Our Own N-layer Integrated Molecular Orbital Molecular Mechanics Research Articles

Two-Step ONIOM Method for the Accurate Estimation of Individual Hydrogen Bond Energy in Large Molecular Clusters.

The study of molecular clusters to understand the properties of condensed systems has been the subject of immense interest. To get insight into these properties, the knowledge of various noncovalent interactions present in these molecular clusters is indispensable. Our recently developed molecular tailoring approach-based (MTA-based) method for the estimation of the individual hydrogen bond (HB) energy in molecular clusters is useful for this purpose. However, the direct application of this MTA-based method becomes progressively difficult with the increase in the size of the cluster. This is because of the difficulty in the evaluation of single-point energy at the correlated level of theory. To overcome this caveat, herein, we propose a two-step method within the our own N-layer integrated molecular orbital molecular mechanics (ONIOM) framework. In this method, the HB energy evaluated by the MTA-based method employing the actual molecular cluster at a low Hartree-Fock (HF) level of theory is added to the difference in the HB energies evaluated by the MTA-based method, employing an appropriate small model system, called the shell-1 model, calculated at high (MP2) and low (HF) levels of theory. The shell-1 model of a large molecular cluster is made up of only a few molecules that are in direct contact (by a single HB) with the two molecules involved in the formation of an HB under consideration. We tested this proposed two-step ONIOM method to estimate the individual HB energies in various molecular clusters, viz., water (Wn, n = 10-16, 18 and 20), (H2O2)12, (H2O3)8, (NH3)n and strongly interacting (HF)15 and (HF)m(W)n clusters. Furthermore, these estimated individual HB energies by the ONIOM method are compared with those calculated by the MTA-based method using actual molecular clusters. The estimated individual HB energies by the ONIOM method, in all these clusters, are in excellent linear one-to-one agreement (R2 = 0.9996) with those calculated by the MTA-based method using actual molecular clusters. Furthermore, the small values of root-mean-square deviation (0.06), mean absolute error (0.04), |ΔEmax| (0.21) and Sε (0.06) suggest that this two-step ONIOM method is a pragmatic approach to provide accurate estimates of individual HB energies in large molecular clusters.

QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update

AbstractComputational enzymology is a rapidly developing area that uniquely provides deep insight into the fundamental processes of biological catalysis at the atomic level. Such in‐depth insight can ultimately be employed in designing potential inhibitors against the targets of interest. Computational enzymology covers a wide range of in‐silico approaches for investigating the enzyme‐catalyzed reaction mechanisms, among which combined quantum mechanics (QM) /molecular mechanics (MM) approaches have gained a lot of attention nowadays. This advanced approach generally involves a QM method (i. e. a method that estimates the electronic structure of the active site) and a simpler MM method (a method that includes the enzyme environment) to understand the enzymatic reactions. The QM/MM method has been widely tested in understanding the molecular mechanisms both at the structural and energetic levels and observed to best correlate with experimental studies of the enzymatic mechanism. It proposes a new mechanism that ultimately opens a new route for designing new potent, efficacious enzyme inhibitors. This review mainly covers wide applications of the ONIOM (Our own N‐layer Integrated molecular Orbital Molecular mechanics) method for decoding the enzymatic catalysis mechanism or designing potential small molecule inhibitors as treatment therapeutics in terms of free energy profiles. Moreover, this article also highlights employing QM/MM method in comprehending the mechanisms for drug metabolism and resistance (owing to mutations). This write‐up may encourage medicinal chemists and molecular biologists to explore this approach to propose more promising therapeutics to improve the quality of treatment.

Multistate QM/QM Extrapolation of UV/Vis Absorption Spectra with Point Charge Embedding.

The simulation of UV/vis absorption spectra of large chromophores is prohibitively expensive with accurate quantum mechanical (QM) methods. Thus, hybrid methods, which treat the core chromophoric region at a high level of theory while the substituent effects are treated with a more computationally efficient method, may provide the best compromise between cost and accuracy. The ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) method has proved successful at describing ground-state processes. However, for excited states, it suffers from difficulties in matching the correct excited states among the different levels of theory. We devised an approach, based on the ONIOM extrapolation formula, to combine two QM levels of theory to extrapolate entire excitation bands rather than individual states. In this contribution, we extend the same QM/QM hybrid scheme to include polarization effects on the core region through point charge embedding. The charges are computed to reproduce the electrostatic potential of the entire chromophore at the low level of theory, with proper constraints to avoid overpolarization issues at the boundary between layers. We test this approach on a variety of model compounds that show how the multistate QM/QM-embedding scheme is able to accurately reproduce the spectrum of the entire system at the high level of theory better than (i) the bare QM/QM hybrid scheme, (ii) the low-level calculation on the entire system, and (iii) the high-level calculation on the core region.

Effect of arsenate substitution on phosphate repository of cell: a computational study.

The structural analogy with phosphate derives arsenate into various metabolic processes associated with phosphate inside the organisms. But it is difficult to evaluate the effect of arsenate substitution on the stability of individual biological phosphate species, which span from a simpler monoester form like pyrophosphate to a more complex phosphodiester variant like DNA. In this study, we have classified the physiological phosphate esters into three different classes on the basis of their structural differences. This classification has helped us to present a concise theoretical study on the kinetic stability of phosphate analogue species of arsenate against hydrolysis. All the calculations have been carried out using QM/MM methods of our Own N-layer Integrated molecular Orbital molecular Mechanics (ONIOM). For quantum mechanical region, we have used M06-2X density functional with 6-31+G(2d,2p) basis set and for molecular mechanics we have used the AMBER force field. The calculated rate constants for hydrolysis show that none of the phosphate analogue species of arsenate has a reasonable stability against hydrolysis.

Point charge embedding for ONIOM excited states calculations.

Hybrid quantum mechanical methods can assist in the interpretation and prediction of the electronic spectra of large molecular structures. In this work, we study the performance of the ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) hybrid method for the calculation of transition energies and oscillator strengths by embedding the core region in a field of fixed point charges. These charges introduce polarization effects from the substituent groups to the core region. We test various charge definitions, with particular attention to the issue of overpolarization near the boundary between layers. To minimize this issue, we fit the charges on the electrostatic potential of the entire structure in the presence of the link atoms used to cap dangling bonds. We propose two constrained fitting strategies: one that produces an average set of charges common to both model system calculations, EE(L1), and one that produces two separate sets of embedding charges, EE(L2). The results from our tests show that indeed electronic embedding with constrained-fitted charges tends to improve the performance of ONIOM compared to non-embedded calculations. However, the EE(L2) charges work best for transition energies, and the EE(L1) charges work best for oscillator strengths. This may be an indication that fixed point charges do not have enough flexibility to adapt to each system, and other effects (e.g., polarization of the embedding field) may be necessary.

Multi-state extrapolation of UV/Vis absorption spectra with QM/QM hybrid methods.

In this work, we present a simple approach to simulate absorption spectra from hybrid QM/QM calculations. The goal is to obtain reliable spectra for compounds that are too large to be treated efficiently at a high level of theory. The present approach is based on the extrapolation of the entire absorption spectrum obtained by individual subcalculations. Our program locates the main spectral features in each subcalculation, e.g., band peaks and shoulders, and fits them to Gaussian functions. Each Gaussian is then extrapolated with a formula similar to that of ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics). However, information about individual excitations is not necessary so that difficult state-matching across subcalculations is avoided. This multi-state extrapolation thus requires relatively low implementation effort while affording maximum flexibility in the choice of methods to be combined in the hybrid approach. The test calculations show the efficacy and robustness of this methodology in reproducing the spectrum computed for the entire molecule at a high level of theory.

Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme.

Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.

Computational modeling of the direct hydride transfer mechanism for the MAO catalyzed oxidation of phenethylamine and benzylamine: ONIOM (QM/QM) calculations

Monoamine oxidases are two isozymic flavoenzymes which are the important targets for drugs used in the treatment of depression, Parkinson and Alzheimer's diseases. The catalytic reaction taking place between the cofactor FAD and amine substrate is still not completely understood. Herein we employed quantum chemical methods on the recently proposed direct hydride transfer mechanism including full active site residues of MAO isoforms in the calculations. Activation free energy barriers of direct hydride transfer mechanism for MAO-A and MAO-B were calculated by ONIOM (our own n-layered integrated molecular orbital + molecular mechanics) method with QM/QM (quantum mechanics:quantum mechanics) approach employing several density functional theory functionals, B3LYP, WB97XD, CAM-B3LYP and M06-2X, for the high layer. The formation of very recently proposed αC-flavin N5 adduct inside the enzyme has been investigated. ONIOM (M06-2X/6-31+G(d,p):PM6) results revealed that such an adduct may form only in MAO-B suggesting slightly different hydride transfer mechanisms for MAO-A and MAO-B.

Isomerization Mechanismof Xylene Catalyzed by H-ZSM-5 Molecular Sieve

The isomerization mechanism of xylene over H-ZSM-5 molecular sieve has been examined using the density functional theory(DFT) and our own-N-layered integrated molecular orbital + molecular mechanics(ONIOM) methods.The structures of intermediate species and transition states are described.The adsorption of reactant and desorption of product significantly affect the tendency of xylene to isomerize.Calculated activation energies suggest that isomerization occurs during the formation of meta-xylene within the extended pore structure of H-ZSM-5 molecular sieve.However,the produced meta-xylene is retained within the pore because of a high desorption energy,and further isomerization to form para-xylene is kinetically favorable.The acid sites within the pores of the molecular sieve allow selective formation of para-xylene.On the external surface of H-ZSM-5 molecular sieve,which lacks the steric constraints of the extended pore structure,xylene isomerizes to form meta-xylene,which can readily desorb from the active site.Such non-selective isomerization decreases the selectivity for para-xylene.Thus,external surface modification of H-ZSM-5 molecular sieve should suppress the non-selective isomerization of xylene,thereby increasing the selectivity for para-xylene by restricting isomerization to inside the pores of the molecular sieve.Calculated relative reaction rate constants for xylene isomerization also indicate that xylene isomerization occurring on the external surface of H-ZSM-5 with meta-xylene as the product has the highest reaction rate.The selectivity for para-xylene is decreased as the reaction temperature is increased.

A Configuration Interaction Picture for a Molecular Environment Using Localized Molecular Orbitals: The Excited States of Retinal Proteins

Electronic excitations of chromophores in proteins and solutions are associated with the electronic response of the molecular environment. The underlying interactions are important origins of solvatochromism. We performed large-scale configuration interaction singles (CIS) calculations (up to 1000 atoms) for retinal chromophores in proteins and methanol solution, in which one-electron processes (polarization and charge-transfer effects of the environment) are included. The present approach also improved the electrostatic potential, as compared to that described by a molecular mechanics (MM) force field. The CIS results were combined with the symmetry adapted cluster (SAC)-CI result using our own N-layer integrated molecular orbital molecular mechanics (ONIOM) method. As compared to the MM description, the CIS reduces the calculated excitation energy by 0.1-0.3 eV and also improves the relative excitation energies among retinal proteins. We applied our localized molecular orbital (LMO) transformation scheme to analyze the CI wave functions. The result clarified the contributions of the amino acids. In bacteriorhodopsin, Tyr185 contributes intermolecular CT excitations. The radial distribution of amino acids' contributions to the CI wave function was also analyzed. The results of the analysis are useful not only for understanding the molecular interactions and the role of amino acids in color tuning, but also for providing insight into the structure of the excited-state wave function for the molecular environment. An excitation-energy decomposition analysis also supported the results of the excited-state wave functions.

In Silico study of carcinogenic o‐Quinone metabolites derived from polycyclic aromatic hydrocarbons (PAHs)

A computational density functional theory study on the structural and electronic properties of several polycyclic aromatic hydrocarbon (PAH) ortho‐quinones was performed and the possible mechanism of DNA‐adduct formation was analyzed to evaluate its thermodynamic viability. Molecular docking techniques were applied to examine the noncovalent interactions developed when a model PAH ortho‐quinone intercalates between the DNA double helix. Quantum‐chemical ONIOM (our Own N‐layer Integrated molecular Orbital molecular Mechanics) calculations within the structure of a DNA fragment were carried out to evaluate the significant steps of noncovalent complex and covalent adduct formation. The solvent effect was also considered by employing a continuum solvation model. The present calculations suggest that initial noncovalent interactions of the PAH o‐quinone within the DNA double helix could determine the feasibility of benzo[a]pyrene‐7,8‐dione‐DNA covalent adduct formation, and that dispersion‐corrected functionals are more suitable for locating the noncovalent complex. Copyright © 2012 John Wiley & Sons, Ltd.

The ONIOM method: its foundation and applications to metalloenzymes and photobiology

AbstractThe ONIOM (our Own N‐layer Integrated molecular Orbital molecular Mechanics) method is one of the most popular, successful, and easily‐to‐implement hybrid quantum mechanics/molecular mechanics (QM/MM) methods to treat complex molecular systems. Hybrid QM/MM methods take advantage of the high accuracy of QM methods and the low computational cost of MM methods. One key feature of the ONIOM method is a simple linear extrapolation procedure, which allows the ONIOM method to be further extended to two‐layer ONIOM(QM1:QM2), three‐layer ONIOM(QM1:QM2:MM), and, in principle, any n‐layer n‐level‐of‐theory methods. Such hierarchical features of the ONIOM method are unique among the hybrid QM/MM methods. This review article provides an overview of the theoretical foundation and recent development of the ONIOM method. Some of its recent applications to metalloenzymes and photobiology will also be highlighted. Prospective ONIOM development for more realistic simulations on the complex systems will be discussed finally. © 2011 John Wiley & Sons, Ltd.This article is categorized under: Electronic Structure Theory > Combined QM/MM Methods

Integrating In Silico and In vitro Approaches to Dissect the Stereoselectivity of Bacillus subtilis Lipase A toward Ketoprofen Vinyl Ester

The asymmetric catalysis, as the character of enzyme, attracts increasing attention from the scientific and industrial communities. In this study, the Bacillus subtilis lipase A, as a model enzyme, is studied systematically to dissect its stereoselectivity toward (rac)-ketoprofen vinyl ester using a combination scheme of molecular docking and quantum mechanical/molecular mechanical (QM/MM) analysis. In this procedure, the rational orientation of the two enantiomers of ketoprofen vinyl ester is obtained with the AutoDock performing, and then, the steric contacts between the enzyme and substrate in the docking outputs are examined visually at the atomic level with a small-probe technique. Subsequently, the binding energies of the enzyme-substrate complexes are calculated using an ONIOM (Our own N-layered Integrated Molecular Orbital + Molecular mechanics)-based QM/MM protocol. The results obtained from the theoretical studies show that the B.subtilis lipase A prefer to hydrolyze the (R )-ketoprofen vinyl ester when compared to its (S )-enantiomer, with a relatively high E (stereoselectivity) value of 31.28 charactering its enantioselectivity. Furthermore, to verify the conclusions from the computational analysis, the B.subtilis lipase A gene is cloned to overexpress the recombinant B.subtilis lipase A, and its stereoselectivity was determined. Satisfactorily, the experimental results are in well agreement with the theoretical predictions because the (R )-ketoprofen vinyl ester is found as the preferring enantiomer of the B.subtilis lipase A, with experimentally measured E value of 36.7. We therefore expect that this in silico-in vitro hybrid approach can provide a new and effective avenue to predict the catalytic activity of and to investigate the molecular mechanism of enzyme-mediated asymmetric catalysis and help in understanding the enzymatic process and in rational enzyme design.

Calculations on the Structure and Spectral Properties of Cytochrome c551 Using DFT and ONIOM Methods

The active site geometry of cytochrome (Cyt) c(551) and its mutated form containing Fe(II) and Fe(III) ions have been calculated using density functional theory (DFT)-based Becke's three-parameter hybrid exchange and Lee-Yang-Parr correlation (B3LYP) method. In addition, calculations have also been carried out using hybrid meta DFT-based M06 functional. The effect of the protein milieu on the active site geometry has also been probed using two-layer via our own N-layered integrated molecular orbital + molecular mechanics (ONIOM) method. Evidence from the calculations reveal that the active site geometry is not significantly affected by the oxidation state of metal ion. The difference in the geometry of the active site and that of the same with the entire protein environment is only minimal, which shows that the protein milieu does not influence the structure of the active site. The calculated electronic transition energies from the time-dependent DFT (TDDFT) calculations are in close agreement with the experimental values. Although there are no significant variations in the active site geometry upon oxidation, the changes in the electronic transition energies have been attributed to the reduction in the overlap of metal ion with the ligand orbitals. In addition, it is found that mutation does not influence the active site geometry and the electronic transition energies. Nevertheless, mutation leads to the formation of more compact structure than the native Cyt c(551).

Oscillator Strengths in ONIOM Excited State Calculations.

We compute oscillator strengths with the ONIOM (Our own N-layer Integrated molecular Orbital molecular Mechanics) hybrid method between ground and valence excited states and compare the results with the high level of theory equation of motion coupled cluster singles and doubles (EOM-CCSD). This work follows our previous studies in which we validated the ability of ONIOM to compute accurate transition energies compared to EOM-CCSD. We test various levels of theory and molecular systems, as well as the effect of the link atom bond length. Our results show that oscillator strengths can be accurately computed with ONIOM, provided that a sensible choice of the partitioning and of the low level method is made. Being able to calculate both the transition energy and the oscillator strength, ONIOM represents a promising approach to completely characterize valence excited states of molecules that are too large to be studied with a conventional high-accuracy method.

Link atom bond length effect in ONIOM excited state calculations

We investigate how the choice of the link atom bond length affects an electronic transition energy calculation with the so-called our own N-layer integrated molecular orbital molecular mechanics (ONIOM) hybrid method. This follows our previous paper [M. Caricato et al., J. Chem. Phys. 131, 134105 (2009)], where we showed that ONIOM is able to accurately approximate electronic transition energies computed at a high level of theory such as the equation of motion coupled cluster singles and doubles (EOM-CCSD) method. In this study we show that the same guidelines used in ONIOM ground state calculations can also be followed in excited state calculations, and that the link atom bond length has little effect on the ONIOM energy when a sensible model system is chosen. We also suggest further guidelines for excited state calculations which can help in checking the effectiveness of the definition of the model system and controlling the noise in the calculation.

Role of Second Coordination Sphere Amino Acid Residues on the Proton Transfer Mechanism of Human Carbonic Anhydrase II (HCA II)

The barrier for the proton transfer in human carbonic anhydrase II (HCA II) has been studied by including the important second coordination sphere residues to the minimalistic model of the active site using B3LYP/6-31+G** level of calculation. Specifically, proton transfer from a zinc-bound water molecule to a histidine residue (His64) mediated by a water bridge (consists of two and three water molecules) has been investigated. The new model contains three functional groups of second coordination sphere residues such as Gln92, Glu117, and Asn244. These residues interact with His94, His119, and His96, respectively. We have calculated the barrier for the proton transfer using the total energies of reactants, transition states, and products. The calculated barrier height for the models with two water and three water molecules are 8.94 and 8.67 kcal/mol, respectively, which are in close agreement with the experimental value of 7.8 kcal/mol obtained from the kinetic experiments and to the range 8-10 kcal/mol predicted from the pK(a) considerations ( Silverman , D. N. Biochim. Biophys. Acta 2000 , 1458 , 88 - 103 . ). In addition, our own N-layered integrated molecular orbital + molecular mechanics (ONIOM) calculations have also been carried out on various model systems to understand the effect of complete environment. It is possible to note from the results that the confinement of water molecules by the protein milieu appreciably decreases the O...O distance between water molecules in the water bridge when compared to the free water dimer which enables the proton transfer from one water to the other and finally to the His64 residue.

EFFECT OF HIGH-LEVEL LAYER SELECTION IN ONIOM ON Na+ ADSORPTION IN ZSM-5 ZEOLITE

Here we present a systematical investigation on the effect of high-level layer selection in our own N-layered integrated molecular orbital + molecular mechanics (ONIOM) method. We used the adsorption of Na+ in the M7 site of ZSM-5 as an instructive example. We embedded n tetrahedral sites (nT= 7, 19, 22, 33) for high-level layer into a low-level layer represented by 75T (denoted as nT@75T). Our calculations showed that 7T@75T behaved poorly in both structure optimization and interaction energy calculation. Hence only including the first coordination circle of the ion (i.e. 7T), as commonly used in literature, is not sufficiently good. However, for n ≥ 19, both structure optimization and interaction energy calculation by ONIOM are in good agreement with the full 75T model calculation. Such a reliable ONIOM calculation needs only 1/10 to 1/5 computational time for each self-consistent field (SCF) iteration as compared to the full 75T model calculation, highlighting its pivotal role in zeolite simulation.

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

Equation of motion coupled-cluster singles and doubles (EOM-CCSD) is one of the most accurate computational methods for the description of one-electron vertical transitions. However, its O(N(6)) scaling, where N is the number of basis functions, often makes the study of molecules larger than 10-15 heavy atoms prohibitive. In this work we investigate how accurately less expensive methods can approximate the EOM-CCSD results. We focus on our own N-layer integrated molecular orbital molecular mechanics (ONIOM) hybrid scheme, where the system is partitioned into regions which are treated with different levels of theory. For our set of benchmark calculations, the comparison of conventional configuration interaction singles (CIS), time-dependent Hartree-Fock (TDHF), and time-dependent density functional theory (TDDFT) methods and ONIOM (with different low level methods) showed that the best accuracy-computational time combination is obtained with ONIOM(EOM:TDDFT), which has a rms of the error with respect to the conventional EOM-CCSD of 0.06 eV, compared with 0.47 eV of the conventional TDDFT.

Investigation of Reverse-Hydrogen Spillover on Zeolite-Supported Palladium Tetramer by ONIOM Method

The present study explores favorable chemical state of zeolite-supported Pd4 clusters using the ONIOM (our-own-N-layered integrated molecular orbital + molecular mechanics) approach, as implemented in the Gaussian03 code. Lowest-energy structures of Pd4 in the gas phase as well as on a zeolite support are found to be in the triplet state. The calculations reveal that reverse hydrogen spillover from bridging OH groups of zeolite support onto Pd4 results in a hydrogenated Pd4H/Zeo((m − 1)H), m = 1−3 species, which are energetically preferable over the bare zeolite-supported form of Pd4/Zeo(mH). The process of single hydrogen transfer from the zeolite support to the Pd4 cluster is found to be exothermic and more favorable than two- and three-proton transfer processes.