Search results for "Interaction energy"

2021

The reaction of :AlAriPr8 (AriPr8 = C6H-2,6-(C6H2-2,4,6-iPr3)2-3,5-iPr2) with ArMe6N3 (ArMe6 = C6H3-2,6-(C6H2-2,4,6-Me3)2) in hexanes at ambient temperature gave the aluminum imide AriPr8AlNArMe6 (1). Its crystal structure displayed short Al-N distances of 1.625(4) and 1.628(3) A with linear (C-Al-N-C = 180°) or almost linear (C-Al-N = 172.4(2)°; Al-N-C = 172.5(3)°) geometries. DFT calculations confirm linear geometry with an Al-N distance of 1.635 A. According to energy decomposition analysis, the Al-N bond has three orbital components totaling -1350 kJ mol-1 and instantaneous interaction energy of -551 kJ mol-1 with respect to :AlAriPr8 and ArMe6N:. Dispersion accounts for -89 kJ mol-1, w…

Weak interactions between trivalent pnictogen centers: computational analysis of bonding in dimers X3E...EX3 (E = pnictogen, X = halogen).

2009

The nature of weak interactions in dimers X(3)E...EX(3) (E = N-Bi, X = F-I) was investigated by wave function and density functional theory (DFT)-based methods. Out of the 20 systems studied, 10 are found to be bound at the CP-MP2 and LMP2 levels of theory. Detailed partition of the interaction energy into different components revealed that dispersion is the primary force holding the dimers together but there also exists an important ionic component whose contribution increases with increasing halogen size. As expected, standard density functionals fail to describe bonding in the studied systems. However, the performance of DFT methods can be easily improved via empirical dispersion correct…

N-Heterocyclic Carbenes with Inorganic Backbones:  Electronic Structures and Ligand Properties

2008

The electronic structures of known N-heterocyclic carbenes (NHCs) with boron, nitrogen, and phosphorus backbones are examined using quantum chemical methods and compared to the experimental results and to the computational data obtained for a classical carbon analogue, imidazol-2-ylidene. The sigma-donor and pi-acceptor abilities of the studied NHCs in selected transition-metal complexes are evaluated using a variety of approaches such as energy and charge decomposition analysis, as well as calculated acidity constants and carbonyl stretching frequencies. The study shows that the introduction of selected heteroatoms into the NHC backbone generally leads to stronger metal-carbene bonds and t…

Molecular Motions within Self-Assembled Dimeric Capsules with Tetraethylammonium Cations as Guest

2001

Hydrogen-bonded, dimeric capsules of calix[4]arenes substituted at the wide rim by four urea functions show unprecedented dynamic features when a tetraethylammonium cation is included as a guest. The seam of hydrogen bonds C=O...(HN)2C=O in the equatorial region which holds the two calixarene counterparts together changes its directionality fast (at 25 degrees C), while the dimer itself is kinetically stable on the NMR time scale. An energy barrier of deltaG++ = 49.9 kJmol(-1) (Tc 276 K) was estimated for this reorientation from variable-temperature (VT) NMR measurements. Lowering the temperature to about -50 degrees C restricts also the rotation of the encapsulated tetraethylammonium catio…

Nitrogen Gas on Graphene: Pairwise Interaction Potentials

2018

We investigate different types of potential parameters for the graphene-nitrogen interaction. Interaction energies calculated at DFT level are fitted with the semi-emperical Improved Lennard-Jones potential. Both a pseudo-atom potential and a full atomistic potential are considered. Furthermore, we consider the influence of the electrostatic part on the parameters using different charge schemes found in the literature as well as optimizing the charges ourselves. We have obtained parameters for both the nitrogen dimer and the graphene-nitrogen system. For the former, the four-charges Cracknell scheme reproduces with high precision the CCSD(T) interaction energy as well as the experimental di…

Ten Facets, One Force Field: The GAL19 Force Field for Water - Noble Metal Interfaces

2020

<div>Understanding the structure of the water/metal interfaces plays an important role in many are as ranging from surface chemistry to environmental processes. Due to their intrinsic complexity, the water/metal interfaces cannot yet be adequately described by quantum mechanical approaches and accurate force-fields are therefore needed. We develop and parametrize GAL19, a novel force-field to describe the interaction of water with two facets (111 and 100) of five metals (Pt, Pd, Au, Ag, Cu). To increase transferability compared to its predecessor GAL17, the water-metal interaction is described as a sum of pair-wise terms. The interaction energy has three contributions: (i) physisorption …

Improved AMYR program: an algorithm for the theoretical simulation of molecular associations, including geometrical and topological characterization …

1991

Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility of carrying out energy minimizations through variable metric methods, as well as the optional calculation of geometrical and topological indices. Program AMYR has been adapted also for high-performance computing and vectorization. An interactive version of the program carries out real-time molecular graphics showing simultaneously the energy prof…

A Computational Study of the Protein-Ligand Interactions in CDK2 Inhibitors: Using Quantum Mechanics/Molecular Mechanics Interaction Energy as a Pred…

2006

ABSTRACT: We report a combined quantum mechanics/molecular mechanics (QM/MM) study to determine the protein-ligand interaction energy between CDK2 (cyclin-dependent kinase 2) and five inhibitors with the N2 -substituted 6-cyclohexylmethoxypurine scaffold. The computational results in this work show that the QM/MM interaction energy is strongly correlated to the biological activity and can be used as a predictor, at least within a family of substrates. A detailed analysis of the protein-ligand structures obtained from molecular dynamics simulations shows specific interactions within the active site that, in some cases, have not been reported before to our knowledge. The computed interaction …

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…

Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues.

2007

Abstract Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. S-1360 is a potent and selective inhibitor of HIV-1 IN. In this work, we have carried out molecular dynamics (MD) simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach, to determine the protein–ligand interaction energy for S-1360 and two analogues. Analysis of the MD trajectories reveals that the strongest protein–inhibitor interactions, observed in the three studied complexes, are established with Lys-159 residue and Mg 2+ cation. Calculations of binding energy using BLYP/MM level of theory reveal that there is a direct rela…