Spectroscopic properties, quantum structure

Inadequate availability of experimental data can considerably inhibit the development of improved energy functions for more accurate simulations of energetic, structural, and spectroscopic properties. This has led to the development of class II force fields such as CFF and the Merck Molecular Force Field (MMFF), which are both based primarily on quantum mechanical calculations of the energy surface. The purpose of MMFF, which has been developed by Thomas Halgren at Merck and Co., is to be able to handle all functional groups of interest in pharmaceutical design. 

Extensive quantum chemical calculations have been reported for sulfur-rich compounds in the past two decades. These calculations were used to investigate molecular structures and spectroscopic properties, as well as to understand the nature chemical bonding and reaction mechanism. Many high-level ab initio calculations were used for interpretation of experimental data and for providing accurate predictions of molecular structures and thermochemical data where no reliable experimental values are available. In recent years, density functional calculations have been extensively tested and used on many first- and second-row compounds. These proven DFT methods look promising for larger systems because for their computational efficiency. 

Molecular mechanics calculations have become a well established tool in the area of coordination chemistry, including the coordination chemistry of nickel375-379 where they are often applied for the analysis or the prediction of structures,380 the computation of isomer or conformer ratios and metal ion selectivities,381,382 and for simulating spectroscopic properties in combination with AOM calculations or by hybrid quantum mechanics/molecular mechanics (QMMM) methods.383,384 Details of the various approaches, e.g., the incorporation of d-electron stabilization energy... 

The first topic has an important role in the interpretation and calculation of atomic and molecular structures and properties. It is needless to stress the importance of electronic correlation effects, a central topic of research in quantum chemistry. The relativistic formulations are of great importance not only from a formal viewpoint, but also for the increasing number of studies on atoms with high Z values in molecules and materials. Valence theory deserves special attention since it improves the electronic description of molecular systems and reactions with the point of view used by most laboratory chemists. Nuclear motion constitutes a broad research field of great importance to account for the internal molecular dynamics and spectroscopic properties. 

There are two very broad, general conclusions resulting from the above review. The first is that MoS2-type nanoparticles are very different than other types of semiconductor nanoparticles. Nanoparticles of several different types of semiconductors, such as CdSe, CdS, and InP, have been extensively studied. Experimental and theoretical studies have elucidated much of their spectroscopy, photophysics, and dynamics. The results reviewed above are, in many places, in sharp contrast with those obtained on other types of quantum dots. This does not come as a surprise. The properties of the bulk semiconductor are reflected in those of the nanoparticle, and properties of layered semiconductors are vastly different from those of semiconductors having three-dimensional crystal structures. Although the electronic and spectroscopic properties of nanoparticles are strongly influenced by quantum confinement effects, the differences in the semiconductors cause there to be few generalizations about semiconductor quantum dots that can be made. 

Many derivatives of fluorescein containing a reactive group at the C-5 position are commercially available [11], Fluorescein isothiocyanate, for example, is widely used as protein tag [12]. These substances have essentially the same spectroscopic properties as the parent compound with the additional capability of binding covalently to proteins. Because of their high emission quantum yields, fluorescein conjugates are extensively used as tracers for microinjection in living cells to gather information on the structure and function of cells, localization of proteins, and cell-to-cell and intracellular diffusion [13-17]. 

Direct labeling of a biomolecule involves the introduction of a covalently linked fluorophore in the nucleic acid sequence or in the amino acid sequence of a protein or antibody. Fluorescein, rhodamine derivatives, the Alexa, and BODIPY dyes (Molecular Probes [92]) as well as the cyanine dyes (Amersham Biosciences [134]) are widely used labels. These probe families show different absorption and emission wavelengths and span the whole visible spectrum (e.g., Alexa Fluor dyes show UV excitation at 350 nm to far red excitation at 633 nm). Furthermore, for differential expression analysis, probe families with similar chemical structures but different spectroscopic properties are desirable, for example the cyanine dyes Cy3 and Cy5 (excitation at 548 and 646 nm, respectively). The design of fluorescent labels is still an active area of research, and various new dyes have been reported that differ in terms of decay times, wavelength, conjugatibility, and quantum yields before and after conjugation [135]. New ruthenium markers have been reported as well [136]. 

In anthracenocryptand 23, exciplexes are formed between the anthracene and nitrogen ion pairs.60,61,63,65,140 In MeOH, the quantum yield dramatically decreases due to the formation, via exciplex intermediates, of nonfluorescent radical ions. Upon addition of an excess of K+, Ag+, or Tl+ to methanolic solutions of 23, 1 1 cryptate-type complexes are formed.61,65 Complexation causes drastic changes in the spectroscopic properties. Cations such as Na+, for example, decrease the intensity of the exciplex emission and increase the intensity of the structured anthracene emission. Heavy-metal ions (Ag+, Tl+) interact strongly with the central ring of anthracene as shown by an exciplex-type emission observed for the Ag+ complex of 23. 

Finally, molybdenum oxide clusters have been prepared as neutral and ionic species in gas phase and studied by quantum chemical methods at various levels of theory. This includes MoO [195-198], MoO , n=l-3 [199], M0O3, Mo04, M0O4H2, Mo205, and M02O6, [200] where the calculations provide a satisfactory description of structural, energetic, and spectroscopic properties. 

As part of the series Topics in Heterocyclic chemistry, this volume titled Bioactive Heterocycles II presents comprehensive and up-to-date reviews on selected topics concerning mainly the usefulness for human health of flavonoids and related compounds, Sophora flavonoids and their functions in Sophora species (Leguminosae), the relationship of biological activity with the diverse structures of heterocycles by quantum chemical calculation, advances in bioactive mesoionic heterocycles, and the spectroscopic properties and application of bioactive phenothiazines including also benzo[a]phenothiazines. 

But second and more important. Priest continues to endorse the inference that because certain properties are primary, they are explanatory. The behavior of matter "at each level may be explained in terms of the structure of the level below. Thus, the behavior of macroscopic bodies and their properties is explained in terms of the (primary) properties of its microscopic (atomic) parts" (Priest, 1989, p. 36). And the behavior of the microscopic parts, which are the bearers of the primary properties, is "explained in terms of their quantum states and properties" (Priest, 1989, p. 36). On the account I have offered, such talk is problematic. The "bare" quantum structure does not explain—all by itself—the microscopic primary property. Reference to the measurement technique must also be included. But perhaps even more important, as I alluded previously, even the quantum structure is not universal or intrinsic. One and the same hunk of matter can have quantum or classical microscopic properties, depending on the time scale of the measurement. It will be of little explanatory importance to refer to the "quantum states and properties" in most spectroscopic measurement situations. To be sure, quantum corrections can be added in if a finer level of explanation is desired, but the "bare" quantum structure doesn t even exist at common... 

Transition metal oxides are the systems which make a challenge to any quantum chemical theory. Thus their theoretical investigation constitute an excellent benchmark for Density Functional Theory in both aspects methodological and practical one. Two transition metal oxide molecules are considered here in detail, VO and MoO, with emphasis put on their electronic structure, spectroscopic properties and metal - oxygen bonding features. Applicability of DFT to various electronic states is discussed and the quality of results within various computational schemes is examined. 

Subjects of recent publications on the spectroscopic properties and electronic structure of porphyrins include the photochemically induced dichroism of [(aetio)Zn]-,380 the absorption spectra of metallo-TPP compounds in SF , Ar, and n-octane matrices,361 the Zeeman effect in the absorption spectra of Pd-porphin in n-octane single crystals,362 the electronic spectra of Cu11- and Niu-corrin derivatives,363 m.c.d. studies on porphyrins,864 866 photoelectron spectra of porphyrins and pyrroles,366 and quantum mechanical calculations on porphyrins.367 368... 

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