Orwik

Helical structure of xylose-DNA.

Synthetic biology and systems chemistry demonstrate a growing interest in modified nucleotides to achieve an enzymatically stable artificial nucleic acid. A potential candidate system is xylose-DNA, in which the 2'-deoxy-beta-D-ribo-furanose is subst... expand abstractituted by 2'-deoxy-beta-D-xylo-furanose. We present here the helical structure and conformational analysis of xylose-DNA on the basis of 35 ns MD simulations of a 29-base-pair DNA duplex. Starting from a right-handed xylose-DNA helix, we observe a remarkable conformational transition from right- to left-handed helix. The left-handed xylose-DNA is highly dynamic, involving screwing and unscrewing motion of the helix. The sugar pucker induced helical changes influence the backbone to adopt the backbone angles for xylose-DNA while retaining the Watson-Crick base pairing and stacking interactions. The results demonstrate the chiral orthogonality of the ribose and xylose based episomes. As far as stability and compactness of information storage is concerned, the ribose based natural DNA is unsurpassed. collapse abstract

Thermodynamically stable noncomposite vortices in mesoscopic two-gap superconductors

In mesoscopic two-gap superconductors with sizes of the order of the coherence length noncomposite vortices are found to be thermodynamically stable in a large domain of the $T - H$ phase diagram. In these phases the vortex cores of one condensate ... expand abstractare spatially separated from the other condensate ones, and their respective distributions can adopt distinct symmetries. The appearance of these vortex phases is caused by a non-negligible effect of the boundary of the sample on the superconducting order parameter and represents therefore a genuine mesoscopic effect. For low values of interband Josephson coupling vortex patterns with $L_1 \neq L_2$ can arise in addition to the phases with $L_1 =L_2$, where $L_1$ and $L_2$ are total vorticities in the two condensates. The calculations show that noncomposite vortices could be observed in thin mesoscopic samples of MgB$_{2}$. collapse abstract

Chemical Bonding in the Boron Buckyball

A symmetry analysis of the valence shell in the boron buckyball B80, shows a perfect match with the symmetry of the valence shell in C60 .The cap atoms participate in the bonding by 30 orbitals which transform as the sigma bonds along the 6-6 edges... expand abstract. Far reaching consequences for chemical and physical properties of B80, which until now only exists in silico, are expected. collapse abstract

The Canonical Form of the Rabi Hamiltonian

The Rabi Hamiltonian, describing the coupling of a two-level system to a single quantized boson mode, is studied in the Bargmann-Fock representation. The corresponding system of differential equations is transformed into a canonical form in which a... expand abstractll regular singularities between zero and infinity have been removed. The canonical or Birkhoff-transformed equations give rise to a two-dimensional eigenvalue problem, involving the energy and a transformational parameter which affects the coupling strength. The known isolated exact solutions of the Rabi Hamiltonian are found to correspond to the uncoupled form of the canonical system. collapse abstract

Tryptophan conformations associated with partial unfolding in ribonuclease T1.

The origin of the biexponential fluorescence decay of Trp in ribonuclease T1 under mildly destabilizing conditions, such as increased pH or temperature, or the presence of detergent, is still not understood. We have performed two extended replica-exc... expand abstracthange molecular dynamics simulations to obtain a detailed representation of the native state at two protonation states corresponding to a high and low pH. At high pH, the appearance of partially unfolded states is evident. We found that this pH-induced destabilization originates from increased global repulsion as well as reduced local favorable electrostatic interactions and reduced H-bonding strength of His(27), His(40), and His(92). At high pH, alternative tryptophan rotamers appear and are linked to a distorted environment of the tryptophan, which also acts as a separate source of ground-state heterogeneity. The total population of these alternative conformations agrees well with the amplitude of the experimentally observed secondary fluorescence lifetime. collapse abstract

A study of the electronic properties of Au nanowires and Au nanoislands on Au(111) surfaces.

By means of ion bombardment of clean Au(111) films, atomically flat nanoparticles of various shapes and sizes were created, ranging from several tens of nm(2) down to only a few nm(2). Both two-dimensional Au islands as well as one-dimensional Au nan... expand abstractowire-like structures have been investigated by means of low-temperature scanning tunneling microscopy and spectroscopy. We were able to probe their local electronic structure in a broad energy range, which was found to be dominated by pronounced size-dependent confinement effects. Mapping of the local density of states revealed complex standing wave patterns that arise due to interference of scattered Au surface state electrons at the edges of the Au nanoparticles. The observed phenomena could be modeled with high accuracy by theoretical particle-in-a-box calculations based on a variational method that can be applied to '2D boxes' of arbitrary polygonal shape and that we have previously successfully applied to explain the electronic wave patterns on Co islands on Au(111). Our findings support the general validity of this particle-in-a-box model. collapse abstract

Hydrolysis of aspartic acid phosphoramidate nucleotides: a comparative quantum chemical study.

L-Aspartic acid has recently been found to be a good leaving group during HIV reverse transcriptase catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. This showed that L-Asp is a good mimic for the pyrophosphate moiety of deoxyade... expand abstractnosine triphosphate. The present work explores the thermochemistry and mechanism for hydrolysis of several models for L-aspartic-dAMP using B3LYP/DGDZVP, MP2/6-311++G** and G3MP2 level of theory. The effect of the new compound is gradually investigated: starting from a simple methyl amine leaving group up to the aspartic acid leaving group. The enzymatic environment was mimicked by involving two Mg(2+) ions and some important active site residues in the reaction. All reactions are compared to the corresponding O-coupled leaving group, which is methanol for methyl amine and malic acid for aspartic acid. With methyl amine as a leaving group a tautomeric associative or tautomeric dissociative mechanism is preferred and the barrier is lower than the comparable mechanism with methanol as a leaving group. The calculations on the aspartic acid in the enzymatic environment show that qualitatively the mechanism is the same as for triphosphate but the barrier for hydrolysis by the associative mechanism is higher for L-aspartic-dAMP than for L-malic-dAMP and pyrophosphate. collapse abstract

Methyne Capping in the Boron Buckyball : A Viable Possibility

We report the electronic structure of methyne boron buckyballs B68(CH)12 and B72(CH)8 obtained by substituting respectively 12 and 8 boron cap atoms by methyne CH groups on the boron buckyball B80. DFT calculations and minimization techniques have ... expand abstractbeen employed to characterize the structural and electronic properties of endo and exo isomers of these molecules in Th symmetry. A vibrational frequencies analysis predicts that only endo-B72(CH)8 corresponds to a true minimum on the potential energy hypersurface with a cohesive energy similar to the boron buckyball. The viable existence of this carboron buckyball opens new perspectives for a synthesis of large boron clusters. collapse abstract

How do rotameric conformations influence the time-resolved fluorescence of tryptophan in proteins? A perspective based on molecular modeling and quantum chemistry.

We discuss the dynamics of tryptophan rotamers in the context of the non-exponential fluorescence decay in proteins. The central question is: how does the ground-state conformational heterogeneity influence the time evolution of tryptophan fluorescen... expand abstractce? This problem is examined here from the theoretical perspective. Three methods at different levels of theory, and with different scopes and computational requirements are reviewed. The Dead-end elimination method is limited to side-chain dynamics and provides an efficient way to detect the stable tryptophan rotamers in a protein. Its application to the study of heterogeneous emission characteristics is illustrated. Molecular dynamics is aimed at the full phase space of the macromolecule in solution, but must rely on classical force fields and laws of evolution. We examine to what extent the molecular mechanics paradigm yields sufficiently accurate thermodynamic results, and what are the possible kinetic implications. Finally Quantum Chemistry is the only theoretical method that allows a direct assessment of the excited states. It is necessarily restricted to small molecular systems, and thus must be used in a hybrid combination with classical methods and electrostatic models. So far understanding of the emitting state has greatly progressed as a result of these calculations, but the actual treatment of the photophysical decay processes at the quantum level has not yet really started. collapse abstract

Unique definition of the Zeeman-splitting g tensor of a Kramers doublet.

It has been widely accepted in the past that the g tensor describing the Zeeman splitting of a Kramers doublet is not uniquely defined. Here we show that with two basic requirements, (i) the invariance of the Zeeman Hamiltonian under symmetry transfo... expand abstractrmations and (ii) its continuous change with the variations of the parameters of the system (geometry and crystal field), a unique determination of the elements of the g tensor is achieved. collapse abstract

A unified perspective on the hydrogen atom transfer and proton-coupled electron transfer mechanisms in terms of topographic features of the ground and excited potential energy surfaces as exemplified by the reaction between phenol and radicals.

The relation between the hydrogen atom transfer (HAT) and proton-coupled electron transfer (PCET) mechanisms is discussed and is illustrated by multiconfigurational electronic structure calculations on the ArOH + R(*) --> ArO(*) + RH reactions. The k... expand abstractey topographic features of the Born-Oppenheimer potential energy surfaces that determine the predominant reaction mechanism are the conical intersection seam of the two lowest states and reaction saddle points located on the shoulders of this seam. The saddle point corresponds to a crossing of two interacting valence bond states corresponding to the reactant and product bonding patterns, and the conical intersection corresponds to the noninteracting intersection of the same two diabatic states. The locations of mechanistically relevant conical intersection structures and relevant saddle point structures are presented for the reactions between phenol and the N- and O-centered radicals, (*)NH2 and (*)OOCH3. Points on the conical intersection of the ground doublet D0 and first excited doublet D1 states are found to be in close geometric and energetic proximity to the reaction saddle points. In such systems, either the HAT mechanism or both the HAT mechanism and the proton-coupled electron transfer (PCET) mechanism can take place, depending on the relative energetic accessibility of the reaction saddle points and the D0/D1 conical intersection seams. The discussion shows how the two mechanisms are related and how they blend into each other along intermediate reaction paths. The recognition that the saddle point governing the HAT mechanism is on the shoulder of the conical intersection governing the PCET mechanism is used to provide a unified view of the competition between the two mechanisms (and the blending of the two mechanisms) in terms of the prominent and connected features of the potential energy surface, namely the saddle point and the conical intersection. The character of the dual mechanism may be understood in terms of the dominant valence bond configurations of the intersecting states, which are zero-order approximations to the diabatic states. collapse abstract

Radial rescaling approach for the eigenvalue problem of a particle in an arbitrarily shaped box.

In the present work we introduce a methodology for solving a quantum billiard with Dirichlet boundary conditions. The procedure starts from the exactly known solutions for the particle in a circular disk, which are subsequently radially rescaled in s... expand abstractuch a way that they obey the new boundary conditions. In this way one constructs a complete basis set which can be used to obtain the eigenstates and eigenenergies of the corresponding quantum billiard to a high level of precision. Test calculations for several regular polygons show the efficiency of the method which often requires one or two basis functions to describe the lowest eigenstates with high accuracy. collapse abstract

The Boron Buckyball has an Unexpected Th Symmetry

The boron buckyball avoids the high symmetry icosahedral cage structure. The previously reported Ih symmetric structure is not an energy minimum in the potential energy surface and exhibits a spontaneous symmetry breaking to yield a puckered cage w... expand abstractith a rare Th symmetry. The HOMO-LUMO gap is twice as large as the reported value and amounts to 1.94 eV at B3LYP/6-31G(d) level. The valence orbital structure of boron buckyball is identical to the one in the carbon analogue. collapse abstract

A CASPT2 study of the electronic spectrum of hexacyanoosmate(III).

CASPT2 calculations reveal that the ligand field splitting parameter Delta(o) of [Os(CN)6]3- is much higher than previously proposed values of +/-38,000 cm(-1). In line with the expected increase down a transition-metal group, Delta(o) is found to be... expand abstract +/-55,000 cm(-1), excluding the possible appearance of ligand field transitions in the UV-vis spectrum. Instead, the calculations confirm that the observed spectrum arises from the three lowest symmetry-allowed ligand-to-metal charge-transfer (LMCT) excitations. Spin-orbit coupling in the ground state is found to be about 4350 cm(-1), leading to a spin-orbit coupling constant zeta of +/-2900 cm(-1). Spin-orbit coupling in the 2T(1u) LMCT states is found not to be negligible, contrary to previous belief. collapse abstract

Vibronic and spin-orbit coupling of a d9 transition-metal ion encapsulated in an icosahedral cage: the (Gamma8+Gamma9)x(g+2h) Jahn-Teller problem.

Interplay between the vibronic and spin-orbit coupling in the (Gamma8+Gamma9)x(g+2h) Jahn-Teller problem, where Gamma8 and Gamma9 are the quartet and sextet spin representation, and g and h denote the fourfold and fivefold degenerate vibrational mode... expand abstracts in icosahedral symmetry, respectively, is studied. A 4d9 or 5d9 transition-metal ion in an icosahedral field may provide a realization of this system. collapse abstract

Effect of the metal environment on the ferromagnetic interaction in the Co-NC-W pairs of octacyanotungstate(V)-Cobalt(II) three-dimensional networks.

State of the art CASSCF and CASPT2 calculations have been performed to elucidate the nature of ferromagnetism of CoII-NC-WV pairs in the three-dimensional compound [[WV(CN)2]2[(micro-CN)4CoII(H2O)2]3.4H2O]n, which has been recently synthesized and in... expand abstractvestigated by a number of experimental techniques (Herrera, J. M.; Bleuzen, A.; Dromzée, Y.; Julve, M.; Lloret, F.; Verdaguer, M. Inorg. Chem. 2003, 42, 7052-7059). In this network, the Co ions are in the high-spin (S = 3/2) state, while the single unpaired electron on the W centers occupies the lowest orbital of the dz2 type of the 5d shell. In agreement with the suggestion made by Herrera et al., we find that the ferromagnetism is due to a certain occupation scheme of the orbitals from the parent octahedral t2g shell on CoII sites, in which the orbital accommodating the unpaired electron is orthogonal to the dz2 orbitals of the surrounding W ions. We investigate the stabilization of such an orbital configuration on the Co sites and find that it cannot be achieved in the ground state of isolated mononuclear fragments [CoII(NC)4(OH2)2]2- for any conformations of the coordinated water molecules and Co-N-C bond angles. On the other hand, it is stabilized by the interaction of the complex with neighboring W ions, which are simulated here by effective potentials. The calculated exchange coupling constants for the CoII-NC-WV binuclear fragments are in reasonable agreement with the measured Curie-Weiss constant for this compound. As additional evidence for the inferred electronic configuration on the Co sites, the ligand-field transitions, the temperature-dependent magnetic susceptibility, and the field-dependent low-temperature magnetization, simulated ab initio for the mononuclear Co fragments, are in agreement with the available data for another compound [WIV[(micro-CN)4-CoII(H2O)2]2.4H2O]n containing diamagnetic W and high-spin Co ions in an isostructural environment. collapse abstract

Jahn and Tellers last case: the icosahedral sextet, gamma(9) x (g+2 h).

Vortices and their relation to ring currents and magnetic moments in nanographenes in high magnetic field.

Much attention has been paid to the role of vortices in the magnetic response properties of superconductors, but less so for molecular systems. Here we present a theoretical analysis on nanographenes subject to a strong homogeneous magnetic field. Th... expand abstracte analysis is based on the simple Hückel-London model, for which we derive the topological definition of vorticity. The results are confirmed by a more elaborate model that includes nonnearest neighbor interaction, the explicit presence of nuclei and all terms due to the magnetic field. We find that due to frontier orbital intersections, large changes in magnetic dipole moments occur. Orbital energy minima and maxima can be related to change of vortex patterns with flux. collapse abstract

Topology-aided molecular design: the platonic molecules of genera 0 to 3.

Tryptophan rotamers as evidenced by X-ray, fluorescence lifetimes, and molecular dynamics modeling.

We investigated the native-state dynamics of the Bacillus caldolyticus cold-shock protein mutant Bc-Csp L66E, using fluorescence and appropriate molecular dynamics methods. Two fluorescence lifetimes were found, the amplitudes of which agree very wel... expand abstractl with tryptophan rotamer populations, obtained from parallel tempering calculations. Rotamer lifetimes were predicted by transition-state theory from high-temperature simulations. Transition pathways were extracted from the transition rates between individual rotameric states. The molecular dynamics also reveal the loop fluctuations in the native state. collapse abstract

Multiquanta vortex entry and vortex-antivortex pattern expansion in a superconducting microsquare with a magnetic dot.

We investigate the nucleation of superconductivity in a microsquare with a magnetic dot on top. The cusplike behavior of the calculated normal-superconducting phase boundaries, T(c)(H), shows a transition between short-period to long-period oscillati... expand abstractons when going from positive to negative applied fields, H. Vorticity changes by more than 1, indicating multiquanta vortex entries, have been detected along this asymmetric T(c)(H) boundary. The dot also expands dramatically the symmetry-consistent vortex-antivortex patterns, thus facilitating their experimental observation. collapse abstract

Oriented 2-cell embeddings of a graph and their symmetry classification: generating algorithms and case study of the möbius-kantor graph.

We discuss a method to derive all symmetry-distinct oriented 2-cell embeddings of a given graph and classify them based on their symmetry. As an example, we apply the algorithm to the highly symmetrical trivalent Möbius-Kantor graph. Considering the ... expand abstractderived 2-cell embeddings as carbon networks leads to some interesting negative curvature carbon allotropes. collapse abstract

Mo2(CN)11:5- A detailed description of ligand-field spectra and magnetic properties by first-principles calculations.

An ab initio multiconfigurational approach has been used to calculate the ligand-field spectrum and magnetic properties of the title cyano-bridged dinuclear molybdenum complex. The rather large magnetic coupling parameter J for a single cyano bridge,... expand abstract as derived experimentally for this complex by susceptibility measurements, is confirmed to a high degree of accuracy by our CASPT2 calculations. Its electronic structure is rationalized in terms of spin-spin coupling between the two constituent hexacyano-monomolybdate complexes. An in-depth analysis on the basis of Anderson's kinetic exchange theory provides a qualitative picture of the calculated CASSCF antiferromagnetic ground-state eigenvector in the Mo dimer. Dynamic electron correlations as incorporated into our first-principles calculations by means of the CASPT2 method are essential to obtain quantitative agreement between theory and experiment. collapse abstract

Hydrogen bonding to pi-systems of indole and 1-methylindole: is there any OH...phenyl bond?

The weak hydrogen-bonded complexes between proton donors and the pi-cloud of indole and 1-methylindole (MI) are investigated theoretically by three different methods: DFT/B3LYP, MPW1B95, and MP2. This study addresses the question as to whether the 1:... expand abstract1 complex can only form between the proton and the pi-cloud of the pyrrole part of indole or if there also exists a 1:1 complex between the proton and the pi-cloud of the phenyl ring. For the water-indole system, the more elaborate MP2 and MPW1B95 methods yield only one minimum with a hydrogen bond to the pyrrole part and weak secondary interactions to the phenyl ring, in agreement with a recent criticism by Van Mourik (Chem. Phys. 2004, 304, 317-319) that the B3LYP functional is unable to account for the dispersion interaction. However, for the 1:1 complexes between MI and 2-propanol, all three methods indicate that both the five-membered and the six-membered rings of the indole chromophore can form pi-complexes. For the MI-trifluoroethanol (TFE) system, it is shown that the ethanol conformation is specific for the interaction site: for the complex to the five-membered ring, TFE is in the cis-gauche conformation, while for the complex to the six-membered ring site, it is in the trans conformation. These results are discussed as a function of local interactions in the systems. collapse abstract

Magnetic anisotropy of Mo(CN)74- anions and fragments of cyano-bridged magnetic networks.

Quantum chemistry calculations of CASSCF/CASPT2 level together with ligand field analysis are used for the investigation of magnetic anisotropy of [Mo(CN)7]4- complexes. We have considered three types of heptacyano environments: two ideal geometries,... expand abstract a pentagonal bipyramid and a capped trigonal prism, and the heptacyanomolybdate fragment of the cyano-bridged magnetic network K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O. At all geometries the first excited Kramers doublet is found remarkably close to the ground one due to a small orbital energy gap in the ligand field spectrum, which ranges between a maximal value in the capped trigonal prism (800 cm(-1)) and zero in the pentagonal bipyramid. The small value of this gap explains (i) the axial form of the g tensor and (ii) the strong magnetic anisotropy even in strongly distorted complexes. Comparison with available experimental data for the g tensor of the mononuclear precursors reveals good agreement with the present calculations for the capped trigonal prismatic complex and a significant discrepancy for the pentagonal bipyramidal one. The calculations for the heptacyanomolybdate fragment of K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O give g(perpendicular)/g(parallel) approximately 0.5 and the orientation of the local anisotropy axis close to the symmetry axis of an idealized pentagonal bipyramid. These findings are expected to be important for the understanding of the magnetism of anisotropic Mo(III)-Mn(II) cyano-bridged networks based on the [Mo(CN)7]4- building block. collapse abstract