Semiempirical Quantum Mechanical Methods Research Articles

VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.

Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.

Development of quantitative structure activity relationships for the binding affinity of methoxypyridinium cations for human acetylcholinesterase

Among the most toxic substances known are the organophosphorus (OP) compounds used as pesticides and chemical warfare agents. Owing to their high toxicity there is a number of efforts underway to develop effective therapies for OP agent exposure. To date all therapies in use treat inhibited acetylcholinesterase (AChE), but are ineffective for the treatment of inhibited AChE, which has undergone a subsequent hydrolysis process, referred to as aging. Toward developing a therapy for treating victims of OP intoxication in the aged state we have developed Quantitative Structure–Activity Relationships (QSARs) based on the AM1 semiempirical quantum mechanical method using the program, CODESSA (COmprehensive Descriptors for Structural and Statistical Analysis). Using this methodology we obtained a multiple correlation QSAR equation which gave R2=0.9359 for a random training set of 38 ligands and R2=0.9236 for prediction on a random test set of 9 ligands.

Development of quantitative structure property relationships for predicting the melting point of energetic materials

The accurate prediction of the melting temperature of organic compounds is a significant problem that has eluded researchers for many years. The most common approach used to develop predictive models entails the derivation of quantitative structure-property relationships (QSPRs), which are multivariate linear relationships between calculated quantities that are descriptors of molecular or electronic features and a property of interest. In this report the derivation of QSPRs to predict melting temperatures of energetic materials based on descriptors calculated using the AM1 semiempirical quantum mechanical method are described. In total, the melting points and experimental crystal structures of 148 energetic materials were analyzed. Principal components analysis was performed in order to assess the relative importance and roles of the descriptors in our QSPR models. Also described are the results of k means cluster analysis, performed in order to identify natural groupings within our study set of structures. The QSPR models resulting from these analyses gave training set R2 values of 0.6085 (RMSE=±15.7°C) and 0.7468 (RMSE=±13.2°C). The test sets for these clusters had R2 values of 0.9428 (RMSE=±7.0°C) and 0.8974 (RMSE=±8.8°C), respectively. These models are among the best melting point QSPRs yet published for energetic materials.

Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase.

The catalytic and allosteric mechanisms of insulin receptor kinase (IRK) are investigated by a combination of ab initio and semiempirical quantum mechanical and molecular mechanical (QM/MM) methods and classical molecular dynamics (MD) simulations. The simulations reveal that the catalytic reaction proceeds in two steps, starting with the transfer of a proton from substrate Tyr to the catalytic Asp1132, followed by the phosphoryl transfer from ATP to substrate Tyr. The enhancement of the catalytic rate of IRK upon phosphorylations in the enzyme's activation loop is found to occur mainly via changes to the free energy landscape of the proton transfer step, favoring the proton transfer in the fully phosphorylated enzyme. In contrast, the effects of the phosphorylations on the phosphoryl transfer are smaller. Equilibrium MD simulations show that IRK phosphorylations affect the protein dynamics of the enzyme before the proton transfer to Asp1132 with only a minor effect after the proton transfer. This finding is consistent with the large change in the proton transfer free energy and the smaller change in the free energy barrier of phosphoryl transfer found by QM/MM simulations. Taken together, the present results provide details on how IRK phosphorylation exerts allosteric control of the catalytic activity via modifications of protein dynamics and free energy landscape of catalytic reaction. The results also highlight the importance of protein dynamics in connecting protein allostery and catalysis to control catalytic activity of enzymes.

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization.

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.

Standards-based curation of a decade-old digital repository dataset of molecular information.

BackgroundThe desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported.ResultsThe procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools.ConclusionsWe recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the “supporting information”) should be conducted in a manner that facilitates automatic periodic curation. Graphical abstractStandards and metadata-based curation of a decade-old digital repository dataset of molecular information.

Structural modifications of graphyne layers consisting of carbon atoms in the sp- and sp 2-hybridized states

A model scheme is proposed for obtaining layered compounds consisting of carbon atoms in the sp- and {vnsp}2-hybridized states. This model is used to find the possibility of existing the following seven basic structural modifications of graphyne: α-, β1-, β2-, β3-, γ1-, γ2-, and γ3-graphyne. Polymorphic modifications β3 graphyne and γ3 graphyne are described. The basic structural modifications of graphyne contain diatomic polyyne chains and consist only of carbon atoms in two different crystallographically equivalent states. Other nonbasic structural modifications of graphyne can be formed via the elongation of the carbyne chains that connect three-coordinated carbon atoms and via the formation of graphyne layers with a mixed structure consisting of basic layer fragments, such as α-β-graphyne, α-γ-graphyne, and β-γ-graphyne. The semiempirical quantum-mechanical MNDO, AM1, and PM3 methods and ab initio STO6-31G basis calculations are used to find geometrically optimized structures of the basic graphyne layers, their structural parameters, and energies of their sublimation. The energy of sublimation is found to be maximal for γ2-graphyne, which should be the most stable structural modification of graphyne.

ChemInform Abstract: Quantum and Molecular Mechanical Monte Carlo Techniques for Modeling Condensed‐phase Reactions

AbstractReview: 98 refs.

Diamond-like phases prepared from graphene layers

The geometrically optimized structure of ten carbon diamond-like phases obtained by crosslinking graphene layers has been calculated using the density functional theory method and the structural parameters, densities, sublimation energies, and densities of electron states have been determined. Bulk moduli of diamond-like phases have been calculated using the PM3 semiempirical quantum-mechanical method. The X-ray powder diffraction patterns have been calculated based on structural parameters. These diffraction patterns can be used to identify new phases.

Self-accelerating decomposition temperature and quantitative structure–property relationship of organic peroxides

This work presents a new approach to predict thermal stability of organic peroxides based on quantitative structure–property relationship methods. The data set consists of self-accelerating decomposition temperature (SADT) of 39 organic peroxides, part of which is obtained from the Recommendations on the Transport of Dangerous Goods and the other part is obtained from C600 calorimetry. Descriptors computed using RM1 semi-empirical quantum mechanical method are selected to describe the above-mentioned 39 molecules. Partial least-squares method and multiple linear regression method are used to select the descriptors and SADT model. At last, a four-descriptor correlation equation is obtained using a cross validation method: a correlation coefficient R>0.9 and a predictive coefficient Q2>0.85.

High-performance, quantum mechanics-based macromolecular x-ray refinement

"Modern, structure based drug discovery (SBDD) is dependent upon accurate protein:ligand structure determination and characterization. In conventional x-ray refinement, the geometry of the ligand within the active site is modeled according to the practitioner's beliefs as expressed in the form of stereochemical restraints provided by the ligand library or CIF file. Further, metal centers, bound species, and so on can be difficult to refine correctly without significant human intervention. Our work has addressed this problem through the integration of DivCon6 - a linear scaling, semiempirical, quantum mechanics (SE-QM) functional - with the Phenix refinement package. With Phenix/DivCon[1], SE-QM is used in ""real-time"" during each microcycle over the course of the refinement. With its inclusion of electrostatics, charge transfer, polarization, dispersion, hydrogen bonds, etcetera, this method is a much more rigorous, robust alternative to conventional stereochemical restraints and is better able to accurately model protein:ligand structures without ""tweaking"" any restraints. We report PM6 refinement results for several key examples including structures with metal coordination spheres, covalent bonds, and other exotic protein:ligand chemistry situations. When compared with the originally deposited PDB structures, we found in all cases that QM refinement leads to ligand structures with much lower strain, and in some cases, the improvement is dramatic and as much 10+ fold. At the same time, SE-QM methods are better able to capture the influence of the surrounding structure (e.g. active site) on the ligand. These interactions are particularly interesting in SBDD as they are often the targets for lead design and optimization, and examples that illustrate how these interactions are captured with SE-QM will also be discussed."

Interaction studies of Alzheimer's Cathepsin B protein with inhibitors in presence and absence of water

Background The accuracy of ligand-protein docking may be affected by the presence of water molecules on the surface of proteins. Water can form complex bridging networks and can play a critical role in dictating the binding mode of ligands. A recent analysis of high-resolution crystal structures of ligand-protein complexes revealed that 85% of the complexes had one or more water molecules bridging the interaction between ligand and protein. For predicting the binding modes and energies of protein-ligand interactions, molecular docking methods are commonly used. In order to obtain an accurate complex geometry and binding energy estimation, an appropriate method for calculating partial charges is essential. AutoDockTools software, widely used as interface for preparing input files, utilizes the either Gasteiger or Kollman partial charge calculation method for both protein and ligand charge calculations. However, it has already been reported that more accurate partial charge calculation and as a consequence, more accurate docking can be achieved by using quantum chemical methods. In common practice so far, the quantum chemical partial charges were applied to the ligands for docking calculations. The newly developed Mozyme function of MOPAC2009 allows fast partial charge calculation of proteins by quantum mechanical semiempirical methods. Thus, in the current study, we use the semi-empirical quantum-mechanical partial charge calculations to investigate the interaction energies and polarization effects of the various components of the binding pocket on a set of Cathepsin B protein. Results The docking accuracy was computed by using the original AutoDock scoring function with the set of 19 protein ligand complexes using Gasteiger, AM1 and PM3 partial charge calculation methods. This helped us to compare the effect of the partial charge calculation method on docking accuracy. It was seen that the docking accuracy in regard to complex geometry significantly increased when partial charges of the ligands and proteins were calculated with the semi-empirical PM3 method. Our results demonstrate that (i) the energetic of the key water molecule are more favorable for the binding site in the Cathepsin B protein (ii) Water bridging and triangle formation were seen between the key amino acid residue and the ligand (iii) The internal energy is significant factor for the binding modes of various ligands. It was also observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations. Out of the 19 complexes analyzed in the course of our study, the geometry of 17 complexes were accurately calculated using PM3 partial charges, while the use of Gasteiger charges resulted in only 8 accurate geometries. Conclusion Our findings indicate that the inclusion of water molecules in ligand-protein docking results in significant increases in docking accuracy when the use of quantum chemical partial charge assignment on both ligand and proteins for predicting the docking simulations.

Comparison of computational studies with the X-ray crystal structure of directly synthesized Bis(D,L-aminobutyric)copper(II) complex

The important feature of the present work is that the crystal data are obtained first time for the directly synthesized complex [Cu(D,L-but)2] from pure zero valent metal and butyric acid in water. Further investigation involves the comparison of structural parameters from the XRD data of the title complex [Cu(D,L-but)2] in solid state with the theoretically optimized structure in the gaseous state and its simulated spectra (vibrational and electronic) are generated. The results show that the structural parameters determined by computational studies and crystal structure studies are in good agreement. In the computational calculations, the geometric optimization is carried out using the MM3 method and electronic spectra are calculated using ZINDO, a semi-empirical quantum mechanical method of Scigress explorer 7.7. The theoretical calculations of HOMO-LUMO energies have revealed that the charge transfer interactions occur within the complex. The crystal data for the [Cu(D,L-but)2] complex are: space group P21/c; a = 11.096(5) A, b = 5.062(4) A, c = 9.475(3) A; β = 92.4°; ρcalc = 1.673 g/cm3; Z = 2.

Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions.

A recent review (Acc. Chem. Res. 2010, 43:142-151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., "on water" and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost.

Frontispiece.

The frontispiece shows the casein kinase 2 (CK2), cyclin-dependent kinase 2 (CDK2), HIV-1 protease (HIV-1 PR) and their inhibitors. Jindřich Fanfrlík and co-workers discuss the latest developments in modern quantum mechanics (QM)-based computer-aided drug design, especially using semiempirical QM methods in their Minireview on page 921 ff.

Physicochemical properties of exogenous molecules correlated with their biological efficacy as protectors against carcinogenesis and inflammation

A large number of molecules referred to here as M, several of which are extracted from plants, belong to different chemical classes and exhibit chemoprotective activity against carcinogenesis and inflammation in rodents and in vitro cell culture. The aim of this article is to review and analyse our previous investigations on linear correlations observed between physicochemical parameters of the tested molecules M and their biological efficacies measured in vivo and/or in vitro. The principal physicochemical parameters studied characterise the energy required to oxidise M into M•+, E(M•+/M), namely its first vertical ionisation potential, and the energy liberated by the addition of an electron to M, i.e. its vertical electron affinity. These physicochemical properties were determined experimentally using diverse techniques and theoretically using mainly semiempirical (AM1) and density functional theory (DFT) quantum mechanical methods.

The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design.

This Minireview discusses the latest developments in modern quantum mechanics (QM)-based computer-aided drug design, especially using semiempirical QM (SQM) methods. It first tackles biochemical and biophysical quantities and the approaches to their measurements. Protein-ligand affinities are determined mostly by noncovalent interactions. The text thus illustrates how these can be accurately treated with SQM methods. Next, a construction of a modern SQM-based scoring function is presented and its applications listed. In summary, SQM-based scoring is a promising modern efficient strategy to be exploited in computer-aided drug design.

Acceleration of Semiempirical Quantum Mechanical Calculations by Extended Lagrangian Molecular Dynamics Approach.

The implementation and performance of the atom-centered density matrix propagation (ADMP) [J. Chem. Phys. 2001, 114, 9758] and the curvy-steps (CURV) methods [J. Chem. Phys. 2004, 121, 1152] are described. These methods solve the electronic Schrödinger equation approximately by propagating the electronic degrees of freedom using the extended Lagrangian molecular dynamics (ELMD) simulation approach. The ADMP and CURV methods are implemented and parallelized to accelerate semiempirical quantum mechanical (QM) methods (such as the MNDO, AM1, PM3, MNDO/d, and AM1/d methods). Test calculations show that both the ADMP and the CURV methods are 2∼4 times faster than the Born-Oppenheimer molecular dynamics (BOMD) method and conserve the total energy well. The accuracy of the ADMP and CURV simulations is comparable to the BOMD simulations. The parallel implementation accelerates the MD simulation by up to 28 fold for the ADMP method and 25 fold for the CURV method, respectively, relative to the speed of the single core BOMD. In addition, a multiple time scale (MTS) approach is introduced to further speed up the semiempirical QM and QM/MM ELMD simulations. Since a larger integration time step is used for the propagation of the nuclear coordinates than that for the electronic degrees of freedom, the MTS approach allows the ELMD simulation to be carried out with a time step that is larger than the time step accessible by the original ADMP and CURV methods. It renders MD simulation to be carried out about 20 times faster than the BOMD simulation, and yields results that are comparable to the single time scale simulation results. The use of the methods introduced in the present work provides an efficient way to extend the length of the QM and QM/MM molecular dynamics simulations beyond the length accessible by BOMD simulation.

Modelling polymers with side chains: MEH-PPV and P3HT

Modelling polymers with side chains is always a challenge once the degrees of freedom are very high. In this study, we present a successful methodology to model poly[2-methoxy-5-(2′-ethyl-hexyloxy)-p-phenylenevinylene] (MEH-PPV) and poly[3-hexylthiophene] (P3HT) in solutions, taking into account the influence of side chains on the polymer conformation. Molecular dynamics and semi-empirical quantum mechanical methods were used for structure optimisation and evaluation of optical properties. The methodology allows to describe structural and optical characteristics of the polymers in a satisfactory way, as well as to evaluate some usual simplifications adopted for modelling these systems. Effective conjugation lengths of 8-14.6 and 21 monomers were obtained for MEH-PPV and P3HT, respectively, in accordance with experimental findings. In addition, anti/syn conformations of these polymers could be predicted based on intrinsic interactions of the lateral branches.