			Home About us Contact

QM/MM Calculations (mm + calculation)

Distribution by Scientific Domains

Chemistry	100%

Distribution within Chemistry

Computational Chemistry & Molecular Modeling	50%
General & Introductory Chemistry	25%

Selected Abstracts

Modeling dioxygen binding to the non-heme iron-containing enzymes

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2006
A. V. Nemukhin
Abstract The structures and properties of the complexes formed upon binding the oxygen molecule to the iron sites in non-heme 2-oxoglutarate-dependent enzymes are characterized by QM(CASSCF)/MM and density functional theory (DFT) calculations. Molecular models for the calculations are constructed following the crystal structure of hypoxia-inducible factor asparaginyl hydroxylase (FIH-1). DFT calculations for the 37-atomic cluster have been carried out at the B3LYP(LANL2DZdp) level. The flexible effective fragment potential method is used as a combined quantum mechanical,molecular mechanical (QM/MM) technique to characterize the fragment of the enzymatic system, including 1,758 atoms in the MM part and 27 atoms in the QM part. In these calculations, the CASSCF(LANL2DZdp) approach is applied in the QM subsystem, and AMBER force field parameters are used in the MM subsystem. With both approaches, equilibrium geometry configurations have been located for different spin states of the system. In DFT calculations, the order of the states is as follows: septet, triplet (+7.7 kcal/mol), quintet (+10.7 kcal/mol). Geometry configurations correspond to the end-on structures with no evidences of electron transfer from Fe(II) to molecular oxygen. In contrast, QM(CASSCF)/MM calculations predict the quintet state as the lowest one, while the septet structure has slightly (<2 kcal/mol) higher energy, and the triplet state is considerably more energetic. In QM/MM calculations, in both quintet and septet states, the electronic configurations show considerable electron charge transfer from iron to oxygen, and the oxidation state of iron in the metal binding site can be characterized as Fe(III). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source]

Conformational analysis, Part 41.

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2006
-unsaturated carbonyl compounds, A modelling, LIS/NMR investigation of the conformations of
Abstract A novel Lanthanide Induced Shift Analysis (LISA) is presented. In this analysis both the paramagnetic and the diamagnetic lanthanide induced chemical shifts are normalised separately in contrast to previous techniques in which only the paramagnetic shifts were normalised. This procedure is used together with molecular mechanics (MMFF94) and ab initio (RHF/6-31G, RHF/6-311G** and B3LYP/6-311G**) calculations to investigate s - cis/s - trans isomerism in some ,,, -unsaturated aldehydes, ketones and esters. In tiglic aldehyde 1 and trans -cinnamaldehyde 4 the s - trans conformer predominates with energy differences ,E (s - cis,s - trans) of 1.64 and 1.76,kcal/mol. In methyl vinyl ketone 2 and trans -cinnamyl methyl ketone 5 the populations of the s - cis and s - trans isomers are almost equal (,E 0.24 and 0.0,kcal/mol) and in methyl crotonate 3 and methyl trans -cinnamate 6 the s - cis conformer is more stable (,E ,0.72 and ,0.41,kcal/mol). These results are in agreement with both the MMFF94 and ab initio calculated energies for the compounds except tiglic aldehyde 1 in which all the calculated values are too large and cinnamyl ketone 5. In this compound the ab initio calculations predict the s - cis form to be more stable than the s - trans in contrast to both the MM calculations and the observed result which give both forms of equal energy. Also in both the MM and ab initio calculations phenyl substitution in the ketone (2 vs. 5) considerably stabilises the s - cis form. This is not observed in practise. In phenyl acetate 7 the B3LYP calculations give two equally stable structures, one planar one non-planar. The MMFF94 and MP2 calculations and the LIS analysis support the existence of only the non -planar conformer in solution, which is also the conformation of phenyl acetate in the crystal. Copyright © 2006 John Wiley & Sons, Ltd. [source]

Tracking Flavin Conformations in Protein Crystal Structures with Raman Spectroscopy and QM/MM Calculations,

ANGEWANDTE CHEMIE, Issue 13 2010
Kjendseth Røhr, Åsmund
Strahlenschäden: Für eine aussagekräftige Analyse von Flavoenzym-Kristallstrukturen muss die Cofaktorkonformation genau bekannt sein. Doch durch Röntgenstrahlen während der Datensammlung erzeugte Photoelektronen können den Flavincofaktor reduzieren und so seine Geometrie ändern (siehe Bild). Parallel zur Datensammlung beobachtete Raman-Schwingungsmoden lieferten wichtige Informationen über den tatsächlichen Flavinzustand. [source]

QM/MM calculation of solvent effects on absorption spectra of guanine

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2010
Maja Parac
Abstract Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited-state calculations were extracted from ground-state molecular dynamics (MD) simulations using the self-consistent-charge density functional tight binding (SCC-DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited-state calculations used time-dependent density functional theory (TDDFT) and the DFT-based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto-N7H and keto-N9H guanine, with particular focus on solvent effects in the low-energy spectrum of the keto-N9H tautomer. When compared with the vertical excitation energies of gas-phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC-DFTB-based rather than B3LYP-based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas-phase and solution spectra, typically ca. 0.1,0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent-induced structural changes and from electrostatic solute,solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010 [source]

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions.

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2002

Abstract QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169,176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (,16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 Å) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product,reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute ,40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1314,1322, 2002 [source]

Modeling dioxygen binding to the non-heme iron-containing enzymes

Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2008
Ying Xiong
Abstract Various quantum mechanical/molecular mechanical (QM/MM) geometry optimizations starting from an x-ray crystal structure and from the snapshot structures of constrained molecular dynamics (MD) simulations have been performed to characterize two dynamically stable active site structures of phosphodiesterase-5 (PDE5) in solution. The only difference between the two PDE5 structures exists in the catalytic, second bridging ligand (BL2) which is HO, or H2O. It has been shown that, whereas BL2 (i.e. HO,) in the PDE5(BL2 = HO,) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+. It has been demonstrated that the results of the QM/MM geometry optimizations are remarkably affected by the solvent water molecules, the dynamics of the protein environment, and the electronic embedding charges of the MM region in the QM part of the QMM/MM calculation. The PDE5(BL2 = H2O) geometries optimized by using the QM/MM method in different ways show strong couplings between these important factors. It is interesting to note that the PDE5(BL2 = HO - ) and PDE5(BL2 = H2O) geometries determined by the QM/MM calculations neglecting these three factors are all consistent with the corresponding geometries determined by the QM/MM calculations that account for all of these three factors. These results suggest the overall effects of these three important factors on the optimized geometries can roughly cancel out. However, the QM/MM calculations that only account for some of these factors could lead to considerably different geometries. These results might be useful also in guiding future QM/MM geometry optimizations on other enzymes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2007
Sérgio Filipe Sousa
Abstract Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great attention in anticancer research over the last decade. However, despite the major accomplishments in the field, some very pungent questions on the farnesylation mechanism still persist. In this study, the authors have analyzed a mechanistic paradox that arises from the existence of several contradicting and inconclusive experimental evidence regarding the existence of direct coordination between the active-site zinc cation and the thioether from the farnesylated peptide product, which include UV,vis spectroscopy data on a Co2+ -substituted FTase, two X-ray crystallographic structures of the FTase-product complex, and extended X-ray absorption fine structure results. Using high-level theoretical calculations on two models of different sizes, and QM/MM calculations on the full enzyme, the authors have shown that the farnesylated product is Zn coordinated, and that a subsequent step where this Zn bond is broken is coherent with the available kinetic results. Furthermore, an explanation for the contradicting experimental evidence is suggested. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source]

Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2003
Pablo A. Molina
Two divide-and-conquer (DAQ) approaches for building multipole-based molecular electrostatic potentials of proteins are presented and evaluated for use in QM/MM calculations. One approach is a further development of the neutralization method of Bellido and Rullmann (J Comput Chem 1989, 10, 479,487) while the other is based on removing part of the electron density before performing the multipole expansion. Both methods create systems with integer charges without using charge renormalization. To determine their performance in terms of location of cuts and distance to QM region, the new DAQ approaches are tested in calculations of the proton affinity of N, of Lys55 in the inhibitor turkey ovomucoid third domain. Finally, the two methods are used to build a variety of MM regions, applied to calculations of the pKa of Lys55, and compared to other computational methodologies in which force field charges are employed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1971,1979, 2003 [source]

How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: A theoretical study

PROTEIN SCIENCE, Issue 4 2006
Yuhui Cheng
Abstract Phosphorylation mediates the function of many proteins and enzymes. In the catalytic subunit of cAMP-dependent protein kinase, phosphorylation of Thr 197 in the activation loop strongly influences its catalytic activity. In order to provide theoretical understanding about this important regulatory process, classical molecular dynamics simulations and ab initio QM/MM calculations have been carried out on the wild-type PKA,Mg2 ATP,substrate complex and its dephosphorylated mutant, T197A. It was found that pThr 197 not only facilitates the phosphoryl transfer reaction by stabilizing the transition state through electrostatic interactions but also strongly affects its essential protein dynamics as well as the active site conformation. [source]

Computational Study of the Phosphoryl Transfer Catalyzed by a Cyclin-Dependent Kinase

CHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2007
Marco De, Vivo Dr.
Abstract A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the ,-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car,Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et,al., Chem. Comm.2003, 1308,1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study (,42,kcal,mol,1 QM vs. ,24,kcal,mol,1 QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family. [source]

QM/MM Modeling of Enantioselective Pybox,Ruthenium- and Box,Copper-Catalyzed Cyclopropanation Reactions: Scope, Performance, and Applications to Ligand Design

CHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2007

Abstract An extensive comparison of full-QM (B3LYP) and QM/MM (B3LYP:UFF) levels of theory has been made for two enantioselective catalytic systems, namely, Pybox,Ru and Box,Cu complexes, in the cyclopropanation of alkenes (ethylene and styrene) with methyl diazoacetate. The geometries of the key reaction intermediates and transition structures calculated at the QM/MM level are generally in satisfactory agreement with full-QM calculated geometries. More importantly, the relative energies calculated at the QM/MM level are in good agreement with those calculated at the full-QM level in all cases. Furthermore, the QM/MM energies are often in better agreement with the stereoselectivity experimentally observed, and this suggests that QM/MM calculations can be superior to full-QM calculations when subtle differences in inter- and intramolecular interactions are important in determining the selectivity, as is the case in enantioselective catalysis. The predictive value of the model presented is validated by the explanation of the unusual enantioselectivity behavior exhibited by a new bis-oxazoline ligand, the stereogenic centers of which are quaternary carbon atoms. [source]

A QM/MM Study of Cisplatin,DNA Oligonucleotides: From Simple Models to Realistic Systems

CHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2006
Arturo Robertazzi
Abstract QM/MM calculations were employed to investigate the role of hydrogen bonding and , stacking in several single- and double-stranded cisplatin,DNA structures. Computed geometrical parameters reproduce experimental structures of cisplatin and its complex with guanine,phosphate,guanine. Following QM/MM optimisation, single-point DFT calculations allowed estimation of intermolecular forces through atoms in molecules (AIM) analysis. Binding energies of platinated single-strand DNA qualitatively agree with myriad experimental and theoretical studies showing that complexes of guanine are stronger than those of adenine. The topology of all studied complexes confirms that platination strongly affects the stability of both single- and double-stranded DNAs: PtNH,,,X (X = N or O) interactions are ubiquitous in these complexes and account for over 70,% of all H-bonding interactions. The , stacking is greatly reduced by both mono- and bifunctional complexation: the former causes a loss of about 3,4 kcal,mol,1, whereas the latter leads to more drastic disruption. The effect of platination on Watson,Crick GC is similar to that found in previous studies: major redistribution of energy occurs, but the overall stability is barely affected. The BH&H/AMBER/AIM approach was also used to study platination of a double-stranded DNA octamer d(CCTG*G*TCC),d(GGACCAGG), for which an experimental structure is available. Comparison between theory and experiment is satisfactory, and also reproduces previous DFT-based studies of analogous structures. The effect of platination is similar to that seen in model systems, although the effect on GC pairing was more pronounced. These calculations also reveal weaker, secondary interactions of the form Pt,,,O and Pt,,,N, detected in several single- and double-stranded DNA. [source]

On the Influence of the Local Environment on the CO Stretching Frequencies in Native Myoglobin: Assignment of the B-States in MbCO

CHEMPHYSCHEM, Issue 10 2006
Markus Meuwly Prof. Dr.
Frequency shifts: The influence of the local electrostatic environment on the ground vibrational level of photodissociated CO in native myoglobin is investigated by performing QM/MM calculations at the DFT level. The distribution of CO frequencies in the FeCO conformation occurs at higher wavenumbers than in the FeOC conformation (see figure). [source]

Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations