Wafer-scale epitaxial modulation of quantum dot density.

Precise control of the properties of semiconductor quantum dots (QDs) is vital for creating novel devices for quantum photonics and advanced opto-electronics. Suitable low QD-densities for single QD devices and experiments are challenging to control during epitaxy and are typically found only in limited regions of the wafer. Here, we demonstrate how conventional molecular beam epitaxy (MBE) can be used to modulate the density of optically active QDs in one- and two- dimensional patterns, while still retaining excellent quality. We find that material thickness gradients during layer-by-layer growth result in surface roughness modulations across the whole wafer. Growth on such templates strongly influences the QD nucleation probability. We obtain density modulations between 1 and 10 QDs/µm2 and periods ranging from several millimeters down to at least a few hundred microns. This method is universal and expected to be applicable to a wide variety of different semiconductor material systems. We apply the method to enable growth of ultra-low noise QDs across an entire 3-inch semiconductor wafer.

Analytical modeling of light transport in scattering materials with strong absorption.

We have investigated the transport of light through slabs that both scatter and strongly absorb, a situation that occurs in diverse application fields ranging from biomedical optics, powder technology, to solid-state lighting. In particular, we study the transport of light in the visible wavelength range between 420 and 700 nm through silicone plates filled with YAG:Ce3+ phosphor particles, that even re-emit absorbed light at different wavelengths. We measure the total transmission, the total reflection, and the ballistic transmission of light through these plates. We obtain average single particle properties namely the scattering cross-section σs, the absorption cross-section σa, and the anisotropy factor µ using an analytical approach, namely the P3 approximation to the radiative transfer equation. We verify the extracted transport parameters using Monte-Carlo simulations of the light transport. Our approach fully describes the light propagation in phosphor diffuser plates that are used in white LEDs and that reveal a strong absorption (L/la > 1) up to L/la = 4, where L is the slab thickness, la is the absorption mean free path. In contrast, the widely used diffusion theory fails to describe this parameter range. Our approach is a suitable analytical tool for industry, since it provides a fast yet accurate determination of key transport parameters, and since it introduces predictive power into the design process of white light emitting diodes.

Reaction of uric acid with peroxynitrite and implications for the mechanism of neuroprotection by uric acid.

Peroxynitrite, a biological oxidant formed from the reaction of nitric oxide with the superoxide radical, is associated with many pathologies, including neurodegenerative diseases, such as multiple sclerosis (MS). Gout (hyperuricemic) and MS are almost mutually exclusive, and uric acid has therapeutic effects in mice with experimental allergic encephalomyelitis, an animal disease that models MS. This evidence suggests that uric acid may scavenge peroxynitrite and/or peroxynitrite-derived reactive species. Therefore, we studied the kinetics of the reactions of peroxynitrite with uric acid from pH 6.9 to 8.0. The data indicate that peroxynitrous acid (HOONO) reacts with the uric acid monoanion with k = 155 M(-1) s(-1) (T = 37 degrees C, pH 7.4) giving a pseudo-first-order rate constant in blood plasma k(U(rate))(/plasma) = 0.05 s(-1) (T = 37 degrees C, pH 7.4; assuming [uric acid](plasma) = 0.3 mM). Among the biological molecules in human plasma whose rates of reaction with peroxynitrite have been reported, CO(2) is one of the fastest with a pseudo-first-order rate constant k(CO(2))(/plasma) = 46 s(-1) (T = 37 degrees C, pH 7.4; assuming [CO(2)](plasma) = 1 mM). Thus peroxynitrite reacts with CO(2) in human blood plasma nearly 920 times faster than with uric acid. Therefore, uric acid does not directly scavenge peroxynitrite because uric acid can not compete for peroxynitrite with CO(2). The therapeutic effects of uric acid may be related to the scavenging of the radicals CO(*-)(3) and NO(*)(2) that are formed from the reaction of peroxynitrite with CO(2). We suggest that trapping secondary radicals that result from the fast reaction of peroxynitrite with CO(2) may represent a new and viable approach for ameliorating the adverse effects associated with peroxynitrite in many diseases.

Reaction of peroxynitrite with melatonin: A mechanistic study.

The pH profile of the peroxynitrite/melatonin reaction suggests that both peroxynitrous acid (ONOOH) and its anion (ONOO-) are reactive toward melatonin, but at physiological pH most of the reaction with melatonin involves ONOOH and the activated form of peroxynitrous acid (ONOOH). The formation of hydroxylated products (mainly 6-hydroxymelatonin) suggests that melatonin also reacts with ONOOH. The overall peroxynitrite/melatonin reaction is first-order in melatonin and first-order in peroxynitrite, but the hydroxylation of melatonin is presumed to be zero-order in melatonin. Melatonin is metabolized in the liver, mainly to 6-hydroxymelatonin, so we do not think this metabolite is a useful biomarker for melatonin's antioxidant activity; however, 6-hydroxymelatonin is a better chain-breaking antioxidant than melatonin and may contribute to the beneficial effects of melatonin in vivo. As is now well-known, CO2 modulates the reactions of peroxynitrite. The reaction of peroxynitrite with melatonin in the absence of added bicarbonate produces mainly 6-hydroxymelatonin and 1,2,3,3a,8, 8a-hexahydro-1-acetyl-5-methoxy-8a-hydroxypyrrolo[2,3-b]indole, with some isomeric 1,2,3,3a,8, 8a-hexahydro-1-acetyl-5-methoxy-3a-hydroxypyrrolo[2,3-b]indole. In the presence of added bicarbonate, product yields decrease and 6-hydroxymelatonin is not formed. These facts suggest that melatonin scavenges reactive species (such as CO3*- and *NO2) that are produced from the peroxynitrite/CO2 reaction. The spectrum of the melatoninyl radical cation is observed both in the absence and in the presence of added bicarbonate, suggesting that the melatoninyl radical cation is the initial product and the hydroxypyrrolo[2, 3-b]indole products are derived from it. Unlike tyrosine, where both nitrated and hydroxylated products can be isolated, nitromelatonin is not found in the final products from the melatonin/peroxynitrite reaction in either the absence or presence of added bicarbonate. However, we suggest that 2-hydroxy-3-nitro- and/or 2-hydroxy-3-peroxynitro-2,3-dihydromelatonin are formed as intermediates and subsequently decompose to give 1,2,3,3a,8, 8a-hexahydro-1-acetyl-5-methoxy-8a-hydroxypyrrolo[2,3-b]indole. Since peroxynitrite/CO2 governs the reactions of peroxynitrite in vivo, we suggest that the hydroxypyrrolo[2,3-b]indole products are the main products from the oxidation of melatonin by peroxynitrite-derived species in vivo, and that these products may serve as indexes for melatonin's antioxidant activity.

Direct and simultaneous ultraviolet second-derivative spectrophotometric determination of nitrite and nitrate in preparations of peroxynitrite.

We have determined the initial concentrations of nitrite and nitrate for three different methods of synthesizing peroxynitrite using an ultraviolet second-derivative spectroscopy method (Fig. 3). As expected, the net nitrogen balance in these preparations (Fig. 4) and the yields of nitrite and nitrate (Table II) indicate that, at pH 6.0, peroxynitrite decomposes to give essentially NO3-. Stock solutions of peroxynitrite prepared using method I (ozonation of azide) consistently contain more NO2- and NO3- than method II (isoamyl nitrite with hydrogen peroxide) and method III (hydrogen peroxide with nitrous acid). Method II gives the least amount of NO2- contaminants, and NO3- impurities are the lowest in method III (Table I).

Nitrosation by peroxynitrite: use of phenol as a probe.

Nitrosation is an important pathway in the metabolism of nitric oxide, producing S-nitrosothiols that may be critical signal transduction species. The reaction of peroxynitrite with aromatic compounds in the pH range of 5 to 8 has long been known to produce hydroxylated and nitrated products. However, we here present evidence that peroxynitrite also can promote the nitrosation of nucleophiles. We chose phenol as a substrate because the nitrosation reaction was first recognized during a study of the CO2-modulation of the patterns of hydroxylation and nitration of phenol by peroxynitrite (Lemercier et al., Arch. Biochem. Biophys. 345, 160-170, 1997). 4-Nitrosophenol, the principal nitrosation product, is detected at pH 7.0, along with 2- and 4-nitrophenols; 4-nitrosophenol becomes the dominant product at pH >/= 8.0. The yield of 4-nitrosophenol continues to increase even after pH 11.1, 1. 2 units above the pKa of phenol, suggesting that the phenolate ion, and not phenol, is involved in the reaction. Hydrogen peroxide is not formed as a by-product. The nitrosation reaction is zero-order in phenol and first-order in peroxynitrite, suggesting the phenolate ion reacts with an activated nitrosating species derived from peroxynitrite, and not with peroxynitrite itself. Under optimal conditions, the yields of 4-nitrosophenol are comparable to those of 2- and 4-nitrophenols, indicating that the nitrosation reaction is as significant as the nitration of phenolic compounds by peroxynitrite. Low concentrations of CO2 facilitate the nitrosation reaction, but excess CO2 dramatically reduces the yield of 4-nitrosophenol. The dual effects of CO2 can be rationalized if O=N-OO- reacts with the peroxynitrite anion-CO2 adduct (O=N-OOCO-2) or secondary intermediates derived from it, including the nitrocarbonate anion (O2N-OCO-2), the carbonate radical (CO*-3), and *NO2. The product resulting from these reactions can be envisioned as an activated intermediate X-N=O (where X is -OONO2, -NO2, or -CO-3) that could transfer a nitrosyl cation (NO+) to the phenolate ion. An alternative mechanism for the nitrosation of phenol involves the one-electron oxidation of the phenolate ion by CO*-3 to give the phenoxyl radical and the oxidation of O=N-OO- by CO*-3 to give a nitrosyldioxyl radical (O=N-OO*), which decomposes to give *NO and O2; the *NO then reacts with the phenoxyl radical giving nitrosophenol. Both mechanisms are consistent with the high yields of NO-2 and O2 during the alkaline decomposition of peroxynitrite and the potent inhibitory effect of N-3 on the nitrosation of phenol by peroxynitrite and peroxynitrite/CO2 adducts. The biological significance of the peroxynitrite-mediated nitrosations is discussed.

Carbon dioxide modulation of hydroxylation and nitration of phenol by peroxynitrite.

We have examined the formation of hydroxyphenols, nitrophenols, and the minor products 4-nitrosophenol, benzoquinone, 2,2'-biphenol, and 4,4'-biphenol from the reaction of peroxynitrite with phenol in the presence and absence of added carbonate. In the absence of added carbonate, the product yields of nitrophenols and hydroxyphenols have different pH profiles. The rates of nitration and hydroxylation also have different pH profiles and match the trends observed for the product yields. At a given pH, the sum of the rate constants for nitration and hydroxylation is nearly identical to the rate constant for the spontaneous decomposition of peroxynitrite. The reaction of peroxynitrite with phenol is zero-order in phenol, both in the presence and absence of added carbonate. In the presence of added carbonate, hydroxylation is inhibited, whereas the rate of formation and yield of nitrophenols increase. The combined maximum yield of o- and p-nitrophenols is 20 mol% (based on the initial concentration of peroxynitrite) and is about fourfold higher than the maximal yield obtained in the absence of added carbonate. The o/p ratio of nitrophenols is the same in the presence and absence of added carbonate. These results demonstrate that hydroxylation and nitration occur via two different intermediates. We suggest that the activated intermediate formed in the isomerization of peroxynitrous acid to nitrate, ONOOH*, is the hydroxylating species. We propose that intermediate 1, O=N-OO-CO2-, or secondary products derived from it, is (are) responsible for the nitration of phenol. The possible mechanisms responsible for nitration are discussed.

Inhibition of peroxynitrite-mediated oxidation of glutathione by carbon dioxide.

Peroxynitrite reacts with CO2 to from an adduct containing a weak O--O bond that can undergo homolytic and/or heterolytic cleavage to give other reactive intermediates. Because the peroxynitrite/CO2 reaction is fast and physiological concentrations of CO2 are relatively high, peroxynitrite-mediated oxidations of biological species probably involve the peroxynitrite-CO2 adduct and its subsequent reactive intermediates. We have examined the reaction of glutathione with peroxynitrite in the presence and absence of added bicarbonate. In the presence of added bicarbonate, CO2 competes with glutathione for peroxynitrite, resulting in a markedly decreased consumption of glutathione compared with that observed in the absence of added bicarbonate. However, the consumption of glutathione still is much higher than predicted from the assumption that the glutathione-peroxynitrite reaction is the only reaction that can consume glutathione in this system. These results suggest that glutathione partially, but not completely, traps intermediate(s) derived from the peroxynitrite and CO2 reaction. Some rate constants for the trapping of the intermediates are estimated by simulating the reactions, and possible mechanisms for the reaction of peroxynitrite with glutathione in the presence of added bicarbonate are discussed.

The catalytic role of carbon dioxide in the decomposition of peroxynitrite.

The fast reaction of peroxynitrite with CO2 and the high concentration of dissolved CO2 in vivo (ca. 1 mM) suggest that CO2 modulates most of the reactions of peroxynitrite in biological systems. The addition of peroxynitrite to CO2 produces of the adduct ONOO-CO2- (1). The production of 1 greatly accelerates the decomposition of peroxynitrite to give nitrate. We now show that the formation of 1 is followed by reformation of CO2 (rather than another carbonate species such as CO3 = or HCO3-). To show this, it is necessary to study systems with limiting concentrations of CO2. (When CO2 is present in excess, its concentration remains nearly constant during the decomposition of peroxynitrite, and the recycling of CO2, although it occurs, can not be detected kinetically). We find that CO2 is a true catalyst of the decomposition of peroxynitrite, and this fundamental insight into its action must be rationalized by any in vivo or in vitro reaction mechanism that is proposed. When the concentration of CO2 is lower than that of peroxynitrite, the reformation of CO2 amplifies the fraction of peroxynitrite that reacts with CO2. Even low concentrations of CO2 that result from the dissolution of ambient CO2 can have pronounced catalytic effects. These effects can cause deviations from predicted kinetic behavior in studies of peroxynitrite in noncarbonate buffers in vitro, and since 1 and other intermediates derived from it are oxidants and/or nitrating agents, some of the reactions attributed to peroxynitrite may depend on the availability of CO2.

Reactions of peroxynitrite with aldehydes as probes for the reactive intermediates responsible for biological nitration.

We have examined the reactions of peroxynitrite with short-chain aliphatic aldehydes to model the reaction of the peroxynitrite anion (ONOO-) with CO2. Aldehydes, like CO2, react rapidly with peroxynitrite and catalyze its decomposition. The pH dependence of the reaction is consistent with the addition of ONOO- (not ONOOH) to the carbonyl carbon atom of the free aldehyde forming a 1-hydroxyalkylperoxynitrite anion adduct (5), which structurally resembles the nitrosoperoxycarbonate adduct (1) formed from the reaction of ONOO- with CO2. Intermediate 5, or the secondary products derived from it, decays to give NO3- and regenerated aldehyde, with small but significant yields of H2O2, organic acids, and organic nitrates. In analogy with the peroxynitrite/CO2 system, it is suggested that 5 undergoes homolytic or heterolytic cleavage at the O-O bond, giving a caged radical pair [RCH(OH)O./ .NO2] (7) or intimate ion pair [RCH(OH)O -/+ NO2] (8). The radicals and ions in intermediates 7 and 8 can recombine within the solvent cage to form 1-hydroxyalkylnitrate [RCH(OH)ONO2] (6), which can then dissociate to give nitrate and regenerate the aldehyde. The aldehyde/ peroxynitrite adducts 5-8 mediate the oxidation of 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) but not the nitration of 4-hydroxyphenylacetate. The significance of these findings is discussed in relation to the mechanism(s) of the CO2-catalyzed isomerization of peroxynitrite to nitrate and biological nitrations involving peroxynitrite/CO2 adducts.

Carbon dioxide catalysis of the reaction of peroxynitrite with ethyl acetoacetate: an example of aliphatic nitration by peroxynitrite.

The reaction of peroxynitrite anion (O=N-OO-) with CO2 results in the formation of an unstable nitrosoperoxycarbonate anion adduct, O=N-OOCO-2 (1). Adduct 1 can serve as a source for several reactive intermediates, including the nitrocarbonate anion (O2N-OCO-2), the carbonate radical ion/nitrogen dioxide radical pair, and the nitronium ion/carbonate ion pair. One or more of these reactive intermediates mediate(s) electrophilic nitrations, for example of tyrosine residues in proteins, which is often observed in peroxynitrite-producing systems. We here report, for the first time, the nitration of an aliphatic substrate, ethyl acetoacetate, by peroxynitrite. The yield of nitration is markedly enhanced in the presence of added carbonate. The major product of this reaction is ethyl 2-nitroacetoacetate. The importance of this reaction is discussed in relation to the possible aliphatic nitrations of amines, sugars, thiols, and thioethers in peroxynitrite-producing biological systems.

Synthesis of peroxynitrite in a two-phase system using isoamyl nitrite and hydrogen peroxide.

A new method for the preparation of high concentrations of peroxynitrite (up to 1 M) is described. The synthesis uses a two-phase system and involves a displacement reaction by the hydroperoxide anion (in the aqueous phase) on isoamyl nitrite (in the organic phase). The product peroxynitrite remains in the aqueous phase, whereas isoamyl alcohol forms a new organic phase along with the unreacted isoamyl nitrite. The aqueous phase contains some 0.15 M isoamyl alcohol and the unreacted hydrogen peroxide, but no isoamyl nitrite. Removal of isoamyl alcohol or traces of isoamyl nitrite is accomplished by washing the aqueous phase with dichloromethane, chloroform, or hexane. A near total removal of hydrogen peroxide is then achieved by passing the solutions through a short column of manganese dioxide. The peroxynitrite in these postprocessed solutions has broad absorption spectrum with a maximum around 302 nm, follows a characteristic first-order decomposition at pH 7.2 and 25 degrees C (k = 0.34 +/- 0.1 s-1), and reacts with organic compounds to give either nitrated or one-electron transfer products. When stored frozen at -20 degrees C, these peroxynitrite solutions decompose at a rate of about 1.7 % per day and should be used within 2-4 weeks. For short-term storage of about 1 week or less, these solutions can be stored at refrigerator temperatures (approximately 5 degrees C) where peroxynitrite has a half-life of about 7 days.

Acceleration of peroxynitrite oxidations by carbon dioxide.

Stopped-flow kinetic studies of the isomerization of peroxynitrite to give nitrate have been performed in carbonate-enriched buffers using pH jump and carbonic anhydrase as probes. The data are consistent with the reaction of CO2 and the peroxynitrite anion rapidly forming an unstable nitrosoperoxy-carbonate anion adduct, O=N-OOCO2- (1). The CO2 catalysis of the isomerization of peroxynitrite is not accompanied by the formation of nitrite, hydrogen peroxide, or other hydroperoxidic material like peroxycarbonate. The reaction proceeds via the transient formation of an oxidant or oxidants that is (are) capable of promoting electrophilic nitration reactions. We propose that O=N-OOCO2- rearranges to give a nitrocarbonate anion, O2N-OCO2- (2) which in turn, may serve as the proximal oxidant in biological systems that produce peroxynitrite. At least four different mechanistic classes of reactions that have been ascribed to peroxynitrite can be envisioned to involve 2: (a) hydrolysis to nitrate, (b) one-electron or (c) two-electron oxidations, and (d) electrophilic nitration. Given the fast reaction of peroxynitrite with carbon dioxide and the ubiquitous presence of the latter, the role of CO2 cannot be neglected in complex peroxynitrite reactions in vitro and in vivo.

Competitive reactions of peroxynitrite with 2'-deoxyguanosine and 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodG): relevance to the formation of 8-oxodG in DNA exposed to peroxynitrite.

We have examined the formation of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodG) in reactions of peroxynitrite with 2'-deoxyguanosine (dG) and calf-thymus DNA. Peroxynitrite reacts with dG at neutral pH, but this reaction does not result in the buildup of 8-oxodG. We also do not find any evidence for the formation of 8-oxodG in calf-thymus DNA upon exposure to peroxynitrite. When 8-oxodG is mixed with 1000-fold excess dG and then allowed to react with peroxynitrite, about 50% of the 8-oxodG is destroyed. The preferential reaction of 8-oxodG is also evident when dG in calf-thymus DNA is partially oxidized in an Udenfriend system and then allowed to react with peroxynitrite. We suggest that 8-oxodG is not produced in peroxynitrite-mediated oxidations of dG and DNA or that it is produced but then is rapidly consumed in further reactions with peroxynitrite. Oxidized DNA bases frequently can be more oxidation sensitive than their corresponding progenitors and, therefore, may be present at] low steady-state concentrations and not represent stable markers of oxidative stress status. The importance of the 8-oxodG/peroxynitrite reaction is discussed in relation to the formation of more stable, secondary oxidation products that might be more useful markers of DNA damage.

Novel kinetics in a biomimetic redox reaction involving NADH and tetrazolium salts in aqueous micellar solutions.

Aqueous micelles of Triton X-100 are shown to catalyze the redox reaction between NADH and 2-p-iodophenyl-3-p-nitrophenyl-5-phenyltetrazolum chloride (INT) at neutral pH. The reaction exhibits a first-order dependence on NADH when INT is saturating; conversely, when NADH is saturating, the dependence is strictly second-order with respect to INT. The second-order dependence of the reaction on INT is also evident in situations where micelles of a cationic detergent are used in place of Triton X-100. The available kinetic evidence indicates the transient formation of a central complex involving the addition of two molecules of INT and one molecule of NADH to a "site" on the micelle where they are held together until completion of the redox process. However, the reaction does not seem to proceed by successive 1-e- steps, suggesting that the second-order dependence on INT has no bearing on the mechanism of redox process. The transfer of reducing equivalents between NADH and INT is shown to be direct and quantitative, with the redox steps confined to a microenvironment, as in the case of enzymatic NAD(P)H-dependent reactions. A mechanism consistent with the hydridic nature of the migrating hydrogen from the C(4) position of the dihydropyridine nucleus of NADH is proposed, assuming that only one molecule of INT in the central complex participates in the actual redox process and that the other molecule of INT acts as a cocatalyst by way of providing the necessary "basicity" at the reaction site.

What does ozone react with at the air/lung interface? Model studies using human red blood cell membranes.

We exposed human red blood cell (RBC) membranes to low levels of ozone and measured the oxidative damage that occurs to the proteins and the unsaturated lipids that are present. Oxidative damage to proteins causes significant decreases in the content of thiol groups, the fluorescence of protein-tryptophan residues, and the activity of membrane-bound acetylcholinesterase. Oxidative damage to lipids causes changes in some of the unsaturated fatty acids (UFA) in the lipid fraction of these RBC membranes. Significant amounts of hexanal, heptanal, and nonanal are formed from the ozonation of UFA. Although no decrease in the amount of oleate is detected, it does undergo ozonation to yield nonanal; thus, as would be expected, product appearance is a more sensitive measure of ozonation than is substrate disappearance. These results imply that both proteins and unsaturated lipids undergo simultaneous and competitive ozonation in human RBC membranes when ozone is the limiting reactant. The ratios of reaction of ozone with different targets can be predicted in reasonably good agreement with the observed values using calculations (W. A. Pryor and R. M. Uppu (1993) J. Biol. Chem. 268, 3120-3126; R. M. Uppu and W. A. Pryor (1994) Chem. Res. Toxicol. 7, 47-55) that take into account the reactivities and relative amounts of protein and lipid functionalities present in the RBC membranes. Similar calculations are used to predict the reaction of ozone with unsaturated lipids and proteins at the air/lung interface, and both UFA and proteins are predicted to react with ozone in the lung, as in RBC membranes.