Biomedical subjects

Yukiteru Katsumoto

Publications and source records attributed to Yukiteru Katsumoto.

9 recordsLinked to original sources

PubMed2006

Dimerization and double proton transfer-induced tautomerism of 4(3H)-pyrimidinone in solution studied by IR spectroscopy and quantum chemical calculations.

The tautomerism and dimerization of 4(3H)-pyrimidinone (4(3H)Pyr) in carbon tetrachloride (CCl4) and chloroform (CHCl3) solutions were investigated using IR spectroscopy and quantum chemical calculations. The observed IR spectra in the NH and OH stretching regions clearly revealed the predominance of the keto tautomer in both solvent systems. The enol form only exists in a very small proportion in the CCl4 solution. The tautomeric constant for the two monomers KT[OH/NH] = 0.012 and DeltaE = 2.62 kcal/mol were estimated at 25 degrees C. This result was supported by the self-consistent reaction field/polarizable continuum (SCRF/PCM) calculation at the MP4(full, SDQ)/aug-cc-pVDZ level, which predicted DeltaE = 3.06 kcal/mol in CCl4. In the C=O stretching region, two bands were observed, suggesting the coexistence of two keto structures at equilibrium. The calculated IR spectra indicated that the bands at 1711 and 1675 cm(-1) arise from the keto monomer and keto-keto (KK) ring dimer, respectively. At elevated temperature, the populations of both the keto and enol monomers increased for the CCl4 solution. The present study revealed that the keto <--> enol tautomerization does not occur in the isolated monomer molecule. The double proton transfer (DPT) reaction in the KK ring dimer presumably plays a substantial role in the population increase of the enol monomer. To our knowledge, this may be the first observation of the tautomerization in a model base pair via the temperature-induced ground-state DPT reaction under a nonpolar liquid environment reported so far. This tautomerism can serve as a mimic circumstance for the spontaneous mutations induced by proton transfer in the DNA base pairs.

Dimerization↗

PubMed2006

Origin of the blue shift of the CH stretching band for 2-butoxyethanol in water.

The blue shift of the isolated CD stretching band of 2-butoxyethanol (C4E1), which is observed for the aqueous solution during the dilution process, has been investigated by infrared (IR) spectroscopy and quantum chemical calculations. Mono-deuterium-labeled C4E1's were employed to remove the severe overlapping among the CH stretching bands. The isolated CD stretching mode of the alpha-methylene in the butoxy group shows a large blue shift, while those of the beta-methylene and methyl groups are not largely shifted. The spectral simulation results for the C4E1/H2O complexes indicate that the large blue shift of the CD stretching band of the butoxy group arises mainly from the hydration of the ether oxygen atom.

Journal Article↗

PubMed2005

Molecular interpretation for the solvation of poly(acrylamide)s. I. Solvent-dependent changes in the C=O stretching band region of poly(N,N-dialkylacrylamide)s.

The solvation of poly(N,N-dimethylacrylamide) (PNdMA) and poly(N,N-diethylacrylamide) (PNdEA) in various protic and aprotic solvents has been studied by using infrared (IR) spectroscopy. Because PNdMA and PNdEA have the same polar functional group, their IR spectra show quite similar solvent effects. Unexpectedly, the solvent-dependent changes of the C=O stretching vibration (nu(C=O)) bands of the two polymers cannot be explained only by dielectric constants of the solvents. Then, infrared spectra of N,N-dimethylacetamide (NdMA) and N,N-diethylacetamide (NdEA), monomer models for PNdMA and PNdEA, respectively, in the same solvents as the polymer solutions have also been examined. Interestingly, the solvent-dependent spectra in the nu(C=O) band region of NdMA and NdEA are correlated with those of PNdMA and PNdEA, respectively, except for slight deviations, which may be ascribed to molecular mobility and/or exclusive volume. These correlations permit one to regard the solvation of the polymers as that of the corresponding monomers. As a result, we have proposed the assignments of nu(C=O) bands for the PNdMA and PNdEA solutions regarding the interactions between solvents and NdMA and NdEA as hydrogen bondings. In the IR spectra of PNdMA and PNdEA in the protic solvents, two C=O bands are mainly observed; one appears at a similar frequency to that of a C=O band observed for the monomer solution, and the other is characteristic of the polymer systems. The former band is likely to reflect the solvation behavior of PNdMA and PNdEA. The results clearly show that the solvation of a polymer can be interpreted at the molecular level using infrared spectroscopy sensitive to solvent effects.

Journal Article↗

PubMed2005

Hydration of short-chain poly(oxyethylene) in carbon tetrachloride: an infrared spectroscopic study.

Hydration of short-chain poly(oxyethylene)s, CH(3)(OCH(2)CH(2))(m)OCH(3) (abbreviated as C(1)E(m)()C(1)) (m = 1-3), in carbon tetrachloride has been studied by infrared spectroscopy. The O-H stretching vibrations of water in ternary solutions with H(2)O:C(1)E(m)C(1):CCl(4) mole ratios of 0.000418:0.005:0.995 to 0.000403:0.04:0.96 were analyzed. Two types of hydrogen bonds are formed in the interaction between water and C(1)E(m)C(1) in carbon tetrachloride; one is a monodentate hydrogen bond, in which only one of the O-H bonds of a water molecule participates in hydrogen bonding, and the other is a bidentate hydrogen bond, in which both of the O-H bonds of a water molecule participate in hydrogen bonding by bridging oxygen atoms separated by two or more monomer units on the polymer chain. An important finding is that the bidentate hydrogen-bond bridge is not formed between the nearest-neighbor oxygen atoms. This experimental observation supports the results of previous molecular dynamics simulations. The shortest oligomer of poly(oxyethylene), i.e., CH(3)OCH(2)CH(2)OCH(3) (1,2-dimethoxyethane) with a single monomer unit, is suggested not to be an adequate model for this polymer with respect to hydrogen bonding to water. The hydrogen bonding in a 1:1 C(1)E(m)C(1)-water adduct in carbon tetrachloride represents primitive incipient hydration of poly(oxyethylene). The present results indicate that both monodentate and bidentate hydrogen bonds are important and the latter is destabilized more rapidly than the former with increasing temperature. This dehydration process can be a potential mechanism of the poly(oxyethylene)-water phase separation.

Carbon Tetrachloride↗

PubMed2005

Geometrical behavior of hydrogen bonding patterns in the alpha-dodecyl-omega-hydroxy-tris(oxyethylene)-water system monitored by near infrared spectroscopy.

Changes in the geometry of hydrogen bonding patterns in the alpha-dodecyl-omega-hydroxy-tris(oxyethylene) (C(12)E(3))-water system have been investigated by near infrared (NIR) spectroscopy. In the 5,300-4,600 cm(-1) region, the characteristic bands for C(12)E(3) and water can be separately investigated, since the combination bands of the OH stretching and its COH bending of alcohols are observed at 5,000-4,650 cm(-1), whereas the combination bands of the OH stretching and its HOH bending of water, at 5,300-5,000 cm(-1). The NIR result has revealed that the addition of water to C(12)E(3) promotes the formation of the OHcdots, three dots, centeredOHcdots, three dots, centeredO hydrogen bonds.

Alcohols↗

PubMed2005

The effect of cooperative hydrogen bonding on the OH stretching-band shift for water clusters studied by matrix-isolation infrared spectroscopy and density functional theory.

Infrared spectra of the water clusters have been measured in the N2 + O2 matrix. The aggregation process of water in the matrix has been monitored by annealing the deposited samples up to 40 K and UV irradiation. The monomer, dimer, cyclic trimer and cyclic pentamer are found as water clusters in the matrix. For the hexamer, several structures such as chair, cage, prism, bag 1 and/or book 1 are likely to exist. By UV irradiation, the cyclic pentamer is predominantly formed from the monomer and dimer. On the other hand, by annealing the deposited sample, several hexamers are formed. The theoretical calculation for water clusters has revealed that the formation of one hydrogen bonding in a hydrogen-bonded chain cooperatively enhances or diminishes the strength of another hydrogen bond. Both proton donor (D) and acceptor (A) participating in a hydrogen-bonding pair DA are capable of forming hydrogen bonding with the other water molecules; D can additionally accept two protons and donate one proton, and A can additionally donate two protons and accept one proton. We have proposed the classification of hydrogen-bonding patterns considering the cooperativity, denoting as d'a'DAd''a'', where d and a are integers indicating the number of proton donors and acceptors to D (the single prime) and A (the double prime), respectively. Then, a magnitude given by MOH = -d' + a' + d'' - a'' has been introduced, which is very useful for connecting the hydrogen-bonding patterns to their OH wavenumbers. As a result, it is revealed that the OH stretching bands of water clusters are characterized by eight indicators (free and MOH = -2, -1, 0, 1, 2, 3 and 4). The classification proposed here is applicable to the OH band analysis for the hydrogen-bonded water and alcohols in a condensed phase.

Computer Simulation↗

PubMed2005

Melting behavior of poly(3-hydroxybutyrate) investigated by two-dimensional infrared correlation spectroscopy.

The melting behavior of a bacterially synthesized biodegradable polymer, poly(3-hydroxybutyrate) (PHB), was investigated by using generalized two-dimensional infrared (2D IR) correlation spectroscopy. Temperature-dependent spectral variations in the regions of the C-H stretching (3100-2850 cm(-1)), C=O stretching (1800-1680 cm(-1)), and C-O-C stretching (1320-1120 cm(-1)) bands were monitored during the melting process. The asynchronous 2D correlation spectrum for the C=O stretching band region resolved two crystalline bands at 1731 and 1723 cm(-1). The intense band at 1723 cm(-1) may be due to the highly ordered crystalline part of PHB, and the weak band at 1731 cm(-1) possibly arises from the crystalline part with a less ordered structure. These crystalline bands at 1731 and 1723 cm(-1) share asynchronous cross peaks with a band at around 1740 cm(-1) assignable to the C=O band due to the amorphous component. This observation indicates that the decreases in the crystalline components do not proceed simultaneously with the increase in the amorphous component. In the 3020-2915 cm(-1) region where bands due to the asymmetric CH3 stretching and antisymmetric CH2 stretching modes are expected to appear, eight bands are identified at 3007, 2995, 2985, 2975, 2967, 2938, 2934, and 2929 cm(-1). The bands at 2985 and 2938 cm(-1) are ascribed to the amorphous part while the rest come from crystal field splitting, which is a characteristic of polymers with a helical structure.

Carbon↗

PubMed2003

Applications of moving window two-dimensional correlation spectroscopy to analysis of phase transitions and spectra classification.

Our recently proposed idea of moving window two-dimensional (2D) correlation spectroscopy, which partitions a data set into series of relatively small submatrices (windows) and calculates their covariance maps in succession, is tested for three convoluted data set. Phase-transition temperatures of oleic acid and poly-(N-isopropylacrylamide) in an aqueous solution are sought by analyzing covariances of their temperature-dependent near-infrared and infrared spectra, respectively, while Raman spectra of three kinds of polyethylene (PE) pellets are investigated to find the spectral differences among them and to classify randomly ordered spectra by a sample-sample (SS) covariance map. The criterion of mean of standard deviation of covariance matrices is used as an indicator of the crucial information present in these matrices so that only a few of them are discussed in details. The results are obtained quickly after very simple calculations and are studied at length. The baseline variation is not removed prior to the calculations but is found to be of use for the determination of the phase-transition temperatures. Randomly ordered Raman spectra of the PE pellets are classified by innovatively used and interpreted SS slice spectra, with the relation to principal component analysis discussed.

Journal Article↗

PubMed2003

Practical algorithm for reducing convex spike noises on a spectrum.

Quantitative data analysis and high-sensitivity measurements by use of Raman and infrared spectroscopy often suffer from noisy spikes such as those due to cosmic rays and water vapor. Since these spikes are unidirectional and isolated, the conventional smoothing techniques do a poor job of removing them. However, a small modification can improve these smoothing techniques significantly. In this paper, we present a simple denoising technique for a single-scan spectrum that is corrupted by convex spikes. In general, the noisy spikes arising from cosmic rays or water vapor have a much narrower bandwidth compared with target "informative" bands in Raman and infrared spectra. This means that these noisy spikes can be separated from the target bands by means of the difference in the bandwidths. The proposed method employs the moving window averaging procedure to distinguish and separate the convex spike. The proposed algorithm allows us to take away the convex spikes from measured spectra without preparing multiply recorded spectra and (much) biasing the measured spectrum.

Acetamides↗