The use of optical spectroscopy in combinatorial chemistry

Infrared and Raman spectroscopy allow direct spectral analysis of the solid‐phase, thus avoiding the tedious cleavage of compounds from the solid support. With diagnostic bands in starting materials or products, infrared and Raman spectroscopy are efficient in monitoring each reaction step directly on the solid phase. Consequently, infrared and Raman spectroscopy have evolved as the premier analytical methodology for direct analysis on the solid support. While infrared transmission spectroscopy is a general analytical method for resin samples, internal reflection spectroscopy is especially suited for solid polymer substrates known as “pins” or “crowns.” Single bead analysis is done best by infrared microspectroscopy, whereas photoacoustic spectroscopy allows totally nondestructive analysis of resin samples. With an automated accessory, diffuse reflection spectroscopy provides a method for high throughput on‐bead monitoring of solid‐phase reactions. Providing identification based on molecular structure, HPLC‐FTIR is, therefore, complementary to LC‐MS. Additionally, Raman spectroscopy as a complement to infrared spectroscopy can be applied to resin samples and—using a Raman microscope—to single beads. Fluorometry as an extremely sensitive spectroscopic detection method allows rapid quantification of organic reactions directly on the resin. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng (Comb Chem) 61:179–187, 1998/1999.     

Role of Fourier transform infrared spectroscopy in the rehearsal phase of combinatorial chemistry: a thin-layer chromatography equivalent for on-support monitoring of solid-phase organic synthesis

The adaptation of diverse organic reactions to solid supports requires significant reaction optimization efforts. A convenient on-support analytical method functionally similar to TLC in solution chemistry is very advantageous. As a TLC-equivalent method, the single bead FTIR is a simple, sensitive, fast, and convenient analytical method to monitor SPOS without stopping the reaction or cleaving the product. As with TLC, single bead FTIR provides a wide range of information such as qualitative assessment, quantitative determination, and reaction kinetics. Studies with the single bead FTIR have not only provided a tool for daily monitoring of the solid-phase reactions, but a way to understand the properties of polymer-bound substrate and the nature of polymer-supported organic reactions. It has assisted in the selection of a wide range of reaction conditions rapidly for SPOS in the rehearsal phase of combinatorial chemistry. Due to its convenience and efficiency, FTIR internal reflection spectroscopy has evolved as a useful analytical methodology for monitoring of combinatorial chemistry reactions directly on polymer surface.     

Introduction to Raman spectrometry]

The frequency shift observed when light is scattered by molecules is called Raman effect. Raman spectroscopy like infrared spectroscopy is a method of studying molecular vibrations. The two methods are complementary, they both give much informations about the structure of molecules and crystals, the nature of chemical bonds and intermolecular interactions. Infrared absorption is allowed if the vibration is accompanied by a variation of electric dipole moment, however Raman scattering will only be observed if a variation of molecular polarizability appears during the vibration. Symetry properties of molecules of crystals lead to the determination of the number of normal vibrational modes and their Raman or infrared activity. The discovery of Laser light source has permitted a great development of Raman instrumentation. Raman spectrometers can easily record the whole spectrum of molecular vibrations (0-4000 cm-1) of samples in solid, liquid or gazeous state. Very small quantities of material are required (several milligrams). Aqueous solutions are easily investigated. Owing to the easy exploration of the low frequency range by modern spectrometers, new areas are opened in the study of the solid state and polymeric chains. Resonance Raman effect allows the spectra of very dilute solutions to be obtained. With the development of rapid scanning systems and electro-optical spectrometers, study of transients species is now possible. Among the physical analysis methods, Raman spectroscopy is now more and more used, and this technic has already been successfully used in numerous biological and biochemical problems.     

A phospholipid bilayer supported under a polymerized Langmuir film

Phospholipid single bilayers supported on a hydrophilic solid substrate are extensively used in the study of the interaction between model membranes and proteins or polypeptides. In this article, the formation of a single dimyristoylphosphatidylcholine (DMPC) bilayer under an octadecyltrimethoxysilane (OTMS) polymerized Langmuir monolayer at the air-water interface is followed by Brewster angle microscopy (BAM) and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). The formation of the bilayer is initiated by injection of dimyristoylphosphatidylcholine small unilamellar vesicles into the aqueous subphase. Brewster angle microscopy allows visualization of the kinetics of formation and the homogeneity of the bilayer. Spectral simulations of the polarization-modulated infrared reflection absorption spectroscopy spectra reveal that the bilayer thickness is 39 +/- 5 A. This system constitutes the first example of a phospholipid bilayer on a "nanoscopic" support and opens the way to studies involving supported bilayers using powerful experimental techniques such as x-ray reflectivity, vibrational spectroscopies, or Brewster angle microscopy.     

Solid-phase sequencing on the gas-phase sequencer

Automated Edman degradation has been successfully used for determining the primary structure of numerous peptides and proteins. Quantitative solid-phase Edman degradation has great potential use for amino acid sequence analysis of synthetic peptides assembled on resin support by the Merrifield procedure. We report here the combined use of a modified gas-phase sequencer program and our improved reversed-phase HPLC analysis for PTH-amino acids to carry out the sequence analysis on synthesized peptide resins. This approach is far more sensitive than using glass beads on the conventional solid-phase sequencer. The peptide was assembled on copoly (styrene-1% divinylbenzene) resin beads at an initial substitution of 0.54 mmol/g. On a routine basis, 10-15 resin beads are used, and a repetitive yield of 94% is obtained: as few as 4 beads can be successfully sequenced. The HPLC PTH-amino acid analysis is sensitive down to subpicomole quantities. This procedure offers a sensitive and rapid analytical tool for checking the purity of peptides as they are being assembled on solid support.     

Microwave‐assisted TFA cleavage of peptides from Merrifield resin

Microwave‐assisted (MW) reactions are of special interest to the chemical community due to faster reaction times, cleaner reactions and higher product yields. The adaptation of MW to solid phase peptide synthesis resulted in spectacular syntheses of difficult peptides. In the case of Merrifield support, used frequently in synthesis of special peptides, the conditions used in product cleavage are not compatible with off‐resin monitoring of the reaction progress. The application of MW irradiation in product removal from Merrifield resin using trifluoroacetic acid (TFA) was investigated using model tetrapeptides and the effects were compared with standard trifluoromethanesulphonic acid (TFMSA) cleavage using elemental analysis as well as chromatographic (HPLC) and spectroscopic (IR) methods. The deprotection of benzyloxycarbonyl and benzyl groups in synthetic bioactive peptides was analyzed using LC‐MS and MS/MS experiments. In a 5 min microwave‐assisted TFA reaction at low temperature, the majority of product is released from the resin, making the analytical scale MW‐assisted procedure a method of choice in monitoring the reactions carried out on Merrifield resin due to the short reaction time and compatibility with HPLC and ESI‐MS conditions. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Chemistry of alpha-hydroxymethylserine: problems and solutions

Further improvements related to the synthesis of peptides containing HmS are presented. Efficient synthetic protocols have been developed to synthesize "difficult" sequences containing a C-terminal HmS residue, MeA-HmS or consecutive HmS. Preparative methods for orthogonal N- and/or C-protected HmS(Ipr) derivatives are described. Their compatibility with standard solution or solid-phase peptide chemistry protocols allows synthetic flexibility toward HmS-containing peptides. In the synthesis of the sterically hindered dipeptides with the C-terminal HmS(Ipr) residue, HATU proves the highest efficiency, as compared with the fluoride and PyBroP/DMAP coupling methods. The HATU method also outperforms the fluoride activation in the solid-phase assembly of HmS homosequence. Specific protocols are described to overcome an undesired cyclization to diketopiperazines that occurs during the removal of Fmoc from dipeptides with the C-terminal HmS(Ipr) or HmS residues, thus precluding their C-->N elongation. The successful protocols involve: (i) the 2+1 condensation using mixed anhydride activation yielding the desired product with the highest optical integrity or (ii) use of the 2-chlorotrityl resin as a solid support sterically suppressing the undesired cleavage due to diketopiperazine formation. The latter approach allows the mild conditions of peptide cleavage from solid support, preserving the isopropylidene protection and minimizing the undesired N-->O-acyl migration that was observed under prolonged acid treatment used for cleaving the HmS peptide from the Wang resin.     

Analytical platform for verification and quantitation of target peptides in human serum: application to cathelicidin

A selective and sensitive, fully automated platform for verification and quantitative determination of target peptides in biofluids is proposed and then validated by development of a method for analysis of cathelicidin in human serum. The method is based on the on-line coupling of solid-phase extraction (SPE) and tandem mass spectrometry with direct infusion. Mass spectrometry analysis was carried out by multiple reaction monitoring using three transitions (one for quantitative analysis and two for qualitative analysis), all them confirmed by in silico fragmentation of the target peptide. Samples were prepared in the SPE workstation on a polymeric divinylbenzene resin by preconcentration, deproteinization, and cleanup, removing salts and interferences after direct injection of human serum. The analytical process required 12 min. The limits of detection and quantitation were 2.5 and 8.25 μg/L, respectively (0.20 and 0.66 pg on column). Repeatability and within-laboratory reproducibility were 2.4% and 2.7%, respectively. A dual-cartridge configuration was used to test recovery of cathelicidin in serum, resulting in 80%. Because quantitative retention in the cartridge was assessed, determination of cathelicidin was validated without using synthetic peptides labeled with stable isotopes. The hyphenated system allows full automation, thereby improving reproducibility and accuracy, as demanded by clinical analysis.     

Exploration research on the fusion of multimodal spectrum technology to improve performance of rapid diagnosis scheme for thyroid dysfunction

The spectral fusion by Raman spectroscopy and Fourier infrared spectroscopy combined with pattern recognition algorithms is utilized to diagnose thyroid dysfunction serum, and finds the spectral segment with the highest sensitivity to further advance diagnosis speed. Compared with the single infrared spectroscopy or Raman spectroscopy, the proposal can improve the detection accuracy, and can obtain more spectral features, indicating greater differences between thyroid dysfunction and normal serum samples. For discriminating different samples, principal component analysis (PCA) was first used for feature extraction to reduce the dimension of high‐dimension spectral data and spectral fusion. Then, support vector machine (SVM), back propagation neural network, extreme learning machine and learning vector quantization algorithms were employed to establish the discriminant diagnostic models. The accuracy of spectral fusion of the best analytical model PCA‐SVM, single Raman spectral accuracy and single infrared spectral accuracy is 83.48%, 78.26% and 80%, respectively. The accuracy of spectral fusion is higher than the accuracy of single spectrum in five classifiers. And the diagnostic accuracy of spectral fusion in the range of 2000 to 2500 cm^?1 is 81.74%, which greatly improves the sample measure speed and data analysis speed than analysis of full spectra. The results from our study demonstrate that the serum spectral fusion technique combined with multivariate statistical methods have great potential for the screening of thyroid dysfunction.     

Inline noninvasive Raman monitoring and feedback control of glucose concentration during ethanol fermentation

Raman spectroscopy as a process analytical technology tool was implemented for the monitoring and control of ethanol fermentation carried out with Saccharomyces cerevisiae. The need for the optimization of bioprocesses such as ethanol production, to increase product yield, enhanced the development of control strategies. The control system developed by the authors utilized noninvasive Raman measurements to avoid possible sterilization problems. Real-time data analysis was applied using partial least squares regression (PLS) method. With the aid of spectral pretreatment and multivariate data analysis, the monitoring of glucose and ethanol concentration was successful during yeast fermentation with the prediction error of 4.42 g/L for glucose and 2.40 g/L for ethanol. By Raman spectroscopy-based feedback control, the glucose concentration was maintained at 100 g/L by the automatic feeding of concentrated glucose solution. The control of glucose concentration during fed-batch fermentation resulted in increased ethanol production. Ethanol yield of 86% was achieved compared to the batch fermentation when 75 % yield was obtained. The results show that the use of Raman spectroscopy for the monitoring and control of yeast fermentation is a promising way to enhance process understanding and achieve consistently high production yield.     

Vibrational spectroscopic approach to the study of acetylcholine and related compounds

The present review reports the coordinated application of three spectroscopic methods (Raman, infrared(IR) and inelastic electron tunneling spectroscopy (IETS)) in the study of the conformation of Ach and some analogues (beta-MeAch, Mu and Nic) in solid state, aqueous solution and in interaction with a surface. Useful correlated information is obtained by Raman and IR spectroscopies on the conformational possibilities of these molecules in transition from solid state to aqueous solution. With this information in hand as well as on the basis of Raman and IR study of the nonenzymatic hydrolysis of Ach, the first detailed experimental investigation of the interaction of Ach and beta-MeAch adsorbed on a surface (A1203) is realised by the IETS method. The results are used to discuss an interaction analogous to that of Ach with receptor and another one analogous to that of Ach and AchE.     

Raman spectroscopy in biomedicine – non-invasive in vitro analysis of cells and extracellular matrix components in tissues

Raman spectroscopy is an established laser-based technology for the quality assurance of pharmaceutical products. Over the past few years, Raman spectroscopy has become a powerful diagnostic tool in the life sciences. Raman spectra allow assessment of the overall molecular constitution of biological samples, based on specific signals from proteins, nucleic acids, lipids, carbohydrates, and inorganic crystals. Measurements are non-invasive and do not require sample processing, making Raman spectroscopy a reliable and robust method with numerous applications in biomedicine. Moreover, Raman spectroscopy allows the highly sensitive discrimination of bacteria. Rama spectra retain information on continuous metabolic processes and kinetics such as lipid storage and recombinant protein production. Raman spectra are specific for each cell type and provide additional information on cell viability, differentiation status, and tumorigenicity. In tissues, Raman spectroscopy can detect major extracellular matrix components and their secondary structures. Furthermore, the non-invasive characterization of healthy and pathological tissues as well as quality control and process monitoring of in vitro-engineered matrix is possible. This review provides comprehensive insight to the current progress in expanding the applicability of Raman spectroscopy for the characterization of living cells and tissues, and serves as a good reference point for those starting in the field.     

Evaluation of silica resins for direct and efficient extraction of DNA from complex biological matrices in a miniaturized format

For DNA purification to be functionally integrated into the microchip for high-throughput DNA analysis, a miniaturized purification process must be developed that can be easily adapted to the microchip format. In this study, we evaluate the effectiveness of a variety of silica resins for miniaturized DNA purification and gauge the potential usefulness for on-chip solid-phase extraction. A micro-solid-phase extraction (muSPE) device containing only nanograms of silica resin is shown to be effective for the adsorption and desorption of DNA in the picogram-nanogram mass range. Fluorescence spectroscopy as well as capillary electrophoresis with laser-induced fluorescence detection is employed for the analysis of DNA recovered from solid-phase resins, while the polymerase chain reaction (PCR) is used to evaluate the amplifiable nature of the eluted DNA. We demonstrate that DNA can be directly recovered from white blood cells with an efficiency of roughly 70%, while greater than 80% of the protein is removed with a 500-nl bed volume muSPE process that takes less than 10 min. With a capacity in the range of 10-30 ng/mg of silica resin, we show that the DNA extracted from white blood cells, cultured cancer cells, and even whole blood on the low microliter scale is suitable for direct PCR amplification. The miniaturized format as well as rapid time frame for DNA extraction is compatible with the fast electrophoresis on microfabricated chips.     

Monitoring of complex industrial bioprocesses for metabolite concentrations using modern spectroscopies and machine learning: application to gibberellic acid production

Two rapid vibrational spectroscopic approaches (diffuse reflectance-absorbance Fourier transform infrared [FT-IR] and dispersive Raman spectroscopy), and one mass spectrometric method based on in vacuo Curie-point pyrolysis (PyMS), were investigated in this study. A diverse range of unprocessed, industrial fed-batch fermentation broths containing the fungus Gibberella fujikuroi producing the natural product gibberellic acid, were analyzed directly without a priori chromatographic separation. Partial least squares regression (PLSR) and artificial neural networks (ANNs) were applied to all of the information-rich spectra obtained by each of the methods to obtain quantitative information on the gibberellic acid titer. These estimates were of good precision, and the typical root-mean-square error for predictions of concentrations in an independent test set was <10% over a very wide titer range from 0 to 4925 ppm. However, although PLSR and ANNs are very powerful techniques they are often described as "black box" methods because the information they use to construct the calibration model is largely inaccessible. Therefore, a variety of novel evolutionary computation-based methods, including genetic algorithms and genetic programming, were used to produce models that allowed the determination of those input variables that contributed most to the models formed, and to observe that these models were predominantly based on the concentration of gibberellic acid itself. This is the first time that these three modern analytical spectroscopies, in combination with advanced chemometric data analysis, have been compared for their ability to analyze a real commercial bioprocess. The results demonstrate unequivocally that all methods provide very rapid and accurate estimates of the progress of industrial fermentations, and indicate that, of the three methods studied, Raman spectroscopy is the ideal bioprocess monitoring method because it can be adapted for on-line analysis.     

Spatially resolved investigation of the oil composition in single intact hyphae of Mortierella spp. with micro-Raman spectroscopy

Zygomycetes are well known for their ability to produce various secondary metabolites. Fungi of the genus Mortierella can accumulate highly unsaturated lipids in large amounts as lipid droplets. However, no information about the spatial distribution or homogeneity of the oil inside the fungi is obtainable to date due to the invasive and destructive analytical techniques applied so far. Raman spectroscopy has been demonstrated to be well suited to investigate biological samples on a micrometre scale. It also has been shown that the degree of unsaturation of lipids can be determined from Raman spectra. We applied micro-Raman spectroscopy to investigate the spatial distribution and composition of lipid vesicles inside intact hyphae. For Mortierella alpina and Mortierella elongata distinct differences in the degree of unsaturation and even the impact of growth conditions are determined from the Raman spectra. In both species we found that the fatty acid saturation in the vesicles is highly variable in the first 600 μm of the growing hyphal tip and fluctuates towards a constant composition and saturation ratio in all of the remaining mycelium. Our approach facilitates in vivo monitoring of the lipid production and allows us to investigate the impact of cultivation parameters on the oil composition directly in the growing hyphae without the need for extensive extraction procedures.     

Solid phase synthesis of a functionalized bis-peptide using "safety catch" methodology

In 1962, R.B. Merrifield published the first procedure using solid-phase peptide synthesis as a novel route to efficiently synthesize peptides. This technique quickly proved advantageous over its solution-phase predecessor in both time and labor. Improvements concerning the nature of solid support, the protecting groups employed and the coupling methods employed over the last five decades have only increased the usefulness of Merrifield's original system. Today, use of a Boc-based protection and base/nucleophile cleavable resin strategy or Fmoc-based protection and acidic cleavable resin strategy, pioneered by R.C. Sheppard, are most commonly used for the synthesis of peptides(1). Inspired by Merrifield's solid supported strategy, we have developed a Boc/tert-butyl solid-phase synthesis strategy for the assembly of functionalized bis-peptides(2), which is described herein. The use of solid-phase synthesis compared to solution-phase methodology is not only advantageous in both time and labor as described by Merrifield(1), but also allows greater ease in the synthesis of bis-peptide libraries. The synthesis that we demonstrate here incorporates a final cleavage stage that uses a two-step "safety catch" mechanism to release the functionalized bis-peptide from the resin by diketopiperazine formation. Bis-peptides are rigid, spiro-ladder oligomers of bis-amino acids that are able to position functionality in a predictable and designable way, controlled by the type and stereochemistry of the monomeric units and the connectivity between each monomer. Each bis-amino acid is a stereochemically pure, cyclic scaffold that contains two amino acids (a carboxylic acid with an α-amine)(3,4). Our laboratory is currently investigating the potential of functional bis-peptides across a wide variety of fields including catalysis, protein-protein interactions and nanomaterials.     

On-line infrared spectroscopy for bioprocess monitoring

One of the major aims of bioprocess engineering is the real-time monitoring of important process variables. This is the basis of precise process control and is essential for high productivity as well as the exact documentation of the overall production process. Infrared spectroscopy is a powerful analytical technique to analyze a wide variety of organic compounds. Thus, infrared sensors are ideal instruments for bioprocess monitoring. The sensors are non-invasive, have no time delay due to sensor response times, and have no influence on the bioprocess itself. No sampling is necessary, and several components can be analyzed simultaneously. In general, the direct monitoring of substrates, products, metabolites, as well as the biomass itself is possible. In this review article, insights are provided into the different applications of infrared spectroscopy for bioprocess monitoring and the complex data interpretation. Different analytical techniques are presented as well as example applications in different areas.     

Characterizing Aeroallergens by Infrared Spectroscopy of Fungal Spores and Pollen

Background

Fungal spores and plant pollen cause respiratory diseases in susceptible individuals, such as asthma, allergic rhinitis and hypersensitivity pneumonitis. Aeroallergen monitoring networks are an important part of treatment strategies, but unfortunately traditional analysis is time consuming and expensive. We have explored the use of infrared spectroscopy of pollen and spores for an inexpensive and rapid characterization of aeroallergens.

Methodology

The study is based on measurement of spore and pollen samples by single reflectance attenuated total reflectance Fourier transform infrared spectroscopy (SR-ATR FTIR). The experimental set includes 71 spore (Basidiomycota) and 121 pollen (Pinales, Fagales and Poales) samples. Along with fresh basidiospores, the study has been conducted on the archived samples collected within the last 50 years.

Results

The spectroscopic-based methodology enables clear spectral differentiation between pollen and spores, as well as the separation of confamiliar and congeneric species. In addition, the analysis of the scattering signals inherent in the infrared spectra indicates that the FTIR methodology offers indirect estimation of morphology of pollen and spores. The analysis of fresh and archived spores shows that chemical composition of spores is well preserved even after decades of storage, including the characteristic taxonomy-related signals. Therefore, biochemical analysis of fungal spores by FTIR could provide economical, reliable and timely methodologies for improving fungal taxonomy, as well as for fungal identification and monitoring. This proof of principle study shows the potential for using FTIR as a rapid tool in aeroallergen studies. In addition, the presented method is ready to be immediately implemented in biological and ecological studies for direct measurement of pollen and spores from flowers and sporocarps.     

X-ray photoelectron spectroscopy and infrared spectroscopy study of maleimide-activated supports for immobilization of oligodeoxyribonucleotides

Surface-tethered nucleic acids are widely applied in solid-phase assays in which complementary strands must be detected against a complex mixture of other sequences. In response to such needs, numerous methods have been developed for immobilizing nucleic acids on solid supports. Often, detailed analysis of associated chemical transformations and of potential side reactions is difficult to obtain. Combined use of planar and high surface area powder supports allows characterization using surface as well as bulk diagnostic techniques. This approach is followed in the present study in which X-ray photoelectron spectroscopy (XPS), transmission infrared spectroscopy (FTIR) and reactivity titrations are used to investigate siliceous supports modified with an aminosilane precursor followed by a maleimide-bearing crosslinker for attachment of nucleic acids. The supports retain maleimide activity for approximately a day when stored under buffer, but deactivation is accelerated under basic conditions or by incomplete conversion of the precursor aminosilane monolayer. Reactions involving the olefinic bond of the imide as well as its carbonyl groups are observed and analyzed. Attachment of sulfhydryl-terminated oligodeoxyribonucleotides is highly site specific, and immobilized strands exhibit excellent hybridization activity. Quantitative use of XPS for label-free determination of DNA coverage based on calibration against reference materials is also described.     

Hemodialysis monitoring using mid‐ and near‐infrared spectroscopy with partial least squares regression

Blood constituents such as urea, glucose, lactate, phosphate and creatinine are of high relevance in monitoring the process of detoxification in ambulant dialysis treatment. In the present work, 2 different vibrational spectroscopic techniques are used to determine those molecules quantitatively in artificial dialysate solutions. The goal of the study is to compare the performance of near‐infrared (NIR) and mid‐infrared (MIR) spectroscopy in hyphenation with partial least squares regression (PLSR) directly by using the same sample set. The results show that MIR spectroscopy is better suited to analyze the analytes of interest. Multilevel multifactor design is used to cover the relevant concentration variations during dialysis. MIR spectroscopy coupled to a multi reflection attenuated total reflection (ATR) cell enables reliable prediction of all target analytes. In contrast, the NIR spectroscopic method does not give access to all 5 components but only to urea and glucose. For both methods, coefficients of determination greater or equal to 0.86 can be achieved in the test‐set validation process for urea and glucose. Lactate, phosphate and creatinine perform well in the MIR with R² ≥ 0.95 using test‐set validation.