Large-amplitude Molecular Motions Research Articles

Structures and conformational dynamics of trans- and cis-crotonaldehydes in excited electronic states: A quantum-chemical study

For trans- and cis-crotonaldehydes CH3CHCHCHO in the triplet and singlet lowest excited electronic states of n,π* and π,π* types, the geometries of conformers, conformer energy differences, and conformational dynamics have been addressed using ab initio multi-reference techniques (CASSCF and CASPT2). The conformers of investigated molecules under study have been shown to possess a symmetry plane in 1,3(n,π*) states and to be significantly non-planar in 1,3(π,π*) states. Couplings of asymmetric internal rotations around CC and CC bonds with others large amplitude molecular motions such as methyl torsion, non-planar distortions of CCHO, CCHC, and CCH(CH3) fragments are discussed. The type of coupling between large-amplitude motions has been shown to be connected with the localization of electronic excitation.

Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase.

Nucleotide-induced conformational closing of the finger domain of DNA polymerase is crucial for its catalytic action during DNA replication. Such large-amplitude molecular motion is often not fully accessible to either direct experimental monitoring or molecular dynamics simulations. However, a coarse-grained model can offer an informative alternative, especially for probing the relationship between conformational dynamics and catalysis. Here we investigate the dynamics of T7 DNA polymerase catalysis using a Langevin-type elastic network model incorporating detailed structural information on the open conformation without the substrate bound. Such a single-parameter model remarkably captures the induced conformational dynamics of DNA polymerase upon dNTP binding, and reveals its close coupling to the advancement toward transition state along the coordinate of the target reaction, which contributes to significant lowering of the activation energy barrier. Furthermore, analysis of stochastic catalytic rates suggests that when the activation energy barrier has already been significantly lowered and nonequilibrium relaxation toward the closed form dominates the catalytic rate, one must appeal to a picture of two-dimensional free energy surface in order to account for the full spectrum of catalytic modes. Our semiquantitative study illustrates the general role of conformational dynamics in achieving transition-state stabilization, and suggests that such an elastic network model, albeit simplified, possesses the potential to furnish significant mechanistic insights into the functioning of a variety of enzymatic systems.

Encoding Molecular Motions in Voxel Maps

This paper builds on the combination of robotic path planning algorithms and molecular modeling methods for computing large-amplitude molecular motions, and introduces voxel maps as a computational tool to encode and to represent such motions. We investigate several applications and show results that illustrate the interest of such representation.

Structure and dynamics of acrolein in 1,3(π,π *) excited electronic states: A quantum-chemical study

The geometrical structure, conformer energy differences, and conformational and vibrational dynamics of acrolein in 1,3(π,π *) electronic states were investigated using a number of single- and multi-reference quantum-chemical methods. Peculiarities of acrolein in the 1(π,π *) state were described with both conformers being significantly non-planar. A Valence Focal-Point Analysis of the conformer energy difference in the 3(π,π *) state was performed. The coupling of the internal rotation about C C and C C bonds with large amplitude molecular motions, such as non-planar distortions of carbonyl, methylene, and methyne fragments was also investigated. The corresponding two-dimensional PES sections were constructed.

Structural Analysis of Transmembrane Halobacterial Tranceducer pHtrII by Multi-Dimensional High-Resolution Solid-State NMR

°Transmembrane protein pHtrII is a transducer which binds to phoborhodopsin. The light excitation of phoborhodopsin is transmitted into the cytoplasm through pHtrII to promote negative photoaxis. We studied uniformly 13 C, 15 N labeled 159residues pHtrII by high-resolution solid-state NMR. The pHtrII (1-159) was econstructed into the deuterated DMPC membranes. High-resolution solid-state 2D NMR was measured under magic-angle spinning at the 1 H resonance frequencies of 500, 600 and 700 MHz . At first, we have assigned 13 C signals of pHtrII (1-159) by using 13 C- 13 C spin diffusion under DARR at -40 o C.Intraresidue correlations across 1-2 bonds were observed at short mixing time. At a long mixing time of 200 ms, intra-residue C α correlations across 3-bonds were obtained. Most amino acids except Tyr and Pro were assigned. The DARR spectra were observed for immobile region of pHtrII. All 13 C signals could not be observed in these dipolar-coupling-based cross-polarization methods because of large-amplitude molecular motions at room temperature. We performed Jcoupling-based HC-INEPT and HCC-TOCSY experiments in order to obtain signals of mobile protein segments. Mobile protein segments make up about 70% of pHtrII (1-159). Many signals in mobile regions were observed in HC and HCC 2D spectra. 13 C and 1 H signals were assigned to amino acid groups were successful in mobile regions. The C α and CO chemical shifts indicate that pHtrII (1-159) mainly forms α -helix structure in lipid bilayer environment.

Nuclear quadrupole hyperfine structure in HC14N/H14NC and DC15N/D15NC isomerization: a diagnostic tool for characterizing vibrational localization

Large-amplitude molecular motions which occur during isomerization can cause significant changes in electronic structure. These variations in electronic properties can be used to identify vibrationally-excited eigenstates which are localized along the potential energy surface. This work demonstrates that nuclear quadrupole hyperfine interactions can be used as a diagnostic marker of progress along the isomerization path in both the HC14N/H14NC and DC15N/D15NC chemical systems. Ab initio calculations at the CCSD(T)/cc-pCVQZ level indicate that the hyperfine interaction is extremely sensitive to the chemical bonding of the quadrupolar 14N nucleus and can therefore be used to determine in which potential well the vibrational wavefunction is localized. A natural bonding orbital analysis along the isomerization path further demonstrates that hyperfine interactions arise from the asphericity of the electron density at the quadrupolar nucleus. Using the CCSD(T) potential surface, the quadrupole coupling constants of highly-excited vibrational states are computed from a one-dimensional internal coordinate path Hamiltonian. The excellent agreement between ab initio calculations and recent measurements demonstrates that nuclear quadrupole hyperfine structure can be used as a diagnostic tool for characterizing localized HCN and HNC vibrational states.

Photophysical Characterization of Natural cis-Carotenoids¶

By means of steady-state fluorescence spectroscopy we explore the photophysics of two lowest lying singlet excited states in two natural 15-cis-carotenoids, namely phytoene and phytofluene, possessing three and five conjugated double bonds (N), respectively. The results are interpreted in relation to the photophysics of all-trans-carotenoids with varying N. The fluorescence of phytofluene is more Stokes-shifted relative to that of phytoene, and is ascribed to the forbidden S1→ S0 transition, with its first excited singlet state (S1) lying 3340 cm−1 below the dipole allowed second excited singlet state (S2), at 77 K. For phytoene the S2 and S1 potential surfaces are closer in energy, probably giving rise to the mixed S2 and S1 fluorescence characteristics. The origin of phytoene fluorescence is discussed and is suggested to be due to the S1→ S0 transition; with the S1 state located 1100 cm−1 below S2 at 77 K. The dependence of the fluorescence quantum yield on temperature and viscosity shows that large amplitude molecular motions are involved in the radiationless relaxation process of phytoene. The transition dipole moment of absorption and emission are parallel in phytoene and nonparallel in phytofluene.

Electroactive Films of Multicomponent Building Blocks

AbstractA ligand consisting of a 2,2′‐bipyridine core and two 4,4′‐bipyridinium arms terminated by a thiol group is prepared following a multistep synthetic procedure. Two of these ligands assemble around a single CuI center as a result of the tetrahedral coordination of their 2,2′‐bipyridine cores by the metal. Both the ligand and the complex adsorb spontaneously on the surface of polycrystalline‐gold electrodes. The surface coverage of the films prepared by immersing a gold substrate into a solution of the ligand increases from monolayer to multilayer values with immersion time. Instead, the complex can only form monolayers. The cyclic voltammograms of the resulting films show the characteristic response for the reversible reduction of the 4,4′‐bipyridinium dications to their radical cations. In the case of the complex, a wave for the monoelectronic oxidation of the metal center can also be observed. The back reduction wave, however, is markedly broader and appears at significantly lower potentials. Model studies in solution indicate that this response is a result of the presence of free thiol groups and is consistent with a change in the coordination geometry of the metal. Specifically, the oxidation of the CuI center to a CuII ion is, presumably, accompanied by the folding of one of the thiol groups back to interact with the metal. Thus, oxidation/reduction cycles of the metal center can, in principle, be exploited to control reversibly large amplitude molecular motions at the electrode/solution interface in the shape of the folding/unfolding of oligomethylene chains.

Intramolecular Charge Transfer Assisted by Conformational Changes in the Excited State of Fluorene-dibenzothiophene-S,S-dioxide Co-oligomers

The strong solvatochromism observed for two fluorene-dibenzothiophene-S,S-dioxide oligomers in polar solvents has been investigated using steady-state and time-resolved fluorescence techniques. A low-energy absorption band, attributed to a charge-transfer (CT) state, is identified by its red shift with increasing solvent polarity. In nonpolar solvents, the emission of these conjugated luminescent oligomers shows narrow and well-resolved features, suggesting that the emission comes from a local excited state (LE), by analogy to their conjugated fluorene-based polymer counterparts. However, in polar solvents, only a featureless broad emission is observed at longer wavelengths (CT emission). A linear correlation between the energy maximum of the fluorescence emission and the solvent orientation polarizability factor Deltaf (Lippert-Mataga equation) is observed through a large range of solvents. In ethanol, below 230 K, the emission spectra of both oligomers show dual fluorescence (LE-like and CT) with the observation of a red-edge excitation effect. The stabilization of the CT emissive state by solvent polarity is accompanied/followed by structural changes to adapt the molecular structure to the new electronic density distribution. In ethanol, above 220 K, the solvent reorganization occurs on a faster time scale (less than 10 ps at 290 K), and the structural relaxation of the molecule (CT(unrelaxed) --> CT(Relaxed)) can be followed independently. The magnitude of the forward rate constant, k(1)(20 degrees C) approximately 20 x 10(9) s(-1), and the reaction energy barrier, E(a) approximately 3.9 kcal mol(-1), close to the energy barrier for viscous flow in ethanol (3.54 kcal mol(-1)), show that large-amplitude molecular motions are present in the stabilization of the CT state.

Water dynamics inside single-wall carbon nanotubes: NMR observations

The dynamics of water (${\mathrm{H}}_{2}\mathrm{O}$ and ${\mathrm{D}}_{2}\mathrm{O}$) molecules adsorbed inside single-wall carbon nanotubes (SWCNTs) of average diameter $13.5\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$ were investigated by means of $^{2}\mathrm{H}$- and $^{1}\mathrm{H}$-NMR between 100 and $300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. Above $220\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, the NMR spectra were substantially narrowed, and indicated that the water is in a liquidlike state with translational and quasifree rotational motions. Below $220\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, where water exhibits long range order inside SWCNTs, the large amplitude molecular motions start to freeze within a time scale of ${10}^{\ensuremath{-}6}\phantom{\rule{0.3em}{0ex}}\mathrm{s}$, while below around $120\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, almost all of the protons become fixed around each atomic site. The results support the dynamic properties and ice-nanotube transition predicted by previous molecular dynamics calculations.

31P double-quantum solid-state NMR study of phosphoroorganic compounds with (O)P–O–P-(O), (S)P–O–P(S) and (S)P–S–P(O) unit

In this work we have tested applicability of the commonly used double quantum recoupling sequence POST-C7 to study of 31P– 31P geometrical constraints for phosphoroorganic model compounds with different chemical shift anisotropy (CSA) and distinct molecular dynamics in the crystal lattice. Our results clearly show that even with large CSA, POST-C7 gives good efficiency of 31P double-quantum excitations. Moreover, large amplitude molecular motion only slightly disturb 31P build-up curve. χ 2 error analysis is used for verification of values and orientations of chemical shift tensors (CST) parameters employed for simulation of POST-C7 buildup curves.

Helium nanodroplet isolation rovibrational spectroscopy: Methods and recent results

In this article, recent developments in helium nanodroplet isolation (HENDI) spectroscopy are reviewed, with an emphasis on the infrared region of the spectrum. We discuss how molecular beam spectroscopy and matrix isolation spectroscopy can be usefully combined into a method that provides a unique tool to tackle physical and chemical problems which had been outside our experimental possibilities. Next, in reviewing the experimental methodology, we present design criteria for droplet beam formation and its seeding with the chromophore(s) of interest, followed by a discussion of the merits and shortcomings of radiation sources currently used in this type of spectroscopy. In a second, more conceptual part of the review, we discuss several HENDI issues which are understood by the community to a varied level of depth and precision. In this context, we show first how a superfluid helium cluster adopts the symmetry of the molecule or complex seeded in it and discuss the nature of the potential well (and its anisotropy) that acts on a solute inside a droplet, and of the energy levels that arise because of this confinement. Second, we treat the question of the homogeneous versus inhomogeneous broadening of the spectral profiles, moving after this to a discussion of the rotational dynamics of the molecules and of the surrounding superfluid medium. The change in rotational constants from their gas phase values, and their dependence on the angular velocity and vibrational quantum number are discussed. Finally, the spectral shifts generated by this very gentle matrix are analyzed and shown to be small because of a cancellation between the opposing action of the attractive and repulsive parts of the potential of interaction between molecules and their solvent. The review concludes with a discussion of three recent applications to (a) the synthesis of far-from-equilibrium molecular aggregates that could hardly be prepared in any other way, (b) the study of the influence of a simple and rather homogeneous solvent on large amplitude molecular motions, and (c) the study of mixed He3/He4 and other highly quantum clusters (e.g., H2 clusters) prepared inside helium droplets and interrogated by measuring the IR spectra of molecules embedded in them. In spite of the many open questions, we hope to convince the reader that HENDI has a great potential for the solution of several problems in modern chemistry and condensed matter physics, and that, even more interestingly, this unusual environment has the potential to generate new sets of issues which were not in our minds before its introduction.

Solid State 13C NMR of 30-Crown-10 Ether and 30-Crown-10.4H2O

The 13C NMR solution spectra of 30-crown-10 ether and its tetrahydrate show only one resonance at all accessible temperatures. In contrast, the solid state 13C NMR spectrum of the 30-crown-10.4H2O shows two resonances in the ratio of 4:1, separated by 1.2 ppm. In the case of 30-crown-10 itself, six resolvable 13C resonances in the ratio of 4:1:1:2:1:1 are observed in the solid with an overall chemical shift dispersion of 5 ppm. The remarkably different spectral behavior of these two systems in the solid state is discussed in terms of the torsional environments of the crystallographically unique carbons and the results of GIAO calculations of isotropic 13C shieldings for simpler model compounds. Results of dipolar dephased 13C CPMAS spectra indicate that 30-crown-10 does not undergo a large amplitude molecular motion, in contrast to earlier results for 18-crown-6. Only a small amount of residual intensity is found in the dipolar dephased spectrum of 30-crown-10.4H2O, indicating that it also is relatively rigid in the solid.

Measurement of heat capacity to gain information about time scales of molecular motion from pico to megaseconds

Molecular motion has primarily a time scale of picoseconds. Quantum mechanical models of small-amplitude vibrations and local, large-amplitude motions can be fitted quantitatively to equilibrium heat capacities. Macroscopic calorimetry, thus yields indirectly the characteristic frequencies of molecular motion in the range of 10 11–10 13 Hz. At lower temperature, much of the large-amplitude molecular motion is restricted to cooperative movements and slows to macroscopic times so that calorimetry can directly measure the kinetics of these changes which may extend the time scales to megaseconds and beyond. In this light, instrumentation and interpretation of differential scanning temperature-modulated calorimetry (DSTMC) are discussed. Six basic thermal effects govern the thermal analysis of linear macromolecules: (1) the vibrational heat capacity; (2) heat capacities arising from large amplitude molecular motion; (3) reversible transitions; (4) annealing; (5) secondary crystallization and (6) primary crystallization. Of these only (1)–(3) are reversible. To these six thermal effects that do not change the molecular integrity, chemical reactions, evaporation, and condensation have to be added for a full thermal analysis. The latter effects have not been treated in this paper.

Dynamics of molecules in crystals from multi-temperature anisotropic displacement parameters. I. theory

A new model for analysing the temperature evolution of anisotropic displacement parameters (ADP's) is presented. It allows for a separation of temperature-dependent from temperature-independent contributions to ADP's and provides a fairly detailed description of the temperature-dependent large-amplitude molecular motions in crystals in terms of correlated atomic displacements and associated effective vibrational frequencies. It can detect disorder in the crystal structure, systematic error in the diffraction data and the effects of non-spherical electron-density distributions on ADP's in X-ray data. The analysis requires diffraction data measured at multiple temperatures.

Variable-Temperature Emission Studies of Solvation Dynamics: Evidence for Coupling of Solvation to Chromophore Structural Dynamics in the Evolution of Charge-Transfer Excited States

Variable-temperature emission data over the range 90−298 K have been collected for a series of bipyridyl complexes of RuII. Spectra obtained for [Ru(dmb)3]2+ (dmb = 4,4‘-dimethyl-2,2‘-bipyridine), [Ru(dpb)3]2+ (dpb = 4,4‘-diphenyl-2,2‘-bipyridine), [Ru(dotb)3]2+ (dotb = 4,4‘-di-o-tolyl-2,2‘-bipyridine), and [Ru(dmesb)3]2+ (dmesb = 4,4‘-dimesityl-2,2‘-bipyridine) in 4:1 EtOH/MeOH show similar trends in terms of both the red shift of the emission spectrum and the thermal breadth of the solvent response as the temperature is increased through the glass-to-fluid transition. In contrast, data collected in 2-MeTHF show a strong dependence on the identity of the chromophore, the details of the spectral evolution qualitatively correlating with changes in the steric demands of the system. The most dramatic effect is observed for [Ru(dmesb)3]2+, in which there is an apparent change in the nature of the emitting species with increasing temperature. These observations suggest a strong coupling of solvation dynamics and solute structure in the low-temperature regime as well as at intermediate temperatures where the structure of the chromophore is evolving in the course of excited-state relaxation. The results underscore the potential importance of specific solvent−solute interactions in the dynamics of solvation for cases in which large-amplitude molecular motion of the chromophore accompanies thermalization of the excited state.

Molecular motion of guests trapped in N-methyl-1,3-diaminopropanecadmium(II) tetracyanonickelate(II) host lattices

The molecular motion of guest molecules in Cd(mtn)Ni(CN)4•0.5G clathrates (mtn = N-methyl-1,3-diaminopropane, G = toluene, nitrobenzene, dichloromethane, and chloroform) were studied by using CP/MAS 13C and 2H NMR techniques. At room temperature, application of 13C CP/MAS NMR with dipolar dephasing showed the presence of large amplitude molecular motion in all cases. Temperature dependent 2H NMR spectra for the toluene-d8 clathrate shows that the methyl group rotated at all temperatures down to 77 K. Also, a 2-site in-plane reorientation process of the entire molecule is activated above 180 K, which goes over into axially symmetric in-plane rotation around 450 K. Severely restricted motions were also observed for the nitrobenzene and haloalkane guests. The rather complicated dynamic behaviour of the guest molecules at low and room temperatures can be attributed to the presence of static disorders which disappear at higher temperatures due to time averaging.

Investigations of the transitions of some tetraalkylammonium halides by DSC, NMR, and X-ray diffraction

The transitions of several symmetric tetraalkylammonium halides were studied by differential scanning calorimetry (DSC), solid-state nuclear magnetic resonance (NMR) and X-ray diffraction. The reversibility of the transitions of Bu 4NI is investigated by cycling of the samples in the DSC. A plastic-crystalline phase is found and characterized. A glass transition is observed for Bu 4NCl at 230 K. Solid-state CP-MAS 13C NMR is performed on Hex 4NI in order to reveal the large-amplitude molecular motion. The DSC transitions are confirmed by changes in the chemical shifts, but additional, more continuous changes are seen. Condis-crystalline phases are probable for the latter two salts. Room-temperature X-ray diffraction on various iodides shows that the appropriate d-spacings increase linearly with size of the alkyl groups.

81Br and 127I NQR and Phase Transitions in CH3NH3 HgBr3 and CH3NH3 HgI3

Abstract The 81Br and 127I NQR spectra were recorded in CH3NH3 HgBr3 and CH3NH HgI3 , respectively. In addition to a phase transition at 338 K, successive phase transitions take place at 127 ± 1, 184±1 and 243±5 K in CH3NH3 HgBr3. On heating, the resonance lines of CH3NH3HgI3 disappear near a phase transition at 328 K and one line appears above this temperature. The temperature variations of the resonance frequencies of the terminal halogen atoms in both crystals are extraordinarily steep. This indicates the large amplitude molecular motions expected for the CH3NH3 cations which are linked to the terminal halogen atoms through N-H ··· X type H-bonding.

A new treatement of the ring-puckering motions by periodic functions in the Hamiltonian

A method is outlined for treating the nonperiodic large amplitude molecular motions by a Hamiltonian which contains only periodic functions. The examples investigated for testing the theory are two pseudo-four-membered ring molecules, cyclopentene (CP) and 2,5-dihydrofuran (DHF) which are doing ring-puckering motions. Our calculations give better results for these two molecules than Malloy's ones [1].