Determination of the anomeric configuration in carbohydrates by longitudinal cross-correlated relaxation studies: application to mono- and disaccharides

The role of cross-correlated relaxation between the anomeric proton chemical shift anisotropy (CSA) and its dipolar relaxation with nearby proton on the longitudinal relaxation in mono- and disaccharides at two magnetic field strengths has been investigated and shown to directly report the identity of their anomeric configuration.     

Determination of chemical shift anisotropy tensors of carbonyl nuclei in proteins through cross-correlated relaxation in NMR.

The principal components and orientations of the chemical shift anisotropy (CSA) tensors of nearly all 13C carbonyl nuclei in a small protein have been determined in isotropic solution by a combination of three complementary cross-correlation measurements.     

Radical cations of branched alkanes in solutions: time-resolved magnetic field effect and quantum chemical studies

Radical cations of heptane and octane isomers, as well as several longer branched alkanes, were detected in irradiated n-hexane solutions at room temperature by the method of time-resolved magnetic field effect (TR MFE). To identify radical cations, the hyperfine coupling constants as determined by simulation of the TR MFE curves were compared to the constants calculated using the density functional theory (DFT) approach. The g-values of the observed radical cations were close to that of the 2,2,3,3-tetramethylbutane radical cation studied earlier by optically detected electron spin resonance (ESR) and TR MFE techniques. No evidence of the decay of the radical cations of branched alkanes to produce olefin radical cations was found, which was further supported by the observation of positive charge transfer from the observed radical cations to cycloalkane molecules. The lifetimes of the radical cations of the branched alkanes were found to be longer than tens of nanoseconds.     

NMR cross-correlated relaxation rates reveal ion coordination sites in DNA

In this work, a novel NMR method for the identification of preferential coordination sites between physiologically relevant counterions and nucleic acid bases is demonstrated. In this approach, the NMR cross-correlated relaxation rates between the aromatic carbon chemical shift anisotropy and the proton-carbon dipolar interaction are monitored as a function of increasing Na(+), K(+), and Mg(2+) concentrations. Increasing the counterion concentration modulates the residence times of the counterions at specific sites around the nucleic acid bases. It is demonstrated that the modulation of the counterion concentration leads to sizable variations of the cross-correlated relaxation rates, which can be used to probe the site-specific counterion coordination. In parallel, the very same measurements report on the rotational tumbling of DNA, which, as shown here, depends on the nature of the ion and its concentration. This methodology is highly sensitive and easily implemented. The method can be used to cross-validate and/or complement direct but artifact-prone experimental techniques such as X-ray diffraction, NMR analysis with substitutionary ions, and molecular dynamics simulations. The feasibility of this technique is demonstrated on the extraordinarily stable DNA mini-hairpin d(GCGAAGC).     

Probing methyl dynamics from 13C autocorrelated and cross-correlated relaxation

An understanding of side-chain motions in protein is of great interest since side chains often play an important role in protein folding and intermolecular interactions. A novel method for measuring dipole-dipole cross-correlated relaxation in methyl groups of uniformly 13C-labeled proteins without deuteration has been developed by our group. The excellent agreement between dynamic parameters of methyl groups in ubiquitin obtained from the cross-correlated relaxation and 13C spin-lattice relaxation and those derived previously from 2H relaxation data demonstrates the reliability of the method. This method was applied to the study of side-chain dynamics of human intestinal fatty acid binding protein (IFABP) with and without its ligand. Binding of oleic acid to the protein results in decreased mobility of most of the methyl groups in the binding region, whereas no significant change in mobility was observed for methyl groups in the nonbinding region.     

Spectroscopic and quantum chemical studies of isocytosine

The methods of electronic and vibrational (IR) spectroscopy were used to study the spectral properties of isocytosine in H₂O, D₂O, chloroform, and hexane in a wide concentration interval. Quantum chemical calculations of tautomeric forms and dimers of isocytosine were carried out. The bands of the calculated and experimental spectra were assigned. The results of the quantum calculations were compared with the experimental data. The spectral bands were classified according to the type of tautomer or dimer to which they belong.Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 24, No. 1, pp. 29–36, January–February, 1988.The authors are grateful to I. M. Ginzberg and L. F. Strelkova for their participation in the discussion of the infrared spectroscopy results.     

Molecular dynamics and quantum chemical studies on nitroglycerine

A constant temperature molecular dynamics study has been performed on PM3 (RHF) geometry optimized nitroglycerine molecule. The dynamics was carried out by using MM+ method at 550 K which is above the explosion point of nitroglycerine. Some molecular orbital characteristics of nitroglycerine at elevated temperatures were computed.     

Perfluoropoly-ether/peroxide compounds: spectroscopic studies and quantum chemical calculations

Perfluoropolyethers (PFPEs) are a class of high performance materials used in a wide range of applications (refrigeration, lubrication, semiconductor industry, etc.). PFPEs containing peroxidic units are intermediate materials for the preparation of commercial end products. In this work we study the spectroscopic properties of ether and peroxides linkages in this class of compounds; nuclear magnetic resonance (NMR) spectra are discussed, FT-Raman data presented. Quantum chemical calculations on model molecules were used as a tool for the interpretation of the Raman experimental data and physical-chemical properties.     

Protein-bound chromophores astaxanthin and phytochromobilin: excited state quantum chemical studies

We present an overview of excited state quantum chemical calculations aimed at elucidating controversial issues regarding the photochemistry of the protein-bound chromophores astaxanthin and phytochromobilin. In particular, we show how the application of time-dependent density functional theory and other single-reference quantum chemical excited state methods have contributed to shed new light on the origin of the >0.5 eV bathochromic shift of the electronic absorption by the carotenoid astaxanthin in the protein macromolecular complex crustacyanin, and the mechanism for C15-Z,syn --> C15-E,anti isomerization of the tetrapyrrole phytochromobilin that underlies the photoactivation of the plant photoreceptor phytochrome. Within the approximation that exciton coupling is neglected, the calculations on astaxanthin provide support for the notion that the bathochromic shift, which is responsible for the slate-blue coloration of lobster shell, is due to polarization rather than a conformational change of the chromophore in the protein-bound state. Furthermore, the polarization is attributed to a hydrogen-bonded protonated histidine residue. The calculations on phytochromobilin, in turn, suggest that a stepwise C15-Z,syn --> C15-E,syn (photochemical), C15-E,syn --> C15-E,anti (thermal) mechanism is much more favorable than a concerted, fully photochemical mechanism, and that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form. Accordingly, the calculations indirectly support the view that the photoactivation of phytochrome does not involve a proton transfer from the chromophore to the surrounding protein.     

Determination of the glycosidic bond angle chi in RNA from cross-correlated relaxation of CH dipolar coupling and N chemical shift anisotropy

A new heteronuclear NMR pulse sequence, the quantitative Gamma(HCN) experiment, for the determination of the glycosidic torsion angle chi in (13)C,(15)N-labeled oligonucleotides is described. The Gamma(HCN) experiment allows measurement of CH dipole-dipole, N chemical shift anisotropy cross-correlated relaxation rates (Gamma(C1'H1',N1)(DD,CSA) and Gamma(C2'H2',N9)(DD,CSA) for pyrimidines Gamma(C1'H1'N9)(DD,CSA) and Gamma(C2'H2',N9)(DD,CSA) for purines). A nucleotide-specific parametrization for the dependence of these Gamma-rates on chi based on (15)N chemical shift tensors determined by solid-state NMR experiments on mononucleosides (Stueber, D.; Grant, D. M. J. Am. Chem. Soc. 2002, 124, 10539-10551) is presented. For a 14-mer and a 30-mer RNA of known structures, it is found that the Gamma(HCN) experiment offers a very sensitive parameter for changes in the angle chi and allows restraining of chi with an accuracy of around 10 degrees for residues which do not undergo conformational averaging. Therefore, the Gamma(HCN) experiment can be used for the determination of chi in addition to data derived from (3)J(C,H)-coupling constants. As shown for the 30-mer RNA, the derived torsion angle information can be incorporated as additional restraint, improving RNA structure calculations.     

Spectroscopic and quantum chemical studies on 4-acryloyl morpholine

Fourier transform infrared (FTIR) and FT-Raman spectra have been recorded and an extensive spectroscopic investigations have been carried out on 4-acryloyl morpholine (4AM). Theoretical quantum chemical studies have also been performed. From the ab initio and DFT analysis using HF, B3LYP and B3PW91 methods with 6-31G(d,p) and 6-311G++(d,p) basis sets the energies, structural, thermodynamical and vibrational characteristics of the compound were determined. The energy difference between the chair equatorial and chair axial conformers of 4AM have been calculated by density functional theory (DFT) method. The optimized geometrical parameters, theoretical wavenumbers and thermodynamic properties of the molecule are compared with the experimental values. The effect of acryloyl group on the characteristic frequencies of the morpholine ring has been analysed. The mixing of the fundamental modes with the help of potential energy distribution (PED) through normal co-ordinate analysis has been discussed.     

Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA

The dependence of N1/9 and C1' chemical shielding (CS) tensors on the glycosidic bond orientation (chi) and sugar pucker (P) in the DNA nucleosides 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine was studied using the calculation methods of quantum chemistry. The results indicate that these CS-tensors exhibit a significant degree of conformational dependence on chi and P structural parameters. The presented data test underlying assumptions of currently established methods for interpretation of cross-correlated relaxation rates between the N1/9 chemical shielding tensor and C1'-H1' dipole-dipole (Ravindranathan et al. J. Biomol. NMR 2003, 27, 365-75. Duchardt et al. J. Am. Chem. Soc. 2004, 126, 1962-70) and highlight possible limitations of these methods when applied to DNA.     

DFT and ab initio quantum chemical studies on p-cyanobenzoic acid

The Fourier transform infrared (FTIR) and FT-Raman spectra of p-cyanobenzoic acid (CBA) have been recorded in the range 4000-400 and 4000-100 cm(-1), respectively. The complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The vibrational frequencies determined experimentally were compared with theoretical wavenumbers obtained from ab initio HF and DFT-B3LYP gradient calculations employing 6-31G**, 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method. The interactions of cyano and carboxylic acid groups with the skeletal vibrational modes were investigated.     

Structure-property relationships in push-pull amino/cyanovinyl end-capped oligothiophenes: quantum chemical and experimental studies

A series of push-pull chromophores built around thiophene-based pi-conjugating spacers and bearing various types of amino donors and cyanovinyl acceptors have been analyzed by means of UV-vis-NIR, IR, and Raman spectroscopic measurements in the solid state as well as in solution. The intramolecular charge transfer (ICT) of these pi-conjugated systems has also been tested by analyzing the ability of the solute molecules to undergo shifts in their fluorescence emission maxima with increasing solvent polarity. These push-pull oligomers also display an attractive electrochemical behavior since they generate stable species both upon oxidation and reduction. Oxidation mainly involves changes in the electron-rich aminooligothienyl half-part of the molecule and leads to the formation of stable cations. On the other hand, reduction to radical anions and dianions is mainly cyanovinyl-centered but also affects the pi-conjugated electron relay. Density functional theory (DFT) calculations have been carried out to help the assignment of the most relevant electronic and vibrational features and to derive useful information about the molecular structure of these NLO-phores.     

The reaction between silylene and ammonia: Some gas-phase kinetic and quantum chemical studies

Time-resolved kinetic studies of the reaction of silylene, SiH₂, generated by 193 nm laser flash photolysis of silacyclopent-3-ene, have been carried out in the presence of ammonia, NH₃. Second order kinetics were observed. The reaction was studied in the gas phase at 10 Torr total pressure in SF₆ bath gas at each of the three temperatures, 299, 340 and 400 K. The second order rate constants (laser pulse energy of 60 mJ +) fitted the Arrhenius equation:noindent Experiments at other pressures showed that these rate constants were unaffected by pressure in the range 10–100 Torr, but showed small decreases in value at 3 and 1 Torr. There was also a weak intensity dependence, with rate constants decreasing at laser pulse energies of 30 mJ +. Ab initio calculations at the G3 level of theory, show that SiH₂+NH₃ should form an initial adduct (donor-acceptor complex), but that energy barriers are too great for further reaction of the adduct. This implies that SiH₂+NH₃ should be a pressure dependent association reaction. The experimental data are inconsistent with this and we conclude that SiH₂ decays are better explained by reaction of SiH₂ with the amino radical, NH₂, formed by photodissociation of NH₃ at 193 nm. The mechanism of this previously unstudied reaction is discussed.     

Ortho effect: The fragmentation of isopropyl 2-hydroxychlorocarbanilates

The mass spectra of isopropyl 2-hydroxychlorocarbanilate indicate a preferential ortho intramolecular rearrangement which yields a chloro 2-benzoxazolinone intermediate ion. A com-parison of the fragmentation of ortho, meta and para hydroxy analogs of isopropyl 3-chlorohydroxy-carbanilate indicates the existence of an ‘ortho effect’ during the fragmentation of isopropyl-chloro 2-hydroxycarbanilates.