David Zorrilla

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

DAMQT‐2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP‐based atomic basin is a new and exclusive feature introduced in DAMQT‐2.1.0. The GUI in DAMQT provides a user‐friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.

Introducing “UCA-FUKUI” software: reactivity-index calculations

A new software (UCA-FUKUI) has been developed to facilitate the theoretical study of chemical reactivity. This program can calculate global parameters like hardness, softness, philicities, and Fukui condensed functions, and also local parameters from the condensed functions. To facilitate access to the program we have developed a very easy-to-use interface. We have tested the performance of the software by calculating the global and local reactivity indexes of a group of representative molecules. Finite difference and frontier molecular orbital methods were compared and their correlation tested. Finally, we have extended the analysis to a set of ligands of importance in coordination chemistry, and the results are compared with the exact calculation. As a general trend, our study shows the existence of a high correlation between global parameters, but a weaker correlation between local parameters.

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

Abstract DAMQT is a package for the analysis of the electron density in molecules and the fast computation of the density, density deformations, electrostatic potential and field, and Hellmann–Feynman forces. The method is based on the partition of the electron density into atomic fragments by means of a least deformation criterion. Each atomic fragment of the density is expanded in regular spherical harmonics times radial factors, which are piecewise represented in terms of analytical functions. This representation is used for the fast evaluation of the electrostatic potential and field generated by the electron density and nuclei, as well as for the computation of the Hellmann–Feynman forces on the nuclei. An analysis of the atomic and molecular deformations of the density can be also carried out, yielding a picture that connects with several concepts of the empirical structural chemistry. Program summary Program title: DAMQT1.0 Catalogue identifier: AEDL_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDL_v1_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: GPLv3 No. of lines in distributed program, including test data, etc.: 278 356 No. of bytes in distributed program, including test data, etc.: 31 065 317 Distribution format: tar.gz Programming language: Fortran90 and C++ Computer: Any Operating system: Linux, Windows (Xp, Vista) RAM: 190 Mbytes Classification: 16.1 External routines: Trolltechs Qt (4.3 or higher) ( http://www.qtsoftware.com/products ), OpenGL (1.1 or higher) ( http://www.opengl.org/ ), GLUT 3.7 ( http://www.opengl.org/resources/libraries/glut/ ). Nature of problem: Analysis of the molecular electron density and density deformations, including fast evaluation of electrostatic potential, electric field and Hellmann–Feynman forces on nuclei. Solution method: The method of Deformed Atoms in Molecules, reported elsewhere [1], is used for partitioning the molecular electron density into atomic fragments, which are further expanded in spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated to density. Restrictions: The current version is limited to 120 atoms, 2000 contracted functions, and l max = 5 in basis functions. Density must come from a LCAO calculation (any level) with spherical (not Cartesian) Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in file GOPENMOL.F90. This statement has not a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intels ifort and Fortran2003 standard. This latter is applied to compilers other than ifort (gfortran uses this one, for instance). Additional comments: The distribution file for this program is over 30 Mbytes and therefore is not delivered directly when download or e-mail is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Largely dependent on the system size and the module run (from fractions of a second to hours). References: [1] J. Fernandez Rico, R. Lopez, I. Ema, G. Ramirez, J. Mol. Struct. (Theochem) 727 (2005) 115.

Ibuprofen Loading in Surfactant-Templated Silica: Role of the Solvent According to the Polarizable Continuum Model

Ibuprofen (an anti-inflammatory drug) has been loaded onto two different surfactant-templated silicas (SBA-15 and MCM-48). To evaluate the effect of the drug-solvent combination on the loading capacity of the silica, we have performed ibuprofen adsorption experiments using 10 different solvents; we have interpreted our experimental results assuming a chemical equilibrium between the ibuprofen adsorbed on the silica and that remaining in solution. To estimate the equilibrium constant for different solvents, we have calculated the free energy in solution for the ibuprofen molecule using the polarizable continuum model (PCM) to take the solvent into account. The results have been analyzed statistically to eliminate the effects of the dispersion of experimental data; results reveal a statistically significant (95-99%) linear relationship between the ibuprofen loading capacity and its free energy in solution calculated with the PCM solvation model. In addition, useful relationships between loading capacity and dielectric constant and molecular size of the solvents are established.

DAMQT 2.0: A new version of the DAMQT package for the analysis of electron density in molecules ☆

Abstract DAMQT 2.0 is a new version of the DAMQT package for the analysis of electron density in molecules and the fast computation of the density, density deformations, electrostatic potential and field, and Hellmann–Feynman forces. Algorithms for the partition of the electron density and the computation of related properties like density deformations, electrostatic potential and field and Hellmann–Feynman forces have been improved and their codes, fully rewritten. MPI versions of the most computational demanding modules are now included in the package for parallel computation. The Graphical User Interface has been also enhanced, with new features including a 2D plotter and significant improvements in the 3D viewer. Program summary Program title: DAMQT 2.0 Catalogue identifier: AEDL_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDL_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GPLv3 No. of lines in distributed program, including test data, etc.: 317,270 No. of bytes in distributed program, including test data, etc.: 40,193,220 Distribution format: tar.gz Programming language: Fortran90 and C++. Computer: Any. Operating system: Linux, Windows (7, 8). RAM: 200 Mbytes Classification: 16.1. Catalogue identifier of previous version: AEDL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180(2009)1654 External routines: Qt (4.8 or higher), OpenGL (3.x or higher), freeGLUT 2.8.x Nature of problem: Analysis of the molecular electron density and density deformations, including fast evaluation of electrostatic potential, electric field and Hellmann–Feynman forces on nuclei. Solution method: The method of Deformed Atoms in Molecules, reported elsewhere [1], is used for partitioning the molecular electron density into atomic fragments, which are further expanded in spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated to density. Restrictions: Density must come from an LCAO calculation (any level) with spherical (not Cartesian) Slater or Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in several files. This statement has not a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel’s ifort and Fortran2003 standard. The latter is applied to compilers other than ifort (gfortran uses this one, for instance). Additional comments: Quick-start guide and User’s manual in PDF format included in the package. User’s manual is also accessible from the Graphical User Interface. The distribution file for this program is over 40 Mbytes and therefore is not delivered directly when downloaded or Email is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Largely dependent on the system size and the module run (from fractions of a second to hours). References: [1] J. Fernandez Rico, R. Lopez, I. Ema and G. Ramirez, J. Mol. Struct. Theochem 727 (2005) 115.

Convergent study of Ru–ligand interactions through QTAIM, ELF, NBO molecular descriptors and TDDFT analysis of organometallic dyes

We report a theoretical study of a series of Ru complexes of interest in dye-sensitised solar cells, in organic light-emitting diodes, and in the war against cancer. Other metal centres, such as Cr, Co, Ni, Rh, Pd, and Pt, have been included for comparison purposes. The metal–ligand trends in organometallic chemistry for those compounds are shown synergistically by using three molecular descriptors: quantum theory of atoms in molecules (QTAIM), electron localisation function (ELF) and second-order perturbation theory analysis of the natural bond orbital (NBO). The metal–ligand bond order is addressed through both delocalisation index (DI) of QTAIM and fluctuation index (λ) of ELF. Correlation between DI and λ for Ru–N bond in those complexes is introduced for the first time. Electron transfer and stability was also assessed by the second-order perturbation theory analysis of the NBO. Electron transfer from the lone pair NBO of the ligands toward the antibonding lone pair NBO of the metal plays a relevant role in stabilising the complexes, providing useful insights into understanding the effect of the ‘expanded ligand’ principle in supramolecular chemistry. Finally, absorption wavelengths associated to the metal-to-ligand charge transfer transitions and the highest occupied molecular orbital (HOMO)--lowest unoccupied molecular orbital (LUMO) characteristics were studied by time-dependent density functional theory.

Topology of molecular electron density and electrostatic potential with DAMQT

Abstract A new version of the DAMQT package incorporating topological analysis of the molecular electron density and electrostatic potential is reported. Evaluation of electron density, electrostatic potential and their first and second derivatives within DAM partition–expansion is discussed, and the pertaining equations are reported. An efficient algorithm for the search of critical points, gradient paths, atomic basins and Hessian analysis is implemented using these equations. 3D viewer built in DAMQT incorporates new facilities for visualization of these properties, as well as for distance and angle measurements. Full control of projection mode is also added to the viewer in DAMQT. Some examples are provided showing the excellent performance for large molecular systems. Program summary Program Title: DAMQT_2.1 Program Files doi: http://dx.doi.org/10.17632/2rxvgbsnhx.1 Licensing provisions: GPLv3 Programming language: Fortran90 and C++ Supplementary material: Quick-start guide and User’s manual in PDF format included in the package. User’s manual is also accessible from the GUI. Nature of problem: Analysis and visualization of the molecular electron density, electrostatic potential, critical points, gradient paths, atomic basins, electric field and Hellmann–Feynman forces on nuclei. Solution method: The method of Deformed Atoms in Molecules, reported elsewhere[1], is used for partitioning the molecular electron density into atomic fragments, which are further expanded in spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated with density, including topological analysis of electron density and electrostatic potential. Restrictions: Density must come from a LCAO calculation (any computational level) with spherical (not Cartesian) Slater or Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in several files. This statement does not have a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel’s ifort and Fortran2003 standard. This latter is applied to compilers other than ifort (gfortran uses this one, for instance). External routines/libraries: Qt (4.8 or higher), OpenGL (3.x or higher), freeGLUT 2.8.x References: [1] J. Fernandez Rico, R. Lopez, I. Ema and G. Ramirez, J. Mol. Struct. Theochem 727 (2005) 115. [2] [3]

Introducing a new bond reactivity index: Philicities for natural bond orbitals

AbstractIn the present work, a new methodology defined for obtaining reactivity indices (philicities) is proposed. This is based on reactivity functions such as the Fukui function or the dual descriptor, and makes it possible to project the information from reactivity functions onto molecular orbitals, instead of onto the atoms of the molecule (atomic reactivity indices). The methodology focuses on the molecules’ natural bond orbitals (bond reactivity indices) because these orbitals have the advantage of being localized, allowing the reaction site of an electrophile or nucleophile to be determined within a very precise molecular region. This methodology provides a “philicity” index for every NBO, and a representative set of molecules has been used to test the new definition. A new methodology has also been developed to compare the “finite difference” and the “frontier molecular orbital” approximations. To facilitate their use, the proposed methodology as well as the possibility of calculating the new indices have been implemented in a new version of UCA-FUKUI software. In addition, condensation schemes based on atomic populations of the “atoms in molecules” theory, the Hirshfeld population analysis, the approximation of Mulliken (with a minimal basis set) and electrostatic potential-derived charges have also been implemented, including the calculation of “bond reactivity indices” defined in previous studies. Graphical abstractA new methodology defined for obtaining bond reactivity indices (philicities) is proposed and makes it possible to project the information from reactivity functions onto molecular orbitals. The proposed methodology as well as the possibility of calculating the new indices have been implemented in a new version of UCA-FUKUI software. In addition, this version can use new atomic condensation schemes and new “utilities” have also been included in this second version.

Software to obtain accurate Gaussian expansions for a wide range of radial functions

is easy to achieve when the exponents βi are assumed to be known, but it is very difficult to realize [1–3] when the values of these exponents must be optimized. The optimization of the exponents is often important, since it leads to a good representation of F(r) with a moderate number of Gaussian functions. This kind of development is useful in the field of quantum chemistry [1–4], as it enables the polycentric integrals

Introducing a new methodology for the calculation of local philicity and multiphilic descriptor: an alternative to the finite difference approximation

ABSTRACT This work presents a new development based on the condensation scheme proposed by Chamorro and Pérez, in which new terms to correct the frozen molecular orbital approximation have been introduced (improved frontier molecular orbital approximation). The changes performed on the original development allow taking into account the orbital relaxation effects, providing equivalent results to those achieved by the finite difference approximation and leading also to a methodology with great advantages. Local reactivity indices based on this new development have been obtained for a sample set of molecules and they have been compared with those indices based on the frontier molecular orbital and finite difference approximations. A new definition based on the improved frontier molecular orbital methodology for the dual descriptor index is also shown. In addition, taking advantage of the characteristics of the definitions obtained with the new condensation scheme, the descriptor local philicity is analysed by separating the components corresponding to the frontier molecular orbital approximation and orbital relaxation effects, analysing also the local parameter multiphilic descriptor in the same way. Finally, the effect of using the basis set is studied and calculations using DFT, CI and Möller–Plesset methodologies are performed to analyse the consequence of different electronic-correlation levels.