Metal-Nucleotide Interactions: Crystal Structures of Alkali (Li+, Na+, K+) and Alkaline Earth (Ca2+, Mg2+) Metal Complexes of Adenosine 2'-Monophosphate

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2'-monophosphate (2'-AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2'-AMP.Li belongs to the monoclinic space group P21 with a = 7.472(3)Å, b = 26.853(6) Å, c = 9.184(1)Å, b = 113.36(1)Å and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P31 and P3121 with a = 8.762(1)Å, c = 34.630(5)Å, Z= 6 and a = 8.931(4), Åc = 34.852(9)Å and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6522 and P21 with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 91.1(0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2'-AMP.Li, 2'-AMP.Na, 2'- AMP.K, 2'-AMP.Ca and 2'-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (cCN = -156.4(2)°) in 2'-AMP.Mg. Ribose moieties adopt C2'-endo puckering in 2'-AMP.Li and 2'-AMP.Ca, C2'-endo-C3'-exo twist puckering in 2'-AMP.Na and 2'-AMP.K and a C3'-endo-C2'-exo twist puckering in 2'-AMP.Mg structure. The conformation about the exocyclic C4'-C5' bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g-) conformation observed in 2'-AMP.Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99Å. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2'-AMP.Na and 2'-AMP.K structures is the involvement of ribose O4' in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42Å forming an octahedron. A classic example of an exception to the existence of the O5'-N3 intramolecular hydorgen bond is the 2'-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11Å. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5' compared to 2' and 3' nucleotides (J. Lawless, E. Edelson, and L. Manring, Am. Chem. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur. J. Biochem. 179, 451-458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245-336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2'-AMP.Na and 2'-AMP.K structures resemble the 2'-AMP.NH4 structure reported in the previous article. 2'-AMP.Li, 2'-AMP.Ca and 2'-AMP.Mg structures display base-ribose O4' stacking. An overview of interaction of monovalent and divalent cations with 2' and 5'-nucleotides has been presented.

Highly efficient spin-conversion effect leading to energy up-converted electroluminescence in singlet fission photovoltaics

Free charge generation in donor-acceptor (D-A) based organic photovoltaic diodes (OPV) progresses through formation of charge-transfer (CT) and charge-separated (CS) states and excitation decay to the triplet level is considered as a terminal loss. On the other hand a direct excitation decay to the triplet state is beneficial for multiexciton harvesting in singlet fission photovoltaics (SF-PV) and the formation of CT-state is considered as a limiting factor for multiple triplet harvesting. These two extremes when present in a D-A system are expected to provide important insights into the mechanism of free charge generation and spin-character of bimolecular recombination in OPVs. Herein, we present the complete cycle of events linked to spin conversion in the model OPV system of rubrene/C60. By tracking the spectral evolution of photocurrent generation at short-circuit and close to open-circuit conditions we are able to capture spectral changes to photocurrent that reveal the triplet character of CT-state. Furthermore, we unveil an energy up-conversion effect that sets in as a consequence of triplet population build-up where triplet-triplet annihilation (TTA) process effectively regenerates the singlet excitation. This detailed balance is shown to enable a rare event of photon emission just above the open-circuit voltage (VOC) in OPVs.

1H NMR study of internal motions and quantum rotational tunneling in (CH3)4NGeCl3

(CH3)4NGeCl3 is prepared, characterized and studied using 1H NMR spin lattice relaxation time and second moment to understand the internal motions and quantum rotational tunneling. Proton second moment is measured at 7 MHz as function of temperature in the range 300-77 K and spin lattice relaxation time (T1) is measured at two Larmor frequencies, as a function of temperature in the range 270-17 K employing a homemade wide-line/pulsed NMR spectrometers. T1 data are analyzed in two temperature regions using relevant theoretical models. The relaxation in the higher temperatures (270-115 K) is attributed to the hindered reorientations of symmetric groups (CH3 and (CH3)4N). Broad asymmetric T1 minima observed below 115 K down to 17 K are attributed to quantum rotational tunneling of the inequivalent methyl groups.

Undamped Oscillations of Collisionless Stellar Systems: Spheres,Spheroids and Discs.

The collisionless Boltzmann equation governing self-gravitating systems such as galaxies has recently been shown to admit exact oscillating solutions with planar and spherical symmetry. The relation of the spherically symmetric solutions to the Virial theorem, as well as generalizations to non-uniform spheres, uniform spheroids and discs form the subject of this paper. These models generalize known families of static solutions. The case of the spheroid is worked out in some detail. Quasiperiodic as well as chaotic time variation of the two axes is demonstrated by studying the surface of section for the associated Hamiltonian system with two degrees of freedom. The relation to earlier work and possible implications for the general problem of collisionless relaxation in self gravitating systems are also discussed.

Magnetization and magnetoresistive response of LiMn2O4 near the charge ordering transition

We report magnetization and magnetoresistance studies of the geometrically frustrated spinel compound LiMn2O4 near its charge ordering temperature. The effect of a 7 T magnetic field is to very slightly shift the transition in the resistivity to lower temperatures resulting in large negative magnetoresistance with significant hysteresis. This hysteresis is not reflected in the magnetization. These observations are compared with what is found in the colossal magnetoresistance and charge ordering perovskite manganese oxides. The manner in which geometric frustration influences the coupling of charge and spin degrees of freedom is examined.

A density matrix renormalization group study of low-lying excitations of polythiophene within a Pariser-Parr-Pople model

Symmetrized density-matrix-renormalization-group calculations have been carried out, within Pariser-Parr-Pople Hamiltonian, to explore the nature of the ground and low-lying excited states of long polythiophene oligomers. We have exploited C-2 symmetry and spin parity of the system to obtain excited states of experimental interest, and studied the lowest dipole allowed excited state and lowest dipole forbidden two photon state, for different oligomer sizes. In the long system limit, the dipole allowed excited state always lies below the lowest dipole forbidden two-photon state which implies, by Kasha rule, that polythiophene fluoresces strongly. The lowest triplet state lies below two-photon state as usual in conjugated polymers. We have doped the system with a hole and an electron and obtained the charge excitation gap and the binding energy of the 1(1)B(u)(-) exciton. We have calculated the charge density of the ground, one-photon and two-photon states for the longer system size of 10 thiophene rings to characterize these states. We have studied bond order in these states to get an idea about the equilibrium excited state geometry of the system. We have also studied the charge density distribution of the singly and doubly doped polarons for longer system size, and observe that polythiophenes do not support bipolarons.

Generalized Burgers equations and Euler–Painlevé transcendents. III

It was proposed earlier [P. L. Sachdev, K. R. C. Nair, and V. G. Tikekar, J. Math. Phys. 27, 1506 (1986); P. L. Sachdev and K. R. C. Nair, ibid. 28, 977 (1987)] that the Euler–Painlevé equations  y(d2y/dη2)+a(dy/dη)2 +f(η)y(dy/dη)+g(η)y2+b(dy/dη) +c=0 represent generalized Burgers equations (GBE’s) in the same way as Painlevé equations represent the Korteweg–de Vries type of equations. The earlier studies were carried out in the context of GBE’s with damping and those with spherical and cylindrical symmetry. In the present paper, GBE’s with variable coefficients of viscosity and those with inhomogeneous terms are considered for their possible connection to Euler–Painlevé equations. It is found that the Euler–Painlevé equation, which represents the GBE ut+uβux=(δ/2)g(t)uxx, g(t)=(1+t)n, β>0, has solutions, which either decay or oscillate at η=±∞, only when −1and, they oscillate over the whole real line when n=−1. Furthermore, the solutions monotonically decay both at η=+∞ and η=−∞, that is, they have a single hump form if β≥βn=(1−n)/(1+n). For β<βn, the solutions have an oscillatory behavior either at η=+∞ or at η=−∞, or at η=+∞ and η=−∞. For β=βn, there exists a single parameter family of exact single hump solutions, similar to those found for the nonplanar Burgers equations in Paper II. Thus the parametric value β=βn seems to bifurcate the families of solutions, which remain bounded at η=±∞. Other GBE’s considered here are also found to be reducible to Euler–Painlevé equations.

Magnetically induced currents and magnetic response properties of molecules

The magnetically induced currents in organic monoring and multiring molecules, in Möbius shaped molecules and in inorganic all-metal molecules have been investigated by means of the Gauge-including magnetically induced currents (GIMIC) method. With the GIMIC method, the ring-current strengths and the ring-current density distributions can be calculated. For open-shell molecules, also the spin current can be obtained. The ring-current pathways and ring-current strengths can be used to understand the magnetic resonance properties of the molecules, to indirectly identify the effect of non-bonded interactions on NMR chemical shifts, to design new molecules with tailored properties and to discuss molecular aromaticity. In the thesis, the magnetic criterion for aromaticity has been adopted. According to this, a molecule which has a net diatropic ring current might be aromatic. Similarly, a molecule which has a net paratropic current might be antiaromatic. If the net current is zero, the molecule is nonaromatic. The electronic structure of the investigated molecules has been resolved by quantum chemical methods. The magnetically induced currents have been calculated with the GIMIC method at the density-functional theory (DFT) level, as well as at the self-consistent field Hartree-Fock (SCF-HF), at the Møller-Plesset perturbation theory of the second order (MP2) and at the coupled-cluster singles and doubles (CCSD) levels of theory. For closed-shell molecules, accurate ring-current strengths can be obtained with a reasonable computational cost at the DFT level and with rather small basis sets. For open-shell molecules, it is shown that correlated methods such as MP2 and CCSD might be needed to obtain reliable charge and spin currents. The basis set convergence has to be checked for open-shell molecules by performing calculations with large enough basis sets. The results discussed in the thesis have been published in eight papers. In addition, some previously unpublished results on the ring currents in the endohedral fullerene Sc3C2@C80 and in coronene are presented. It is shown that dynamical effects should be taken into account when modelling magnetic resonance parameters of endohedral metallofullerenes such as Sc3C2@C80. The ring-current strengths in a series of nano-sized hydrocarbon rings are related to static polarizabilities and to H-1 nuclear magnetic resonance (NMR) shieldings. In a case study on the possible aromaticity of a Möbius-shaped [16]annulene we found that, according to the magnetic criterion, the molecule is nonaromatic. The applicability of the GIMIC method to assign the aromatic character of molecules was confirmed in a study on the ring currents in simple monocylic aromatic, homoaromatic, antiaromatic, and nonaromatic hydrocarbons. Case studies on nanorings, hexaphyrins and [n]cycloparaphenylenes show that explicit calculations are needed to unravel the ring-current delocalization pathways in complex multiring molecules. The open-shell implementation of GIMIC was applied in studies on the charge currents and the spin currents in single-ring and bi-ring molecules with open shells. The aromaticity predictions that are made based on the GIMIC results are compared to other aromaticity criteria such as H-1 NMR shieldings and shifts, electric polarizabilities, bond-length alternation, as well as to predictions provided by the traditional Hückel (4n+2) rule and its more recent extensions that account for Möbius twisted molecules and for molecules with open shells.

Excitation and relaxation energies of trans-stilbene: Confined singlet, triplet, and charged bipolarons

The π-electronic excitations and excited-state geometries of trans-stilbene (tS) are found by combining exact solutions of the Pariser-Parr-Pople (PPP) model and semiempirical Parametric Method 3 (PM3) calculations. Comprehensive comparisons with tS spectra are obtained and related to the fluorescence and topological alternation of poly(paraphenylenevinylene) (PPV). The one-photon absorption and triplet of tS correspond, respectively, to singlet and triplet bipolarons confined to two phenyls, while the tS2- ground state is a confined charged bipolaron. Independent estimates of the relaxation energy between vertical and adiabatic excitation show the bipolaron binding energy to depend on both charge and spin, as expected for interacting π electrons in correlated or molecular states. Complete configuration interaction within the PPP model of tS accounts for the singlet-triplet gap, for the fine-structure constants and triplet-triplet spectra, for two-photon transitions and intensities, and for one-photon spectra and the radiative lifetime, although the relative position of nearly degenerate covalent and ionic singlets is not resolved. The planar PM3 geometry and low rotational barrier of tS agree with resolved rotational and vibrational spectra in molecular beams. PM3 excitation and relaxation energies for tS bipolarons are consistent with experiment and with PPP results. Instead of the exciton model, we interpret tS excitations in terms of states that are localized on each ring or extended over an alternating chain, as found exactly in Hückel theory, and find nearly degenerate transitions between extended and localized states in the singlet, triplet, and dianion manifolds. The large topological alternation of the extended system increases the ionicity and interchanges the order of the lowest one- and two-photon absorption of PPV relative to polyenes.

Twinning of quasicrystals and related structures

We consider for the first time twinning in quasicrystals and related structures in a systematic manner. The twinning operations are considered in the framework of six-dimensional crystallography. The number of twin variants and the symmetry of twinned aggregates are also discussed. It is shown that essentially two different types of interface can arise between any two twin variants.

1H NMR study of molecular dynamics and phase transition in (NH4)2ZnBr4

The proton second moment (M2) and spin-lattice relaxation time (T1) have been measured in (NH4)2ZnBr4 in the range 77-300 K. The room-temperature spectrum shows a structure which disappears around 243 K. The signal is strong and narrow even at 77 K. Proton T1 shows a maximum at 263 K, caused by spin rotation interaction and decreases with decreasing temperature till 235 K, where it shows a sudden increase. Below 235 K, again it decreases and shows a slope change around 216.5 K (reported Tc). From 216.5 K, T1 decreases continuously without exhibiting any minimum down to 77 K. The narrow line at 77 K, and absence of a T1 minimum down to 77 K indicate the possibility of quantum mechanical tunnelling in this system. Motional parameters such as activation energy and pre-exponential factor have been evaluated for the reorientational motion of the NH+4 ion.

Photochemical intramolecular gamma-hydrogen abstraction in a ketone and an alkene and the role of tunneling of hydrogen

Intramolecular gamma-hydrogen abstraction reactions were examined in pentane-2-one and 2-methyl-1-pentene in their lowest triplet states using the AM1 semi-empirical molecular orbital method with the complete geometry optimization in the unrestricted Hartree-Fock frame. The results reveal that the oxygen atom of the carbonyl group and the end carbon atom of the olefinic bond acquire high free valence and spin density indices in their respective lowest triplet states, leading to abstraction of hydrogen from the gamma-position relative to the carbonyl and olefinic bonds. The theoretical energy profiles fit with a polynomial and the probability of tunneling of hydrogen was estimated by the WKB (Wentzel, Kramer and Brillouin) method. The results, after thermal averaging of the rate constants, reveal that tunneling of hydrogen is significant at room temperature.

Theoretical studies of the spin states of macrocyclic aza-amido binuclear copper (II) complexes

The spin and charge excitation gaps and charge and spin density distributions have been studied in macrocyclic binuclear aza-amido copper (II) complexes employing a model Hamiltonian. The spin gaps depend on the σ-orbital occupancies, and for small gaps, the exchange integral between the σ orbitals of the bridging oxygen atoms, KOO, which is sensitive to geometry, determines the low-lying spin excitations. The singlet—singlet gaps also depend upon the σ-orbital occupancy but are weakly dependent upon KOO.

Quantum Dots and Nanoroads of Graphene Embedded in Hexagonal Boron Nitride

The quest for novel two-dimensional materials has led to the discovery of hybrids where graphene and hexagonal boron nitride (h-BN) occur as phase-separated domains. Using first-principles calculations, we study the energetics and electronic and magnetic properties of such hybrids in detail. The formation energy of quantum dot inclusions (consisting of n carbon atoms) varies as 1/root n, owing to the interface. The electronic gap between the occupied and unoccupied energy levels of quantum dots is also inversely proportional to the length scale, 1/root n-a feature of confined Dirac fermions. For zigzag nanoroads, a combination of the intrinsic electric field caused by the polarity of the h-BN matrix and spin polarization at the edges results in half-metallicity; a band gap opens up under the externally applied ``compensating'' electric field. For armchair nanoroads, the electron confinement opens the gap, different among three subfamilies due to different bond length relaxations at the interfaces, and decreasing with the width.

Temperature dependence of infrared and Raman modes in polymeric RbC60

Temperature dependence of the intra-molecular vibrational modes Of C-60 in the quasi-1D polymeric RbC60, across the low temperature transition at similar to50 K, has been probed through infrared (IR) and Raman spectroscopies. With the lowering of temperature, the split IR modes of RbC60 are seen to harden but below 50 K a small but definitive signature of an anomalous softening is observed. In addition, the background IR transmission shows an increase below 50 K with the opening of a well defined gap in the electronic spectrum. The implications of these results, along with those of Raman measurements, are discussed in terms of the interaction of intra-molecular phonons with electrons and spin excitations in the system. (C) 2002 Published by Elsevier Science Ltd.