Mechanism and kinetics of excited-state relaxation in internally hydrogen-bonded molecules - 2-/2'-hydroxy-5'-methylphenyl/-benzotriazole in solution
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Huston, A. L.↗
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Picosecond kinetics of excited state decay processes in internally hydrogen-bonded polymer photostabilizers
A construction of economically practical solar energy conversion devices could be based on the employment of inexpensive, visible-radiation transparent, durable, light-fast materials. Difficulties arise in connection with the availability of such materials. Plastics which are not particularly susceptible to solar ultraviolet degradation are, in general, expensive, while less expensive optically transparent films are susceptible to deterioration when exposed to solar radiation. However, techniques are known for protecting polymers from photochemical degradation. According to these techniques, the composition or structure of polymeric material is modified by incorporation of photostabilizers. Two classes of ultraviolet absorbers are used as commercial photostabilizers. These classes include 2-hydroxybenzophenone (HB) and 2-(2-prime -hydroxyphenyl)benzotriazole (HPB). The present investigation is concerned with the results of spectroscopic and kinetics measurements related to the study of the mechanism of excited-state relaxation of polymer photostabilizers in the class HB and HPB.
Huston, A. L.↗
Direct observation of the excited-state proton transfer and decay kinetics of internally hydrogen-bonded photostabilizers in copolymer films
The excited-state dynamics of a 2-hydroxyphenylbenzotriazole (HPB) photostabilizer copolymerized with polystyrene are reported. HPB fluorescence from these copolymer films is observed at approximately 630 nm, characteristic of the proton-transferred excited state of HPB, and it has a risetime of less than 10 ps and a decay time of 28 + or - 4 ps at room temperature. Measurement of the relative fluorescence quantum yield as a function of temperature gives the activation energy for nonradiative decay of this state to be E/hc = 259 + or 25/cm.
Oconnor, D. B.↗
Process for selective monoaddition to silanes containing two silicon-hydrogen bonds and products thereof
A process for the selective monoadditon of an olefin or acetylene to a siloxane which contains two reactive Si--H bonds to produce a product in which only one of the two Si--H functions has added across the olefin or acetylene is disclosed. A process for making unsymmetrical siloxanes from symmetrical dihydrosiloxanes and products of both of these processes are also disclosed. Products are represented by the formula I in which R.sup.1 and R.sup.4 are different: ##STR1##.
Crivello, James V.↗
Manipulating hydrogen bond dissociation rates and mechanisms in water dimer through vibrational strong coupling
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Qi Yu↗
An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals
Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.
Jackels, C. F.↗
An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals
Ab initio quantum chemical techniques have been used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types were identified. Basic sets of polarized double-zeta quality and large scale configuration interaction wave functions have been utilized. Based upon electronic energies, the covalently-bonded HOOOH species is found to be 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen-bonded HO-HO2 species is found to have an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen-bonded form is found to be planar, to possess one relatively 'normal' hydrogen bond, and to have lowest energy 3A-prime and 1A-prime states that are essentially degenerate. The 1A-double prime and 3A-double prime excited states produced by rotation of the unpaired OH electron into the molecular plane are found to be very slightly bound.
Jackels, C. F.↗
Structures of aspartic acid-96 in the L and N intermediates of bacteriorhodopsin: analysis by Fourier transform infrared spectroscopy
The light-induced difference Fourier transform infrared spectrum between the L or N intermediate minus light-adapted bacteriorhodopsin (BR) was measured in order to examine the protonated states and the changes in the interactions of carboxylic acids of Asp-96 and Asp-115 in these intermediates. Vibrational bands due to the protonated and unprotonated carboxylic acid were identified by isotope shift and band depletion upon substitution of Asp-96 or -115 by asparagine. While the signal due to the deprotonation of Asp-96 was clearly observed in the N intermediate, this residue remained protonated in L. Asp-115 was partially deprotonated in L. The C = O stretching vibration of protonated Asp-96 of L showed almost no shift upon 2H2O substitution, in contrast to the corresponding band of Asp-96 or Asp-115 of BR, which shifted by 9-12 cm-1 under the same conditions. In the model system of acetic acid in organic solvents, such an absence of the shift of the C = O stretching vibration of the protonated carboxylic acid upon 2H2O substitution was seen only when the O-H of acetic acid is hydrogen-bonded. The non-hydrogen-bonded monomer showed the 2H2O-dependent shift. Thus, the O-H bond of Asp-96 enters into hydrogen bonding upon conversion of BR to L. Its increased hydrogen bonding in L is consistent with the observed downshift of the O-H stretching vibration of the carboxylic acid of Asp-96.
NASA Discipline Exobiology↗
A Brief Review of Chaotropic vs. Kosmotropic Salts on the Degree of Saturation of Membrane Fatty Acids: Implications for Preservation of Environmental Biomarkers
Water activity is well known to have a significant impact on habitability, due to the presence of salts. However, salt composition is also important for habitability, as it can impact microbial activity and biomolecular interactions since certain salts are known to disrupt hydrogen bonding. Chaotropic agents disrupt hydrogen bonding in aqueous solutions leading to increased entropy (chaos) whereas kosmotropic agents are compounds that promote hydrogen bonding (order). The Hofmeister series (Fig. 1) shows the ordering of ions in terms of their ability to stabilize and induce precipitation or aggregation of proteins.
M B Wilhelm↗
Database of non-canonical base pairs found in known RNA structures
Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.
NASA Discipline Exobiology↗
Quantitation of buried contamination by use of solvents. Part 1: Solvent degradation of amine cured epoxy resins
The solubility and/or swelling of cured epoxy resins was studied using the solubility parameter method. Determination of solubility parameters were found in order to select solvents for solvent-assisted degradation of cured epoxy polymers used in spacecraft. A method for improving recovery of seeded spores is suggested for assay of buried contaminants. Three commercial epoxy resins were cured using four different alkyl amines. For each resin-amine combination, three levels of amine were used, corresponding to 1/3, 2/3, and all of the amine required to react with the oxirane groups of the resin. The solubility parameters of the 36 resulting model compounds were determined in poorly and moderately hydrogen-bonded solvents. No strongly hydrogen-bonded solvents caused dissolution or swelling. The tolerance of cured resins is discussed in terms of polymer structure.
Rheineck, A. E.↗
Base pairing and base mis-pairing in nucleic acids
In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.
Wang, A. H. J.↗
Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations
In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.
NASA Discipline Exobiology↗
Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase
Thiamin pyrophosphate (TPP), the biologically active form of vitamin BI, is a cofactor of enzymes catalyzing reactions involving the cleavage of a carbon-carbon bond adjacent to an oxo group. TPP-dependent enzymes show a common mechanism of TPP activation by: (1) forming the ionic N-H...O(sup -) hydrogen bonding between the N1' atom of the aminopirymidine ring of the coenzyme and intrinsic gamma-carboxylate group of glutamate and (2) imposing an "active" V-conformation that brings the N4' atom of the aminopirymidine to the distance required for the intramolecular C-H.. .N hydrogen bonding with the thiazolium C2 atom. Within these two hydrogen bonds that rapidly exchange protons, protonation of the N1' atom is strictly coordinated with the deprotonation of the 4' -amino group and eventually abstraction of the proton from C2. The human pyruvate dehydrogenase Elp, component of human pyruvate dehydrogenase complex, catalyzes the irreversible decarboxylation of the pyruvate followed by the reductive acetylation of the lipoyl group of dihydrolipoyl acyltransferase. Elp is alpha(sub 2)beta(sub2)-heterotetrameric with a molecular mass of I54 kDa, which has two catalytic sites, each providing TPP and magnesium ion as cofactors and each formed on the interface between the PP and PYR domains. The dynamic nonequivalence of two otherwise chemically equivalent catalytic sites has been observed and the flip-flop mechanism was suggested, according to which two active sites affect each other and in which different steps of the catalytic reaction are performed in each of the sites at any given moment. Based on specific futures of human pyruvate dehydrogenase including rigid and flexible connections between domains that bind the cofactor we propose a mechanistic model for the flip-flop action of this enzyme. We postulate that the dynamic protein environment drives the exchange of tautomers in the 4' -aminopyrimidine ring of the cofactor through a concerted shuttl-like motion of tightly connected domains. The dynamic exchange of those tautomers, in turns, is required during the reactions of pyruvate decarboxylation and reductive acetylation of lipoamide. Thus the shuttle-like motion of the domains is coordinated with the reactions of decarboxylation and acetylation, which are carried out in each of the cofactor sites resulting in a flip-flop action of the enzyme. The structure-derived mechanism of action of human pyruvate dehydrogenase may be likely common for other TPP-dependent enzymes.
Dominiak, Paulina↗
Composition and properties of the so-called 'diamond-like' amorphous carbon films
The composition of amorphous 'diamond-like' films made by direct low energy ion beam deposition, R.F. discharge and sputtering was determined by nuclear reaction analysis, IR spectroscopy and microcombustion chemical analysis. The nuclear reaction analysis showed very similar hydrogen depth profiles for all three types of samples. The atomic ratio of hydrogen to carbon was approximately 0.2 at the film surface and rose to approximately 1.0 at a depth of 500 A. The integrated intensity of the C-H stretching band at about 2900 per cm indicates that the amount of chemically bonded hydrogen is less than the total hydrogen content. Combustion analysis confirmed the overall atomic ratio of hydrogen to carbon determined by nuclear reaction analysis. The chemical state of the non-bonded hydrogen was not determined; however, the effective diffusion coefficient computed from the hydrogen depth profile was extremely low. This indicates either that the films are exceedingly impermeable or that the non-bonded hydrogen requires an additional activated step to leave the films, e.g., desorption or chemical reaction.
Angus, J. C.↗
Silica/Polymer and Silica/Polymer/Fiber Composite Aerogels
Aerogels that consist, variously, of neat silica/polymer alloys and silica/polymer alloy matrices reinforced with fibers have been developed as materials for flexible thermal-insulation blankets. In comparison with prior aerogel blankets, these aerogel blankets are more durable and less dusty. These blankets are also better able to resist and recover from compression . an important advantage in that maintenance of thickness is essential to maintenance of high thermal-insulation performance. These blankets are especially suitable as core materials for vacuum- insulated panels and vacuum-insulated boxes of advanced, nearly seamless design. (Inasmuch as heat leakage at seams is much greater than heat leakage elsewhere through such structures, advanced designs for high insulation performance should provide for minimization of the sizes and numbers of seams.) A silica/polymer aerogel of the present type could be characterized, somewhat more precisely, as consisting of multiply bonded, linear polymer reinforcements within a silica aerogel matrix. Thus far, several different polymethacrylates (PMAs) have been incorporated into aerogel networks to increase resistance to crushing and to improve other mechanical properties while minimally affecting thermal conductivity and density. The polymethacrylate phases are strongly linked into the silica aerogel networks in these materials. Unlike in other organic/inorganic blended aerogels, the inorganic and organic phases are chemically bonded to each other, by both covalent and hydrogen bonds. In the process for making a silica/polymer alloy aerogel, the covalent bonds are introduced by prepolymerization of the methacrylate monomer with trimethoxysilylpropylmethacrylate, which serves as a phase cross-linker in that it contains both organic and inorganic monomer functional groups and hence acts as a connector between the organic and inorganic phases. Hydrogen bonds are formed between the silanol groups of the inorganic phase and the carboxyl groups of the organic phase. The polymerization process has been adapted to create interpenetrating PMA and silica-gel networks from monomers and prevent any phase separations that could otherwise be caused by an overgrowth of either phase. Typically, the resulting PMA/silica aerogel, without or with fiber reinforcement, has a density and a thermal conductivity similar to those of pure silica aerogels. However, the PMA enhances mechanical properties. Specifically, flexural strength at rupture is increased to 102 psi (=0.7 MPa), about 50 times the flexural strength of typical pure silica aerogels. Resistance to compression is also increased: Applied pressure of 17.5 psi (=0.12 MPa) was found to reduce the thicknesses of several composite PMA/silica aerogels by only about 10 percent.
Ou, Danny↗
Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes
We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.
NASA Discipline Number 52-20↗
The Application B3LYP to Large Systems
The application of density functional theory (DFT), using the B3LYP functional, to a series of chemical problems is described. The first involves the calculation of silica-adsorbate bond energies, including both chemical bonds and weak hydrogen bonding. The calculation of vibrational frequencies for large organic systems is discussed. For the closed shell neutral systems, the B3LYP results are similar to the self- consistent- field results, however, for the positive ions, only the B3LYP level of theory is accurate and sufficiently inexpensive to allow the study of large systems. The final application involves the calculation of successive metal-ligand bond energies. The B3LYP bond energies and entropies are shown to be in good agreement with experiment.
Bauschlicher, Charles W.↗