Molecular conformation methods

Traditionally, molecular mechanics has not been the method of choice for predicting transition structures. However, since it is the only method viable for many large molecules, some elforts have been made to predict transition structures. Since the bonds are explicitly defined in molecular mechanics methods, it is not possible to simply find a point that is an energy maximum, except for conformational intermediates. 

Ah initio calculations of polymer properties are either simulations of oligomers or band-structure calculations. Properties often computed with ah initio methods are conformational energies, polarizability, hyperpolarizability, optical properties, dielectric properties, and charge distributions. Ah initio calculations are also used as a spot check to verify the accuracy of molecular mechanics methods for the polymer of interest. Such calculations are used to parameterize molecular mechanics force fields when existing methods are insulficient, which does not happen too often. 

S. Piofeta, Ji., Conformational Analysis of Aliphatic Amines by Quantum and Molecular Mechanical Methods, Pb.D. Dissertation, University of Georgia, 1978, available from University Microfilms International, Arm Arbor, Mich. 

The melting points, optical rotations, and uv spectral data for selected prostanoids are provided in Table 1. Additional physical properties for the primary PGs have been summarized in the Hterature and the physical methods have been reviewed (47). The molecular conformations of PGE2 and PGA have been determined in the soHd state by x-ray diffraction, and special H and nuclear magnetic resonance (nmr) spectral studies of several PGs have been reported (11,48—53). Mass spectral data have also been compiled (54) (see Mass spectrometry Spectroscopy). 

Figure 6 A schematic representation of two clustering methods, m which each point represents a single molecular conformation and the circles are the similarity cutoff distances used to define the clusters, (a) Three clusters are defined when overlapping clusters are grouped together, (h) Five clusters are defined when the overlaps are removed from one of the overlapping clusters.

The geometries and relative energies of the different conformations of model chalcogen diimides E(NR)2 (E = S, Se R = H, Me, Bu and SiMe3) have been investigated by using ab initio and DET molecular orbital methods.The cis,trans conformation is predicted to be most stable with the exception of the parent molecules E(NH)2 and the unsymmetrical systems RNSNH, for which the cis,cis conformation is slightly more stable than the cis, trans isomer. 

The molecular mechanics method has been applied to the calculation of conformational properties of the thiane, dithiane and trithiane oxide systems which are... 

Gundertofte, K., Liljefors, T., Norrby, P.-O., Pettersson, I. A comparison of conformational energies calculated by several molecular mechanics methods. 

As it was mentioned in Section 9.4.1, 3D structures generated by DG have to be optimized. For this purpose, MD is a well-suited tool. In addition, MD structure calculations can also be performed if no coarse structural model exists. In both cases, pairwise atom distances obtained from NMR measurements are directly used in the MD computations in order to restrain the degrees of motional freedom of defined atoms (rMD Section 9.4.2.4). To make sure that a calculated molecular conformation is rehable, the time-averaged 3D structure must be stable in a free MD run (fMD Sechon 9.4.2.5J where the distance restraints are removed and the molecule is surrounded by expMcit solvent which was also used in the NMR measurement Before both procedures are described in detail the general preparation of an MD run (Section 9.4.2.1), simulations in vacuo (Section 9.4.2.2) and the handling of distance restraints in a MD calculation (Section 9.4.2.3) are treated. Finally, a short overview of the SA technique as a special M D method is given in Sechon 9.4.2.6. 

As described in Section 9.4, the determination and refinement of molecular conformations comprehends three main methods DG, MD and SA. Other techniques like Monte Carlo calculations have only a limited applicability in the field of structure elucidation. In principle, it is possible to exclusively make use of DG, MD or SA, but normally it is strongly suggested to combine these methods in order to obtain robust and reliable structural models. Only when the results of different methods match a 3D structure should be presented. There are various ways of combining the described techniques and the procedural methods may differ depending on what kind of molecules are investigated. However, with the flowchart in Fig. 9.13 we give an instruction on how to obtain a reliable structural model. 

Finally, Burkhard Luy, Andreas Frank and Horst Kessler discuss Conformational Analysis of Drugs by Nuclear Magnetic Resonance Spectroscopy . The determination and refinement of molecular conformations comprehends three main methods distance geometry (DG), molecular dynamics (MD) and simulated anneahng (SA). In principle, it is possible to exclusively make use of DG, MD or... 

The examples cited above are of molecules which are not strictly speaking noorigid, although they have more than one well-defined equilibrium configuration. The 1,2-dichloroetbane molecule discussed above is a classic example. With the aid of computer programs that have been developed to treat this problem, it has become possible to calculate wifi) confidence the equilibrium conformations of such molecules, as well as the energy differences and the tunneling barriers between them. It is appropriate here to summarize briefly the so-called molecular mechanics method that is currently employed to obtain these results. 

The final step in the molecular-mechanics calculation of molecular conformation involves the minimization of the energy Approximations are involved whose importance is not always clear. Usually, all first derivatives with respect to the various internal coordinates are set equal to zero - although these coordinates are often not independent (see Section 10.6). Furthermore, the final conformation obtained depends on the assumed initial structure. Therefore, (he method must be applied with care and a certain amount of chemical intuition. In spite of these uncertainties the molecular mechanics method has been employed with considerable success, particularly in the conformational analysis of branched alkanes. For molecules containing hetero-atoms, it can be applied, but with somewhat less confidence. 

When the data in this table are plotted, the graph shown in Fig. 33 is obtained. From this one can calculate a pKa of 2.85 for displacement of benzimidazole in D2O. In addition, since room temperature is above the coalescence temperature, it is possible to set a lower limit on the exchange rate between coordinated and uncoordinated benzimidazole of 3.1 X 102 sec-1. From Fig. 33 one can, by extrapolation, calculate the C(20)-methyl resonance of the base-on and "base-off forms to be 0.41 and 1.05 respectively. These numbers can be used, with the assumption of fast exchange, to determine the relative amounts of "base-on and base-off" species from the observed C(20)-chemical shift for any arbitrary sample. Such information would be useful, for instance, when investigating the displacement of benzimidazole by other Lewis bases. Thus for the simple case of benzimidazole displacement we have shown that NMR provides a method for studying the molecular conformation of vitamin B12. 

Finally, as in macro-Raman experiments, orientation-insensitive spectra can also be calculated for spectromicroscopy. A method has been developed recently for uniaxially oriented systems and successfully tested on high-density PE rods stretched to a draw ratio of 13 and on Bombyx mori cocoon silk fibers [65]. This method has been theoretically expanded to biaxial samples using the K2 Raman invariant and has proved to be useful to determine the molecular conformation in various polymer thin films [58]. 

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