Quantum mechanical calculations are performed on 116 conformers of the protein ubiquitin (Lange et al., Science 2008, 320, 1471–1475). The results indicate that the heat of formation (HOF), dipole moment, energy of the frontier orbitals HOMO and LUMO, and HOMO-LUMO gap fluctuate within their corresponding ranges. This study thus provides a link between the conformational dynamics of a protein a...

Vibrational spectra of NO ligands adsorbed on cationic gold clusters are obtained using IR multiphoton dissociation spectroscopy. We observe a strong oscillation of the NO stretching frequency with increasing cluster size that reveals a clear odd-even dependence in the strength of the NO bond. For the corresponding CO complexes, no oscillation is found. This behaviour can be understood on the b...

UNLABELLED Many chemical concepts hinge on the notion of an orbital called the lowest unoccupied molecular orbital, or LUMO. This hypothetical orbital and the much more concrete highest occupied molecular orbital (HOMO) constitute the two "frontier orbitals", which rationalize a great deal of chemistry. A viable LUMO candidate should have a sensible energy value, a realistic shape with amplitud...

Chemists use one set of orbitals when comparing to a structural formula, hybridized AOs or NBOs for example, and another for reasoning in terms of frontier orbitals, MOs usually. Chemical arguments can frequently be made in terms of energy and/or electron density without the consideration of orbitals at all. All orbital representations, orthogonal or not, within a given function space are relat...

We investigate the structures, NMR chemical shifts, absorption spectra, frontier molecular orbitals, and transition density matrices of pi-stacked polyfluorenes by ab initio calculations. For F1-F4, we consider two different conformations, syn and anti. The simulated 1H NMR chemical shifts are in good agreement with the previous experiment, and the significantly upfielded chemical shifts explai...

Charge transport through a molecular junction comprising an oligomer of p-phenylene-vinylene between gold contacts has been investigated using density-functional theory and the nonequilibrium Green’s function method. The influence of the contact gap geometry on the transport has been studied for elongated and contracted gaps, as well as various molecular conformations. The calculated current-vo...

To accelerate reactive events in molecular dynamics simulations we introduce a general bias potential scheme which depends only on the electronic degrees of freedom of the reactive system. This electronic reaction coordinate, which is expressed in terms of a penalty function of the one-electron orbital energies, has been applied to study different reaction pathways of s-cis-butadiene. Three dif...

An azobenzene molecule Disperse Red 1 with strongly delocalised frontier orbitals has been studied with a number of density-functional theory (DFT) related approaches. The purpose is two-fold: to interpret observed photoabsorption and to compare the performance of various DFT-based approximations. The planarity of the vacuum conformation of the lower energy trans conformation is found to be sig...

The G-quadruplexes are four-stranded nucleic acid structures with guanine-rich sequences that play important biological roles in, for example, regulating telomerase association and activity. Recent evidence supports the hypothesis that the telomeric G-quadruplex DNA represents a target of novel anticancer drug medication. In this work, we present results of the molecular electrostatic potential...