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Conformational Analysis
In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers. Conformations that correspond to local maxima on the energy surface are the transition states between the local-minimum conformational isomers. Rotations about single bonds involve overcoming a rotational energy barrier to interconvert one conformer to another. If the energy barrier is low, there is free rotation and a sample of the compound exists as a rapidly equilibrating mixture of multiple conformers; if the energy barrier is high enough then there is restricted rotation, a molecule may exist for a rel ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cis–trans Isomerism
''Cis''–''trans'' isomerism, also known as geometric isomerism or configurational isomerism, is a term used in chemistry that concerns the spatial arrangement of atoms within molecules. The prefixes "''cis''" and "''trans''" are from Latin: "this side of" and "the other side of", respectively. In the context of chemistry, ''cis'' indicates that the functional groups (substituents) are on the same side of some plane, while ''trans'' conveys that they are on opposing (transverse) sides. ''Cis''–''trans'' isomers are stereoisomers, that is, pairs of molecules which have the same formula but whose functional groups are in different orientations in three-dimensional space. ''Cis-trans'' notation does not always correspond to E–Z notation, ''E''–''Z'' isomerism, which is an ''Absolute configuration, absolute'' stereochemical description. In general, ''cis''–''trans'' stereoisomers contain double bonds that do not rotate, or they may contain ring structures, where the rotation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Carbohydrate Conformation
Carbohydrate conformation refers to the overall three-dimensional structure adopted by a carbohydrate (saccharide) molecule as a result of the through-bond and through-space physical forces it experiences arising from its molecular structure. The physical forces that dictate the three-dimensional shapes of all molecules—here, of all monosaccharide, oligosaccharide, and polysaccharide molecules—are sometimes summarily captured by such terms as " steric interactions" and " stereoelectronic effects" (see below). Saccharide and other chemical conformations can be reasonably shown using two-dimensional structure representations that follow set conventions; these capture for a trained viewer an understanding of the three-dimensional structure via structure drawings (see organic chemistry article, and "3D Representations" section in molecular geometry article); they are also represented by stereograms on the two dimensional page, and increasingly using 3D display technologies on compu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Macrocycles
Macrocycles are often described as molecules and ions containing a ring of twelve or more atoms. Classical examples include the crown ethers, calixarenes, porphyrins, and cyclodextrins. Macrocycles describe a large, mature area of chemistry. Synthesis The formation of macrocycles by ring-closure is called macrocylization. Pioneering work was reported for studies on terpenoid macrocycles. The central challenge to macrocyclization is that ring-closing reactions do not favor the formation of large rings. Instead, small rings or polymers tend to form. This kinetic problem can be addressed by using high-dilution reactions, whereby intramolecular processes are favored relative to polymerizations. Some macrocyclizations are favored using template reactions. Templates are ions, molecules, surfaces etc. that bind and pre-organize compounds, guiding them toward formation of a particular ring size. The crown ethers are often generated in the presence of an alkali metal cation, whic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cycloalkane
In organic chemistry, the cycloalkanes (also called naphthenes, but distinct from naphthalene) are the monocyclic saturated hydrocarbons. In other words, a cycloalkane consists only of hydrogen and carbon atoms arranged in a structure containing a single ring (possibly with side chains), and all of the carbon-carbon bonds are single. The larger cycloalkanes, with more than 20 carbon atoms are typically called ''cycloparaffins''. All cycloalkanes are isomers of alkenes. The cycloalkanes without side chains are classified as small (cyclopropane and cyclobutane), common (cyclopentane, cyclohexane, and cycloheptane), medium (cyclooctane through cyclotridecane), and large (all the rest). Besides this standard definition by the International Union of Pure and Applied Chemistry (IUPAC), in some authors' usage the term ''cycloalkane'' includes also those saturated hydrocarbons that are polycyclic. In any case, the general form of the chemical formula for cycloalkanes is C''n''H2(' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cyclohexane Conformation
In organic chemistry, cyclohexane conformations are any of several three-dimensional shapes adopted by molecules of cyclohexane. Because many compounds feature structurally similar six-membered rings, the structure and dynamics of cyclohexane are important prototypes of a wide range of compounds. The internal angles of a regular, flat hexagon are 120°, while the preferred angle between successive bonds in a carbon chain is about 109.5°, the tetrahedral angle (the arc cosine of −). Therefore, the cyclohexane ring tends to assume non-planar (warped) conformations, which have all angles closer to 109.5° and therefore a lower strain energy than the flat hexagonal shape. Consider the carbon atoms numbered from 1 to 6 around the ring. If we hold carbon atoms 1, 2, and 3 stationary, with the correct bond lengths and the tetrahedral angle between the two bonds, and then continue by adding carbon atoms 4, 5, and 6 with the correct bond length and the tetrahedral angle, we can var ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Klyne–Prelog System
In stereochemistry, the Klyne–Prelog system (named for William Klyne and Vladimir Prelog) for describing conformations about a single bond offers a more systematic means to unambiguously name complex structures, where the torsional or dihedral angles are not found to occur in 60° increments. Klyne notation views the placement of the substituent on the front atom as being in regions of space called anti/syn and clinal/periplanar relative to a reference group on the rear atom. A plus (+) or minus (–) sign is placed at the front to indicate the sign of the dihedral angle. Anti or syn indicates the substituents are on opposite sides or the same side, respectively. Clinal substituents are found within 30° of either side of a dihedral angle of 60° (from 30° to 90°), 120° (90°–150°), 240° (210°–270°), or 300° (270°–330°). Periplanar substituents are found within 30° of either 0° (330°–30°) or 180° (150°–210°). Juxtaposing the designations produces the fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Strain (chemistry)
In chemistry, a molecule experiences strain when its chemical structure undergoes some stress which raises its internal energy in comparison to a strain-free reference compound. The internal energy of a molecule consists of all the energy stored within it. A strained molecule has an additional amount of internal energy which an unstrained molecule does not. This extra internal energy, or strain energy, can be likened to a compressed spring.Anslyn and Dougherty, ''Modern Physical Organic Chemistry'', University Science Books, 2006, Much like a compressed spring must be held in place to prevent release of its potential energy, a molecule can be held in an energetically unfavorable conformation by the bonds within that molecule. Without the bonds holding the conformation in place, the strain energy would be released. Summary Thermodynamics The equilibrium of two molecular conformations is determined by the difference in Gibbs free energy of the two conformations. From this ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enantiomer
In chemistry, an enantiomer ( /ɪˈnænti.əmər, ɛ-, -oʊ-/ ''ih-NAN-tee-ə-mər''; from Ancient Greek ἐνάντιος ''(enántios)'' 'opposite', and μέρος ''(méros)'' 'part') – also called optical isomer, antipode, or optical antipode – is one of two stereoisomers that are non-superposable onto their own mirror image. Enantiomers are much like one's right and left hands, when looking at the same face, they cannot be superposed onto each other. No amount of reorientation will allow the four unique groups on the chiral carbon (see Chirality (chemistry)) to line up exactly. The number of stereoisomers a molecule has can be determined by the number of chiral carbons it has. Stereoisomers include both enantiomers and diastereomers. Diastereomers, like enantiomers, share the same molecular formula and are non-superposable onto each other however, they are not mirror images of each other. A molecule with chirality rotates plane-polarized light. A mixture of equals a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dihedral Angle
A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimensions, a dihedral angle represents the angle between two hyperplanes. The planes of a flying machine are said to be at positive dihedral angle when both starboard and port main planes (commonly called wings) are upwardly inclined to the lateral axis. When downwardly inclined they are said to be at a negative dihedral angle. Mathematical background When the two intersecting planes are described in terms of Cartesian coordinates by the two equations : a_1 x + b_1 y + c_1 z + d_1 = 0 :a_2 x + b_2 y + c_2 z + d_2 = 0 the dihedral angle, \varphi between them is given by: :\cos \varphi = \frac and satisfies 0\le \varphi \le \pi/2. Alternatively, if an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Butane Conformations And Relative Energies
Butane () or ''n''-butane is an alkane with the formula C4H10. Butane is a gas at room temperature and atmospheric pressure. Butane is a highly flammable, colorless, easily liquefied gas that quickly vaporizes at room temperature. The name butane comes from the root but- (from butyric acid, named after the Greek word for butter) and the suffix -ane. It was discovered by the chemist Dr. Walter Snelling in 1912. It was found dissolved in crude petroleum in 1864 by Edmund Ronalds, who was the first to describe its properties. Butane is one of a group of liquefied petroleum gases (LP gases). The others include propane, propylene, butadiene, butylene, isobutylene, and mixtures thereof. Butane burns more cleanly than gasoline and coal. Density The density of butane is highly dependent on temperature and pressure in the reservoir. For example, the density of liquid phase is 571.8±1 kg/m3 (for pressures up to 2MPa and temperature 27±0.2 °C), while the density of liqu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Drug Design
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it. Drug design frequently but not necessarily relies on computer modeling techniques. This type of modeling is sometimes referred to as computer-aided drug design. Finally, drug design that relies on the knowledge of the three-dimensional structure of the biomolecular target is known as structure-based drug design. In addition to small molecules, biopharmaceuticals including peptides and especially therapeutic antibodies a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
