Unknown Species

13 A Menagerie of Molecules from Michl and Balqi Superstrained Molecules 

The bonding sitnation in the qnatemary carbons of 4 seems somewhat similar to that for the apical carbon of pyramidane (Chapter 2), a view suggested by the presence of prominent regions of electrostatic charge (electrostatic potential), approximating lone pairs, at these carbons (c Chapter 2, Fig. 2.5). 

Molecule 5, C5H4 Removal of an appropriate pair of hydrogens from 3 gives, as an alternative to 4, molecule 5, tetracyclo[2.1.0.0 . 0 ]pentane, pyramidane. This was still unknown as of early 2007, despite having sparked a fair amount of interest (19 references in Chemical Abstracts) because it is the canonical molecule with a pyramidal carbon atom. Pyramidane was discussed in Chapter 2. Noteworthy are the facts that it has a lone pair at the apex (prominent electrostatic potential region), and that computations provide good evidence that it will prove to be reasonably stable, perhaps even isolable at room temperature. 

13 A Menagerie of Moleeules from Miehl and Balaji Superstrained Moleeules 

Molecule 6 is two tetrahedranes sharing a face. We saw in Chapter 6 and in cormection with 4 (above) that tetrahedrane is ejqrected to isomerize in a strongly exothermic reaction to cyclobutadiene. If we transpose this expectation unflinchingly to the case of 6, then we are hypothesizing the isomerization of 6 to 11  

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The question marks indicate uncertainty, as the molecule is an unknown species. 

In Surface Analysis by Laser Ionization (SALI), a probe beam such as an ion beam, electron beam, or laser is directed onto a surfiice to remove a sample of material. An untuned, high-intensity laser beam passes parallel and close to but above the sur-fiice. The laser has sufficient intensity to induce a high degree of nonresonant, and hence nonselective, photoionization of the vaporized sample of material within the laser beam. The nonselectively ionized sample is then subjected to mass spectral analysis to determine the nature of the unknown species. SALI spectra accurately reflect the surface composition, and the use of time-of-flight mass spectrometers provides fast, efficient and extremely sensitive analysis. 

Dissolved inorganic carbon is present as three main species which are H2CO3, HCOs and CO. Analytically we have to approach the carbonate system through measurements of pH, total CO2 or DIC, alkalinity (Aik), and PcOj- In an open carbonate system there are six unknown species H", OH , PcOj/ H2CO3, HCOs, and CO . The four equilibrium constants connecting these species are K, Ki, Kh, and fCw. The values of these equilibrium constants vary with T, P, and S (Millero, 1995). To solve for the six rmknowns we need to measure two of the four analytical parameters (Stumm and Morgan, 1996). Direct measurement of Pco is the best approach, but if that is not possible then the most accurate and precise pair (Dickson, 1993) is Total CO2 by the coulometric method Johnson et al., 1993) and pH by the colorimetric method (Clayton et ah, 1995). 

Maier and co-workers condensed formaldehyde and elemental silicon at 12 K in an argon matrix and photolyzed the mixture to form silaketene H2SiCO, which is similar in structure to the silylene-CO adduct mentioned above. The reactants first form siloxiranylidene 49 (which equilibrates with an unknown species postulated as the planar/linear silaketene 50 when exposed to 313-nm-wavelength light) and then forms complex 51 when photolyzed at 366 nm (Scheme 15). This species could also be formed by photolyzing diazidosilane 52 in the presence of CO, and complex 51 equilibrates with SiCO (53) and H2. The CO infrared shift for this bent structure was calculated at 2129 cm , which is shifted —80cm from the calculated value of free CO, at 2210 cm. The experimentally observed value was reported at 2038-2047 cm at 12 K. 

The computational prediction of vibrational spectra is among the important areas of application for modem quantum chemical methods because it allows the interpretation of experimental spectra and can be very instrumental for the identification of unknown species. A vibrational spectrum consists of two characteristics, the frequency of the incident light at which the absorption occurs and how much of the radiation is absorbed. The first quantity can be obtained computationally by calculating the harmonic vibrational frequencies of a molecule. As outlined in Chapter 8 density functional methods do a rather good job in that area. To complete the picture, one must also consider the second quantity, i. e., accurate computational predictions of the corresponding intensities have to be provided. 

Both the identification of a species and the determination of the kinetics of its formation or decay can be achieved with longer pathlength cells, such as that depicted in Figure 2.103. In kinetic experiments, however, there is the proviso that the experiment can be performed before natural convection currents interfere with the measurements i.e. the operator must be certain that the removal of a chromophore from the optical path is due to reaction and not due to convection currents. It should be noted that the strength of UV-visible spectroscopy does not lie primarily in the identification of unknown species as the information it provides is not of a molecularly specific nature. 

For reasons of roundoff errors due to water being the dominant species, a simplification is introduced for dilute solutions (Morel and Hering, 1993). One unknown and one equation are simultaneously eliminated from the set of conservation equations which make the recipe. The unknown species HzO is expressed as a function of the unknowns OH- and H+, which assigns OH- a — 1 H+ coefficient, and the OH- conservation equation (first column in Table 6.1) is left out. 

This matrix can be derived from Table 6.1 by expressing the unknown species H20 as a function of OH- and H+, then removing the OH" conservation equation, i.e., removing the corresponding column. 

Now, prior to the computation of the unknown species spectra Auk, the known contribution Yk is subtracted from Y. 

Figure 4-45 represents the situation graphically. The parts of C and A in light grey represent the contributions of the known species, dark grey characterises the unknown species. 

Excluding activity coefficients, three relationships are required in addition to the nine thermodynamic equilibria in order to calculate concentrations of the 12 unknown species. These relationships are the mass balances for magnesium and chloride, and the electroneutrality equation. 

The activity coefficients that are significant in determining the concentrations of the unknown species are the activity coefficients of Mg++, Ca++, SO3, SO4, and HSO3. The activity coefficient of Ca + is assumed to be equal to that of Mg++, and that of SOo equal to that of S0. The method for calculating the activity coefficients of Mg, SO4, and HSO3 was presented previously ( ). The activity coefficients of the neutral dissolved species and the fugacity coefficient of S02(g) are assumed equal to unity, as in (J ). 

The synthesis of solid derivatives homo- and heteroatomlc polyanions has to date principally featured the simplest of techniques to obtain generally the least soluble and most stable of the Ions possible from either en or NHg. There is no question that many other species exist in solution if not as solids, as evidenced by Zlntl s results, numerous color changes observed during reactions of alloys with crypt solutions, several seml-quantltatlve analyses of either unsatisfactory crystals or solutions formed In mixed metal reactions (14,37), and new NMR signals from unknown species In a wide variety of systems (23,24,38). The solution chemistries alone deserve a great deal more attention. 

Super or near-critical water is being studied to develop alternatives to environmentally hazardous organic solvents. Venardou et al. utilized Raman spectroscopy to monitor the hydrolysis of acetonitrile in near-critical water without a catalyst, and determined the rate constant, activation energy, impact of experimental parameters, and mechanism [119,120]. Widjaja et al. tracked the hydrolysis of acetic anhydride to form acetic acid in water and used BTEM to identify the pure components and their relative concentrations [121]. The advantage of this approach is that it does not use separate calibration experiments, but stiU enables identihcation of the reaction components, even minor, unknown species or interference signals, and generates relative concentration profiles. It may be possible to convert relative measurements into absolute concentrations with additional information. 

The branched f -alkane series are biomarkers because of the locale of their occurrence and the presence of only alternate pseudohomologs (even- or odd-carbon numbers only). Their inferred origin is from probable microbial precursors of unknown species, where methylation and ethylation, diethylation, butylation and ethylation occurred during biosynthesis... 

Rh s(CO)iis they revealed the presence of an unidentified complex which was suggested to be the previously unknown species Rh4(a-CO)i2-The BTEM protocol is an extremely powerful technique to recover pure component spectra of unknown species, even when present at very low concentrations. This was illustrated by a detailed mechanistic study of the promoting effect of HMn(CO)5 on the Rh4(CO)i2 catalyzed hydroformylation of 3,3-dimethylbut-l-ene [22], A dramatic increase in the hydroformylation rate was found when both metals were used simultaneously. Detailed in situ FTIR measurements using the BTEM protocol indicated the presence of homometallic complexes only during catalysis. The metal complexes that were identified under catalytic conditions were RC(0)Rh(C0)4, Rh4(CO)i2, Rh5(CO)i5, HMn(CO)s, and Mn2(CO)io (see Figure 6.6). The kinetics of product formation showed an overall product formation rate, Eq. (3) ... 

For the aminotroponiminate (ATI) system, the active species has been shown not to be the monomeric cationic alkyl proposed originally. Indeed, labeling experiments indicate that (ATl)AlEf and (ATIlAKi-Bu)" primarily undergo chain transfer to monomer, whereas another, as yet unknown, species... 

While a constant flux of OH was assumed in generating curves C and D of Fig. 16.12, this is obviously only a simplified construct taken to represent some species that forms OH in subsequent reactions. The flux of this unknown species appears to depend on the particular chamber and chamber history and is roughly proportional to the light intensity. It was also found that it increases significantly with temperature, relative humidity, and N02 concentrations but is independent of total pressure and the NO concentration (Carter et al., 1982). 

Likewise any reactivity-based definition would require some arbitrary choice of reaction rate. Which reaction would be used What minimal rate would be required What conditions of temperature, solvent, or acidity would be chosen for the definition As a practical matter, such a dehnition could not be applied to any unknown species for the simple reason that reaction rates are, at this point in time, notoriously difficult to predict from first principles. 

Representing the data in terms of a small number of primary factors is a very efficient way of storing information. This approach is frequently used in spectroscopic libraries, designed to identify unknown species by comparing their spectra with ones filed in the library. 

How can this enigma be answered Put away a sample of pure harmaline, with its spectral identification, onto the shelf for 50 or 100 years, and then re-analyze it Who knows, but what might be needed for this conversion is heat, or a bit of iron catalyst, or some unknown species of South American mold. Acid is certainly known to promote this oxidation. It would be very much worth while to answer this question because some, perhaps much, of the results of human pharmacological studies that involve harmaline as a metabolic poison, may be influenced by the independent action of harmine as a harmaline contaminant. 

As we have previosly noted for the phosphine chalcogenides2, we seek, as a minimum, two related objectives from calculations such as these an understanding of the bonding in these unusual systems and prediction of the structure and properties of unknown species. Unfortunately, as regards the prediction of unknown species, few data are available on any of the molecules studied so that we cannot calibrate these calculations against experiment. We have also noted previously1,2 that basis sets of at least double zeta quality with polarization and diffuse terms, full geometry optimization and some form of electron... 

The systematic procedure is to write as many independent algebraic equations as there are unknowns (species) in the problem. The equations are generated by writing all the chemical equilibrium conditions plus two more the balances of charge and of mass. There is only one charge balance in a given system, but there could be several mass balances. 

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