Structure, stability and bonding of the leapfrog B24 0 ,±1,±2.

Two new structural motifs of the B24 clusters are constructed by use of the leapfrog transformation. The resulting leapfrog B24 has either a bowl shape with a square vacancy or a quasi-planar 2D close-packed triangular boron sheet. The neutral and ionic forms of the latter are found to be more stable than their homologous leapfrog bowl clusters, with the exception of the dicationic B24 +2 . While the leapfrog isomer is less stable than the tubular double ring in the neutral state, it becomes competitive in some ionic states. The nucleus independent chemical shift, electron localization function, ring current maps and the electronic structure of leapfrog B24 clusters reveal them to behave as aromatics.

A comparison of the chemical bonding and reactivity of Si8H8O12 and Ge8H8O12: A theoretical study.

We have analyzed the chemical bonding and reactivity in the cubic molecule octahydridosilsesquioxane, Si8H8O12, and its counterpart Ge8H8O12 by means of ab initio quantum chemical methods and group theory. Density functional theory and MP2 methods combined with the basis sets 6-311+G(d) and 6-311++G(2d,p) were used for geometry optimization and vibrational frequency analysis. The geometries of Si8H8O12 and Ge8H8O12 are unstable under Oh symmetry and distort to the rare Th molecular symmetry. The energy gained from this pseudo-Jahn-Teller distortion ranges from 0.78 to 6.14 kcal mol-1 depending on methodological treatment. The Fukui functions and the molecular electrostatic potential were both used as DFT-based reactivity descriptors. Our study shows that Si8H8O12 and Ge8H8O12 are both hard amphoteric molecules. The cavity within each cage is acidic and able to encapsulate hard small bases such as F-. The exterior of the cages is basic and can form stable exohedral complexes with hard acids, as in the case of H+. The insertion of F- in Si8H8O12 and Ge8H8O12 cages gives the most stable endohedral complexes of the series studied, characterized by formation energies of -3.50 and -3.45 eV at CAM-B3LYP/6-311+G(d) and -3.61 and -3.68 eV at the MP2/6-311++G(d,p) level, respectively. The calculated formation energies of the exohedral and endohedral complexes align with the DFT reactivity descriptor analysis.

Ansatz for the Jahn-Teller triplet instability.

A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering distortions, which transform as the five quadrupolar modes. The solution of the corresponding vibronic Hamiltonian is constructed using the analytical method introduced by Bargmann, as an alternative to existing group-theoretical techniques based on coefficients of fractional parentage. It involves the construction of an ansatz that incorporates SO(5) to SO(3) symmetry breaking. The resulting Jahn-Teller equations are derived and solved in terms of radial polynomials and Gegenbauer functions.

Formation of the quasi-planar B50 boron cluster: topological path from B10 and disk aromaticity.

The lowest-lying isomer of the B50 boron cluster is confirmed to have a quasi-planar shape with two hexagonal holes. By applying a topological (leap-frog) dual operation followed by boron capping, we demonstrated that such a quasi-planar structure actually comes from the smallest elongated B102-, and its high thermodynamic stability is due to its inherent disk aromaticity arising from its 32 valent π electrons that fully occupy a disk configuration of [(1σ)2(1π)4(1δ)4(2σ)2(1φ)4(2π)4(1γ)4(2δ)4(1η)4]. The aromatic character of the quasi-planar B50 is further supported by a strong diatropic magnetic current flow. The sudden appearance of a quasi-planar B50 again points out that the growth pattern of pure boron clusters is still far from being completely understood.

Valence bonds in planar and quasi-planar boron disks.

Planar and quasi-planar boron clusters with a disk-like shape are investigated in search of common bonding characteristics. Methods used involve molecular orbital calculations based on Density Functional Theory (DFT), and valence bond partitioning using Adaptive Natural Density Partitioning (AdNDP) analysis. For high-symmetry cases the proposed bonding schemes are confirmed using the group-theoretical induction method. The focus is on the electron occupation of delocalized in-plane 3-center and 4-center bonds. For disks consisting of concentric rings this inner electron count is found to be equal to a multiple of the vertex count of the inner polygon. For two concentric rings the multiplying factor is four, for three concentric rings it is eight. The appropriate bonding schemes are presented which explain these results. Some giant clusters with two hexagonal holes are also discussed.

The Quantization of the E ⊗ e Jahn-Teller Hamiltonian.

The E ⊗ e Jahn-Teller Hamiltonian in the Bargmann-Fock representation gives rise to a system of two coupled first-order differential equations in the complex field, which may be rewritten in the Birkhoff standard form. General leapfrog recurrence relations are derived, from which the quantized solutions of these equations can be obtained. The results are compared to the analogous quantization scheme for the Rabi Hamiltonian.

Xylonucleic acid: synthesis, structure, and orthogonal pairing properties.

There is a common interest for studying xeno-nucleic acid systems in the fields of synthetic biology and the origin of life, in particular, those with an engineered backbone and possessing novel properties. Along this line, we have investigated xylonucleic acid (XyloNA) containing a potentially prebiotic xylose sugar (a 3'-epimer of ribose) in its backbone. Herein, we report for the first time the synthesis of four XyloNA nucleotide building blocks and the assembly of XyloNA oligonucleotides containing all the natural nucleobases. A detailed investigation of pairing and structural properties of XyloNAs in comparison to DNA/RNA has been performed by thermal UV-melting, CD, and solution state NMR spectroscopic studies. XyloNA has been shown to be an orthogonal self-pairing system which adopts a slightly right-handed extended helical geometry. Our study on one hand, provides understanding for superior structure-function (-pairing) properties of DNA/RNA over XyloNA for selection as an informational polymer in the prebiotic context, while on the other hand, finds potential of XyloNA as an orthogonal genetic system for application in synthetic biology.

Is C50 a superaromat? Evidence from electronic structure and ring current calculations.

The fullerene-50 is a 'magic number' cage according to the 2(N + 1)(2) rule. For the three lowest isomers of C50 with trigonal and pentagonal symmetries, we calculate the sphericity index, the spherical parentage of the occupied π-orbitals, and the current density in an applied magnetic field. The minimal energy isomer, with D3 symmetry, comes closest to a spherical aromat or a superaromat. In the D5h bond-stretch isomers the electronic structure shows larger deviations from the ideal spherical shells, with hybridisation or even reversal of spherical parentages. It is shown that relative stabilities of fullerene cages do not correlate well with aromaticity, unlike the magnetic properties which are very sensitive indicators of spherical aromaticity. Superaromatic diamagnetism in the D3 cage is characterized by global diatropic currents, which encircle the whole cage. The breakdown of sphericity in the D5h cages gives rise to local paratropic countercurrents.

Jahn-Teller distortion in polyoligomeric silsesquioxane (POSS) cations.

We investigated the symmetry breaking mechanism in cubic octa-tert-butyl silsesquioxane and octachloro silsesquioxane monocations (Si8O12(C(CH3)3)8(+) and Si8O12Cl8(+)) using density functional theory (DFT) and group theory. Under Oh symmetry, these ions possess (2)T2g and (2)Eg electronic states and undergo different symmetry breaking mechanisms. The ground states of Si8O12(C(CH3)3)8(+) and Si8O12Cl8(+) belong to the C3v and D4h point groups and are characterized by Jahn-Teller stabilization energies of 3959 and 1328 cm(-1), respectively, at the B3LYP/def2-SVP level of theory. The symmetry distortion mechanism in Si8O12Cl8(+) is Jahn-Teller type, whereas in Si8O12(C(CH3)3)8(+) the distortion is a combination of both Jahn-Teller and pseudo-Jahn-Teller effects. The distortion force acting in Si8O12(C(CH3)3)8(+) is mainly localized on one Si-(tert-butyl) group, while in Si8O12Cl8(+) it is distributed over the oxygen atoms. The main distortion forces acting on the Si8O12 core arise from the coupling between the electronic state and the vibrational modes, identified as 9t2g + 1eg + 3a2u for the Si8O12(C(CH3)3)8(+) and 1eg + 2eg for Si8O12Cl8(+).

Cooperative dynamics of a DNA polymerase replicating complex.

Engineered DNA polymerases continue to be the workhorses of many applications in biotechnology, medicine and nanotechnology. However, the dynamic interplay between the enzyme and the DNA remains unclear. In this study, we performed an extensive replica exchange with flexible tempering (REFT) molecular dynamics simulation of the ternary replicating complex of the archaeal family B DNA polymerase from the thermophile Thermococcus gorgonarius, right before the chemical step. The convoluted dynamics of the enzyme are reducible to rigid-body motions of six subdomains. Upon binding to the enzyme, the DNA double helix conformation changes from a twisted state to a partially untwisted state. The twisted state displays strong bending motion, whereby the DNA oscillates between a straight and a bent conformation. The dynamics of double-stranded DNA are strongly correlated with rotations of the thumb toward the palm, which suggests an assisting role of the enzyme during DNA translocation. In the complex, the primer-template duplex displays increased preference for the B-DNA conformation at the n-2 and n-3 dinucleotide steps. Interactions at the primer 3' end indicate that Thr541 and Asp540 are the acceptors of the first proton transfer in the chemical step, whereas in the translocation step both residues hold the primer 3' terminus in the vicinity of the priming site, which is crucial for high processivity.

Quantum rules for planar boron nanoclusters.

This article presents the use of free particle models to obtain quantum rules for planar boron clusters, with nuclearities in the range from seven to twenty. The information obtained from the models is being compared with electronic structure calculations based on the DFT method. Separate rules for in-plane and out-of-plane bonding are derived. In-plane bonding is precise on the cluster boundary and forms a network of alternating triangular 3c-2e bonds on the inside. The out-of-plane bonding is strongly delocalized and only depends on the global shape and size of the cluster.

The boron conundrum: which principles underlie the formation of large hollow boron cages?

Extensive optimisation calculations are performed for the B(80) isomers in order to find out which principles underlie the formation of large hollow boron cages. Our analysis shows that the most stable isomers contain triangular B(10) or rhombohedral B(16) building blocks. The lowest-energy isomer has C(3v) symmetry and is characterised by a belt of three interconnected B(16) units and two separate B(10) units. At the B3LYP/6-31G(d) level of theory, this newly discovered isomer is 2.29, 1.48, and 0.54 eV below the leapfrog B(80) of Szwacki et al., the T(h) -B(80) of Wang, and the D(3d) -B(80) of Pochet et al., respectively. Our C(3v) isomer is therefore identified as the most stable hollow cage isomer of B(80) presently known. Its HOMO-LUMO gap of 1.6 eV approaches that of the leapfrog B(80). The leapfrog principle still remains a reliable scheme for producing boron cages with larger HOMO-LUMO gaps, whereas the thermodynamically most stable B(80) cages are formed when all pentagonal faces are capped. We show that large hollow cages of boron retain a preference for fullerene frames. The additional capping is in accordance with the following rules: preference for capping of pentagonal faces, formation of B(10) and/or B(16) units, homogeneous distribution of the hexagonal caps, and hole density approaching 1/9. Although our most stable B(80) isomer still remains higher in energy than the B(80) core-shell structure, we show that by applying the bonding principles to larger structures it is possible to construct boron cages with higher stabilisation energy per boron atom than the core-shell structure; a prototypical example is B(160). This clearly shows the continuous competition between the two suggested construction schemes, namely, the formation of multiple-shell structures and hollow cages.

Particle on a boron disk: ring currents and disk aromaticity in B20(2-).

The B20(2-) cluster is predicted to exhibit a planar sheet-like structure with a circular circumference. Orbital plots and energy correlations demonstrate the close correspondence between the electronic structure of B20(2-) and the Bessel functions describing the waves of a quantum mechanical particle confined to a disk. The π-band of B20(2-), and its B19(-) congener, contains 12 π-electrons, forming a (1σ)(2)(1π)(4)(1δ)(4)(2σ)(2) configuration, which corresponds to a "disk aromaticity" electron count. The analogy not only applies to the π-band, but also extends to the 50 valence σ-electrons. The occupied σ-orbitals are assigned on the basis of radial and angular nodes of the scalar disk waves. The magnetic response of the cluster was examined by Nucleus Independent Chemical Shift (NICS) values and current density calculations based on the ipsocentric model. B20(2-) is found to exhibit a remarkable inner paratropic current in the σ-channel and an outer diatropic current in the π-channel. The orbital excitations responsible for the antiaromaticity in σ and the disk-aromaticity in π are identified.

Jahn-Teller instability in cationic boron and carbon buckyballs B80+ and C60+: a comparative study.

This paper investigates the Jahn-Teller effect in the icosahedral cation B(80)(+) and compares the descent in symmetry with that in C(60)(+). For both cations the icosahedral ground state is a (2)H(u) state, which exhibits a H ⊗ (g ⊕ 2h) Jahn-Teller instability. A detailed construction of the potential energy surface of B(80)(+) using different DFT methods including B3LYP/6-31G(d), VWN/6-31G(d), PBE/TZP and PBE/6-31G(d) shows that, contrary to C(60)(+), which prefers D(5d) symmetry, the ground state of B(80)(+) adopts S(6) point group symmetry. A D(3d) structure is identified as a saddle point among the S(6) minima of B(80)(+). The distortion of D(3d) to S(6) in B(80)(+) is attributed to a superposition of Jahn-Teller and pseudo-Jahn-Teller effects. Imaginary modes, transforming as the g(g) representation, which are present in neutral icosahedral B(80), form the dominant symmetry breaking active modes. The pronounced difference between the JT effects in the boron and carbon buckyball cations is due to the plasticity of the boron caps. The calculated Jahn-Teller stabilization of B(80)(+) is nearly 1549 cm(-1) (PBE/TZP), which exceeds the stabilization of 596 cm(-1) computed for C(60)(+) at the same level.

Disk aromaticity of the planar and fluxional anionic boron clusters B20(-/2-).

The presence of excess electrons modifies the structural landscape and tends to extend the planarity of boron clusters. While the neutral B(20) is tubular, both the anion and dianion B(20)(-/2-) become planar. Geometrical features of the stable anions suggest the existence of a new type of cluster that is planar and doubly cyclic with one atom located at the center (see figure), as well as being fluxional.

Influence of the nucleobase and anchimeric assistance of the carboxyl acid groups in the hydrolysis of amino acid nucleoside phosphoramidates.

Nucleoside phosphoramidates (NPs) are a class of nucleotide analogues that has been developed as potential antiviral/antitumor prodrugs. Recently, we have shown that some amino acid nucleoside phosphoramidates (aaNPs) can act as substrates for viral polymerases like HIV-1 RT. Herein, we report the synthesis and hydrolysis of a series of new aaNPs, containing either natural or modified nucleobases to define the basis for their differential reactivity. Aqueous stability, kinetics, and hydrolysis pathways were studied by NMR spectroscopy at different solution pD values (5-7) and temperatures. It was observed that the kinetics and mechanism (P-N and/or P-O bond cleavage) of the hydrolysis reaction largely depend on the nature of the nucleobase and amino acid moieties. Aspartyl NPs were found to be more reactive than Gly or ß-Ala NPs. For aspartyl NPs, the order of reactivity of the nucleobase was 1-deazaadenine>7-deazaadenine>adenine>thymine≥3-deazaadenine. Notably, neutral aqueous solutions of Asp-1-deaza-dAMP degraded spontaneously even at 4 °C through exclusive P-O bond hydrolysis (a 50-fold reactivity difference for Asp-1-deaza-dAMP vs. Asp-3-deaza-dAMP at pD 5 and 70 °C). Conformational studies by NMR spectroscopy and molecular modeling suggest the involvement of the protonated N3 atom in adenine and 1- and 7-deazaadenine in the intramolecular catalysis of the hydrolysis reaction through the rare syn conformation.

Solution structure and conformational dynamics of deoxyxylonucleic acids (dXNA): an orthogonal nucleic acid candidate.

Orthogonal nucleic acids are chemically modified nucleic acid polymers that are unable to transfer information with natural nucleic acids and thus can be used in synthetic biology to store and transfer genetic information independently. Recently, it was proposed that xylose-DNA (dXNA) can be considered to be a potential candidate for an orthogonal system. Herein, we present the structure in solution and conformational analysis of two self-complementary, fully modified dXNA oligonucleotides, as determined by CD and NMR spectroscopy. These studies are the initial experimental proof of the structural orthogonality of dXNAs. In aqueous solution, dXNA duplexes predominantly form a linear ladderlike (type-1) structure. This is the first example of a furanose nucleic acid that adopts a ladderlike structure. In the presence of salt, an equilibrium exists between two types of duplex form. The corresponding nucleoside triphosphates (dXNTPs) were synthesized and evaluated for their ability to be incorporated into a growing DNA chain by using several natural and mutant DNA polymerases. Despite the structural orthogonality of dXNA, DNA polymerase ß mutant is able to incorporate the dXNTPs, showing DNA-dependent dXNA polymerase activity.

Reactivity of amino acid nucleoside phosphoramidates: a mechanistic quantum chemical study.

Recent experimental evidence (Maiti et al. Chem.-Eur. J., submitted) indicates that hydrolysis of nucleoside phosphoramidates is subjected to anchimeric influence by carboxyl moieties in the leaving group but also by the base in the nucleotide. A quantum chemical analysis of these findings is presented. First the intrinsic hydrolysis mechanism is investigated for simplified model compounds, and then both amino acid and nucleoside substituents are included. It is found that hydrolysis is assisted by the α-carboxyl group via formation of a five-membered intermediate and that the barrier for the reaction of this intermediate toward the product state can be influenced by the nucleobase. The adenine base protonated on N3 interacts with the transition state and considerably lowers the barrier for hydrolysis. The influence of several base modifications is explained by calculating the pK(a) for protonation on N3.

Fourteen-electron ring model and the anomalous magnetic circular dichroism of meso-triarylsubporphyrins.

The MCD spectra of meso-triarylsubporphyrins show a sign anomaly which is correlated with the acceptor properties of the aryl substituent. From the spectra, magnetic moments of the excited states are determined. In the context of a simplified orbital model, the sign change is attributed to the quenching of the magnetic moment of the LUMO by acceptor orbitals of the substituent. The actual calculation of this moment presents a major challenge to computational methods. It is shown that wave function techniques based on CASSCF underestimate the covalency effects that are responsible for the quenching. In contrast, a CI method based on DFT orbitals yields excellent results, which fully support the orbital model.

Normal mode analysis of Trp RNA binding attenuation protein: structure and collective motions.

The Trp RNA-binding protein (TRAP) has a toroidal topology and a perfect 11-fold symmetry, which makes it an excellent candidate for a vibrational study of elastic properties. Normal mode analysis in combination with correlation matrix calculations was used to detect collective low-frequency motions in TRAP. The results reveal the presence of highly correlated modes at the lower end of the spectrum, which directly reflect the annular and toroidal topology. The integral of the correlations over the low-frequency torsional part of the vibrational spectrum further demonstrates the relative rigidity of the 11 monomer building blocks of TRAP. The internal flexibility of each monomer and the effects of Trp-binding were also examined. The study clearly shows the determining influence of symmetry and topology on the elastic properties and also offers a detailed view on the Trp affinity of TRAP.