Open Molecule Foundation

The Open Molecule Foundation, available online at http //www.xml-cml.org/, accessed on August 14,2002. 

The chemical markup language (CML), under development by the Open Molecule Foundation for description of chemical structures for Internet transmission. 

Molecular orbital theory is more complex than the hybrid orbital approach, but the foundations of the model are readily accessible. Though complex, molecular orbital theory opens the door to many fascinating aspects of modem chemistry. In this section, we introduce the molecular orbital approach through diatomic molecules. 

In Science, every concept, question, conclusion, experimental result, method, theory or relationship is always open to reexamination. Molecules do exist Nevertheless, there are serious questions about precise definition. Some of these questions lie at the foundations of modem physics, and some involve states of aggregation or extreme conditions such as intense radiation fields or the region of the continuum. There are some molecular properties that are definable only within limits, for example, the geometrical stmcture of non-rigid molecules, properties consistent with the uncertainty principle, or those limited by the negleet of quantum-field, relativistic or other effects. And there are properties which depend specifically on a state of aggregation, such as superconductivity, ferroelectric (and anti), ferromagnetic (and anti), superfluidity, excitons. polarons, etc. Thus, any molecular definition may need to be extended in a more complex situation. 

Cohen and Turnbull [20,21] laid down the foundation for the free volume concept in modeling self-diffusion in simple van der Waals liquids. They considered that the volume in a liquid is composed of two parts, the actual volume occupied by the liquid molecules and the free volume surrounding these molecules opened up by thermal fluctuation. Increasing temperature increases only the free volume and not the occupied volume. The average free volume per molecule, vf, can be defined as... 

Physical chemistry is the science that describes the course of a chemical reaction. We have a solid foundation in the theoretical description of chemical reactions. Reactions occur under the rule of thermodynamics that defines equilibrium states where in a closed system (no changes in the number of molecules) no net reaction occurs. In an open system with continuous changes of the number of molecules (flow), this... 

The required statistical foundations have been outlined in chapter 1.3. Basically, two approaches are open, the canonical and the grand canonical. In the former, the adsorbate is considered as a closed system, characterized by the number of adsorbate molecules N. the area A and the temperature T. By model considerations, the canonical partition function Q(N.A.T) is formulated from... 

Statistical thermodynamics of monolayers is the obvious pendant of phenomenological classical thermodynamics, discussed in the previous section. In this approach some model assumptions are made on the properties and interactions of molecules, moving from a molecular picture to macroscopic properties, using statistical strategies, the foundations of which were laid down in chapter 1.3. Basically two approaches are open ... 

Four-component theories for the calculation of electronic structures as described in detail in this review have become mature particularly in the last decade as a highly accurate tool for any kind of system be it an atom, molecule or solid. Theoretical as well as methodological understanding gave detailed insight into the foundations of relativistic electronic structure theory. Some fundamental questions are still open as we have explicated, especially in the first two sections of this review, and they will certainly be tackled and answered in the years to come. Methodological advances will also continue to be made. 

When this evolutionary synthesis was formulated, people did not know what are genes. In this sense, the development of synthetic evolution theory can be compared to the initial steps of thermodynamics Fourier, for instance, formulated correct heat conduction equation (and developed powerful methods to solve it — Fourier series) without any knowledge of what was heat. But once molecular nature of heat was understood, the science of thermodynamics received its natural foundation in statistical mechanics. Similarly, once the nature of genes, as the sequences of DNA coding for particular proteins, was understood — it opened up the doors for molecular understanding of evolution. And since the molecules involved are, of course, biopolymers of DNA, RNA, and proteins — we should touch upon this topic in this book. That is why we invite you to the discussion of physics underpinnings of evolution. 

Tour has also attracted the interest of the National Science Foundation and others in his mission to teach chemistry, physics, biology, and materials science at the nanomolecular level through the animated adventures of actual molecules chemically synthesized in his Rice University laboratory. This project, called NanoKids , seeks to open up science with computer animation, music, and a MTV style and make nanoscale science learning fun and simple. 

Abstract In this chapter we examine some basic concepts of quantum chemistry to give a solid foundation for the other chapters. We do not pretend to review all the basics of quantum mechanics but rather focus on some specific topics that are central in the theoretical description of magnetic phenomena in molecules and extended systems. First, we will shortly review the Slater-Condon rules for the matrix elements between Slater determinants, then we will extensively discuss the generation of spin functions. Perturbation theory and effective Hamiltonians are fundamental tools for understanding and to capture the complex physics of open shell systems in simpler concepts. Therefore, the last three sections of this introductory chapter are dedicated to standard Rayleigh-Schrddinger perturbation theory, quasi-degenerate perturbation theory and the construction of effective Hamiltonians. 

Three essential elements provide the foundation for continuum mechanics. First, we must have a kinematical framework for mathematically describing the motion of material particles — not molecules, but differential portions of a physical entity, or body. Second, conservation principles for mass, charge, linear and angular momenrnm, and energy serve as fundamental, universal postulates. Various forms of the transport theorem enable translation of conservation principles between recognizable forms for closed and open... 

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