The dipole moment in the lowest singlet pi formed from pi state of indole determined by the optical Stark effect

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Simulations of the Absorption and Fluorescence of Indole in Aqueous Solution and at a Nonpolar/Polar Interface

Theoretical results are presented on the absorption and fluorescence of indole in aqueous solution as well as at the air/water surface. We use a combined quantum chemical statistical mechanical model with explicit solvent. An approximate ab initio complete active space self-consistent field description of the indole molecule is used, coupled to a discrete polarizable water medium. From the bulk simulations, strong support is found for the interchange mechanism, which explains the unusual solvent shift of the fluorescence of indole or tryptophan in a polar surrounding by a solvent induced switch of the fluorescing state. Two mechanisms are given to explain the different shifts for indole at the interface. First, a dielectric depletion effect, which is expected from the reduction of the amount of polar media. Second, an interface-specific effect, which derives from the stronger hydrogen bond formation at the surface. The latter effect acts to increase the shift for both absorption and emission at the surface as compared to the bulk. From these results, the intrinsic probe photophysics of tryptophan in proteins is discussed in terms of the properties of the protein/solvent interface and the orientation of the amino acid.

Temperature excursion infrared (TEIR) spectroscopy used to study hydrogen bonding between water and biomolecules

Water is a highly polar molecule that is capable of making four H-bonding linkages. Stability and specificity of folding of water-soluble protein macromolecules are determined by the interplay between water and functional groups of the protein. Yet, under some conditions, water can be replaced with sugar or other polar protic molecules with retention of protein structure. Infrared (IR) spectroscopy allows one to probe groups on the protein that interact with solvent, whether the solvent is water, sugar or glycerol. The basis of the measurement is that IR spectral lines of functional groups involved in H-bonding show characteristic spectral shifts with temperature excursion, reflecting the dipolar nature of the group and its ability to H-bond. For groups involved in H-bonding to water, the stretching mode absorption bands shift to lower frequency, whereas bending mode absorption bands shift to higher frequency as temperature decreases. The results indicate increasing H-bonding and decreasing entropy occurring as a function of temperature, even at cryogenic temperatures. The frequencies of the amide group modes are temperature dependent, showing that as temperature decreases, the amide group H-bonds to water strengthen. These results are relevant to protein stability as a function of temperature. The influence of solvent relaxation is demonstrated for tryptophan fluorescence over the same temperature range where the solvent was examined by infrared spectroscopy.

Experimental measurement of the induced dipole moment of an isolated molecule in its ground and electronically excited states: Indole and indole–H2O

Reported here are measurements of the magnitude and orientation of the induced dipole moment that is produced when an indole molecule in its ground S(0) and electronically excited S(1) states is polarized by the attachment of a hydrogen bonded water molecule in the gas phase complex indole-H(2)O. For the complex, we find the permanent dipole moment values mu(IW)(S(0)) = 4.4 D and mu(IW)(S(1)) = 4.0 D, values that are substantially different from calculated values based on vector sums of the dipole moments of the component parts. From this result, we derive the induced dipole moment values mu(I) (*)(S(0)) = 0.7 D and mu(I) (*)(S(1)) = 0.5 D. The orientation of the induced moment also is significantly different in the two electronic states. These results are quantitatively reproduced by a purely electrostatic calculation based on ab initio values of multipole moments.

Stark absorption spectroscopy of indole and 3-methylindole

Indole and 3-methylindole (3-MI) doped into a polymethylmethacrylate (PMMA) film are studied by the Stark absorption (electroabsorption) spectroscopy. The 1La and 1Lb absorption bands are distinguished and the change in permanent dipole moment on 1La excitation is determined by a model fit to the measured absorption and electroabsorption spectra. Analysis of the spectra, measured at normal incidence and magic angle conditions, proved the essential role of the electric-field-induced orientation/alignment effects for polar indole and 3-MI molecules in the PMMA environment at room temperature.

Optical activity of a nucleotide-sensitive tryptophan in myosin subfragment 1 during ATP hydrolysis

The xanthene probes 5'-iodoacetamido-fluorescein and -tetramethylrhodamine specifically modify skeletal muscle myosin subfragment 1 (S1) at the reactive thiol residue (SH1) and fully quench the fluorescence emission from tryptophan residue 510 (Trp510) in S1 (T.P. Burghardt and K. Ajtai, Biophys. Chem., 60 (1996) 119; K. Ajtai and T.P. Burghardt, Biochemistry, 34 (1995) 15943). The difference between the fluorescence intensity obtained from S1 and probe-modified S1 comes solely from Trp510 in chymotryptic S1, a protein fragment that contains five tryptophan residues. The rotary strength and quantum efficiency of Trp510 were measured using difference signals from fluorescence detected circular dichroism (FDCD) and fluorescence emission spectroscopy. These structure-sensitive signals indicate that the binding of nucleotide or nucleotide analogs to the active site of S1 causes structural changes in S1 at Trp510 and that a one-to-one correspondence exists between Trp510 conformation and transient states of myosin during contraction. The Trp510 rotary strength and quantum efficiency were interpreted structurally in terms of the indole side-chain conformation using model structures and established computational methods.

The conformation of xanthene dyes in the myosin sulfhydryl one binding site. Part I. Methods and model systems

Derivatives of the fluorescent probes fluorescein and rhodamine specifically and covalently modify the highly reactive thiol (SH1) of myosin subfragment 1 (S1). Both probes develop circular dichroism (CD) upon modification of SH1 at the visible absorption band of the chromophore. A model system of chiral complexing agents (aromatic chiral amines) interacting with fluorescein in solvent develops a CD signal that mimics that produced by S1. The model system suggests that a specific interaction of the probe with an aromatic chiral residue in the SH1 binding pocket induces the CD signal. Several other spectroscopic signals, including absorption and fluorescence intensity and anisotropy, characterize the fluorescein or rhodamine binding to SH1. A coupled dipole method is adapted to interpret these spectroscopic signals in terms of the probe-S1 complex conformation. The computation of the orientation of the principal hydrodynamic frame (PHF) of S1 from its crystallographic alpha-carbon backbone structure permits the known orientation of the probe in the PHF of S1 to further constrain the conformation of the probe-S1 complex. The coupled dipole interpretation of spectroscopic data combined with constraints relating the probe dipole orientation to the PHF of S1 determines the conformation of the probe-S1 complex. The methods developed here are applied to the spectroscopic signals from fluorescein or rhodamine in the SH1 binding site of S1 to obtain an atomic resolution model of the probe-S1 conformation [Ajtai and Burghardt, Biochemistry, 34 (1995) 15943-15952].

Protein: nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes

Low singlet transition energies and line strengths were calculated for the cytosine:indole:guanine complex by the INDO/1S-CI method. The chromophores were arranged in three sets of 270 intercalating geometries. Calculations were executed in the supermolecule model with single excited configurations. Errors due to basis set extension and incomplete configuration representation were assessed, for all chromophore pairs, by full BSSE correction calculations and inclusion of double-excited configurations. The intercalation-induced perturbations of the principal transitions are characterized by but not limited to (a) a decrease in strength of [pi*,pi] transitions, (b) increase in strength in [pi*,n] transitions, (c) splitting of [pi*,pi] transitions into components of unequal strength, and (d) energy and strength dependence in mixed transitions on rise and shift movements of the nucleic acid bases. These predictions are in accord with absorption, fluorescence emission, and scattering, and resonance Raman spectroscopic data on oligonucleotides and analogous aromatic complexes. The calculations suggest that major differences in intercalating coordinations are discernible in the near-uv spectroscopic domain of proteins and nucleic acids.

Electronic states of the indole-acrylamide molecular pair

A model is suggested for tryptophan fluorescence quenching by acrylamide based on the prediction that acrylamide can absorb a photon from the excited indole moiety and then dissipate the optical energy into a sink of fast exchanging conformations. Semiempirical electronic structure calculations of the indole-acrylamide pair indicate little actual intermolecular orbital mixing at van der Waals contact distances. However, the two lowest singlet transitions of the molecular pair, assigned to the acrylamide (pi *)----n(O) line and to the indole 1Lb----1A1 line, respectively, vary significantly in energies and in transition and excited state moments with the geometry of interaction between the two entities. The distribution of optimal quenching coordinations depends separately on the benzene and pyrrole portions and has a distinctly non-spherical shape at these distances.