Spectrum Hybrid Methods

Multivariate calibration methods are in general not analyte specific. Calibration models are built based on correlations in the data, which may be owing to the analyte or to systematic or spurious effects. One way to effectively boost the model specificity is through incorporation of additional analyte-specific information such as its pure spectrum. Hybrid methods merge additional spectral information with calibration data in an implicit calibration scheme. In the following section, we present two of these methods developed in our laboratory. 

Since the suggestion of the sequential QM/MM hybrid method, Canuto, Coutinho and co-authors have applied this method with success in the study of several systems and properties shift of the electronic absorption spectrum of benzene [42], pyrimidine [51] and (3-carotene [47] in several solvents shift of the ortho-betaine in water [52] shift of the electronic absorption and emission spectrum of formaldehyde in water [53] and acetone in water [54] hydrogen interaction energy of pyridine [46] and guanine-cytosine in water [55] differential solvation of phenol and phenoxy radical in different solvents [56,57] hydrated electron [58] dipole polarizability of F in water [59] tautomeric equilibrium of 2-mercaptopyridine in water [60] NMR chemical shifts in liquid water [61] electron affinity and ionization potential of liquid water [62] and liquid ammonia [35] dipole polarizability of atomic liquids [63] etc. 

If only a small set of ligands should be docked, one can choose from the full spectrum of methods since then the computing time is only a minor issue. The most promising approaches are probably the hybrid methods combining a very efficient search technique in a first phase with a very exact scoring and optimization technique in the second phase. The first phase is of importance since it guarantees a broad sampling within the solution space. The second phase then tries to find the local minima and scores them as reliably as possible. 

DNLM 1. Neurotransmitters—physiology. 2. Histochemistry— methods. 3. In Situ Hybridization— methods. 4. Chromatography, Liquid— methods, 5. Spectrum Analysis, Mass— methods. W1 ME 9616J V. 72 1997/QV 126 N4939 1997]... 

Ahneida, C., Azevedo, N. R, Fernandes, R. M., Keevil, C. W., Vieira, M. J. (2010). Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Salmonella spp. in a broad spectrum of samples. Applied and Environmental Microbiology, 76(13), 4476-4485. http //dx.doi.org/10.1128/AEM.01678-09 PMCID PMC2897454. 

Clearly, it would be more efficient to have a conceptual framework to guide development, or at least show where fundamental limits might lie. A complete theory of MALDI should quantitatively predict the observed mass spectrum as a function of variables such as matrix choice, analyte physical and chemical properties, concentrations, preparation method, laser characteristics (wavelength, spatial and temporal properties), local environment (such as ambient pressure or substrate temperature), and ion extraction method. Here we focus only on ionization mechanisms and do not address all factors affecting a MALDI experiment. Some of these are discussed in other contributions to this volume. Only mechanisms involving molecular matrices and laser excitation are included, methods that depend primarily on properties of the substrate, such as nanoparticles or stmctured surfaces (such as DIOS) are not Hybrid methods, such as laser ablation into electrosprays, are also out of our scope, but vacuum and higher-pressure (e.g., atmospheric pressure) MALDI are both considered to have the same underlying mechanisms discussed here. 

Figure 11.12. Si electrode and NW hybrid device, (a) Schematic of a single LED fabricated by the method outlined in Fig. 11.11. (b) I-V behavior for a crossed p-n junction formed between a fabricated p+-Si electrode and an n-CdS NW. (c) EL spectrum from the forward biased junction, (d) SEM image of a CdS NW assembled over seven p+-silicon electrodes on a SOI wafer (e) EL image recorded from an array consisting of a CdS NW crossing seven p+-Si electrodes. The image was acquired with +5V applied to each silicon electrode while the CdS NW was grounded. [Reprinted with permission from Ref. 59. Copyright 2005 Wiley-VCH Verlag.]...

In an attempt to aid interpretation of the IR spectrum of MbCO we decided to model the full protein by use of a hybrid quantum mechanics/molecular mechanics approach (QM/MM), to evaluate changes in the CO stretching frequency for different protein conformations. The QM/MM method used [44] combines a first-principles description of the active center with a force-field treatment (using the CHARMM force field) of the rest of the protein. The QM-MM boundary is modeled by use of link atoms (four in the heme vinyl and propionate substituents and one on the His64 residue). Our QM region will include the CO ligand, the porphyrin, and the axial imidazole (Fig. 3.13). The vinyl and propionate porphyrin substituents were not included, because we had previously found they did not affect the properties of the Fe-ligand bonds (Section 3.3.1). It was, on the other hand, crucial to include the imidazole of the proximal His (directly bonded to the... 

As was the case for the absorption spectrum, different calculations of the band MCD of ZnP and MgP have produced different interpretations of the observed spectral features. Solheim et al. have recently calculated the MCD spectra of ZnP, MgP, and NiP using their complex polarization propagator method and a hybrid... 

Although PCR and PLS are powerful methods, they are not without their limitations. In particular, implicit calibration methods can be susceptible to chance correlations. Thus, when the calculated b is applied to a future spectrum in which those correlations are not present, increased error is likely. It may be possible to improve implicit calibration and limit spurious correlations by incorporating additional information about the system or analytes. This combination of features from implicit and explicit calibration methods is termed hybrid calibration. 

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