Gert van der Zwan's research while affiliated with Vrije Universiteit Amsterdam and other places

Publications (82)

Article
The paper mentioned in the title contains inaccuracies and misleading interpretations that seriously misrepresent basic knowledge about tautomerism in azo dyes. Therefore, we aim in this Letter to correct the most obvious mistakes, to address the misrepresentation of the main issues of tautomerism, and to give a better understanding of the basic pr...
Article
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Simple models, in particular those based on Onsager's point dipole in a spherical cavity embedded in a polarizable medium, played an important role in understanding equilibrium and dynamical interaction between solvent polarization and classical reaction kinetics. After a brief review of some crucial results, and an application to the interaction o...
Article
Binding of the antihistamine drug brompheniramine (BPA) to human serum albumin (HSA) is studied by measuring quenching of the fluorescence and room temperature phosphorescence (RTP) of tryptophan. The modified Stern-Volmer equation was used to derive association constants and accessible fractions from the steady-state fluorescence data. Decay assoc...
Article
The Escherichia coli DNA repair enzyme AlkB is a 2-oxoglutarate (2OG)-dependent Fe(2+) binding dioxygenase that removes methyl lesions from DNA and RNA. To date, nine human AlkB homologues are known: ABH1 to ABH8 and the obesity-related FTO. Similar to AlkB, these homologues exert their activity on nucleic acids, although for some homologues the bi...
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The spectroscopy and kinetics of the tyrosinase catalyzed trans-resveratrol oxidation were investigated by measuring both UV-vis absorption spectra over the 200-500 nm range and Raman spectra over the 600-1800 cm(-1) region. Room temperature UV-vis absorption spectra, as a function of time, showed the presence of two isosbestic points located at λ(...
Article
UV resonance Raman spectroscopy was used to characterize the binding of three first-generation histamine H(1) receptor antagonists-tripelennamine (TRP), mepyramine (MEP), and brompheniramine (BPA)-to human serum albumin (HSA) at pH 7.2 and pH 9.0. Binding constants differ at these pH values, which can be ascribed to the different extent of protonat...
Article
A paper by Amat et al. [2] reported that the ATP-driven oxidation of luciferin to electronically excited oxyluciferin catalyzed by luciferase was accelerated when ATP was priorly irradiated at non-resonant optical frequencies (NROF) at 635 and 830nm. In another paper by Amat et al. [3], increased fluorescence intensities of ATP–Mg complexes, which...
Article
Ultraviolet Resonance Raman (UVRR) spectroscopy—a Raman technique that combines high sensitivity with high selectivity and does not suffer from background fluorescence—is applied to the fluorescent H1 antihistamines tripelennamine (TRP) and mepyramine (MEP) in aqueous solution to elucidate their molecular structure as a function of pH. In a previou...
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We have studied the effect of urea-induced unfolding on the electron transfer process of yeast iso-1-cytochrome c and its mutant K72AK73AK79A adsorbed on electrodes coated by mixed 11-mercapto-1-undecanoic acid/11-mercapto-1-undecanol self-assembled monolayers. Electrochemical measurements, complemented by surface enhanced resonance Raman studies,...
Article
Hybrid bilayer lipid membranes (HBMs) were built on roughened silver electrodes exhibiting surface-enhanced Raman scattering (SERS) activity. The HBM consisted of a first layer of octadecanethiol (ODT) directly bound to the electrode surface, on which a second layer of 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) was obtained by self-assembl...
Article
In a paper by Amat et al. (Modification of the intrinsic fluorescence and biochemical behavior of adenosine triphosphate ATP after irradiation with visible and near-infrared laser light, J. Photochem. Photobiol. B 81 (2005) 26-32) it was shown that the conversion of glucose to glucose-6-phosphate by hexokinase in vitro was accelerated when ATP, whi...
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The thermodynamics of the electron transfer (ET) process for beef heart and yeast cytochromes c and the Lys72Ala/Lys73Ala/Lys79Ala mutant of the latter species subjected to progressive urea-induced unfolding was determined electrochemically. The results indicate the presence of at least three protein forms which were assigned to a low-temperature a...
Article
Enantioselective phosphorescence lifetime detection was combined with chiral cyclodextrin-based electrokinetic chromatography for the analysis of camphorquinone (CQ). A time-gated detection system based on a pulsed light-emitting diode for excitation at 465 nm was developed for the online lifetime determination. The background electrolyte for the c...
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Ultrafast transient absorption spectroscopy of wild-type bacteriorhodopsin (WT bR) and 2 tryptophan mutants (W86F and W182F) is performed with visible light excitation (pump) and UV probe. The aim is to investigate the photoinduced change in the charge distribution with 50-fs time resolution by probing the effects on the tryptophan absorption bands...
Article
Excited-state quantum chemical calculations of two 2-alkyloamino-6-methyl-4-nitropyridine N-oxides are presented. Several different calculation methods and different basis sets were used, which all lead to similar results, although the precise values of excited-state energies and excited-state dipole moments differ. All methods used predict that in...
Article
Electronic absorption, emission, and excitation spectra, and fluorescence lifetimes of two H1 antihistamines--tripelennamine and mepyramine--are investigated in detail to ascertain their usefulness as fluorescent probes for ligand binding to G-protein coupled receptors. The photophysical behavior of these compounds in aqueous solution is complex du...
Article
The structure and electronic spectra of 2-methylamino-6-methyl-4-nitropyridine N-oxide (2M6M) were investigated. The X-ray structure of 2M6M molecule shows that it crystallizes in the monoclinic system of the P21/n space group and forms internally hydrogen-bonded [NH…O=2.563(3)Ǻ] monomers linked by the same type of intermolecular [2.799(3)Ǻ] hydrog...
Article
We report on photoluminescence decay measurements of CdSe nanoparticles over several decades of intensities and times, and as a function of size and temperature. A model is proposed for the multi-exponential decay kinetics, and their temperature dependence, in which a major role is played by the now well established presence of a large ground-state...
Article
Cyclic voltammetry was employed to determine the formal reduction potential and heterogeneous electron-transfer rate constant of cytochrome c immobilized on three different metal substrates chemically modified with 11-mercaptoundoecanoic acid. The metal substrates include smooth gold and silver electrodes as well as nanoscopically rough silver elec...
Article
Bovine cytochrome c (cyt c) was adsorbed on a polycrystalline gold electrode coated with 4-mercaptopyridine and 11-mercapto-1-undecanoic acid self-assembled monolayers (SAMs) and the thermodynamics and kinetics of the heterogeneous protein-electrode electron transfer (ET) reaction were determined by cyclic voltammetry. The E°′ values for the immobi...
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The authors measured the elec. field induced linear dichroism for a wide range of sizes of CdSe nanocrystals. Large ground-state dipole moments were obsd., esp. for the smallest crystals. In these, the authors found a very large anisotropy of the absorption and most of the dipole strength is along the direction of the ground-state dipole moment. Fo...
Article
Three newly discovered drug metabolizing mutants of cytochrome P450 BM3 (van Vugt-Lussenburg et al., Identification of critical residues in novel drug metabolizing mutants of Cytochrome P450 BM3 using random mutagenesis, J Med Chem 2007;50:455-461) have been studied at an atomistic level to provide structural explanations for a number of their char...
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Surface-enhance resonance Raman scattering spectra of the heme–thiolate enzyme cytochrome P450 2D6 (CYP2D6) adsorbed on Ag electrodes coated with 11-mercaptoundecanoic acid (MUA) were obtained in various experimental conditions. An analysis of these spectra, and a comparison between them and the RR spectra of CYP2D6 in solution, indicated that the...
Article
The influence of pH on the redox properties of cytochrome c (cyt c) adsorbed on roughened silver electrodes chemically modified with a self-assembled monolayer (SAM) of 11-mercapto-1-undecanoic acid (MUA) was studied with voltammetric techniques in combination with surface-enhanced resonance Raman scattering (SERRS). The experiments were performed...
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Cytochrome P450 2D6 (CYP2D6) is one of the most important cytochromes P450 in humans. Resonance Raman data from the T309V mutant of CYP2D6 show that the substitution of the conserved I-helix threonine situated in the enzyme’s active site perturbs the heme spin equilibrium in favor of the six-coordinated low-spin species. A mechanistic hypothesis is...
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Full-text available
To combine voltammetric techniques with surface-enhanced resonance Raman scattering (SERRS), cytochrome c (cyt c) was immobilized on a roughened silver electrode chemically modified with a self-assembled monolayer (SAM) of 4-mercaptopyridine (PySH). All measurements were performed on the same electrode in a homemade spectroelectrochemical cell suit...
Article
The aim of the current report is to shed light on the tautomerism of 4-((Phenylimino)methyl) naphthalene-1-ol in solution, which was studied by UV-Vis spectroscopy and quantum chemical calculations. It was found that this compound does not have the typical tautomeric behavior of its analog 4-Phenylazo-naphthalen-1-ol. The complicated equilibrium be...
Article
Electrospray ionization mass spectrometry was used to investigate complex formation of different metal complexes in a continuous-flow ligand-exchange reactor. A computer program was developed based on normal equilibrium calculations to predict the formation of various metal-ligand complexes. Corresponding to these calculations, infusion electrospra...
Article
In this work we modeled the circular dichroism (CD) spectrum of LHCII, the main light harvesting antenna of photosystem II of higher plants. Excitonic calculations are performed for a monomeric subunit, taken from the crystal structure of trimeric LHCII from spinach [Liu, Z. F., Yan, H. C., Wang, K. B., Kuang, T. Y., Zhang, J. P., Gui, L. L., An, X...
Article
Surface-enhanced resonance Raman scattering (SERRS) from dilute solutions (down to nanomolar concentrations) of human mono-oxygenase CYP2D6 is observed using aqueous dispersions of Ag nanoparticles (hydrosol) coated with self-assembled monolayers (SAMs) of mercaptoalkanoic acids of two different lengths. From a direct comparison with its resonance...
Article
The bacteriophage T4 capsid protein gp23 was studied using time-resolved and steady-state fluorescence of the intrinsic protein fluorophore tryptophan. In-vitro gp23 consists mostly of monomers at low temperature but forms hexamers at room temperature. To extend our knowledge of the structure and hexamerization characteristics of gp23, the temperat...
Article
We present ultrafast pump-probe studies on chem. prepd. CdSe nanocrystals. Upon pulsed optical excitation we find pronounced oscillations, indicating strong coupling to a LO phonon mode. From the polarization dependence of the signal addnl. information about the very first coherent events of exciton dynamics is obtained. The obsd. anisotropy behavi...
Chapter
Viable biological systems occur on a wide scale of dimensions ranging from sizes of 30 meters for mammals (blue whale), and 120 meters for plants (sequoia tree), down to 10−6 meters for single cellular organisms.
Article
The crystal structure of 2-butylamino-6-methyl-4-nitropyridine N-oxide (2B6M) was resolved on the basis of X-ray diffraction. Solid 2B6M occurs in the form of a doubly hydrogen-bonded dimer with squarelike hydrogen-bonding network composed of two intra- (2.556(2) A) and two intermolecular (2.891(2) A) N-H...O type hydrogen bonds. The molecule thus...
Article
To date, a successful combination of surface-enhanced resonance Raman spectroscopy (SERRS) and electrochemistry to study heme proteins is inhibited by the problems raised by the prerequisite to use silver as electrode metal. This paper indicates an approach to overcome these problems. It describes a quick and reproducible procedure to prepare silve...
Article
Cytochrome P450 2D6 (CYP2D6) is one of the most important drug-metabolizing enzymes in humans. Resonance Raman data, reported for the first time for CYP2D6, show that the CYP2D6 heme is found to be in a six-coordinated low-spin state in the absence of substrates, and it is perturbed to different extents by bufuralol, dextromethorphan, and 3,4-methy...
Article
Absorption and circular dichroism (CD) spectra of light-harvesting (LH)1 complexes from the purple bacteria Rhodobacter (Rba.) sphaeroides and Rhodospirillum (Rsp.) rubrum are presented. The complexes exhibit very low intensity, highly nonconservative, near-infrared (NIR) CD spectra. Absorption and CD spectra from several mutant and reconstituted L...
Article
In this work, we investigate the origin and characteristics of the circular dichroism (CD) spectrum of various light-harvesting 1 (LH1) complexes. The near-infrared (NIR) CD signal of these core antennae is strongly nonconservative, and the nature of this nonconservativity is under examination in this paper. So far, on the basis of the high-resolut...
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Enzyme structure and dynamics may play a main role in substrate binding and the subsequent steps in the CYP (cytochrome P450) catalytic cycle. In the present study, changes in the structure of human CYP2D6 upon binding of the substrate are studied using steady-state and time-resolved fluorescence methods, focusing not only on the emission of the tr...
Article
The spectroscopic properties of two asymmetric indolylmaleimide derivatives, 4-bromo-3-(1'H-indol-3'-yl)maleimide and 4-methyl-3-(1'H-indol-3'-yl)maleimide, are investigated. The bromo derivative was crystallized and its X-ray structure was determined. Both compounds are strongly colored while their separate components (indole and maleimide) absorb...
Article
The ultrafast evolution of the electric field within bacteriorhodopsin was measured by monitoring the absorption changes of a tryptophan residue after excitation of retinal. The Trp absorption decreases within the first 200 femtoseconds and then recovers on time scales typical for retinal isomerization and vibrational relaxation. A model of exciton...
Article
Arcyriarubin A and arcyriaflavin A, two strongly emissive and intensely colored natural products containing both two indoles and a maleimide unit, are investigated (in the flavin the two indole moieties are coupled by a cyclization). The photophysical properties of these compounds were studied in several solvents using UV-vis absorption, steady-sta...
Article
Excited-state intramolecular proton transfer (ESIPT) occurring in the salicylic acid (SA) derivative 5-methoxysalicylic acid (5-MeOSA) in an apolar solvent (cyclohexane) and in the presence of the hydrogen bond accepting agent diethyl ether (DEE) is investigated. Analysis of the directly measured subnanosecond time-resolved emission spectra (TRES)...
Article
The time-resolved fluorescence properties of the bacteriophage T4 capsid protein gp23 are investigated. The structural characteristics of this protein are largely unknown and can be probed by recording time-resolved and decay-associated fluorescence spectra and intensity decay curves using a 200 ps-gated intensified CCD-camera. Spectral and decay d...
Article
In this work we investigate the origin and characteristics of the circular dichroism (CD) spectrum of rhodopin glucoside and lycopene in the light-harvesting 2 complex of Rhodopseudomonas acidophila and Rhodospirillum molischianum, respectively. We successfully model their absorption and CD spectra based on the high-resolution structures. We assume...
Article
A new citrate-reduced silver hydrosol coated with omega-mercaptoalkanoic acids (mercaptopropionic and mercaptoundecanoic acids) self-assembled monolayers was prepared and characterized with surface-enhanced Raman spectroscopy. The structure and the quality of the coating monolayers are discussed and compared to similar coated and uncoated silver hy...
Article
The possibilities of a 200 ps gated intensified charge-coupled device (CCD) camera to record time-resolved fluorescence were explored using the fluorescing amino acid tryptophan and its derivative Nacetyl-tryptophan amide (NATA) as model compounds. The results were compared to complementary data from time-correlated single-photon counting (TCSPC) e...
Article
Surface-enhanced resonance Raman spectra of cytochrome c on silver electrodes coated with self-assembled monolayers of mercaptopropionic acid were recorded at different potentials using 50 microL of a micromolar solution. For this purpose, a linearly moving, low-volume, small spectroelectrochemical cell was designed and used together with a Raman m...
Article
The temperature dependence of fluorescence excitation spectra is investigated. This gives information on melittin folding equilibrium complementary to that obtained from fluorescence emission studies. A fit of the excitation spectra of melittin with three Gaussian functions gives good results. It suggests that in melittin a reversal of La and Lb el...
Article
The applicability of homogeneous on-line continuous-flow, multi-protein biochemical assays was demonstrated for the interaction between fluorescein-biotin and streptavidin and for digoxin and anti- digoxigenin using electrospray quadrupole time-of-flight mass spectrometry (Q-TOF MS). In the on-line continuous-flow biochemical MS-based system, sever...
Article
The applicability of a homogeneous on-line continuous-flow, multi-protein biochemical assay was demonstrated for the interaction between fluorescein-biotin and streptavidin and for digoxin and anti-digoxigenin using electrospray quadrupole time-of-flight mass spectrometry (Q-TOF MS). In the on-line continuous-flow biochemical MS-based system severa...
Article
Spectral and photophysical properties of substituted salicylic anions are investigated by steady-state and time-resolved fluorescence spectroscopy for a variety of electron donating substituents at the positions para to the hydroxyl and carboxylic groups. Next to the usual excited-state intramolecular proton transfer in aqueous solution, an excited...
Article
We studied the fluorescence dynamics of the light-harvesting-2 complex of Rhodopseudomonas acidophila both with and without an externally applied electric field. The fluorescence emission spectrum of the complex shows (small) spectral shifts of the average emission wavelength on a time scale of 300 ps. The shifts are temperature dependent and resul...
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We investigated the temperature-mediated reassociation of the B820 subunit of Rs. rubrum to form a light-harvesting 1 complex (LH 1). By combining several spectroscopic techniques with global spectral data analysis fitting, we present evidence for the occurence of two spectral intermediates that appear during the reassociation process. At high temp...
Article
Full-text available
Salicylic anion absorption and emission are studied in a variety of solvents and solvent mixtures. The large Stokes shift observed for this anion is taken to be indicative of a rapid excited state proton transfer reaction to its keto form. The changes in the Stokes shift in the various solvents can be well-correlated with changes in polarity/polari...
Article
Photophysical properties of several basically important aromatic azodyes (1-phenylazo-2-naphthol and 2-phenylazo-1-naphthol) and Schiff bases (N-(2-hydroxy-1-naphthylmethylidene) aniline and N-(1-hydroxy-2-naphthylmethylidene) aniline) all containing an intramolecular hydrogen bond were studied by both steady-state and time-resolved fluorescence sp...
Article
The absorption (OD) and circular dichroism (CD) spectra of LH2 complexes from various purple bacteria have been measured and modeled. Based on the lineshapes of the spectra we can sort the LH2 complexes into two distinguishable groups: "acidophila"-like (type 1) and "molischianum"-like (type 2). Starting from the known geometric structures of Rhodo...
Article
The spectral properties of several aromatic azo dyes of fundamental importance (4-phenylazo-1-naphthol, 1-phenylazo-2-naphthol and 2-phenylazo-1-naphthol) and Schiff bases (N-(2-hydroxy-1-naphthylmethylidene)aniline and N-(1-hydroxy-2-naphthylmethylidene)aniline) are investigated at temperatures down to 100 K. The observed spectral changes are inte...
Article
We calc. the effects of relatively strong elec. fields, corresponding to typical values for the fields inside glasses and proteins, on the spectroscopic properties of a simple two-level mol. Disorder in the elec. field strength is employed as a phys. source for inhomogeneous broadening. A striking result is that a Gaussian probability distribution...
Article
The effects of increasing concentration (10-7-2.5 x 10-3 mol/g) of Erythrosin B (Ery B) in poly(vinyl alcohol) films on its visible absorption spectrum have been investigated. In a concentration range of 2 x 10-7-10-5 mol/g, no effects on the absorption spectrum are found. By contrast, within this concentration range, time-resolved fluorescence exp...
Article
This paper describes the absorbance properties of pigments in disordered films. The fluorescence quenching of pigment systems at low concentrations are usually attributed to the presence of so-called statistical pairs. We show that, if line broadening mechanisms are taken into account such as homogeneous and inhomogeneous broadening and statistical...
Article
Eenergy transfer in the B800 ring of the LH2 antenna of the purple bacteria Rhodopseudomonas (Rps.) acidophila and Rhodospirillum (Rs.) molischianum was studied at room temperature using three-pulse echo peak shift (3PEPS) and transient grating (TG) techniques. From the transient grating experiments, we found the B800 → B850 energy transfer rates t...
Article
In this paper the circular dichroism and absorption spectra of the LH2 complex of Rhodopseudomonas acidophila, for which the atomic structure is known, are analyzed. We show that an analysis based on the distribution of the excitations in real space, and their correlations, to unravel the relation between the atomic structure of the light-harvestin...
Chapter
The light-harvesting antenna protein LH2 of photosynthetic purple bacteria has been the subject of intensive study since the structures of the LH2 complexes of Rhodospirillum molischianum [1] and Rhodopseudomonas acidophila [2] were resolved a few years ago. The LH2 complex is a ring shaped structure with 8 [1] or 9 [2] subunits, each of which bind...
Article
In this paper, we report the circular dichroism (CD) spectra of two types of LH2-only mutants of Rhodobacter sphaeroides. In the first, only the wild type LH2 is present, while i the second, the B800 binding site of LH2 has been either destabilized or removed. For the first time, we have identified a band in the CD spectrum of LH2, located at appro...
Article
The dielectric relaxation of acetonitrile-water mixtures is measured at 298.15 K. From the resulting complex permittivity spectra, two relaxation processes are found. The low-frequency process is attributed to water molecules that reside in a micro-phase of relatively stable clusters. The high-frequency process is attributed to both acetonitrile an...
Article
The published crystal structure of the LH2 complex of Rhodopseudomonas acidophila is used to calculate absorption and CD spectra of this system. An important parameter, the zero crossing of the CD spectrum with respect to the absorption maximum, is shown to be sensitive to structural changes. The changes in spectral properties as a function of vary...
Article
The origin of the nonconservative nature of the circular dichroism (CD) spectrum of bacteriochlorophyll dimers is investigated. It is shown that coupling between the Qy and Qx transitions can, under rather restricting circumstances, lead to an asymmetrical CD spectrum: only for a limited set of relative orientations of the monomers within the dimer...
Article
The quasi-lattice quasi-chemical (QLQC) model and the stepwise solvent exchange (SSE) model are both used in solvation chemistry to describe preferential solvation of solutes in binary mixtures. A critical assessment of the SSE model reveals a basic flaw. The usual assumption in the SSE model, that the activity coefficients of the solvent molecules...
Article
The quasi-lattice quasi-chemical model has been modified in order to predict the enthalpy of transfer of alkali-metal halides in binary solvent mixtures from the solvation properties in the pure solvents and from the excess enthalpy and Gibbs energy of mixing of the solvents. In mixtures with a negative Gibbs energy of mixing, there is an approxima...
Article
We investigated and extended models describing the influence of director fluctuations (DF) on the orientational dynamics of individual (dissolved) molecules. The models are divides in two categories. On one hand the traditional models, relying on a seperation in time scales between the DF and the individual motion of the molecule. On the other high...
Article
We study the dynamics of an axisymmetric particle suspended in a fluid. The approach we use is based on the induced forces method. We then obtain formal expressions for the friction tensors from which one derives explicit formulas for the friction coefficients depending on the shape of the particle, valid in the long-particle limit. Some particular...
Article
The influence of director fluctuations on a probe molecule dissolved in a nematic liquid crystal is calculated to all orders using the gaussian properties of the director field. Consequences for the N.M.R. spectrum and relaxation through quadrupolar interaction of the probe molecule are indicated. It is found that the equilibrium distribution of mo...