Molecular Mechanics Method Research Articles

Simulation of gas chromatographic separation based on random diffusion

色谱分离过程中的粒子扩散问题是色谱动力学研究的基础,深入理解粒子的扩散行为对优化分离操作条件、提升色谱性能和开发新型色谱柱尤为关键。现有的模拟方法多集中于局部过程的热力学研究,而整体的扩散分离过程报道并不多见。为此,该文基于微尺度受限空间内随机扩散的方法,通过动态追踪粒子的运动轨迹,实现粒子在气相色谱开管柱内的扩散全过程模拟。基于前期烷烃同系物的分离模拟研究,结合Kovats保留指数,分别建立了吸附步数与温度、吸附步数与碳数的函数关系,由此获得不同类型的同系物在不同温度条件下的分离参数系统。以醇类同系物的分离验证模拟的可靠性,结果表明保留时间的相对误差基本控制在5%以内,而峰宽相对误差在0.75%~60%之间。峰宽误差较大的原因在于:(1)参数化计算过程中未能充分迭代以及使用外推法;(2)模型中忽略了醇分子之间的氢键作用。该文提出的模拟方法虽然可以准确地预测色谱保留时间以及合理描述色谱峰的基本形貌特征,但尚有进一步发展空间,特别是增加对分子间相互作用的细节处理,例如可参考分子力学的方法建立分子间势函数和吸附步数的关系,利用分子力学计算的能量来取代参数化的吸附步数,从而实现更为精确的分离过程模拟。总体而言,该文所提出的模拟方法为优化色谱分离操作条件和开发新型色谱分离技术提供了有价值的参考。

A Bioinformatics Research of Active Compounds Curcuma xanthorriza in Arthritis Disease

Curcuma xanthorriza roxb. or commonly known as ginger is a plant that grows in the tropics which is known as a million benefits plant, one of which is for the treatment of Arthritis. The main active compounds that act as anti-inflammatory which refer to arthritis are curcumin and demethoxycurcumin. The purpose of this study was to analyze the active compounds contained in ginger which play an important role in the treatment of arthritis. Bioinformatics analysis was carried out using the ChemOffice 2016 software using the molecular mechanics method. The 2-dimensional structure analysis uses the ChemDraw program, while the 3-dimensional structure analysis uses the Chem3D program. From the data optimization results using the molecular mechanics method, the following results are obtained: The total energy produced in the compounds curcumin, d-camphor, demethoxycurcumin, p-tolymethilcarbinol, starch, respectively 17.4573 kcal / mol; 29,2006 kcal / mol; 13.8948 kcal / mol; -0.6574 kcal / mol; and 29,6089 kcal / mol. Based on the research data obtained, it can be concluded that the active compounds curcumin and demethoxycurcumin are compounds that act as anti-inflammatory triggers for arthritis. It is proven that the results of the MM2 method are in accordance with the related theory.
 Keyword: curcuma, anti-inflammatory, molecular mechanics, curcumin, demethoxycurcumin..
 
 Keywords: Anti-inflammatory; Curcuma; Curcumin, Demethoxycurcumin; Molecular mechanics

TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics.

Fast and accurate assessment of small-molecule dihedral energetics is crucial for molecular design and optimization in medicinal chemistry. Yet, accurate prediction of torsion energy profiles remains challenging as the current molecular mechanics (MM) methods are limited by insufficient coverage of drug-like chemical space and accurate quantum mechanical (QM) methods are too expensive. To address this limitation, we introduce TorsionNet, a deep neural network (DNN) model specifically developed to predict small-molecule torsion energy profiles with QM-level accuracy. We applied active learning to identify nearly 50k fragments (with elements H, C, N, O, F, S, and Cl) that maximized the coverage of our corporate compound library and leveraged massively parallel cloud computing resources for density functional theory (DFT) torsion scans of these fragments, generating a training data set of 1.2 million DFT energies. After training TorsionNet on this data set, we obtain a model that can rapidly predict the torsion energy profile of typical drug-like fragments with DFT-level accuracy. Importantly, our method also provides an uncertainty estimate for the predicted profiles without any additional calculations. In this report, we show that TorsionNet can accurately identify the preferred dihedral geometries observed in crystal structures. Our TorsionNet-based analysis of a diverse set of protein-ligand complexes with measured binding affinity shows a strong association between high ligand strain and low potency. We also present practical applications of TorsionNet that demonstrate how consideration of DNN-based strain energy leads to substantial improvement in existing lead discovery and design workflows. TorsionNet500, a benchmark data set comprising 500 chemically diverse fragments with DFT torsion profiles (12k MM- and DFT-optimized geometries and energies), has been created and is made publicly available.

The influence of crack on the Si anode performance in Na- and Mg-ion batteries: An atomic multiscale study

Based on multiscale simulations coupled with quantum mechanical and molecular mechanical methods, we present the impact of crack on the performance of Si anode in Na-ion batteries (NIBs) and Mg-ion batteries (MIBs). We found that crack can offer more stable sites to host interstitials than defect-free Si and form binding energy gradients near the crack front. Moreover, the crack tip may significantly enhance the binding strength, enabling it to insert Na and Mg into the Si anode thermodynamically. The crack creates a fast channel into the tip along its propagation direction, causing Na and Mg to accumulate at the crack tip, similar to the case of Li. Furthermore, since diffusion out is more challenging, Na and Mg prefer to diffuse into the crack. Finally, the crack may trap interstitials and lower the charging and discharging rate of NIBs and MIBs.

QM/MM study on enzymatic mechanism in sinigrin biosynthesis

As the major and abundant type of glucosinolates (GL) in plants, sinigrin has potential functions in promoting health and insect defense. The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds, which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase (SOT). However, due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL, little is known about this sulfonation process. Fortunately, the crystal structure of SOT 18 from Arabidopsis thaliana (AtSOT18) containing the substance (sinigrin) similar to 3-methylthiopropyl GL has been determined. To understand the enzymatic mechanism, we employed molecular dynamics (MD) simulation and quantum mechanics combined with molecular mechanics (QM/MM) methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18. The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism. Moreover, Lys93, Thr96, Thr97, Tyr130, His155, and two enzyme peptide chains (Pro92-Lys93 and Gln95-Thr96-Thr97) play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry. Particularly, His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process. The presently proposed concerted dissociative mechanism explains the role of AtSOT18 in sinigrin biosynthesis, and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.

Theoretical Study on the Light-Emitting Mechanism of Multifunctional Thermally Activated Delayed Fluorescence Molecules

Multifunctional thermally activated delayed fluorescence (TADF) molecules have recently attracted great attention. The light-emitting mechanisms of the TADF molecule PTZ-AQ with aggregation-induced emission (AIE) and mechanochromic luminescence (MCL) in three different aggregation states are studied using the combined quantum mechanics and molecular mechanics (QM/MM) method as well as the thermal vibration correlation function method. It is found that different aggregation patterns would induce different intermolecular interaction and molecular geometries. The different energy diagram of excited states also induce variation of emission colors and (reverse) intersystem crossing processes. By comparing with the light-emitting properties in solvent, the AIE property is confirmed, which is induced by enhanced radiative rate and decreased nonradiative rates in aggregation. The bicolor switch mechanism for the molecule in the solid state should have a close relationship with the dihedral angle change between the donor and the acceptor. The calculation results provide valuable information for understanding the light-emitting mechanism of the PTZ-AQ based polymorphs with AIE and MCL properties, which would favor the design of a new type multifunctional TADF molecules.

The mechanism of intramolecular halogen bonding enhanced the quantum efficiency of ultralong organic phosphorescence in the aggregated state.

Ultralong organic phosphorescence (UOP) has broad application prospects in many fields, but realizing its high quantum efficiency is still full of challenges. One of the main reasons is that the internal luminescence mechanism is unclear and theoretical investigations to reveal the inner structure-property relationship are highly desired. Herein, the internal mechanism of halogen bonding enhancing the quantum efficiency of UOP is studied through the combination of quantum mechanics and molecular mechanics methods coupled with the thermal vibration correlation function (TVCF) method. Geometric and electronic data are obtained by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations. Transition properties, energy gaps, intermolecular interactions, excited state dynamics as well as Huang-Rhys factors and reorganization energies are analyzed in detail. The results show that the high phosphorescence quantum efficiency benefits from the fast intersystem crossing (ISC) process and the slow non-radiative decay process. The halogen bonding, which cooperates with the effects of aromatic carbonyl and heavy atoms, not only accelerates the ISC rate by increasing the spin-orbit coupling effect, but also restricts the molecular motion and reduces the non-radiative energy consumption. Furthermore, through wise molecular design, an efficient UOP molecule with fast ISC and slow non-radiative decay rates is proposed. This work provides an insight into realizing efficient UOP emission via intramolecular halogen bonding.

Triplet exciton dynamics of pure organics with halogen substitution boosted two photon absorption and room temperature phosphorescence: A theoretical perspective

Organic room temperature phosphorescence (RTP) molecules have shown promising applications in organic light emitting diodes and vivo imaging. Thus, triplet exciton dynamics in solid phase should be revealed and the molecule should possess large two photon absorption (TPA) cross sections under near-infrared excitation. The effects of halogen substitution and intermolecular interaction on RTP and TPA properties are studied at molecular level for a series of derivatives. Surrounding environment in solid phase is considered by combined quantum mechanics and molecular mechanics method. Intermolecular interactions are evaluated by the independent gradient model and calculated through the molecular force field energy decomposition method. Minimum energy crossing point, Huang-Rhys factor and reorganization energy are discussed, triplet exciton dynamics are investigated by thermal vibration correlation function method. Results indicate that the largest TPA cross sections are found for molecule in water. The halogen substitution can enlarge the proportion of (π, π*) and facilitate the intersystem crossing process. Restricted intramolecular rotation motions of dihedral angle in low frequency regions are found for Br-Np-Cz-BF2 in solid phase. While enhanced vibrations of bond length and bond angle in high frequency regions are detected for I-Np-Cz-BF2. Effects of halogen substitution and intermolecular interaction on triplet exciton dynamics are highlighted.

Formation and characterization of furfuryl mercaptan-β-cyclodextrin inclusion complex and its thermal release characteristics

Abstract Furfuryl mercaptan has the aroma characteristics of coffee. However, it is unstable during storage of coffee brew and roasted coffee. In order to enhance the stability of furfuryl mercaptan, furfuryl mercaptan-β-cyclodextrin inclusion complex was synthesized using the precipitation method in this work. Fourier transform infrared spectroscopy, x-ray diffraction, and thermogravimetric analysis (TG) were used to characterize the resulting products. The interaction of furfuryl mercaptan with β-cyclodextrin was investigated by the molecular mechanics (MM) method. These changes in FTIR and XRD gave supporting evidence for the successful formation of furfuryl mercaptan-β-cyclodextrin inclusion complex. The TG results showed that the formation of furfuryl mercaptan-β-cyclodextrin inclusion complex could improve the thermal stability of furfuryl mercaptan and provide a long-lasting effect. The structure of furfuryl mercaptan-β-cyclodextrin inclusion complex with the minimum energy was obtained by MM2 calculation, and the minimum binding energy was –77.0 kJ mol−1 at –1.96 × 10–10 m.

Proofreading experimentally assigned stereochemistry through Q2MM predictions in Pd-catalyzed allylic aminations

The palladium-catalyzed enantioselective allylic substitution by carbon or nitrogen nucleophiles is a key transformation that is particularly useful for the synthesis of bioactive compounds. Unfortunately, the selection of a suitable ligand/substrate combination often requires significant screening effort. Here, we show that a transition state force field (TSFF) derived by the quantum-guided molecular mechanics (Q2MM) method can be used to rapidly screen ligand/substrate combinations. Testing of this method on 77 literature reactions revealed several cases where the computationally predicted major enantiomer differed from the one reported. Interestingly, experimental follow-up led to a reassignment of the experimentally observed configuration. This result demonstrates the power of mechanistically based methods to predict and, where necessary, correct the stereochemical outcome.

A Localized Planarization Strategy in Hole Mobility Modulation of Disordered Triphenylamine‐Based Organic Semiconductors

AbstractHole mobility plays a critical role in organic semiconductors, which is synergistically controlled by many factors closely interrelated to the molecular configuration, for example, the degree of molecular planarization. But at present, analysis from quantitative ab initio models to assess this correlation is lacking. Here, a series of triphenylamine‐based materials are designed and investigated to build a system with different levels of planarization. The key parameters in the Marcus equation are calculated with quantum and molecular mechanics methods and the hole mobilities are evaluated. Compared with non‐planar and fully planar molecules, localized planar molecules exhibit low reorganization energy, high transfer integral, and moderate energy disorder. Considering the conjugation and rigidity effects, a localized planarization strategy is demonstrated to design functional triphenylamine‐based materials by keeping a balance of the three factors above and enhanced hole mobilities are predicted. This strategy will shed light on mobility optimization and the applications of triphenylamine‐based materials.

A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.

Antibiotic resistance is a major threat to global public health. β-lactamases, which catalyze breakdown of β-lactam antibiotics, are a principal cause. Metallo β-lactamases (MBLs) represent a particular challenge because they hydrolyze almost all β-lactams and to date no MBL inhibitor has been approved for clinical use. Molecular simulations can aid drug discovery, for example, predicting inhibitor complexes, but empirical molecular mechanics (MM) methods often perform poorly for metalloproteins. Here we present a multiscale approach to model thiol inhibitor binding to IMP-1, a clinically important MBL containing two catalytic zinc ions, and predict the binding mode of a 2-mercaptomethyl thiazolidine (MMTZ) inhibitor. Inhibitors were first docked into the IMP-1 active site, testing different docking programs and scoring functions on multiple crystal structures. Complexes were then subjected to molecular dynamics (MD) simulations and subsequently refined through QM/MM optimization with a density functional theory (DFT) method, B3LYP/6-31G(d), increasing the accuracy of the method with successive steps. This workflow was tested on two IMP-1:MMTZ complexes, for which it reproduced crystallographically observed binding, and applied to predict the binding mode of a third MMTZ inhibitor for which a complex structure was crystallographically intractable. We also tested a 12-6-4 nonbonded interaction model in MD simulations and optimization with a SCC-DFTB QM/MM approach. The results show the limitations of empirical models for treating these systems and indicate the need for higher level calculations, for example, DFT/MM, for reliable structural predictions. This study demonstrates a reliable computational pipeline that can be applied to inhibitor design for MBLs and other zinc-metalloenzyme systems.

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

Exploring the Mechanism of Shikimate Kinase through Quantum Mechanical and Molecular Mechanical (QM/MM) Methods

The chemical step of Shikimate Kinase Helicobacter pylori, involving the transfer of a phosphoryl group, has been studied by using quantum mechanical and molecular mechanical (QM/MM) methods. Understanding the mechanism of this chemical step, present in bacteria and other microorganisms but absent in humans, can lead to the development of novel drugs for the treatment of common diseases caused by those pathogenic organisms. Different mechanisms including associative, dissociative, and concerted have been proposed up to now but there is not a consensus on the type of pathway that the reaction follows. Herein, we found that the mechanism has features from the associative and concerted types. An analysis of the free energy landscape of the chemical step reveals that the reaction is a two-step process without a well-defined intermediate state.

Advanced nonlinear buckling analysis of a compressed single layer graphene sheet using the molecular mechanics method

The standard molecular mechanics (MM) method with the DREIDING force field (see Mayo et al. The Journal of Physical Chemistry, 1990, 94: 8897–8909) and the molecular structural mechanics (MSM) method with Bernoulli–Euler beam elements are used to study the quasi-static nonlinear buckling and post-buckling behavior of a compressed nearly square single layer graphene sheet (SLGS) for different types of boundary conditions. The novelty of this study is the finding that well-calibrated parameter sets provide similar values of buckling forces/modes and similar post-buckling deformations for stable equilibrium configurations of SLGSs in simulations using the standard MM and MSM methods. In addition, the effect of accounting for non-bonded van der Waals (vdW) forces on the advanced post-buckling deformation modes of compressed SLGSs was studied for the first time. It is shown that the column-like post-buckling deformation modes of compressed SLGSs obtained without the inclusion of vdW interatomic forces are similar to the well-known ones for the planar Euler elastica, and the advanced post-buckling modes obtained with the inclusion of interatomic vdW forces are qualitatively different from the corresponding modes for the planar Euler elastica. In addition, the study shows the theoretical possibility of the existence of post-buckling out-of-plane equilibrium configurations whose stability is provided by attractive vdW forces.

A molecular model to study FosA enzyme inhibition

Fosfomycin resistance protein (FosA) is a metalloenzyme known for catalyzing a nucleophilic addition reaction of glutathione to the epoxide ring of Fosfomycin, a broad-spectrum antibiotic used to combat Gram-positive pathogens. The reaction leads fosfomycin to lose its pharmacological effect, thus promotes antibiotic resistance. A small-molecule FosA inhibitor has been discovered. ANY1 (3-bromo-6-[3-(3-bromo-2-oxo-1H-pyrazolo[1,5-a]pyrimidin-6-yl)-4-nitro-1H-pyrazol-5-yl]-1H-pyrazolo[1,5-a]pyrimidin-2-one) is competitive with the antibiotic for binding the active site of the enzyme. Through Molecular Mechanics methods, using the AMBER force field, we carry out molecular dynamics simulations and binding free energy calculations to investigate the most important interactions between the enzyme and inhibitor. Our results were able to reproduce the trend of experimental data with R2 of 77.51%. Furthermore, we have shown that electrostatic and van der Waals interactions, as well as cavitation energies, are favorable for maintaining the enzyme-inhibitor complex, while reactive field energies and non-polar interactions act in an unfavorable way for interactions between FosA and ANY1.

(Invited) Toward a Molecular Understanding of Photoinduced Charge Separation Process in Organic Solar Cells with Computational Approaches

Photoinduced charge separation (CS) process plays important roles in various fields such as natural and artificial photosynthesis, solar cell, and light-emitting diode. To investigate the photoinduced CS process theoretically, the CS state is often regarded as “static exciton” and described by several parameters such as free energy difference and electronic coupling between initial and final states according to Marcus theory. However, dynamical effects such as nuclear motions and spin-orbit coupling (SOC) are recently being recognized as important factors for controlling the CS efficiency. Therefore, the CS state should be considered as “dynamic exciton.” To analyze the dynamic exciton theoretically, we need to treat the photoexcited reaction dynamics quantum mechanically, where the locally excited and CS states, electronic coupling and SOC dynamically fluctuates. In addition, surrounding environment such as solvent are also important and required to be explicitly considered because the charge distribution of CS state is much different from that of initial state. It is impossible to treat all the systems including surroundings quantum mechanically. Therefore, combined quantum mechanical and molecular mechanical (QM/MM) method, in which an important subsystem is described quantum mechanically whereas the other surrounding is treated by molecular mechanics force field, is an essential tool. However, even the QM/MM method still requires large computational cost for the analysis of dynamic exciton because the calculation time of excited state is much longer than that of ground state. To overcome this difficulty, we have been developing several methods combining the QM/MM method and molecular dynamics simulation efficiently. In this presentation, we will show several applications toward a molecular understanding of photoinduced CS process in organic solar cells.

Enzyme Models-From Catalysis to Prodrugs.

Enzymes are highly specific biological catalysts that accelerate the rate of chemical reactions within the cell. Our knowledge of how enzymes work remains incomplete. Computational methodologies such as molecular mechanics (MM) and quantum mechanical (QM) methods play an important role in elucidating the detailed mechanisms of enzymatic reactions where experimental research measurements are not possible. Theories invoked by a variety of scientists indicate that enzymes work as structural scaffolds that serve to bring together and orient the reactants so that the reaction can proceed with minimum energy. Enzyme models can be utilized for mimicking enzyme catalysis and the development of novel prodrugs. Prodrugs are used to enhance the pharmacokinetics of drugs; classical prodrug approaches focus on alternating the physicochemical properties, while chemical modern approaches are based on the knowledge gained from the chemistry of enzyme models and correlations between experimental and calculated rate values of intramolecular processes (enzyme models). A large number of prodrugs have been designed and developed to improve the effectiveness and pharmacokinetics of commonly used drugs, such as anti-Parkinson (dopamine), antiviral (acyclovir), antimalarial (atovaquone), anticancer (azanucleosides), antifibrinolytic (tranexamic acid), antihyperlipidemia (statins), vasoconstrictors (phenylephrine), antihypertension (atenolol), antibacterial agents (amoxicillin, cephalexin, and cefuroxime axetil), paracetamol, and guaifenesin. This article describes the works done on enzyme models and the computational methods used to understand enzyme catalysis and to help in the development of efficient prodrugs.

Importance of Lattice Constants in QM/MM Calculations on Metal-Organic Frameworks.

Metal-organic frameworks (MOFs) are crystalline materials with novel physical and chemical properties. Computational simulations have become powerful complements to experiment for understanding catalysis in MOFs and developing new MOFs and their applications. However, due to their relatively large and complex structures, MOFs can be burdensome for fully quantum mechanical calculations. A combined quantum mechanical and molecular mechanical (QM/MM) method that combines the accuracy of fully quantum mechanical methods and the efficiency of MM methods is therefore attractive. In this study, we employ a QM/MM method for the study of two classes of chemical process in a MOF: the conversion of reaction intermediates in an Ir-containing borylation catalyst supported on MOF UiO-67 and the diffusion of a diborylated methane molecule in the pristine UiO-67 framework. We compare the QM/MM results with full-quantum mechanical results on large systems to validate the accuracy of the applied QM/MM method. In the first case, we consider a model of the entire system by partitioning it into subsystems that interact covalently, and in the second case the subsystem interaction is mainly steric. We observe that the QM/MM results agree with the full-quantum mechanical results within an average of 4 kcal/mol in the first case with strong electronic interactions and within an average of 3 kcal/mol in the case with only noncovalent interactions. An important lesson learned from the present study is that the quantitative results are very sensitive to the lattice constants predicted by the MM method used in the QM/MM calculations.

Multiscale Quantum Refinement Approaches for Metalloproteins.

Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.