Quantum Mechanical Density Functional Theory Research Articles

Origin of the Energy Barrier to Chemical Reactions ofO2on Al(111): Evidence for Charge Transfer, Not Spin Selection

Dissociative adsorption of molecular oxygen on the Al(111) surface exhibits mechanistic complexity that remains surprisingly poorly understood in terms of the underlying physics. Experiments clearly indicate substantial energy barriers and a mysteriously large number of adsorbed single oxygen atoms instead of pairs. Conventional first principles quantum mechanics (density functional theory) predicts no energy barrier at all; instead, spin selection rules have been invoked to explain the barrier. In this Letter, we show that correct barriers arise naturally when embedded correlated electron wave functions are used to capture the physics of the interaction of O(2) with the metal surface. The barrier originates from an abrupt charge transfer (from metal to oxygen), which is properly treated within correlated wave function theory but not within conventional density functional theory. Our potential energy surfaces also identify oxygen atom abstraction as the dominant reaction pathway at low incident energies, consistent with measurements, and show that charge transfer occurs in a stepwise fashion.

The reaction mechanism of the enantioselective Tsuji allylation: inner-sphere and outer-sphere pathways, internal rearrangements, and asymmetric C-C bond formation.

We use first principles quantum mechanics (density functional theory) to report a detailed reaction mechanism of the asymmetric Tsuji allylation involving prochiral nucleophiles and nonprochiral allyl fragments, which is consistent with experimental findings. The observed enantioselectivity is best explained with an inner-sphere mechanism involving the formation of a 5-coordinate Pd species that undergoes a ligand rearrangement, which is selective with regard to the prochiral faces of the intermediate enolate. Subsequent reductive elimination generates the product and a Pd(0) complex. The reductive elimination occurs via an unconventional seven-centered transition state that contrasts dramatically with the standard three-centered C-C reductive elimination mechanism. Although limitations in the present theory prevent the conclusive identification of the enantioselective step, we note that three different computational schemes using different levels of theory all find that inner-sphere pathways are lower in energy than outer-sphere pathways. This result qualitatively contrasts with established allylation reaction mechanisms involving prochiral nucleophiles and prochiral allyl fragments. Energetic profiles of all reaction pathways are presented in detail.

Combined Theoretical and Experimental Study of the Complexation of a Hexaarylbenzene-Based Receptor with the Potassium Cation

In this study, non-covalent binding interactions of the hexaarylbenzene-based receptor (R) with the potassium cation have been investigated. Employing quantum mechanical density functional theory calculations, the most probable structure of the KR + complex species was predicted. In this complex, the K+ cation synergistically interacts with the polar ethereal oxygen fence and with the central hydrophobic benzene bottom via cation–π interaction. The strength of the KR + complex was evaluated experimentally by affinity capillary electrophoresis. From the dependence of the effective electrophoretic mobility of the receptor R on the concentration of the potassium ion in the background electrolyte, the thermodynamic binding (stability, association) constant (K KR) of the KR + complex in methanol was evaluated as log10 K KR = 3.20 ± 0.22.

Bambus[6]uril as a ditopic ion-pair molecular receptor for Cs+I−

Quantum mechanical density functional theory (DFT) calculations were used to derive the most probable structure of the bambus[6]uril·Cs+I− electroneutral complex species. In this complex, the considered anion I−, included in the macrocyclic cavity, is bound by 12 weak hydrogen bonds between methine hydrogen atoms on the convex face of glycoluril units and the I− anion, whereas the cesium cation Cs+ interacts only with two carbonyl oxygen atoms of the parent macrocyclic receptor. The interaction energy of the resulting complex, involving the Boys–Bernardi counterpoise corrections of the basis set superposition error, was found to be −472.4 kJ/mol.

Alkaloids from the Root of Isatis indigotica

Seventeen new alkaloids (1-17) and 14 known analogues have been isolated from an aqueous extract of the root of Isatis indigotica. The structures and absolute configurations of these compounds were determined by extensive spectroscopic data analysis, including 2D NMR, single-crystal X-ray crystallography using anomalous scattering of Cu Kα radiation, and electronic circular dichroism spectra calculations based on the quantum-mechanical time-dependent density functional theory. Compounds 1, 2, and 3 are the first examples of natural products with unique linkages between a molecule of 2-(4-methoxy-1H-indol-3-yl)acetonitrile and 2-(1H-indol-3-yl)acetonitrile, 2-(4-methoxy-1H-indol-3-yl)acetonitrile, and 4-hydroxyphenylethane, respectively. Compounds (-)-4 and (+)-4 represent the first natural products with the pyrrolo[2,3-b]indolo[5,5a,6-b,a]quinazoline skeleton. Some structural assignments for the new alkaloids suggest that the assignments made for certain previously reported alkaloids require revision. Compounds 1-3 and arvelexin (18) show antiviral activity against the influenza virus A/Hanfang/359/95 (H3N2), with IC(50) values of 3.70-12.35 μM, and 17 inhibits Coxsackie virus B3 replication with an IC(50) of 6.87 μM.

Linking of amino-capped quinonediimines by divalent transition metal ions: Synthesis, characterization, and comparison to electronic structure calculations

Quantum mechanical density functional theory (DFT) calculations are reported for novel, self-assembled transition metal linked dimers of N,N′-bis (3′-carboxy,4′-aminophenyl)-1,4-quinonediimine, with the metals manganese, iron, cobalt, nickel, copper and zinc each in the +2 oxidation state. Infrared spectroscopy detected systematic changes in the carbon–nitrogen double bond involving the imine nitrogen atoms, from 1457cm−1 for manganese complex to 1622cm−1 for the iron complexes. The calculated electronic band gaps of the complexes compare favorably to those for the uncomplexed quinonediimines. The synthesis of the compounds demonstrates a feasible route to the design of a tunable architecture of linear molecular wires derived from properly derivatized quinonediimines.

Modeling Adsorption in Metal–Organic Frameworks with Open Metal Sites: Propane/Propylene Separations

We present a new approach for modeling adsorption in metal-organic frameworks (MOFs) with unsaturated metal centers and apply it to the challenging propane/propylene separation in copper(II) benzene-1,3,5-tricarboxylate (CuBTC). We obtain information about the specific interactions between olefins and the open metal sites of the MOF using quantum mechanical density functional theory. A proper consideration of all the relevant contributions to the adsorption energy enables us to extract the component that is due to specific attractive interactions between the π-orbitals of the alkene and the coordinatively unsaturated metal. This component is fitted using a combination of a Morse potential and a power law function and is then included into classical grand canonical Monte Carlo simulations of adsorption. Using this modified potential model, together with a standard Lennard-Jones model, we are able to predict the adsorption of not only propane (where no specific interactions are present), but also of propylene (where specific interactions are dominant). Binary adsorption isotherms for this mixture are in reasonable agreement with ideal adsorbed solution theory predictions. We compare our approach with previous attempts to predict adsorption in MOFs with open metal sites and suggest possible future routes for improving our model.

Theoretical study on the complexation of bambus[6]uril with the cyanate and thiocyanate anions

Quantum mechanical density functional theory (DFT) calculations were used to derive the most probable structures of the bambus[6]uril·OCN− and bambus[6]uril·SCN− anionic complex species. In these two C 3 symmetric complexes, each of the two considered anions, included in the macrocyclic cavity, is bound by 12 weak hydrogen bonds between methine hydrogen atoms on the convex face of glycoluril units and the respective anion.

Molecular simulation studies for intercalation of photoactive dyes into layered double hydroxide

Molecular simulation studies were performed to explore the properties of functionalized Mg–Al layered double hydroxides (LDHs). Using molecular dynamics (MD) simulations, the intercalation of photoactive dyes (methyl orange, MO) into a Mg:Al 2:1 LDH system were studied, for which some limited experimental data have been reported (J. Colloid Interface Sci. 2008, 318, 337). The interlayer structure, hydrogen bonding, and consequent swelling of LDH compounds containing MO molecules were shown on the molecular level. Quantum mechanical density functional theory was also employed in order to get the geometry optimization and atomic charges. The concentration profiles, mean square displacement (MSD), and self-diffusion coefficient were calculated using the trajectory files on the basis of MD simulations, and the results indicated that the MO molecules were much more stable when intercalated into the LDH layers. The orientation of the intercalated MO molecules was measured at the interface of the LDH layers. The tail vectors of the MO molecule were tilted with an average angle from 70° to 76°, and most of the angular distribution is about 74.15°, which had a good agreement with the experimental data 74.1°.

Stability and crystal structures of iron carbides: A comparison between the semi-empirical modified embedded atom method and quantum-mechanical DFT calculations

Iron carbides play a crucial role in steel manufacturing and processing and to a large extent determine the physical properties of steel products. The modified embedded atom method (MEAM) in combination with Lee's Fe-C potential is a good candidate for molecular dynamics simulations on larger Fe-C systems. Here, we investigate the stability and crystal structures of pure iron and binary iron carbides using MEAM and compare them with the experimental data and quantum-mechanical density functional theory calculations. The analysis shows that the Fe-C potential gives reasonable results for the relative stability of iron and iron carbides. The performance of MEAM for the prediction of the potential energy and the calculated lattice parameters at elevated temperature for pure iron phases and cementite are investigated as well. The conclusion is that Lee's MEAM Fe-C potential provides a promising basis for further molecular dynamics simulations of Fe-C alloys and steels at lower temperatures (up to 800 K).

Nuclear Inelastic Scattering and Mössbauer Spectroscopy as Local Probes for Ligand Binding Modes and Electronic Properties in Proteins: Vibrational Behavior of a Ferriheme Center inside a β-Barrel Protein

In this work, we present a study of the influence of the protein matrix on its ability to tune the binding of small ligands such as NO, cyanide (CN(-)), and histamine to the ferric heme iron center in the NO-storage and -transport protein Nitrophorin 2 (NP2) from the salivary glands of the blood-sucking insect Rhodnius prolixus. Conventional Mössbauer spectroscopy shows a diamagnetic ground state of the NP2-NO complex and Type I and II electronic ground states of the NP2-CN(-) and NP2-histamine complex, respectively. The change in the vibrational signature of the protein upon ligand binding has been monitored by Nuclear Inelastic Scattering (NIS), also called Nuclear Resonant Vibrational Spectroscopy (NRVS). The NIS data thus obtained have also been calculated by quantum mechanical (QM) density functional theory (DFT) coupled with molecular mechanics (MM) methods. The calculations presented here show that the heme ruffling in NP2 is a consequence of the interaction with the protein matrix. Structure optimizations of the heme and its ligands with DFT retain the characteristic saddling and ruffling only if the protein matrix is taken into account. Furthermore, simulations of the NIS data by QM/MM calculations suggest that the pH dependence of the binding of NO, but not of CN(-) and histamine, might be a consequence of the protonation state of the heme carboxyls.

A Theoretical Study of Metal–Metal Cooperativity in the Homogeneous Water Gas Shift Reaction

The possibility of metal-metal cooperativity in improving the yield of the homogeneous water gas shift reaction (WGSR) has been investigated through full quantum mechanical density functional theory calculations. The calculations indicate that bimetallic catalysts would be likely to be more highly active than mononuclear metal-based catalysts for the WGSR. The results have implications for the design of improved WGSR catalysts in the future.

Molecular engineering of microporous crystals: (IV) Crystallization process of microporous aluminophosphate AlPO 4-11

The products of microporous aluminophosphate AlPO 4-11 crystallized for different periods of time were freeze-dried and characterized by XRD and NMR techniques. Six crystallographically distinct Al- and P-centered large fragments and 34 small fragments of dimer (Al–P), trimer (Al–P–Al and P–Al–P), tetramer (Al–P 3 and P–Al 3), pentamer (Al–P 4 and P–Al 4), and 4- and 6-membered rings were extracted from the framework of AlPO 4-11. Each of the six large fragments contained two completed coordination layers surrounding the centered atom. The shielding tensors of the Al and P atoms of the fragments were calculated using the quantum mechanics density functional theory. The experimentally observed chemical shifts of Al or P from the well-crystallized AlPO 4-11 were assigned to the shielding tensors of the center atoms of the six large fragments and were further used as references in the determination of the chemical shifts of the Al or P atoms in the small fragments. A comparison of the calculated chemical shifts of the Al and P atoms in the small fragments to the experimental data of the products isolated at different crystallization periods suggested that the fragments of dimers, trimers of the form Al–P–Al, tetramers of the form P–Al 3, and pentamers may exist in the crystallization process of AlPO 4-11. On the basis of these observations regarding the putative small fragments, a possible crystallization process of AlPO 4-11 was proposed.

Theoretical study on the protonation of bambus[6]uril

Quantum mechanical density functional theory (DFT) calculations were used to derive the most probable structures of the bambus[6]uril·H3O+ and bambus[6]uril·(H3O+)2 cationic complex species. In these two complexes, each of the considered H3O+ ions is bound by three strong linear hydrogen bonds to the three corresponding carbonyl oxygens of the parent macrocyclic receptor.

Molecular Modeling of Hydrotalcite Structure Intercalated with Transition Metal Oxide Anions: CrO42– and VO43–

Molecular dynamics (MD) simulations are used to study the interlayer structure, hydrogen bonding, and energetics of hydration of Mg/Al (2:1 and 4:1) layered double hydroxide (LDH) or hydrotalcite (HT) intercalated with oxymetal anions, CrO(4)(2-), and VO(4)(3-). The ab initio forcefield COMPASS is employed for the simulations. The charge on the oxymetal anions is determined by quantum mechanical density functional theory. The structural behavior of the oxymetal anions in LDH directly relates to the energetic relationships, with electrostatic and H-bonding interactions between the anions, hydroxide sites of the metal hydroxide layers, and the interlayer water molecules. Distinct minima in the hydration energy indicate the presence of energetically well-defined structural states with specific water content. The experimentally identified variability in the retention of the CrO(4)(2-) and VO(4)(3-) is well reflected in the calculations and self-diffusion coefficients obtained from the simulations give insight into the mobility of the intercalated species.

Affinity capillary electrophoresis and quantum mechanical calculations applied to the investigation of hexaarylbenzene‐based receptor binding with lithium ion

In this study, two complementary approaches, affinity capillary electrophoresis (ACE) and quantum mechanical density functional theory (DFT) calculations, have been employed for quantitative characterization and structure elucidation of the complex between hexaarylbenzene (HAB)-based receptor R and lithium ion Li(+) . First, by means of ACE, the apparent binding constant of LiR(+) complex (K LiR +) in methanol was determined from the dependence of the effective electrophoretic mobilities of LiR(+) complex on the concentration of lithium ions in the 25 mM Tris/50 mM chloroacetate background electrolyte (BGE) using non-linear regression analysis. Prior to regression analysis, the effective electrophoretic mobilities of the LiR(+) complex were corrected to reference temperature 25 °C and constant ionic strength 25 mM. The apparent binding constant of the LiR(+) complex in the above methanolic BGE was evaluated as logK LiR + = 1.15±0.09. Second, the most probable structures of nonhydrated LiR(+) and hydrated LiR(+)·3H(2)O complexes were derived by DFT calculations. The optimized structure of the hydrated LiR(+)·3H(2)O complex was found to be more realistic than the nonhydrated LiR(+) complex because of the considerably higher binding energy of LiR(+)·3H(2)O complex (500.4 kJ/mol) as compared with LiR(+) complex (427.5 kJ/mol).

Oxide clusters as source of the third oxygen atom for the formation of carbonates in alkaline earth dehydrated zeolites

In our paper, we show that carbonates can be formed with almost no energetic barrier from CO 2 and metal-oxide binuclear MO X M species (M = Mg, Ca, Sr, Ba, with X = 1–4, depending on the cation) in alkaline earth zeolites, mordenite (MOR) and phillipsite (PHI), on the basis of quantum mechanical density functional theory (DFT) calculations at both isolated cluster and 3D periodic levels. The participation of MO X M species ( X = 1 and 3) explains the source of the third O atom in CO 3 species in dehydrated zeolites, on the basis of a good agreement between the calculated and experimental positions of the asymmetric and symmetric CO 3 vibration bands, of the ratio of their intensities, and of the weak dependence versus the cation and framework type. The reaction of formation of dimethylcarbonate from CaCO 3Ca in the 8-membered (8R) ring of MOR and methanol has also been considered, suggesting the carbonate activity as the source of CO 2 at elevated temperatures.

Impact of Chemical Impurities on the Crystalline Cement Clinker Phases Determined by Atomistic Simulations

The presence of chemical substitutions is believed to play a crucial role in the hydration reactions, structure, and elastic properties of cement clinker phases. Hence, substitutions are of great technological interest, as more efficient production of cement clinkers would result in a reduction of CO2 emissions, as well as possible economic benefits. Here we use a combination of classical and quantum mechanical simulation methods to study the detailed physicochemical changes of the clinker phases alite (Ca3SiO5) and belite (Ca2SiO4) when Mg2+, Al3+ and Fe3+ guest ions are incorporated into their structure. Using classical force field methods, we considered random substitutions among possible sites and different compositions in order to identify the preferential substitution sites on the crystalline structures. Then, the resulting structural changes that take place to accommodate the guest ions are investigated and discussed in detail. Using quantum mechanical density functional theory calculations the ele...

Parameter estimation by Density Functional Theory for a lattice-gas model of Br and Cl chemisorption on Ag (1 0 0)

We study Bromine and Chlorine chemisorption on a Ag (1 0 0) surface, using a lattice-gas model and the quantum-mechanical Density Functional Theory (DFT) method. In this model the Br and Cl ions adsorb at the fourfold hollow sites of the Ag (1 0 0) surface, which can be represented by a square lattice of adsorption sites. Five different coverages were used for each kind of adsorbate. For each adsorbate and coverage, we obtained the minimum-energy configuration, its energy, and its charge distribution. From these data we calculated dipole moments, lateral interaction energies, and binding energies. Our results show that for Br the lateral interactions obtained by fitting to the adsorption energies obtained from the DFT calculation are consistent with long-range dipole–dipole lateral interactions obtained using the dipole moments calculated from the DFT charge distribution. For Cl we found that, while the long-range dipole–dipole lateral interactions are important, short-range attractive interactions are also present. Our results are overall consistent with parameter estimates previously obtained by fitting room-temperature Monte Carlo simulations to electrochemical adsorption isotherms [I. Abou Hamad, et al., J. Electroanal. Chem. 554 (2003) 211; Electrochim. Acta 50 (2005) 5518].

Zinc(II) and PPi Selective Fluorescence OFF–ON–OFF Functionality of a Chemosensor in Physiological Conditions

A fluorescent chemosensor based on a quinoline derivative, L(2) (OFF state), selectively senses Zn(2+) by effective chelate-enhanced fluorescence (ON state), which further shows selectivity toward PPi over competing anions like Pi, AMP, and ATP via fluorescence quenching (OFF state) in a 100% aqueous HEPES buffer (pH 7.4). A plausible mode for the selective binding of PPi to 1 has been demonstrated by quantum mechanical density functional theory calculations and high-resolution mass spectrometry analysis.