Geometry in solution

One very popular technique is an adaptation of the Born model for orbital-based calculations by Cramer and Truhlar, et. al. Their solvation methods (denoted SMI, SM2, and so on) are designed for use with the semiempirical and ah initio methods. Some of the most recent of these methods have a few parameters that can be adjusted by the user in order to customize the method for a specific solvent. Such methods are designed to predict ACsoiv and the geometry in solution. They have been included in a number of popular software packages including the AMSOL program, which is a derivative of AMPAC created by Cramer and Truhlar. 

The monomeric [NbCl3(py)3] has been used for the preparation of [Nb(NCS)3(py)3].593 Ks[Nb(CN)g], obtained by electrosynthesis,536 is the only X-ray-characterized monomeric homoleptic Nb111 compound. A dodecahedral D2d geometry with two sets of Nb—C distances was found in the solid.635 IR data suggest a change to a D4d geometry in solution. 13CNMR data are compatible with either a D or a fluxional Did polyhedron. 

D3 symmetry. 32> This conformation is adopted by trimesitylborane (1 g) in the solid state, and the low-temperature H-nmr spectra of divers triarylboranes which have substituents other than hydrogen in all six ortho positions are consistent with this geometry in solution. At higher temperatures, the spectra of such molecules reflect rapid stereoisomerizations which are interpreted in terms of flip mechanisms. 

One of the most prominent hydrogen-bonded systems is DNA. Despite numerous experimental and theoretical investigations on vibrational spectra of nucleic acid bases [7-13], information on inter- and intramolecular interactions in base pairs and DNA oligomers is still limited [14-25]. A recent example is the work on single adenine-uracil (AU) base pairs in the Watson-Crick geometry in solution, which showed an enhancement of vibrational energy... 

Nuclear Overhauser effect (NOE) experiments clarified the preference of the cis-trans-geometry in solution for cyclic lactams 19. For 19a-c, X-ray geometries (Section 14.10.3.1) retain in solution, and NOEs were observed between the methylene protons next to the ring carbonyl and the NCH2 protons, whereas no such NOE was observed in 19d <2002CC2656>. 

Lodewyk et al. " have extended the approach of Jain et al. to include C chemical shifts. The RMSE results for the C chemical shifts of their recommended computational models are listed in Table 2.8. Errors are larger than for proton chemical shifts, but quite reasonable results can again be had with modest computational effort. Again, it is important to note that optimization of the geometry in solution is unnecessary. Tantillo maintains a Web site compiling the recommended methods and scahng factors for H and C chemical shift prediction. 

Heteronuclear NOE experiments provided evidence for the anti geometry in solution. Enhancement at the aldehydic (but not the phenyl) proton absorption was observed upon irradiation of the fluorine atoms, see ref. 67. 

In practice we often neglect the distinction between AG and AGg(x), although sometimes it is important to optimize the geometry in solution or to at least include the conformational part. (If one did try to include the rotational part, one would run into the problem that the 3 gas-phase rotations are converted in liquid solution into low-frequency librations that are strongly coupled to low-energy solvent motions). In the rest of this section... 

The calculated individual contributions to the total aqueous solvation free energies of 30 organic compounds are given in Table 1. The electrostatic (SCRF) contributions were calculated using semiempirical AMI (Austin Model 1 [60,61]) method. The dispersion energies were calculated using INDO/1 parameterization [62] and AMI optimized molecular geometries in solution. A comparison of different columns in Table 1 with the experimental solvation... 

Mascharak et al. 63) have prepared a structural BLM model PMAH containing pyrimidine, imidazole, and primary and secondary amine building blocks. The iron -PMAH complex was studied by X-ray absorption, magnetic circular dichroism, and resonance Raman spectroscopy 63). This Fe-BLM model exhibits a five-coordinate, square pyramidal geometry in the solid state and a distorted octahedral geometry in solution with a solvent molecule at the sixth position. Similar spectral features have been found for Fe -BLM. This PMAH-Fe" complex binds O2 to generate PMAH-Fe "-OOH, a low-spin hydroperoxo-iron(III) complex 64) able to promote the lipid peroxidation as BLM 65). 

Although this article focuses on skeletal isomerism and extends the concept to those compounds with different geometries in solution, it deals only with examples... 

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