Crystallization data, analysis

J. R. Helliwell, P. A. Machin, and M. Z. Papiz, Computational Aspects of Protein Crystal Data Analysis, Proceedings of the Daresbury Study Weekend 23-24 January, 1987, in Daresbury Lab. Rep. DL/SCI/R25, 1987, Daresbury Laboratory, Daresbury, UK, 1989. 

Machin P (1987) In Helliwell JR, Machin PA, Papiz MZ (eds) Computational aspects of protein crystal data analysis. Proceedings of a Daresbury Study Weekend DL/SCI/R25... 

Of all the piezoelectric crystals that are available for use as shock-wave transducers, the two that have received the most attention are x-cut quartz and lithium-niobate crystals (Graham and Reed, 1978). They are the most accurately characterized stress-wave transducers available for stresses up to 4 GPa and 1.8 GPa, respectively, and they are widely used within their stress ranges. They are relatively simple, accurate gauges which require a minimum of data analysis to arrive at the observed pressure history. They are used in a thick gauge mode, in which the shock wave coming through the specimen is... 

The comparison with experiment can be made at several levels. The first, and most common, is in the comparison of derived quantities that are not directly measurable, for example, a set of average crystal coordinates or a diffusion constant. A comparison at this level is convenient in that the quantities involved describe directly the structure and dynamics of the system. However, the obtainment of these quantities, from experiment and/or simulation, may require approximation and model-dependent data analysis. For example, to obtain experimentally a set of average crystallographic coordinates, a physical model to interpret an electron density map must be imposed. To avoid these problems the comparison can be made at the level of the measured quantities themselves, such as diffraction intensities or dynamic structure factors. A comparison at this level still involves some approximation. For example, background corrections have to made in the experimental data reduction. However, fewer approximations are necessary for the structure and dynamics of the sample itself, and comparison with experiment is normally more direct. This approach requires a little more work on the part of the computer simulation team, because methods for calculating experimental intensities from simulation configurations must be developed. The comparisons made here are of experimentally measurable quantities. 

SIMS, and SNMS in rare cases, such as for HgCdJTei samples or some polymers, the sample structure can be modified by the incident ion beam. These effects can often be eliminated or minimized by limitii the total number of particles incident on the sample, increasing the analytical area, or by cooling the sample. Also, if channeling of the ion beam occurs in a crystal sample, this must be included in the data analysis or serious inaccuracies can result. To avoid unwanted channelii, samples are often manipulated during the analysis to present an average or random crystal orientation. 

Crystal data and details of data collection, data reduction and final refinement are reported in Table 1. The procedure for data collection and processing, which included a correction for scan-truncation effects, were similar to those recently described for syn-l,6 8,13-biscarbonyl[14]annulene [10] and citrinin [11], Figure 1 shows the numbering scheme adopted in the present analysis. 

Trimethylenemethane is a special type of alkene that does not exist as the free compound. Various synthetic equivalents to the synthon 43 shown below have been reported. Trost, in particular, has exploited these compounds in 1,3-dipolar cycloaddition reactions.138 139 A metal-bound, isolated trimethylenemethane species was recently reported by Ando (Scheme 6). It resulted from the complexation of an ero-methylenesila-cyclopropene with group 8 carbonyls (Fe, Ru).140,140a The structure was proved by X-ray crystal structure analysis.29Si NMR data were consistent with the -structure shown. 

Most recently, we have been able to obtain the in situ surface EXAFS spectrum of a half-monolayer of underpotentially deposited copper on a bulk Pt(lll) single crystal pretreated with iodine. The spectrum shown in Fig. 23 is a bit noisy (due to limited number of scans) but at least five well-defined oscillations can be observed. Preliminary data analysis indicates that the copper adatoms sit on threefold hollow sites with copper neighbors at 2.80 0.03 A. This distance is very close to the Pt—Pt distance in the (111) direction and indicates the presence of a commensurate... 

Seebach and Brenner have found that titanium enolates of acyl-oxazolidinones are added to aliphatic and aromatic nitroalkenes in high diastereoselectivity and in good yield. The effect of bases on diastereoselectivity is shown in Eq. 4.59. Hydrogenation of the nitro products yields y-lactams, which can be transformed into y-amino acids. The configuration of the products is assigned by comparison with literature data or X-ray crystal-structure analysis. 

Scarsdale, J. N., C. Van Alsenoy, V. J. Klimkowski, L. Schafer, and F. A. Momany. 1983. Ab Initio Studies of Molecular Geometries. 27. Optimized Molecular Structures and Conformational Analysis of N-Acetyl-N-methylalaninamide and Comparison with Peptide Crystal Data and Empirical Calculations. J. Am. Chem. Soc. 105,3438-3445. 

Insertion and rearrangement steps were also observed in the reaction of 1 with B2C1443 (Scheme 14). Compounds 52 and 53 were characterized by NMR spectroscopic or mass-spectrometric data, compound 54 by an X-ray crystal structure analysis. 54 may be regarded as a borane-stabilized boranediyl, consisting of a Me5C5B nido-cluster unit (Fig. 8). 

Differentiation of vapor responses of the colloidal crystal film was accomplished with spectral measurements of the shape changes of the diffraction peak. Selectivity of response was obtained by applying multivariate data analysis to correlate these spectral changes to the effects of species of different chemical nature and to establish the identity and concentration of species. 

There are many types of data in chemistry that are not specifically covered in this book. For example, we do not discuss NMR data. NMR spectra of solutions that do not include fast equilibria (fast on the NMR time scale) can be treated essentially in the same way as absorption spectra. If fast equilibria are involved, e.g. protonation equilibria, other methods need to be applied. We do not discuss the highly specialised data analysis problems arising from single crystal X-ray diffraction measurements. Further, we do not investigate any kind of molecular modelling or molecular dynamics methods. While these methods use a lot of computing time and power, they are more concerned with data generation than with data analysis. 

The relatively recent development27 of the direct methods of crystal structure analysis has produced a great increase in the number of crystal structures reported in the literature, particularly with regard to the possible hydrogen bonds (also for biological molecules). Hence, the classical spectroscopic data on hydrogen bonding in solution are backed up by X-ray diffraction analysis data. 

Crystal data (by X-ray diffraction analysis) and calculation of net 7r-electron population for 7V,7V-dialkyl-p-nitroaniline and for 3,5- and 2,6-dimethyl-4-nitroaniline indicate that... 

K. Pollanen, A. Hakkinen, S-P. Reinikinen, J. Rantanen, M. Kaijalainen, M. Louhi-Kultanen and L. Nystrom, IR spectroscopy together with multivariate data analysis as a process analytical tool for in-hne monitoring of crystallization process and solid-state analysis of crystalline product, J. Pharm. Biomed. Anal., 38, 275-284 (2005). 

The theoretician uses these programs to predict structure, either of single molecules or of assemblages of molecules, using X-ray or NMR data, when available, to test his predictions (13-15). It has been known for a long time that even the earlier molecular mechanics programs can predict the structures of certain types of molecules with excellent reliability. For the cyclic alkanes, an accuracy comparable to that of the best X-ray crystal structure analysis can be obtained. In fact, the method is more widely applicable since neither compound nor crystals are necessary (1 . 

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