Molecular depiction

Cuissart, B., Touffet, F., Cremilleux, B., Bureau, R., and Rault, S. (2002) The maximum common substructure as a molecular depiction in a supervised classification context experiments in quantitative structure/biodegradability relationships. J. Chem. Inf. Comput. Sci. 42, 1043-1052. 

Subsequent crystallographic studies detailing a related natural product rapamycin (Figure 3.9)140 provided a molecular depiction of these complexes. In a refined 2.0 A structure by Clardy,141 rapamycin provides a two-faced binding wherein the C2-C12 region binds to FKBP12 and the C16-C23 region interacts with FRB. 

In the next sample problem, we use molecular depictions to find the formula, name, and mass. 

SAMPLE PROBLEM 3.9 Using Molecular Depictions to Solve... 

We can use atomic masses, not ionic masses, because electron loss equals electron gain, so electron mass is balanced. In the next two sample problems, the name or molecular depiction is used to find a compound s molecular or formula mass. 

Using Molecular Depictions to Determine Formula, Name, and Mass... 

Using Molecular Depictions in a Limiting-Reactant Problem... 

The surface forces apparatus of crossed mica cylinders (Section VI-4D) has provided a unique measurement of friction on molecular scales. The apparatus is depicted in Fig. VI-3, and the first experiments involved imposing a variation or pulsing in the sepa-... 

The first step consists of the molecular adsorption of CO. The second step is the dissociation of O2 to yield two adsorbed oxygen atoms. The third step is the reaction of an adsorbed CO molecule with an adsorbed oxygen atom to fonn a CO2 molecule that, at room temperature and higher, desorbs upon fomiation. To simplify matters, this desorption step is not included. This sequence of steps depicts a Langmuir-Hinshelwood mechanism, whereby reaction occurs between two adsorbed species (as opposed to an Eley-Rideal mechanism, whereby reaction occurs between one adsorbed species and one gas phase species). The role of surface science studies in fomuilating the CO oxidation mechanism was prominent. 

In the above discussion it was assumed that the barriers are low for transitions between the different confonnations of the fluxional molecule, as depicted in figure A3.12.5 and therefore the transitions occur on a timescale much shorter than the RRKM lifetime. This is the rapid IVR assumption of RRKM theory discussed in section A3.12.2. Accordingly, an initial microcanonical ensemble over all the confonnations decays exponentially. However, for some fluxional molecules, transitions between the different confonnations may be slower than the RRKM rate, giving rise to bottlenecks in the unimolecular dissociation [4, ]. The ensuing lifetime distribution, equation (A3.12.7), will be non-exponential, as is the case for intrinsic non-RRKM dynamics, for an mitial microcanonical ensemble of molecular states. 

The first classical trajectory study of iinimoleciilar decomposition and intramolecular motion for realistic anhannonic molecular Hamiltonians was perfonned by Bunker [12,13], Both intrinsic RRKM and non-RRKM dynamics was observed in these studies. Since this pioneering work, there have been numerous additional studies [9,k7,30,M,M, ai d from which two distinct types of intramolecular motion, chaotic and quasiperiodic [14], have been identified. Both are depicted in figure A3,12,7. Chaotic vibrational motion is not regular as predicted by tire nonnal-mode model and, instead, there is energy transfer between the modes. If all the modes of the molecule participate in the chaotic motion and energy flow is sufficiently rapid, an initial microcanonical ensemble is maintained as the molecule dissociates and RRKM behaviour is observed [9], For non-random excitation initial apparent non-RRKM behaviour is observed, but at longer times a microcanonical ensemble of states is fonned and the probability of decomposition becomes that of RRKM theory. 

Figure Bl.4.3. (a) A schematic illustration of the THz emission spectrum of a dense molecular cloud core at 30 K and the atmospheric transmission from ground and airborne altitudes (adapted, with pennission, from [17]). (b) The results of 345 GHz molecular line surveys of tlu-ee cores in the W3 molecular cloud the graphics at left depict tire evolutionary state of the dense cores inferred from the molecular line data [21],...

Zeolites (section C2.13) are unique because they have regular pores as part of their crystalline stmctures. The pores are so small (about 1 nm in diameter) that zeolites are molecular sieves, allowing small molecules to enter the pores, whereas larger ones are sieved out. The stmctures are built up of linked SiO and AlO tetrahedra that share O ions. The faujasites (zeolite X and zeolite Y) and ZSM-5 are important industrial catalysts. The stmcture of faujasite is represented in figure C2.7.11 and that of ZSM-5 in figure C2.7.12. The points of intersection of the lines represent Si or A1 ions oxygen is present at the centre of each line. This depiction emphasizes the zeolite framework stmcture and shows the presence of the intracrystalline pore stmcture. In the centre of the faujasite stmcture is an open space (supercage) with a diameter of about 1.2 nm. The pore stmcture is three dimensional. 

Another way to overcome the step-size restriction fc < is to use multiple-time-stepping methods [4] or implicit methods [17, 18, 12, 3). In this paper, we examine the latter possibility. But for large molecular systems, fully implieit methods are very expensive. For that reason, we foeus on the general class of scmi-implicit methods depicted in Fig. 1 [12]. In this scheme. Step 3 of the nth time step ean be combined with Step 1 of the (n - - l)st time step. This then is a staggered two-step splitting method. We refer to [12] for further justification. 

This German stamp depicts a molecular model of urea and was issued in 1982 to commemorate the bun dredth anniversary of Woh ler s death The computer graphic that opened this in troductory chapter is also a model of urea... 

FIGURE 12 7 The mechanism of Friedel-Crafts alkylation The molecular model depicts the cyclohexadienyl cation intermediate formed in step 1... 

Some classes of compounds are so prone to fragmentation that the molecular ion peak IS very weak The base peak m most unbranched alkanes for example is m/z 43 which IS followed by peaks of decreasing intensity at m/z values of 57 71 85 and so on These peaks correspond to cleavage of each possible carbon-carbon bond m the mol ecule This pattern is evident m the mass spectrum of decane depicted m Figure 13 42 The points of cleavage are indicated m the following diagram... 

---