Structure, determination

Structure determination by LEED (quantitative LEED) consists of three main parts, namely as visualized in Eigure 3.2.1.31, the 

Compare experimentai with modei intensities via R-factor 

Vary modei parameters in a structurai search or find  

When the model calculations are carried out as a function of N model parameters, 

R-factor Rp on a model parameter p, with all other pjs fixed at their exact value. In panel (b), the determination of error limits Ap, via the variance of the R-factor, var(Rp), is defined. 

The proof of structure of many of the coumarins in the Tables has come as a result of the ingenious and enlightened use of a variety of organic chemical techniques by many researchers and the reader is referred to the particular references quoted for each compound. Assignment of structure to a new coumarin is a two-fold problem of initially identifying the different substituent groups and then allocating these to their correct position on the coumarin nucleus. 

With the development of spectroscopic techniques it is now often a straightforward matter to arrive fairly rapidly at a possible structure. It is one of the main purposes of this review to enable the reader to identify tentatively a coumarin and then, from the Tables, to establish whether or not it is new. 

Suppose that a molecule has several probable structures, each of which belongs to a different point group. Then the number of infrared- and Raman-active fundamentals should be different for each stmcture. Therefore, the most probable model can be selected by comparing the observed number of infrared- and Raman-active fundamentals with that predicted theoretically for each model. 

Td Activity Number of Fundamentals XeF Stretching FXeF Bending 

TABLE 1.11b. Number of Fundamentals for Square-Planar Xep4 

Another example is given by the XeF ion, which has the three possible structures shown in Fig. 1.21. The results of vibrational analysis for each are summarized in Table 1.12. It is seen that the numbers of IR-active vibrations are 5,6, and 3 and those of Raman-active vibrations are 6, 9, and 3, respectively, for the D3 , C41 , and D5/ structures. As discussed in Sec. 2.7.3, the XeF ion exhibits three IR bands (550-400, 290, and 274 cm ) and three Raman bands (502, 423, and 377 cm ). Thus, a pentagonal planar structure is preferable to the other two structures. The somewhat unusual structures thus obtained for XeF4 and XeF5 can be rationalized by the use of the valence shell electron-pair repulsion (VSEPR) theory (Sec. 2.6.3). 

This method is widely used for elucidation of the molecular structure of inorganic, organic, and coordination compounds. In Part 11 and Appendix HI, the number of infrared- and Raman-active fundamentals is compared for XY3 (planar, Da, and pyramidal, Cj,), XY4 (square-jJanar, D4/ and tetrahedral, Td), XYj (trigonal-bipyramidal, Dj, and tetragonal-pyramidal, 4 ) and other molecules. Recently, the structures of various metal carbonyl compounds (Sec. III-16) have been determined by this simple technique. 

It should be noted, however, that this method does not give a clear-cut answer if the predicted numbers of infrared- and Raman-active fundamentals are similar for various probable structures. Furthermore, a practical difhculty arises in determining the number of fundamentals from the observed spectrum, since the intensities of overtone and combination bands are sometimes comparable to those of fundamentals when they appear as satellite bands of the fundamental. This is panicularly true when overione and combination bands are enhanced anomalously by Fermi resonance (accidental degeneracy). For example, the frequency of the first overtone of the 1/2 vibration of CO2 (667cm ) is very close to that of the vibration (1337 cm ). Since these two vibrations belong to the same symmetry species ( p, they interact with 

Ta Activity Number of Fundamentals XcF Stretching FXeF Bending 

To calculate the vibrational frequencies, it is necessary first to express both the potential and the kinetic energies in terms of some common coordinates (Sec. 1-3). Internal coordinates (Sec. 1-8) are more suitable for this purpose than rectangular coordinates, since (1) force constants expressed in terms of internal coordinates have clearer physical meanings than those expressed in terms of rectangular coordinates, and (2) a set of internal coordinates does not involve translational and rotational motion of the molecule as a whole. 

When correlating the number of infrared-active CO-stretching modes with molecular structure, the phase in which measurements are made has some bearing on the effective molecular symmetry and must therefore be considered. Measurement of the infrared spectra of compounds in the gas phase is ideal because mtermolecular interactions can be neglected the selection rules which determine the number and activity of the CO-stretching modes are those associated with the point group of the isolated molecule. Because of the limited volatility of many carbonyl complexes and their tendency to decompose at higher temperatures, gas-phase measurements have been limited chiefly to the binary carbonyls (44). It 

X-Ray analysis alone provides an absolute method for determining the molecular structure of a compound in the solid state. However, a consideration of the number of CO-stretching frequencies observed in the infrared spectrum of a carbonyl complex has proved invaluable in providing information about its structure both in the solid state and, more particularly, in solution. Applications of this latter approach to problems of molecular structure may now be discussed. As was noted in previous discussions, certain limitations must be considered in applying this method these will be taken into account. 

Complex Position of substituents Point group Infrared-active CO-stretching inodes 

The isomers M(CO) 4L2 may be readily distinguished as only one infrared-active CO-stretching vibration is predicted for the trans species, whereas 

Compounds with trigonal bipyramidal configurations also display isomerism the point groups and infrared active CO-stretching vibrations are given in Table II assuming all ligands have spherical symmetry. 

Isomers and Point Gboups of Substituted Octahedral Carbonyl Complexes 

The ease with which the active principle can be isolated and purified depends very much on the structure, stability, and quantity of the compound. 

Penicillin proved a difficult compound to isolate and purify. Although Fleming recognized the antibiotic qualities of penicillin and its remarkable non-toxic nature to man, he disregarded it as a useful drug since it appeared too unstable. He could isolate it in solution, but whenever he tried to remove the solvent, the drug was destroyed. Now that we know the structure of penicillin (Chapter 9), its instability under the purification procedures of the day is understandable and it was not until the development of a new procedure called freeze-drying that a successful isolation of penicillin was achieved. 

Other advances in isolation techniques have occurred since those days and in particular in the field of chromatography. There are now a variety of chromatographic techniques available to help in the isolation and purification of a natural product. 

In the past, determining the structure of a new compound was a major hurdle to overcome. It is sometimes hard for present-day chemists to appreciate how difficult structure determinations were before the days of NMR and IR spectroscopy. A novel structure which may now take a week s work to determine would have provided two or three decades of work in the past. For example, the microanalysis of cholesterol was carried out in 1888 to get its molecular formula, but its chemical structure was not fully established until an X-ray crystallographic study was carried out in 1932. 

Structures had to be degraded to simpler compounds, which were further degraded to recognizable fragments. From these scraps of evidence, possible structures were proposed, but the only sure way of proving the theory was to synthesize these structures and to compare their chemical and physical properties with those of the natural compound or its degradation products. 

The structures of dibenzazonines have been determined on the basis of degradation studies and/or spectroscopic properties. Structural determinations are further confirmed by comparison with synthetic samples. 

Erybidine (1) crystallizes as colorless needles and has the characteristic UV absorption at 284 nm. Its 1H-NMR spectrum shows the presence of an /V-methyl (2.82) and three methoxyl groups [3.92 (3H) and 3.87 (6H)]. Treatment with diazomethane gives a tetramethoxy derivative identified as O-methylerybidine (9) on the basis of degradation studies and comparison with a synthetic sample, thus establishing the monophenolic nature of the alkaloid. The hydroxyl group of 

The above data clearly suggest a dibenzazonine structure with two methoxyl and two hydroxyl groups as substituents, their locations being determined by nuclear Overhauser effect difference spectroscopy experiments (Fig. 1). Several derivatives of crassifolazonine (2) were prepared and characterized (2a-2c). Final proof for the proposed structure of crassifolazonine (2) was obtained by its total synthesis (15). 

LUIS CASTEDO EXPOSITO AND DOMINGO DOMINGUEZ FRANCISCO 

Laurifonine (4) was isolated as an amorphous powder whose dibenzazonine structure was suggested by UV absorption bands at 221 and 283 nm. The H-NMR spectrum has signals for an 7V-methyl (2.32) and three aromatic methoxyl groups (3.90, 3.80, and 3.76) that were located at C-2, C-l 1, and C-12 by identification of degradation products. The aromatic part of the H-NMR spectrum confirms this type of substitution, exhibiting two singlets at 6.72 and 6.68 for two para protons while H-l resonates as a doublet (7.05, J = 2.5 Hz), H-3 as a double doublet (6.80, J = 8.5 and 2.5 Hz), and H-4 as a doublet (7.18, J = 8.5 Hz) (23). 

More than half a century passes from initial research the pharmacist Otto Paul Unverdorben (1806-1873) had conducted in 1826 to elucidate the structure, when Adolf von Baeyer was able to dispose of the final uncertainties regarding indigo s chemical constitution in 1883. 

Baeyer confirmed his results by the total synthesis of oxindole, isatin and indole. Nitration ofphenylacetic acid, isolation of the o-nitro isomer, and reduction of the latter followed by ring closure gave oxindole. Reaction with nitrous acid ( .e. potassium nitrate and sulfuric acid) gave isatin oxime, from which by reduction, dehydrogenation with iron(lll) chloride and final hydrolysis, isatin itself was obtained. 

O Baeyer had tried out zinc dust distillation for the first time as a synthetic route to indole. In connection with the structure determination of many natural products, this later proved a valuable method for the transformation of phenols into hydrocarbons. 

Baeyer synthesised indole by reduction of o-nitrocinnamic acid with iron and potassium hydroxide (Baeyer-Emmerling indole synthesis). 

All this work was novel, but did not answer the question concerning the structure of indigo. As we shall see, with oxindole, Bayer had chosen the wrong substitution pattern. 

As we have seen in the previous sections, a crystallizable polymer melt that has been sohdified under quiescent conditions possesses a two-phase structure consisting of chain-folded crystals organized as spherulites in an amorphous matrix. Because the mechanical, optical, electrical, thermal, and transport properties of the two phases are generally quite different from each other, the observed behavior will be a weighted average of the properties of the two phases. We can expect the weighting function to be the fraction of the crystalline or amorphous phase, with the size and size distribution of the domains often playing a relatively minor role. 

For perfect alignment, (p is zero and/ equals unity. For perpendicular orientation, (f is a right angle and / equals — Further, a zero value of the orientation factor implies random orientation, which occurs at (f = 54.7°. 

In summary, then, it is necessary to measure the fiaction of crystals, the crystalline orientation factor the amorphous orientation factor and possibly the size and size distribution of crystals in order to relate polymer structure to polymer properties. Although the extent of crystallinity is generally measured using density or heat-of-fusion methods, orientation is determined with the help of optical birefringence, dichroism, sonic modulus, or x-ray diffraction [60]. The size of crystals is observed with an optical or electron microscope. 

The simplest method of determining the mass fraction crystallinity X of an unfilled, semicrystalline homopolymer is to measure the density p of a representative sample. If the material is free of voids and impurities, the total volume V of unit mass of polymer is given by 

Example 11.6 When a fiber made from PET is dropped in a density gradient column made from toluene and carbon tetrachloride, it comes to rest 70% of the way down the column. What is the percent crystallinity For PET, is equal to 1.335 g/cm and p is equal to 1.455 g/cm.  

NM R experiments (ID and 2D, homonuclear and heteronuclear) are the preeminent techniques for the determination of molecular structures. However, careful application and analysis of mass spectral data can provide sufficient information to postulate tentative structures. In this respect, the application of tandem MS experiments, sometimes in conjunction with selective derivatization of the unknown compound, can be very informative about the stmcture. The high-resolution mass spectral data are critical to the support of NMR-deduced stmctures by providing molecular formulae for unknowns. 

The range of spectroscopic techniques now available means that it is often a straightforward matter to arrive at a possible structure for a new isocoumarin. Key references are given in the Tables relating to the structure elucidation of the natural isocoumarins. Carbon-13 nuclear magnetic resonance spectroscopy has proved to be of use in determination of the structures of the more complex isocoumarins 139). The C-NMR data for some simple isocoumarin derivatives have been listed (227, 265). 

Crystal structure determinations have been used to confirm the structures of duclauxin (127) 221), cladosporin (86) (266), hydrangenol (40) 249), agrimolide (93) 13), dehydroaltenusin (118) 238), gilmaniel-lin (124) 68) and antibiotic AI-77-B (152) (259). The absolute configuration has been determined by crystal structure methods for naph-thalic anhydride (123) 143) and actinobolin (145) 302, 307). 

Circular dichroism has been used to correlate the absolute configuration at C-3 of dihydroisocoumarins, for example mellein (19), agrimo- 

The first investigation of the bitter principles in enmei-so was carried out in 1910 and isolation of a crystalline bitter substance was reported by Yagi (2). In 1954, antibacterial activity was reported for the extract (5). In 1958, isolation of enmein, one of the major diterpenoid constituents, initiated structure determination and investigation of other constituents. Since then, our knowledge of the diterpenoids of Rabdosia species has developed to a remarkable degree. Particular interest has centered on their antitumor activity. For previous reviews of the chemistry of Rabdosia diterpenoids, the reader is referred to Ref. (4—7). 

The chemical investigation of Rabdosia plants began with isolation of the bitter principles of enmei-so (R, japonica and R. trichocarpa). During the first period (1958—1966), the main effort was devoted to the structure elucidation of enmein, one of the major constituents. After this was 

Because of the wide variety of reactions available to synthetic chemists, it is possible to devise syndietic strategies for just about any target that we wish. 

Organic Chemistry An Intermediate Text, Second Edition, by Robert V. Hoffman ISBN 0-471-45024-3 Copyright 2004 John Wiley Sons, Inc. 

Vibrational spectroscopy is useful in identification of protonic entities and their configuration. It can determine the type of association for instance, whether M-OH entities form infinite chains, cyclic or open dimers, and the position of a proton in strong, symmetric hydrogen bonds where it can distinguish a truly centred proton from a statistically symmetrical case . 

All the phenalenones so far isolated from plants are derivatives of 9-phenyl-lH-phenalen-1-one (44). All the related compounds occurring with them may be regarded as metabolic oxidation products phenyl-naphthalides, phenylnaphthalic anhydrides, quinonemethides derived from oxa- and aza-phenalenones, derivatives of lH-naphtho[2,l,8- wia]-xanthen-l-one (45) and a phenalenone dimer. 

Oxidation of the dimethyl ethers gave the two dimethoxyphenyl-naphthalic anhydrides (49) and (50) which were then decarboxylated to give respectively l,2-dimethoxy-6-phenylnaphthalene (51) and 1,2-dimethoxy-8-phenylnaphthalene (52). These were identified by unequivocal total synthesis. Further oxidation of both anhydrides (49) and (50) gave biphenyl-2,3,4-tricarboxylic acid (53) which was decarboxylated to biphenyl. 

The scanning tunneling microscope (STM) [2] and the atomic force microscope [3] are fascinating new techniques which enable us to see directly the stmcture of the interfaces. The application of these techniques to electrochemistry is far from trivial, and much progress has been achieved from the initial experiments [4, 5], in which 

While the atomic force microscope (AFM) is a relative newcomer [11, 12], it has some advantages over the STM because it does not measure currents, and therefore does not interfere with the electrochemistry. 

In STM the tips are held 1-2 nanometers above the surface of the electrodes. 

If the tip is close enough to the surface there will be a tunneling current, which is an exponential function of the tip to surface distance. This causes very strong variations in current intensity when the tip is moved up or down, the current may typically vary by an order of magnitude when the tip is moved 0.1 nm ( 1 angstrom) in the z direction. This means that the vertical resolution can be as much as 0.001 nm. The image provided by the STM is really more an electron density map of the surface, and the real positions of the atoms are related to this map through form factors that are known to a certain approximation. 

Low resolution scans are certainly less sensitive to these form factors and provide extremely useful morphology information. 

The crystal stractures of P.Y. 185 and P.R. 260 have been determined from single crystals by X-ray stracture analysis (Table 14.2) [18]. Because of the extremely low solubility of P.Y. 139, single crystals could not be obtained. Therefore, the crystal stracture of 

The resulting hydrogen bond network propagates in sheets of the P.R. 260 molecules parallel to the crystallographic [Oil] plane. In these sheets the molecules 

The seiection of moiecuies beiongs to one sheet. Dashed lines represent intra- and intermoiecuiar hydrogen bonds. 

For comparison, a specific packing energy SPE = PE/mol. mass has been defined. The SPE values of the investigated isoindohne differs significantly. The specific packing energy of P.Y. 139 exceeds the corresponding value of P.R. 260 by 42%, and thus marks P.Y. 139 as the intrinsically more stable solid. 

Data analyses software are often provided by the manufacturers of the diffraction equipment. However, special attention needs to be exercised when analyzing data from nonroutine samples. 

Molecular Model. Amino acid analyses of all these three silk fibroins show a uniformly high content of alanine ([Ala] ). There is an option in linked-atom least-squares (LALS) program to indicate two molecular chains by defining the constraints for only one of them. Here, the geometry for Ala is for the D-Ala and not L-Ala. The molecular conformation must satisfy both the sterical and mathematical requirements. Hence, we have chosen initial p and for Ala and Gly residues to be the same as that of Marsh et al. s (1955) results, and the main chain was constructed with appropriate helical parameters together with bond lengths and angles. 

Molecular and Crystal Structure for Repeating Unit. The refinement was carried out for the crystal structure in which two antiparallel molecules related by a two-fold rotation axis parallel to the c-axis. In order to get appropriate packing parameters, the discrepancy factors Rq (conventional R factor) and (weighted Rq factor) and the shortest contact between non-bonded atoms were calculated. Here, Rq and R were defined by 

A dipeptide Ala-Gly was used as chemical repeating unit for refinement. The weight of each reflection w was fixed to 1. 

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The crystal structure determines not only the arrangement of atoms in the lattice but also the external form of the crystal. 

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Woodruff D P, Cowie B C C and Ettem a A R H F 1994 Surface structure determination using x-ray standing waves a simple view J. Rhys.. Condens. 6 10 633—45... 

Doll R and Van Hove M A 1996 Global optimization in LEED structure determination using genetic algorithms Surf. Sc 355 L393-8... 

B1.22 Surface characterization and structural determination optical methods... 

B1.23 Surface structural determination particle scattering methods... 

Kim C, Hefner C and Rabalais J W 1997 Surface structure determination from ion scattering images Surf. Sc/. 388 LI 085-91... 

Tidsweii i M, Lucas C A, Markovic N M and Ross P N 1995 Surface structure determination using anomaious x-ray scattering Underpotentiai deposition of copper on Pt(111) Phys. Rev. B 51 10 205-8... 

To find appropriate empirical pair potentials from the known protein structures in the Brookhaven Protein Data Bank, it is necessary to calculate densities for the distance distribution of Ga-atoms at given bond distance d and given residue assignments ai,a2- Up to a constant factor that is immaterial for subsequent structure determination by global optimization, the potentials then ciiiergo as the negative logarithm of the densities. Since... 

E. Pretsch, T. Cletc, J. Seibl, W. Simon, Tables of Spectral Data for Structure Determination of Organic Compounds, Springer-Verlag, Berlin, 1989. 

Structure determination of the products obtained by alkylation was established previously by ... 

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