Development of glycyl radical parameters for the OPLS-AA/L force field

On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.     

The microwave spectrum of the C3 sugars: glyceraldehyde and 1,3-dihydroxy-2-propanone and the dehydration product 2-hydroxy-2-propen-1-al

The triose sugars with empirical formula, C₃H₆O₃, consist of the aldehyde form, glyceraldehyde, and the ketone form, 1,3-dihydroxy-2-propanone. Recently, the simplest sugar, glycolaldehyde (CH₂OHCHO) was identified in the Sgr B2(N) molecular cloud by Hollis et al. (Astrophys. J. (Lett.) 540 (2000) L107), providing the incentive to pursue the present study. The microwave spectra of the triose sugars were obtained with the NIST Fourier-transform pulsed-nozzle microwave spectrometers equipped with heated nozzles. A few tenths of a gram of solid sample was placed in the nozzle base, which was heated to between 105 and 135 °C and pressurized with inert carrier gas. Broad spectral survey scans were carried out from 10 to 20 GHz for samples of both compounds. In the glyceraldehyde sample study, three conformers of the parent species were identified as well as 1,3-dihydroxy-2-propanone. In addition, three decomposition products were also identified: formic acid, trans-methyl glyoxal, and a previously experimentally unknown compound: 2-hydroxy-2-propen-1-al. Ab initio calculations were carried out with the Gaussian 98 program at the MP2/6-311++G** level to aid in the identification of each of the new species. The survey scan of the 1,3-dihydroxy-2-propanone sample confirmed the identification of this species initially assigned in the glyceraldehyde study. The 1,3-dihydroxy-2-propanone survey also exhibited spectra from the same three decomposition products initially observed in the glyceraldehyde work. However, the three conformers of glyceraldehyde were not present in the spectra of 1,3-dihydroxy-2-propanone.     

Microwave spectrum of the heterodimers: CH3OH-CO2 and CH3OH-H2CO

Molecular complexes, dimers and heterodimers often show interesting structures, large amplitude internal motions and orientations for reaction coordinates. These properties were the motivations for the current study of the rotational spectra of the heterodimers, CH₃OH-CO₂ and CH₃OH-H₂CO, in a pulsed nozzle Fourier-transform microwave (FTMW) spectrometer. In addition to studying the normal isotopic forms, several isotopologues containing ¹³C or deuterium substituted atoms of each heterodimer were analyzed in order to obtain structural data of the complexes. All species showed splittings from internal rotation of the methyl group and splittings on the b-type transitions of the CH₃OH-H₂CO species suggesting rotation of the H₂CO group between equivalent structural forms. Stark effect measurements on each of the parent species provided dipole moment components. Theoretical ab initio results are compared to the experimentally determined molecular parameters.     

The Role of Aromatic Residues in Stabilizing the Secondary and Tertiary Structure of Avian Pancreatic Polypeptide

Avian Pancreatic Polypeptide is a 36 residue protein that exhibits a tertiary fold. Results of previous experimental and computational studies indicate that the structure of aPP is stabilized more by non-bonded interactions than by the hydrophobic effect. Aromatic residues are known to participate in a variety of long range non-bonded interactions, with both backbone atoms and the atoms of other side-chains, which could be responsible, in part, for the stability of both the local secondary structure and the tertiary fold. The effect of these aromatic interactions on the stability of aPP was calculated using BHandHLYP/cc-pVTZ. Aromatic residues were shown to participate in multiple hydrogen bonded and weakly polar interactions in the secondary structure. The energies of the weakly polar interactions are comparable with those of hydrogen bonds. Aromatic residues were also shown to participate in multiple weakly polar interactions across the tertiary fold, again with energies similar to those of hydrogen bonds.     

Organic compounds in the C3H6O3 family: Microwave spectrum of cis-cis dimethyl carbonate

Geometry optimization calculations on 13 members of the C₃H₆O₃ family of organic species have been carried out to determine their relative binding energies. Dimethyl carbonate [(CH₃)₂CO₃] is one of the lower energy species in this family, which includes the C₃-sugars 1,3-dihydroxyacetone and glyceraldehyde. The microwave spectrum of dimethyl carbonate has been measured over the frequency range 8.4-25.3 GHz with several pulsed-beam Fourier-transform microwave spectrometers and from 227 GHz to 350 GHz with direct absorption spectrometers. The spectrum of the lowest-energy cis-cis conformer of dimethyl carbonate has been assigned, and ab initio electronic structure calculations of the three possible conformers have been performed. Stark effect measurements were carried out on the cis-cis conformer to provide accurate determinations of the dipole moment components.     

The a-Type K = 0 Microwave Spectrum of the Methanol Dimer

The rotational spectrum of (CH₃OH)₂ has been observed in the region 4-22 GHz with pulsed-beam Fabry-Perot cavity Fourier-transform microwave spectrometers at NIST and at the University of Kiel. Each a-type R(J), K_a = 0 transition is split into 15 states by tunneling motions for (CH₃OH)₂, (¹³CH₃OH)₂, (CH₃OD)₂, (CD₃OH)₂, and (CD₃OH)₂. The preliminary analysis of the methyl internal rotation presented here was guided by the previously developed multidimensional tunneling theory which predicts 16 tunneling components for each R(J) transition from 25 distinct tunneling motions. Several isotopically mixed dimers of methanol have also been measured, namely ¹³CH₃OH, CH₃OD, CD₃OH, and CD₃OD bound to ¹²CH₃OH. Since the hydrogen bond interchange motion (which converts a donor into an acceptor) would produce a new and less favorable conformation from an energy viewpoint, it does not occur and only 10 tunneling components are observed for these mixed dimers. The structure of the complex is similar to that of water dimer with a hydrogen bond distance of 2.035 Å and a tilt of the acceptor methanol of 84° from the O-H-O axis. The effective barrier to internal rotation for the donor methyl group of (CH₃OH)₂ is ν₃ = 183.0 cm⁻¹ and is one-half of the value for the methanol monomer (370 cm⁻¹), while the barrier to internal rotation of the acceptor methyl group is 120 cm⁻¹.     

Asymptotic region of charge density oscillation around impurities in dilute copper based alloys—II

The wipe-out number for the first order quadrupole effect in the NMR of matrix nuclei was measured in dilute Cu-Ag, Cu-Ga and Cu-Ge alloys in order to study the asymptotic behavior of the charge density oscillation around different non-transitional metal impurities. The measured values of the wipe-out numbers were compared with the predictions from Friedel's theory by using the phase shifts calculated by Blatt, Kohn-Vosko, Alfred-Van Ostenburg. “Empirical” phase shifts (η₀, η₁, η₂) for the Cu-Zn, Cu-Ga and Cu-Ge alloys were determined on the basis of Faber-Ziman diagrams. The values of the experimentally determined first order wipe-out number, the residual resistivity, and the Knight shift measured on the smelts, were described by these phase shifts.     

On the self-consistency of the Lane model

The conditions for the self-consistency of the Lane potential are investigated by fitting the (p, p), (p, n?) and (n, n) differential cross sections in pairs. It is concluded that the model is correct only for average potentials to the accuracy of average potentials. The Lane potential can only be found by fitting (p, p) and (p, n?) data, and its real and imaginary parts should not be allowed to vary independently.