ONIOM
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Kinetic Regime Change in the Tandem Dehydrative Aromatization of Furan Diels–Alder Products Open
Renewable production of p-xylene from [4 + 2] Diels–Alder cycloaddition of 2,5-dimethylfuran (DMF) and ethylene with H–Y zeolite catalyst in n-heptane solvent is investigated. Experimental studies varying the solid acid catalyst concentrat…
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On the Difference Between Additive and Subtractive QM/MM Calculations Open
The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the sy…
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Embedded Mean-Field Theory Open
We introduce embedded mean-field theory (EMFT), an approach that flexibly allows for the embedding of one mean-field theory in another without the need to specify or fix the number of particles in each subsystem. EMFT is simple, is well-de…
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Density Functional Theory (DFT) Study To Unravel the Catalytic Properties of M-Exchanged MFI, (M = Be, Co, Cu, Mg, Mn, Zn) for the Conversion of Methane and Carbon Dioxide to Acetic Acid Open
The conversion of greenhouse gases, such as CO2 and CH4, to value chemicals is a major challenge, because of the high stability of both molecules. In this study, density functional theory (DFT) calculations with long-range corrections and …
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Selecting Chiral BINOL‐Derived Phosphoric Acid Catalysts: General Model To Identify Steric Features Essential for Enantioselectivity Open
Choosing the optimal catalyst for a new transformation is challenging because the ideal molecular requirements of the catalyst for one reaction do not always simply translate to another. Large groups at the 3,3′ positions of the binaphthol…
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Protic vs aprotic ionic liquid for CO2 fixation: A simulation study Open
The cycloaddition of CO2 with epoxides catalyzed by ionic liquids (ILs) has been a widely ongoing studied hot topic over the years. Recent experimental research has shown that the protic ionic liquids (PILs) behave stronger hydrogen proton…
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DFT Study of Closed and Open Sites of BEA, FAU, MFI, and BEC Zeolites Substituted with Tin and Titanium Open
DFT with long-range corrections and ONIOM along with a polarizable-continuum model were used to analyze zeolites BEA, FAU, MFI, and BEC substituted with Sn and Ti. The preferential substitution sites for Ti and Sn in the different framewor…
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Ordered Solvents and Ionic Liquids Can Be Harnessed for Electrostatic Catalysis Open
Herein, we employ classical molecular dynamics simulations using the Drude oscillator-based polarizable force field, quantum chemical calculations, and ONIOM multiscale calculations to study (a) how an external field orders the solvent env…
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ONIOM(QM:QM′) Electrostatic Embedding Schemes for Photochemistry in Molecular Crystals Open
Understanding photoinduced processes in molecular crystals is central to the design of highly emissive materials such as organic lasers and organic light-emitting diodes. The modeling of such processes is, however, hindered by the lack of …
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Theoretical Distribution of the Ammonia Binding Energy at Interstellar Icy Grains: A New Computational Framework Open
The binding energies (BE) of molecules on the interstellar grains are crucial in the chemical evolution of the interstellar medium (ISM). Both temperature-programmed desorption (TPD) laboratory experiments and quantum chemistry computation…
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Adsorption in zeolites using mechanically embedded ONIOM clusters Open
We have explored mechanically embedded three-layer QM/QM/MM ONIOM models for computational studies of binding in Al-substituted zeolites.
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<span>fromage</span> : A library for the study of molecular crystal excited states at the aggregate scale Open
The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investi…
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Joint Experimental, in Silico, and NMR Studies toward the Rational Design of Iminium-Based Organocatalyst Derived from Renewable Sources Open
An efficient organocatalyst for iminium-ion based asymmetric Diels-Alder (DA) reactions has been rationally designed. The most influential structure-activity relationships were determined experimentally, while DFT calculations and NMR stud…
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How accurate are approximate quantum chemical methods at modelling solute–solvent interactions in solvated clusters? Open
In this paper, the performance ofab initiocomposite methods, and a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water.
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Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase Open
The NADPH-dependent QueF nitrile reductases catalyze the unprecedented four-electron reduction of nitrile to amine. QueF nitrile reductases can be found in the tRNA biosynthetic pathway of many bacteria and are potential antimicrobial drug…
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Modeling emission features of salicylidene aniline molecular crystals: A QM/QM’ approach Open
A new computational protocol relying on the use of electrostatic embedding, derived from QM/QM' ONIOM calculations, to simulate the effect of the crystalline environment on the emission spectra of molecular crystals is here applied to the …
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High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with<i>PHENIX</i>/<i>DivCon</i>: the impact of mixed Hamiltonian methods on ligand and protein structure Open
Conventional macromolecular crystallographic refinement relies on often dubious stereochemical restraints, the preparation of which often requires human validation for unusual species, and on rudimentary energy functionals that are devoid …
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Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study Open
In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH)(PW 11 O 39 )] 4− (ZrK) have been investigated using the hybrid two‐layer QM/MM (ONIOM) method. These reactions ha…
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ONIOM meets <b><i>xtb</i></b>: efficient, accurate, and robust multi-layer simulations across the periodic table Open
The ONIOM multi-layer scheme is implemented in the xtb software package and enables the combination of the GFN method family with DFT and WFT for fast and accurate multi-layer simulations throughout the periodic table.
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Assessment of Multi-Scale Approaches for Computing UV–Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches Open
Computational simulation of UV/vis spectra in condensed phases can be performed starting from converged molecular dynamics (MD) simulations and then performing quantum mechanical/molecular mechanical (QM/MM) computations for a statisticall…
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TriplatinNC and Biomolecules: Building Models Based on Non-covalent Interactions Open
The class of polynuclear platinum(II) compounds have demonstrated a great interest because their high activity against cancer cells. Among these new compounds, the TriplatinNC also called AH78, demonstrated surprising antitumor activity, i…
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The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study Open
This paper deals with the development and first validation of a composite approach for the simulation of chiroptical spectra in solution aimed to strongly reduce the number of full QM computations without any significant accuracy loss. The…
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Theoretical Determination of Size Effects in Zeolite-Catalyzed Alcohol Dehydration Open
In the upgrading of biomass pyrolysis vapors to hydrocarbons, dehydration accomplishes a primary objective of removing oxygen, and acidic zeolites represent promising catalysts for the dehydration reaction. Here, we utilized density functi…
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Templating and Catalyzing [2+2] Photocycloaddition in Solution Using a Dynamic G‐Quadruplex Open
We describe a templating/covalent capture strategy that enables photochemical formation of 8 cyclobutanes in one noncovalent assembly. This process was characterized by experiment and quantum mechanical/molecular mechanics (ONIOM) calculat…
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Asparagine Tautomerization in Glycosyltransferase Catalysis. The Molecular Mechanism of Protein <i>O</i>-Fucosyltransferase 1 Open
O-glycosylation is a post-translational protein modification essential to life. One of the enzymes involved in this process is protein O-fucosyltransferase 1 (POFUT1), which fucosylates threonine or serine residues within a specific sequen…
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Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain Open
A proteolytic reaction of papain with a simple peptide model substrateN-methylacetamide has been studied.
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The Catalytic Mechanism of the Marine‐Derived Macrocyclase PatGmac Open
Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti‐HIV). Despite their desirability, efficient design and production of these compounds has n…
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Light‐Activated Reversible Imine Isomerization: Towards a Photochromic Protein Switch Open
Mutants of cellular retinoic acid‐binding protein II (CRABPII), engineered to bind all‐ trans ‐retinal as an iminium species, demonstrate photochromism upon irradiation with light at different wavelengths. UV light irradiation populates th…
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Quantum Simulation of Molecules in Solution Open
Quantum chemical calculations on quantum computers have been focused mostly on simulating molecules in the gas phase. Molecules in liquid solution are, however, most relevant for chemistry. Continuum solvation models represent a good compr…
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Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors Open
In this work, we performed a study to assess the interactions between the ricin toxin A (RTA) subunit of ricin and some of its inhibitors using modern semiempirical quantum chemistry and ONIOM quantum mechanics/molecular mechanics (QM/MM) …