The inability to describe charge redistribution from regions I to II at the high level of theory imposes limitations on the general applicability of the our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method. In this report, we exploit the most inexpensive components of an ONIOM QM:QM calculation to provide a new method which has the ability to describe such charg...

Energy partitioning of pharmaceutical cocrystals by molecule-pair interaction and ONIOM energies identifies the driving force their formation, leading to in silico conformational sampling for predicting API-cocrystal combinations experiment.

Calculation of the free energy profile for hydrolysis of phosphohistidine using ONIOM methodology indicates a much tighter transition state in the enzyme active site compared to that in explicit water and elucidates the role of active site residues in catalysis.

We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this...

The properties, interactions, and reactions of cyclic water clusters (H(2)O)(n=1-5) on model systems for a graphite surface have been studied using pure B3LYP, dispersion-augmented density functional tight binding (DFTB-D), and integrated ONIOM(B3LYP:DFTB-D) methods. Coronene C(24)H(12) as well as polycircumcoronenes C(96)H(24) and C(216)H(36) in monolayer, bilayer, and trilayer arrangements we...

The first example of intramolecular nucleophilic addition of an alcohol to a fullerene double bond is described. In particular, the straightforward one-step reaction of commercially available sarcosine, hydroxyacetaldehyde, and [60]fullerene, in refluxing chlorobenzene, affords a structurally complex novel pyrrolidinofullerene endowed with a furan ring simultaneously fused to both the pyrrolidi...

We present ONIOM calculations using density functional theory (DFT) as the high and AM1 as the medium level that explore the abilities of different hexapeptide sequences to terminate the growth of a model for the tau-amyloid implicated in Alzheimer's disease. We delineate and explore several design principles (H-bonding in the side chains, using antiparallel interactions on the growing edge of ...

Nicotinamidase (Nic) is a key zinc-dependent enzyme in NAD metabolism that catalyzes the hydrolysis of nicotinamide to give nicotinic acid. A multi-scale computational approach has been used to investigate the catalytic mechanism, substrate binding and roles of active site residues of Nic from Streptococcus pneumoniae (SpNic). In particular, density functional theory (DFT), molecular dynamics (...

Photosystem II (PSII) of photosynthesis has the unique ability to photochemically oxidize water. Recently an engineered bacterioferritin photochemical 'reaction centre' (BFR-RC) using a zinc chlorin pigment (ZnCe6) in place of its native heme has been shown to photo-oxidize bound manganese ions through a tyrosine residue, thus mimicking two of the key reactions on the electron donor side of PSI...