Ab initio calculation of excited state dipole polarizability - Application to the first 1, 3 Σ + g,u states of Li 2

Firstly, imaginary frequency-dependent dipole polarizabilities of Li in its ² S ground state and the first ² P excited state are calculated from a time-dependent gauge-invariant method using effective core pseudo-potentials and the multi-configuration one-electron wave function. C₆ dispersion coefficients of the 2 s + 2 s and 2 s + 2 p dissociations are deduced and also compared with all-electron values. Then, static polarizabilities of Li₂ in its ground and first excited ^{1, 3} Σ ⁺ _g,u states are obtained at interatomic distance corresponding to the energy minimum of each state. Received 10 May 2001 and Received in final form 14 September 2001     

Molecular beam deflection experiments on mixed clusters

Gas phase Ti-C₆₀ clusters are studied by molecular beam electric deflection. The permanent dipole moment of the TiC₆₀ molecule is determined. It is equal to 8.1±1.5 D. This dipole is due to a transfer of electron from the transition metal atom to the C₆₀ cage. No dipole is observed for Ti(C₆₀)₂ molecules. This is in agreement with the symmetrical dumbbell-like structure that has been previously proposed. Received 22 November 2000     

Susceptibility and electric dipole in metal C 60 compounds

The permanent electric dipole moment of metal atom-C₆₀ compounds is measured. A column (alkali) and a row (transition metals) of the periodic table are systematically investigated. Most of the experimental results are obtained at high temperature when the atom is mobile on the C₆₀ cage. For a given example (NaC₆₀), the dipole moment is also measured by a different method at low temperature and both results are consistent. For alkali, the results are compared to ab initio calculations. A good agreement is obtained, both for absolute values and for the evolution of the bonding in the alkali column. For transition metals, the relative values of the dipole moments are in qualitative agreement with the ionic character of the compounds.     

Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that ≈40-base molecules can undergo kinetic transitions between two well-defined “open” and “closed” states, on a timescale ≈1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed. Our dynamical model is also applied to the unzipping of long (kilo-basepair) DNA molecules at constant force. Received 29 July 2002 / Received in final form 5 February 2003 Published online: 16 April 2003 RID="a" ID="a"e-mail: cocco@ldfc.u-strasbg.fr RID="b" ID="b"e-mail: jmarko@uic.edu RID="c" ID="c"e-mail: monasson@lpt.ens.fr     

Static electric dipole polarizabilities of Na clusters

The static electric dipole polarizability of Na _N clusters with even N has been calculated in a collective, axially averaged and a three-dimensional, finite-field approach for , including the ionic structure of the clusters. The validity of a collective model for the static response of small systems is demonstrated. Our density functional calculations verify the trends and fine structure seen in a recent experiment. A pseudopotential that reproduces the experimental bulk bond length and atomic energy levels leads to a substantial increase in the calculated polarizabilities, in better agreement with experiment. We relate remaining differences in the magnitude of the theoretical and experimental polarizabilities to the finite temperature present in the experiments. Received 8 November 1999     

Ab initio calculations of the second dynamic hyperpolarizability of LiH by means of Floquet theory approach

Floquet theory is used to describe the response of a molecule to applied radiation electric field. The method of ab initio calculation of frequency dependent (hyper)polarizabilities based on combination of perturbation theory with the finite field method has been developed. Electron correlation is taken into account by means of the CIPSI algorithm. The total wave function expansion involves spectral, pseudo-spectral states and polynomial terms. The developed approach is applied to the calculation of the second hyperpolarizability of the lithium hydride molecule subjected to the superposition of harmonic and static electric fields. The method can be used to calculate the higher order nonlinear properties of molecules. Received 23 November 2000 and Received in final form 25 March 2001     

Sphere packing, helices and the polytope {3, 3, 5}

The packing of tetrahedra in face contact is well-known to be relevant to atomic clustering in many complex alloys. We briefly review some of the structures that can arise in this way, and introduce methods of dealing with the geometry of the polytope {3, 3, 5}, which is highly relevant to an understanding of these structures. Finally, we present a method of projection from S₃ to E₃ that enables coordinates for the key vertices of the collagen model of Sadoc and Rivier to be calculated. Received 27 March 2001     

Non perturbative approach for a polar and polarizable linear molecule in an inhomogeneous electric field: Application to molecular beam deviation experiments

A non perturbative approach is used to solve the problem of a rigid linear molecule with both a permanent dipole moment and a static dipole polarizability, in a static electric field. Eigenenergies are obtained and compared to perturbative low field and high field approximations. Analytical expressions for the orientation parameters and for the gradient of the energy are given. This non perturbative approach is applied to the simulation of beam deviation experiments in strong electric field. Results of simulations are given for inhomogeneous alkali dimers. For LiNa, the simulations are compared to experimental data. For LiK, deviation profiles have been simulated in order to prepare future experiments on this molecule. Received 21 July 1999 and Received in final form 22 September 1999     

A DFT study of electron or hole localization in a peptide containing asparagin

The mechanisms of protein degradation induced by ionisation are of great interest for radiobiology, improvement of mass spectroscopy and industrial processes such as radio sterilisation. Sequences containing asparagin are very sensitive especially if surrounded by glycine. Very few techniques allow a satisfying understanding of the processes induced by creation of an anionic or cationic site in a peptide. We used the methods of quantum chemistry (DFT/B3LYP with 6-31G^* basis set) to characterise the geometry modifications induced in the cations or in the anions derived from peptide Gly Asn Gly. The cationic sites are localised mostly close to the first peptidic bond and induce a lengthening of the Ca-C(O) bond. Conversely the anionic sites are localised on a carbonyl function. Implications are discussed considering the radiolytic products and the proposed mechanisms. Received 21 January 2002 Published online 13 September 2002     

Fibril stability in solutions of twisted -sheet peptides: a new kind of micellization in chiral systems

The problem of fibril (fibre) formation in chiral systems is explored theoretically being supported by experiments on synthetic de novo 11-mer peptide forming self-assembled -sheet tapes. Experimental data unambiguously indicate that the tapes form fibrils of nearly monodisperse thickness ca . 8-10 nm. Fibril formation and stabilisation are attributed to inter-tape face-to-face attraction and their intrinsic twist, correspondingly. The proposed theory is capable of predicting the fibril aggregation number and its equilibrium twist in terms of molecular parameters of the primary tapes. The suggested novel mechanism of twist stabilisation of finite aggregates (fibrils) is different to the well-known stabilisation of micelles in amphiphilic systems, and it is likely to explain the formation and stability of fibrils in a wide variety of systems including proteinaceous amyloid fibres, sickle-cell hemoglobin fibres responsible for HbS anemia, corkscrew threads found in chromonics in the presence of chiral additives and native cellulose microfibrillar crystallites. The theory also makes it possible to extract the basic molecular parameters of primary tapes (inter-tape attraction energy, helical twist step, elastic moduli) from the experimental data. Received 7 May 1999 and Received in final form 15 February 2000     

Magnetic order in the Shastry-Sutherland model

We investigate the influence of energetic disorder, viscous damping and an external field on the electron transfer (ET) in DNA. The double helix structure of the λ-form of DNA is modeled by a steric oscillator network. In the context of the base-pair picture two different kinds of modes representing twist motions of the base pairs and H-bond distortions are coupled to the electron amplitude. Through the nonlinear interaction between the electronic and the vibrational degrees of freedom localized stationary states in the form of standing electron-vibron breathers are produced which we derive with a stationary map method. We show that in the presence of additional energetic disorder the degree of localization of such breathers is enhanced. It is demonstrated how an applied electric field initiates the long-range coherent motion of breathers along the bases of a DNA strand. These moving electron-vibron breathers, absorbing energy from the applied field, sustain energetic losses due to the viscous friction caused by the aqueous solvent as well as the impact of a moderate amount of energetic disorder. Moreover, it is illustrated that with the choice of the amplitude and frequency of the external field, the breather can be steered to a desired lattice position achieving control of the ET. Received 5 July 2002 Published online 29 November 2002     

Localization properties of electronic states in a polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.     

Quantum diffusion in polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate quantum diffusion of an electron in a model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with fluctuation of the parameters due to the impact of colored noise. The randomness is introduced by fluctuations of distance between two consecutive bases along the stacked base pairs. We demonstrate that in the model the decay time of the correlation can control the spread of the electronic wavepacket. Furthermore it is shown that in a motional narrowing regime the averaging over fluctuation causes ballistic propagation of the wavepacket, and in the adiabatic regime the electronic states are affected by localization.     

Static anisotropic and isotropic electric dipole polarizabilities of Na n F n-1 clusters

Recently, electric susceptibilities of Na_nF_n-1 clusters have been measured by deflecting a molecular beam in an inhomogeneous electric field. The analysis of the deflection of a cluster by the electric field needs the calculation of the electric properties. We present the calculation of the static anisotropic and average dipolar polarizabilities within a model in which the Na_nF_n-1 clusters ( 2 n 23) are treated as one electron embedded in the field of n ions Na⁺ and of n - 1 ions F^-. The accuracy of the results is evaluated and discussed on small clusters (n 5) in comparison with ab initio calculations. The relationship between the polarizabilities, the electronic localization and the geometric structure is discussed. Received 10 September 2002 Published online 3 July 2003     

Deformation in cooperative molecular motors

We implement a model to represent the effect of the deformation of the backbone of a system of motor proteins while sliding on a track filament. This model incorporates a nearest neighbor interaction term among the motors for the deformation energy. Correlations induced by this term result in increased motor force for inter-particle distances small compared to the ratchet period. Received 20 February 2001 and Received in final form 31 May 2001     

Hydration of nucleic acid components in dependence on nucleotide composition and relative humidity: a Monte Carlo simulation

What role does the nucleotide composition play in the process of formation of hydrated environment of nucleic acids? Can one estimate the hydration of nucleic acids on the level of their components? In order to resolve these questions we have completed an extensive computer simulation of the hydration of nucleic acids components - deoxynucleoside monophosphates distinguished by nucleotide composition. The energetic characteristics of systems containing deoxynucleoside monophosphates and water clusters of various dimensions are received. Our results demonstrate that deoxynucleoside monophosphates containing guanine and/or cytosine residues hydrated more strongly because of formation of more hydrogen bonds with water molecules in small water clusters, i.e. at low values of relative humidity. With increasing of number of water molecules in a water cluster the energetic preference of deoxynucleoside monophosphates containing guanine and/or cytosine residues decreases, and for water clusters corresponding to a state of a dilute aqueous solution the hydration of all types of deoxynucleoside monophosphates does not differ in a great degree. Deoxynucleoside monophosphates containing guanine and/or cytosine residues cause the greater destruction of the water structure compensated by the greater interaction with the nearest water molecules for all levels of relative humidity. Received 25 December 2001 and Received in final form 22 March 2002 Published online 13 September 2002     

The secondary structure of RNA under tension

We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second-order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a macroscopic end-to-end distance at high forces. At low temperatures, the sequence inhomogeneities modify the critical behaviour. We provide numerical evidence for the universality of the critical exponents which, by extrapolation of the scaling laws to zero force, contain useful information on the ground-state (f = 0) properties. This provides a good method for quantitative studies of scaling exponents characterizing the collapsed globule. In order to get rid of the blurring effect of thermal fluctuations, we restrict ourselves to the ground state at fixed external force. We analyze the statistics of rearrangements, in particular below the critical force, and point out its implications for force-extension experiments on single molecules. Received 18 June 2002 and Received in final form 23 September 2002 RID="a" ID="a"e-mail: muller@ipno.in2p3.fr     

Helix coil mixing in twist-storing polymers

Twist-storing polymers respond with elastic energy penalty to coherent or random twisting along the local chain axis away from its equilibrium, which can be straight (as in “ribbons”) or helical (as in DNA and other biopolymers). Here we study the equilibrium conformation of such polymers, focusing on the thermodynamic balance between twist and writhe, resulting from the competition between the random coil entropy and the potential energy stored in superhelical portions of the polymer chain. Two macroscopic variables characterise such a chain, the end-to-end distance R and the link number Lk, which is a topological invariant of a given polymer with clamped ends. We find that with increasing link number Lk, the chain accommodates its excess twist in growing plectonemes, unless forced out of this state by stretching its end-to-end distance R. We calculate the force-extension relation, which exhibits crossovers between different deformation regimes. Received 16 November 2000 and Received in final form 6 February 2001     

Solute effects on the helix-coil transition

We discuss the effects of the solvent composition on the helix-coil transition of a polypeptide chain. We use a simple model to demonstrate that improving the hydrogen-bonding ability of the solvent can make the transition less cooperative, without affecting the transition temperature. This effect is very different from other solvent effects which primarily influence the melting transition rather than the cooperativity. Received 10 December 2001 and Received in final form 22 March 2002