Linear Format

Sample line notations for Aspirin Molecule [ 6]0C(=0)C1=CC=CC=C1C(0)=0 (SMARTS) 

InChIKey=FNJSWIPFHMKRAT-UHFFFAOYSA-N (InChl Key) C0C(=0)clccccclC(0)=0 (SMILES) 

---

CLAIMS BIBLIO iacludes an abstract and claim ia additioa to basic bibliographic information for chemical and chemically related U.S. patents from 1950 and for all patents from 1963. AH claims are searchable and ptintable from 1971 claims for many patents are not avaHable from 1971 to 1974. Prom 1972, many tides have been enhanced with additional keywords to describe the iavention more clearly and to iadicate the presence of a drawiag chemical stmctures have beea coaverted so that they display ia linear format. Many company names have been standardized, and USPTO classification is updated aimuaHy to reflect reclassification projects. 

Most metals and ceramics have elastic elongation of less than 2%. Stretching in these materials involves the movement of atoms. In contrast, polymers can be easily elongated because the applied stress promotes linear formation of the polymer backbone. 

It is a common practice to describe mass dependent isotope fractionation processes by a single linear curve on a three-isotope-plot (Matsuhisa et al. 1978). The resulting straight lines are referred to as terrestrial mass fractionation lines and deviations from it are used as indicating nonmass-dependent isotope effects. The three-isotope-plot is based on the approximation of a power law function to linear format. To describe how far a sample plots off the mass-dependent fractionation line, a new term has been introduced A 0, A Mg, A S, etc. Several definitions of A have been introduced in the literature, which have been discussed by Assonov and Bren-ninkmeijer (2005). The simplest definition is given by ... 

Except for very simple systems, initial rate experiments of enzyme-catalyzed reactions are typically run in which the initial velocity is measured at a number of substrate concentrations while keeping all of the other components of the reaction mixture constant. The set of experiments is run again a number of times (typically, at least five) in which the concentration of one of those other components of the reaction mixture has been changed. When the initial rate data is plotted in a linear format (for example, in a double-reciprocal plot, 1/v vx. 1/[S]), a series of lines are obtained, each associated with a different concentration of the other component (for example, another substrate in a multisubstrate reaction, one of the products, an inhibitor or other effector, etc.). The slopes of each of these lines are replotted as a function of the concentration of the other component (e.g., slope vx. [other substrate] in a multisubstrate reaction slope vx. 1/[inhibitor] in an inhibition study etc.). Similar replots may be made with the vertical intercepts of the primary plots. The new slopes, vertical intercepts, and horizontal intercepts of these replots can provide estimates of the kinetic parameters for the system under study. In addition, linearity (or lack of) is a good check on whether the experimental protocols have valid steady-state conditions. Nonlinearity in replot data can often indicate cooperative events, slow binding steps, multiple binding, etc. 

Recently-reported pyrimido[4,5-, pyrimidine 168, prepared as in Equation (90), has been reported as a Janus-AT heterocycle, where the molecule is designed to have the hydrogen-bonding characteristics of both a diaminopurine and uracil/thymine <2007JOC466>. Crystallographic studies show that 168 forms a linear formate-bridged supra-molecular array. 

Restriction map of pBR322 in circular and linear format. Designed by CGC Scientific, a provider of software tools for biologists. http //www.fermentas.com... 

Until the late 1970s, the Wiswesser Line Notation (WLN) was the only widely recognized format in which to code chemical structures in a computer-readable linear format. It was invented by William J. Wiswesser (1952), and his work was recognized and honored with the Skolnik Award for outstanding contributions to and achievements in the theory and practice of chemical information science by the American Chemical Society in 1980. The WLN was quickly adopted by major chemical companies to store and retrieve machine-readable, 3D-chemical structure information in a 2D, linear array, and is still in use today. 

The name SMILES comes from Simplified Molecular Input Line Entry System (Weininger 1988). It is a linear format for description of molecules and reactions developed by Daylight Chemical Information Systems, Inc. SMILES was designed with the intention to be both human readable and writable, which makes it unique among the other chemical formats described in this chapter. 

Even though InChl (discussed in the next section) is quickly gaining support as the linear format of choice, the fact that SMILES can be read and written by humans... 

InChI is a very recent member of the family of chemical formats (McNaught 2006). It is a linear format that was developed in cooperation with NIST and IUPAC and has several important features that distinguish it from other formats. Unlike the other formats discussed above, it cannot describe reactions—only compounds. 

S YBYL Line Notation (Ash et al. 1997) is a linear format that to some extent resembles SMILES. The most important feature that these two formats have in common is human readability. However, the authors of SLN have made several design decisions that make it different from SMILES in several important points ... 

It is even more important to keep such limitations in mind when one format is used as an intermediary because the conversion is not possible in a direct way. Choosing a linear format for this task would inadvertently lead to loss of information about geometry of the converted structure, even though both the original and the final format it. 

When publishing chemical structures for search engines, all file-based formats are usually out of the question. The reason is simple Search engines work on the scale of characters and words and are not prepared to compare whole files. Thus, we remain with the selection of available widespread linear formats SMILES, InChl, and InChIKey. 

Linear formats are usually not good candidates for primary data storage, simply because they do not contain the molecular geometry. Therefore, it is advisable to use one of the file-based formats for this purpose—either Molfile or CML. These are very similar in their capabilities and have good support in various chemical software packages, with Molfile usually having slightly smaller files and even wider support than CML. 

However, file-based formats are not directly comparable when a search in a database is performed and special chemistry-aware tools have to be used. For the purpose of searching in the database, linear formats might be more useful. This topic is discussed in the following subsection. 

Fig. 56.1 An example of pattern notes, an alternative to the more commonly used linear format.

D. These disk systems store data in linear format and store data in sequential access. 

Restrictors are required at the ends of SFC columns to maintain supercritical conditions throughout the column and to limit overall flow. Several options exist, with frit restrictors being the most popular, followed by integral and linear formats. The frit restrictor is... 

In Equation 5 the index of the crystallization reaction, n, and z, are calculated from its linear format (Eq. 6) as the slope and intercept at Ln(f) = 0, respectively. The F values to calculate by linear regression (Eq. 6) n and z are, most of the time, between F < 0.25 and F S 0.75. These F values are considered to assure constant radial growth rate and no crystal impingement. 

Fig. 12. Linear format of the Avrami equation for crystallization of a 26% blend of palm stearin in sesame oil at 24.5°C (A) and 26.5°C (B). Cooling rate used I C/min.

---