Studied on the interactions of antibody-porphyrin by circular dichroism and ultraviolet-visible spectrophotometry

Circular dichoism and UV-vis measurements were used to study the interaction between porphyrin and monoclonal antibodies ( McAbs). McAbs-porphyrin complex formation is usually accompanied by significant bathochromic shift and hyperchromicity changes of the absorption maxima in the porphyrin soret band region. Induced CD spectra in the same region (350 similar to 450 nm) were detected upon complex formation. They follow Lamb-Beer's law and exhibit isosbestic behavior. Both the UV-Vis and induced CD spectra of the antibody: porphyrin complex remain unchanged over a broad pH range ( pH 6 similar to 11), indicating remarkable stability of the complex and reflecting the dominant role of hydrophobic interaction between the hapten benzophenone and the antibody combining site.

Decomposition of circular dichroism of norepinephrine by singular value decomposition-least square method

Singular value decomposition - least squares (SVDLS), a new method for processing the multiple spectra with multiple wavelengths and multiple components in thin layer spectroelectrochemistry has been developed. The CD spectra of three components, norepinephrine reduced form of norepinephrinechrome and norepinephrinequinone, and their fraction distributions with applied potential were obtained in three redox processes of norepinephrine from 30 experimental CD spectra, which well explains electrochemical mechanism of norepinephrine as well as the changes in the CD spectrum during the electrochemical processes.

Circular dichroism and resonance Raman comparative studies of wild type cytochrome c and F82H mutant

The UV-visible, circular dichroism (CD), and resonance Raman (RR) spectra of the wild type yeast iso-1-cytochrome c (WT) and its mutant F82H in which phenylalanine-82 (Phe-82) is substituted with His are measured and compared for oxidized and reduced forms. The CD spectra in the intrinsic and Soret spectral region, as well as RR spectra in high, middle, and low frequency regions, are discussed. From the analysis of the spectra, it is determined that in the oxidized F82H the two axial ligands to the heme iron are His-18 and His-82 whereas in the reduced form the sixth ligand switches from His-82 to Met-80 providing the coordination geometry similar to that of WT. Based on the spectroscopic data, the conclusion is that the porphyrin macrocycle is less distorted in the oxidized F82H compared to the oxidized WT. Similar distortions are present in the reduced form of the proteins. Frequency shifts of Raman bands, as well as the decrease of the or-helix content in the CD spectra, indicate more open conformation of the protein around the heme. (C) 2000 John Wiley & Sons, Inc.

Circular dichroism spectro electrochemical and voltammetric studies of vitamin B-2

Electroreduction of vitamin B-2 (VB2) was studied by in situ circular dichroism (CD) spectroelectrochemistry (SEC) with a long optical path length thin layer cell (LOPLTLC). The results showed that the electroreduction of VB2 in phosphate buffer solution (PBS) (PH 6.8) was a two-electron electrochemical process with weak adsorption of the reactant at the glassy carbon (GC) electrode surface. The CD spectra change of VB2 in the reduction process was explained with the theory of electronic states. We also treated the CD spectra with a singular value decomposition least square (SVDLS) method, and have found not only the number of components and their spectra, but also the fraction distribution of each component in the electroreduction process of VB2.

Investigation of thermal unfolding process of cyanic adduct of horseradish peroxidase by Fourier transform infrared and circular dichroism spectrometry

Detailed circular dichroism(CD) and Fourier transform infrared (FTIR) studies have been carried out to monitor thermal unfolding of horseradish peroxidase isoenzyme C(HRP) inhibited by CN(HRP-CN). The results suggest that HRP-CN is quite different from native HRP with different spin states of Fe of heme and different coordinated states. Cyanide becomes the sixth ligand of Fe(I) of heme and the hydrogen-binding network is destroyed partly at the same time, which cause the drastic decrease of thermal stability of HRP. The FTIR and Soret-CD spectra analysis demonstrate that during the heating process there is an intermediate state(I') which has both partly destroyed secondary and tertiary structures of native HRP, then it is the appearance of protein aggregation state(A) after fully unfolding. The unfolding pathway thus can be shown as follows: I -->I'-->U -->A.

The electrochemically induced conformational transition of disulfides in bovine serum albumin studied by thin layer circular dichroism spectroelectrochemistry

The conformational transition of disulfides in bovine serum albumin (BSA) induced by electrochemical redox reaction of disulfides were monitored by in-situ circular dichroism (CD) spectroelectrochemistry, with a long optical path thin layer cell and analyzed by a singular value decomposition least square (SVDLS) method. Electrochemical reduction of disulfides drives the left-handed conformation of disulfides changed into the right-handed. At open circuit, eight of the 17 disulfides were of left-handed conformation. Four of the 17 disulfides took part in the electrochemical reduction with an EC mechanism. Only one-fourth of the reduced disulfides returned to left-handed conformation in the re-oxidation process. Some parameters of the electrochemical reduction process, i.e. the number of electrons transferred and electron transfer coefficient, n=8, alphan=0.15, apparent formal potential, E-1(0') = -0.65(+/-0.01) V, standard heterogeneous electron transfer rate constant, k(1)(0) = (2.84 +/- 0.14)x 10(-5) cm s(-1) and chemical reaction equilibrium constant, K-c=(5.13 +/- 0.12) x 10(-2), were also obtained by double logarithmic analysis based on the near-UV absorption spectra with applied potentials. (C) 2001 Elsevier Science B.V. All rights reserved.

In-situ circular dichroism spectroelectrochemical study on the redox process of norepinephrine

The redox process of norepinephrine in pH = 7.0 phosphate buffer solution at glassy carbon electrode was studied by circular dichroism spectroelectrochemistry with a long optical path thin layer cell. The spectroelectrochemical data were analyzed with the double logarithm method. According to the double logarithsmic plot results, the mechanism of electrochemical oxidation of norepinephrine is an irreversible process with a subsequent chemical reaction (EC) to form a norepinephrinechrome. Both of norepinephrinequinone and norepinephrinechrome are followed E mechanisms. Some kinetic parameters about the electrochemical process, i.e. the electron transfer coefficient and number of electron transfered, alpha n = 0.38, the formal potential, E-1(0)' = 0.20 V, the standard heterogenous electron transfer rate constant, k(1)(0) = 1.2 x 10(-4) cm s(-1) for the oxidation of norepinephrine, alpha n = 0.37, E-2(0)' = 0.25 V and k(2)(0) = 4.4 x 10(-5) cm . s(-1) for the reduction of norepinephrinequnone and alpha n = 0.33, E-3(0)' = -0.25V and k(3)(0) = 1.1 x 10(-4) cm . s(-1) for the reduction of norpinephrinechrome, were also estimated.

Investigation of the self-accelerating process of ascorbic acid by in-situ circular dichroism spectroelectrochemistry

The electrode reaction process of ascorbic (Vc) was studied by in-situ circular dichroic(CD) spectroelectrochemistry with a long optical path thin layer cell on glassy carbon(GC) electrode. The spectroelectrochemical data were analyzed by the double logarithmic method together with nonlinear regression. The results suggested that the mechanism of Ve in pH 7.0 phosphate buffer solution at GC electrode was a two-electron irreversible electrooxidation followed by adsorption of the oxidation product. That is a self-accelerated process. Some kinetic parameters at free and at adsorbed electrode surface, i.e, the formal potentials, E-0' = 0.09 V, E-a(0') = 0.26 +/- 0.02 V; the electron transfer coefficient and number of transfered electron, alpha n = 0.41, alpha(a)n = 0.07;the standard heterogeneous electron transfer rate constant, k(0) = 8.0 x 10(-5) cm.s(-1), k(a)(0) = 1.9 x 10(-4) cm.s(-1) and adsorption constant, beta = 102.6 were also estimated.

Vibrational spectroscopy and DFT calculations of the di-amino acid peptide L-aspartyl-L-glutamic acid in the zwitterionic state

Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the linear di-amino acid peptide L-aspartyl-L-glutamic acid (L-Asp-L-Glu); the solution state Raman spectrum has also been obtained for the N,O-deuterated derivative. SCF-DFT calculations at the B3-LYP/cc-pVDZ level established that the structure and vibrational spectra of L-Asp-L-Glu can be interpreted using a model of the peptide with ten hydrogen-bonded water molecules, in conjunction with the conductor-like polarizable continuum solvation method. The DFT calculations resulted in the computation of a stable zwitterionic structure, which displays trans-amide conformation. The vibrational spectra were computed at the optimised molecular geometry, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.

Vibrational spectroscopy and DFT calculations of di-amino acid cyclic peptides. Part I: cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(t-Ala-Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid-state and aqueous protonated samples, as well as their corresponding N-deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3-LYP/cc-pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas-phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di-amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C-2 and C-1 symmetries for the six-membered rings of cyclo(L-Ala-L-Ala) and cydo(L-Ala-Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cydo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L-AlaGly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis-peptide linkage are shown to be significantly different from those of the trans-peptides. For example, deuterium shifts have shown that the cis-amide I vibrations found in cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Ala-Gly) have larger N-H contributions compared to their trans-amide counterparts. Compared to trans-amide II vibrations, cis-amide II vibrations show a considerable decrease in N-H character.

IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)

B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ~ 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring.

Vibrational spectra and crystal structure of the di-amino acid peptide cyclo(L-Met-L-Met): Comparison of experimental data and DFT calculations

Experimental Raman and FT-IR spectra of solid-state non-deuterated and N-deuterated samples of cyclo(L-Met-L-Met) are reported and discussed. The Raman and FT-IR results show characteristic amide I vibrations (Raman: 1649 cm-1, infrared: 1675 cm-1) for molecules exhibiting a cis amide conformation. A Raman band, assigned to the cis amide II vibrational mode, is observed at sim1493 cm-1 but no IR band is observed in this region. Cyclo(L-Met-L-Met) crystallises in the triclinic space group P1 with one molecule per unit cell. The overall shape of the diketopiperazine (DKP) ring displays a (slightly distorted) boat conformation. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. B3-LYP/cc-pVDZ calculations of the structure of the molecule predict a boat conformation for the DKP ring, in agreement with the experimentally determined X-ray structure. Copyright © 2009 John Wiley & Sons, Ltd.

DFT calculations of the structures and vibrational spectra of the [Fe(bpy)(3)](2+) and [Ru(bpy)(3)](2+) complexes

Structures of the [M(bpy)(3)](2+) complexes (M = Fe and Ru) have been calculated at the B3-LYP/DZVP level. IR and Raman spectra were calculated using the optimised geometries, employing a scaled quantum chemical force field, and compared with an earlier normal coordinate analysis of [Ru(bpy)(3) ](2+) which was based upon experimental data alone, and the use of a simplified model. The results of the calculations provide a highly satisfactory fit to the experimental data and the normal coordinate analyses, in terms of potential energy distributions, allow a detailed understanding of the vibrational spectra of both complexes. Evidence is presented for Jahn-Teller distortion in the E-1 MLCT excited state. (C) 2008 Elsevier B.V. All rights reserved.

Vibrational spectra of α-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding

The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.