Absolute configuration retention of a configurationally labile ligand during dynamic processes of thiolate protected gold clusters.

Monolayer protected metal clusters are dynamic nanoscale objects. For example, the chiral Au(2-PET) cluster (2-PET: 2-phenylethylthiolate) racemizes at moderate temperature. In addition, ligands and metal atoms can easily exchange between clusters.

Real-time time-dependent density functional theory implementation of electronic circular dichroism applied to nanoscale metal-organic clusters.

Electronic circular dichroism (ECD) is a powerful spectroscopy method for investigating chiral properties at the molecular level. ECD calculations with the commonly used linear-response time-dependent density functional theory (LR-TDDFT) framework can be prohibitively costly for large systems. To alleviate this problem, we present here an ECD implementation within the projector augmented-wave method in a real-time-propagation TDDFT framework in the open-source GPAW code.

Efficient Amino Acid Conformer Search with Bayesian Optimization.

Finding low-energy molecular conformers is challenging due to the high dimensionality of the search space and the computational cost of accurate quantum chemical methods for determining conformer structures and energies. Here, we combine active-learning Bayesian optimization (BO) algorithms with quantum chemistry methods to address this challenge. Using cysteine as an example, we show that our procedure is both efficient and accurate.

Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory.

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag + -mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range.

Silver-Stabilized Guanine Duplex: Structural and Optical Properties.

Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag-mediated guanine duplex with two nucleobases per strand, G-Ag-G.