A new ingenious combination of rank annihilation factor analysis (RAFA) and self-modeling to enhance the unambiguous resolution of multicomponent spectra.

In the article, a novel chemometric method for resolution of three-component spectral mixtures is presented and thoroughly scrutinized. Its main core is based on the concept of 'soft' data self-modeling using the SVD factorization (SVD-SM). Each spectrum is then represented as an element of the geometric object known as a simplex which, in this case, takes a form of a triangle. Since its vertices are defined by the spectra of the mixture's pure components, the carried out analysis comes down to a proper determination of the vertices locations. As opposed to the conception of doing so by estimating the areas of feasible solutions (AFS), the idea of unambiguous identification of the simplex's sides is introduced. This may be achieved through a neat application of the rank annihilation factor analysis (RAFA), which allows for generation of two-component difference spectra, whose point representations mark the edges of the searched triangle. Consequently, the obtained final results remain highly unique. In the paper, basics and details of the outlined hybrid RAFA-SVD-SM method are critically discussed from both conceptual and practical points of view. Finally, effectiveness of the proposed algorithm (written in MATLAB) is (successfully) validated on a few series of experimental quenched fluorescence spectra. The high enough recovery rate of the individual component spectra qualifies the proposed approach to be a justifiable alternative for the several well-established chemometric methods tested in the study, including GRAM and PARAFAC.

Searching for Alternatives to the Savitzky-Golay Filter in the Spectral Processing Domain.

An elegant, well-established effective data filter concept, proposed originally by Abraham Savitzky and Marcel J.E. Golay, is undoubtedly a very effective tool, however not free from limitations and drawbacks. Despite the latter, over the years it has become a "monopolist" in many fields of spectra processing, claiming a "commercial" superiority over alternative approaches, which would potentially allow to obtain equivalent or in some cases even more reliable results. In order to show that basic operations performed on spectral datasets, like smoothing or differentiation, do not have to be equated to the application of the one particular single algorithm, several of such alternatives are briefly presented within this paper and discussed with regard to their practical realization. A special emphasis is put on the fast Fourier methodology (FFT), being widespread in the general domain of signal processing. Finally, a user-friendly Matlab routine, in which the outlined algorithms are implemented, is shared, so that one can select and apply the technique of spectral data processing more adequate for their individual requirements without the need to code it prior to use.

Intermolecular interactions of tetracyanoethylene (TCNE) and fumaronitrile (FN) with minor amines: A combined UV-Vis and EPR study.

In this paper, the nature of interactions between two cyanocarbons-tetracyanoethylene (TCNE) and fumaronitrile (FN)-and a series of four secondary amines possessing a general formula C4HxN (x = 5-11) is thoroughly scrutinized. For all of the TCNE-amine pairs, tricyanovinylation (TCV) reaction is observed; however, only for pyrrole, it is accompanied with a visible charge-transfer (CT) complex formation-no such chemical individuals, characteristic for TCNE, have been noticed for aliphatic and alicyclic amines. On the contrary, FN forms such complexes with all the amines studied. Interestingly, a rather unexpected reaction of FN with alicyclic amines has been observed. The recorded electron paramagnetic resonance (EPR) spectra indicate the presence of both TCNE●- and FN●- radicals in the analyzed samples, assigned to a complete charge (electron) transfer process within the CT complexes, whose efficiency can be additionally enhanced by photoirradiation. The origination of the former radical, whose presence is observed also in the TCNE-diethylamine mixture, is as well proposed to result indirectly from the TCV reaction, occurring for this system. Finally, the superhyperfine structure of EPR spectra, indicating the existence of some secondary interactions of the radicals with surrounding compounds, is discussed. Formation of CT complexes and tricyanovinylates has been investigated and characterized with UV-Vis spectroscopy, while the presence of (cyano)radicals in the analyzed mixtures has been evidenced by (photoinduced) EPR measurements. Interpretation of the experimental results is also supplemented with computer simulations including density functional theory calculations.

Do Spectra Live in the Matrix? A Brief Tutorial on Applications of Factor Analysis to Resolving Spectral Datasets of Mixtures.

In spite of a rapid growth of data processing software, that has allowed for a huge advancement in many fields of chemistry, some research issues still remain problematic. A standard example of a troublesome challenge is the analysis of multi-component mixtures. The classical approach to such a problem consists of separating each component from a sample and performing individual measurements. The advent of computers, however, gave rise to a relatively new domain of data processing - chemometry - focused on decomposing signal recorded for the sample rather than the sample itself. Regrettably, still a very few chemometric methods are practically used in everyday laboratory routines. The Authors believe that a brief 'user-friendly' guide-like article on several 'flagship' algorithms of chemometrics may, at least partly, stimulate an increased interest in the use of these techniques among researchers specializing in many fields of chemistry. In the paper, five different techniques of factor analysis are used for the analysis of a three-component system of fluorophores. These algorithms, applied on the excitation-emission spectra, recorded for the 'unknown' mixture, allowed to unambiguously determine its composition without the need for physical separation of the components. An example of using chemometric methods for physical chemistry research is also provided. For each presented technique of the data analysis, a short description of its theoretical background followed by an example of its practical performance is given. In addition, the Reader is supplemented with a basic information on matrix algebra, detailed experimental 'recipes', reference specialist literature and ready-to-use MATLAB codes.

Unravelling the nature of a toluene-fumaronitrile complex.

In this research, the occurrence and anomalous increase of an additional absorption band observed in the spectrum of fumaronitrile dissolved in toluene are explained and characterized. The formation of a stable ground-state complex between these two molecules is evidenced by both experimental and theoretical studies. TD-DFT calculations show that the presence of an unexpected signal in the absorption spectra originates from the photoinduced intermolecular charge-transfer process occurring within this system. The mechanism and the efficiency of the adduct formation were investigated using both spectral measurements (UV-Vis, IR) and quantum-mechanical calculations (DFT). The influence of the solvent polarity on the complex stability was also evaluated. Since the forces responsible for the adduct formation turn out to be of a rather weak, dispersive character, the related equilibrium stability constant is relatively low and becomes even lower with the increase in solvent polarity. Finally, the system was analyzed for the expected fluorescence emission of the resulting complex, but none was observed.

Compensation of temperature effects on spectra through evolutionary rank analysis.

Spectra measured in various ranges of temperature are usually slightly different from each other in shape and position of the bands. Although the displayed inconsistencies are rather small, yet may lead to incorrect analysis and interpretation of the collected spectrothermal data. Thus the unspecific spectral effects induced by temperature, in particular the thermal shifts and broadening of the bands, have to be compensated. In the paper, a simple two-step method of thermospectral dataset uniformisation is presented. Thermally induced 'movement' of the bands is approximated as a linear function of the difference of temperatures, so the co-shifting of the spectra is done linearly. Thermal broadening is mimicked by convoluting the low-temperature signal (spectrum) with a Gaussian or Lorentzian spreading filter. Proper widths (values of FWHM) of these filters, used to uniform the whole dataset, are assumed to depend on the difference of temperatures, in a form of one-parameter functions. This assumption, which has been empirically confirmed, is a fundamental premise of the method of Partial Compensation for Thermal Broadening (PCTB). Optimal values of the parameters of all the functions, used to compensate both thermal shifting and broadening, are found by the Evolutionary Rank Analysis (ERA) applied on an evolving data matrix. Efficiency of the proposed approach was verified on the UV-Vis thermospectral dataset of one-component model systems. In addition, since the method is aimed at making uniformed the thermospectral datasets of multi-component systems with similar spectral properties of individual components, the two-component conformer system of t-APE (trans-1-(2'-anthryl)-2-phenylethene) has also been analyzed.

π-π-Induced aggregation and single-crystal fluorescence anisotropy of 5,6,10b-tri-aza-acephenanthrylene.

The structural origin of absorption and fluorescence anisotropy of the single crystal of the π-conjugated heterocyclic system 5,6,10b-tri-aza-acephenan-thrylene, TAAP, is presented in this study. X-ray analysis shows that the crystal framework in the space group P [Formula: see text] is formed by centrosymmetric dimers of face-to-face mutually oriented TAAP molecules joined by π-π non-covalent interactions. The conformation of the TAAP molecule is stabilized by intramolecular C-H⋯N(sp2), N(sp2)H⋯π(CN), and C-H⋯O(sp2) hydrogen bonds. The presence of weak π-π interactions is confirmed by quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analysis. The analysis of the optical spectra of TAAP in solution and in the solid state does not allow the specification of the aggregation type. DFT calculations for the dimer in the gas phase indicate that the lowest singlet excitation is forbidden by symmetry, suggesting H-type aggregation, even though the overall absorption spectrum is bathochromically shifted as for the J-type. The experimental determination of the permanent dipole moment of a TAAP molecule in 1,4-dioxane solution indicates the presence of the monomer form. The calculated absorption and emission spectra of the crystal in a simple approximation are consistent with the experimentally determined orientation of the absorption and emission transition dipole moments in TAAP single crystals. The electrostatic interaction between monomers with a permanent dipole moment (ca 4 D each) could result in the unusual spectroscopic JH-aggregate behaviour of the TAAP dimer.

Fast Decomposition of Three-Component Spectra of Fluorescence Quenching by White and Grey Methods of Data Modeling.

'White' and 'grey' methods of data modeling have been employed to resolve the heterogeneous fluorescence from a fluorophore mixture of 9-cyanoanthracene (CNA), 10-chloro-9-cyanoanthracene (ClCNA) and 9,10-dicyanoanthracene (DCNA) into component individual fluorescence spectra. The three-component spectra of fluorescence quenching in methanol were recorded for increasing amounts of lithium bromide used as a quencher. The associated intensity decay profiles of differentially quenched fluorescence of single components were modeled on the basis of a linear Stern-Volmer plot. These profiles are necessary to initiate the fitting procedure in both 'white' and 'grey' modeling of the original data matrices. 'White' methods of data modeling, called also 'hard' methods, are based on chemical/physical laws expressed in terms of some well-known or generally accepted mathematical equations. The parameters of these models are not known and they are estimated by least squares curve fitting. 'Grey' approaches to data modeling, also known as hard-soft modeling techniques, make use of both hard-model and soft-model parts. In practice, the difference between 'white' and 'grey' methods lies in the way in which the 'crude' fluorescence intensity decays of the mixture components are estimated. In the former case they are given in a functional form while in the latter as digitized curves which, in general, can only be obtained by using dedicated techniques of factor analysis. In the paper, the initial values of the Stern-Volmer constants of pure components were evaluated by both 'point-by-point' and 'matrix' versions of the method making use of the concept of wavelength dependent intensity fractions as well as by the rank annihilation factor analysis applied to the data matrices of the difference fluorescence spectra constructed in two ways: from the spectra recorded for a few excitation lines at the same concentration of a fluorescence quencher or classically from a series of the spectra measured for one selected excitation line but for increasing concentration of the quencher. The results of multiple curve resolution obtained by all types of the applied methods have been scrutinized and compared. In addition, the effect of inadequacy of sample preparation and increasing instrumental noise on the shape of the resolved spectral profiles has been studied on several datasets mimicking the measured data matrices. Graphical Abstract ᅟ.

Infrared Spectroscopy and Born-Oppenheimer Molecular Dynamics Simulation Study on Deuterium Substitution in the Crystalline Benzoic Acid.

In this study we present complementary computational and experimental studies of hydrogen bond interaction in crystalline benzoic acid and its deuterated and partially deuterated derivatives. The experimental part of the presented work includes preparation of partially deuterated samples and measurement of attenuated total reflection (ATR)-FTIR spectra. Analysis of the geometrical parameters and time course of dipole moment of crystalline benzoic acid and its deuterated and partially deuterated derivatives by Born-Oppenheimer molecular dynamics (BOMD) enabled us to deeply analyze the IR spectra. Presented simulations based on BOMD gave us opportunity to investigate individual motion and its contribution to the IR spectra. The band contours calculated using Fourier transform of autocorrelation function are in quantitative agreement with the experimental spectra. Characterization of single bands was carried out by "normal coordinate analysis". The salient point of our study is a comparison of the spectra of the deuterated and partially deuterated crystalline benzoic acid with that of the nondeuterated one. Furthermore, we have applied the principal component analysis for analysis of the number of components in partially deuterated systems. In this study, we reveal that the arrangements of hydrogen and deuterium atoms in partially deuterated samples are random.

Resolution of conformer-specific all-trans-1,6-diphenyl-1,3,5-hexatriene UV absorption spectra.

All-trans-1,6-diphenyl-1,3,5-hexatriene (ttt-DPH) exists in solution as a mixture of s-trans,s-trans and s-cis,s-trans conformers. The latter is higher in energy, and its contribution increases with increasing temperature. ttt-DPH UV absorption spectra broaden with increasing temperature and undergo blue shifts with decreasing polarizability. We describe here the resolution of two spectrothermal matrices of ttt-DPH UV absorption spectra into two conformer-specific components. The first matrix consists of DPH spectra measured in n-dodecane in the 283 to 374 K T range and the second of ttt-DPH absorption spectra measured in the even numbered n-alkanes (n-C(8)-n-C(16)) at temperatures selected to achieve isopolarizability (284-372 K). Principal component analysis (PCA) treatments showed that reasonable two-component systems are attained by compensation for T-induced broadening and shifting in the pure conformer spectra. The self-modeling (SM) method used to resolve the n-C(12) matrix is successfully tested on a simulated matrix closely mimicking ttt-DPH experimental spectra in n-C(12). Compensation for nonlinear effects yields robust two-component matrices from the experimental spectra. Their resolution into pure component spectra is based on the application of the Lawton and Sylvestre (LS) non-negativity criterion at the spectral onset to define the spectrum of the low energy s-trans-conformer and the optimum linearity van't Hoff (vH) plot criterion to find the spectrum of the higher-energy s-cis-conformer. Resolved spectra are somewhat sensitive to the choice of the spectral region in which the LS criterion is applied. The surprising result is that both resolutions lead to the conclusion that the molar fraction of the s-cis-conformer equals, or even exceeds, the molar fraction of the s-trans-conformer as the highest T's employed in our study are approached.

Photoisomerization of cis,cis-1,4-diphenyl-1,3-butadiene in glassy media at 77 K: the bicycle-pedal mechanism.

The cis-trans photoisomerization of cis,cis-1,4-diphenyl-1,3-butadiene in a soft isopentane glass at 77 K gives significant two-bond photoisomerization in contrast to solution and hard glassy media where only one-bond photoisomerization takes place.

Photoisomerization of cis-1-(2-naphthyl)-2-phenylethene in methylcyclohexane at 77 K: no hula-twist.

The cis-trans photoisomerization of cis-1-(2-naphthyl)-2-phenylethene (c-NPEA and c-NPEB) was studied in methylcyclohexane glass at 77 K. The progress of the reaction was followed by fluorescence spectroscopy. Formation of the extended trans conformer (t-NPEB) is revealed by the growth of sharp vibronic bands on the broad structureless fluorescence spectrum of c-NPE. Principal component analysis with self-modeling of a matrix consisting of spectra generated by irradiation of c-NPE at different excitation wavelengths and spectra of t-NPE measured under the same conditions as a function of excitation wavelength reveals that the diabatic photoisomerization is a completely conformer-specific one-bond twist process: c-NPEB --> t-NPEB. These observations are consistent with observations in solution at ambient temperature. They demonstrate unequivocally that free volume restrictions imposed by the amorphous glassy environment do not open a hula-twist process.

Resolution of three fluorescence components in the spectra of all-trans-1,6-diphenyl-1,3,5-hexatriene under isopolarizability conditions.

all-trans-1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescence in solution consists of emissions from the S1 (2(1)A(g)) and S2 (1(1)B(u)) states of the s-trans,s-trans conformer (s-t-DPH) and emission from the S1 state of the s-cis,s-trans conformer (s-c-DPH). The contribution of s-c-DPH fluorescence increases upon excitation at longer wavelengths, and both minor emissions, s-c-DPH and 1(1)B(u) s-t-DPH fluorescence, contribute more at higher temperatures (Ts). Resolution of a spectrothermal matrix of DPH fluorescence spectra by principal component analysis with self-modeling (PCA-SM) is hampered by T-dependent changes in the spectra of the individual components. We avoided differential polarizability-dependent spectral shifts by measuring the spectra in n-alkanes (Cn, C8 to C16 with n even) at T values selected to keep the index of refraction constant, hence under isopolarizability conditions. Compensation of the spectra for T-induced broadening allowed resolution of the spectral matrix into its three components. The optimum van't Hoff plot gives Delta H = 2.83 kcal/mol for s-c-DPH/s-t-DPH equilibration, somewhat smaller than the 3.4 kcal/mol calculated value, and the optimum Boltzmann distribution law plot gives Delta E(ab) = 4.09 kcal/mol for 1(1)B(u)/2(1)A(g) equilibration. The 1(1)B(u) fluorescence spectrum bears mirror-image symmetry with the DPH absorption spectrum, and the energy gap, 1431 cm(-1), is consistent with the 1615 cm(-1) difference between the lowest energy bands in the 1(1)B(u) and 2(1)A(g) fluorescence spectra. The results give V(ab) = 198 +/- 12 cm(-1) for the vibronic matrix coupling element between the 2(1)A(g) and 1(1)B(u) states. Fluorescence quantum yields and lifetimes under isopolarizability conditions reveal an increase in the effective radiative rate constant of s-t-DPH with increasing T.

Conformer-specific photoconversion of 25-hydroxytachysterol to 25-hydroxyprevitamin D3: role in the production of vitamin Ds.

The photochemical goal in the production of vitamin Ds (Vit Ds) is to maximize the conversion of the provitamins (Pros) to the previtamins (Pres) while minimizing stoichiometric losses to undesirable over-irradiation products. The last step in the syntheses, the [1,7]-sigmatropic rearrangement of the Pres to the Vits, is thermally induced. The competition between cis-trans photoisomerization and photocyclization of the Pres is known to be highly excitation-wavelength specific. It inspired Havinga's nonequilibration of excited rotamers (NEER) principle and more recent alternative explanations. In contrast, the photochemistry of tachysterol has been reported to be relatively unexceptional with Tachy --> Pre quantum yields in the 0.10-0.13 range, independent of lambdaexc. Examination of the spectrum of the 25-hydroxy derivative of tachysterol (HOTachy) reveals vibronic structure between 295 and 260 nm and a broad structureless shoulder between 330 and 295 nm. These features are consistent with absorption by at least two Tachy conformers. We show that these conformers differ dramatically in their trans-to-cis photoisomerization efficiency. The Tachy --> Pre quantum yield at 313 nm (0.42) in degassed methanol solution is substantially higher than at 254 nm (0.12). On the basis of recent theoretical predictions, it is likely that 313 nm selectively excites the cEc HOTachy conformer which gives photoisomerization much more efficiently than do the other expected conformers (cEt, most abundant, and tEt). Efficient conversion of HOPro D3 to HOPre D3 is accomplished by a two-stage 254/313-nm irradiation sequence. Use of 313 nm in the second step is preferable to previously proposed much longer wavelengths that were hardly absorbed by HOTachy.