Symmetry in chemistry from the hydrogen atom to proteins

Fundamental studies of vibrational resonance phenomena by multivalued resummation of the divergent Rayleigh-Schrödinger perturbation theory series: deciphering polyad structures of three H216O isotopologues

A fundamental quantitative study of the vibrational resonances of three H₂¹⁶O H,D-isotopologues with a quartic Watson Hamiltonian was carried out using the resummation of the high-order (∼λⁿ, n ≤ 203) divergent Rayleigh-Schrödinger perturbation theory (RSPT) series by quartic Padé-Hermite multivalued diagonal approximants PH^[m,m,m,m,m], m ≤ 40. The resonance condition between a pair of states is formulated as the existence of a common complex energy solution branch point inside the unit circle: |E(λ_j)|,  Re(λ_j)² + Im(λ_j)² ≤ 1. For the matrix formulation of the vibrational problem (VCI), the existence of common branch points is governed by the Katz theorem and they can be found as roots of discriminant polynomials. The main branches of the Padé-Hermite approximants typically reproduce VCI energies with high accuracy while alternative branches often fit nearby resonant states. The resummation of the RSPT series for H₂O and D₂O (up to the tenth polyad) revealed not only Fermi and Darling-Dennison resonances, but also unusual (0,2,-5) and (5,-2,0) resonance effects matching the (5,2,5) polyad structure, while the (3,2,1) structure was rigorously confirmed for HDO. It is demonstrated that the (5,2,5) polyad structure ensures good organization of high-energy resonating states and breaks down the classic (2,1,2) structure. The advocated methodology of quantitative description of resonance phenomena and revealing polyad structures is suitable for larger molecules and can be adapted to linear molecules and symmetric tops. Its application ensures rigorous classification of vibrational states and can be used in quantitative vibration-rotation spectroscopy.

Actual Symmetry of Symmetric Molecular Adducts in the Gas Phase, Solution and in the Solid State

This review discusses molecular adducts, whose composition allows a symmetric structure. Such adducts are popular model systems, as they are useful for analyzing the effect of structure on the property selected for study since they allow one to reduce the number of parameters. The main objectives of this discussion are to evaluate the influence of the surroundings on the symmetry of these adducts, steric hindrances within the adducts, competition between different noncovalent interactions responsible for stabilizing the adducts, and experimental methods that can be used to study the symmetry at different time scales. This review considers the following central binding units: hydrogen (proton), halogen (anion), metal (cation), water (hydrogen peroxide).

Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity

We will consider in this chapter supersecondary structures (SSS) as a set of secondary structure elements (SSEs) found in protein domains. Some SSS arrangements/topologies have been consistently observed within known tertiary structural domains. We use them in the context of repeating supersecondary structures that self-assemble in a symmetric arrangement to form a domain. We call them protodomains (or protofolds). Protodomains are some of the most interesting and insightful SSSs. Within a given 3D protein domain/fold, recognizing such sets may give insights into a possible evolutionary process of duplication, fusion, and coevolution of these protodomains, pointing to possible original protogenes. On protein folding itself, pseudosymmetric domains may point to a "directed" assembly of pseudosymmetric protodomains, directed by the only fact that they are tethered together in a protein chain. On function, tertiary functional sites often occur at protodomain interfaces, as they often occur at domain-domain interfaces in quaternary arrangements.First, we will briefly review some lessons learned from a previously published census of pseudosymmetry in protein domains (Myers-Turnbull, D. et al., J Mol Biol. 426:2255-2268, 2014) to introduce protodomains/protofolds. We will observe that the most abundant and diversified folds, or superfolds, in the currently known protein structure universe are indeed pseudosymmetric. Then, we will learn by example and select a few domain representatives of important pseudosymmetric folds and chief among them the immunoglobulin (Ig) fold and go over a pseudosymmetry supersecondary structure (protodomain) analysis in tertiary and quaternary structures. We will point to currently available software tools to help in identifying pseudosymmetry, delineating protodomains, and see how the study of pseudosymmetry and the underlying supersecondary structures can enrich a structural analysis. This should potentially help in protein engineering, especially in the development of biologics and immunoengineering.

Gauge symmetry, chirality and parity effects in four-particle systems: Coulomb's law as a universal function for diatomic molecules

Following recent work in search for a universal function (Van Hooydonk, Eur. J. Inorg. Chem., (1999), 1617), we test four symmetric +/- a(n)Rn potentials for reproducing molecular potential energy curves (PECs). Classical gauge symmetry for 1/R-potentials results in generic left right asymmetric PECs. A pair of symmetric perturbed Coulomb potentials is quantitatively in accordance with observed PECs. For a bond, a four-particle system, charge inversion (a parity effect, atom chirality) is the key to explain this shape generically. A parity adapted Hamiltonian reduces from ten to two terms and to a soluble Bohr-like formula, a Kratzer (1 - Re/R)2 potential. The result is similar to the combined action of spin and wave function symmetry upon the Hamiltonian in Heitler-London theory. Analytical perturbed Coulomb functions varying with (1 - Re/R) scale attractive and repulsive branches of PECs for 13 bonds H2, HF, LiH, KH, AuH, Li2, LiF, KLi, NaCs, Rb2, RbCs, Cs2 and I2 in a single straight line. The 400 turning points for 13 bonds are reproduced with a deviation of 0.007 A at both branches. For 230 points at the repulsive side, the deviation is 0.003 A. The perturbed electrostatic Coulomb law is a universal molecular function. Ab initio zero molecular parameter functions give PECs of acceptable quality, just using atomic ionisation energies. The function can be used as a model potential for inverting levels and gives a first principle's comparison of short- and long-range interactions, important for the study of cold atoms. Wave-packet dynamics, femto-chemistry applied to the crossing of covalent and ionic curves, can provide evidence for this theory. We anticipate this scale/shape invariant scheme applies to smaller scales in nuclear and high-energy particle physics. For larger gravitational scales (Newton 1/R potentials), problems with super-unification are discussed. Reactions between hydrogen and antihydrogen, feasible in the near future, will probably produce normal H2.