Search

A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin. [ABSTRACT FROM AUTHOR]

Silver clusters develop within DNA strands and become optical chromophores with diverse electronic spectra and wide-ranging emission intensities. These studies consider a specific cluster that absorbs at 400 nm, has low emission, and exclusively develops with single-stranded oligonucleotides. It is also a chameleon-like chromophore that can be transformed into different highly emissive fluorophores. We describe four characteristics of this species and conclude that it is highly oxidized yet also metallic. One, the cluster size was determined via electrospray ionization mass spectrometry. A common silver mass is measured with different oligonucleotides and thereby supports a Ag10 cluster. Two, the cluster charge was determined by mass spectrometry and Ag L3-edge X-ray absorption near-edge structure spectroscopy. Respectively, the conjugate mass and the integrated white-line intensity support a partially oxidized cluster with a +6 and +6.5 charge, respectively. Three, the cluster chirality was gauged by circular dichroism spectroscopy. This chirality changes with the length and sequence of its DNA hosts, and these studies identified a dispersed binding site with ~20 nucleobases. Four, the structure of this complex was investigated via Ag K-edge extended X-ray absorption fine structure spectroscopy. A multishell fitting analysis identified three unique scattering environments with corresponding bond lengths, coordination numbers, and Debye-Waller factors for each. Collectively, these findings support the following conclusion: a Ag10+6 cluster develops within a 20-nucleobase DNA binding site, and this complex segregates into a compact, metal-like silver core that weakly links to an encapsulating silver-DNA shell. We consider different models that account for silver-silver coordination within the core. [ABSTRACT FROM AUTHOR]

Superatom state-resolved dynamics of the Au25(SC8H9)18- monolayer-protected cluster (MPC) were examined using femtosecond two-dimensional electronic spectroscopy (2DES). The electronic ground state of the Au25(SC8H9)18- MPC is described by an eight-electron P-like superatom orbital. Hot electron relaxation (200 ± 15 fs) within the superatom D manifold of lowest-unoccupied molecular orbitals was resolved from hot hole relaxation (290 ± 20 fs) in the superatom P states by using 2DES in a partially collinear pump-probe geometry. Electronic relaxation dynamics mediated by specific superatom states were distinguished by examining the time-dependent cross-peak amplitudes for specific excitation and detection photon energy combinations. Quantification of the time-dependent amplitudes and energy positions of cross peaks in the 2.21/1.85 eV (excitation/detection) region confirmed that an apparent energetic blue shift observed for transient bleach signals results from rapid hot electron relaxation in the superatom D states. The combination of structurally precise MPCs and state-resolved 2DES can be used to examine directly the influence of nanoscale structural modifications on electronic carrier dynamics, which are critical for developing nanocluster-based photonic devices. [ABSTRACT FROM AUTHOR]

Ruthenium clusters of the type [Ru3(μ3-O)(OAc)6(CO)(L)(nic)], where L = 4-dimethylaminopyridine (dmap) and nic = isonicotinic acid, form hydrogen-bonded mixed-valence dimers upon a single electron reduction. Electrochemical responses show two overlapping reduction waves, indicating the presence of a thermodynamically stable mixed-valence dimer with considerable electronic coupling across the hydrogen bond. Electronic spectra of the singly reduced hydrogen-bonded mixed-valence dimer reveal two intervalence charge transfer bands in the near-infrared region consistent with a Robin-Day class II system. These bands are assigned as metal-to-metal and metal-to-bridge charge transfer, and their behavior is best described by a semiclassical three state model. Infrared spectroscopy suggests localized behavior indicating electron transfer between the two clusters is slower than 1010 s–1. [ABSTRACT FROM AUTHOR]