FT-Raman spectroscopy of biological molecules

Raman spectroscopy of biological molecules is often very difficult if not impossible due to a large fluorescence background from absorbing species, either from the molecule itself or an impurity. Photobleaching is occasionally successful in photochemically removing fluorescent impurities, but the majority of samples are not responsive to such treatment. Resonance enhancement of an absorbing species allows acquisition of Raman spectra in spite of competing fluorescence. However, the resonance Raman spectrum is characteristic of the chromophore only and little structural information is obtained from the spectrum about other parts of the molecule which are not resonantly enhanced. The newly developed technique of FT-Raman spectroscopy proves to be a solution to both of these problems for biological materials. Excitation with infrared wavelengths prevents electronic absorptions which give rise to fluorescence. In addition, the obtained spectra are completely nonresonant, allowing detection of vibrational modes of all parts of the molecule including the chromophore. We will present nonresonant, fluorescence free spectra of a range of biologically significant molecules including phospholipids and porphyrins.     

Physical properties and spectra of IO, IO- and HOI studied by ab initio methods

Structure and properties of the IO, IO- and HOI species, which are of potential importance for the ozone destruction catalytic cycle in the troposphere, have been calculated together with the EPR, NMR and UV-visible spectra by ab initio methodology with account of spin-orbit coupling (SOC) effects. Multi-configuration self-consistent field calculations with linear and quadratic response techniques and the multi-reference configuration interaction method have been employed. Photodissociation of these species, crucial for the catalytic ozone-destruction cycle, is critically reviewed and analyzed. Calculations predict that the singlet-triplet (S-T) transition to the lowest triplet state (X1 A' --> 3A') should be responsible for the weak long-wavelength tail absorption (approximately 450-560 nm) and photodissociation of the HOI molecule. The second, more intense, band around 400 nm is produced by two overlapping S-S and S-T transitions. In order to check this assignment of the HOI photodissociation the isoelectronic IO- anion and IO radical have been studied by the same methods. Comparison with the EPR spectrum of the IO radical indicates that the methods are reliable which gives credit to the accuracy of the HOI spectral interpretation. NMR spectra of HOI and IO- molecules and some other properties are calculated for the first time.     

Computational high-frequency overtone spectra of the water-ammonia complex

We have computed vibrational high-frequency overtone spectra of the water-ammonia complex, H(2)O-NH(3), and its isotopomers. The complex has been modeled as two independently vibrating monomer units. The internal coordinate Hamiltonians for each monomer unit have been constructed using exact gas phase kinetic energy operators. The potential energy and dipole moment surfaces have been calculated with the explicitly correlated coupled cluster method CCSD(T)-F12A and the valence triple-ζ VTZ-F12 basis around the equilibrium geometry of the complex. The vibrational eigenvalues have been calculated variationally and the eigenfunctions obtained have been used to compute the intensities of the absorption transitions. In H(2)O-NH(3), the water molecule acts as the proton donor and its symmetry is broken. The hydrogen-bonded OH bond oscillator undergoes a large redshift and intensity enhancement compared to the free hydrogen bond. Broken degeneracy of the asymmetric vibrations, quenched inversion splittings, and blueshift of the symmetric bending mode are the most visible changes in the ammonia unit.     

Spectroscopic and quantum chemical study of the novel compound cyclopropylmethylselenol

An investigation into the properties of the novel compound cyclopropylmethylselenol has been undertaken by use of Stark-modulation microwave spectroscopy and high-level quantum chemical calculations. Ground-state spectra belonging to six isotopomers of a single conformer of the molecule were recorded and assigned. This conformer, predicted to be the lowest in energy by a series of quantum chemical calculations, possesses a synclinal arrangement of the H-C-C-Se atoms. In addition to the assignment of these ground-state spectra, transitions attributable to vibrationally excited states of the 78Se- and 80Se-containing isotopomers were identified. A tentative assignment of these excited-state spectra to specific vibrational modes has been made with the assistance of a density functional theory calculation at the B3LYP/6-311++G(3df,2pd) level of theory. Close agreement was found between experimental ground-state rotational constants and ab initio equilibrium values calculated at the MP2/aug-cc-pVTZ level of theory. Good agreement was also noted between certain r(s) principal axis coordinates of atoms in the molecule and the corresponding ab initio r(e) values. Limited evidence in favor of the formation of a weak intramolecular hydrogen bond between the H atom of the selenol group and electron density associated with the cyclopropyl ring is discussed.     

Confocal laser microspectroscopic Rabi-flopping study of an iron oxide emitter surface used for Rydberg matter generation

Rydberg matter (RM) is a novel metal-like material in the form of electronically excited clusters of atoms (e.g. K and H) or molecules (e.g. H(2)). It is used as the inverted laser medium for IR in the RM laser. RM has recently been formed in its lowest state, which is proposed to be metallic hydrogen [Energy and Fuels 19 (2005) 2235]. An emitter material (K-doped iron oxide catalyst) that forms RM is studied by a specialized spectroscopic method, needed to detect the Rydberg states on the emitter surface. The spectroscopic method is phase-delay Rabi-flopping; it gives spectra from the time delay due to the periodic motion of the optical nutation vector. The formation of Rydberg species in the form of complexes K*-M (M a general small molecule) and (K-M)* is studied. So-called avoided transitions in K(+) ions are detected, of the same type as observed as transitions in the RM laser by stimulated emission. The formation and detection of Rydberg complexes containing H and H(2) is of great interest for metallic hydrogen production. Complexes with M=CH(2), H(2)O (or OH), CHO, H(2) and M'H are observed. Avoided transitions in RM clusters K(N)(*) are also identified. The identification of H containing Rydberg complexes on the surface indicates that metallic hydrogen is formed by the same cluster desorption route as other RM clusters.     

Optical excitations in star-shaped fluorene molecules

A detailed study of the low-energy optical transitions in two families of star-shaped molecules is presented. Both families have 3-fold rotational symmetry with oligofluorene arms attached to a central core. In one family, the core of the molecule is a rigid meta-linked truxene, while the other is a meta-linked benzene moiety. The low-energy transitions were studied both experimentally and using time-dependent density functional theory (TD-DFT). The optical transitions of these new star-shaped molecules were compared with corresponding linear oligofluorenes. Both families of star-shaped molecules showed higher absorption and fluorescence dipoles and photoluminescence quantum yields than straight chain oligofluorenes. TD-DFT calculations show that absorption takes place across the entire molecule, and after excited state relaxation, the emission results from a single arm. In both theory and experiment the transition dipole moments show an approximate n(0.5) dependence on the number of fluorene units in each arm.     

Structure, dipole moment and large amplitude motions of 1-benzofuran

The rotational spectrum of 1-benzofuran has been investigated by three different rotational spectroscopy techniques: (i) millimeterwave absorption free jet spectroscopy, useful for a fast assignment of the spectrum; (ii) molecular beam Fourier transform microwave spectroscopy, sensitive to detect less abundant isotopic species in natural abundance; (iii) waveguide conventional microwave spectroscopy, useful for the study of intramolecular dynamics, through the rotational spectra of the vibrational satellites of low energy modes. Besides the rotational spectrum of the ground state of the normal species, the spectra of 9 singly substituted 13C and 18O isotopomers in natural abundance, and of 6 vibrational satellites, have been measured. Precise structural parameters for the molecule, as well as information on the potential energy surface of the low energy vibrations, have been obtained. The dipole moment components have been determined to be micro(a)= 0.216 (2) and micro(b)= 0.720 (3) D, respectively.     

Interaction of low-energy electrons with linear diphenylethynyl derivatives in the gas phase

The gas phase electron impact spectroscopy has been used to study the relative efficiency of excitation into singlet states and energies of singlet-triplet transitions for two electroactive organic materials, anthracene and biphenyl-containing diphenylethynyl derivatives. The probability of the lowest singlet-triplet transition in anthracene-containing molecule was found to be much higher than that in anthracene which is connected with triple bonds. No noticeable contribution of the triple bonds into singlet spectra of the studied molecules was observed. There are a number of intense transitions in the range higher than 10 eV. The optical spectrum calculated using the density functional theory is in good agreement with experimental electron energy loss and optical absorption spectra.     

Multipole moments and polarizabilities of nonpolar diatomic molecules through quantum solvation in solid parahydrogen: the quadrupole moment of N2

It is shown in this paper that from the study of the induced infrared absorption spectra of homonuclear diatomic molecules solvated as impurities in a molecular quantum solid, it is possible to extract information about the rovibrational matrix elements of the multipole moments and polarizability of the embedded molecule. Theoretical expressions are derived for the integrated absorption coefficients of various multipole-field-induced double transitions involving guest-host pairs in a solid para-H(2) matrix. The intensities of some of the quadrupole moment induced transitions involving the N(2)-para-H(2) pair have been measured. From a comparison of the experimental and theoretical intensities, rovibrational matrix elements of the quadrupole moment of N(2) are determined in its ground vibrational state.     

Studies on the occurrence of atoms and molecules of aluminum, gallium, indium and their monohalides in an electrothermal carbon furnace

Molecular absorption spectra of monohalides (MX; X = F, Cl and Br) of aluminum, gallium and indium have been observed, where the monohalide species were produced in the electrothermal carbon furnace. In the spectra, some characteristic band structures have been identified for each metal halide. Generally, aluminum halides and/or metal fluorides provided clear and sharp band structures. The spectral bandwidth, background absorptions, and co-existing cations influenced the analytical features of molecular absorption spectrometry utilizing the monohalide bands. The time-dependent signal profiles of atoms and molecules at the stage of atomization in the carbon furnace have been observed for discussing the mechanisms of atomization and molecule formation of the Group III elements. Alkali and alkaline earth ions enhanced the molecular absorptions of monohalides, and transition metal ions reduced the background absorptions due to cutting the oxide. In addition, the application of the molecular absorptions of monohalides to the determination of trace halogens has also been investigated using the electrothermal vaporization technique.     

Theoretical studies on the electronic structures and absorption spectra of substituted benzenes with one- and two-dimensional charge transfer character

The electronic structures and absorption spectra of one- and two-dimensional charge transfer (CT) molecules based on para-nitroaniline (pNA) and 1,3-diamino-4,6-dinitro- benzene (DADB) have been studied theoretically via semi-empirical and ab initio methods. It is found that the behaviors of optical absorption are strongly influenced by the dimension of CT. Different from the well-known one-dimensional CT molecule of pNA, which shows one intense absorption related to the π → π^* CT transition, two-dimensional CT molecule of DADB exhibits more absorption peaks associated with various low-lying CT transitions in near ultraviolet range. In addition, the relative orientations of transition dipole moment and ground state dipole moment in one- and two-dimensional charge transfer molecules were also discussed.     

Can ortho-para transitions for water be observed?

The spectrum of water can be considered as the juxtaposition of the spectra of two molecules, with different total nuclear spin: ortho-H2O, and para-H2O. No transitions have ever been observed between the two different nuclear-spin isotopomers. The interconversion time is unknown and it is widely assumed that interconversion is forbidden without some other intervention. However, weak nuclear spin-rotation interaction occurs and can drive ortho to para transitions. Ab initio calculations show that the hyperfine nuclear spin-rotational coupling constants are about 30 kHz. These constants are used to explore the whole vibration-rotation spectrum with special emphasis on the coupling between nearby levels. Predictions are made for different spectral regions where the strongest transitions between ortho and para levels of water could be experimentally observed.     

Study on the sonodynamic activity and mechanism of promethazine hydrochloride by multi-spectroscopic techniques

In this paper, the bovine serum albumin (BSA) was selected as a target molecule, the sonodynamic damage to protein in the presence of promethazine hydrochloride (PMT) and its mechanism were studied by the means of absorption, fluorescence and circular dichroism (CD) spectra. The results of hyperchromic effect of absorption spectra and quenching of intrinsic fluorescence spectra indicate that the ultrasound-induced BSA molecules damage is enhanced by PMT. The damage degree of BSA molecules increases with the increase of ultrasonic irradiation time and PMT concentration. The results of synchronous fluorescence, three-dimensional fluorescence and CD spectra confirmed that the synergistic effects of ultrasound and PMT induced the damage of BSA molecules. The results of oxidation-extraction photometry with several reactive oxygen species (ROS) scavengers indicate that the damage of BSA molecules could be mainly due to the generation of ROS and both (1)O(2) and OH are the important mediators of the ultrasound-induced BSA molecules damage in the presence of PMT.     

INDO/SCF-CI calculations and structural spectroscopic studies of some complexes of 4-hydroxyacetanilide

The electronic energies among different possible structures of 4-hydroxyacetanilide (paracetamol) (PA) molecule, were calculated using INDO method and it has been concluded that its structure has C(s) point group symmetry of the cis-form. The ionization potential, electron affinity, dipole moment and binding energy have been calculated. The calculated electronic transitions of the cis-form of PA using SCF-CI method have good coincidence with the electronic absorption spectrum. The temperature effect on the electronic spectrum of PA confirms the presence of one conformer only. The electronic spectra of PA compound were studied in different polar- and non-polar solvents and the hydrogen bonding as well as the orientation energies of the polar solvents were determined from the mixed solvents studies. Complexes of PA with various metal ions such as, Cu(II), Zn(II) or Fe(II) ions of ratio 2:1, respectively, have been prepared and their structure has been confirmed by elemental analysis, atomic absorption spectra, IR spectra and (1)H NMR spectra and finally it can be concluded that the structure of the complexes has C2h point group symmetry in which two PA molecules are chelated to any one of the metal ions, Cu(II), Zn(II) and Fe(II) ions.     

Anlysenstörungen durch strukturierten Untergrund in der Atomabsorptionsspektrometrie

In atomic absorption spectrometry the determination of the spectral background is very difficult. The problem of the background measurement is namely to determine the spectral background under the very narrow resonance line, which cannot be resolved by the monochromator. The normal method of background measurement with a source of continuous radiation is correct only in that case when the background is a spectral continuum, e.g., a dissociation continuum of molecules. The background measurement may be faulty, if the background is due to line-rich electronic excitation spectra of molecules. The actual background is totally dependent upon whether or not a rotational line of the molecular spectrum coincides with the, atomic absorption line. This cannot be deduced from measurements obtained from those atomic absorption instruments normally used. Therefore in order to avoid systematic errors in atomic absorption analysis a systematic study of interfering molecular spectra with high resolution instruments is the only way to solve this problem.     

Theoretical investigation of the electronically excited states of chlorine hydrate

As a step toward a first principles characterization of the optical properties of chlorine hydrate, we have calculated the electronic absorption spectrum of a chlorine molecule trapped in dodecahedral (H2O)20 and hexakaidodecahedral (H2O)24 cages. For comparison, spectra were also calculated for an isolated Cl2 molecule as well as for selected Cl2(H2O)n, n < or =8, clusters cut out of the Cl2(H2O)20 cluster, allowing us to follow the evolution of the low-lying excited states with increasing number of surrounding water molecules. Although encapsulation of a chlorine molecule within the water cages has relatively little effect on its low-lying valence transitions, it does result in a large number of solvent-to-solute charge-transfer transitions at energies starting near 48,000 cm(-1).     

Ab initio potential energy surface and predicted microwave spectra for Ar--OCS dimer and structures of Arn--OCS (n = 2-14) clusters

An ab initio potential energy surface for the Ar--OCS dimer was calculated using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)] with a large basis set containing bond functions. The interaction energies were obtained by the supermolecular approach with the full counterpoise correction for the basis set superposition error. The CCSD(T) potential was found to have two minima corresponding to the T-shaped and the collinear Ar--SCO structures. The two-dimensional discrete variable representation method was employed to calculate the rovibrational energy levels for five isotopomers Ar--OCS, Ar--OC34S, Ar--O13CS, Ar--18OCS, and Ar--17OCS. The calculated pure rotational transition frequencies for the vibrational ground state of the five isotopomers are in good agreement with the observed values. The corresponding microwave spectra show that the b-type transitions (Delta Ka = +/-1) are significantly stronger than the a-type transitions (Delta Ka = 0). Minimum-energy structures of the Ar2--OCS trimer were been determined with MP2 optimization, whereas the minimum-energy structures of the Arn--OCS clusters with n = 3-14 were obtained with the pairwise additive potentials. It was found that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The 14 nearest neighbor Ar atoms form the first solvation shell around the OCS molecule.     

Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study

The solvent effect on the absorption spectra of coumarin 120 (C120) in water was studied utilizing the combined quantum mechanical∕molecular mechanical (QM∕MM) method. In molecular dynamics (MD) simulation, a new sampling scheme was introduced to provide enough samples for both solute and solvent molecules to obtain the average physical properties of the molecules in solution. We sampled the structure of the solute and solvent molecules separately. First, we executed a QM∕MM MD simulation, where we sampled the solute molecule in solution. Next, we chose random solute structures from this simulation and performed classical MD simulation for each chosen solute structure with its geometry fixed. This new scheme allowed us to sample the solute molecule quantum mechanically and sample many solvent structures classically. Excitation energy calculations using the selected samples were carried out by the generalized multiconfigurational perturbation theory. We succeeded in constructing the absorption spectra and realizing the red shift of the absorption spectra found in polar solvents. To understand the motion of C120 in water, we carried out principal component analysis and found that the motion of the methyl group made the largest contribution and the motion of the amino group the second largest. The solvent effect on the absorption spectrum was studied by decomposing it in two components: the effect from the distortion of the solute molecule and the field effect from the solvent molecules. The solvent effect from the solvent molecules shows large contribution to the solvent shift of the peak of the absorption spectrum, while the solvent effect from the solute molecule shows no contribution. The solvent effect from the solute molecule mainly contributes to the broadening of the absorption spectrum. In the solvent effect, the variation in C-C bond length has the largest contribution on the absorption spectrum from the solute molecule. For the solvent effect on the absorption spectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.     

Quantitative spectroscopic and theoretical study of the optical absorption spectra of H2O, HOD, and D2O in the 125-145 nm region

The room temperature absorption spectra of water and its isotopomers D2O and HOD have been determined in absolute cross section units in the 125 to 145 nm wavelength region using synchrotron radiation. The experimental results for these B band spectra are compared with results from quantum mechanical calculations using accurate diabatic ab initio potentials. A Monte Carlo sampling over the initial rotational states of the molecules is applied in order to calculate the cross sections at a temperature of 300 K. The overall rotation of the water molecule is treated exactly. Both for the experimental and for the theoretical spectrum an analysis is made in terms of a component attributed to rapid direct dissociation processes and a component attributed to longer-lived resonances. The agreement between the results from experiment and theory is excellent for H2O and D2O. In the case of HOD in the results of theory two more resonances are found at low energy. It is demonstrated that the width of the resonances of 0.04 eV is the result of overlapping and somewhat narrower resonances in the spectra of molecules differing in rotational ground state.     

Spectroscopic studies on polymeric cobalt(II) and nickel(II) complexes with bridging succinonitrile and succinonitrile isotopomer ligands

A series of cobalt(II) and nickel(II) complexes were synthesized using succinonitrile and its [1,4-13C2], [15N2]-, [2,2,3,3-2H4]- and [1,4-13C,-2,2,3,3-2H4]- isotopomers as bridging ligands. Spectroscopic studies, as well as X-ray powder diffraction profiles, were used to identify the nature of the octahedral coordination sphere of the central metal ions and to assign the vibrational spectra in full detail. The succinonitrile ligands were found to be in trans configuration in all the complexes studied and to be coordinated via the lone pairs of their nitrile nitrogens. The rule of mutual exclusion was found to be fulfilled for the succinonitrile ligands under the Ci symmetry of the complexes and the vibrations of the succinonitrile ligands were found to appear in either the infrared or the Raman spectra. All succinonitrile isotopomers exhibited blue-shifts of 43-71 cm(-1) upon coordination, while most of the other vibrations remained unchanged or underwent small shifts of only a few wavenumbers. The mass differences of the succinonitrile isotopomers were found to shift mainly the vibrations of the respective affected part of the molecules in comparison with the normal succinonitrile. The exchange of the halides, which are coordinated to the central metal ion, was also found to influence the vibrations of the associated water molecules and we could identify vibrational bands arising due to the H-bond interaction between the halides and the water molecules. Finally, we showed that all complexes under consideration have, spectroscopically, the same symmetry.