In this Account we describe recent advances in two ab initio electronic structure methods, localized perturbation approaches and density functional theory, that allow accurate calculations including electron correlation to be carried out for systems with hundreds of atoms. Application of these methods to large-scale modeling of biological systems is discussed. Localized perturbation methods are...

The calculation of X-ray emission spectroscopy with equation of motion coupled cluster theory (EOM-CCSD), time-dependent density functional theory (TDDFT), and resolution of the identity single excitation configuration interaction with second-order perturbation theory (RI-CIS(D)) is studied. These methods can be applied to calculate X-ray emission transitions by using a reference determinant wi...

Density functional theory (DFT) is now extensively used as a research tool for the investigation of structure and reactivity of biological systems; however, its high computational demands still restrict the applicability of DFT to systems of a few tens up to one hundred atoms. A combined quantum mechanical/molecular mechanical (QM/MM) approach is applicable as an important method to study whole...

Acetylene hydratase is a tungsten-dependent enzyme that catalyzes the nonredox hydration of acetylene to acetaldehyde. Density functional theory calculations are used to elucidate the reaction mechanism of this enzyme with a large model of the active site devised on the basis of the native X-ray crystal structure. Based on the calculations, we propose a new mechanism in which the acetylene subs...

Key factors affecting the parallel efficiency of archetypical quantumchemical calculations are discussed. Effective load balancing schemes are proposed. Introduction of the memory affinity to the balancing process is shown to result in super-linear scaling.

Particulate contamination formed by homogeneous clustering reactions of silicon hydrides within silicon chemical vapor deposition processes is an important source of yield loss during semiconductor processing. On the other hand, intentional synthesis of silicon nanoparticles may be of great interest because of the unique optical and electronic properties of nanostructured silicon. Kinetic model...

More recently medical chemistry research has been focused on proteins that drive and controlcell cycle progression. Among them, the cyclin dependent kinases (cdk’s) are a group ofserine/threonine kinases, which rule the transition between successive stages of the cell cycle. Theactivity of cdk’s is regulated by multiple mechanisms, including binding to cyclins, which is a broadclass of positive...

We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC appro...

Proton-energy differences, ammonia adsorption, and D/H-exchange barriers for methane at selected isolated Brønsted sites in zeolites FAU, MFI, BEA, ERI, and CHA are studied by combined quantum-chemicalclassical (QM/MM) calculations in an attempt to understand the factors that determine the reactivity at these Brønsted sites. The barrier of the D/H-exchange reaction for methane was found to corr...