Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.

We explore the ability of four quantum mechanical (QM)/molecular mechanical (MM) models to accurately identify the native pose of six HIV-1 protease inhibitors and compare them with the AMBER force field and ChemScore and GoldScore scoring functions. Three QM/MM scoring functions treated the ligand at the HF/6-31G*, AM1d, and PM3 levels; the fourth QM/MM function modeled the ligand and active site at the PM3-D level. For the discrimination of native from non-native poses, solvent-corrected HF/6-31G*:AMBER and AMBER functions exhibited the best overall performance.

The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections.

Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added dispersion correction have been used to study stabilising carbohydrate-aromatic and amino acid-aromatic interactions. The interaction energy for three simple sugars in different conformations with benzene, all give interaction energies close to 5 kcal mol(-1). Our original parameterization of PM3 (PM3-D) seriously overestimates this value, and has prompted a reparametrization which includes a modified core-core interaction term.

A computational study of the intramolecular deprotonation of a carbon acid in aqueous solution.

Proton transfer reactions are the rate-limiting steps in many biological and synthetic chemical processes, often requiring complex cofactors or catalysts to overcome the generally unfavourable thermodynamic process of carbanion intermediate formation. It has been suggested that quantum tunnelling processes enhance the kinetics of some of these reactions, which when coupled to protein motions may be an important consideration for enzyme catalysis. To obtain a better fundamental and quantitative understanding of these proton transfer mechanisms, a computational analysis of the intramolecular proton transfer from a carbon acid in the small molecule, 4-nitropentanoic acid, in aqueous solution is presented.

The non-covalent functionalisation of carbon nanotubes studied by density functional and semi-empirical molecular orbital methods including dispersion corrections.

Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added empirical dispersion correction have been used to study the binding of a series of small molecules and planar aromatic molecules to single-walled carbon nanotubes (CNTs). For the small molecule set, the PM3-D method gives a mean unsigned error (MUE) in the binding energies of 1.2 kcal mol(-1) when judged against experimental reference data for graphitic carbon.

Density Functional and Semiempirical Molecular Orbital Methods Including Dispersion Corrections for the Accurate Description of Noncovalent Interactions Involving Sulfur-Containing Molecules.

We describe the use of density functional theory (DFT-D) and semiempirical (AM1-D and PM3-D) methods having an added empirical dispersion correction, to treat noncovalent interactions between molecules involving sulfur atoms. The DFT-D method, with the BLYP and B3LYP functionals, was judged against a small-molecule database involving sulfur-π, S-H···S, and C-H···S interactions for which high-level MP2 or CCSD(T) estimates of the structures and binding or interaction energies are available. This database was also used to develop appropriate AM1-D and PM3-D parameters for sulfur.

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules.

Semi-empirical calculations including an empirical dispersive correction are used to calculate intermolecular interaction energies and structures for a large database containing 156 biologically relevant molecules (hydrogen-bonded DNA base pairs, interstrand base pairs, stacked base pairs and amino acid base pairs) for which MP2 and CCSD(T) complete basis set (CBS) limit estimates of the interaction energies are available. The dispersion corrected semi-empirical methods are parameterised against a small training set of 22 complexes having a range of biologically important non-covalent interactions. For the full molecule set (156 complexes), compared to the high-level ab initio database, the mean unsigned errors of the interaction energies at the corrected semi-empirical level are 1.

Semiempirical Molecular Orbital Scheme To Study Lanthanide(III) Complexes: PM3 Parameters for Europium, Gadolinium, and Ytterbium.

Semiempirical parameters for europium, gadolinium, and ytterbium have been developed for use in the PM3 method to allow the structure and energetics of complexes containing lanthanide(III) ions to be accurately modeled. At the semiempirical level, the lanthanide(III) ion is represented by a +3 core and has a minimal basis of 6s5d6p (9 atomic orbitals), the 4f electrons being included within the electronic core. Training sets containing up to 19 lanthanide complexes, with data computed at the density functional theory (DFT) level, have been employed for each lanthanide(III) ion.

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted.

The nature and function of the catalytic centres of the DMSO reductases.

Density functional theory calculations have been performed to probe aspects of the function of the reaction centres of the DMSO reductase enzymes, in respect of catalysis of oxygen atom transfer (OAT). The first comparison between Mo and W at the active site of these enzymes has been accomplished by a consideration of the reaction profile for OAT from DMSO to [MoIV(OMe)(S2C2H2)2]1- versus that for the corresponding reaction with [WIV(OMe)(S2C2H2)2]1-. Both reaction profiles involve two transition states separated by a well-defined intermediate; however, whilst the second transition state (TS2) is clearly rate-limiting for the Mo system, the two transition states have a similar energy for the W system.

Development of parameter sets for semi-empirical MO calculations of transition metal systems: iron parameters for iron-sulfur proteins.

A semi-empirical parameter set for iron has been developed which is appropriate for the study of iron-sulfur proteins having a single iron atom, by fitting to density-functional theory (DFT) calculations obtained for a series of small models of iron-containing proteins. These parameters are obtained using a modified BFGS optimisation procedure previously used to obtain semi-empirical parameters for the main group elements. The modifications to this procedure for obtaining parameters for transition metal atoms are outlined.

Promotion of oxygen atom transfer in Mo and W enzymes by bicyclic forms of the pterin cofactor.

Density functional theory calculations suggest that bicyclic structures of the "molybdopterin" in DMSO reductases may have an important catalytic role in oxygen atom transfer reactions.

The use of methods involving semi-empirical molecular orbital theory to study the structure and reactivity of transition metal complexes.

The electronic structure of molecular systems containing transition metal atoms is traditionally studied using methods based on density functional theory (DFT). Although such an approach has been quite successful, the treatment of large systems, be they transition metal complexes, bioinorganic molecules or the solid state, is still extremely computationally demanding at this level, and may not be practical for many systems of interest. In this paper we describe how semi-empirical MO methods can be used to overcome these computational bottlenecks, yet still provide predictions of the necessary accuracy.

Carbonyl-ene reactions catalyzed by bis(oxazoline) copper (II) complexes proceed by a facile stepwise mechanism: DFT and ONIOM (DFT:PM3) studies.

The mechanism of a carbonyl-ene addition reaction catalyzed by a bis(oxazoline) copper (II) complex has been studied using DFT methods. We find that the reaction proceeds by a stepwise mechanism with very low barriers and have identified the role of the metal catalyst. We find that the more computationally economic ONIOM method gives accurate geometries for the stationary structures on the potential energy surface but that accurate energetics must be calculated at the full DFT level.