Nuclear magnetic resonance computational study

Ketimines and aldimines proved to be good substrates [73]. Based on the structure modification, nuclear magnetic resonance (NMR) study, kinetic study, and computational study, they proposed a double hydrogen bond structure between the acidic N-H protons and the imine lone pair to activate the electrophile toward the attack by the cyanide ion (Figure 2.15) [74]. The catalyst system is applicable to the Mannich-type reaction of N-Boc-aldimine with ketene silyl acetals to give corresponding P-amino esters in 86-98% ee (Scheme 2.25) [75]. Hydrophospho-nylation of aldimines with bis(2-nitrobenzyl)phosphite by means of (4d) furnished a-amino phosphonates in good enantioselectivity (Scheme 2.26) [76]. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

Left and center Two gramicidin A molecules associate to span a cell membrane. Right Axial view showing ion channel. [Structure from B. Roux, "Computational Studies of the Gramicidin Channel." Acc. Chem. Res. 2002,35,366. based on solid-state nuclear magnetic resonance. Schematic at left from L. Stryer. Biochemistry,... 

Crystal reaction study mechanistic tools, 296 computer simulation, 297 electronic spectroscopy, 298 electron microscopy, 298 electron paramagnetic resonance (EPR), 299 nuclear magnetic resonance (NMR), 298 Raman spectroscopy, 299 Crystal reaction study techniques crystal mounting, 308 decomposition limiting, 309 polarized IR spectroscopy, 309 temperature control, 308 Cycloreversions, adiabatic photochemical involving anthracenes, 203 excited state properties of lepidopterenes, 206... 

Computational efforts to describe the conformational preferences of (R,R)-tartaric acid and its derivatives - mainly for isolated molecules - were made recently [18-25]. The conformations of these molecules also attracted attention from experimental chemists [22-40]. (/ ,/ [-tartaric acid and its dimethyl diester were observed in crystals, in conformations with extended carbon chain and planar a-hydroxy-carboxylic moieties (T.v.v and Tas for the acid and the ester, respectively) [25-28] (see Figure 2). The predominance ofthe T-structure was also shown by studies of optical rotation [31], vibrational circular dichroism (VCD) [23], Raman optical activity [32, 35], and nuclear magnetic resonance (NMR) [22, 33, 34]. The results of ab-initio and semiempirical calculations indicated that for the isolated molecules the Tsv and T as conformers were those of lowest energy [22, 21, 23, 25]. It should be noted, however, that early interpretations of NMR and VCD studies indicated that for the dimethyl diester of (/ ,/ [-tartaric acid the G+ conformation is favored [36-38]. 

In addition, this procedure was quite tedious and time consuming. Therefore, in recent years when physical methods for assaying molecules in mixtures—methods such as nuclear magnetic resonance (NMR), gas chromatography, and others—have become available, a renaissance in the study of redistribution reactions has taken place. These methods allowed a rapid, quantitative, and precise determination of all of the reaction products present in a mixture. Also, equilibrium reactions could be carried out in much smaller sample sizes, thus permitting the study of exotic, hard-to-obtain compounds. Redistribution reactions—the kinetics as well as the equilibria—can now be measured directly in sealed NMR tubes. Furthermore, the relatively recent widespread availability to chemists of high-speed computers, in addition to these modern analytical tools, has facilitated the use of the appropriate mathematics even when highly complicated. 

Nuclear magnetic resonance (NMR) spectroscopy has been used to directly observe varied persistent superelectrophilic species. Although H and 13C NMR have been the most often used techniques, there have also been applications of 15N, 170, and 19F NMR in their structural characterization. Coupled with theoretical computational methods capable of estimating NMR chemical shifts, these studies have been very useful in the study of superelectrophiles. 

Jeffrey C. Hoch, Flemming M. Poulsen, and Christina Redfield, Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, Proceedings of a NATO Advanced Research Workshop on Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, held June 13-18, 1990, in 11 Ciocco, Italy, in NATO ASI Series, Ser. A Life Sciences, Vol. 225, Plenum, New York, 1991. 

Recent single-molecule experimental studies of proteins provide more detailed views of protein motions, and confirm that a wide variety of timescales is involved in, e.g., catalytic action of enzymes [7,14,15,19,33], Of course, molecular dynamics simulations have been used to probe motions in single proteins for many years, and advances in both theory and computational science have made simulations a powerful approach to building theoretical understanding of protein dynamics [1], The recent introduction of accelerated molecular dynamics methods is helpful in this context [11]. Although detailed dynamical information is sacrificed to the enhanced sampling of conformational space in these methods, which have been shown to access conformational fluctuations that are revealed by nuclear magnetic resonance experiments on the millisecond... 

Since the publication of CHEC-II(1996), there has been little advance, with respect to ring-fused oxiranes, in experimental structural methods (e.g., nuclear magnetic resonance (NMR), ultraviolet (UV), and Raman spectroscopy). However, there has been considerable interest in the use of theoretical computational studies to probe structural and reactivity issues, particularly with regard to highly labile oxiranes fused to small rings. 

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