Using valence bond theory to understand electronic excited states: Application to the hidden excited state (2(1)A(g)) of C2nH2n+2 (n=2-14) polyenes

A valence bond (VB) method is presented and applied to calculate the hidden excited states, 2(1)A(g), and other covalent excited states of polyenes from C4H6 to C28H30. The ground rules needed to understand the results are qualitatively outlined and used to discuss the asymptotic behavior of these molecules as n goes to infinity. The theory enables to understand in a coherent and lucid manner excited state properties, such as the makeup of the various states, their energies and geometries, the puzzling increase of the C=C frequency in the excited state, the opposite bond alternation properties of the ground and excited state, isomerization patterns, soliton characteristics, etc

Calculation of transition dipole moment in fluorescent proteins : Towards efficient energy transfer

Förster Resonance Energy Transfer (FRET) between fluorescent proteins (FPs) is widely used to construct fluorescent sensor proteins, to study intracellular protein–protein interactions and to monitor conformational changes in multidomain proteins. Although FRET depends strongly on the orientation of the transition dipole moments (TDMs) of the donor and acceptor fluorophores, this orientation dependence is currently not taken into account in FRET sensor design. Similarly, studies that use FRET to derive structural constrains typically assume a ¿2 of 2/3 or use the TDM of green fluorescent protein, as this is the only FP for which the TDM has been determined experimentally. Here we used time-dependent density functional theory (TD-DFT) methods to calculate the TDM for a comprehensive list of commonly used fluorescent proteins. The method was validated against higher levels of calculation. Validation with model compounds and the experimentally determined TDM of GFP shows that the TDM is mostly determined by the structure of the p-conjugated fluorophore and is insensitive to non-conjugated side chains or the protein surrounding. Our calculations not only provide TDM for most of the currently used FPs, but also suggest an empirical rule that can be used to obtain the TDMs for newly developed fluorescent proteins in the future

Density embedded VB/MM: A hybrid ab initio VB/MM with electrostatic embedding

A hybrid QM/MM method that combines ab initio valence-bond (VB) with molecular mechanics (MM) is presented. The method utilizes the ab initio VB approach to describe the reactive fragments and MM to describe the environment thus allows VB calculations of reactions in large biological systems. The method, termed density embedded VB/MM (DE-VB/MM), is an extension of the recently developed VB/MM method. It involves calculation of the electrostatic interaction between the reactive fragments and their environment using the electrostatic embedding scheme. Namely, the electrostatic interactions are represented as one-electron integrals in the ab initio VB Hamiltonian, hence taking into account the wave function polarization of the reactive fragments due to the environment. Moreover, the assumptions that were utilized in an earlier version of the method, VB/MM, to formulate the electrostatic interactions effect on the off-diagonal matrix elements are no longer required in the DE-VB/MM methodology. Using DE-VB/MM, one can calculate, in addition to the adiabatic ground state reaction profile, the energy of the diabatic VB configurations as well as the VB state correlation diagram for the reaction. The abilities of the method are exemplified on the identity S(N)2 reaction of a chloride anion with methyl chloride in aqueous solution. Both the VB configurations diagram and the state correlation diagram are presented. The results are shown to be in very good agreement with both experimental and other computational data, suggesting that DE-VB/MM is a proper method for application to different reactivity problems in biological systems

CB2 cannabinoid receptor agonist enantiomers HU-433 and HU-308: An inverse relationship between binding affinity and biological potency

The significance of the results reported is in two areas. (i) Because the cannabinoid receptor type 2 (CB2) agonists seem to be general protective agents, HU-433, a new specific CB2 agonist, may be of major therapeutic importance. (ii) Enantiomers usually have different activity profiles. We report now that HU-433 and its enantiomer HU-308 are both specific CB2 agonists, but whereas HU-433 is much more potent than HU-308 in the rescue of ovariectomy-induced bone loss and ear inflammation, its binding to the CB2 receptor (through which the activity of both enantiomers takes place) is substantially lower compared with HU-308. This situation questions the usefulness of universal radioligands for comparative binding studies

A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes

The catalytic power of enzymes containing coenzyme B12 cofactor has been, in some respects, the “last bastion” for the strain hypothesis. The present work explores the origin of this effect by using simulation methods that overcome the sampling difficulties of previous energy minimization studies. It is found that the major part of the catalytic effect is due to the electrostatic interaction between the ribose and the protein, and that the strain contribution is very small. Remarkably, enzymes can use electrostatic effects even in a radical process, when the charge distribution of the reacting fragments does not change significantly during the reaction. Electrostatic catalysis can, in such cases, be obtained by attaching a polar group to the leaving fragment and designing an active site that interacts more strongly with this group in the product state than in the reactant state. The finding that evolution had to use this trick provides further evidence to the observation that it is extremely hard to catalyze enzymatic reactions by nonelectrostatic factors. The trick used by B12 enzymes may, in fact, be a very powerful new strategy in enzyme design