Quantum Mechanical Density Functional Theory Research Articles

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

We have coupled hybrid quantum mechanics (density functional theory; Car-Parrinello)/molecular mechanics molecular dynamics simulations to a grand-canonical scheme, to calculate the in situ redox potential of the Cu(2+) + e(-) --> Cu(+) half reaction in azurin from Pseudomonas aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and finite-temperature fluctuations of the protein structure are both essential for a correct quantitative description of the electronic properties of this system. We report a redox potential shift with respect to copper in water of 0.2 eV (experimental 0.16 eV) and a reorganization free energy lambda = 0.76 eV (experimental 0.6-0.8 eV). The electrostatic field of the protein plays a crucial role in fine tuning the redox potential and determining the structure of the solvent. The inner-sphere contribution to the reorganization energy is negligible. The overall small value is mainly due to solvent rearrangement at the protein surface.

Quantum mechanical vs. empirical potential modeling of uranium dioxide (UO2) surfaces: (111), (110), and (100)

To evaluate the stability, potential reactivity, and relaxation mechanisms on different uraninite surfaces, surface energy values were calculated and structural relaxation was determined for the (111), (110), and (100) crystallographic faces of uranium dioxide (UO 2 ) using quantum mechanical (density functional theory) and empirical potential computational methods. Quantum mechanical results are compared with empirical potential results, which use surface slab models with two different geometries, as well as various different empirical force fields. The strengths and weaknesses of the different approaches are evaluated, and surface stabilizing mechanisms such as relaxation, charge redistribution, and electronic stabilization are investigated. Quantum mechanical (q.m.) surface energy results are in agreement with the relative surface energy trends resulting from calculations using three different empirical potential sets for uranium and oxygen (two from Catlow 1977; one from Meis and Gale 1998), and with empirical force-field values published in the literature (Abramowski et al. 1999, 2001). The (111) surface consistently has the lowest surface energy (0.461 J/m 2 from q.m. calculations) and the smallest amount of surface relaxation, followed by the (110) surface (0.846 J/m 2 ; q.m.), and the (100) surface (1.194 J/m 2 ; q.m.) (quantum mechanical surface energy values in parentheses are for surface slabs with a thickness of four UO 2 units). Differences exist, however, in the absolute values of surface energies calculated as a function of potential set used. Quantum mechanical values are consistently lower than values calculated using empirical potential methods. A fourth potential set is presented that is derived from fitting electrostatic and short-range repulsive parameters to experimental bulk properties and surface energies and relaxations from quantum mechanical calculations.

Mechanisms of Amine-Catalyzed Organosilicate Hydrolysis at Circum-Neutral pH

Mono- and polyamines can catalyze the hydrolysis and condensation of organosilicate starting materials in biomimetic silica synthesis pathways at circum-neutral pHs and room temperature. Our study is focused on understanding the mechanistic role of amines in catalyzing the hydrolysis process that precedes condensation. We have conducted (29)Si NMR experimental studies over a range of temperature and pHs for the hydrolysis rates of trimethylethoxysilane (TMES), a model compound with only one hydrolyzable bond, combined with quantum mechanical hybrid density functional theory calculations of putative intermediate and transition-state structures for TMES and tetramethyl orthosilicate (TMOS). Comparison of calculated energies with experimentally determined activation energies indicates that amine catalysis of TMES is primarily a consequence of the amine's acidity at neutral pH. The proton released by the amine is transferred to the organosilicate, producing a protonated ethoxy leaving group that can be displaced by water in an S(N)2 reaction. For TMOS, the activation energy of proton-transfer coupled with S(N)2 substitution is comparable to that for Corriu's nucleophile-activated nucleophilic displacement, such that the mechanism of amine-catalyzed hydrolysis is dependent mostly on the ambient pH conditions as well as the type of amine. The relevance of our results to biological silica precipitation is discussed.

Adsorption of H, NH x, BH x and BBr x on a (110) surface of c-BN: A quantum-mechanical DFT study

The adsorption of H, NH x , BH x and BBr x ( x = 1, 2 and 3) on hydrogen-terminated (110) surfaces of c-BN has been investigated theoretically. Density Functional Theory (DFT) methods were used in order to study the adsorption processes of these different species on both nitrogen and boron sites at the surfaces. With one exception, all adsorption processes were found to be exothermic and in the order; BBr· ≫ BH 2· ≈H· > BH· ≫ NH· ≈ BBr 2· > NH 2· ≫ BH 3· > NH 3· > BBr 3· for a nitrogen site, and NH 2· > NH· > BBr· > H· > BH· > BH 2· ≈ BBr 2· ≫ BBr 3· ≈ NH 3· ≈BH 3· for a boron site. The exception was NH 3 being bonded to a surface N site, for which the reaction was slightly endothermic. The various modeling parameters that were used in the calculations of these adsorption energies have been chosen by performing series of extensive test calculations, in which the effect of these parameters (e.g. template size, vacuum depth, atom constraints) on bond-strength have been carefully estimated. Moreover, a semi-empirical method has been evaluated with the purpose to study the usefulness of this type of method for the polar BN compound.

Quantum Mechanical Modeling of Self-Assembly and Photoinduced Electron Transfer in PNA-Based Artificial Living Organisms

In order to support the creation of both artificial living organisms in the USA LANL "Protocell Assembly" project and programmable nano-biorobots in the EU "Programmable Artificial Cell Evolution" project, we used quantum mechanical (QM), density functional theory (DFT), the semiempirical PM3 method, and molecular mechanics (MM) software to investigate various complex photosynthetic systems based on peptide nucleic acid (PNA) in a water environment. Quantum mechanical DFT PBEPBE simulations, including electron correlations, confirm that water molecules that surround all the photosynthetic complex of the LANL protoorganism are main constructing factors and stabilize this system consisting of: PNA fragment attached by covalent bond sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule, lipid precursor molecule and fragment of lipid molecules mono layer. The absorption spectrum shift to the red wavelengths in the complex artificial protocell photosynthetic center might be used as the measure of the complexity of this system. The electron pi-pi* transitions in the first and third excited states are from HOMO and HOMO-1 located on the conjugated water molecules and sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO of the lipid precursor molecule as calculated using the time dependent (TD) PBEPBE/6-31G model. Electron charge tunneling in the first and third excited states should induce metabolic photodissociation of the lipid precursor molecule because of localization of the transferred electron cloud on the head (waste) of the lipid precursor molecule. TD electron correlation PBEPBE/6-31G calculations show that in the different energies of excitation, the charge transfer tunneling is from sensitizer to lipid precursor and cytosine molecules. One should note that in a water solvent, the electron charge transfer pi-pi* transition in the fifth and sixth excited state is from the HOMO and HOMO-1 located on the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO+2 located on the cytosine-PNA fragment molecule. Investigation results indicate that strong back electron tunneling from the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the cytosine molecule in the LANL artificial photosynthetic system exists.

Chlorination−Methylation of the Hydrogen-Terminated Silicon(111) Surface Can Induce a Stacking Fault in the Presence of Etch Pits

Recently, we reported STM images of the methylated Si(111) surface [prepared through chlorination-alkylation of the Si(111)-H surface] taken at 4.7 K, indicating that the torsion angle of the methyl group with respect to the subsurface silicon layer is phi = 23 +/- 3 degrees . Repulsions between H atoms in adjacent methyl groups are minimized at 30 degrees , while repulsions between H atoms and second layer Si atoms are minimized at 60 degrees . The experimental result of 23 degrees is surprising because it suggests a tendency of the methyl group toward the eclipsed configuration (0 degrees ) rather than staggered (60 degrees ). In contrast, extensive fully periodic quantum mechanical Density Functional Theory studies of this surface give an equilibrium torsion angle of 37.5 degrees , indicating a tendency toward the staggered configuration. This discrepancy can be resolved by showing that the CH3 on the step edges and etch pits interacts repulsively with the CH3 on the surface terraces unless a stacking fault is introduced between the first and second silicon layers of the Si(111)-CH3 surface terraces. We propose that this could occur during the chlorination-alkylation of the Si(111)-H surface. This stacking fault model predicted phi = 22.5 degrees measured with respect to the bulk (corresponding to phi = 37.5 degrees with respect to the second layer Si atoms). This model can be tested by measuring the orientation of the CH3 within the etch pits, which should have phi = 37.5 degrees , or by making a surface without etch pits, which should have phi = 37.5 degrees .

Structure Determination of the 4d Metal Diborides: A Quantum Mechanical Study

Metal diborides (MB(2)) often have interesting thermal, mechanical, and superconducting properties. MgB(2) was put into focus some years ago for its high transition temperature (39 K) in combination with its simple AlB(2) structure. The boron structure in MB(2) is assumed to be dependent on the electron transfer from the nearby positioned metal atoms. An electronic and structural comparison has been performed here for various initially planar and puckered transition-metal borides, using quantum mechanical density functional theory (DFT) calculations under periodic boundary conditions. In comparison to MgB(2), the experimentally planar transition-metal diborides (ZrB(2), NbB(2), and MoB(2)) and the experimentally puckered ones (TcB(2), RuB(2), RhB(2), and PdB(2)) have been examined. The results indicate that the energetic stability generally follows the experimentally obtained results. The metals that are less electronegative than boron donate electrons to boron, which in turn induce planar boron structures (graphitic-like). The metals that prefer to be planar donate more than one electron, while the trend for metals which favor puckered B structures is that they donate less than one electron per metal atom. Two donated electrons per metal atom (or very close to) will result in the most stable AlB(2) structure.

First-principle study of nitrogen incorporation in amorphous carbon

First-principle calculations using quantum-mechanical density functional theory are carried out to study nitrogen incorporation in amorphous carbon, in which the structural models from liquid quench containing 64 atoms are introduced. The properties simulated for N incorporated amorphous carbon are in agreement with the available experimental results. The topological and electronic properties for nitrogen incorporation structures with various densities are investigated, and it is found that the bonding configuration of nitrogen atoms strongly depends on the density and the nitrogen concentration in the network. The simulations provide a qualitative support for a low nitrogen doping efficiency observed in the experiment since no true doping (N atoms substitutionally occupy C sites, leading to a donor level below conduction band mobility edge E c ) exists in any cases studied. For the tetrahedral amorphous carbon (at density of 2.9 g/cm 3) with a low concentration of nitrogen (1.6 at% and 3.2 at%), the incorporated N atoms are found to adopt the auto-compensated sites or to be in threefold coordination. In particular, a new threefold C defect is found, which is introduced by nitrogen auto-compensation. Nitrogen incorporated amorphous carbon (2.0 g/cm 3) leads to the formation of a graphite-like structure with twofold nitrogen coordination.

Hierarchical Multiscale Mechanism Development for Methane Partial Oxidation and Reforming and for Thermal Decomposition of Oxygenates on Rh

A thermodynamically consistent C1 microkinetic model is developed for methane partial oxidation and reforming and for oxygenate (methanol and formaldehyde) decomposition on Rh via a hierarchical multiscale methodology. Sensitivity analysis is employed to identify the important parameters of the semiempirical unity bond index quadratic exponential potential (UBI-QEP) method and these parameters are refined using quantum mechanical density functional theory. With adjustment of only two pre-exponentials in the CH4 oxidation subset, the C1 mechanism captures a multitude of catalytic partial oxidation (CPOX) and reforming experimental data as well as thermal decomposition of methanol and formaldehyde. We validate the microkinetic model against high-pressure, spatially resolved CPOX experimental data. Distinct oxidation and reforming zones are predicted to exist, in agreement with experiments, suggesting that hydrogen is produced from reforming of methane by H2O formed in the oxidation zone. CO is produced catalytically by partial oxidation up to moderately high pressures, with water-gas shift taking place in the gas-phase at sufficiently high pressures resulting in reduction of CO selectivity.

Hierarchical, multiscale surface reaction mechanism development: CO and H 2 oxidation, water–gas shift, and preferential oxidation of CO on Rh

A hierarchical multiscale parameter refinement approach was used to develop microkinetic models for CO and H 2 oxidation, and CO–H 2 coupling for water–gas shift (WGS) and preferential oxidation (PROX) of CO on Rh. The rate parameters were estimated with a combination of quantum mechanical density functional theory (DFT), the semi empirical unity bond index-quadratic exponential potential method, and transition-state theory. To improve the predictive ability, selected pre-factors of the CO and H 2 oxidation reaction mechanisms were optimized against multiple experimental data sets, such as ignition, molecular beam, and laser-induced fluorescence. Thermodynamic consistency of rate parameters was ensured over a wide temperature range by a combination of statistical mechanics and constraints-based optimization. DFT calculations were used to estimate cross adsorbate–adsorbate CO–H interactions. It is shown that the coupling between the two fuels arising from these interactions is essential for PROX of CO. Important reaction pathways in the WGS and PROX chemistries are discussed. For example, it is shown that the oxidation of CO by OH via the carboxyl intermediate, and not by O, is the dominant path in PROX. Thus, hydrogen acts as a “catalyst” for CO combustion under certain conditions. Finally, the mechanisms are validated against additional sets of redundant experimental data.

Excited state intramolecular proton transfer in anionic and cationic species of 2-(2′-amino-3-pyridyl)benzimidazole

Excited state intramolecular proton transfer (ESIPT) process has been studied in the monoanionic and monocationic species of 2-(2′-amino-3-pyridyl)benzimidazole (2-A3PyBI) in aqueous and organic solvents. Dual fluorescence is observed from monocationic (aqueous and alcoholic solvents, partly from non-polar and polar aprotic ones) and monoanionic species in aqueous media. Presence of different species has been characterized with the help of absorption, fluorescence excitation and fluorescence spectroscopy, as well as, time resolved fluorimetry. The electronic structure calculations were performed on each species using semi-empirical quantum mechanical AM1 method and density functional theory B3LYP with 6-31G** basis set using Gaussian 98 program to characterize the particular ionic species. Presence of electron withdrawing pyridine N atom and negative charge on the benzimidazole moiety plays the vital role in increasing the rate of ESIPT process.

Energetics of hydrogen coverage on group VIII transition metal surfaces and a kinetic model for adsorption/desorption

We determined the binding energy of hydrogen to the closest packed surface for all nine group VIII transition metals as a function of surface coverage using quantum mechanics (density functional theory with the generalized gradient approximation) with periodic boundary conditions. The study provides a systematic comparison of the most stable surfaces of the nine group VIII transition metals, leading to results consistent with available surface science studies. We then use these to develop a simple thermodynamic model useful in estimating the surface coverage under typical heterogeneous catalysis conditions and compare these results to temperature programmed desorption experiments.

Excited state prototropism in 2-aminonicotinic acid: effect of solvents and acid–base concentrations

Absorption, fluorescence excitation and fluorescence spectroscopy combined with time-dependent spectrofluorimetry have been used to study the effect of solvents and acid–base concentration on the spectral characteristics of 2-aminonicotinic acid (2-ANA). The 2-ANA exists as a molecular species in non-polar and polar aprotic solvents and zwitterion (ZI-1) in polar protic solvents. Dual emission is observed from ZI and the monoanion (MA) of 2-ANA, suggesting that excited state intramolecular proton transfer (ESIPT) is observed from the amino proton to the carbonyl oxygen, followed by structural reorganization. Single normal Stokes shifted fluorescence is observed from the monocation (MC) of 2-ANA, indicating that the carboxylate ion is more effective than COOH group in ESIPT process. The dication (DC1) is formed by the protonation of N and >C O moieties and dianion by deprotonation of NH 2 and COOH groups. Electronic molecular structure calculations were performed on each species using semi-empirical quantum mechanical AM1 method and density functional theory (DFT) B3LYP using 6-31G ** basis sets with Gaussian 98 to assign the structure to the various species.

Spectral characteristics of various prototropic species of 2-(3′-aminophenyl)pyrido[3,4-d]imidazole

Spectral characteristics of the prototropic species of 2-(3′-aminophenyl)pyrido [3,4-d]imidazole (3-APPI) have been studied in three non-aqueous and aqueous solvents, using absorption, fluorescence excitation and fluorescence spectroscopy, as well as, time dependent spectrofluorimetry. Acid concentration in ether is controlled by trifluoroacetic acid (TFA), whereas in other three solvents H 2SO 4 is used. Semi-empirical quantum mechanical calculations (AM1) and density functional theory (DFT) calculations have been carried out on all kinds of neutral and ionic species. Combining the experimental and theoretical results, the spectral characteristics have been assigned to various cationic and monoanionic species. It has been shown that: (i) only one kind of monoanion (MA) is formed by the deprotonation of N H moiety and one kind of trication (TC), (ii) two kinds of monocations (MC1 and MC3) in the ground (S 0) and first excited singlet (S 1) states in polar aprotic and protic solvents, whereas only one monocation (MC3) is formed in ether + TFA system. p K a values for the various prototropic reactions were determined in S 0 and S 1 states and discussed.

Intra- and intermolecular proton transfer in methyl-2-hydroxynicotinate

Spectral characteristics of methyl 2-hydroxynicotinate (MEHNA) have been studied using absorption, fluorescence excitation and fluorescence spectroscopy, as well as, using single photon counting nanosecond spectrofluorimeter. MEHNA is present as enol in less polar solvents and keto in polar media. In non-polar solvents, large Stokes shifted fluorescence band is assigned to phototautomer, formed by excited state intramolecular proton transfer (ESIPT), whereas fluorescence is only observed from keto form in polar solvents. In aqueous and polar solvents monocation (MC) is formed by protonating the exo carbonyl oxygen atom in the ground state (S0) and in the first excited singlet state (S1), MC is obtained by protonating carbonyl oxygen atom of the ester. It is formed by ESIPT from exo carbonyl proton to carbonyl oxygen atom of the ester. Dication is formed by protonating both the oxygen atoms. Two kinds of monoanions formed by deprotonating phenolic proton or >N–H proton of keto suggest the presence of enol and keto in aqueous solution. In cyclohexane MC is formed by protonating carbonyl oxygen in both S0 and S1 states. The electronic structure calculations were performed on each species using semi-empirical quantum mechanical AM1 method and density functional theory B3LYP with 6-31G** basis set using Gaussian 98 program, along with potential energy mapping, to characterize the particular species.

Accurate pKa Determination for a Heterogeneous Group of Organic Molecules

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energetics of gas-phase protonation. The electrostatic contribution to the solvation energies of protonated and deprotonated compounds were calculated by solving the Poisson equation using atomic charges generated by fitting the electrostatic potential derived from the molecular wave functions in vacuum. The combination of gas-phase and electrostatic solvation energies by means of the thermodynamic cycle enabled us to compute pKa values for the 26 compounds, which cover six distinct chemical groups (carboxylic acids, benzoic acids, phenols, imides, pyridines and imidazoles). The computational procedure for determining pKa values is accurate and transferable with a root-mean-square deviation of 0.53 and 0.57 pKa units and a maximum error of 1.0 pKa and 1.3 pKa units for Becke-half&half and B3LYP DFT functionals, respectively.

Intra- and intermolecular proton transfer in methyl-2-hydroxynicotinate

Spectral characteristics of methyl 2-hydroxynicotinate (MEHNA) have been studied using absorption, fluorescence excitation and fluorescence spectroscopy, as well as, using single photon counting nanosecond spectrofluorimeter. MEHNA is present as enol in less polar solvents and keto in polar media. In non-polar solvents, large Stokes shifted fluorescence band is assigned to phototautomer, formed by excited state intramolecular proton transfer (ESIPT), whereas fluorescence is only observed from keto form in polar solvents. In aqueous and polar solvents monocation (MC) is formed by protonating the exo carbonyl oxygen atom in the ground state (S0) and in the first excited singlet state (S1), MC is obtained by protonating carbonyl oxygen atom of the ester. It is formed by ESIPT from exo carbonyl proton to carbonyl oxygen atom of the ester. Dication is formed by protonating both the oxygen atoms. Two kinds of monoanions formed by deprotonating phenolic proton or >N–H proton of keto suggest the presence of enol and keto in aqueous solution. In cyclohexane MC is formed by protonating carbonyl oxygen in both S0 and S1 states. The electronic structure calculations were performed on each species using semi-empirical quantum mechanical AM1 method and density functional theory B3LYP with 6-31G** basis set using Gaussian 98 program, along with potential energy mapping, to characterize the particular species.

The Role of Adsorbate–Adsorbate Interactions in the Rate Controlling Step and the Most Abundant Reaction Intermediate of NH3Decomposition on Ru

N–N adsorbate–adsorbate interactions on a Ru(0001) surface are first estimated using quantum mechanical density functional theory (DFT) calculations, and subsequently incorporated, for the first time, in a detailed microkinetic model for NH3 decomposition on Ru using the unity bond index-quadratic exponential potential (UBI–QEP) method. DFT simulations indicate that the cross N–H interactions are relatively small. Microkinetic model predictions are compared to ultra-high vacuum temperature programmed desorption and atmospheric fixed bed reactor data. The microkinetic model with N–N interactions captures the experimental features quantitatively. It is shown that the N–N interactions significantly alter the rate determining step, the most abundant reaction intermediate, and the maximum N*-coverage, compared to mechanisms that ignore adsorbate–adsorbate interactions.

Molecular Dynamics Simulation of Structure and Thermodynamic Properties of Poly(dimethylsilamethylene) and Hydrocarbon Solubility Therein: Toward the Development of Novel Membrane Materials for Hydrocarbon Separation

Molecular dynamics simulation is used to model the structure and thermodynamic properties of a novel rubbery polymer with promising membrane properties for hydrocarbon separation. A realistic united atom force field is developed based on extensive density functional theory quantum mechanics calculations for a model dimer and volumetric data at various temperatures and pressures. Both a constant bond length and a flexible bond length model are examined. Well-equilibrated structures of the polymer melt at various conditions are used to evaluate numerous thermodynamic properties, such as the isothermal compressibility, thermal expansion coefficient, and cohesive energy density, and structural properties, including intra- and intermolecular distribution functions and the static structure factor. The microscopic structure of the free volume of the polymer matrix and its evolution with time affects the diffusion of penetrant molecules considerably; they are calculated accurately using the Greenfield and Theodorou geometric analysis. The solubilities of various n-alkanes from methane to n-hexane at 300 and 400 K are calculated using the Widom test particle insertion technique. In all cases, simulation results are in good agreement with literature experimental data for the volumetric properties of the polymer melt and the solubility coefficients of n-alkanes in the polymer. In a forthcoming publication, the transport properties of these systems and the underlying molecular mechanisms will be examined.

Density functional theory study of the d(10) series (H3P)3M(eta 1-SO2) and (MenPh(3-n)P)3M(eta 1-SO2) (M = Ni, Pd, Pt; n = 0-3): SO2 pyramidality and M-S bond dissociation energies.

Quantum mechanical density functional theory (DFT) and coupled DFT/molecular mechanics (QMMM) studies of the compounds (H(3)P)(3)M(eta(1)-SO(2)) and (Me(n)Ph(3-n)P)(3)M(eta(1)-SO(2)) (M = Ni, Pd, Pt; n = 0-3) model the experimental data well, particularly the planar/pyramidal geometries at sulfur. Bond dissociation energy (BDE) calculations confirm that Pd/Pt systems with pyramidal SO(2) ligands exhibit M-S BDEs smaller by 30-50% than Ni systems with planar SO(2). However, scans of the potential energy surfaces show that flexing the planar/pyramidal torsion angle within ranges of 20-30 degrees requires little energy. Bond energy decomposition calculations indicate that the electrostatic Delta E(elstat) term determines the BDE for Pd/Pt molecules where the sulfur is pyramidal, whereas all three terms matter when the sulfur is planar, as for Ni compounds. However, this accounts only for a fraction of the BDE differences; orbital energy matching accounts for the balance.