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

The CO/CO 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 + O → 2CO conversion has been elucidated. Our results show that the Fe center in CFO plays the key role as a catalyst in the CO/CO conversion.

Single site Fe on the (110) surface of γ-AlO: 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 Fe position with the quartet spin state.

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 Zn(μ-O)(COO) 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.

Structure and Energetics of (111) Surface of γ-AlO: 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), has been optimized by the density functionals along with the full electron basis sets by using periodic boundary condition. This newly modeled (111) surface is characterized by the same stability as that of the (110) surface, and its surface energy amounts to 2.

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

The reaction of the multisite coordination ligand (HL) with Co(Ac)·4HO in the absence of any base affords a homometallic tetranuclear mixed-valence complex, [Co(L)(CHCO)(CHOH)]·EtO (1). This mixed-valence metallogrid [Co(L)(CHCO) (CHOH)]·EtO (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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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(.

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.

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.

Structural and electronic property responses to the arsenic/phosphorus exchange in GC-related DNA of the B-form.

The suggestion that phosphorus/arsenic replacement in DNA can play a role in living things has generated great controversy (Wolfe-Simon et al., Science 2011, 332, 1163). Examined here theoretically are substitution effects on Watson-Crick base pairing and base stacking patterns in realistic DNA subunits.

Electron attachment to the cytosine-centered DNA single strands: does base stacking matter?

Electron attachment to the trimer of nucleotide, dGpdCpdG, has been investigated by a quantum mechanical approach at a reliable level of theory. The study of the electron attached dGpdCpdG species demonstrates that cytosine contained DNA single strands have a strong tendency to capture low-energy electrons and to form electronically stable cytosine-centered radical anions. The comparative study of the model molecules pdCpdG and dGpdCp reveals that base stacking has little contribution to the adiabatic electron affinity (AEA) of cytosine in DNA single strands.

Low energy electron attachment to the adenosine site of DNA.

To evaluate the role of adenosine in low energy electron (LEE) induced DNA strand breaks, theoretical investigations of the LEE attachment induced C-O σ bonds and N-glycosidic bond breaking of 2'-deoxyadenosine-3',5'-diphosphate (3',5'-dAMP) were performed at the B3LYP/DZP++ level of theory. The results indicate that, although adenine-rich oligonucleotides are capable of capturing the near 0 eV electron to form the electronically stable radical anions in the gas phase, it is unlikely to undergo either C-O σ bond cleavage or the glycosidic processes due to the low electron detachment energy (VDE) of 3',5'-dADP(-) unit (0.26 eV).

The electronic spectra of the sandwich stacked PFBT: a theoretical study.

Stacked models that include 9,9'-bis(6''-N,N,N-trimethylammonium)hexyl]fluorene-co-alt-4,7-(2,1,3-benzothiadiazole)dibromide (F(BT)F) monomer sandwiched between two stacked 2,1,3-benzothiadiazole (BT) units were explored using theoretical approaches. Molecular structures and the optical characteristics of the investigated species were investigated at the M06-2X/6-311G(d,p)//TD-M06-2X/6-311G(d,p) level of theory. In all models, the electronic excitation to the lowest singlet ππ* excited state (S1(ππ*)) is governed by the highest occupied molecular orbital to lowest unoccupied molecular orbital (HOMO → LUMO) transitions.

Exploring a reaction mechanism for acetato ligand replacement in paddlewheel tetrakisacetatodirhodium (II,II) complex by ammonia: computational density functional theory study.

This study focuses on the first step of interaction between DNA and the paddle-wheel dirhodium complex. The ammonia molecule was used to model the oligonucleotide sequence. The reaction was considered in neutral and acidic conditions, in gas phase, and in solvent, using the COSMO model.