CIRCUMSTELLAR AND INTERSTELLAR SYNTHESIS OF ORGANIC MOLECULES

We review the formation and evolution of complex circumstellar and interstellar molecules. A number of promising chemical routes are discussed which may lead to the formation of polycyclic aromatic hydrocarbon molecules, fullerenes, and unsaturated hydrocarbon chains in the outflows from stars. Some of the problems with these chemical schemes are pointed out as well. We also review the role of grains in the formation of complex molecules in interstellar molecular clouds. This starts with the formation of simple molecules in an ice grain mantle. UV photolysis and/or thermal polymerization can convert some of these simple molecules into more complex polymeric structures. Some of these species may be released to the gas phase, particularly in the warm regions around newly formed stars. Methanol and formaldehyde seem to play an important role in this drive towards molecular complexity and their chemistry is traced in some detail.     

Effect of structural modifications on the spectroscopic properties and dynamics of the excited states of peridinin

The spectroscopic properties and dynamics of the lowest excited singlet states of peridinin and two derivatives have been studied by steady-state absorption and fast-transient optical spectroscopic techniques. One derivative denoted PerOlEs, possesses a double bond and a methyl ester group instead of the r-ylidenebutenolide of peridinin. Another derivative denoted PerAcEs, is the biosynthetic precursor of peridinin and possesses a triple bond and a methyl ester group corresponding to the r-ylidenbutenolide function. Ultrafast time-resolved spectroscopic experiments in the visible and near-infrared regions were performed on the molecules and reveal the energies and regarding the structural features and interactions responsible for the unusual solvent-induced changes in the steady-state and transient absorption spectra and dynamics of dynamics of the excited electronic states. The data also provide information peridinin.     

Exploring hydrogen bond in the excited state leading toward intramolecular proton transfer: detailed analysis of the structure and charge density topology along the reaction path using QTAIM

Excited state intramolecular proton transfer (ESIPT) reaction along the O-H[Symbol: see text][Symbol: see text][Symbol: see text][Symbol: see text]O hydrogen bond of o-hydroxy benzaldehyde (OHBA), methyl salicylate (MS) and salicylic acid (SA) was investigated by ab-initio quantum chemical calculation and theory of atoms and molecules (QTAIM) for the first time. Variation in several geometric as well as QTAIM parameters along the reaction coordinate was monitored in the fully relaxed excited state potential energy curve (PEC) obtained from intrinsic reaction coordinate (IRC) analysis. Although, the excited state barrier height for the forward reaction (?E (0) (#) ) reduces substantially in all the systems, MS and SA do not show any obvious asymmetry for proton transfer. For MS and SA, the crossover of the bond index as well as the lengths of the participating bonds at the saddle point is assigned due to this symmetry in accordance with bond energy - bond order (BEBO) model, which does not hold true in OHBA both in the ground and excited states. Bond ellipticity, covalent and metallic character were examined for different structures along the reaction path within the QTAIM framework. The QTAIM analysis was found to be able to uniquely distinguish between the ground and excited states of the OHBA molecule as well as both determining the effects on the bonding character of adding different substituent groups and differentiating between the ESIPT reactions in the SA and MS molecules.     

The effect of oxygen on the amplitude of photodriven electron transfer across the lipid bilayer-water interface.

The surprisingly small effect of oxygen on photoelectron transfer in pigmented lipid bilayers is traced to a short lifetime of the excited states. Decreasing the oxygen concentration by greater than 100-fold decreases the half saturating concentration of acceptor by only threefold and has no effect on the maximum photovoltage observed at acceptor saturation. This holds true for both magnesium octaethylporphyrin and chlorophyll with both ferricyanide and methyl viologen as acceptors. Since oxygen quenches excited states at near the encounter limit, the lifetime of reactive state must be short, less than 100 ns. About 100-fold higher concentrations of acceptor are required to quench the fluorescence (in liposomes) than to saturate the photoeffect. Thus the reactive state is most likely the triplet. The short life of the excited state is caused by concentration quenching, i.e., their reaction with ground state molecules. The increase of photovoltage with increasing pigment concentration shows that this quenching in a condensed form of the pigment produces ions that lead to the observed photovoltage by interfacial reaction of the anion with acceptor.     

A fluorescence-probe study of the interaction of cycloheptaamylose arenes and amphiphillic molecules

The inclusion of the fluorescence probe pyrene within the void of cycloheptaamylose has been demonstrated by the nature of the fluorescence spectra of the arene, the lifetime of the fluorescence, and the rate of reaction of excited states of the arene with quencher molecules. The data suggest two equilibria processes, namely, an initial, fast inclusion of the arene, followed by a slower aggregation of the resulting cycloamylose-pyrene complexes. Addition of surfactant molecules, below the critical micelle concentration (c.m.c.), to the pyrene-cycloamylose solution leads to complexing of the three components of the system and thence to an increase in the hydrophobicity of the arene environment. Above the c.m.c., micelles of the surfactants are formed and the arene is transferred from the cycloamylose to the micelle. The fluorescence measurements establish conditions for varying the hydrophobicity of the arene environment. Preliminary kinetic data show that the rates of quenching of the excited states of the arene by such molecules as I^- and CH₃NO₂ are significantly decreased by inclusion in the dextrin. The data suggest systems that may be used to study molecular details of the reactions of excited states with quencher molecules.     

Interstellar molecules

Summary The study of interstellar molecules broadly includes two areas of interest. One area uses the unique ability of molecules to act as probes of the physical conditions in the cold, dense, visually opaque component of the interstellar medium. The physical properties of this and other components of the interstellar medium are summarized. The other area deals with the chemistry of interstellar molecules, recent aspects of which are emphasized in this review. Gas-phase chemistry, shock chemistry, and grain surface chemistry are discussed in the context of recent observations. No present observations suggest that surface reactions are relevant, but neither can they be ruled out. Ion-molecule reactions are clearly operative, at least for the simpler species. Chemical isotope fractionation is reviewed, andd it is concluded that the complexities of the chemistry allow no cosmological conclusions to be drawn from observations of deuterium in interstellar molecules, while the presence of¹³C in interstellar molecules permits an estimate of the¹²C/¹³C ratio which is consistent with the current concepts of the nucleosynthesis history of the Galaxy. Possible connections between interstellar molecules and the early molecular history of the solar system are discussed.This is the first of a series of papers which will appear in the Synthesis section of the Journal of Molecular Evolution pertaining to the topic Organic Molecules in the Solar System and Beyond.Operated by Associated Universitites, Inc., under contract with the National Science Foundation     

Rotovibrational states of the water molecule on the sun

The infrared spectrum of water observed in sunspots is complex and dense, with bands separated by approximately 0.01 cm^?1. For top asymmetrical molecules, there is no theoretical approach that allows for the calculation of rotovibrational energy with such precision. Experimentally derived rotovibracional energy levels of water at high temperatures combined with variational calculations have been used for the band assignments. These energy levels are employed to refine the analysis of a small portion of the infrared absorption spectrum. Such procedure has allowed for the identification of additional 55 bands to the 70 already identified as rotovibrational transitions of the water molecule. Our new assignments, which include pure and cross transitions, offer additional evidence of the existence of water on the sun, but above all they illustrate the complexity of the solar spectrum that involves states with higher levels of rotational excitation. Given the conditions on the sun, more molecules of water would occur in excited electronic states, which include apolar and paramagnetic states, generating intense bands in the spectrum. Since there is an analytical solution for the rotovibrational transitions of linear molecules, we were able to identify 16 bands relative to the excited electronic states ¹B₂ and ³A₁ in the sunspot spectrum. Density functional B3LYP/AUG-cc-pVTZ calculations of the electric and magnetic dipole are employed to discuss some consequences of the presence of excited states of water in the dynamics of sunspots and solar magnetic field.     

Role of interstellar molecules in prebiological evolution

Three generations of organic molecules in space are considered: interstellar molecules, molecules synthesised in protosolar cloud and molecules synthesised on the Earth. It is shown that there is no possibilities for amino acid polymers to be synthesised under interstellar cloud conditions. Molecules of the second generation were disintegrated during the Earth accumulation period. The problem of the origin of life is connected with the evolution of molecules of the third generation.     

Nonlinear optical absorption of photosynthetic pigment molecules in leaves

A mathematical formulation of the relationship between optical absorption coefficient of photosynthetic pigment molecules and light intensity was developed. It showed that physical parameters of photosynthetic pigment molecule (i.e., light absorption cross-section of photosynthetic pigment molecule, its average lifetime in the excited state, total photosynthetic pigment molecules, the statistical weight, or degeneracy of energy level of photosynthetic pigment molecules in the ground state and in the excited state) influenced on both the light absorption coefficient and effective light absorption cross-section of photosynthetic pigment molecules. Moreover, it also showed that both the light absorption coefficient and effective light absorption cross-section of photosynthetic pigment molecules were not constant, they decreased nonlinearly with light intensity increasing. The occupation numbers of photosynthetic pigment molecules in the excited states increased nonlinearly with light intensity increasing.     

Solvent-assisted excited state proton transfer and photoacidity of 2-hydroxypyridine. A nonadiabatic dynamics study

Reactions involving proton transfer, especially those taking place in excited states (ESPT), received considerable attention. These reactions underlie many biological and biochemical processes that are vital to life. DNA mutations excited state funnelling and transport phenomena are just examples. Among many molecules undergoing this type of photoreactions, phenols show a unique property, the so-called photoacidity. In the present communication, solvent (methanol and ammonia) assisted excited state proton transfer and photo acidity of 2-hydroxypyridine (2HP) are investigated at the DFT M06-2X / def2pvv level of theory. Excited states of 2HP and its complexes with methanol and ammonia were examined at two levels. First, sampling a Wigner distribution of 300 points, the photoabsorption spectra were simulated within the nuclear ensemble approximation. Second, simulation of the dynamics of the excited states with the surface hopping method. Several separate spectral windows with three hundred trajectories each, were considered. Lifetime of excited states and photochemical channels observed were discussed.     

Investigation of the mechanism for rapid heating of nitrogen and air in gas discharges

A rapid heating of nitrogen-oxygen mixtures excited by gas discharges is investigated numerically with allowance for the following main processes: the reactions of predissociation of highly excited electronic states of oxygen molecules (which are populated via electron impact or via the quenching of the excited states of N₂ molecules), the reactions of quenching of the excited atoms O(¹ D) by nitrogen molecules, the VT relaxation reactions, etc. The calculated results adequately describe available experimental data on the dynamics of air heating in gas-discharge plasmas. It is shown that, over a broad range of values of the reduced electric field E/N, gas heating is maintained by a fixed fraction of the discharge power that is expended on the excitation of the electronic degrees of freedom of molecules (for discharges in air, η_E?28%). The lower the oxygen content of the mixture, the smaller the quantity η_E. The question of a rapid heating of nitrogen with a small admixture of oxygen is discussed.     

The Diffuse Interstellar Bands: A Tracer For Organics In The Diffuse Interstellar Medium?

The diffuse interstellar bands (DIBs) are absorption bands seen in the spectra of stars obscured by interstellar dust. DIBs are recognized as a tracer for free, organic molecules in the diffuse interstellar medium (ISM). The potential molecular carriers for the DIBs are discussed with an emphasis on neutral and ionized polycyclic aromatic hydrocarbons (PAHs) for which the most focused effort has been made to date. From the combined astronomical, laboratory and theoretical study, it is concluded that a distribution of free neutral and ionized complex organics (PAHs, fullerenes, unsaturated hydrocarbons) represents the most promising class of candidates to account for the DIBs. The case for aromatic hydrocarbons appears particularly strong. The implied widespread distribution of complex organics in the diffuse ISM bears profound implications for our understanding of the chemical complexity of the ISM, the evolution of prebiotic molecules and its impact on the origin and the evolution of life on early Earth through the exogenous delivery (cometary encounters and metoritic bombardments) of prebiotic organics.     

Ab initio study of singlet excited states of bicyclo[2.2.0]hexasilane and tricyclo[4.2.0.02,5]octasilane

The singlet excited states in the optimized geometries of bicyclo[2.2.0]hexasilane and tricyclo[4.2.0.0^2,5]octasilane are studied theoretically using the ab initio molecular orbital method at the RHF/3-21G^* level with the all-singles CI approximation. These molecules are found to have zigzag structures in both the ground states and the singlet excited states corresponding to the lowest absorptions, and the estimated Stokes shifts between the lowest absorption and fluorescence are similar to the experimental values.     

One- and two-photon induced QD-based energy transfer and the influence of multiple QD excitations.

Due to the increased use of quantum dots (QDs) in diverse laser microscopies, it is interesting to study the excitation pump power and excitation wavelength dependence of QD-based energy transfer (ET) processes. The ET in QD conjugates with phthalocyanines (Pcs) was studied with femtosecond time-resolved pump-probe spectroscopy upon one- and two-photon excitation. At the used excitation wavelengths only the QDs are excited and become the energy donors. Due to the matched spectral overlap of QD photoluminescence and Pc absorption, the ET occurs on a picosecond time scale. The ET process shows strong pump power dependence whereby an increase in excitation power results in multiple QD excitations and in shorter excited state lifetimes on the QDs due to Auger relaxation. As a result, high excitation pump power leads also to an accelerated ET to the acceptor molecules from the initially multiply excited states of the QDs. Excited state quenching studies as function of pump power suggest that ET occurs mainly from the lowest one-exciton state (n = 1) and only to a minor extent from the multiply excited states (n > 1). For the short-lived, multiply excited states the ET competes inefficiently with Auger recombinations and energy transfer efficiencies of phi(ET)(n=1>) approximately 20%, phi(ET)(n=2>) approximately 7%, phi(ET)(n=3>) < or = 2% were obtained. Also after two-photon excitation the ET efficiency is highest from the one-exciton state. The experimentally determined ET efficiencies were compared with theoretical ET efficiencies upon multiple excitations. In both cases the ET efficiency decreases with the increase in excitation pump power.     

Messenger RNA for glutamine synthetase: its partial purification, translation in a cell-free system and its regulation by hydrocortisone.

We have verified that the enzymatic hydroxylation of carcinogenic aromatic hydrocarbons produces product molecules in electronically excited states. Introduction of the carcinogen benzo[α]pyrene into liver microsomes from 3-methylcholanthrene-induced rats results in a significant chemiluminescence which is shown for the first time to be correlated with the enzymatic hydroxylation of the parent carcinogen. The kinetics of the chemiluminescence implicate the intermediate epoxide as the precursor to the excited state product molecules.     

THE SEARCH FOR INTERSTELLAR GLYCINE

Millimeter arrays can be used to identify hot young molecular cores which contain large, highly saturated interstellar molecules, including biomolecules. These cores are prime locations for searching for interstellar glycine. The current status of the interstellar glycine search is discussed.     

Photophysics of pyrene-labelled compounds of biophysical interest.

The effects of the chemical constitution and structure of the substituent on the excited state dynamics of several model fluorescent pyrene-labelled molecules of biophysical interest have been examined. Nine new 1-substituted pyrenyl compounds, Py-NH-CO-C2H5, Py-NH-CO-Leu-Boc, Py-CH2-NH-CO-C2H5, Py-CH2-NH-CO-Leu-Boc, Py-CO-NH-C3H7, Py-CO-NH-Leu-OMe, Py-CH2-CO-NH-C3H7, Py-CH2-CO-NH-Leu-OMe and Py-C3H6-CO-NH-Leu-OMe, have been synthesized and their electronic spectra, fluorescence quantum yields and excited state lifetimes measured. These data have been used to calculate the radiative, kr, and non-radiative decay constants of their S1 states and the values of these constants correlated with the structures of the tethers. Non-radiative S1 decay rates (mainly intersystem crossing to T1) vary in parallel with the radiative rates so that the excited state lifetimes and radiative rate constants change considerably with the structure of the substituent whereas the quantum yields of fluorescence do not. An excellent correlation between [epsilon]max of the S1-S0 transition and either kr or the excited state lifetime is observed as long as no additional intermolecular or intramolecular excited state decay process of significant rate competes with the 'normal' radiative and non-radiative (ISC) decay processes of the pyrenyl chromophore. This correlation may have predictive value. Rates of bimolecular quenching of the S1 states of these molecules by molecular oxygen have been measured. The quenching process is diffusion-controlled with a spin statistical factor of 1, indicating that the S1-T1 electronic energy spacings of all the derivatives exceed the O2(1Deltag-3Sigmag-) electronic excitation energy of ca. 1 eV.     

Mass spectrometry of uronic acid derivatives. Part V. Fragmentation of methyl derivatives of methyl 4-deoxy-beta-L-threo-hex-4-ehopyranosiduronic-acid.

The basic fragmentation mechanism of methyl(methyl 4-deoxy-2,3-di-O-methyl-β-l-threo-hex-4-enopyranosid)uronate has been deduced by deuteromethylation analysis, metastable transition measurements, and by interpreting the spectra of weakly excited foregoing molecules. The differences in fragmentation of partially methylated derivatives of methyl 4-deoxy-β-l-threo-hex-4-enopyranosiduronic acid compared to that of the fully methylated substance are discussed in detail and the criteria are proposed for identification of the compounds concerned by mass spectrometry.     

Species-specific differences in the intermediate states of human and Syrian hamster prion protein detected by high pressure NMR spectroscopy

Human (huPrP) and Syrian hamster (ShaPrP) prion proteins have barriers for mutual infectivity, although they fold into almost an identical structure. The pressure responses of huPrP and ShaPrP characterized by high pressure NMR spectroscopy show differences in their excited states, as monitored by pressure-induced chemical shifts and intensity changes of individual residues in the (15)N/(1)H HSQC spectra. Both proteins fluctuate rapidly between two well folded (native) conformations N(1) and N(2) and less frequently between N and the excited states I(1) and I(2) with local disorder that may present structural intermediates on the way to PrP(Sc). These four structural states can be observed in the hamster and human PrP. At ambient pressure, less than 5 molecules of 10,000 are in the intermediate state I(2). From the structural point of view, the different states are mutually different, particularly in positions strategically important for generating species barriers for infection. The results point to the notion that excited state conformers are important for infection and that their structural differences may crucially determine species barriers for infection.     

Electronic excitations of biomolecules studied by quantum chemistry

Significant methodological advances have been made over the past ten years in developing reliable quantum chemical methods for the treatment of electronically excited states. These methods can nowadays be used routinely by the experienced researcher to accurately compute excitation spectra of medium-sized organic molecules; results have been reported for several popular photobiological systems, including green fluorescent protein. First steps are currently being taken to account for the solvochromic shifts of chromophore excitations caused by particular protein environments and to dynamically simulate photochemical reactions in the excited states.