An extensive proton nuclear magnetic resonance (nmr) study is reported for all common purine and pyrimidine 5'-ribo-and deoxyribonucleotides at 220 MHz.Spectra for these nucleotides were measured in D20 solutions at 20 f 2' and signal assignments made with the aid of selected "-'H and 3'P-'H decoupling experiments.Complete sets of accurate chemical shifts and coupling constants were derived for each nucleotide by iterative procedures and yielded close agreement between observed and calculated spectra. The nmr parameters have been utilized in a quantitative evaluation of several key nucleotide conformational features including equilibrium conformations of ribose and deoxyribose rings, preferred exocyclic group orientations, and base-ribose ring orientation. A quantitative conformational analysis was made for the D-ribose and D-deoxyribose rings of all the 5'-riboncleotides following procedures analogous to those developed recently by Altona and Sundaralingam. The analysis is based on an assumption of a rapidly equilibrating mixture between N type [C(3')-endo, C(2')-exo] and S type [C(2')-endo, C(3')-exo] conformers, N * S. With the aid of graphical plots quantitative estimates were made of pseudorotational angle, P, degree of pucker, T, and ring conformer populations. The results show that the pseudorotational parameters (P, T) do not vary significantly between nucleotides and are generally within ranges found in the crystalline state. An S-type conformation is favored in both ribo-and deoxyribonucleotides at 20° with the equilibrium lying somewhat more in favor of the S conformer in the latter, i.e., 70:30 vs. 60:40. Possible effects of electronegativity change upon pseudorotationa1 parameters were explored and it was concluded that no particular advantage is gained by using adjusted Karplus expressions for individual ring molecular fragments at the present accuracy of measured coupling constants. A confor-T h e structure, conformations, and interactions of purine and pyrimidine nucleosides and 5'-ribo-and deoxyribonucleotides have been the subject of extensive investigations in recent years (Sundaralingam

In order to obtain information about the conformational features in a polyribonucleotide at the nearest neighbor level, detailed nuclear magnetic resonance studies of the dinucleoside monophosphates ApA, ApG, GpA, UpU, CpC, UpC, and CpU were undertaken. Proton spectra were recorded at 100, 220, 270, or 300 MHz for D2O solutions, 0.01-0.03 M, pD 7.4 at 20+/-2 degrees C. Spectra of ApA, ApG, UpU, and UpC were also recorded in the temperature range of 70-90 degrees C. Unambiguous signal assignments of all proton resonances were made with the aid of selectively deuterated dimers. Complete, accurate sets of nuclear magnetic resonance (NMR) parameters were derived for each nucleotidyl unit by simulation-iteration methods. A complete set of chemical shift and coupling constant data was also obtained for all the constituent monomeric units at a concentration and ionization state comparable to that of the dimers. Conformational properties were evaluated quantitatively for most of the bonds in the dinucleoside monophosphates using procedures developed in earlier studies. All of the dimers have a flexible conformational framework in aqueous solution. While flexibility is allowed and alternate conformations are accessible, these molecules nevertheless attempt to achieve conformational identity by showing preferences--sometimes overwhelming preferences--for certain orientations. Thus the ribose rings exist as equilibrium mixtures of C2'-endo in equilibrium C3'-endo conformers with a bias for the C3'-endo pucker in most cases. The C4'-C5' bonds of both nucleotidyl units show significant preference (70-85%) for a gg conformation. Similarly, the dominant conformer (80-90%) about C5'-O5' is g'g'. Even though an unambiguous determination of the orientation about C3'-O3' cannot be made, there is suggestive evidence that the orientation of the 3' phosphate group is coupled to the ribose conformational equilibrium and it is likely that a 3Eg- in equilibrium 2Eg+ equilibrium exists with a bias for the 3Eg- coupled conformation in which the H3'-C3'-O3'-P dihedral angle is about 34-38 degrees. The individual nucleotidyl units in the dimers differ in several key ways from corresponding monomer conformations. Specifically, the ribose equilibrium C2'-endo in equilibrium C3'-endo shifts in favor of C3'-endo upon dimerization, the only exception being UpU. The C4'-C5' and C5'-O5' bonding network in the dimer forms a stable conformational unit and no correlation exists in the dimers between the conformational preference of this fragment and ribose conformer population. The temperature data for the dimers and dimerization data clearly indicate that the transition C2'-endo leads to C3'-endo is directly related to XCN changes brought about by dimerization and stacking...

The detailed conformational features and dynamics of heterodinucleoside monophosphates ApU, ApC, GpU, GpC, UpA, CpA, UpG, and CpG have been studied in aqueous solution by high field nuclear magnetic resonance (NMR) spectroscopy. Analysis of the resultant NMR parameters leads to a number of discernible trends throughout the series. Thus the ribose rings of the dimers exist as equilibrium mixtures of C(2')-endo(2E) in equilibrium C(3')-endo(3E) conformers with a proclivity for the 3E pucker in most cases; the C(4')-C(5') bonds of both nucleotidyl units show significant preference (74-96%) for a gg conformation and the dominant conformer (85-89%) about C(5')-O(5') is g'g'. Orientation about the C(3')-O(3') bond is coupled to the ribose conformational equilibrium and the system exists with a bias for the 3Eg- coupled conformation in which the H(3')-C(3')-O(3')-P dihedral angle occupies the narrow range of 33-35 degrees. Dimerization, on the average, causes about 10% increase in gg and g'g' populations and the g-domain becomes increasingly populated about the C(3')-O(3') bond. The ribose equilibrium 2E in equilibrium 3E shifts in favor of 3E upon dimerization, the effect being very conspicuous for the pu-py series (similar to 40 yields 60%) and less noticeable for the py-pu systems (similar to 47 yields 58%), clearly suggesting a correlation between sequence and ribose conformational equilibrium. The temperature and dimerization data for the heterodinucleoside monophosphates show that the transition 2E yields 3E is directly related to XCN changes induced by dimerization and stacking. Analysis of the ribose coupling data shows that the percentage populations of stacked species vary from dimer to dimer with GpC displaying a maximum of 45% stacked population and UpG about 10%. However, in general, the pu-py dimers show a higher preference (27-45%) for stacked conformations than py-pu dimers (10-25%). It is proposed that the pronounced deshielding of H(5') of the 5'-nucleotidyl units upon dimerization is associated with the presence of right-handed stacks (g-g-), whereas the chemical shift trends of H(5') and H(5') of 3'-nucleotidyl units are due to the presence of left-handed stacks (g+g+) in all the dimers. In pu-py dimers, the population of the g-g- species is found to be greater than that of g+g+. Also the population of g-g- stacks in pu-py dimers is generally greater than in their corresponding matched py-pu dimers. Thus the base sequence has not only an explicit effect on the overall populations of stacked species, but also on the handedness of the stacks. The present results further confirm the interdependence of conformational bonds throughout the nucleotidyl framework.

This paper reports on the measurement of fluid (water) pressure distribution at a soft (polyurethane) pad/steel interface. The distribution of the interfacial fluid pressure has been measured with a specially-designed fixture over the typical range of normal loads and velocities used in the chemical mechanical polishing/planarization of silicon wafers. The results show that, for most cases, the leading two-thirds of the fixture exhibits a subambient pressure, and the trailing third a positive pressure. The average pressure is sub-ambient and may be of the order of 50∼100% of the normal load applied. An analytical model has been developed to predict the magnitude and distribution of the interfacial fluid pressure. The predictions of this model fit the experimental results reasonably well, especially for low sliding velocities. [S0742-4787(00)00902-4]

A preliminary model for the contact mechanics and fluid mechanics of the chemical mechanical polishing process is presented. Only the basic equations of elastic contact surface mechanics and hydrodynamic lubrication are required. Although the model is highly idealized, no ad hoc assumptions or adjustable parameters are required. Some new experimental results are presented, reinforcing the counterintuitive experimental determination of suction fluid pressure below the pad. The model correctly predicts the magnitude of the suction pressure and the effect of load, speed, and roughness. © 1999 The Electrochemical Society. All rights reserved.