Solvent effect hybridization

The relationship between the structure of 1,2,4-thiadiazolidines and their H NMR spectral solvent effects has been studied by measurement of the NMR chemical shift differences (Av) of 39 derivatives in various solvents (CgDg, CCU) for methyl or methylene groups attached to an sp2-hybridized nitrogen, Av correlates linearly with Hammett a constants and for those attached to an sp3 4-hybridized nitrogen, with Taft a° constants <1982AHC285>. 

The solvation models are used to predict the properties of small molecules and large biomolecules employing different levels of theory. In the prediction of solvent effect using electronic structure calculation, semiempirical, HF, post-HF, and DFT-based hybrid methods have been widely used [2-11], Since a wealth of literature is... 

Compounds in which the carbons are sp3 hybridized display the same confused situation. Erickson 78> reports that the trans vicinal H—H coupling constant of c//-dibromosuccinic anhydride (which is reasonably rigid) varies from 2.5 Hz in CHC13 to 6.0 Hz in acetone and dioxane. The same paper reports that the meso dibromosuccinic anhydride and the two corresponding dichloro compounds do not display any solvent dependence of their coupling constants. (Erickson also reports that lJc.H of the dl- dibromide decreases from 172 Hz in chloroform to 166 Hz in acetone and 165 Hz in dioxane exactly the opposite behavior from that observed for any other 1JC H coupling ever studied). It is at least possible that these data result from chemical degradation of the solute rather than from true solvent effects as discussed here. 

An interesting alternative that combines the advantages of both classical and quantum mechanics is to use hybrid QM/MM models, first introduced by Arieh Warshel for modeling enzymatic reactions [7]. Here, the chemical species at the active site are treated using high-level (and therefore expensive) QM models, which are coupled to a force field that describes the reaction environment. Hybrid models can thus take into account solvent effects in homogeneous catalysis, support structure and interface effects in heterogeneous catalysis, and enzyme structure effects in biocatalysis. 

Computational methods to study solvent effects on NMR (Sadlej Pecul) and EPR (Barone, Cimino Pavone) parameters are presented and discussed within the PCM as well their generalizations to hybrid continuum/discrete approaches in which the presence of specific interactions (e.g. solute-solvents H-bonds) is explicitly taken into account by including some solvent molecules strongly interacting with the solute. 

As a first reassuring statement, we can say that trends in chemical shifts of 13C are somewhat parallel to those of H, so that some of the feeling for H spectra may carry over to l3C spectra. Furthermore, the concept of additivity of substituent effects (see Sections 4.7.1 and 4.7.6) is useful for both spectra. The 13C shifts are related mainly to hybridization, substituent electronegativity, and diamagnetic anisotropy (to a lesser extent) solvent effects are important in both spectra. Chemical shifts for I3C are affected by... 

Although a single covalent structure written in terms of new hybrids obtained by mixing xa and xb could reproduce the wavefunction Er of Eq. (14), as Coulson and Fischer did in their H2 VB study [20], in this Section the role of each contribution will be examined separately in order to analyze the solvent effect. 

Gao, J., Hybrid Quantum and Molecular Mechanical Simulations An Alternative Avenue to Solvent Effects in Organic Chemistry. Accounts of Chemcal Research (1996) 29 298-305. 

Broo A, Pearl G, Zemer MC (1997) Development of a hybrid quantum chemical and molecular mechanics method with application to solvent effects on the electronic spectra of uracil and uracil derivatives. Journal of Physical Chemistry A 101 2478—2488. 

Macroscopic solvent effects can be described by the dielectric constant of a medium, whereas the effects of polarization, induced dipoles, and specific solvation are examples of microscopic solvent effects. Carbenium ions are very strong electrophiles that interact reversibly with several components of the reaction mixture in addition to undergoing initiation, propagation, transfer, and termination. These interactions may be relatively weak as in dispersive interactions, which last less than it takes for a bond vibration (<10 14 sec), and are thus considered to involve "sticky collisions. Stronger interactions lead to long-lived intermediates and/or complex formation, often with a change of hybridization. For example, onium ions are formed with -donors. Even stable trityl ions react very rapidly with amines to form ammonium ions [41], and with water, alcohol, ethers, and esters to form oxonium ions. Onium ion formation is reversible, with the equilibrium constant depending on the nucleophile, cation, solvent, and temperature (cf., Section IV.C.3). 

No systematic study of the effect of different solvation models has been performed. A few reports have compared specific cases such as the study of cationic and anionic alanines, which shows a significant improvement in the chemical shift prediction using polarized continuum method (PCM) or better stiU a hybrid solvation approach (Section 1.4.3). However, the linear scaling correction discussed below can often account for the systematic solvent effect and so sometimes one can get away without any solvent computation at all. 

The Intention of this volume is to give a flavour of the types of problems in biochemistry that theoretical calculations can solve at present, and to illustrate the tremendous predictive power these approaches possess. With these aspects in mind, I have tried to gather some of the leading scientists in the field of theoretical/computational biochemistry and let them present their work. You will hence find a wide range of computational approaches, from classical MD and Monte Carlo methods, via semi-empirical and DFT approaches on isolated model systems, to Car-Parrinello QM-MD and novel hybrid QM/MM studies. The systems investigated also cover a broad range from membrane-bound proteins to various types of enzymatic reactions as well as inhibitor studies, cofactor properties, solvent effects, transcription and radiation damage to DNA. 

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