6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over-stabilization of alpha-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "Amber" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in Amber of two sets of backbone phi/psi dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the phi/psi dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems.

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Comparison of multiple Amber force fields and development of improved protein backbone parameters.

1. Introduction 2. Theoretical foundations 3. Propagation and focusing of optical fields 4. Spatial resolution and position accuracy 5. Nanoscale optical microscopy 6. Near-field optical probes 7. Probe-sample distance control 8. Light emission and optical interaction in nanoscale environments 9. Quantum emitters 10. Dipole emission near planar interfaces 11. Photonic crystals and resonators 12. Surface plasmons 13. Forces in confined fields 14. Fluctuation-induced phenomena 15. Theoretical methods in nano-optics Appendices Index.

/pdf/principles-of-nano-optics-1hz998yqo8.pdf

Principles of nano-optics

To say that this is the best book on the quantum theory of fields is no praise, since to my knowledge it is the only book on this subject But it is a very good and most useful book The original was written in German and appeared in 1942 This is a translation with some minor changes A few remarks have been added, concerning meson theory and nuclear forces, also footnotes referring to modern work in this field, and finally an appendix on the symmetrization of the energy momentum tensor according to Belinfante Quantum Theory of Fields Prof Gregor Wentzel Translated from the German by Charlotte Houtermans and J M Jauch Pp ix + 224, (New York and London: Interscience Publishers, Inc, 1949) 36s

Quantum Theory of Fields

Ranging from the physics of elementary particles to the structure of viruses, the subject matter of this book stresses the importance of optical activity and chirality in modern science and will be of interest to a wide range of scientists. Using classical and quantum methods with a strong emphasis on symmetry principles, the volume develops the theory of varied optical activity and related phenomena from the perspective of molecular scattering of polarized light. First Edition Hb (1983): 0-521-24602-4

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Molecular Light Scattering and Optical Activity

The spectroscopic analysis of large biomolecules is important in applications such as biomedical diagnostics and pathogen detection, and spectroscopic techniques can detect such molecules at the nanogram level or lower. However, spectroscopic techniques have not been able to probe the structure of large biomolecules with similar levels of sensitivity. Here, we show that superchiral electromagnetic fields, generated by the optical excitation of plasmonic planar chiral metamaterials, are highly sensitive probes of chiral supramolecular structure. The differences in the effective refractive indices of chiral samples exposed to left- and right-handed superchiral fields are found to be up to 10(6) times greater than those observed in optical polarimetry measurements, thus allowing picogram quantities of adsorbed molecules to be characterized. The largest differences are observed for biomolecules that have chiral planar sheets, such as proteins with high β-sheet content, which suggests that this approach could form the basis for assaying technologies capable of detecting amyloid diseases and certain types of viruses.

/pdf/ultrasensitive-detection-and-characterization-of-4vm2e080ni.pdf

Ultrasensitive detection and characterization of biomolecules using superchiral fields

The intensity of Rayleigh and Raman scattering from optically active molecules is shown to be slightly different in right and left circularly polarized incident light. The circular intensity differential of the Rayleigh line is dependent on components of the optical activity tensor, and that of the Raman lines is a function of the variation of the optical activity with the vibrational coordinates. This circular intensity differential might be of the order of 10-3 times that of the Rayleigh or Raman intensity.

Laurence D. Barron

Papers

Molecular Light Scattering and Optical Activity

Ultrasensitive detection and characterization of biomolecules using superchiral fields

Rayleigh and Raman scattering from optically active molecules

Raman scattering of circularly polarized light by optically active molecules

Absolute Asymmetric Synthesis under Physical Fields: Facts and Fictions.