SIMULATION OF IR SPECTRA

Selzer, P., Schuur, J. and Gasteiger, J. (1996). Simulation of IR Spectra with Neural Networks Using the 3D-MoRSE Code. In Software Development in Chemistry - Vol. 10 (Gasteiger, J., ed.), Fachgruppe Chemie-Information-Computer (CIC), Frankfurt am Main (Germany), pp. 293-302. 

Figure 5.2 Simulation of experimental bands of carboxylic acid dimers. Propynoic and propy-noic-D acids simulated on the basis of the first simplest theory (6) (upper spectra). Experimental spectra are drawn with full fines and predicted transitions as vertical bars. More recent simulations of IR spectra of acetic acid dimers are shown in the lower spectra, where greyed portion is experiment and thick line is theoretical reconstitution. Reproduced with permission from 1. Boumay and Y. Marechal, 1. Chem. Phys., 55 (1971) 1230 and from ref. (13). Copyright 2006, American Institute of Physics.

Theoretical simulations of IR spectra of different hydrogen-bonded crystals and gaseous complexes, presented in Sections III.A-III.F, based on the quantum-mechanical model presented in Section II, show that this model quantitatively explains details of the fine structure of the IR spectra and reproduces well deu-teration and temperature effects. The model takes into account the following mechanisms ... 

Schrader B, Bougeard D, Niggemann W (1980) Determination of the Structures of Organic Molecules by Computer-Evaluation and Simulation of IR and Raman Spectra. In Computational Methods in Chemistry, IBM Research Symposia-Series. Plenum Press, New York Schrader B, Heinrich P, Wyzgol R (1990a) US patent 4,941,742 Franz patent 2 625 318 UK patent 2 214 291... 

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 apphcation of QM/Continuum approaches to IR spectroscopy follows exacdy the same path commonly apphed to isolated molecules. The simulation of the spectra is obtained with two calculations one to obtain the equihbrium geometry of the solvated molecule and the other to compute the vibrational frequencies and intensities at the equihbrated geometry, as required by the standard harmonic approximation (HA). The frequencies (intensities) are calculated as the derivatives of the energy (dipole) with respect to nuclear displacements. The difference is that now the energy includes the solute—solvent interaction term and this imphes that in the calculation of its derivatives the variation of the molecular cavity has to be taken into account as it is generally anchored on the solute atoms. 

To simulate the IR spectra of stratified media containing an arbitrary number of layers, there exist two approaches—the application of recursion relationships... 

Electronic absorption and diffuse reflectance spectra (ESDR) were obtained with a "Specord M-40" spectrophotometer. IR spectra were recorded with a "Perkin Elmer FT-IR 1725X" spectrophotometer provided with diffuse reflectance accessory for solid samples. EPR spectra were recorded with a SE/X-2543 spectrometer at 77 K and 300 K. Primary treating and simulation of EPR spectra were carried out by special algorithms using IBM PC/XT type computers. 

The knowledge of the evolution with time of the molecular dipole moments is mandatory for the calculation of IR spectra with MD simulations. In the modem theory of polarization, the dipole moment of the (periodic) box cell is calculated with the Berry phase representation, as implemented in the CPMD and CP2K packages [98]. Briefly, in the limit where the F point approximation applies, the electronic contribution to the cell dipole moment (where a = x,y, z) is given by [99]... 

Another approach to the calculation of IR spectra of hydrogen-bonded complexes is based on linear response theory, in which the spectral density is the Fourier transform of the autocorrelation function of the dipole moment operator involved in the IR transition [62,63]. Recently Car-Parrinello molecular dynamics (CPMD) [73] has been used to simulate IR spectra of hydrogen-bonded systems [64-72]. 

In this chapter we present the results of theoretical studies [74, 75] of the vibrational spectra of hexagonal, cubic, and amorphous ice in the O—H and O—D stretching regions, including simulation of IR and Raman spectra, the effects of isotopic dilution on the IR and polarized Raman spectra, and computational modeling of the observed influence of dilution on the properties of vibrationally excited states. In the crystalline isotopomers the properties of the spectra and the vibrationally excited states are determined by complex interplay between the... 

A third approach uses two different methods to simulate IR spectra. The first uses harmonic frequencies and intensities of a semiempirical calculation, and the second a list of 40 substructures expected to be typical of IR spectra. Both types of data serve as input for back-propagation neural networks, which are trained with the quantum chemical or the structural information. The quantum chemical and the substructure approaches both exhibited similiar performance concerning... 

Figure 10.2-9. Application of a counterpropagation neural network as a look-up table for IR spectra sinnulation, The winning neuron which contains the RDF code in the upper layer of the network points to the simulated IR spectrum in the lower layer.

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,... 

Fig. 8. Theoretical simulation of VCD (top) and IR absorption (bottom) spectra of alanine dodecapeptides for the amide V bands for a fully a-helical conformation (left) and a fully left-handed 3i-helical conformation (right). The simulations are for the same three isotopically labeled (13C on the amide C=0 for four Ala residues selected in sequence) peptides as in Figure 7 N-terminal tetrad (4AL1), middle (4AL2), and C-terminal (4AL4). The 13C feature is the same for all sequences, confirming the experimentally found unfolding of the C-terminus. The agreement with the shapes in Figure 7 is near quantitative. Reprinted from Silva, R. A. G. D., Kubelka, J., Decatur, S. M., Bour, R, and Keiderling, T. A. (2000a). Proc. Natl. Acad. Sci. USA 97, 8318-8323. 2000 National Academy of Science, U.S.A.

A formally antiaromatic 1,4-dihydropyrazinothiadiazole has been prepared and characterized by single crystal X-ray spectroscopy. The antiaromatic character of which has been supported computationally using NICS measurements <20070L1073>. CHIH-DFT computational studies on acenaphtho[l,2-f]-l,2,5-thiadiazole 1,1-dioxide led to simulations of its infrared (IR) and ultraviolate (LJV) spectra, the dipole moment and polarizability <2007JMT373>. 4,6-Dinitrobenzothiadiazole was determined to have an electrophilic reactivity of —8.40 which corresponds to a pK z° of 7.86 for Meisenheimer complexation with water and is close to the demarcation boundary (E = —8.5) between super-and normal-electrophiles and between reactive dienophiles and inert partners in Diels-Alder adduct formation <20070BC1744>. 

FIGURE 14. Theoretically simulated and experimental vibrational circular dichroism (VCD) and infrared (IR) spectra of (2S,3S)-2,3-dimethylaziridine [(2S,3S)-159] carbon tetrachloride in the region 700-1600 cm-1. Reproduced from Reference 149 by permission of the National Research Council of Canada... 

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