International Journal of Molecular Sciences

20 pages, 927 KiB

Open AccessReview

Binding and Docking Interactions of NO, CO and O₂ in Heme Proteins as Probed by Density Functional Theory

by Vangelis Daskalakis¹ and Constantinos Varotsis^2,*

¹ Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, P.O. Box 1527,GR-711 10 Heraklion, Greece

² Department of Chemistry, University of Crete, P.O. Box 2208, 71003, Voutes – Heraklion, Greece

Int. J. Mol. Sci. 2009, 10(9), 4137-4156; https://doi.org/10.3390/ijms10094137 - 22 Sep 2009

Cited by 16 | Viewed by 15504

Abstract

Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O₂ with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, [...] Read more.

Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O₂ with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, whereas indirect interactions result by ligands in the same coordination sphere. Interactions play a crucial role in stabilizing transition states in catalysis or altering ligation chemistry. We have probed, by Density Functional Theory (DFT), the perturbation degree in the stretching vibrational frequencies of CO, NO and O₂ molecules in the presence of electrostatic interactions or hydrogen bonds, under conditions simulating the inner cavities. Moreover, we have studied the vibrational characteristics of the heme bound form of the CO and NO ligands by altering the chemistry of the proximal to the heme ligand. CO, NO and O₂ molecules are highly polarizable exerting vibrational shifts up to 80, 200 and 120 cm^-1, respectively, compared to the non-interacting ligand. The importance of Density Functional Theory (DFT) methodology in the investigation of the heme-ligand-protein interactions is also addressed. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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29 pages, 1633 KiB

Open AccessReview

Periodic Density Functional Theory Investigation of the Uranyl Ion Sorption on Three Mineral Surfaces: A Comparative Study

by Jérôme Roques^*, Edouard Veilly and Eric Simoni

Université Paris-Sud 11, Institut de Physique Nucléaire, IPNO bât 100, UMR 8608, F-91406 Orsay, France

Int. J. Mol. Sci. 2009, 10(6), 2633-2661; https://doi.org/10.3390/ijms10062633 - 4 Jun 2009

Cited by 34 | Viewed by 21509

Abstract

Canister integrity and radionuclides retention is of prime importance for assessing the long term safety of nuclear waste stored in engineered geologic depositories. A comparative investigation of the interaction of uranyl ion with three different mineral surfaces has thus been undertaken in order [...] Read more.

Canister integrity and radionuclides retention is of prime importance for assessing the long term safety of nuclear waste stored in engineered geologic depositories. A comparative investigation of the interaction of uranyl ion with three different mineral surfaces has thus been undertaken in order to point out the influence of surface composition on the adsorption mechanism(s). Periodic DFT calculations using plane waves basis sets with the GGA formalism were performed on the TiO₂(110), Al(OH)₃(001) and Ni(111) surfaces. This study has clearly shown that three parameters play an important role in the uranyl adsorption mechanism: the solvent (H₂O) distribution at the interface, the nature of the adsorption site and finally, the surface atoms’ protonation state. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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Graphical abstract

10 pages, 63 KiB

Open AccessArticle

Nature of Copper Active Sites in CuZSM-5: Theory and Experiment

by Ewa Broclawik^1,*, Jerzy Datka², Barbara Gil² and Pawel Kozyra²

¹ Institute of Catalysis, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland

² Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Cracow, Poland

Int. J. Mol. Sci. 2002, 3(4), 435-444; https://doi.org/10.3390/i3040435 - 25 Apr 2002

Cited by 15 | Viewed by 9574

Abstract

We report here a concise resume reporting the way of constructing the model of an active site composed of transition metal cation exchanged in zeolites. The main goal was to devise the model of CuZSM-5 capable of describing geometrical and electronic properties of [...] Read more.

We report here a concise resume reporting the way of constructing the model of an active site composed of transition metal cation exchanged in zeolites. The main goal was to devise the model of CuZSM-5 capable of describing geometrical and electronic properties of metal sites and adsorption complexes with small molecules. The models were built up starting from simple ring structures encountered in ZSM-5 framework to fused rings’ model selected as the representative of α position for hosting the exchanged cation. Geometrical and electronic properties of the basal model, composed of the extended framework cluster with Cu⁺ or Cu²⁺ cation, and adsorption complexes with diatomic molecules were extracted from DFT calculations. The stress was put here on direct confirmation of structural changes on copper reduction/oxidation and adsorption. Electron donor/acceptor properties of the sites combined with electronic properties of adsorbed molecules led to the proposal for the mechanism of NO activation by Cu⁺ZSM-5: transfer of electrons from copper d orbitals to antibonding states of NO should cause large weakening of the bond, which was evidenced also by IR measurements. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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12 pages, 425 KiB

Open AccessArticle

Zeolite-Catalyzed Hydrocarbon Formation from Methanol: Density Functional Simulations

by Niranjan Govind^*, Jan Andzelm, Kurt Reindel and George Fitzgerald

Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, USA

Int. J. Mol. Sci. 2002, 3(4), 423-434; https://doi.org/10.3390/i3040423 - 25 Apr 2002

Cited by 49 | Viewed by 12878

Abstract

We report detailed density functional theory (DFT) calculations of important mechanisms in the methanol to gasoline (MTG) process in a zeolite catalyst. Various reaction paths and energy barriers involving C-O bond cleavage and the first C-C bond formation are investigated in detail using [...] Read more.

We report detailed density functional theory (DFT) calculations of important mechanisms in the methanol to gasoline (MTG) process in a zeolite catalyst. Various reaction paths and energy barriers involving C-O bond cleavage and the first C-C bond formation are investigated in detail using all-electron periodic supercell calculations and recently developed geometry optimization and transition state search algorithms. We have further investigated the formation of ethanol and have identified a different mechanism than previously reported [1], a reaction where water does not play any visible role. Contrary to recent cluster calculations, we were not able to find a stable surface ylide structure. However, a stable ylide structure built into the zeolite framework was found to be possible, albeit a very high reaction barrier. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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16 pages, 83 KiB

Open AccessArticle

The O-H Bond Dissociation Energies of Substituted Phenols and Proton Affinities of Substituted Phenoxide Ions: A DFT Study

by Asit K. Chandra¹ and Tadafumi Uchimaru^2,*

¹ Research Institute of Innovative Technology for the Earth (RITE), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, Tsukuba 305-8565, Japan

² National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, Tsukuba 305-8565, Japan

Int. J. Mol. Sci. 2002, 3(4), 407-422; https://doi.org/10.3390/i3040407 - 25 Apr 2002

Cited by 148 | Viewed by 16404

Abstract

The accurate O-H bond dissociation enthalpies for a series of meta and para substituted phenols (X-C₆H₄-OH, X=H, F, Cl, CH₃, OCH₃, OH, NH₂, CF₃, CN, and NO₂) have been [...] Read more.

The accurate O-H bond dissociation enthalpies for a series of meta and para substituted phenols (X-C₆H₄-OH, X=H, F, Cl, CH₃, OCH₃, OH, NH₂, CF₃, CN, and NO₂) have been calculated by using the (RO)B3LYP procedure with 6-311G(d,p) and 6-311++G(2df,2p) basis sets. The proton affinities of the corresponding phenoxide ions (XC₆H₄-O-) have also been computed at the same level of theory. The effect of change of substituent position on the energetics of substituted phenols has been analyzed. The correlations of Hammett’s substituent constants with the bond dissociation enthalpies of the O-H bonds of phenols and proton affinities of phenoxide ions have been explored. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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12 pages, 373 KiB

Open AccessArticle

First Principles Molecular Dynamics Study of Catalysis for Polyolefins: the Ziegler-Natta Heterogeneous System.

by Mauro Boero^1,*, Kiyoyuki Terakura^2,3 and Michele Parrinello⁴

¹ Reserach Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology (RICS-AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan

² Joint Research Center for Atom Technology (JRCAT-AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305- 8562 Japan

³ Research Institute for Computational Science, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan

⁴ Swiss Center for Scientific Computing (CSCS), via Cantonale, Galleria 2, CH-6928 Manno, Switzerland and ETH Hönggerberg HCI, CH-8093 Zurich, Switzerland

Int. J. Mol. Sci. 2002, 3(4), 395-406; https://doi.org/10.3390/i3040395 - 25 Apr 2002

Cited by 4 | Viewed by 10503

Abstract

We review part of our recent ab initio molecular dynamics study on the Ti-based Ziegler-Natta supported heterogeneous catalysis of α-olefins. The results for the insertion of ethylene in the metal-carbon bond are discussed as a fundamental textbook example of polymerization processes. Comparison with [...] Read more.

We review part of our recent ab initio molecular dynamics study on the Ti-based Ziegler-Natta supported heterogeneous catalysis of α-olefins. The results for the insertion of ethylene in the metal-carbon bond are discussed as a fundamental textbook example of polymerization processes. Comparison with the few experimental data available has shown that simulation can reproduce activation barriers and the overall energetics of the reaction with sufficient accuracy. This puts these quantum dynamical simulations in a new perspective as a virtual laboratory where the microscopic picture of the catalysis, which represents an important issue that still escapes experimental probes, can be observed and understood. These results are then discussed in comparison with a V-based catalyst in order to figure out analogies and differences with respect to the industrially more successful Tibased systems. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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35 pages, 242 KiB

Open AccessArticle

Can Unrestricted Density-Functional Theory Describe Open Shell Singlet Biradicals?

by Jürgen Gräfenstein, Elfi Kraka, Michael Filatov and Dieter Cremer^*

Department of Theoretical Chemistry, G¨oteborg University, Reutersgatan 2, S-413 20 G¨oteborg, Sweden

Int. J. Mol. Sci. 2002, 3(4), 360-394; https://doi.org/10.3390/i3040360 - 25 Apr 2002

Cited by 192 | Viewed by 20171

Abstract

Unrestricted density functional theory (UDFT) can be used for the description of open-shell singlet (OSS) biradicals provided a number of precautions are considered. Biradicals that require a two-determinantal wave function (e.g. OSS state of carbenes) cannot be described by UDFT for principal reasons. [...] Read more.

Unrestricted density functional theory (UDFT) can be used for the description of open-shell singlet (OSS) biradicals provided a number of precautions are considered. Biradicals that require a two-determinantal wave function (e.g. OSS state of carbenes) cannot be described by UDFT for principal reasons. However, if the overlap between the open-shell orbitals is small (the single electrons are located at different atomic centers) errors become small and, then, the principal failure of UDFT in these cases is not apparent and may even be disguised by the fact that UDFT has the advantage of describing spin polarization better than any restricted open shell DFT method. In the case of OSS biradicals with two- or multiconfigurational character (but a onedeterminantal form of the leading configuration), reasonable results can be obtained by broken-symmetry (BS)-UDFT, however in each case this has to be checked. In no case is it reasonable to lower the symmetry of a molecule to get a suitable UDFT description. Hybrid functionals such as B3LYP perform better than pure DFT functionals in BS-UDFT calculations because the former reduce the self-interaction error of DFT exchange functionals, which mimics unspecified static electron correlation effects, so that the inclusion of specific static electron correlation effects via the form of the wavefunction becomes more effective. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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22 pages, 293 KiB

Open AccessArticle

Chemical Reactivity Dynamics and Quantum Chaos in Highly Excited Hydrogen Atoms in an External Field: A Quantum Potential Approach

by P. K. Chattaraj^* and B. Maiti

Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India

Int. J. Mol. Sci. 2002, 3(4), 338-359; https://doi.org/10.3390/i3040338 - 25 Apr 2002

Cited by 17 | Viewed by 9532

Abstract

Dynamical behavior of chemical reactivity indices like electronegativity, hardness, polarizability, electrophilicity and nucleophilicity indices is studied within a quantum fluid density functional framework for the interactions of a hydrogen atom in its ground electronic state (n = 1) and an excited electronic state [...] Read more.

Dynamical behavior of chemical reactivity indices like electronegativity, hardness, polarizability, electrophilicity and nucleophilicity indices is studied within a quantum fluid density functional framework for the interactions of a hydrogen atom in its ground electronic state (n = 1) and an excited electronic state (n = 20) with monochromatic and bichromatic laser pulses. Time dependent analogues of various electronic structure principles like the principles of electronegativity equalization, maximum hardness, minimum polarizability and maximum entropy have been found to be operative. Insights into the variation of intensities of the generated higher order harmonics on the color of the external laser field are obtained. The quantum signature of chaos in hydrogen atom has been studied using a quantum theory of motion and quantum fluid dynamics. A hydrogen atom in the electronic ground state (n = 1) and in an excited electronic state ( n = 20) behaves differently when placed in external oscillating monochromatic and bichromatic electric fields. Temporal evolutions of Shannon entropy, quantum Lyapunov exponent and Kolmogorov – Sinai entropy defined in terms of the distance between two initially close Bohmian trajectories for these two cases show marked differences. It appears that a larger uncertainty product and a smaller hardness value signal a chaotic behavior. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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14 pages, 78 KiB

Open AccessArticle

The Concept of Density Functional Theory Based Descriptors and its Relation with the Reactivity of Molecular Systems: A Semi-Quantitative Study

by K. R. S. Chandrakumar and Sourav Pal^*

Theoretical Chemistry Group, Physical Chemistry Division, National Chemical Laboratory, Pune - 411 008, India

Int. J. Mol. Sci. 2002, 3(4), 324-337; https://doi.org/10.3390/i3040324 - 25 Apr 2002

Cited by 78 | Viewed by 12528

Abstract

In this present paper, we have made an attempt to explain the theoretical basis for the empirical hardness/softness concepts to address the reactivity of molecular complexes in a semi-quantitative way within the framework of density functional theory. A model based on local hard-soft-acid-base [...] Read more.

In this present paper, we have made an attempt to explain the theoretical basis for the empirical hardness/softness concepts to address the reactivity of molecular complexes in a semi-quantitative way within the framework of density functional theory. A model based on local hard-soft-acid-base principle has been proposed. The results obtained using some prototype charge transfer complexes, Lewis acid-base complexes and hydrogen-bonded complexes as examples, are in good agreement with the standard ab initio values. Although the model contains ad hoc parameters, it may form the basis of semi-quantitative description of inter-molecular interactions using hardness/softness parameters. The limitation, weakness and other critical issues of the present model are also discussed. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

14 pages, 120 KiB

Open AccessArticle

Use of Local Softness for the Interpretation of Reaction Mechanisms

by Asit K. Chandra¹ and Minh Tho Nguyen^2,*

¹ National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 5, Tsukuba 305-8565, Japan

² Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium

Int. J. Mol. Sci. 2002, 3(4), 310-323; https://doi.org/10.3390/i3040310 - 25 Apr 2002

Cited by 101 | Viewed by 11526

Abstract

The application of reactivity parameters derived from density functional theory in a local sense, in particular the softness and Fukui function, to interpret and predict the mechanisms of various organic reactions has been discussed. Local softness is shown to be successful in determining [...] Read more.

The application of reactivity parameters derived from density functional theory in a local sense, in particular the softness and Fukui function, to interpret and predict the mechanisms of various organic reactions has been discussed. Local softness is shown to be successful in determining the site-selectivity and regiochemistry and can be used as an alternative to the traditional frontier orbital theory. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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34 pages, 504 KiB

Open AccessArticle

Chemical Reactivity as Described by Quantum Chemical Methods

by P. Geerlings^* and F. De Proft

Eenheid Algemene Chemie, Free University of Brussels (VUB), Pleinlaan 2,1050 Brussels,Belgium

Int. J. Mol. Sci. 2002, 3(4), 276-309; https://doi.org/10.3390/i3040276 - 25 Apr 2002

Cited by 161 | Viewed by 16160

Abstract

Density Functional Theory is situated within the evolution of Quantum Chemistry as a facilitator of computations and a provider of new, chemical insights. The importance of the latter branch of DFT, conceptual DFT is highlighted following Parr's dictum "to calculate a molecule is [...] Read more.

Density Functional Theory is situated within the evolution of Quantum Chemistry as a facilitator of computations and a provider of new, chemical insights. The importance of the latter branch of DFT, conceptual DFT is highlighted following Parr's dictum "to calculate a molecule is not to understand it". An overview is given of the most important reactivity descriptors and the principles they are couched in. Examples are given on the evolution of the structure-property-wave function triangle which can be considered as the central paradigm of molecular quantum chemistry to (for many purposes) a structure-property-density triangle. Both kinetic as well as thermodynamic aspects can be included when further linking reactivity to the property vertex. In the field of organic chemistry, the ab initio calculation of functional group properties and their use in studies on acidity and basicity is discussed together with the use of DFT descriptors to study the kinetics of S_N2 reactions and the regioselectivity in Diels Alder reactions. Similarity in reactivity is illustrated via a study on peptide isosteres. In the field of inorganic chemistry non empirical studies of adsorption of small molecules in zeolite cages are discussed providing Henry constants and separation constants, the latter in remarkable good agreement with experiments. Possible refinements in a conceptual DFT context are presented. Finally an example from biochemistry is discussed : the influence of point mutations on the catalytic activity of subtilisin. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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23 pages, 283 KiB

Open AccessArticle

Applications of the Information Theory to Problems of Molecular Electronic Structure and Chemical Reactivity

by Roman F. Nalewajski

Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Cracow, Poland

Int. J. Mol. Sci. 2002, 3(4), 237-259; https://doi.org/10.3390/i3040237 - 25 Apr 2002

Cited by 39 | Viewed by 11113

Abstract

Recent studies on applications of the information theoretic concepts to molecular systems are reviewed. This survey covers the information theory basis of the Hirshfeld partitioning of molecular electron densities, its generalization to many electron probabilities, the local information distance analysis of molecular charge [...] Read more.

Recent studies on applications of the information theoretic concepts to molecular systems are reviewed. This survey covers the information theory basis of the Hirshfeld partitioning of molecular electron densities, its generalization to many electron probabilities, the local information distance analysis of molecular charge distributions, the charge transfer descriptors of the donor-acceptor reactive systems, the elements of a “thermodynamic” description of molecular charge displacements, both “vertical” (between molecular fragments for the fixed overall density) and “horizontal” (involving different molecular densities), with the entropic representation description provided by the information theory. The average uncertainty measures of bond multiplicities in molecular “communication” systems are also briefly summarized. After an overview of alternative indicators of the information distance (entropy deficiency, missing information) between probability distributions the properties of the “stockholder” densities, which minimize the entropy deficiency relative to the promolecule reference, are summarized. In particular, the surprisal analysis of molecular densities is advocated as an attractive information-theoretic tool in the electronic structure theory, supplementary to the familiar density difference diagrams. The subsystem information density equalization rules satisfied by the Hirshfeld molecular fragments are emphasized: the local values of alternative information distance densities of subsystems are equal to the corresponding global value, characterizing the molecule as a whole. These local measures of the information content are semi-quantitatively related to the molecular density difference function. In the density functional theory the effective external potentials of molecular fragments are defined, for which the subsystem densities are the ground-state densities. The nature of the energetic and “entropic” equilibrium conditions is reexamined and the entropy representation forces driving the charge transfer in molecular systems are introduced. The latter combine the familiar Fukui functions of subsystems with the information densities, the entropy representation “intensive” conjugates of the subsystem electron densities, and are shown to exactly vanish for the “stockholder” charge distribution. The proportionality relations between charge response characteristics of reactants, e.g., the Fukui functions, are derived. They are shown to follow from the minimum entropy deficiency principles formulated in terms of both the subsystems electron densities and Fukui functions, respectively. Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

3 pages, 25 KiB

Open AccessEditorial

Special Issue on Application of Density Functional Theory in Chemical Reactions

by Abhijit Chatterjee

Environmental Management Group, National Institute of Advanced Industrial Science and Technology, AIST TOHOKU, 4-2-1 Nigatake, Miyagino-ku, Sendai 983-8551, Japan

Int. J. Mol. Sci. 2002, 3(4), 234-236; https://doi.org/10.3390/i3040234 - 25 Apr 2002

Cited by 6 | Viewed by 6913

Abstract

Rapid advances are taking place in the application of density functional theory (DFT) to describe complex chemical reactions.[...] Full article

(This article belongs to the Special Issue Application of Density Functional Theory)

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