bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tutorial on automated Patterson interpretation to find heavy atoms
Authors: Sheldrick G M 
Published: November 2023

Abstract
The algorithms employed for automatic location of heavy atoms via the Patterson function in the programs SHELXS-86 and SHELXS-90 are discussed, and are illustrated in the form of two tutorial exercises. As a small molecule crystallographer participating in a macromolecular computing school, I have tried to choose a topic of importance to both small molecule and macromolecular crystallographers, namely the location of heavy atoms via the Patterson function. In the case of heavy atom derivatives of proteins this Patterson would be calculated using the isomorphous difference structure factors. At least a quarter of organic and inorganic structures are solved by the heavy atom method, and the preparation of heavy atom derivatives is almost obligatory for proteins if no suitable search model is available for molecular replacement. Despite this, there is a striking lack of user-friendly computer programs, general for all space groups and types of problem, for the automatic location of heavy atoms, in sharp contrast to the situation in small-molecule direct methods. This seems to be simply an historical accident; the necessary theory has be well understood for at least 40 years, and the computer resources required are modest.
Exponential density: exact fitting of structure moduli by entropy maximization
Authors: Collins D M , Prince E 
Published: November 2023

Abstract
Electron density given as an exponential function can be made to fit subsets of structure moduli exactly by a constrained nonlinear optimization. A dual method is used in which the problem is solved in a space of dimension equal to the number of structure factor constraints. Entropy is the objective function to be maximized. On the joint basis that density must be everywhere positive and exactly match the experimental constraints, the result is shown to be the most general obtainable from an initial phase assignment. If there are other acceptable maps, they cannot be as flat as the electron density map given by this algorithm.
Modelling the architecture of large RNA molecules: a three-dimensional model for group I ribozymes
Authors: Westhof E , Jaeger L , Dumas, P , Michel F 
Published: November 2023

Abstract
Approaches for modelling proteins and nucleic acids are discussed in parallel. While knowledge-based modelling is nowadays the most powerful method for proteins, it is yet inadequate for nucleic acids. For modelling nucleic acids, especially RNA molecules, one has to rely either on chemical and enzymatic probing at the nucleotide level or on comparative sequence analysis if enough sequences with appropriate randomness are available. With either method, one can hopefully obtain sufficient information not only for determining the 2D structure but also for constructing the 3D architecture of complex RNA molecules. ‘ The application of comparative sequence analysis together with graphic modelling to group I ribozymes is presented.
Development of indigenous technology for the manufacture of modern silicon materials
Authors: Murthy A R Vasudeva 
Published: November 2023

Abstract
The importance of modern silicon materials to the industrial development of India was realized by the scientists in the Departments of Inorganic and Physical Chemistry and Physics at the Indian Institute of Science in Bangalore over three decades ago. A programme was initiated for the standardization of preparative methods for high purity silicon compounds on a laboratory scale. The technical know-how generated at the Institute has since been transferred to industry for the manufacture of a few of these silicon compounds, which include silicon tetrachloride and ethyl silicate-40. The scale of operations for these compounds runs into hundreds of tons per year. In quality, they conform well to international standards and are also competitive with regard to price in the world market. These two products not only meet the current industrial needs of the country, but also serve to meet the growing demands of a number of industrially advanced countries. Further collaborative programmes with industry are in progress. The industry has put up a plant to manufacture about 30 tons yr- of polycrystalline silicon and 10 tons of electronic grade silicon for single crystals and wafers. Other silicon materials like silane, fumed silica, silicon nitride, etc. are also under development.
Binary systems, Bakhuis Roozeboom diagram
Authors: Koningsveld R , Stockmayer W H , Nies E 
Published: November 2023

Abstract
The phase rule (59) reads f=4 −Pfor binary systems, and we therefore have the following possibilities for phase equilibrium:
One-phase equilibrium: f= 3; freedom of choice for p, T, and x 2; three-dimensional regions in p(T, x 2) space; trivariant equilibria.
Two-phase equilibrium: f= 2; freedom of choice for the possible combinations ( p, T), ( p, x 2), or (T, x 2); ruled surfaces in p(T, x 2) space; bivariant equilibria.
Three-phase equilibrium: f= 1; choice of one intensive variable fixes the other two; space curves in p(T, x 2) space; univariant equilibria.
Four-phase equilibrium: f= O; non-variant equilibrium, only at a single set of values of p, T, x 2; a quadruple pointin p(T, x 2) space.
If a vapour phase is involved, it is customary to use the index 1 to denote the more volatile of the two components.
Physical Adsorption: Forces and Phenomena
Authors: Bruch L W , Cole Milton W , Zaremba Eugene 
Published: November 2023

Abstract
About twenty years ago, as a rapid expansion of surface physics was underway, Greg Dash and Bill Steele published a pair of influential monographs on physical adsorption defining the language and identifying a family of issues that are common to most work in the field. In the intervening years, many workers have contributed to the growth of understanding of physical adsorption. At present, we appear to be in a period of consolidation and it seemed appropriate to us to attempt a monograph that would incorporate the progress that has been made. This book is the result of our efforts.
Monolayer Examples
Authors: Bruch L W , Cole Milton W , Zaremba Eugene 
Published: November 2023

Abstract
In this chapter we survey several examples of physically adsorbed monolayers chosen according to two criteria: (1) to demonstrate the interesting variety of physical phenomena present and (2) to illustrate the outstanding features of the general theory in Chapters 4 and 5. Fluid phases (dilute gases and liquids) have correlation lengths that usually are small except near the gas-liquid critical point, but in the monolayer the correlation length may reach thousands of angstroms near a melting transition (Specht et al. 1985; Nuttall et al. 1994). Further, the spatially periodic external potential arising from the substrate lattice may cause the fluid density to be quite nonuniform. The solid phases have sharp diffraction patterns and present a most diverse set of structures in the monolayer regime; we emphasize the types of lattices and their evolution under increased temperature and lateral stress.
Travelling Waves
Authors: Gray Peter , Scott Stephen K 
Published: November 2023

Abstract
In the previous chapter we dealt with the existence and spontaneous formation of stable spatially non-uniform patterns. Here, we consider another form of spatial behaviour. We envisage a (long) tube, initially containing a spatially uniform distribution of reactants. The spontaneous reaction converting these reactants to products is exceedingly slow but can be initiated at one end, perhaps by the local addition of some key intermediates (such as an autocatalyst), by local heating, or by a spark (which often serves to achieve both of the former). We are interested to see if and how the reaction can then propagate along the whole length of the tube. Uthe reactants are gaseous and the process is exothermic, the reaction zone will typically move quickly and we talk of a flame. For reactions in dilute solutions the propagation is typically much slower, and we talk of a chemical wave.
Principles of Nuclear Magnetic Resonance in One and Two Dimensions
Authors: Ernst Richard R , Bodenhausen Geoffrey , Wokaun Alexander 
Published: November 2023

Abstract
Nuclear magnetic resonance spectroscopy is one of the most powerful and versatile techniques now available for the study of molecular structure and reaction mechanisms. Written by recognised experts in the field, this classic account of modern NMR spectroscopy was heralded on its first publication in 1987 as "the lasting text of its age" Nature. Now available in paperback, it provides a thoroughly comprehensive review of modern NMR techniques and the underlying principles. It describes the study of solutions and solids using one- and two-dimensional spectroscpy, providing both a solid theoretical foundation and a description of practical procedures. The material is presented in an intuitive manner within a rigorous mathematical framework, and is extensively illustrated throughout. This important work was written at the ETH in Zurich, one of the world's leading institutions in advanced NMR methods, which has played a key role in the development of Fourier spectroscopy, two-dimensional spectroscopy, and Fourier-transform NMR imaging. Available in paperback for the first time, the book provides the definitive account of the field, and is without question "a must.....for every self-respecting NMR spectroscopist" Journal of Magnetic Resonance.
Multiple Quantum Coherence And Applications
Authors: Goldman Maurice 
Published: November 2023

Abstract
In the following it will be necessary to distinguish positive from negative multiple quantum coherence. The somewhat arbitrary convention is that +k quantum coherence corresponds to matrix elements of the form (8.3), that is to the case when a contains operators which, when acting on some kets, raise m by k units. Likewise, -k quantum coherence corresponds to matrix elements of the form (8.2). We give below some examples of the order of coherence produced by operators present in the density matrix:
Introduction
Authors: Child M S 
Published: November 2023

Abstract
Semiclassical mechanics is a short-wavelength link between classical and quantum mechanics, similar to that between wave and geometrical optics. Its object is to maintain contact with the structure imposed by classical mechanics, without sacrificing quantum mechanical accuracy, or, in the vivid words of Berry and Mount (1972), to ‘sew quantum mechanical flesh onto classical bones’. The overriding principles are that the classical phase space is divided into ‘accessible’ and ‘inaccessible’ regions characteristic of the type of motion, and that the boundaries of these regions impose a classical structure, which is evidenced in the quantum mechanics by interference in the bright accessible regions and exponential decay into the shadow regions. The strength of the classical skeleton is that this structure is maintained whether the observations are made in coordinate space, quantum number space, or some mixed representation. In all cases the central quantity is the classical action, whose dimensions are those of Planck’s constant; on one hand it guides the classical motion, according to the minimum action principle, and on the other it adds a phase to each classical trajectory, which gives rise both to quantum mechanical interference and, by a mathematical extension, to quantum mechanical tunnelling.
Matrix Elements
Authors: Child M S 
Published: November 2023

Abstract
The calculation of matrix elements raises several interesting points. In the first place it immediately raises the question of normalization of the semiclassical wavefunctions, which is addressed in Section 5.1. The conclusion is that the JWKB normalization factors for bound and continuum states differ only by a factor dependent on the density of states. Secondly Section 5.2 shows how an angle–action representation for the wavefunction leads directly to the Heisenberg correspondence between matrix elements and classical Fourier components. Thirdly Franck–Condon and curve-crossing matrix elements often show informative interference patterns which are clearly revealed by the stationary phase and uniform approximations outlined in Section 5.3. Finally the more awkward non-curve-crossing cases examined in Section 5.4 provide a further illustration of the uniform approximation approach.
Non-Separable Bound Motion
Authors: Child M S 
Published: November 2023

Abstract
Quantization problems for non-separable bound systems are best appreciated in the light of knowledge of the possible phase space structures, discussed in Section 7.1. Emphasis is placed on the role of the so-called invariant tori, which are generalizations of the phase orbits of Section 4.1. Section 7.2 describes how the simplest situations may be quantized by an extension of the Bohr-Sommerfeld approach, due to Einstein (1917), Brillouin (1926a, b), and Keller (1958) (EBK). However, resonant situations, in which the frequencies of motion in different degrees of freedom are rationally related, introduce two types of complication. The first is that unstable resonances inevitably lead to bifurcation into two or more coexisting types of motion at a given energy, which means that different procedures are required in different parts of phase space and that non-classical corrections may be important at the boundaries between these different regions. Section 7.3 shows how difficulties of this type may be handled by methods due to Jaffe and Brumer (1980) and Sibert et al. (1982 ), while Section 7.4 offers an alternative to the above methods, based on a Fourier representation of the torus due originally to Percival and Pomphrey (1973, 1976). The second type of complication, which is more serious, is that interactions between several such resonances may lead to classical chaos; the extent to which such chaotic systems may be quantized by classical perturbation and adiabatic switching techniques is explored in Sections 7.5 and 7.6. Finally Section 7.7 deals with quantization by use of periodic orbits as suggested by Gutzwiller (1967, 1969, 1970, 1991) and Berry and Tabor (1976, 1977). Reviews of the various approaches have been given by Percival (1977), Handy (1980), Noid et al. (1981), and Ezra et al. (1987).
The ClassicalS Matrix
Authors: Child M S 
Published: November 2023

Abstract
The classical S matrix is a natural extension of the semiclassical phase shift employed in Sections 8.1 –8.3. A simple example appeared earlier in eqn (8.121) in a context that recognized a tacit distinction between the treatment of translational and internal degrees of freedom. In the more general approach, described below, all degrees of freedom are treated equivalently in a manner applicable to arbitrary non-separable processes, with specific reference to inelastic and reactive scattering and photodissociation. Two different formulations have been adopted. One due to Pechukas (1969) and Miller (1970, 1974, 1976) starts from the Feynman path integral approach to quantum mechanics (see Feynman and Hibbs 1965), as discussed in Appendix C in the context of the theory of transformations in classical and quantum mechanics. The other, due to Marcus (1970) and coworkers, which is based on a direct JWKB type of approximation for the scattering wavefunction, is expounded in Section 9.1 in a way that leads naturally to the uniform approximations that make the difference between an intuitively attractive and a quantitatively reliable theory. Reviews of the two approaches have been given by Miller (1974, 1976) and Child (1974a, 1976a).
Reactive Scattering
Authors: Child M S 
Published: November 2023

Abstract
Some aspects of the theory of reactive scattering carry over from the classical S matrix theory discussed in the previous chapter. In particular the reactive tunnelling calculations of George and Miller (1972) and Stine and Marcus (1972) were among the earliest applications of the complex classical trajectory technique. However, the reactive context introduces a number of severe complications in the light of which the present discussion is restricted to models in which the atoms involved are assumed to be constrained to a line. The first remaining complication concerns the choice of coordinate system, because no single system allows an equally convenient description of the dynamics in the reactants, products, and interaction regions of the potential energy surface. Section 10.1 describes the three most commonly used types of system. The second complication is that chemical reaction dynamics is almost invariably inhibited by one or more bottlenecks or transition states between reactants and products. Some trajectories pass through them unimpeded, others are reflected directly back towards reactants, while yet others may be trapped between them for significant periods and it is this diversity of behaviour that restricts the validity of the classical S matrix approach. Nevertheless the nature and properties of these bottlenecks is now very wen characterized. Section l0.2 gives an outline, taken from the authoritative review by Pollak (1985), while Section 10.3 discusses the consequences in relation to interference effects and quantum mechanical resonances. Finally Section 10.4 refers to the nature of effective (vibrationally adiabatic) barriers to vibrationally state-selected reactions and to the general phenomenon of reactive tunnelling in a state-selected context.
Boron trifluoride/aluminium trichloride-mediated conjugate addition and substitution reactions
Authors: Ibuka Toshiro , Yamamoto Yoshinori 
Published: November 2023

Abstract
The conjugate addition and the substitution reactions of ordinary organo-copper reagents are the most important carbon–carbon bond-forming processes in synthetic organic chemistry today. However, owing to either moderate reactivity of the conventional organocopper reagents or severe steric hindrance in the substrates, the attempted conjugate addition to certain α,β-unsaturated carbonyl compounds or substitution to allylic and propargy-lic systems often gives none of the desired products. Failure to react with ordinary organocuprates has undoubtedly detracted from the application of organocopper reactions in synthesis.
Alkyne carbocupration and polyene synthesis
Authors: Normant J -F 
Published: November 2023

Abstract
The addition of organocopper reagents to terminal alkynes and to acetylene represents an efficient way to synthesize vinylcopper reagents with a given geometry. The addition proceeds in a Markownikov way in a purely syn-specific fashion. Two approaches may be considered. With terminal alkynes (eqn 1), RCu is preferably prepared from a Grignard reagent which can be primary or secondary, and the solvent can be ether, THF, or ether-dimethyl sulfide.
Techniques for chemical studies
Authors: Buback M , Hinton C 
Published: November 2023

Abstract
Chemical reactions in fluid phases have several interesting aspects, particularly in the supercritical fluid state where both the temperature, T, and the pressure, P, are above the critical values: (i) the availability of an extended range of pressures and temperatures offers opportunities to run a process under conditions which optimize the kinetics and selectivity; (ii) since the solvent properties can be significantly varied in the supercritical fluid state, homogeneity of the reaction mixture may be easily obtained and phase separation for product recovery may be achieved after the reaction without major problems; (iii) additional advantages of carrying out chemical processes in supercritical phases accrue from the excellent heat- and masstransfer properties in these states; (iv) free-radical polymerizations in extended ranges of pressure and temperature are particularly important since the kinetics of the process and the properties of the polymeric product are tied together.
Structures of metal alkoxides and oxoalkoxides
Authors: Struchkov Yuri T , Turova Nataljya Ya. , Yanovsky Alexander I 
Published: November 2023

Abstract
Although metal alkoxides and oxoalkoxides lie on the border between organic and coordination chemistry, their crystal structures are appropriate to organic crystal chemistry, involving molecular type packings. Moreover their crystal and molecular structures give some insight into their reactivity and chemical transformations.
Aza crowns
Authors: Parker David 
Published: November 2023

Abstract
Macrocyclic polyamines are versatile ligands that form well-defined complexes with a wide range of metal ions. The selectivity and stability of metal complex formation is a sensitive function of the number of nitrogen binding sites, their relative disposition and the conformation of the macrocyclic ligand. The importance of this domain of coordination chemistry is reflected in the growing number of applications of functionalised aza crowns. For example, selectivity in complex formation is being harnessed in the development of polymer-supported aza crowns for the separation of metal ions, while the kinetic stability of many of the metal complexes has permitted the development of radiolabelled complexes for in vivo use. Protonated polyamines bind strongly to charge dense anions and selectivity in the binding of monoand polyphosphate anions has been defined.
Equilibria in dilute solutions in water
Authors: Williams R J P , Da Silva J J R Frausto 
Published: November 2023

Abstract
In Chapter 3 we have shown that, on bringing together volumes of two different ideal gases, A and B, they form a homogeneous mixture, which, at equilibrium, is totally randomised, that is, disordered. We also referred to the possibilities of weak interactions between A and B, which give deviations from perfect or ideal gas behaviour, and stronger ones, which may lead to the formation of gaseous compounds, AnBm, at equilibrium with A+B. An example is H20 in an equilibrium mixture with H2 and 02 when the temperature is kept &gt; 3000°C. The mixture of the three gases is still homogeneous and disordered, but some order, structure, in H20 has appeared. The reasons for such ordering were described in Chapter 2. In the case of two bulk liquids similar considerations apply, but in these cases miscibility is more limited and phase separation frequently occurs (see Chapter 4). In liquids and particularly in liquid/solid and solid/solid mixtures, we often observe a higher degree of order in the phase distribution of the two components A and B, up to the limit of pure co-operative compound formation, which is absent in the mixtures of gases. In all these cases the mixing of similar mole fractions of components only was considered, starting from two, A and B, and then going forward to larger numbers.