Florent Xavier Gadéa

Building-Block Approach for Determining Low-Frequency Normal Modes of Macromolecules

Normal mode analysis of proteins of various sizes, ranging from 46 (crambin) up to 858 residues (dimeric citrate synthase) were performed, by using standard approaches, as well as a recently proposed method that rests on the hypothesis that low‐frequency normal modes of proteins can be described as pure rigid‐body motions of blocks of consecutive amino‐acid residues. Such a hypothesis is strongly supported by our results, because we show that the latter method, named RTB, yields very accurate approximations for the low‐frequency normal modes of all proteins considered. Moreover, the quality of the normal modes thus obtained depends very little on the way the polypeptidic chain is split into blocks. Noteworthy, with six amino‐acids per block, the normal modes are almost as accurate as with a single amino‐acid per block. In this case, for a protein of n residues and N atoms, the RTB method requires the diagonalization of an n × n matrix, whereas standard procedures require the diagonalization of a 3N × 3N matrix. Being a fast method, our approach can be useful for normal mode analyses of large systems, paving the way for further developments and applications in contexts for which the normal modes are needed frequently, as for example during molecular dynamics calculations. Proteins 2000;41:1–7.

Theoretical study of the visible photodissociation spectrum of Ar3

Abstract The six A′ potential energy surfaces were computed by a DIM-like method involving a valence-bond quasidiabatic basis. Transition dipole moments were also determined using a similar method. The 4D dynamics of this system (restricted to a molecular plane fixed in space) was obtained with the HWD method (hemiquantal dynamics with the whole DIM basis) and the visible photoabsorption spectrum was determined with the help of a 1D full quantum mechanical program applied to each normal mode. The photoabsorption spectrum of Ar3+ was calculated in the range 440–710 nm. It corresponds to photodissociation since the excited Ar3+ ions almost all dissociate into the Ar+ +Ar+Ar channel by a rapid explosion of the cluster, and only very few into Ar2+ +Ar. It is dominated by a transition to the second excited state along with a symmetric stretching motion. We found a prominent 80 nm wide peak centered at 530 nm, with a maximum cross section of 4.2 × 10−16cm2. The Ar2+ formation results from a transition to the first excited state under low-energy laser excitation and is controlled by non-adiabatic transitions.

Ab initio calculations for Ar2+, He2+ and He3+, of interest for the modelling of ionic rare-gas clusters

Abstract Large CI ab initio calculations are performed for Ar2+, He2+ and He3+. For both ionic dimers a complete set of accurate data is determined, including the various electronic states and the transition moments to be used for spectroscopical studies and for modelling larger ionic rare-gas clusters. Spectroscopic constants for Ar2+ are in remarkable agreement with the experimental results. The study for He3+ confirms the failure of the minimal DIM model for helium ions.

Theoretical study of an unusual reactive collision Cs(7p)+H2→CsH+H. Diabatic approach of the collinear collision potential energy surfaces

The Cs(7p)+(X 1∑+g, v=0) H2→(X 2∑+, v=0) CsH+H reactive collision was recently experimentally observed from a crossed beam experiment by Crepin et al. This reaction is rather unusual since it starts from a highly excited state of the system (11th potential surface) and must reach the ground state surface in the product channel without energy loss. Accurate nonempirical CI calculations of the potential energy surface for the collinear collision are reported, using large basis sets and a nonempirical relativistic pseudopotential for the Cs atom. The adiabatic potential surfaces, which exhibit irregular behavior, are reinterpreted in terms of an ab initio nearly diabatic effective Hamiltonian spanned by five neutral repulsive channels Cs(6s)×H2, Cs(6p)×H2,..., Cs(7p)×H2 and an ionic very flat Cs+H−2 channel which tends to the product wave function (Cs+H−)×H. The intersection of these diabatic potential surfaces are accessible from the entrance energy and this picture supports a harpooning mechanism, the 7p e...

A theoretical study of mutual neutralization in Li + H collisions

First principles calculations of mutual neutralization in and collisions have been performed for low energies (0.68-50.0 eV). A diabatic representation is used for eight electronic states determined directly within an ab initio calculation. For the comparison with the recent merged-beam experiment the finite acceptance angle of the detector has been taken into account. An improved ionic diabatic curve, corrected for deficiencies in the ab initio electron affinity of H, has also been used. The large cross section at low energy for this mutual neutralization is due predominantly to the almost optimal efficiency for the non-adiabatic transition to the neutral Li(3s)H(1s) state. The calculated cross section exceeds experiment by no more than about 20%, indicating that the neutral-ionic diabatic crossings and couplings are accurately evaluated by the ab initio approach.

AB INITIO STUDY OF THE LIH+ MOLECULE, ELECTRONIC INTERACTION ANALYSIS AND LIH UV PHOTOELECTRON SPECTRUM

Abstract All adiabatic curves of LiH + dissociating into Li(2s, 2p, 3s, 3p, 3d) + H + and Li + + H (1s, 2s, 2p) are determined by an ab initio approach involving a non-empirical pseudopotential for the Li(ls 2 ) core and core valence correlation corrections. The resulting spectroscopic constants and vibrational level spacings of all these states are presented. From the usual semiclassical approximations an analysis of the high energy vibrational level spacing is performed allowing for accurate long range extrapolations. For the lowest curves dissociating into Li + + H (1s) and Li (2s) + H + an analysis of the main electronic interactions is carried out from a diabatic model and reveals the importance of the binding charge delocalisation effects versus the polarisation (charge localised) ones. In addition the LiH photoelectron spectrum is calculated. An interesting feature of that spectrum is that both bound-bound and bound-free transitions coexist due to the particular shape of the LiH and LiH + potential energy curves.

Theoretical and experimental determination of the lowest excited states of the Kr*2 excimer

The potential energy curves of the Kr*2 excimer dissociating into Kr (4s24p6 1S0)+Kr*(4s24p55s) are determined (i) theoretically from ab initio CI calculation and semiempirical SO coupling and (ii) experimentally from the temperature dependence of absorption profiles. The results are carefully examined with the help of theoretical simulation of line profiles using semiclassical or quantal models.

Theory of Fano profiles

The theory of Fano profiles currently presented in the framework of scattering theory can also be investigated from model Hamiltonians projected in the basis of discrete states. It is shown that the wave operator approach of quantum dynamics applied to these models simultaneously provides the lineshapes and the dynamics of the quasi-bound states of interest. An analytical expression which generalizes Fano profiles is presented.

Nonradiative lifetimes for LiH in the A state using adiabatic and diabatic schemes

Accurate positions and nonradiative lifetimes of states belonging to the adiabatic A state of LiH are estimated. The results coming from a Golden Rule treatment in the adiabatic scheme present excellent agreement with those obtained through a diabatic close coupling calculation. That confirms the accuracy reached in both approaches and also in the treatment of the diabatic–adiabatic transformation. It involves, in particular, an effective phase control that is needed to properly estimate nonadiabatic couplings. Also, a powerful numerical procedure to obtain energy profiles in the diabatic close coupling frame is described and applied in this work.

Theoretical study of the CsH molecule: adiabatic and diabatic potential energy curves and dipole moments

For nearly all states dissociating below the ionic limit, we perform an adiabatic and diabatic study for 1?+ and 3?+ electronic states dissociating into Cs (6s, 6p, 5d, 7s, 7p, 6d, 8s and 4f) + H (1s). Furthermore, we present the adiabatic results for the 1?5 1,3? and 1?3 1,3? states. The calculations rely on an ab initio pseudopotential, semi-empirical operator core-valence correlation and full valence CI approaches, combined to an efficient diabatization procedure. For the low-lying states, our spectroscopic constants and vibrational level spacing are in very good agreement with the available experimental data. Diabatic potentials and dipole moments are analysed, revealing the strong imprint of the ionic state in the 1?+ adiabatic states. The H electron affinity correction was accounted for by the use of the efficient diabatization method. This leads to a better agreement with the available experimental data. Experimental suggestions are also given for the higher excited states based on their unusual behaviour.