Imaging molecules

Figure 9.1 Tetrahedral carbon atoms and their mirror images. Molecules of the type CH3X and CH2XY are identical to their mirror images, but a molecule of the type CHXYZ is not. A CHXYZ CH3X X l X hK vh H ...

To appreciate the difference between the two cis isomers, look carefully at the complex and its mirror image (or better, build models). No matter how we twist and turn the molecules, we cannot superimpose the mirror image molecule on the original molecule. It is like trying to superimpose your right hand on your left hand. The two molecules are, in fact, two distinct compounds. Optical isomers can also occur whenever four different groups form a tetrahedral complex, but not if they form a square-planar complex. 

For example, (7) is trans-2-methylcyclohexanol in addition the chirality of C-l and C-2 should be designated by the R/S) notation, and the correct systematic name is therefore (lR,2R)-2-methylcyclohexanol (7a), since the mirror image molecule, (lS,2S)-2-methylcyclohexanol (7b) is also the trans isomer. The cis isomer is also chiral, and diastereoisomeric with the trans isomer the two enantiomers would be (lS,2R)-2-methylcyclohexanol (24a) and ( R,2S)-2-methylcyclohexanol (24b). 

Chirality (handedness, from Greek cheir = hand) is the term used for objects, including molecules, which are not superposable with their mirror images. Molecules which display chirality, such as (S)-(+)-lactic acid (/, Fig. 1) are called chiral. Chirality is often associated with a chiral center (formerly called an asymmetric atom ), such as the starred carbon atom in lactic acid (Fig. 1) but there are other elements that give rise to chirality the chiral axis as in allenes (see below) or the chiral plane, as in certain substituted paracyclophanes.1,2)... 

Since the enantiomeric resolution of tartaric acid in 1848 by Pasteur, a longstanding issue is whether mirror-image molecules are energetically identical with respect to the origin of biomolecular homochirality [100]. In 1860 Pasteur first conjectured that the homochirality may come from certain intrinsically handed force existing in the Universe [1]. In 1898, Kipping and Pope reported experimental results in relation to NaC103 with l- and d-... 

Since the historical PV weak force origin /3-decay experiment of 60Co [ 106], theoreticians presumed that the tiny parity violating WNC at molecular and subatomic levels may also allow a distinction between mirror image molecules at the macroscopic level as well. This is because PV-WNC at the molecular level may be a candidate for the homochiral scenario under terrestrial and extraterrestrial conditions [1,2,104,109-118]. The WNC, however, did not induce any observable PV effects between enantiomers in their ground states because of the minuscule PV energy difference (PVED) of 10 19 eV and/or negligibly small 10 - % ee in racemates. Theoreticians also proposed several possible amplification mechanisms at reproducible detection levels within laboratory time scales and at terrestrial locations [113,117,118]. 

The study of organic molecules on surfaces has been an early application of STM. Smith [10] has found that liquid crystal molecules can be adsorbed on graphite and imaged with atomic resolution by STM in ambient conditions. Organic molecules were also studied by STM in vacuum [11-13]. After true atomic resolution by AFM became feasible, several groups imaged molecules in vacuum by AFM [14-16]. 

Fig. 5. Surface diffusion of the rigid rodlike molecule 4-trans-2-(pyrid-4-yl-vinyl) benzoic acid on Pd(110). In (a) and (b) two consecutive STM images taken at 361 K are shown which demonstrate the 1-dim motion. Arrows indicate molecules whose position changed circles mark fractionally imaged molecules moving under the STM tip in the course of the measurement, (c) Model for the flat adsorption geometry explaining the two observed molecular orientations in the STM data. The length of the molecule is 12.5 A. (d) Arrhenius plot of single molecule hopping rates [75].

Fig. 3 Orange and lemon odor in mirror image molecules R-(+)- and S-(-)-limonene, respectively...

The mirror image of trans- 1,2-dichlorocyclopentane is different from (nonsuper-imposable with) the original molecule. These are two different compounds, and we should expect to discover two mirror-image isomers of trans- 1,2-dichlorocyclopentane. Make models of these isomers to convince yourself that they are different no matter how you twist and turn them. Nonsuperimposable mirror-image molecules are called enantiomers. A chiral compound always has an enantiomer (a nonsuperimposable mirror image). An achiral compound always has a mirror image that is the same as the original molecule. Let s review the definitions of these words. 

Mirror-image molecules have nearly identical physical properties. Compare the following properties of (K)-2-bromobutane and (S)-2-bromobutane. 

A molecule whose geometrical structure is not identical to its mirror image possesses chirality. For example, enantiomers are mirror-image structures of a chiral molecule. Two mirror-image molecules are identified as l- and D-enantiomers. Amino acids and deoxyribose in DNA are chiral molecules. Asy mmetry in biochemistry requires the constant catalytic production of the preferred enantiomer in the reactions between enantiomers, a process known as racemization. In systems with appropriate chiral autocatalysis, instability may appear. Due to random fluctuations, the instability occurs accompanying the bifurcation of asymmetric states in which one enantiomer dominates. These states of broken symmetry can be observed in the following simple model reaction scheme with chiral autocatalysis (Kondepudi and Prigogine, 1999)... 

Schmidt, Karen F. Mirror-Image Molecules. Science News 143 (May 29,1993) 348-350. 

Mirror-image molecules that are not superimposable are called enam tiomers (Greek enantio, opposite ). Enantiomers are related to each oth as a right hand is related to a left hand and result whenever a tetrahedral carbon is bonded to four different substituents (one need not be H). For example, lactic acid (2-hydroxypropanoic acid) exists as a pair of enantiomers because there are four different groups (-H, -OH, -CH , -COOK) bonded to the central carbon atom. The enantiomers are called ( + )-Iactac acid and (—)-lactic acid. 

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