First-Principles Study on Polymorphs of AgVO3: Assessing to Structural Stabilities and Pressure-Induced Transitions

In this paper, we present a comprehensive theoretical study, based on density-functional theory calculations, and which focuses on the structural and electronic properties of silver vanadium oxide (AgVO3) in the monoclinic [Cm (β-AgVO3), C2/c (α-AgVO3), and Cc], orthorhombic (Amm2), and cubic (Pm3̅m) phases from 0–30 GPa. The structural and electronic properties, the stability of different phases, and the pressure-induced solid–solid phase transitions of AgVO3 have been previously studied. The effects of pressure on the band structures, energy–gap values, density of states, and vibrational frequencies are also studied. Numerical and analytical calculations are conducted to obtain the lattic…

Toward an understanding of the selectivity in domino reactions. A DFT study of the reaction between acetylenedicarboxylic acid and 1, 3-Bis(2-furyl)propane

The mechanism of the domino reaction between acetylenedicarboxylic acid and 1,3-bis(2-furyl)propane has been theoretically studied in the framework of density functional theory. This domino process comprises two consecutive cycloaddition reactions: the first one is initialized by the nucleophilic attack of the C5 position of the furan ring to a conjugate position of acetylenedicarboxylic acid to give a zwitterionic intermediate, which by a subsequent ring-closure process affords an oxanorbornadiene intermediate. The second reaction is an intramolecular concerted cycloaddition of this intermediate to give the final dioxapentacyclic adduct. For the second cycloaddition, which corresponds to t…

Theoretical approach for determining the relation between the morphology and surface magnetism of Co3O4

Abstract Precisely controlling the different aspects of the morphology and magnetic properties of metal oxides are fundamental to materials design. A theoretical approach, based on the Wulff construction and magnetization density (M) index, is presented to clarify the relation between the morphology and surface magnetism. The M index allows us to evaluate the uncompensated spins at the (1 0 0), (1 1 0), (1 1 1) and (1 1 2) surfaces of Co3O4 with a spinel structure. The investigated morphologies show an excellent agreement with the experimental results, with the main contribution coming from the (1 0 0) and (1 1 1) magnetic planes. The present results are also helpful in clarifying the intri…

Designing a Transition State Analogue for the Disfavored Intramolecular Michael Addition of 2-(2-Hydroxyethyl)acrylate Esters

The rate-determining steps for the intramolecular 1,2 and 1,4 addition reactions in basic medium of methyl 2-(2-hydroxyethyl)acrylate to give the corresponding γ-lactone and tetrahydrofuran, respec...

Theoretical Study of Catalytic Efficiency of a Diels–Alderase Catalytic Antibody: An Indirect Effect Produced During the Maturation Process

The Diels–Alder reaction is one of the most important and versatile transformations available to organic chemists for the construction of complex natural products, therapeutics agents, and synthetic materials. Given the lack of efficient enzymes capable of catalyzing this kind of reaction, it is of interest to ask whether a biological catalyst could be designed from an antibody-combining site. In the present work, a theoretical study of the different behavior of a germline catalytic antibody (CA) and its matured form, 39 A-11, that catalyze a Diels–Alder reaction has been carried out. A free-energy perturbation technique based on a hybrid quantum-mechanics/molecular-mechanics scheme, togeth…

Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase

Two different transition structures (TSs) have been located and characterized for the chorismate conversion to prephenate in Bacillus subtilis chorismate mutase by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) calculations. GRACE software, combined with an AM1/CHARMM24/TIP3P potential, has been used involving full gradient relaxation of the position of ca. 3300 atoms. These TSs have been connected with their respective reactants and products by the intrinsic reaction coordinate (IRC) procedure carried out in the presence of the protein environment, thus obtaining for the first time a realistic enzymatic reaction path for this reaction. Similar QM/MM computational schemes h…

A Quantum Mechanic/Molecular Mechanic Study of the Wild-Type and N155S Mutant HIV-1 Integrase Complexed with Diketo Acid

Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral resistance to diketo acids (DKAs) appears when some amino acid residues of the IN active site are mutated. Mutations represent a fascinating experimental challenge, and we invite theoretical simulations for the disclosure of still unexplored features of enzyme reactions. The aim of this work is to understand the molecular mechanisms of HIV-1 IN drug resistance, which will be useful for designing anti-HIV inhibitors with unique resistance profiles. In this study, we use mo…

Electronic fluxes during diels-alder reactions involving 1,2-benzoquinones: mechanistic insights from the analysis of electron localization function and catastrophe theory

By means of the joint use of electron localization function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero-Diels-Alder reaction of 4-methoxy-1,2-benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and electron pair rearrangements through the reaction progress in terms of the different ways o…

General and Theoretical Aspects of the Metal Enolates

1 General Aspects 2 Structure of the Metal Enolates 3 Spectroscopy of the Metal Enolates 4 Reactivity of the Metal Enolates 5 Acknowledgments Keywords: general and theoretical aspects of metal enolates; metal enolate structure; calcium and magnesium enolates; spectroscopy of metal enolates - NMR spectroscopy; UV spectroscopy; enolate, applied to anionic structure with two carbon atoms bound through double bond; IR spectroscopy; generalized gradient approximation (GGA-DFT) for adsorption modes of acetone

Geometry, electronic structure, morphology, and photoluminescence emissions of BaW1-xMoxO4 (x = 0, 0.25, 0.50, 0.75, and 1) solid solutions: Theory and experiment in concert

Abstract The design of a solid solution with tunable electro-optical properties and multifunctionality is a promising strategy for developing novel materials. In this work, BaW1-xMoxO4 (x = 0, 0.25, 0.5, 0.75, and 1) solid solutions have been successfully prepared for the first time by a co-precipitation method. Their crystal structure and phase composition were determined by X-ray diffraction and Rietveld refinements. Fourier transform infrared and micro Raman spectroscopy in combination with field-emission scanning electron microscopy (FE-SEM) were used to describe the microstructures and chemical compositions of the synthesized materials. The influence of chemical composition on morpholo…

An ab initio study of the unimolecular decomposition mechanism of formamidine. 4-31G Characterization of potential energy hypersurface

Ab initio MO calculations have been carried out for the unimolecular decomposition of formamidine. The Hartree–Fock method in LCAO approximation with the 4-31G basis set was used. The 4-31G potential hypersurface has been further studied. The stationary points (R, TS, and P) were localized. A reaction analysis by correlation of bond-order indices and localized molecular orbitals demonstrated that the decomposition is an asynchronous process. The TS can be described as four-membered ring.

Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis.

Glycine N-methyltransferase (GNMT) is an S-adenosyl-l-methionine dependent enzyme that catalyzes glycine transformation to sarcosine. Here, we present a hybrid quantum mechanics/molecular mechanics (QM/MM) computational study of the reaction compared to the counterpart process in water. The process takes place through an SN2 mechanism in both media with a transition state in which the transferring methyl group is placed in between the donor (SAM) and the acceptor (the amine group of glycine). Comparative analysis of structural, electrostatic, and electronic characteristics of the in-solution and enzymatic transition states allows us to get a deeper insight into the origins of the enzyme's c…

A theoretical study on the thermal ring opening rearrangement of 1H-bicyclo[3.1.0]hexa-3,5-dien-2-one: a case of two state reactivity

The molecular mechanism of the thermal rearrangement of singlet 1H-bicyclo[3.1.0]hexa-3,5-dien-2-one to give triplet 4-oxocyclohexa-2,5-dienylidene has been investigated using density functional theory (B3LYP and M05-2X functionals) as well as ab initio CASSCF and CASPT2 multiconfigurational methods. The reactant has a singlet ground state while the product can be found in three low lying electronic states P((3)B(1)), P((1)B(1)), and P((1)A'). Therefore, the molecular mechanism of this ring opening rearrangement may involve up to three different potential energy surfaces of two spin multiplicities: two singlet (closed shell, CS, and open shell, OS) and one triplet. The stationary points on …

Toward an Understanding of Molecular Mechanism of Domino Cycloadditions. Density Functional Theory Study of the Reaction between Hexafluorobut-2-yne and N,N‘-Dipyrrolylmethane

Understanding the Nature of the Molecular Mechanisms Associated with the Competitive Lewis Acid Catalyzed[4+2] and[4+3] Cycloadditions between Arylidenoxazolone Systems and Cyclopentadiene: A DFT Analysis

The molecular mechanisms of the reactions between aryliden-5(4H)-oxazolone 1, and cyclopentadiene (Cp), in presence of Lewis acid (LA) catalyst to obtain the corresponding [4+2] and [4+3] cycloadducts are examined through density functional theory (DFT) calculations at the B3LYP/6-31G* level. The activation effect of LA catalyst can be reached by two ways, that is, interaction of LA either with carbonyl or carboxyl oxygen atoms of 1 to render [4+2] or [4+3] cycloadducts. The endo and exo [4+2] cycloadducts are formed through a highly asynchronous concerted mechanism associated to a Michael-type addition of Cp to the beta-conjugated position of alpha,beta-unsaturated carbonyl framework of 1.…