Theoretical DFT Study on the Mechanisms of CO/CO2 Conversion in Chemical Looping Catalyzed by Calcium Ferrite.

The CO/CO2 conversion mechanism on the calcium ferrite (CFO) surface in chemical looping was explored by a computational study using the density functional theory approach. The CFO catalytic reaction pathway of 2CO + O2 → 2CO2 conversion has been elucidated. Our results show that the Fe center in CFO plays the key role as a catalyst in the CO/CO2 conversion. Two energetically stable spin states of CFO, quintet and septet, serve as the effective catalysts. The presence of the triplet O2 molecule caused the conversion of these two spin-state structures into each other along the catalytic reaction pathway. A double release of CO2 was predicted following this reaction mechanism. The rate-determining step is the formation of the 2CO2-CFO complex (P4) in the quintet state (19.0 kcal/mol). The predicted energy barriers for all the steps suggest that the proposed pathway is plausible.

Single site Fe on the (110) surface of γ-Al2O3: insights from a DFT study including the periodic boundary approach.

Examination of the stable (110) surface of γ-alumina reveals that there are three different types of sites available to host a single Fe atom. With the carefully calibrated density functional approach (M12-L/SV), three types of Fe single sites on the (110) surface of γ-alumina have been investigated under the periodic boundary conditions. The most stable Fe replacement site on the (110) surface of γ-alumina has been found to be represented by the tri-coordinated FeI position with the quartet spin state. The replacement of Al by Fe atoms at the Al site leads to charge redistributions of the neighboring O atoms. However, sublayer charge distribution is less affected. A significant contribution of p orbitals of the O atoms in the surface phase to the LUMO has been found for the tri-coordinated FeI substitution on the (110) surface. The corresponding oxygen atoms (OA and OA1) have been activated due to the existence of FeI in their neighborhood. The loosened neighboring AlIII-OA bonds match this activation. This activation of O suggests the existence of an important source of the reactive O during the Fe catalytic oxidation of CO processes.

The crucial roles of guest water in a biocompatible coordination network in the catalytic ring-opening polymerization of cyclic esters: a new mechanistic perspective.

The ring-opening polymerization (ROP) of cyclic esters/carbonates is a crucial approach for the synthesis of biocompatible and biodegradable polyesters. Even though numerous efficient ROP catalysts have been well established, their toxicity heavily limits the biomedical applications of polyester products. To solve the toxicity issues relating to ROP catalysts, we report herein a biocompatible coordination network, CZU-1, consisting of Zn4(µ4-O)(COO)6 secondary building units (SBUs), biomedicine-relevant organic linkers and guest water, which demonstrates high potential for use in the catalytic ROP synthesis of biomedicine-applicable polyesters. Both experimental and computational results reveal that the guest water in CZU-1 plays crucial roles in the activation of the Zn4(µ4-O)(COO)6 SBUs by generating µ4-OH Brønsted acid centers and Zn-OH Lewis acid centers, having a synergistic effect on the catalytic ROP of cyclic esters. Different to the mechanism reported in the literature, we propose a new reaction pathway for the catalytic ROP reaction, which has been confirmed using density functional theory (DFT) calculations, in situ diffuse reflectance IR Fourier transform spectroscopy (DRIFTS), and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF MS). Additionally, the hydroxyl end groups allow the polyester products to be easily post-modified with different functional moieties to tune their properties for practical applications. We particularly expect that the proposed catalytic ROP mechanism and the developed catalyst design principle will be generally applicable for the controlled synthesis of biomedicine-applicable polymeric materials.

Structure and Energetics of (111) Surface of γ-Al2O3: Insights from DFT Including Periodic Boundary Approach.

The (111) surface of γ-alumina has been reexamined, and a new (111) surface model has been suggested. The local structure of this new surface of γ-alumina, (111)n, has been optimized by the density functionals along with the full electron basis sets by using periodic boundary condition. This newly modeled (111)n surface is characterized by the same stability as that of the (110) surface, and its surface energy amounts to 2.561 J/m2, only about 0.002 J/m2 larger than that of (110). Three different types of the tricoordinated Al centers have been identified on (111)n. Molecular orbital (MO) analysis and the population analysis demonstrate that one type of Al, Al(I), is a nonpaired electron center. The singly occupied MO on Al(I) center is expected to play an important role in the catalytic activities of the γ-alumina. Moreover, the neighboring Al (Al(III)) on the (111)n surface provides suitable acceptance position for the electron donating groups. The defected surfaces of (111)n are found to be having a similar stability. The detachment of Al(I) from the (111)n surface results in disappearance of the nonpaired electron centers. Meanwhile, the attachment of Al(I) on (111)n surface will produce rich nonpaired electron centers on this new surface. Therefore, this newly defined surface is expected to attract the research interests in the catalytic activities of γ-alumina.

A mixed-valence metallogrid [CoCo] with an unusual electronic structure and single-ion-magnet characterization.

The reaction of the multisite coordination ligand (H2L) with Co(Ac)2·4H2O in the absence of any base affords a homometallic tetranuclear mixed-valence complex, [Co4(L)4(CH3CO2)2(CH3OH)2]·Et2O (1). This mixed-valence metallogrid [Co4(L)4(CH3CO2)2 (CH3OH)2]·Et2O (1) has been theoretically and experimentally analyzed to assign the valence and spin state in the form of trans-[Co-Co-Co-Co]. HF-EPR reveals the presence of axial anisotropy (D = -34.4 cm-1) with a significant transverse component (E = 9.5 cm-1) in the local high spin cobalt centers. Slow magnetic relaxation effects were observed in the presence of a dc field, demonstrating field-induced single ion magnetic behavior, which is associated with the unusual electronic structure of Co(ii) within the metallogrid.

Electron interaction with a DNA duplex: dCpdC:dGpdG.

Electron attachment to double-stranded cytosine-rich DNA, dCpdC:dGpdG, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 eV. The excess electron may reside on the nucleobase at the 5' position (dC˙(-)pdC:dGpdG) or at the 3' position (dCpdC˙(-):dGpdG). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dC1H˙pdC:dG2-H(-)pdG and dCpdC2H˙:dGpdG1-H(-). These distonic radical anions are found to be approximately 1 to 4 kcal mol(-1) more stable than the normal radical anions. Intra-strand cytosine π→π transition energies are below the electron detachment energy. Inter-strand π→π transitions of the excess electron from C to G are predicted to be less than 2.79 eV. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex.

A copper-based layered coordination polymer: synthesis, magnetic properties and electrochemical performance in supercapacitors.

A copper-based layered coordination polymer ([Cu(hmt)(tfbdc)(H2O)]; hmt = hexamethylenetetramine, tfbdc = 2,3,5,6-tetrafluoroterephthalate; Cu-LCP) has been synthesized, and it has been structurally and magnetically characterized. The Cu-LCP shows ferromagnetic interactions between the adjacent copper(II) ions. Density functional theory calculations on the special model of Cu-LCP support the occurrence of ferromagnetic interactions. As an electrode material for supercapacitors, Cu-LCP exhibits a high specific capacitance of 1274 F g(-1) at a current density of 1 A g(-1) in 1 M LiOH electrolyte, and the capacitance retention is about 88% after 2000 cycles.

Photoinduced electron detachment and proton transfer: the proposal for alternative path of formation of triplet states of guanine (G) and cytosine (C) pair.

A viable pathway is proposed for the formation of the triplet state of the GC Watson-Crick base pair. It includes the following steps: (a) a low-energy electron is captured by cytosine in the GC pair, forming the cytosine base-centered radical anion GC(-•); and (b) photoradiation with energy around 5 eV initiates the electron detachment from either cytosine (in the gas phase) or guanine (in aqueous solutions). This triggers interbase proton transfer from G to C, creating the triplet state of the GC pair. Double proton transfer involving the triplet state of GC pair leads to the formation of less stable tautomer G(N2-H)(•)C(O2H)(•). Tautomerization is accomplished through a double proton transfer process in which one proton at the N3 of C(H)(•) migrates to the N1 of G(-H)(•); meanwhile, the proton at the N2 of G transfers to the O2 of C. This process is energetically viable; the corresponding activation energy is around 12-13 kcal/mol. The base-pairing energy of the triplet is found to be ∼3-5 kcal/mol smaller than that of the singlet state. Thus, the formation of the triplet state GC pair in DNA double strand only slightly weakens its stability. The obtained highly reactive radicals are expected to cause serious damage in the DNA involved in biochemical processes, such as DNA replication where radicals are exposed in the single strands.

Electron interaction with phosphate cytidine oligomer dCpdC: base-centered radical anions and their electronic spectra.

Computational chemistry approach was applied to explore the nature of electron attachment to cytosine-rich DNA single strands. An oligomer dinucleoside phosphate deoxycytidylyl-3',5'-deoxycytidine (dCpdC) was selected as a model system for investigations by density functional theory. Electron distribution patterns for the radical anions of dCpdC in aqueous solution were explored. The excess electron may reside on the nucleobase at the 5' position (dC(•-)pdC) or at the 3' position (dCpdC(•-)). From comparison with electron attachment to the cytosine related DNA fragments, the electron affinity for the formation of the cytosine-centered radical anion in DNA is estimated to be around 2.2 eV. Electron attachment to cytosine sites in DNA single strands might cause perturbations of local structural characteristics. Visible absorption spectroscopy may be applied to validate computational results and determine experimentally the existence of the base-centered radical anion. The time-dependent DFT study shows the absorption around 550-600 nm for the cytosine-centered radical anions of DNA oligomers. This indicates that if such species are detected experimentally they would be characterized by a distinctive color.

Spin-orbit corrected potential energy surface features for the I ((2)P(3/2)) + H2O → HI + OH forward and reverse reactions.

Using the CCSD(T) method with relativistic correlation consistent basis sets up to cc-pVQZ-PP, the entrance complex, transition state, and exit complex for the endothermic reaction I + H2O → HI + OH have been studied. The vibrational frequencies and the zero-point vibrational energies of the five stationary points for the title reaction are reported and compared with the limited available experimental results. Opposite to the valence isoelectronic F + H2O system, but similar to the Cl + H2O and Br + H2O reactions, the I + H2O reaction is endothermic, in this case by 46 kcal mol(-1). After the zero-point vibrational energy and spin-orbit coupling corrections, the endothermic reaction energy is predicted to be 48 kcal mol(-1), which agrees well with experimental values. For the reverse reaction HI + OH → I + H2O the transition state lies below the reactants, consistent with the experimental negative temperature dependence for the rate constants.

Benchmarking the Electron Affinity of Uracil.

The Weizmann Bruecker doubles composite method W1BD has been applied in a benchmark study of electron attachment to the nucleobase uracil. The largest computations involved the BD method with a basis set of 760 contracted Gaussian functions, namely augh-cc-pVQZ+2df. The predictions demonstrate that the adiabatic electron affinity (AEA) of uracil is definitely positive. The most relable value for the AEA of uracil should be 0.024 ± 0.013 eV. Other high level methods such as CASPT2 and G4 theory also predict the AEA of uracil with reasonable accuracy. Both the Hartree-Fock and MP2 approaches severely underestimate the AEA. The latter two methods are not recommended for the study of electron attachment to the DNA/RNA bases. On the other hand, some commonly used Density functional theory approaches, especially, M06-2X, are promising candidates for the study of electron-DNA/RNA interactions.

How Small Can a Catenane Be?

Catenanes are playing an increasingly important role in supramolecular chemistry. In attempting to identify the minimum number of carbon atoms in a viable catenane, the B3LYP, BP86, M06-2X, MM3, and MM4 methods were applied to study representative [2]catenane models, which consist of two mechanically interlocked saturated n-cycloalkanes ([CnH2n]2). The structures, energy variations, and electron density differences vary nearly monotonically from n = 18 to 11. For example, the B3LYP/DZP++ dissociation energies [CnH2n]2 → 2CnH2n are 101, 121, 159, 191, 222, 252, 290, and 323 kcal/mol from n = 18 to 11, respectively. However, there is much variation among the energetic predictions with the B3LYP, BP86, M06-2X, MM3, and MM4 methods. The distances of the longest C-C single bond in each catenane are 1.593 (n = 18), 1.604 (n = 17), 1.631 (n = 16), 1.640 (n = 15), 1.667 (n = 14), 1.669 (n = 13), 1.680 (n = 12), and 1.689 Š(n = 11). These results display something of a shoulder in the vicinity of n = 14. This may suggest that [C15H30]2 is the smallest catenane that will resist fragmentation under specified laboratory conditions.

From formamide to adenine: a self-catalytic mechanism for an abiotic approach.

Mechanisms for abiotic reaction pathways from formamide (H2NCHO) to adenine are presented herein. Formamide is a simple C1 building block hypothesized to be a precursor to many protometabolic compounds. On the basis of a step-by-step mechanism of the reaction pathways, formamide is suggested to be more reactive in addition reactions than HCN. In addition to its simplicity, the formamide self-catalyzed mechanism is energetically (kinetically) more viable than either a water-catalyzed mechanism or noncatalyzed processes. Moreover, this self-catalyzed mechanism accounts for the yields of purine and adenine previously observed in experiments. This mechanism may elucidate processes that were vital for the emergence of life on the early earth.

From formamide to purine: a self-catalyzed reaction pathway provides a feasible mechanism for the entire process.

A formamide self-catalyzed mechanistic pathway that transforms formamide to purine through a five-membered ring intermediate has been explored by density functional theory calculations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest and lowest energy reaction pathway. All necessary reactants, including catalysts, are generated from a single initial compound, formamide. The most catalytically effective form of formamide is found to be the imidic acid isomer. The catalytic effect of formamide has been found to be much more significant than that of water. The self-catalytic mechanism revealed here provides a pathway with the lowest energy barriers among all reaction routes previously published. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-member ring-closing, and deamination. Overall, a five-membered ring-closing is the rate-determining step in the present catalytic route, which is consistent with our previous mechanistic investigations. The activation energy of this rate-controlling step (ca. 27 kcal/mol) is significantly lower than the rate-determining step (ca. 34 kcal/mol) in the pathway from 4-aminoimidazole-5-carboxamidine described by Schleyer's group (Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 17272-17277) and in the pyrimidine pathway (ca. 44 kcal/mol) reported by Sponer et al. (J. Phys. Chem. A 2012, 116, 720-726). The self-catalyzed mechanistic pathway reported herein is less energetically demanding than previously proposed routes.

From formamide to purine: an energetically viable mechanistic reaction pathway.

A step-by-step mechanistic pathway following the transformation of formamide to purine through a five-membered ring intermediate has been explored by density functional theory computations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest reaction pathway. All necessary reactants are generated from a single starting compound, formamide, through energetically viable reactions. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-membered ring-closure, and deamination. On the basis of the study of noncatalytic pathways, catalytic water has been found to provide energetically viable step-by-step mechanistic pathways. Among these reaction steps, five-member ring-closure is the rate-determining step. The energy barrier (ca. 42 kcal/mol) of this rate-control step is somewhat lower than the rate-determining step (ca. 44 kcal/mol) for a pyrimidine-based pathway reported previously. The mechanistic pathway reported herein is less energetically demanding than for previously proposed routes to adenine.

The electronic spectra and the H-bonding pattern of the sulfur and selenium substituted guanines.

The density functional theory (DFT) with B3LYP, M05-2x, and M06-2x functionals, along with the 6-311+G(d, p) basis set, were used in the study of the UV absorption spectra and the H-bonding pairing patterns of the sulfur and selenium substituted guanines. The time-dependent DFT calculations reveal that the red-shifts of the transition energies predicted for guanine for the first gas-phase observable transition amount to 55 nm for S6mG and 86 nm for Se6mG, respectively. These changes in the transition energies are qualitatively comparable to the experimental data for substituted guanines in DNA. The density deformation map reveals that both sulfur and selenium atoms exhibit lesser conjugated with the purine ring, which leads to the small transition energies in S6mG and Se6mG. The decrease in binding energy (3 kcal/mol) of Se6mGmC as compared to that of mGmC is well related to the observation of the melting temperature difference ΔT(m) ~3.9 °C for the Se-DNA versus DNA. The molecular recognition (mGmC pairing) pattern is found to be changed significantly due to the replacement of O6 by S or Se. The substantial base-base plane twisting revealed in this study suggests that the base stacking in the DNA might be interrupted. This study shows that the red-shifts of the transition energies predicted by the M05-2x and M06-2x functionals are close to those revealed by the B3LYP calculations. As M05-2x and M06-2x offer better descriptions for the dispersion interactions, they provide efficient approaches to investigate the influences of the base-stacking on the transition energies.

Isoguanine formation from adenine.

Several possible mechanisms underlying isoguanine formation when OH radical attacks the C(2) position of adenine (A C 2) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A C 2⋅⋅⋅OH reactant complexes is formed, leading to C(2)-H(2) bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG 1 or isoG 2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20 kcal mol(-1) , indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH(⋅) →isoG+H(⋅) reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG 1 has the lowest energy. Our findings explain why only the N(1)H and O(2)H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.

Could hydrolysis of arsenic substituted DNA be prevented? Protection arises from stacking interactions.

Investigation of the hydrolysis of dinucleoside-arsenate-deoxyguanylyl-3',5'-deoxyguanosine (dGAsdG(-)) reveals that base-stacking in DNA increases the resistance of As-DNA towards hydrolysis. Base-stacking raises the activation energy of hydrolysis. Hydrolysis of As-DNA is found to be endothermic. The hydrolysis stability of As-DNA should be higher than that estimated based on arsenate diester models.

Electron attachment to solvated dGpdG: effects of stacking on base-centered and phosphate-centered valence-bound radical anions.

To explore the nature of electron attachment to guanine-centered DNA single strands in the presence of a polarizable medium, a theoretical investigation of the DNA oligomer dinucleoside phosphate deoxyguanylyl-3',5'-deoxyguanosine (dGpdG) was performed by using density functional theory. Four different electron-distribution patterns for the radical anions of dGpdG in aqueous solution have been located as local minima on the potential energy surface. The excess electron is found to reside on the proton of the phosphate group (dGp(H-)dG), or on the phosphate group (dGp(.-)dG), or on the nucleobase at the 5' position (dG(.-)pdG), or on the nucleobase at the 3' position (dGpdG(.-)), respectively. These four radical anions are all expected to be electronically viable species under the influence of the polarizable medium. The predicted energetics of the radical anions follows the order dGp(.-)dG>dG(.-)pdG>dGpdG(.-)>dGp(H-)dG. The base-base stacking pattern in DNA single strands seems unaffected by electron attachment. On the contrary, intrastrand H-bonding is greatly influenced by electron attachment, especially in the formation of base-centered radical anions. The intrastrand H-bonding patterns revealed in this study also suggest that intrastrand proton transfer might be possible between successive guanines due to electron attachment to DNA single strands.