Search results for "Density Functional Theory."
showing 10 items of 935 documents
Cubane-Type Mo3FeS44+,5+ Complexes Containing Outer Diphosphane Ligands: Ligand Substitution Reactions, Spectroscopic Studies, and Electronic Structu…
2012
A general protocol to access Mo(3)FeS(4)(4+) clusters selectively modified at the Fe coordination site is presented starting from the all-chlorine Mo(3)(FeCl)S(4)(dmpe)(3)Cl(3) (1) [dmpe = 1,2-bis(dimethylphosphane-ethane)] cluster and tetrabutylammonium salts (n-Bu(4)NX) (X = CN(-), N(3)(-), and PhS(-)). Clusters Mo(3)(FeX)S(4)(dmpe)(3)Cl(3) [X = CN(-) (2), N(3)(-) (3), and PhS(-) (4)] are prepared in high yield, and comparison of geometric and redox features upon modification of the coordination environment at the Fe site at parity of ligands at the Mo sites is also presented. The existence of the cubane-type Mo(3)FeS(4)(4+,5+) redox couple is demonstrated by cyclic voltammetry and for co…
Ligand-Stabilized Au13Cux (x = 2, 4, 8) Bimetallic Nanoclusters: Ligand Engineering to Control the Exposure of Metal Sites
2013
Three novel bimetallic Au-Cu nanoclusters stabilized by a mixed layer of thiolate and phosphine ligands bearing pyridyl groups are synthesized and fully characterized by X-ray single crystal analysis and density functional theory computations. The three clusters have an icosahedral Au13 core face-capped by two, four, and eight Cu atoms, respectively. All face-capping Cu atoms in the clusters are triply coordinated by thiolate or pyridyl groups. The surface ligands control the exposure of Au sites in the clusters. In the case of the Au13Cu8 cluster, the presence of 12 2-pyridylthiolate ligands still leaves open space for catalysis. All the 3 clusters are 8-electron superatoms displaying opti…
Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution
2012
We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06-2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substra…
Can multiscale simulations unravel the function of metallo-enzymes to improve knowledge-based drug discovery?
2019
Metallo-enzymes are a large class of biomolecules promoting specialized chemical reactions. Quantum-classical quantum mechanics/molecular mechanics molecular dynamics, describing the metal site at quantum mechanics level, while accounting for the rest of system at molecular mechanics level, has an accessible time-scale limited by its computational cost. Hence, it must be integrated with classical molecular dynamics and enhanced sampling simulations to disentangle the functions of metallo-enzymes. In this review, we provide an overview of these computational methods and their capabilities. In particular, we will focus on some systems such as CYP19A1 a Fe-dependent enzyme involved in estroge…
A Molecular Electron Density Theory Study of the Reactivity of Azomethine Imine in [3+2] Cycloaddition Reactions
2017
The electronic structure and the participation of the simplest azomethine imine (AI) in [3+2] cycloaddition (32CA) reactions have been analysed within the Molecular Electron Density Theory (MEDT) using DFT calculations at the MPWB1K/6-311G(d) level. Electron localisation function (ELF) topological analysis reveals that AI has a pseudoradical structure, while the conceptual DFT reactivity indices characterise this TAC as a moderate electrophile and a good nucleophile. The non-polar 32CA reaction of AI with ethylene takes place through a one-step mechanism with low activation energy, 5.3 kcal/mol-1. A bonding evolution theory (BET) study indicates that this reaction takes place through a non-…
A Molecular Electron Density Theory Study of the Chemoselectivity, Regioselectivity, and Diastereofacial Selectivity in the Synthesis of an Anticance…
2019
The [3 + 2] cycloaddition (32CA) reaction of an &alpha
Density functional theory fragment descriptors to quantify the reactivity of a molecular family: Application to amino acids
2007
By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a b…
Structural and Theoretical Basis for Ligand Exchange on Thiolate Monolayer Protected Gold Nanoclusters
2012
Ligand exchange reactions are widely used for imparting new functionality on or integrating nanoparticles into devices. Thiolate-for-thiolate ligand exchange in monolayer protected gold nanoclusters has been used for over a decade; however, a firm structural basis of this reaction has been lacking. Herein, we present the first single-crystal X-ray structure of a partially exchanged Au(102)(p-MBA)(40)(p-BBT)(4) (p-MBA = para-mercaptobenzoic acid, p-BBT = para-bromobenzene thiol) with p-BBT as the incoming ligand. The crystal structure shows that 2 of the 22 symmetry-unique p-MBA ligand sites are partially exchanged to p-BBT under the initial fast kinetics in a 5 min timescale exchange reacti…
Quantum Chemical Parametrization and Spectroscopic Characterization of the Frenkel Exciton Hamiltonian for a J-Aggregate Forming Perylene Bisimide Dye
2012
Quantum chemical and quantum dynamical calculations are performed for a bay-substituted perylene bisimide dye up to its hexameric aggregate. The aggregate structure is determined by employing the self-consistent charge density functional tight-binding (SCC-DFTB) approach including dispersion corrections. It is characterized by a stabilization via two chains of hydrogen bonds facilitated by amide functionalities. Focusing on the central embedded dimer, the Coulomb coupling for this J-aggregate is determined by means of the time-dependent density functional theory (TDDFT) to be -514 cm(-1). Exciton vibrational coupling is treated within the shifted oscillator model from which five strongly co…
Toward an Understanding of the Catalytic Role of Hydrogen-Bond Donor Solvents in the Hetero-Diels−Alder Reaction between Acetone and Butadiene Deriva…
2006
A detailed theoretical investigation of the catalytic role of hydrogen-bond- (HB-) donor molecules (water, methanol, chloroform, dichloromethane, and chloromethane) in the hetero-Diels-Alder reaction between acetone and N,N-dimethyl-1-amino-3-methoxy-1,3-butadiene is presented. This work extends a previous study (Domingo, L. R.; Andres, J. J. Org. Chem. 2003, 68, 8662) in which the importance of weak HB-donor solvents to catalyze more effectively than solvents with a higher dielectric constant but no HB-donor capability was analyzed. Now, based on density functional theory (DFT) at B3LYP/6-31+G(d) level calculations, different techniques for analyzing the nature of HB interaction, namely, n…