DAMQT: A package for the analysis of electron density in molecules

López, Rafael; Rico, J. Fernández; Ramı́rez, G.; Ema, I.; Zorrilla, David

doi:10.1016/j.cpc.2009.03.004

Cited by 24 publications

(22 citation statements)

References 32 publications

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“…This criterion involves to retain as much as possible the sphericity of each atom fragment, characteristic of isolated atoms, and the two-center distribution is partitioned according to the fast convergence of the multipolar expansion of the long-range potential of the molecular fragments toward the one of the full (i.e., molecule) distribution [21,22]. The result is a detailed picture of the molecular electron density as regions of electron accumulation and depletion nicely reproducing the notions expected from chemical intuition [15]. This approach has a similarity with the idea of electronic density differences in solid state, providing the same power to interpret molecular phenomena.…”

Section: Theorymentioning

confidence: 89%

Nuclear fukui functions and the deformed atoms in molecules representation of the electron density: Application to gas‐Phase RDX (hexahydro‐1,3,5‐trinitro‐1,3,5‐ triazine) electronic structure and decomposition

Moraes

Borges

2011

Int J of Quantum Chemistry

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ABSTRACT:The electronic structure and the onset of decomposition processes of the four conformers of the RDX molecule were studied through the density functional theory (DFT) along with the B3LYP functional and the 6-311þG(2d,p) Gaussian basis set. The computed DFT electron density was decomposed into atomic contributions using the deformed atoms in molecules (DAM) method, which allowed us to identify regions of electron accumulation and electron depletion of each conformer. The nuclear Fukui functions nuclear stiffness and nuclear reactivity index were then calculated. Both functions are atomic vectors, intrinsic molecular properties, which provide information for the onset of the fragmentation process, were further discussed through the analysis of the DAM electron density. The computed, decomposed electronic structures indicate that equatorial (E) NO 2 (nitro) groups are less bulky than axial (A) groups, with the Additional Supporting Information may be found in the online version of this article. former contributing more than the latter to the increase of the ring delocalized electrons and, therefore, to the lower stability of conformers with more E groups. Concerning the decomposition, the RDX NANO 2 bond cleavage is the most probable process for the AAA, AEE, and EEE conformers, while for the AAE conformer, HONO elimination is favored in partial agreement with previous study.

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Section: Theorymentioning

confidence: 89%

Nuclear fukui functions and the deformed atoms in molecules representation of the electron density: Application to gas‐Phase RDX (hexahydro‐1,3,5‐trinitro‐1,3,5‐ triazine) electronic structure and decomposition

Moraes

Borges

2011

Int J of Quantum Chemistry

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“…Such a method was also used by Hansen and Coppens 24 for computing electrostatic potential and its derivatives. Later, Rico and López et al [18][19][20][21][22] proposed an efficient DAM procedure for evaluation of molecular scalar fields such as MED and MESP by partitioning into atomic contributions. However, the difference between the DAM and Coppens-Hansen method comes from two sources: the way in which the density is partitioned into pseudoatomic fragments and the functions chosen for representing the radial factors.…”

Section: A Deformed Atoms In Molecules Methodsmentioning

confidence: 99%

“…20,21 This DAM method of evaluating the MED and MESP has been implemented in the package DAMQT. 22 The advantage of this method is that the calculation of function and its derivatives is very rapid and is dependent only on the expansion parameter l max . Considering this, the MED and MESP evaluated by DAM, along with the gradients, are employed in conjunction with the topography building code reported in Ref.…”

Section: A Deformed Atoms In Molecules Methodsmentioning

confidence: 99%

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Rapid topography mapping of scalar fields: Large molecular clusters

Yeole

López

Gadre

2012

The Journal of Chemical Physics

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An efficient and rapid algorithm for topography mapping of scalar fields, molecular electron density (MED) and molecular electrostatic potential (MESP) is presented. The highlight of the work is the use of fast function evaluation by Deformed-atoms-in-molecules (DAM) method. The DAM method provides very rapid as well as sufficiently accurate function and gradient evaluation. For mapping the topography of large systems, the molecular tailoring approach (MTA) is invoked. This new code is tested out for mapping the MED and MESP critical points (CP's) of small systems. It is further applied to large molecular clusters viz. (H 2 O) 25 , (C 6 H 6 ) 8 and also to a unit cell of valine crystal at MP2/6-31+G(d) level of theory. The completeness of the topography is checked by extensive search as well as applying the Poincaré-Hopf relation. The results obtained show that the DAM method in combination with MTA provides a rapid and efficient route for mapping the topography of large molecular systems.

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“…44 Recently, our group used another atom-centered partition scheme, the deformed atoms in molecules (DAM) model 45,46 to partition electron density of four conformers of hexahydro-1,3,5-trinitro-1,3,5-triazine energetic molecule, known as RDX, and examined their electronic structure and fragmentation modes. 47 Partition of the molecular charge according to DMA was developed with the main purpose of evaluating intermolecular interactions, being also useful to investigate accurately molecular charge distributions.…”

Section: Partition Of the Electron Densitymentioning

confidence: 99%

Probing topological electronic effects in catalysis: thiophene adsorption on NiMoS and CoMoS clusters

Borges¹,

Silva²

2012

J. Braz. Chem. Soc.

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Um método teórico geral em duas etapas para estudar redistribuições eletrônicas em processos catalíticos é apresentado. Na primeira etapa, teoria do funcional da densidade (DFT) é usada para otimizar completamente duas geometrias: o aglomerado que representa o catalisador e o sistema aglomerado mais molécula adsorvida. Na segunda etapa, a densidade eletrônica molecular convergida é dividida em multipolos centrados em sítios atômicos obtidos segundo uma análise de multipolos distribuídos, que fornece informação topológica detalhada da redistribuição de carga do catalisador e da molécula, antes e depois da adsorção. Esta abordagem é aplicada para a adsorção de tiofeno sobre a borda metálica 10 -10 dos catalisadores Ni(Co)MoS e comparada com a mesma reação em MoS 2 não-substituído. Energias de adsorção, geometrias e a análise de multipolos calculada indicam uma fraca adsorção do tiofeno em ambas as situações. Um modelo coulombiano para a ligação química mostra que a magnitude da ligação metal-enxofre na superfície dos catalisadores de Ni(Co)MoS promovidos é consideravelmente menor do que em MoS 2 não substituído, desta forma confirmando a origem do aumento da atividade de hidrodessulfurização (HDS) nestes catalisadores.A general two-step theoretical approach to study electronic redistributions in catalytic processes is presented. In the first step, density functional theory (DFT) is used to fully optimize two geometries: the cluster representing the catalyst and the cluster plus adsorbed molecule system. In the second step, the converged electron density is divided into multipoles centered on atomic sites according to a distributed multipole analysis which provides detailed topological information on the charge redistribution of catalyst and molecule before and after adsorption. This approach is applied to thiophene adsorption on the 10 -10 metal edge of Ni(Co)MoS catalysts and compared to the same reaction on bare MoS 2 . Calculated adsorption energies, geometries and multipole analysis indicate weak thiophene chemisorption on both cases. A Coulombic bond model showed that surface metal-sulfur bond strengths in Ni(Co)MoS promoted catalysts are considerably smaller than in bare MoS 2 , thus confirming the origin of the enhancement of hydrodesulfurization (HDS) activity in these catalysts.

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DAMQT: A package for the analysis of electron density in molecules

Cited by 24 publications

References 32 publications

Nuclear fukui functions and the deformed atoms in molecules representation of the electron density: Application to gas‐Phase RDX (hexahydro‐1,3,5‐trinitro‐1,3,5‐ triazine) electronic structure and decomposition

Nuclear fukui functions and the deformed atoms in molecules representation of the electron density: Application to gas‐Phase RDX (hexahydro‐1,3,5‐trinitro‐1,3,5‐ triazine) electronic structure and decomposition

Rapid topography mapping of scalar fields: Large molecular clusters

Probing topological electronic effects in catalysis: thiophene adsorption on NiMoS and CoMoS clusters

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