The analytic generalized Born approximation is an efficient electrostatic model that describes molecules in solution. Here it is modified to permit a more accurate description of large macromolecul...

/pdf/modification-of-the-generalized-born-model-suitable-for-r7y74akg5g.pdf

Modification of the Generalized Born Model Suitable for Macromolecules

The structure of the protein–solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein–solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density ≈10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces.

https://www.embl-hamburg.de/biosaxs/reprints/cryson_1998.pdf

Protein hydration in solution: Experimental observation by x-ray and neutron scattering

Preface Acknowledgements 1. Global transitions in proteins 2. Molecular forces in biological structures 3. Conformations of macromolecules 4. Molecular associations 5. Allosteric interactions 6. Diffusion and Brownian motion 7. Fundamental rate processes 8. Association kinetics 9. Multi-state kinetics 10. Enzyme catalysis 11. Ions and counter-ions 12. Fluctuations 13. Ion permeation and membrane potential 14. Ion permeation and channel structure 15. Cable theory 16. Action potentials References Appendix 1. Expansions and series Appendix 2. Matrix algebra Appendix 3. Fourier analysis Appendix 4. Gaussian integrals Appendix 5. Hyperbolic functions Appendix 6. Polar and spherical coordinates.

/pdf/molecular-and-cellular-biophysics-4wltyfc0iy.pdf

Molecular and cellular biophysics

The gauche energy, the t-g barrier, and the cis barrier in n-butane and n-hexane have been investigated using high-level ab initio electronic structure calculations. CCSD(T)/cc-pVTZ//MP2/6-311G(2df,p) calculations yield a gauche energy in n-butane of 0.59 kcal/mol, which after correction for zero-point and thermal vibrational effects is within 0.05 kcal/mol of the values obtained from recent experiments. Calculations at the same level yield t-g and cis barrier energies in n-butane of 3.31 and 5.48 kcal/mol, respectively, supporting the traditional view that the cis barrier in n-butane is much higher than the t-g barrier. We found that torsional potential functions previously parametrized to reproduce the measured low-lying torsional vibrational transitions in the trans and gauche conformers of n-butane and which yield only a small energy difference between the barriers can be modified to reproduce both the spectroscopic data and the large quantum chemistry energy difference between barriers. For the centr...

Quantum Chemistry Study of Conformational Energies and Rotational Energy Barriers in n-Alkanes

High-resolution (e,2e) measurements of the valence electronic structure and momentum-space electron density distributions of n-butane have been exhaustively reanalyzed in order to cope with the presence of two stable structures in the gas phase, namely the all-staggered and gauche conformers. The measurements are compared to a series of Boltzmann-weighted simulations based on the momentum-space form of Kohn−Sham (B3LYP) orbital densities, and to ionization spectra obtained from high-level [ADC(3)] one-particle Green's Function calculations. Indubitable improvements in the quality of the simulated (e,2e) ionization spectra and electron momentum profiles are seen when the contributions of the gauche form of n-butane are included. Both the one-electron binding energies and momentum distributions consistently image the distortions and topological changes that molecular orbitals undergo due to torsion of the carbon backbone, and thereby exhibit variations which can be traced experimentally. With regard to the ...

Probing molecular conformations with electron momentum spectroscopy: the case of n-butane.

The trans‐gauche energy difference for n‐butane dissolved in CH2Cl2 and in CCl4 has been measured by the method of Raman band intensities. In methylene chloride, ΔE was observed to be 537±70 cal/mol, a value indistinguishable from that reported for pure liquid butane. A slightly lower value 438±80 cal/mol was observed for the CCl4 solution.

An investigation of the conformational equilibrium of n‐butane in a solvent using Raman spectroscopy

An investigation of the conformational equilibrium of n-butane in a solvent using raman spectroscopy

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An investigation of the conformational equilibrium of n‐butane in a solvent using Raman spectroscopy

An investigation of the conformational equilibrium of n-butane in a solvent using raman spectroscopy