Circular dichroism and 13C nuclear magnetic resonance spectroscopy of pennisetin from pearl millet

The conformation and stability of pearl millet prolamin (pennisetin) were examined by using circular dichroism and C-13 nuclear magnetic resonance spectroscopy. The far UV spectrum of pennisetin in 70% (v/v) aqueous ethanol showed the presence of predominant alpha-helical structure and its occurrence in the alpha + beta class of protein. The far and near UV spectra of pennisetin in ethanol: trifluoroethanol also supported this observation. However pennisetin showed the presence of some helical structure in 8 M urea which is known to be a highly unordered structure forming solvent. A decrease in alpha helical content of native pennisetin was observed with rise in temperature from 5-75-degrees-C and this effect of temperature was found to be reversible. A C-13 NMR spectrum of pennisetin in 70% ethanol suggested a high degree of molecular mobility in ethanol. Comparison of the cross polarization spectrum with the single pulse excitation spectrum suggested pennisetin to be a heterogeneous protein.

Effects of molecular size in solvation dynamics

The effects of molecular size on the dynamics of polar solvation are studied by using a microscopic theory which includes the translational relaxation modes of the solvent consistently. It is shown that while in the absence of the translational contribution the solvation rate increases with the size of the solute (in agreement with the conclusions of the nonequilibrium MSA theory),a complete reversal of the solute size dependence occurs when translational modes make a significant contribution to the solvent polarization relaxation.

Dynamics of activationless reactions in solution

Recent picosecond and subpicosecond laser spectroscopy experiments have revealed several chemically and biologically important reactions in solution in which the reaction potential surface does not present a barrier to the motion along the reaction coordinate.The dynamics of these reactions display diverse and interesting behavior. They include the dependence of relaxation rate on the solvent viscosity, the solvent polarity, the temperature, and the wavelength of the exciting light. In this article we review the recent developments in the theoretical description of activationless processes in solution and compare them with the available experimental results

Two forms of Pf1 Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit

Inovirus is a helical array of alpha-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Ab initio molecular orbital calculations on ion-molecule and ion pair-molecule complexes of the water-lithium cyanide system

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets were performed on a series of ion-molecule and ion pair-molecule complexes for the H2O + LiCN system. Stabilisation energies (with counter-poise corrections), geometrical parameters, internal force constants and harmonic vibrational frequencies were evaluated for 16 structures of interest. Although the interaction energies are smaller, the geometries and relative stabilities of the monohydrated contact ion pair are reminiscent of those computed for the complexes of the individual ions. Thus, interaction of the oxygen lone pair with lithium leads to a highly stabilised C2v structure, while the coordination of water to the cyanide ion involves a slightly non-linear hydrogen bond. Symmetrical bifurcated structures are computed to be saddle points on the potential energy surface, and to have an imaginary frequency for the rocking mode of the water molecule. On optimisation the geometries of the solvent shared ion pair structures (e.g. Li+cdots, three dots, centered OH2cdots, three dots, centered CN−) revealed a proton transfer from the water molecule leading to hydrogen bonded forms such as Li-O-Hcdots, three dots, centered HCN. The variation in the force constants and harmonic frequencies in the various structures considered are discussed in terms of ion-molecular and ion pair-molecule interactions.

Desorptio/fotoionisaatio ilmanpaineessa takavarikoitujen huumausaineiden, steroidien ja räjähdysaineiden tutkimuksessa

Tutkimuksen tarkoituksena oli selvittää desorptio/fotoionisaatio ilmanpaineessa tekniikan (engl. desorption atmospheric pressure photoionization, DAPPI) soveltuvuutta rikosteknisen laboratorion näytteiden analysointiin. DAPPI on nopea massaspektrometrinen ionisaatiotekniikka, jolla voidaan tutkia yhdisteitä suoraan erilaisilta pinnoilta. DAPPI:ssa käytetään lämmitettyä mikrosirua, joka suihkuttaa höyrystynyttä liuotin- ja kaasuvirtausta kohti näytettä. Näytteen pinnan komponentit desorboituvat lämmön vaikutuksesta, jonka jälkeen ionisoituminen tapahtuu VUV-lampun emittoimien fotonien avulla.DAPPI:lla tutkittiin takavarikoituja huumausaineita, anabolisia steroideja ja räjähdysaineita sekä niiden jäämiä erilaisilta pinnoilta. Lisäksi kartoitettiin DAPPI:n mahdollisuuksia ja rajoituksia erilaisille näytematriiseille ilman näytteiden esikäsittelyä. Takavarikoitujen huumausaineiden tutkimuksessa analysoitiin erilaisia tabletteja, jauheita, kasvirouheita, huumekasveja (khat, oopium, kannabis) ja sieniä. Anabolisia steroideja tunnistettiin tableteista sekä ampulleista, jotka sisälsivät öljymäistä nestettä. Jauheet ripoteltiin kaksipuoliselle teipille ja analysoitiin siltä. Muut näytteet analysoitiin sellaisenaan ilman minkäänlaista esikäsittelyä, paitsi nestemäisten näytteiden kohdalla näyte pipetoitiin talouspaperille, joka analysoitiin DAPPI:lla. DAPPI osoittautui nopeaksi ja yksinkertaiseksi menetelmäksi takavarikoitujen huumausaineiden ja steroidien analysoimisessa. Se soveltui hyvin rikoslaboratorion erityyppisten näytteiden rutiiniseulontaan ja helpotti erityisesti huumekasvien ja öljymäisten steroidiliuosten tutkimusta. Massaspektrometrin likaantuminen pystyttiin ehkäisemään säätämällä näytteen etäisyyttä sen suuaukosta. Likaantumista ei havaittu huolimatta näytteiden korkeista konsentraatioista ja useita kuukausia jatkuneista mittauksista. Räjähdysaineiden tutkimuksessa keskityttiin seitsemän eri räjähdysaineen DAPPI-MS-menetelmän kehitykseen; trinitrotolueeni (TNT), nitroglykoli (NK), nitroglyseriini (NG), pentriitti (PETN), heksogeeni (RDX), oktogeeni (HMX) ja pikriinihappoä Nämä orgaaniset räjähteet ovat nitraattiyhdisteitä, jotka voidaan jakaa rakenteen puolesta nitroamiineihin (RDX ja HMX), nitroaromaatteihin (TNT ja pikriinihappo) sekä nitraattiestereihin (PETN, NG ja NK). Menetelmäkehityksessä räjähdysainelaimennokset pipetoitiin polymetyylimetakrylaatin (PMMA) päälle ja analysoitiin siitä. DAPPI:lla tutkittiin myäs autenttisia räjähdysainejäämiä erilaisista matriiseista. DAPPI:lla optimoitiin jokaiselle räjähdysaineelle sopiva menetelmä ja yhdisteet saatiin näkymään puhdasaineina. Räjähdysainejäämien analysoiminen erilaisista rikospaikkamateriaaleista osoittautui haastavammaksi tehtäväksi, koska matriisit aiheuttivat itsessään korkean taustan spektriin, josta räjähdysaineiden piikit eivät useimmiten erottuneet tarpeeksi. Muut desorptioionisaatiotekniikat saattavat soveltua paremmin haastavien räjähdysainejäämien havaitsemiseksi.

Desorption from concentrated polymer solutions in good and poor solvents

The objective of the study was to investigate the effects of the nature of solvent and polymer concentration on the mass-transfer coefficients in desorption of solvents and to develop a correlation to predict them. Desorption was experimentally studied in a Lewis cell with concentrated binary solutions of polymer in good and poor solvents. The range of parameters covered are polymer weight fraction between 0.25 and 0.6, Reynolds number between 3 and 100; Schmidt number between 1.4 X lo6 and 2.5 X lo8, and Sherwood number between 3.5 X lo2 and 1.2 X lo4. Desorption from moderately concentrated solutions (polymer weight fraction -0.25) is gas-phase controlled. Studies with more concentrated solutions showed that the effects of solvent and concentration were such that corrections due to concentration-dependent diffusivity and viscosity as well as high flux had to be applied to the mass-transfer coefficients before they could be correlated.

Electronic absorption and emission spectroscopic investigations of the interaction of the fullerenes, C60 and C70, with amines and aromatic molecules

Electronic absorption spectroscopy and fluorescence spectroscopy have been used to investigate the interaction of the fullerenes C60 and C70 with diethylaniline, and with aromatic solvents such as benzene. C60 interacts weakly with aromatic amines in the ground state while C70 does not interact at all. Steady state fluorescence emission and lifetime measurements show that both C60 and C70 form excited state complexes (exciplexes) with the amines in non-aromatic solvents such as methylcyclohexane, but not in benzene. In benzene, only fluorescence quenching is observed due to the interaction between the π systems of the aromatic solvent and the fullerene in the ground state. This is also borne out by the systematic study of solvent effects on the absorption and emission spectra of the fullerenes.

Interaction of C60 and C70 with aromatic amines in the ground and excited states. Evindence for fullerene—benzene interaction in the ground state

While C60 interacts with aromatic amines such as dimethylaniline in the ground state, C70 does not. Fluorescence spectroscopic studies, including lifetime measurements, show the formation of exciplexes of both C60 and C70 with aromatic amines in nonaromatic solvents such as methylcyclohexane. Exciplexes are however not formed in benzene solvent, due to π—π interaction between benzene and the fullerene. Based on spectroscopic absorption measurements, it is shown that both C60 and C70 do indeed interact with benzene in the ground state.

Two forms of PF1 INOVIRUS: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the assymetric unit

Inovirus is a helical array of agr-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Molecular expression for dielectric friction on a rotating dipole: Reduction to the continuum theory

Recently we presented a microscopic expression for dielectric friction on a rotating dipole. This expression has a rather curious structure, involving the contributions of the transverse polarization modes of the solvent and also of the molecular length scale processes. It is shown here that under proper limiting conditions, this expression reduces exactly to the classical continuum model expression of Nee and Zwanzig [J. Chem. Phys. 52, 6353 (1970)]. The derivation requires the use of the asymptotic form of the orientation‐dependent total pair correlation function, the neglect of the contributions of translational modes of the solvent, and also the use of the limit that the size of the solvent molecules goes to zero. Thus, the derivation can be important in understanding the validity of the continuum model and can also help in explaining the results of a recent computer simulation study of dielectric relaxation in a Brownian dipolar lattice.

Solvation dynamics in a Brownian dipolar lattice. Comparison between computer simulation and various molecular theories of solvation dynamics

Several recent theoretical and computer simulation studies have considered solvation dynamics in a Brownian dipolar lattice which provides a simple model solvent for which detailed calculations can be carried out. In this article a fully microscopic calculation of the solvation dynamics of an ion in a Brownian dipolar lattice is presented. The calculation is based on the non‐Markovian molecular hydrodynamic theory developed recently. The main assumption of the present calculation is that the two‐particle orientational correlation functions of the solid can be replaced by those of the liquid state. It is shown that such a calculation provides an excellent agreement with the computer simulation results. More importantly, the present calculations clearly demonstrate that the frequency‐dependent dielectric friction plays an important role in the long time decay of the solvation time correlation function. We also find that the present calculation provides somewhat better agreement than either the dynamic mean spherical approximation (DMSA) or the Fried–Mukamel theory which use the simulated frequency‐dependent dielectric function. It is found that the dissipative kernels used in the molecular hydrodynamic approach and in the Fried–Mukamel theory are vastly different, especially at short times. However, in spite of this disagreement, the two theories still lead to comparable results in good agreement with computer simulation, which suggests that even a semiquantitatively accurate dissipative kernel may be sufficient to obtain a reliable solvation time correlation function. A new wave vector and frequency‐dependent dissipative kernel (or memory function) is proposed which correctly goes over to the appropriate expressions in both the single particle and the collective limits. This form is expected to lead to better results than all the existing descriptions.

Structure and conformation of the calcium complex of cyclo(Ala-Leu-Pro-Gly)2 in two crystal forms

Crystal structures of two different forms of the calcium perchlorate complex of cyclo(Ala-Leu-Pro-Gly)2 have been determined and refined using X-ray crystallographic techniques. Orthorhombic form: C32H52N8O8.Ca(ClO4)2.7H2O.2CH3OH, space group C222(1), a = 14.366, b = 18.653, c = 19.824 A, Z = 4, R = 0.068 for 2208 observed reflections. Monoclinic form: C32H52N8O8.Ca(ClO4)2.4H2O, space group C2, a = 21.096, b = 10.182, c = 11.256 A, beta = 103.33 degrees, Z = 2, R = 0.075 for 2165 observed reflections. The cyclic peptide molecule in both the structures has the form of a twofold symmetric, slightly elongated bowl. Type II' beta-turns, involving Gly and Ala at the corners, exist at the two ends of the molecule. The interior of the molecule is substantially hydrophilic, and the external surface of the bowl is largely hydrophobic. The calcium ion is located at the centre of the mouth of the bowl-like molecule. In both crystal forms, four peptide carbonyl oxygens from the cyclic peptide and two solvent oxygens coordinate to the metal ion. The mode of complexation may be described as incomplete encapsulation as, for example, in the case of metal complexes of antamanide. In the crystal structures the complex ions are held together by hydrogen bonds involving perchlorate ions and water molecules. The molecular structure observed in the crystals is entirely consistent with the results of solution studies, which also indicate the conformation of the cyclic peptide in the complex to be similar to that of the uncomplexed molecule.

Structure of Sesbania Mosaic Virus at 4·7 Å Resolution and Partial Sequence of the Coat Protein

Sesbania mosaic virus (SMV) is a plant virus infecting Sesbania grandiflora plants in Andhra Pradesh, India. Amino acid sequence of the tryptic peptides of SMV coat protein were determined using a gas phase sequenator. These sequences showed identical amino acids at 69% of the positions when aligned with the corresponding residues of southern bean mosaic virus (SBMV).Crystals diffracting to better than 3 Å resolution were obtained by precipitating the virus with ammonium sulphate. The crystals belonged to rhombohedral space group R3 with α = 291·4 Å and α = 61·9°. Three-dimensional X-ray diffraction data on these crystals were collected to a resolution of 4·7 Å, using a Siemens-Nicolet area detector system. Self-rotation function studies revealed the icosahedral symmetry of the virus particles, as well as their precise orientation in the unit cell. Cross-rotation function and modelling studies with SBMV showed that it is a valid starting model for SMV structure determination. Low resolution phases computed using a polyalanine model of SBMV were subjected to refinement and extension by real-space electron density averaging and solvent flattening. The final electron density map revealed a polypeptide fold similar to SBMV. The single disulphide bridge of SBMV coat protein is retained in SMV. Four icosahedrally independent cation binding sites have been tentatively identified. Three of these sites, related by a quasi threefold axis, are also found in SBMV. The fourth site is situated on the quasi threefold axis. Aspartic acid residues, which replace Ile218 of SBMV from the quasi threefold-related subunits are suitable ligands to the cation at this site

Folding of a Donor-Containing Ionene by Intercalation with an Acceptor

Cationic ionenes that bear electron-rich 1,5-dialkoxynaphthalene (DAN) units within the alkylene segment were allowed to interact with different types of electron-deficient, acceptor-containing molecules in an effort to realize intercalation-induced folding of the ionenes; the collapse of the chains was expected to occur in such a way that the donor and acceptor units become arranged in an alternating fashion. Several acceptor-bearing molecules were prepared by the derivatization of pyromellitic dianhydride and naphthalene tetracarboxylic dianhydride with two different oligoethylene glycol monomethyl ether monoamines. This yielded acceptor molecules with different water solubility and allowed the examination of solvophobic effects in the folding process. UV/Vis spectroscopic studies were carried out by using a 1:1 mixture of the DAN-ionenes and different acceptor molecules in water/DMSO solvent mixtures. The intensity of the charge-transfer (CT) band was seen to increase with the water content in the solvent mixture, thereby suggesting that the intercalation is indeed aided by solvophobic effects. The naphthalene diimide (NDI) bearing acceptor molecules consistently formed significantly stronger CT complexes when compared to the pyromellitic diimide (PDI) bearing acceptor molecules, which is a reflection of the stronger pi-stacking tendency of the former. AFM studies of drop-cast films of different ionene-acceptor combinations revealed that compact folded structures are formed most effectively under conditions in which the strongest CT complex is formed.