e.g. alkoxyacetylene or ketene acetal as illustrated in eqns (3.1) and (3.2), and therefore we started to investigate this problem. To our satisfaction, various isocyanates were prepared and isolated with the aid of these reagents, since only a carboxylic ester, which is unreactive to isocyanates, was formed as a side-product of the reaction.
Phosphorylation
Authors: Mukaiyama Teruaki
Published: November 2023

Among the dehydrations described in Chapter 2, intramolecular dehydration by the use of polyphosphoric esters proceeded along with hydrolysis of pyrophosphoric bonds, which are involved in polyphosphoric esters. Turning our attention to this point, I discussed with the members of my laboratory a possible extension to intermolecular dehydration and decided to start a study on phosphorylation, which is important for the synthesis of nucleotides, oligonucleotides, and coenzymes.
Deoxygenation reactions: oxidationreduction condensation
Authors: Mukaiyama Teruaki
Published: November 2023

Through our further discussions on the development of dehydration reactions using organic dehydrating agents, such as isocyanates, vinyl ethers, and imidoyl phosphate (see Chapter 2), we visualized that a dehydrating agent is characterized by its high reactivity toward water. For instance, phosphorus trichloride is usually kept sealed in an ampoule in the laboratory, and when exposed to air it reacts with moisture to form a white mist.
Oxidation-reduction condensation: the synthesis of peptides and nucleotides
Authors: Mukaiyama Teruaki
Published: November 2023

Phosphorylation of bromocyanoacetamide with phosphonate proceeds through the initial formation of an enol phosphate of the amide via a phosphonium salt, which is a reactive species responsible for the reaction with an alcohol to produce the corresponding phosphate along with a stable carboxamide.
Synthetic reactions with the onium salts of aza-arenes
Authors: Mukaiyama Teruaki
Published: November 2023

As mentioned in preceding chapters, the dehydration reaction has been a major subject of interest over the years as it is one of the most fundamental organic reactions. The importance of this reaction is apparent when one considers the wide variety of biological substances, such as peptides and oligonuclcotides, which arc formed mostly by intermolecular dehydration.
The selective aldol reaction and Michael reaction
Authors: Mukaiyama Teruaki
Published: November 2023

In the first half of the 1970s, we investigated the characteristics of alkylthioboranes based on the concept of ‘elements in combination’ as described in Chapter 7,1 and we explored new reactions of significant interest. Further extension of research to investigate new characteristics of alkylthioboranes seemed quite promising, because the combination of two different elements in this particular case could create an unexpected and novel reactivity. In fact, we found that an aldol product was formed smoothly in the reaction of alkylthioborane, ketene, and aldehyde. One example, shown in eqn (13.1), is the formation of [3-hydroxy thioester by the reaction of dibutyl-S-butylthioborane, aldehyde, and ketene. We then started an investigation of the mechanism of this reaction.
Epilogue
Authors: Mukaiyama Teruaki
Published: November 2023

Synthetic organic chemistry in Japan has made great progress since the days when I began my own research after graduating from the Tokyo Institute of Technology, and now occupies a prominent position in the world.
Oscillations In A Closed Isothermal System: Ma Them A Ti Cal Analysis
Authors: Gray Peter , Scott Stephen K
Published: November 2023

The previous chapter has provided some indication of the behaviour which can be exhibited by the simple cubic autocatalysis model. In order to make a full analysis, it is convenient both for algebraic manipulation and as an aid to clarity to recast the rate equations in dimensionless terms. This is meant to be a painless procedure (and beloved of chemical engineers even though traditionally mistrusted by chemists). We aim wherever possible to make use of symbols which can be quickly identified with their most important constituents: thus for the dimensionless concentration of A we have a, with /3 for the dimensionless concentration of B.
Thermokinetic Oscillations In A Closed System
Authors: Gray Peter , Scott Stephen K
Published: November 2023

This chapter and chapter 5 study the prototypical thermokinetic oscillator. Thermal feedback replaces autocatalysis, and the Arrhenius temperature dependence of rate coefficients supplies non-linearity in the scheme

In the preceding chapters we investigated the basic patterns of behaviour which might be exhibited by a reaction scheme which involved a certain form of chemical feedback under isothermal conditions. Here we make a similar analysis for systems with purely first-order chemical reactions but under conditions in which the heat produced by the natural exothermicity can lead to departures from isothermal operation. Feedback is then provided from thermal coupling as the increase in temperature of the reacting mixture leads to an increase in the local value of the reaction rate constant.
Reaction In A Non-Isothermal Cstr: Stationary States And Singularity Theory
Authors: Gray Peter , Scott Stephen K
Published: November 2023

Chapter 6 considered isothermal autocatalysis in an open system; here we study a classic case of thermal feedback. A rich variety of stationary-state patterns (bifurcation diagrams) are generated and considered here alongside those of the previous isothermal example. Flow diagrams are again illuminating and singularity theory provides a systematic approach. After study a reader should be able to:
Chemical Diffusion Pattern Formation (Turing Structures)
Authors: Gray Peter , Scott Stephen K
Published: November 2023

In this chapter we investigate some of the ways in which spatial patterns can arise in closed chemical systems. Coloured patterns can arise when a reaction is carried out in thin layers, in a petri dish for instance, corresponding to spatial variations in chemical concentrations. Thus in the BelousovZhabotinskii reaction, blue concentric circles indicating local regions of high Ce4+ concentration travel through a red background of Ce3+ to form target patterns. The latter are moving in time, i.e. they are a form of travelling wave, about which we will say more in the next chapter. Here we are interested in the possible spontaneous formation of stationary patterns.
Manipulation of Nuclear Spin Hamiltonians
Authors: Ernst Richard R , Bodenhausen Geoffrey , Wokaun Alexander
Published: November 2023

A major advantage of NMR in comparison with other forms of spectroscopy is the possibility of manipulating and modifying the nuclear spin Hamiltonian at will, almost without any restriction, and to adapt it to the special needs of the problem to be solved. Many infra-red and ultraviolet spectra cannot be interpreted because of the enormous complexity of incompletely resolved signal patterns. In NMR, however, it is very often possible to simplify complex spectra by modifying the Hamiltonian to an extent which permits a successful analysis. The ease of manipulation of nuclear spin Hamiltonians is unique for purely practical reasons. Because nuclear interactions are weak, it is possible to introduce competitive perturbations of sufficient strength to override certain interactions. In optical spectroscopy, the relevant interactions are of much higher energy, and similar manipulations are virtually impossible.
Two-Dimensional Fourier Spectroscopy
Authors: Ernst Richard R , Bodenhausen Geoffrey , Wokaun Alexander
Published: November 2023

The extension of spectroscopy to two and more dimensions stems from the recognition that the properties of a molecular system cannot be fully characterized by a conventional one-dimensional (ID) spectrum. Even an ensemble of one-spin systems is a non-linear system, as mentioned in Chapter 4, and is only incompletely characterized by its impulse response or transfer function. This holds even more so for coupled spin systems. Many ambiguities remain in ID spectra, such as the assignment of multiplets and the identification of connected transitions. Two dimensional (2D) spectroscopy is a general concept which makes it possible to acquire more detailed information about the system under investigation. Since the first proposal in 1971 (6.1) and the first experimental realization in 1974 (6.2—6.5) an astonishing number of powerful 2D techniques have been invented, tested, and applied to problems in physics, chemistry, biology, and medicine.
Two-Dimensional Separation ofof Interactions
Authors: Ernst Richard R , Bodenhausen Geoffrey , Wokaun Alexander
Published: November 2023

The interpretation of NMR spectra in liquid or solid phases is often impeded by the complexity of overlapping resonances. When the Hamiltonian is composed of terms of different physical origin, such as chemical shifts or dipolar or scalar couplings, it is often possible to render spectra more intelligible by separating various interactions in orthogonal frequency domains. Two-dimensional separation is preferable to decoupling techniques, since there is no loss of information. In the course of 2D separation, the number of peaks is conserved. The primary advantage lies in the fact that overlapping resonances are unravelled. The separation of interactions by 2D spectroscopy can be compared with two-dimensional chromatography. In a one-dimensional thin layer or paper chromatogram, the separation of the constituents by elution with a given solvent is often incomplete. Elution with a second solvent in a perpendicular direction may then achieve full separation.
Nonequilibrium Phenomena in Polyatomic Gases
Authors: Mccourt Frederick R W , Beenakker Jan J M , Kohler Walter E , Kuscer Ivan
Published: November 2023

Properties of the effective cross sections which have been utilized in the expressions for nonequilibrium phenomena in dilute polyatomic gases are discussed, and interrelationships amongst them elucidated. Then, the evaluation of such effective cross sections from molecular scattering theory is outlined. The temperature dependence of the effective cross sections as determined experimentally is discussed, and for molecular hydrogen, compared with the results of full quantum scattering calculations. Transport phenomena in rarefied gases, the modelling of the surface scattering operator and the derivation of boundary-layer effects (with and without magnetic fields present) are covered in four chapters. Aspects of the collisionless gas regime are then dealt with in a separate chapter. The penultimate chapter covers relevant mathematical material, and the final chapter provides tables of experimental data and effective cross sections deducted from these data wherever possible. This book completes this major two-volume work on Non-equilibrium phenomena in polyatomic gases, and stands as a definitive treatise in this area of chemical physics. Volume 1, on dilute gases, was published in August 1990.
Molecular Scattering Theory
Authors: Mccourt Frederick R W , Beenakker Jan J M , Kohler Walter E , Kuscer Ivan
Published: November 2023

Since the scattering of particles is usually analyzed quantum mechanically, the greater part of this chapter will be devoted to quantum mechanical scattering theory. However, as will be shown in the last section, classical theory based upon the evaluation of trajectories can also provide useful approximations, except for the very lightest molecules. The analysis leads to scattering amplitudes, S -matrix elements, and differential scattering cross sections, which provide the raw material for the evaluation of effective cross sections - the ultimate goal from the viewpoint of this book. Recipes for such evaluation were given in the preceding chapter. Although there are persistent discrepancies between quantum mechanical and classical evaluations of differential cross sections for small scattering angles and low energies, such differences are largely washed out in the calculation of effective cross sections and consequently cheaper classical calculations can often be employed.
Introduction
Authors: Scott Stephen K
Published: November 2023

This quantitative interpretation of experimental results from chemical systems is frequently based on the construction and subsequent analysis of kinetic mechanisms or models. This process can work in two directions. If we can confidently predict the chemistry, in terms of the individual reactions which are likely to occur between all the possible chemical species in the system, we can then write down the reaction rate equations based on the law of mass action. The reaction rate equations specify the rates at which the species concentrations change with time, and how these rates depend upon those concentrations. The idea here is to break the overall reaction up into a number of component or elementary steps.
Mappings
Authors: Scott Stephen K
Published: November 2023

The idea of a mapping in a dynamical system can be treated at various levels. At its simplest it can be accepted as a ‘game’. Even in this form it is instructive and has the advantage of requiring nothing more than a non-programmable calculator for the reader to participate. Later, we will see that the lessons learnt are of surprising relevance to the behaviour in chemical reactions.
Flows I. Two-variable systems
Authors: Scott Stephen K
Published: November 2023

In the previous chapter we investigated the behaviour of simple mappings. These showed ‘stationary states’ and bifurcations to periodicity, aperiodicity, and periodic windows. Even if we cannot claim to have completely understood these responses, a number of patterns with some definite structure have clearly emerged. Now we turn to models described by differential equations. In order to bring out the relevant features most clearly, we will employ the simplest of the model chemical schemes: the cubic autocatalator (Merkin et al. 1986, 1987a,h; Gray and Scott 1986, 1990a,b).
Flows II: Three-variable systems
Authors: Scott Stephen K
Published: November 2023

The previous chapter revealed a great deal about the behaviour of two variable chemical systems. Despite the variety of bifurcation phenomena, only two structurally-stable responses were found: stationary-state operation or simple period-I limit cycles. More complex patterns, such as oscillations that repeat every other excursion (period-2), are forbidden with only two variables by the restriction that trajectories may not, in general, cross on the phase plane (which is a two-dimensional surface). If we consider models or systems with more than two variables, the phase space becomes at least three dimensional.
Forced systems
Authors: Scott Stephen K
Published: November 2023

In the previous chapter we have considered models that have distinct variables, such as concentrations or local temperature, and parameters. The parameters are under our control and stay fixed when we want them to-only varying should we wish so. Thus the inflow concentrations or ambient temperature are fixed in time. In this chapter we investigate the types of behaviour possible when one or more of the parameters is varied in time (or does so of its own volition in spite of our wishes). Specifically we will be interested in the case where this time variation is periodic and in situations where the system without this additional periodicity can abo oscillate or show multistability. Again. this chapter will deal mainly with models and theory: practical aspects and real experimental systems come where appropriate in Chapters 8 to 12.
Experimental methods
Authors: Scott Stephen K
Published: November 2023

This chapter sets out to link the various theoretical methods described in the previous chapters to their application in experimental situations. In the latter case we must learn to cope with the ‘real world’ limitations on the availability and precision of our data. The theoretician or computer modeller is generally in an atypically privileged position in this respect. In principle, all species concentrations can be made available at any fixed time interval or other choice of sampling condition. The data can be obtained, and the parameters maintained constant, to almost arbitrary precision (within the confines of a computing budget). Such control over the raw data allows further manipulation such as constructing limit cycles or other attractors. Poincare sections, etc. to be made with relative ease.
Heterogeneous catalysis
Authors: Scott Stephen K
Published: November 2023

Heterogeneous catalytic systems have seemed a natural and fertile field for non-linear behaviour and only solution-phase reactions have been more widely studied. The oxidation of carbon monoxide over many metal surfaces in particular seems to have been the subject of deep investigations perhaps because of its technological as well as fundamental significance. Heterogeneous catalysis is widely applied in the chemical industry as a whole-the petrochemical industry in particular-and so there has been both motivation and support for any increase in understanding and control of such reactions. It might also be added that many theoreticians have also taken advantage of the ‘grey areas’ of uncertainty in the form of appropriate reaction rate laws, using putative surface reactions (and their enzyme equivalents) as an excuse for almost any otherwise unbelievable but convenient polynomial or transcendental form.
Quantum Description Of Nmr
Authors: Goldman Maurice
Published: November 2023

We are now equipped with the necessary mathematical background to analyse NMR in quantum-mechanical terms. In this chapter, the analysis is restricted to standard NMR, essentially the free-induction decay following a single r.f. pulse. The first section deals with the case when the only interaction experienced by the spins is the Zeeman interaction with an external field. It illustrates the way in which quantum mechanics is used in practice and its main result is a quantum justification of the equation of motion of the magnetization derived in Chapter 1 by a purely classical approach. The second section is a simplified description of chemical shifts and indirect interactions and of their influence on the NMR spectra. For such a simple problem, it will already become apparent that the formal machinery developed in the previous chapters is far superior to the classical or naive quantum methods, as regards the ease and the simplicity with which quantitative results are obtained.
Phase Integral Approximations
Authors: Child M S
Published: November 2023

The simplest representation for the quantum mechanical wavefunction in terms of classical quantities is due to Jeffreys (1925), Wentzel (1926), Kramers (1926), and Brillouin (1926a,b). It generalizes the free-motion form, ψ = exp(ipx/h), by allowing for variation in the momentum p(x) as a function of position, a correction that replaces the exponent by a phase integral, ∫p(x) dx, and introduces a normalization term related to the local velocity. A similar description may also be applied in classically forbidden regions by allowing the momentum to become imaginary, p(x) = i|p(x)|, provided that the local de Broglie wavelength, λ.(x) = h/p(x), varies sufficiently slowly with x. Details are given in Section 2.1 and discussed at greater length by Froman and Froman (1967) and Froman (1980).
Quantization
Authors: Child M S
Published: November 2023

Questions of quantization turn on a proper treatment of normally isolated regions where the JWKB description, expressed by eqn (2.13), breaks down. The most obvious of such special regions are those around the classical turning points, at each of which the analysis in Sections 2.2 and 2.3 yields an associated so-called Maslov (1972) phase correction of π/4; Delos (1986) and Littlejohn and Robbins (1987) discuss this Maslov correction from a more fundamental standpoint and Appendix A and parts of Section 11.2 bear on its choice. Other special regions around potential singularities are most conveniently handled by introducing a Langer (1932) correction term to the physical potential function (see Section 2.3). It is shown in Section 3.1 that systems with no other complications may be quantized by the Bohr-Sommerfeld rule

(3.1)∮p(q)dq=(n+δ)h,  n=0,1,2,3⋯

where n is the quantum number and b is a Maslov index, which takes the values ½, 0, ½ for vibrational, plane rotational, and orbital motion respectively.
Angle–Action Variables
Authors: Child M S
Published: November 2023

The Bohr–Sommerfeld quantization rule, 12π∮pdq =(n+δ)ℏ,

arose in Section 3.1 from the boundary conditions on the JWKB wave function. Here it is set in the context of classical angle–action theory from which it evolved (Bohr 1913). The idea is that any bound periodic motion can be simply described in special action-angle variables, termed here (1, α), such that the action, defined in Cartesian variables by the equation
Atom–Atom Scattering
Authors: Child M S
Published: November 2023

Atomic collisions are normal1y termed elastic or inelastic. The former lead simply to momentt1m transfer between the collision partners, or equivalently to a change in the direction of their motions; the latter lead also to a simultaneous transfer of energy between internal motion and translation. This chapter lays the foundations of the theory in the elastic context and indicates, in the final section, how it generalizes to the inelastic case. The theory stems from the seminal papers of Ford and Wheeler (1959) which precipitated the recent revival of interest in semiclassical mechanics. The review by Berry and Mount (1972) was also very influential.
Principles
Authors: Procter Garry
Published: November 2023

In order to achieve asymmetric synthesis, at least one component of the reaction must be chiral and non-racemic. If there is no asymmetric component in the reaction, then transition states which lead to enantiomers will themselves be enantiomeric, equal in energy, and a racemate must be formed. In principle, the use of a chiral, non-racemic substrate, reagent, solvent, or catalyst should lead to asymmetric synthesis. In general terms, any feature of the reacting system which would cause the possible transition states for the reaction to be diastereoisomeric (where they would normally be enantiomeric) could lead to the preferential formation of one diastereoisomer or enantiomer. This follows because transition states which are diastereoisomeric need not be of the same energy and consequently one of the possible products could be formed more rapidly. The various possibilities will be considered in this chapter.
Additions to carbonyl compounds
Authors: Procter Garry
Published: November 2023

The addition of a nucleopbile to a carbonyl group is a fundamental reaction of organic chemistry, and a cornerstone of organic synthesis. As such it is impossible to cover all such reactions which are relevant to asymmetric synthesis in one chapter. Enantioselective reduction of ketones is covered in Chapter 7 along with the reduction of other functional groups, and asymmetric aldol reactions of aldehydes is the subject of Chapter 5. Accordingly, this chapter is concerned mainly with the addition of nucleophiles to ketones and aldehydes in which one or more new chiral centres are formed and which result in non-racemic products. The most straightforward and commonly encountered example of this type of process is the addition of non-chiral nucleophiles to chiral aldehydes and ketones, and this will be the subject of the first part of this chapter. This in itself constitutes a large area of organic synthesis, and selected examples will be used to illustrate the important general principles and applications.
Hydrolysis and esterification
Authors: Procter Garry
Published: November 2023

There are two general approaches to the use of hydrolysis and esterification in asymmetric synthesis, and usually both involve the use of enzymes as asymmetric catalysts. In one case the asymmetric catalyst is used in a kinetic resolution process in which one enantiomer of a racemic mixture reacts more rapidly than its antipode. In the example shown (Fig. 9.1) the lipase-catalysed hydrolysis of the (1R,2R)-enantiomer of 9.1 is rapid. In effect, the (1S,.2S) enantiomer is not a substrate for the enzyme, and essentially all of the fastreacting antipode is hydrolysed to the alcohol. As in all simple resolution procedures, the yield of an individual enantiomer cannot be greater than fifty per cent, and the two enantiomerlc components, ester (1S,2S)-9.l and alcohol 9.2 still need to be separated.