Ab initio study of naphtho-homologated DNA bases

Naphtho-homologated DNA bases have been recently used to build a new type of size-expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naphtho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like forms of naphtho-thymine (yyT) and naphtho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naphtho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.     

A family of enneanuclear iron(II) single-molecule magnets

Complexes [Fe₉(X)₂(O₂CMe)₈{(2‐py)₂CO₂}₄] (X^?=OH^? ( 1 ), N₃^? ( 2 ), and NCO^? ( 3 )) have been prepared by a route previously employed for the synthesis of analogous Co₉ and Ni₉ complexes, involving hydroxide substitution by pseudohalides (N₃^?, NCO^?). As indicated by DC magnetic susceptibility measurements, this substitution induced higher ferromagnetic couplings in complexes 2 and 3 , leading to higher ground spin states compared to that of 1 . Variable‐field experiments have shown that the ground state is not well isolated from excited states, as a result of which it cannot be unambiguously determined. AC susceptometry has revealed out‐of‐phase signals, which suggests that these complexes exhibit a slow relaxation of magnetization that follows Arrhenius behavior, as observed in single‐molecule magnets, with energy barriers of 41 K for 2 (τ₀=3.4×10^?12 s) and 44 K for 3 (τ₀=2.0×10^?11 s). Slow magnetic relaxation has also been observed by zero‐field ⁵⁷Fe Mössbauer spectroscopy. Characteristic integer‐spin electron paramagnetic resonance (EPR) signals have been observed at X‐band for 1 , whereas 2 and 3 were found to be EPR‐silent at this frequency. ¹H NMR spectrometry in CD₃CN has shown that complexes 1 – 3 are stable in solution.     

Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian

The need to simulate large-sized molecules or to deal with large series of compounds is a challenging topic in computational chemistry, which has stimulated the development of accurate semiempirical methods, such as the recently reported Recife Model 1 (RM1; J Comput Chem 2006, 27, 1101). Even though RM1 may prove to be of value simply due to the enhanced quantitative accuracy in gas phase, it is unclear how the new parameters optimized for RM1 affect the suitability of this semiempirical Hamiltonian to study chemical processes in condensed phases. To address this question, we report the parametrization of the MST/RM1 continuum model for neutral solutes in water, octanol, chloroform and carbon tetrachloride, and for ions in water. The results are used to discuss the transferability of the solvation parameters implemented in previous MST/AM1 and MST/PM3 models.     

Microwave‐assisted synthesis of new regioisomeric 6,7‐dihydroindeno[1,2‐e]pyrimido[4,5‐b][1,4]diazepin‐5(5aH)‐ones

Novel 11‐amino‐6‐aryl‐6,7‐dihydroindeno[1,2‐e] pyrimido[4,5‐b][1,4]diazepin‐5(5aH)‐ones 4a‐f were prepared regioselectively by the tricomponent reaction of 4,5,6‐triaminopyrimidine 1, 1,3‐indandione 2 and aromatic aldehydes 3a‐f. The bicomponent approach, using 2,4,5,6‐tetraaminopyrimidine 5 and 2‐aryl‐ideneindandiones 6a‐f as reagents, afforded 9,11‐diamino‐6‐aryl‐6,7‐dihydroindeno[1,2‐e]pyrimido[4,5‐b]‐[1,4]diazepin‐5(5aH)‐ones 7a‐f in good yields and the regioisomeric 8,10‐diamino derivatives 8a‐c in lower yields. Both, bi‐ and tricomponent approaches were performed by microwave irradiation and all products were fully characterized by detailed NMR measurements.     

Reversible core-interconversion of an iron(III) dihydroxo bridged complex

Complexes [Fe(Hhbi)(2)(NO(3))].2EtOH (1.2EtOH) and [Fe(2)(mu-OH)(2)(Hhbi)(4)].2H(2)O.8EtOH (2.2H(2)O.8EtOH) crystallize in the orthorhombic Fdd2 and P4(2)2(1)2 space groups, respectively (Hhbi(-) = the monoanion of 2-(2'-hydroxyphenyl benzimidazole). Complex 1 exhibits paramagnetic relaxation as evidenced by Mossbauer spectroscopy, and significant axial zero-field splitting (1.5 cm(1) 相似文献   

Biosynthesis of the cyclooligomer depsipeptide beauvericin, a virulence factor of the entomopathogenic fungus Beauveria bassiana

Beauvericin, a cyclohexadepsipeptide ionophore from the entomopathogen Beauveria bassiana, shows antibiotic, antifungal, insecticidal, and cancer cell antiproliferative and antihaptotactic (cell motility inhibitory) activity in vitro. The bbBeas gene encoding the BbBEAS nonribosomal peptide synthetase was isolated from B. bassiana and confirmed to be responsible for beauvericin biosynthesis by targeted disruption. BbBEAS utilizes D-2-hydroxyisovalerate (D-Hiv) and L-phenylalanine (Phe) for the iterative synthesis of a predicted N-methyl-dipeptidol intermediate, and forms the cyclic trimeric ester beauvericin from this intermediate in an unusual recursive process. Heterologous expression of the bbBeas gene in Escherichia coli to produce the 3189 amino acid, 351.9 kDa BbBEAS enzyme provided a strain proficient in beauvericin biosynthesis. Comparative infection assays with a BbBEAS knockout B. bassiana strain against three insect hosts revealed that beauvericin plays a highly significant but not indispensable role in virulence.     

Structure, recognition properties, and flexibility of the DNA.RNA hybrid

Molecular dynamics is used to investigate the properties of the DNA.RNA hybrid in aqueous solution at room temperature. The structure of the hybrid is intermediate between A and B forms but, in general, closer to the canonical A-type helix. All the riboses exhibit North puckerings, while 2'-deoxyriboses exist in North, East, and South puckerings, the latter being the most populated one. The molecular recognition pattern of the DNA.RNA hybrid is a unique combination of those of normal DNA and RNA duplexes. Finally, the results obtained from essential dynamics and stiffness analysis demonstrate the large and very asymmetric flexibility of the hybrid and the strong predilection that each strand (DNA or RNA) has on the nature of their intrinsic motions in the corresponding homoduplexes. The implications of the unique structural and dynamic properties of the DNA.RNA hybrid on the mechanism of cleavage by RNase H are discussed.     

The first example of a hetero-tetranuclear [(VO)Gd](2) complex: synthesis, crystal structure and magnetic properties of [VOLGd(hfa)(2)CH(3)OH](2).2CH(3)OH.2(CH(3))(2)CO

A cyclic tetranuclear [V(IV)O-Gd(III)](2) complex with VO and Gd ions alternately arrayed, behaves, from the magnetic point of view, as two independent dinuclear entities each having a S= 4 ground state, as a consequence of an active and ferromagnetic VO-Gd interaction through the double phenoxo bridge and a magnetically inactive VO-Gd interaction through the amide bridge.     

Tree level gravity—scalar matter interactions in analogy with Fermi theory of weak interactions using only a massive vector field

In this paper we work in perturbative quantum gravity coupled to scalar matter at tree level and we introduce a new effective model in analogy with the Fermi theory of weak interaction and in relation with a previous work where we have studied only the gravity and its self-interaction. This is an extension of the I.T.B. model (Intermediate-Tensor-Boson) for gravity also to gravitationally interacting scalar matter. We show that in a particular gauge the infinite series of interactions containing n gravitons and two scalars could be rewritten in terms of only two Lagrangians containing a massive field, the graviton and, obviously, the scalar field. Using the S-matrix we obtain that the low energy limit of the amplitude reproduces the local Lagrangian for the scalar coupled to gravity.     

Entangled and disentangled evolution for a single atom in a driven cavity

For an atom in an externally driven cavity, we show that special initial states lead to near-disentangled atom-field evolution, and superpositions of these can lead to near maximally entangled states. Somewhat counterintutively, we find that (moderate) spontaneous emission in this system actually leads to a transient increase in entanglement beyond the steady-state value. We also show that a particular field correlation function could be used, in an experimental setting, to track the time evolution of this entanglement.