Chemicals structure

Early chemical studies of persimmon tannin were often done with insufficiently purified tannin fractions. It was reported in 1923 that the elemental formula of persimmon tannin might be C14H20O9, and in 1962, it was proposed that the major component of persimmon tannin was leucodelphinidin-3-glucoside. Further studies done by Itoo et al. showed that persimmon tannin might have a more complex 

Chemical structure and the polarity determine dissolution of polymers. If the bonds in polymer and solvent are similar, then the energy of interaetion between homogeneous and heterogeneous moleeules is nearly identieal whieh faeilitates solubility of polymer. If the chemical structure of polymer and solvent moleeule differ greatly in polarity, then swelling and dissolution does not happen. It is refleeted in an empirieal rule that like dissolves like . 

Nonpolar polymers (polyisoprene, polybutadiene) mix infinitely with alkanes (hexane, oetane, ete.) but do not mix with sueh polar liquids as water and aleohols. Polar polymers (eellulose, polyvinylalcohol, ete.) do not mix with alkanes and readily swell in water. Polymers of the average polarity dissolve only in liquids of average polarity. For example, polystyrene is not dissolved or swollen in water and alkanes but it is dissolved in aromatie hydrocarbons (toluene, benzene, xylene), methyl ethyl ketone and some ethers. Polymethylmethacrylate is not dissolved nor swollen in water nor in alkanes but it is dissolved in dichloroethane. Polychloroprene does not dissolve in water, restrictedly swells in gasoline and dissolves in 1,2-dichloroethane and benzene. Solubility of polyvinylchloride was considered in terms of relationship between the size of a solvent molecule and the distance between polar groups in polymer.  

The above examples are related to the concept of the one-dimensional solubility parameter. However the effects of specific interactions between some functional groups can change compatibility of the system. ChloroaUcanes compared with esters are known to be better solvents for polymethylmethacrylate. Aromatic hydrocarbons although having solubility parameters much higher than those of alkanes, dissolve some rubbers at least as well as alkanes. Probably it is related to increase in entropy change of mixing that has a positive effect on solubility. 

The molecular mass of polymer significantly influences its solubility. With molecular mass of polymer increasing, the energy of interaction between chains also increases. The separation of long chains requires more energy than with short chains. 

Even polymers with the same chemical composition can show differences in the intrinsic viscosity depending on the chemical structure. Polymers with different tacticities (for example the poly(propylene) in Fig. 5.13) show an expansion of the coil in theta-solvents from atactic to iso- and syndiotactic structures. The different coil expansions are caused by different short-range interactions between the side groups [47] (see The influence of the tacticity of a polymer in Chap. 6). In good solvents, the coil expansion is dominated by the solvation of the polymer chain. In this case, there are no observable differences in the intrinsic viscosity of poly(propylenes) with different tacticities. The same observation is made for poly(styrene) in different good solvents in Fig. 6.14. 

A comparison of polymers with different polymer backbones is shown in Fig. 5.13 for the non-ionic polymers poly(ethylene oxide) (PEO), poly(acrylamide) (PAAm), and methyl cellulose (ME) in aqueous solution. The heteroatom in the backbone of PEO leads to an expanded coil structure compared to PAAm with the heteroatom in the side chain. Cellulose derivatives have in addition to the heteroatom the ring structure of the anhydroglucose unit in the polymer backbone. The methyl cellulose in this example has a less expanded coil than the synthetic PAAm and PEO. Again, it is hard to distinguish between the influence of the solvation of the polar backbone and the pure steric hindrance of the different backbone structures. 

The influence of ionic groups in the side chain of the polymer on the intrinsic viscosity is shown in Fig. 5.13 for the sodium salt of poly(acrylic acid) (PAAcNa) 

In-silico screening is one way to expand the chemical space beyond what has been reported after some 200 years of chemistry. While Chemical Abstracts and Beilstein might contain millions of chemical structures, there is another real chemical world that has yet to be mined and that is lost chemistry, the chemistry that was done but never reported. Current estimates are that on the order of 80% of the chemistry performed over the past years has not been published. It is to be found in files and lab books around the world, on dusty shelves, or destroyed long ago and lost forever. How some of the lost chemistry can be retrieved and evaluated is not our subject here. The visible chemistry that is real, the actual compounds in vials, is the center of the current focus. 

A good compound library is a corporate asset, it deserves a place on the balance sheet of any company engaged in drug discovery and development There are two more global statements that can be made about compound libraries before looking at the individual metrics that really matter  

Money and time are inseparable. Getting a billion-dollar drug into the market even just one month earlier can achieve an extra 100 million in revenue Library metrics are not confined to making the drug discovery process more effective they are as relevant in the downstream activities of drug development, process development, and clinical trials, where the big money is spent. 

So what makes a compound library good or bad, or indifferent What is going through the minds of the people who decide what compounds to add to the library, to delete or to screen, and what are the equally relevant but practical issues that need more full appreciation  

Chemists have their own very special shorthand depiction of a chemical compound, the chemical stmcture. A two-dimensional molecular structure drawing contains a wealth of information from which chemists and biologists can form opinions based on their experience and intuition. Much of the time, their thought processes will be the same, sometimes not. It depends on what particular aspect of the discovery/development process concerns them most. 

In much of their work biologists need to have an understanding of the structures of molecules, and of molecular aggregates such as exist in the membranes and interiors of cells. A very general account of chemical structure is given in this chapter. Emphasis 

The conformation of a polymer chain is the three dimensional spatial arrangement of the chain as determined by the rotation about backbone bonds. The conformation and configuration of the polymer molecules have a great influence on the properties of the polymer component. It is described by the polarity, flexibility and the regularity of the macromolecule. The helix is a typical ordered conformation type for polymers that contain regular chain microstructure. Typically carbon atoms are tetra-valent, which means that in a saturated organic compound they are surrounded by four substituent in a symmetric tetrahedral geometry. 

In HDPE, chains fold to form the lamellae and propagate outwards three dimensionally, creating a sphere-like formation. This sphere-like 

In common with other materials the end groups and sequence distribution of PAEK can be determined by techniques such as nuclear magnetic resonance (NMR) and FTIR. There is a substantial amount of literature on this subject. However, whereas measurement of crystallinity is frequently necessary, it is relatively unusual for end users to be concerned with detailed information on chemical structure. It is easy to distinguish the basic PAEK by FHR (e.g., measuring the relative intensity of the carbonyl infrared absorption) or by measuring the melting point and glass transition by DSC. 

Fluorine end groups are typically determined by F-NMR and can be compared with results on model compounds [42]. Hydroxyl end groups can be measured by FTIR - the levels in commercial polymers are very low. Fluorine is typically found to be a common end group, reflecting the use of excess fluoromonomer so as to avoid the presence of relatively unstable hydroxyl groups. C-NMR has been used in conjunction with model compounds to identify other end groups. 

Blundell, R. Crick, B. Fife, J. Peacock, A. Keller and A. Waiddon, Journal of Materials Science, 1989,24, 6, 2057. 

Medellm-Rodriguez and P.J. Phillips, Polymer Engineering and Science, 1996, 36, 5, 703. 

Shulz and B. Hsiao, Journal of Macromolecular Science Physics, 1998, B37, 5, 667. 

Polymers with delocalized % electrons are usually semiconducting compounds. The specific conductivity depends on two factors the transport of the individual charge within the macromolecule itself and the transport from molecule to molecule. 

For good intramolecular electron transport to be achieved, the molecule must be as planar as possible. The more extended the delocalized 7c-electron system, the better will be the conductivity. The specific conductivity thus increases sharply in the series coronene, ovalene, circumanthracene, graphite (Table 14-3). The activation energy El of the electronic conduction, which can be calculated using 

Incorporated heteroatoms perturb the n resonance system, thus increasing conductivity (violanthrene as opposed to violanthrone). Poly-(carbazene) and poly(azasulfene) also show considerably higher conductivity than poly(vinylene). It can be quite generally assumed that all conducting and semiconducting polymers are conjugated, but not all the (formally) conjugated polymers are semiconductors. 

The intermolecular passage of electrons is made easier when the molecular chains are in a high state of order. Crystalline poly(acetylene) thus has a specific conductivity which is four orders of magnitude higher than that of amorphous poly(acetylene). For high levels of crystallization to be possible, the crystal unit cells must be constructed as simply as possible. 

The passage of electrons occurs more readily when the macromolecules are cross-linked. Such cross-linking systems with conjugated double 

The atomic composition of polymers encompasses primarily non-metallic elements such as carbon (C), hydrogen (H) and oxygen (O). In addition, recurrent elements are nitrogen (N), chlorine (Cl), fluoride (F) and sulfur (S). The so-called semi-organic polymers contain other non-metallic elements such as silicon (Si) in silicone or polysiloxane, as well as bor or beryllium (B). Although other elements can sometime be found in polymers, because of their very specific nature, we will not mention them here. The properties of the above elements lead to specific properties that are common of all polymers. These are  

There are various ways that the monomers can arrange during polymerization however, we can break them down into two general categories uncross-linked and cross-linked. Furthermore, the uncross-linked polymers can be subdivided into linear and branched polymers. The most common example of uncross-linked polymers that present the various degrees of branching is polyethylene (PE). 

Another important family of uncross-linked polymers are copolymers. Copolymers are polymeric materials with two or more monomer types in the same chain. A copolymer that is composed of two monomer types is referred to as a bipolymer (i.e., PS-HI), and one that is formed by three different monomer groups is called a terpolymer (i.e., ABS). Depending on how the different monomers are arranged in the polymer chain, one distinguishes between random, alternating, block, or graft copolymers, discussed later in this chapter. 

Although thermoplastics can cross-link under specific conditions, such as gel formation when PE is exposed to high temperatures for prolonged periods of time, thermosets, and 

Step Linear Polycondensation Polyamides Polycarbonate Polyesters Polyethers Polyimide Siloxanes 

The specific conductivity of a polymer depends on two factors charge carrier transport within the individual molecule and transport from molecule to molecule. 

Of course, inter- and intramolecular electron transport cannot be rigorously separated from each other. For example, intermolecular electron passage is facilitated by molecular chains being in a high state of order. Thus, the specific conductivity of crystalline poly(acetylene) is four orders of magnitude higher than for the amorphous polymer. The electronic conductivity of amorphous polymers is promoted by molecular cross-linking. 

For example, poly(p-phenylene), polymerized by converting p-dichloro-benzene with sodium, has practically linear polymer chains and only a relatively low specific conductivity of 10 cm presumably because the 

Cross-linked polymers produced in this way cannot be worked easily. In this respect, charge transfer complexes from polymeric donors and acceptors are more advantageous. The poly(2-vinyl pyridine) and iodine complex, for example, has a specific conductivity of 10 H cm . It is used as a cathode in Li/h batteries for implantable heart pacemakers. This solid state battery has a higher energy density than the best lead accumulators and a lifetime of about ten years. 

Polyethylene exhibits a range of tensile strengths and flexibilities, is generally tough, can be readily extruded or molded, and is relatively inexpensive. These characteristics guarantee that the various families of polyethylene find major use as a commodity polymer. Due to its large number of variants, we use polyethylene in a wider rai e of applications than any other polymer. 

There are seven principal variants of polyethylene, which are shown schematically in Fig. 18.2. Within each family there is a range of products that share the same general characteristics. 

The homogalacturonans (HGs) are galacturonans unsubstituted, also called smooth regions. The bonds between monomers are 

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In principle, extractive distillation is more useful than azeotropic distillation because the process does not depend on the accident of azeotrope formation, and thus a greater choice of mass-separating agent is, in principle, possible. In general, the solvent should have a chemical structure similar to that of the less volatile of the two components. It will then tend to form a near-ideal mixture with the less volatile component and a nonideal mixture with the more volatile component. This has the effect of increasing the volatility of the more volatile component. 

As in the case of density or specific gravity, the refractive index, n, for hydrocarbons varies in relation to their chemical structures. The value of n follows the order n paraffins < n naphthenes < n aromatics and it increases with molecular weight. 

Group the component in a petroleum fraction, which is possible if the normal boiling temperature and the standard specific gravity are known. This method gives correct results when the chemical structure is simple as in the case of a paraffin or naphthene. 

Generate the data from the method of contributing groups which requires knowledge of the chemical structure and some careful attention. 

With regards to the overall balance of combustion, the chemical structure of the motor or heating fuel, e.g., the number of carbon atoms in tbe chain and the nature of the bonding, does not play a direct role the only important item is the overall composition, that is, the contents of carbon, hydrogen, and — eventually— oxygen in the case of alcohols or ethers added to the fuel. 

Table 5.4 gives the specific energies of selected organic liquid compounds. Compared with the isooctane chosen as the base reference, the variations from one compound to another are relatively small, on the order of 1 to 5%, with the exception of some particular chemical structures such as those of the short chain nitroparaffins (nitromethane, nitroethane, nitropropane) that are found to be energetic . That is why nitromethane, for example, is recommended for very small motors such as model airplanes it was also used in the past for competitive auto racing, for example in the Formula 1 at Le Mans before being forbidden for safety reasons. 

The RON and MON of hydrocarbons depend closely on their chemical structure. Figure 5.4 shows how the RON varies with the boiling point of each family of hydrocarbons. 

For diesel engines, the fuel must have a chemical structure that favors auto-ignition. This quality is expressed by the cetane number. 

The procedure for determining the cetane number in the CFR engine is not extremely widespread because of its complexity and the cost of carrying it out. There also exist several methods to estimate the cetane number of diesel fuels starting from their physical characteristics or their chemical structure. 

The smoke point corresponds to the maximum possible flame height (without smoke formation) from a standardized lamp (NF M 07-028). The values commonly obtained are between 10 and 40 mm and the specifications for TRO fix a minimum threshold of 25 mm. The smoke point is directly linked to the chemical structure of the fuel it is high, therefore satisfactory, for the linear paraffins, lower for branched paraffins and much lower still for naphthenes and aromatics. 

To avoid these problems, refiners commonly use additives called detergents" (Hall et al., 1976), (Bert et al., 1983). These are in reality surfactants made from molecules having hydrocarbon chains long enough to ensure their solubility in the fuel and a polar group that enables them to be absorbed on the walls and prevent deposits from sticking. The most effective chemical structures are succinimides, imides, and fatty acid amines. The required dosages are between 500 and 1000 ppm of active material. 

A primary class of additives is that of the detergents. We will examine in turn the role they play in motor fuels and the chemical structures that are necessary. 

Chemical Structures Effective in Improving the Gasoline Octane Number... 

SIMS is, strictly speaking, a destructive teclmique, but not necessarily a damaging one. In the dynamic mode, used for making concentration depth profiles, several tens of monolayers are removed per minute. In static SIMS, however, the rate of removal corresponds to one monolayer per several hours, implying that the surface structure does not change during the measurement (between seconds and minutes). In this case one can be sure that the molecular ion fragments are truly indicative of the chemical structure on the surface. 

Uchida M, Tanizaki T, Gda T and Ka]iyama T 1991 Control of surface chemical-structure and functional property of Langmuir-Blodgett-film composed of new polymerizable amphiphile with a sodium-sulfonate Maoromoieouies 24 3238-43... 

Both methods suggest that the chemical structure of A A (cis double bonds connected by two single bonds) allows the fatty acid to access the cyclooxygenase active site of PGHS-1 through a narrow hydrophobic channel and to bind in a shape favorable for the cyclooxygenation reaction. 

Chemists major task is to make compounds with desired properties. Society at large is not interested in beautiful chemical structures, but rather in the properties that these structures might have. The chemical industry can only sell properties, but it does so by conveying these properties through chemical structures. Thus, the first fundamental task in chemistry is to make inferences about which structure might have the desired property (Figure 1-2). 

The DENDRAL project initiated in 1964 at Stanford was the prototypical application of artificial intelligence techniques - or what was understood at that time under this name - to chemical problems. Chemical structure generators were developed and information from mass spectra was used to prune the chemical graphs in order to derive the chemical structure associated with a certain mass spectrum. 

To know how to transform a chemical structure into a language for computer representation and manipulation... 

To learn more about connection tables and matrix representations of chemical structures... 

In chemistry, chemical structures have to be represented in machine-readable form by scientific, artificial languages (see Figure 2-2). Four basic approaches are introduced in the following sections trivial nomenclature systematic nomenclature chemical notation and mathematical notation of chemical structures. 

The systematic lUPAC nomenclature of compounds tries to characterize compounds by a unique name. The names are quite often not as compact as the trivial names, which are short and simple to memorize. In fact, the lUPAC name can be quite long and cumbersome. This is one reason why trivial names are still heavily used today. The basic aim of the lUPAC nomenclature is to describe particular parts of the structure (fi agments) in a systematic manner, with special expressions from a vocabulary of terms. Therefore, the systematic nomenclature can be, and is, used in database systems such as the Chemical Abstracts Service (see Section 5.4) as index for chemical structures. However, this notation does not directly allow the extraction of additional information about the molecule, such as bond orders or molecular weight. 

Neither a trivial name nor the systematic nomenclature, which both represent the structure as an alphanumerical (text) string, is ideal for computer proccs.sing. The reason is that various valid compound names can describe one chemical structure (Figure 2-6). As a consequence, the name/structure correlation is unambiguous but not unique. Nowadays, programs can translate names to structures, and. structitrcs to names, to make published structures accessible in electronic journals (see also Chapter (I, Section 2 in the Handbook). 

Figure 2-6. Various logical compound names can describe one chemical structure.

The Wiswesser Line Notation (WLN) was introduced in 1946, in order to organize and to systematically describe the cornucopia of compounds in a more concise manner. A line notation represents a chemical structure by an alphanumeric sequence, which significantly simplifies the processing by the computer [9-11], (n many cases the WLN uses the standard symbols for the chemical elements. Additionally, functional groups, ring systems, positions of ring substituents, and posi-... 

The WLN was applied to indexing the Chemical Structure Index (CSI) at the Institute for Scientific Information (ISI) [13] and the Ituiex Chemicus Registry System (ICRS) as well as the Crossbow System of Imperial Chemical Industries (ICl). With the introduction of connection tables in the Chemical Abstracts Service (CAS) in 1965 and the advent of molecular editors in the 1970s, which directly produced connection tables, the WLN lost its importance. 

The ROSDAL syntax is characterized by a simple coding of a chemical structure using alphanumeric symbols which can easily be learned by a chemist [14]. In the linear structure representation, each atom of the structure is arbitrarily assigned a unique number, except for the hydrogen atoms. Carbon atoms are shown in the notation only by digits. The other types of atoms carry, in addition, their atomic symbol. In order to describe the bonds between atoms, bond symbols are inserted between the atom numbers. Branches are marked and separated from the other parts of the code by commas [15, 16] (Figure 2-9). The ROSDAL linear notation is rmambiguous but not unique. 

In 1986, David Weininger created the SMILES Simplified Molecular Input Line Entry System) notation at the US Environmental Research Laboratory, USEPA, Duluth, MN, for chemical data processing. The chemical structure information is highly compressed and simplified in this notation. The flexible, easy to learn language describes chemical structures as a line notation [20, 21]. The SMILES language has found widespread distribution as a universal chemical nomenclature... 

SLN is easy to learn and its use is intuitive. The language uses only six basic components to specify chemical structures. Four of them are hsted in Table 2-3 and can be compared directly with the SMILES notation of Section 2,3.3. 

HvaluaMon of line notations for representing u chemical structure. 

Chemists have been used to drawing chemical structures for more than a hundred years. Nowadays, structures are not only drawn on papei but they are also available in electronic form on a computer for publications, for presentations, or for the input and outptit with computer programs. For these applications, well-known software such as ISIS/Draw (MDL [31] or ChemWindow (Bio-Rad Sadtier [32]) arc used (see Section 2,12), The structures generated with these programs arc... 

Another approach applies graph theory. The analogy between a structure diagram and a topological graph is the basis for the development of graph theoretical algorithms to process chemical structure information [33-35]. 

A connection table has been the predominant form of chemical structure representation in computer systems since the early 1980s and it is an alternative way of representing a molecular graph. Graph theory methods can equally well be applied to connection table representations of a molecule. 

If the indexing of the atoms is changed, the CT will have a different appearance. Thus, the representation of a chemical structure in a CT is unambiguous but not unique, which can only be achieved by canonicalization (see below). 

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