Interaction of adenine adducts with thymine: a computational study

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions. The differences in their geometrical structures, energetic properties, and hydrogen-bonding strengths have also been compared with Watson-Crick adenine-thymine base pair (A-T). Single-point energy calculations at MP2/6-311++G** levels on B3LYP/6-31+G* optimized geometries have also been carried out to better estimate the hydrogen-bonding strengths. The basis set superposition error corrected hydrogen-bonding strength sequence at MP2/6-311++G**//B3LYP/6-31+G* for the most stable complexes is found to be EA(2)-T(I) (15.30 kcal/mol) > EA(1)-T(II) (14.98 kcal/mol) > EA(3)-T(II) (14.68 kcal/mol) > epsilonA(2)-T(I) (14.54 kcal/mol) > epsilonA(3)-T(II) (14.22 kcal/mol) > epsilonA(3)-T(II) (13.64 kcal/mol) > A-T (13.62 kcal/mol). The calculated reaction enthalpy value for epsilonA(2)-T(I) is 10.05 kcal/mol, which is the highest among the etheno adduct-thymine complexes and about 1.55 kcal/mol more than those obtained for Watson-Crick A-T base pair and the reaction enthalpy value for EA(1)- T(II) is 10.22 kcal/mol, which is highest among the ethano addcut-thymine complexes and about 1.72 kcal/mol more than those obtained for Watson-Crick A-T base pair. The aim of this research is to provide fundamental understanding of adenine adduct and thymine interaction at the molecular level and to aid in future experimental studies toward finding the possible cause of DNA damage.     

Interaction of molecular hydrogen with open transition metal centers for enhanced binding in metal-organic frameworks: a computational study

Molecular hydrogen is known to form stable, "nonclassical" sigma complexes with transition metal centers that are stabilized by donor-acceptor interactions and electrostatics. In this computational study, we establish that strong H2 sorption sites can be obtained in metal-organic frameworks by incorporating open transition metal sites on the organic linkers. Using density functional theory and energy decomposition analysis, we investigate the nature and characteristics of the H2 interaction with models of exposed open metal binding sites {half-sandwich piano-stool shaped complexes of the form (Arene)ML(3- n)(H2)n [M=Cr, Mo, V(-), Mn(+); Arene = C6H5X (X=H, F, Cl, OCH3, NH2, CH3, CF3) or C6H3Y2X (Y=COOH, X=CF3, Cl; L=CO; n=1-3]}. The metal-H2 bond dissociation energy of the studied complexes is calculated to be between 48 and 84 kJ/mol, based on the introduction of arene substituents, changes to the metal core, and of charge-balancing ligands. Thus, design of the binding site controls the H2 binding affinity and could be potentially used to control the magnitude of the H2 interaction energy to achieve reversible sorption characteristics at ambient conditions. Energy decomposition analysis illuminates both the possibilities and present challenges associated with rational materials design.     

Quantum mechanical approach to the chemisorption of molecular hydrogen on defect magnesium oxide surfaces

Quantum mechanical theoretical calculations have been performed on the linear atomic chain in order to simulate the interaction of molecular hydrogen with the defects present at the surface of activated MgO. The total energy of the system, the relative energy of the various molecular orbitals, and the electronic charge distribution have been computed for various lattice parameters (d _O-O = 4.0–4.8 Å) as a function of the H-H (or O-H) separation. A symmetrical motion of the hydrogen nuclei with respect to the central Mg²⁺ vacancy was assumed. It is shown that chemisorption of hydrogen on surface O^–ions sites results in the formation of pseudo-hydroxyl groups. For a small lattice parameter (4.0 Å), no stable state of molecular hydrogen has been found while an increase in the lattice parameter results in a uniform increase of the calculated activation energy for the molecular hydrogen activation process. A mechanism is proposed which is not so different from that put forward for the hydrogen activation by transition metal complexes. Molecular hydrogen is found to act as an electron donor.     

Kinetic adsorption energy distributions of rough surfaces: a computational study

The adsorption energy distribution usually refers to localized monolayers of adsorbate at thermodynamic equilibrium. Many papers have been published that analyze its influence on adsorption isotherms, heats of adsorption, and adsorption kinetics. However, the adsorption energy distribution, in its classical thermodynamic equilibrium sense, may be not as useful as expected. This is because many important processes involving adsorption have dynamic character and reactant particles have a finite time for penetration of the adsorbent. The above suggests that some adsorption centers located in less accessible fragments of the surface can be invisible in a dynamic process. However, under conditions allowing the thermodynamic equilibrium such adsorption centers could noticeably contribute to the adsorption energy distribution. The aim of this work is to measure the adsorption energy distributions of special rough surfaces using a dynamic method. This method is based on the molecular dynamics simulation of an ideal gas flowing over a sample surface. The ideal gas particles penetrate the surface, and at the moment of collision of a gas particle with the surface the Lennard-Jones potential energy is calculated. This energy can be identified with the adsorption energy at a given point on the surface. The surfaces used in the calculations have been created using two surface growth models (i.e., random deposition and ballistic deposition). The application of these highly disordered surfaces enables us to draw some general conclusions about the properties of real surfaces that are usually far from any deterministic geometry.     

Interaction of hydrogen with surfaces of silicates: single crystal vs. amorphous

We have studied how the formation of molecular hydrogen on silicates at low temperature is influenced by surface morphology. At low temperature (<30 K), the formation of molecular hydrogen occurs chiefly through weak physical adsorption processes. Morphology then plays a role in facilitating or hindering the formation of molecular hydrogen. We studied the formation of molecular hydrogen on a single crystal forsterite and on thin films of amorphous silicate of general composition (Fe(x)Mg((x-1)))(2)SiO(4), 0 < x < 1. The samples were studied ex situ by Atom Force Microscopy (AFM), and in situ using Thermal Programmed Desorption (TPD). The data were analysed using a rate equation model. The main outcome of the experiments is that TPD features of HD desorbing from an amorphous silicate after its formation are much wider than the ones from a single crystal; correspondingly typical energy barriers for diffusion and desorption of H, H(2) are larger as well. The results of our model can be used in chemical evolution codes of space environments, where both amorphous and crystalline silicates have been detected.     

Reactivity of hydrogen species on oxide surfaces

Hydrogen species on oxides are widely involved in oxides-catalyzed reactions such as H_2/hydrocarbon oxidation, hydrogenation/dehydrogenation, water-gas shift, and water-splitting reactions. Thus identifications of hydrogen species on oxide surfaces and their reactivity are important for fundamental understanding of these oxides-catalyzed reactions. In this Feature Article, we briefly review our research progress on the reactivity of various hydrogen species on oxides, including surface hydroxyl species,hydride species and hydrated protons. We have successfully developed effective strategies of using gas-phase atomic H to controllably create oxygen vacancies and prepare various hydrogen species on oxide model catalysts under ultra-high vacuum(UHV) conditions and using well-defined oxide nanocrystals with different surface structures and oxygen vacancy concentrations to study the H_2-oxide interaction under ambient or even higher H_2 pressures. Reactivity of various hydrogen species on oxide surfaces has been identified, including local oxygen vacancy-controlled reactivity of OH species, oxygen vacancystabilized hydride species, homolytic dissociation of H2 at oxygen vacancies of reduced oxide surfaces into hydride species accompanied by surface oxidation, photoexcited holes-stimulated desorption of hydride species, electron-stimulated desorption of hydride and OH species, and photoexcited electrons-stimulated desorption of hydrated protons. Strong influences of oxygen vacancies in oxides on both stability and reactivity of various hydrogen species on oxide surfaces are highlighted.     

Understanding hydrogen adsorption in metal-organic frameworks with open metal sites: a computational study

Recent experimental investigations show that the open metal sites may have a favorable impact on the hydrogen adsorption capacity of metal-organic frameworks (MOFs); however, no definite evidence has been obtained to date and little is known on the interactions between hydrogen and the pore walls of this kind of MOFs. In this work, a combined grand canonical Monte Carlo simulation and density functional theory calculation is performed on the adsorption of hydrogen in MOF-505, a recently synthesized MOF with open metal sites, to provide insight into molecular-level details of the underlying mechanisms. This work shows that metal-oxygen clusters are preferential adsorption sites for hydrogen, and the strongest adsorption of hydrogen is found in the directions of coordinatively unsaturated open metal sites, providing evidence that the open metal sites have a favorable impact on the hydrogen sorption capacity of MOFs. The storage capacity of hydrogen of MOF-505 at room temperature and moderate pressures is predicted to be low, in agreement with the outcome for hydrogen physisorption in other porous materials.     

Sonochemical synthesis of cerium oxide nanoparticles-effect of additives and quantum size effect

Cerium oxide (CeO(2)) nanoparticles were prepared sonochemically, by using cerium nitrate and azodicarbonamide as starting materials, and ethylenediamine or tetraalkylammonium hydroxide as additives. The additives have a strong effect on the particle size and particle size distribution. CeO(2) nanoparticles with small particle size and narrow particle size distribution are obtained with the addition of additives; while highly agglomerated CeO(2) nanoparticles are obtained in the absence of additives. Monodispersed CeO(2) nanoparticles with a mean particle size of ca. 3.3 nm are obtained when tetramethylammonium hydroxide (TMAOH) is used as the additive and the molar ratio of cerium nitrate/azodicarbonamine/TMAOH is 1/1/1. Blue shifts of the absorption peak and the absorption edges of the products are observed in the UV-Vis absorption spectra as a result of the quantum size effect. The samples have been characterized using powder XRD, TEM, DLS, and absorption spectra.     

The catalytic activity of proline racemase: a quantum mechanical/molecular mechanical study

The enzyme proline racemase from the eukaryotic parasite Trypanosoma cruzi (responsible for endemic Chagas disease) catalyzes the reversible stereoinversion of chiral Calpha in proline. We employed a new combined quantum mechanical and molecular mechanical (QM/MM) potential to study the reaction mechanism of the enzyme. Three critical points were found: two almost isoenergetic minima (M1a and M2a), in which the enzyme is bound to L- and D-Pro, respectively, and a transition state (TSCa), unveiling a highly asynchronous concerted process. A systematic analysis was performed on the optimized geometries to point out the key role played by some residues in stabilizing the transition state.     

Interaction of atomic hydrogen with single-walled carbon nanotubes: a density functional theory study

We have studied the interaction of atomic hydrogen with (5,5) and (10,0) single-walled carbon nanotubes (SWNT) using density functional theory. These calculations use Gaussian orbitals and periodic boundary conditions. We compare results from the local spin density approximation, generalized gradient approximation (GGA), and hybrid density functionals. We have first kept the SWNT geometric structure fixed while a single H atom approaches the tube on top of a carbon atom. In that case, a weakly bound state with binding energies from -0.8 to -0.4 eV was found. Full geometry relaxation leads to a strong SWNT deformation, weakening the nearest C-C bonds and increasing the binding energy by about 1 eV. Full hydrogen coverage of the (5,5) SWNT converts this metallic nanotube into an insulator with a band gap of 3.4 eV for the GGA functional and 4.8 eV for the hybrid functional. Hybrid functionals perform similar to pure density functional theory functionals for the calculation of binding energies while band gaps critically depend on the functional choice.     

Interaction of oxide surfaces with water: environmental transmission electron microscopy of MgO hydroxylation.

Environmental transmission electron microscopy (ETEM) is opening an important window for in situ studies of interaction of water with oxides. Studies of MgO smoke nanocrystals under partial pressures of water ranging from 10 mTorr to 10 Torr found their {100} neutral surfaces to be extremely resistant to dissociative adsorption of water and hydroxylation, in agreement with recent theoretical predictions. ETEM observations of electron irradiation driven MgO smoke nanocrystal hydroxylation displayed the anticipated volume expansion, but revealed complex shape changes with elongations toward oxide corners. The reaction rate was found to increase with electron flux at constant water pressure. In situ selected area diffraction studies of MgO single crystals showed that the hydroxide grows with its basal (0001) plane parallel to the polar MgO (111) planes. This is the same crystallographic relationship as in dehydroxylation experiments, but with four variants. Electron energy loss spectroscopy found oxygen K-edge changes consistent with bulk hydroxylation.     

Nitric oxide binding to ferric cytochrome P450: a computational study

The interaction between nitric oxide (NO) and the active site of ferric cytochrome P450 was studied by means of density functional theory (DFT), at the generalized gradient approximation level, and of the SAM1 semiempirical method. The electrostatic effects of the protein environment were included in our DFT scheme by using a hybrid quantum classical approach. The active-site model consisted of an iron(III) porphyrin, the adjacent cysteine residue, and one coordinated water molecule. For this system, spin populations and relative energies for selected spin states were computed. Interestingly, the unpaired electron density, the HOMO, and the LUMO were found to be highly localized on the iron and in an appreciable extent on the sulfur coordinated to the metal. This provides central information about the reactivity of nitric oxide with the active site. Since the substitution of a molecule of H2O by NO has been proposed as being responsible for the inhibition of the cytochrome in the presence of nitric oxide, we have analyzed the thermodynamic feasibility of the ligand exchange process. The structure of the nitrosylated active site was partially optimized using SAM1. A low-spin ground state was obtained for the nitrosyl complex, with a linear Fe-N-O angle. The trends found in Fe-N-O angles and Fe-N lengths of the higher energy spin states provided a notable insight into the electronic configuration of the complex within the framework of the Enemark and Feltham formalism. In relation to the protein environment, it was assessed that the electrostatic field has significant effects on several computed properties. However, in both vacuum and protein environments, the ligand exchange reaction turned out to be exergonic and the relative orders of spin states of the relevant species were the same.     

A quantum mechanical study of the reactivity of (SiO)2-defective silica surfaces

The reactivity of the strained (SiO)(2)-four atom ring defect at the silica surfaces has been studied in a cluster approach adopting the ONIOM2[B3LYP6-31+G(d,p):MNDO] method to compute the ring opening reaction by interaction with H(2)O and NH(3). The vibrational "fingerprints" of the isolated defect are computed at 921, 930, and 934 cm(-1) in reasonable agreement with experimental evidence on amorphous silica outgassed at T>900 K. The opening of the (SiO)(2)-four-member ring by the considered molecules is exergonic and the actual value depends on the possible constraints enforced on the reaction products by the silica surrounding. The free kinetic energy barriers result from the interplay between the nucleophilic/electrophilic character of the adsorbed molecule and are 22 and 25 kcal mol(-1) for NH(3) and H(2)O, respectively. All free energy profiles envisage an activated complex in which the nucleophilic part of the molecule interacts on the coordinatively strained silicon atom of the (SiO)(2) defect followed by the proton transfer from the coordinated molecule towards the oxygen of the defective ring. Calculations show that this step can be speed up by the presence of more than one adsorbed molecule or even more (about seven orders of magnitude), by the copresence of water molecules acting as "proton transfer helpers." In these cases, the free energy barriers decrease to approximately 13 and 15 kcal mol(-1) for NH(3) and H(2)O, respectively. For the case of H(2)O adsorption, benchmark test calculations reveal that MP2, BLYP, and B3LYP energy profiles are in very good agreement with each other, whereas for PBE, both the reaction energy and the activation barrier are underestimated. Present data also show that the molecular model mimicking the (SiO)(2) defect is far less reactive than what appears to occur on the real defect at the surface of amorphous silica. So, only a combination of some further geometrical strains imparted by the solid on the (SiO)(2) defect, not accounted for by the cluster models, and higher adsorbate loadings are needed to reharmonize experiment and simulation. Notwithstanding, the vibrational features of the reaction products have been characterized and support the available experimental measurements.     

The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.     

Interaction of uranyl ion with few molecules of water: thought (computational) scenarios with hydrogen bonding motif

The interaction of the uranyl ion $\hbox{UO}_{2}^{2+}$ with one, two and three molecules of water is computationally modeled. It is demonstrated that the dihydration potential energy surface of $\hbox{UO}_{2}^{2+}$ is partitioned into two bonding regions which correspondingly determine the weak and strong regime of solvation: if the former describes the traditional filling of the first solvation shell, the latter develops, via the hydrogen bonding interaction, to the metastable complex [UO₂(OH)]⁺-H₃ O⁺ with a rather short lifetime. An addition of water molecule from infinity to its H₃ O⁺ side results in the formation of the Zundel cation and spontaneous dissociation into the latter and [UO₂(OH)]⁺. “…we are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation.” Joseph Louis Gay-Lussac Memoires de la Sociétè d’Arcueil 2, 207 (1808)¹      

Hydrogen abstraction from poly(propylene) and poly(propylene oxide) by hydroxyl radicals: a computational quantum semi-empirical study

The reaction of hydrogen abstraction by hydroxyl radicals on two substrates (poly(propylene) and poly(propylene oxide)) was studied using three quantum semi-empirical methods (MNDO, AM1, PM3). The calculations were performed as a function of the site of abstraction (hydrogen atom on a secondary or tertiary carbon atom), and of the calculation method. In each case, we localised the transition state and showed that this transition state occurs early along the reaction coordinate. The results concerning the activation energies depend on the sites and the calculation methods. The calculated results were compared to experimental ones.     

Conformational behaviour of phenylpyrimidines. a quantum mechanical study

The conformational behaviour of isomeric phenylpyrimidines has been studied by STO-3G ab-initio computations. The results show that the torsional angle between the two rings increases with the number of H-H v$\text{i}$cinal interactions and a planar equilibrium conformation is obtained only in the absence of these interactions (2-phenylpyrimidine). A Fourier expansion of the torsional potential suggests that the first two terms are sufficient for a good fitting, except in the case of two H-H interactions (5-phenylpyrimidine), where the second term dominates and the first and third terms are of the same order of magnitude.     

Adsorption of organic substances on broken clay surfaces: a quantum chemical study

Hydrogen-bonded interactions between local defect structures on broken clay surfaces modeled as molecular clusters and the organic molecules acetic acid, acetate, and N-methylacetamide (NMA) have been investigated. Density functional theory and polarized basis sets have been used for the computation of optimized interaction complexes and formation energies. The activity of the defect structures has been characterized as physical or chemical in terms of the strength of the hydrogen bonds formed. Chemical defects lead to significantly enhanced interactions with stronger hydrogen bonds and larger elongation of OH bonds in comparison to the physical defects. The type of interaction with the defect structure significantly influences the planarity of the model peptide bond in NMA. Both cases, enhancement of the planarity by increase of the CN double bond character and strong deviations from planarity, are observed.     

Molecular mechanical devices based on quinone-pyrrole and quinone-indole dyads: a computational study

A set of intramolecularly connected dyads consisting of a quinone unit and a pyrrole or indole moiety have been designed and evaluated in quantum-chemical calculations. It is shown computationally for several systems, depending on the length and attachment points of the interconnecting chains, that a reduction of the quinone to the semiquinone radical anion or quinolate dianion state leads to a reversible intramolecular reorientation from a pi-stacked to a T-stacked arrangement. In the rearranged structures, a hydrogen bond from the pyrrole or indole N-H function to the semiquinone or quinolate pi-system is created upon reduction. In some systems, hydrogen bonds to the semiquinone or quinolate oxygen atoms are partly feasible and will be preferred over T-stacking. The choice of systems has been based on recent computational observations related to photosystem I. Systems with pyrrole or indole units should provide a better basis for the envisioned molecular motor than recently proposed quinone-benzene dyads. The intramolecular interactions modify the quinone redox potentials. Electronic g-tensors have been computed for the semiquinone states. These reflect characteristically the presence and nature of hydrogen bonds to the semiquinone and represent suitable electron paramagnetic resonance spectroscopic probes for the preferred structures. Intramolecular proton transfer is possible in the dianionic state.     

Rearrangement and hydrogen scrambling pathways of the toluene radical cation: a computational study

A computational study is undertaken to provide a unified picture for various rearrangement reactions and hydrogen scrambling pathways of the toluene radical cation (1). The geometries are optimized with the BHandHLYP density functional, and the energies are computed with the ab initio CCSD(T) method, in conjunction with the 6-311+G(d,p) basis set. In particular, four channels have been located, which may account for hydrogen scrambling, as they are found to have overall barriers lower than the observed threshold for hydrogen dissociation. These are a stepwise norcaradiene walk involved in the Hoffman mechanism, a rearrangement of 1 to the methylenecyclohexadiene radical cation (5) by successive [1,2]-H shifts via isotoluene radical cations, a series of [1,2]-H shifts in the cycloheptatriene radical cation (4), and a concerted norcaradiene walk. In addition, we have also investigated other pathways such as the suggested Dewar-Landman mechanism, which proceeds through 5, via two consecutive [1,2]-H shifts. This pathway is, however, found to be inactive as it involves too high reaction barriers. Moreover, a novel rearrangement pathway that connects 5 to the norcaradiene radical cation (3) has also been located in this work.