Simulation of spectra

When there is no spectrum in the library that can be used to elucidate a chemical structure, interpretative methods are needed. The methods of pattern recognition and of artificial intelligence must then be used. As a result, different chemical structures will be obtained as candidates for the unknown molecule. To verify an assumed structure, simulation of spectra becomes important. In a final step, the simulated spectrum could be compared with that measured. 

High-performance methods for routine simulations of IR and mass spectra are not yet available. In IR spectroscopy, the best simulations are obtained on the basis of quantum-chemical approaches. 

The increments used here in the NMR simulation represent in a more general sense molecular descriptors that can be defined as follows [5]  

The molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment. 

With this definition, we can consider the structure representations of molecules in Section 7.2 as topological descriptors. At present, more than 5000 molecular descriptors can be computed [5]. They can be categorized by their data types (Table 7.11) or by their dimensionality (Table 7.12). 

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Other methods consist of algorithms based on multivariate classification techniques or neural networks they are constructed for automatic recognition of structural properties from spectral data, or for simulation of spectra from structural properties [83]. Multivariate data analysis for spectrum interpretation is based on the characterization of spectra by a set of spectral features. A spectrum can be considered as a point in a multidimensional space with the coordinates defined by spectral features. Exploratory data analysis and cluster analysis are used to investigate the multidimensional space and to evaluate rules to distinguish structure classes. 

Figure 1. Flow chart of the Polymer Analysis program. The program Is entered from a larger program, NMRl. A database must be chosen or created for the spectrum at hand and a statistical model chosen. Options In the main menu Include calculation of probabilities associated with the model, simulation of spectra, and modification of the peak table or database.

The growing importance of quantum-chemical calculations is dealt with in a short section, with emphasis on the consideration of relativistic effects, especially in systems containing mercury. These calculations aim at optimization of structures, determination of bond energies, simulation of spectra, and estimation of spectral parameters, independent of but complementary to experiments. 

This benefit comes at a cost, which arises from significantly reduced S/N and some interpretive difficulty as compared to IR. Developments on the latter front are bringing the theoretical prediction capability of VCD for small molecules to a level demonstrably superior to that for ECD (Freedman and Nafie, 1994 Stephens et al., 1994 Stephens and Devlin, 2000), especially for peptide spectra (Kubelka et al., 2002). Most previous protein applications of VCD used empirically based analyses (Keiderling, 1996, 2000). Theoretical methods are limited when applied to large molecules such as proteins however, a hybrid approach using ab initio determination of spectral parameters with modest-sized molecules for transfer to large peptides has made simulation of spectra for large peptides possible (Bour et al., 1997 Kubelka et al., 2002). Theoretical techniques for simulation of small-molecule VCD are the focus of several previous reviews (Stephens and Lowe, 1985 Freedman and Nafie,... 

Molecular spectra can be analyzed for spectrometric or for spectroscopic purposes. The term spectrometric usually refers to compound identification (linking a signal to a known structure) and to the determination of its concentration. The term spectroscopic stands for interpretation of the spectrum in terms of structure (chemical, electronic, nuclear, etc.). In this chapter we will look as some theoretical and practical aspects of a key spectrometric application of bioEPR, namely, the determination of the concentration of paramagnets, also known as spin counting. Subsequently, we consider the generation of anisotropic powder EPR patterns in the computer simulation of spectra, a basic technique that underlies both spectrometric and spectroscopic applications of bioEPR. 

The combined effects of the dipolar and exchange interactions produce a complex frequency-dependent EPR spectrum, which can however be analysed by performing numerical simulations of spectra recorded at different microwave frequencies. When centre A is a polynuclear centre, the value of its total spin Sa = S, is determined by the strong exchange coupling between the local spins S, of the various metal sites. In this case, the interactions between A and B consist of the summation of the spin-spin interactions between Sb and all the local spins S, (Scheme II). The quantitative analysis of these interactions can therefore yield the relative arrangement of centres A and B as well as information about the coupling within centre A. 

The semiquinone biradical produced in the photocycle of bacterial photosynthetic reaction centres was trapped at 77 K and examined at 9.6, 35, and 94 GHz.16 Simulations of spectra at the multiple resonant frequencies using the simulated annealing method revealed the spatial and electronic structure of the biradical. The value of r was found to be 17.2 + 0.2 A, which is in good agreement with the value of 17.4 0.2 A obtained in an X-ray crystal structure. This study shows the power of high-frequency EPR combined with data obtained at lower frequencies. 

Quantitative simulation of spectra as outlined above is complicated for particle films. The material within the volume probed by the evanescent field is heterogeneous, composed of solvent entrapped in the void space, support material, and active catalyst, for example a metal. If the particles involved are considerably smaller than the penetration depth of the IR radiation, the radiation probes an effective medium. Still, in such a situation the formalism outlined above can be applied. The challenge is associated with the determination of the effective optical constants of the composite layer. Effective medium theories have been developed, such as Maxwell-Garnett 61, Bruggeman 62, and other effective medium theories 63, which predict the optical constants of a composite layer. Such theories were applied to metal-particle thin films on IREs to predict enhanced IR absorption within such films. The results were in qualitative agreement with experiment 30. However, quantitative results of these theories depend not only on the bulk optical constants of the materials (which in most cases are known precisely), but also critically on the size and shape (aspect ratio) of the metal particles and the distance between them. Accurate information of this kind is seldom available for powder catalysts. 

Simulation of spectra for (R)-acacpnH2 and its trifluoro derivative indicates that the syn conformation, predominant in solution, is that having the pn methyl group anti to the N atom, as found in the solid state.101 A similar conformer distribution is expected also for acacenH2 in view of the similarity of absorption spectra. In conclusion, it appears that these compounds exist in solution essentially in a unique conformation, maintained by strong intramolecular hydrogen bonds. 

Once the desired structure is generated the user should be able to use its representation (the connection table) in many different ways to store it, to combine it with other structures, supplement it with textual information, to decompose it to fragments, add it to a collection, use it as a target or query compound in different searches or procedures, use it in different applications such as simulation of spectra, determination of properties, etc. calculate molecular formula, draw it on a plotter, etc. 

The LAOCOON II program has been used to calculate theoretical spectra for l,3,4,6-tetra-0-acetyl-2,5-0-methylene-D-mannitol-1,1,6,6-d4 (76 p. 73),192 and in the iterative analysis and simulation of spectra of methyl 2,3- and 3,4-anhydroglycopyranosides86 (LAOCN3 was also used), the protons of the sugar portion of many nucleosides,104-105-107 109 for example, 2 -deoxyadenosine251 (84), and adenosine 5 -phosphate126 (55 p. 60). 

Water clusters containing simple ions are another area of current experimental and theoretical interest. Accordingly, they are also the subject of EA studies. Chaudhury et al. [113] have used EA methods on empirical potentials to obtain optimized structures of halide ions in water clusters, which they then subjected to AMI calculations for simulation of spectra. EA applications to alkali cations in TIP4P water clusters [114,115] have led to explanations of experimental mass-spectroscopic signatures of these systems, in particular the lack of magic numbers for the sodium case and some of the typical magic numbers of the potassium and cesium cases, and the role of dodecahedral clathrate structures in these species. 

Till recently, computations of vibronic spectra have been limited to small systems or approximated approaches, mainly as a consequence of the difficulties to obtain accurate descriptions of excited electronic states of polyatomic molecules and to computational cost of full dimensional vibronic treatment. Recent developments in electronic structure theory for excited states within the time-dependent density functional theory (TD-DFT) and resolution-of-the-identity approximation of coupled cluster theory (R1-CC2) and in effective approaches to simulate electronic spectra have paved the route toward the simulation of spectra for significantly larger systems. 

IRG2959 (Scheme 12.1) was used as aprobe of molecular motion in cotton fibers. TR ESR spectra of IRG2959 consist of spectra of RPs in a liquid-like and in crystalline environments. Simulation of spectra led to the conclusion that radicals participate in 3D and in 2D motion. Observation of a contribution of SCRP suggested that approximately 50% of radicals are trapped in cages of cotton fibers during the time of the experiment (0.5 0.s). ... 

The reader is referred to the monograph by Sandstrom for a detailed treatment of the subject of dynamic NMR. A helpful tool in evaluating NMR spectra of species in chentical exchange is to perform simulations of spectra, which... 

FIGURE 4.15. Simulated 60-, 100-, and 300-MHz spectra of acrylonitrile 300-MHz experimental spectrum (in CDCh) for comparison. For reference to simulation of spectra, see footnote reference to Bruker Instruments program in Section 4.8. 

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