Geometry and Conformation

The structure, geometry, and conformation of solid 2,4-diphenyl-6-methyldihydropyrimidine (20) were determined by X ray diffraction.24 The analysis has shown clearly that the crystalline form of this compound has a 1,4-dihydro structure (20a) with a nonplanar ring. Atoms N-l and C-4 are out 

Olofson and co-workers28 obtained evidence for homoaromaticity of the l,l,4-trimethyl-l,4-dihydro-l,2,4,5-tetrazinium cation (23) from a crystal-structure determination. The quaternary nitrogen N-l is tetrahedral, causing the ring to assume the boat shape. There is evidence for substantial delocalization of the N-4 electron pair (hybridization between sp2 and sp3), whereas N-l is 0.51 A, while N-4 is only 0.26 A above the N-2—C-3—N-5— C-6 plane. It should be noted that the crystal structures of 22 and 23 have remarkable similarities. Both molecules are in the boat conformation with their prows twice as high as their sterns. Also, carbons occupy these apices in 

while nitrogens occupy these sites in 23. Molecule 23 is slightly flatter than 22, and subsequently the increased boat character of the latter molecule is reflected in a decreased rate of ring inversion from the one boat form to the other. It should be noted that all attempts to decrease ring inversion in 1,2-dihydropyrimidine (21) under the conditions reported24 failed. The reason for this failure probably lies in the close proximity of C-2 to the plane, which acts to increase the rate of inversion. 

To confirm the structures of NaBH4 reduction products of 1,2,4-triazines, Japanese workers recently published an X-ray study, showing that the product has the 2,5-dihydro structure (25). The dihydrotriazine ring was found to take the boat conformation, which, because of the delocalization of the n electrons and lone-pair electrons of N-2, was significantly squashed.33 

Streitwieser, Jr., Molecular Orbital Theory for Organic Chemistry, p. 275. Wiley, New 

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Calculations on larger molecules have been carried out using molecular mechanics techniques and the Merck force field.- This method has proven to be suitable for the calculation of equilibrium geometries and conformational energy differences. 

Crippen, G. M. Distance Geometry and Conformational Calculations, Research Studies Press, Wiley, New York, 1981. 

AMX, this is possible, because there are three nonselective relaxation-rate values for three unknown py values (pam. Pax, Pmx)- For a system in which y > 3 proton spins, this analysis cannot be unambiguously applied, because there are j(j — )/2 values of py to be determined from j measured R (ns) values. However, under favorable circumstances (see Section IV), depending on the relative disposition of the proton spins in the molecular frame, some Py values may be disregarded. This affords a good estimate of the appropriate Py values, and, hence, information about molecular geometry and conformation. 

Gharge Transport in Single Au Alkanedithiol Au Junctions Coordination Geometries and Conformational Degrees of Freedom. Journal of the American Chemical Society, 130, 318-326. 

We will now consider the studies devoted to the next two linear polyenes 1,3,5-hexatriene and 1,3,5,7-octatetraene. First, we will present the results corresponding to geometries and conformational energies computed for these compounds. We will then discuss the computed frequencies and force fields. 

Molecular mechanics methods achieve good structural accuracy for classical molecules, whereas their reliability for species with particular combinations of atoms may be questionable, particularly for molecules containing heteroatoms, which affect geometry and conformation via the position of their lone-pairs. Force-field programs, for example, often fail to calculate the geometry... 

Romers, C., Geometry and Conformational Properties of Some Five- and Six-Membered Heterocyclic Compounds Containing Oxygen and Sulfur, 4, 39. 

The purpose of this brief survey was to demonstrate that, despite the criticisms which may be made of the use of any semi-empirical quantum technique for structural and conformational studies, the CNDO/2 and Extended CNDO/2 formalisms are definitely reliable tools for theoretical conformational analyses in inorganic and coordination chemistry. Moreover, if these tools are combined with the most suitable experimental techniques (i.e. microwave spectroscopy and electron diffraction) in that field, many problems of geometry and conformation can be solved in a way that neither of these approaches could have accomplished alone. 

Crippen, G.M. Distance geometry and conformational calculations. In Chemometrics Research Studies, Vol. 1, Bawden, D. (ed.) John Wiley, Chichester, UK, 1981. 

R.J. Abraham, S.L.R. Ellison, P. Schonholzer, W.A. Thomas, A theoretical and crystallographic study of the geometries and conformations of fluoro-olefins as peptide analogs. Tetrahedron 42 (1986) 2101-2110. 

One approach is to construct a more flexible description of electron motions in terms of a combination of Hartree-Fock descriptions for ground and excited states. Configuration interaction (Cl) and Moller-Plesset (MP) models are two of the most commonly used models of this type. The so-called second-order Moller-Plesset model (MP2) is the most practical and widely employed. It generally provides excellent descriptions of equilibrium geometries and conformations, as well as thermochemistry, including the thermochemistry of reactions where bonds are broken and formed. Discussion is provided in Section n. 

An alternative approach to improve upon Hartree-Fock models involves including an explicit term to account for the way in which electron motions affect each other. In practice, this account is based on an exacf solution for an idealized system, and is introduced using empirical parameters. As a class, the resulting models are referred to as density functional models. Density functional models have proven to be successful for determination of equilibrium geometries and conformations, and are (nearly) as successful as MP2 models for establishing the thermochemistry of reactions where bonds are broken or formed. Discussion is provided in Section II. 

Molecular mechanics models differ both in the number and specific nature of the terms which they incorporate, as well as in the details of their parameterization. Taken together, functional form and parameterization, constitute what is termed a force field. Very simple force fields such as SYBYL, developed by Tripos, Inc., may easily be extended to diverse systems but would not be expected to yield quantitatively accurate results. On the other hand, a more complex force field such as MMFF94 (or more simply MMFF), developed at Merck Pharmaceuticals, while limited in scope to common organic systems and biopolymers, is better able to provide quantitative accounts of molecular geometry and conformation. Both SYBYL and MMFF are incorporated into Spartan. 

As commented previously, molecular mechanics models are applicable only to investigation of equihbrium geometries and conformations. 

Molecular mechanics models are restricted to the description of molecular equilibrium geometry and conformation. They are the method of choice for conformational searching on complex systems. 

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