A fluctuating quantum model of the CO vibration in carboxyhemoglobin

In this paper, we present a theoretical approach to construct a fluctuating quantum model of the CO vibration in heme-CO proteins and its interaction with external laser fields. The methodology consists of mixed quantum-classical calculations for a restricted number of snapshots, which are then used to construct a parametrized quantum model. As an example, we calculate the infrared absorption spectrum of carboxy-hemoglobin, based on a simplified protein model, and found the absorption linewidth in good agreement with the experimental results.     

Experimental measurement of single-wall carbon nanotube torsional properties

We report on the characterization of nanometer-scale torsional devices based on individual single-walled carbon nanotubes as the spring elements. The axial shear moduli of the nanotubes are obtained through modeling of device reaction to various amounts of applied electrostatic force and are compared to theoretical values.     

Mechanics and Friction at the Nanometer Scale

In this overview, we will give an introduction to experiments in which manipulation is used a means of uncovering the intrinsic response and dynamical behavior of small objects. Experiments done on individual particles reveal new and rich behaviors that are inaccessible to averaging methods. Experiments exploring the stiffness and toughness of carbon nanotubes will be presented showing that nanometer scale engineered materials can far outperform current engineering materials. Through AFM manipulation, imaging and force measurements, the stiffness of this material was found to equal or exceed diamond. Their toughness is also extraordinary. Due to their near crystalline perfection, carbon nanotubes are able to undergo strains exceeding 15% during bending without damage. Through AFM manipulation experiments, these large deformations have been shown to be highly reversible. Experiments in which the lateral force of manipulation of small objects across surfaces is measured show that friction at the nanometer scale occurs without wear processes and is an intrinsic property of the particular interface. Results are also presented showing anisotropic behavior in friction and movement due to commensurate lattice effects. At the nanometer scale, the contacting surfaces can be nearly perfect so that commensurate effects are not partially averaged out by many differently oriented domains. It has been shown that friction can very over an order of magnitude depending on the relative orientation of the contacting surfaces. The relative orientation of object and substrate lattices also can determine the modes of motion. In some cases the particle is confined to move in one direction. In other cases the relative orientation determines whether the particle rolls, rotates in-plane or slides. These effects may have implications on the fundamental mechanisms of friction. They provide a laboratory for testing different geometrical configurations of atoms sliding on atoms. The results may also have implications in the design of nanometer scale electromechanical mechanisms.     

Torsional response and stiffening of individual multiwalled carbon nanotubes

We report on the characterization of torsional oscillators which use multiwalled carbon nanotubes as the spring elements. Through atomic-force-microscope force-distance measurements we are able to apply torsional strains to the nanotubes and measure their torsional spring constants, and estimate their effective shear moduli. The data show that the nanotubes are stiffened by repeated flexing. We speculate that changes in the intershell mechanical coupling are responsible for the stiffening.     

Dissociation behavior of a bifunctional tempo‐active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry

We have synthesized a homobifunctional active ester cross‐linking reagent containing a TEMPO (2,2,6,6‐tetramethylpiperidine‐1‐oxy) moiety connected to a benzyl group (Bz), termed TEMPO‐Bz‐linker. The aim for designing this novel cross‐linker was to facilitate MS analysis of cross‐linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO‐Bz‐linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof‐of‐principle study was to evaluate the potential of the TEMPO‐Bz‐linker for chemical cross‐linking studies to derive 3D‐structure information of proteins. Our studies were motivated by the well documented instability of the central NO―C bond of TEMPO‐Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO―C bond of the TEMPO‐Bz‐linker. This leads to the formation of complementary open‐shell peptide radical cations, while precursor ions that are protonated at the TEMPO‐Bz‐linker itself exhibit a charge‐driven formation of even‐electron product ions upon collision activation. MS³ product ion experiments provided amino acid sequence information and allowed determining the cross‐linking site. Our study fully characterizes the CID behavior of the TEMPO‐Bz‐linker and demonstrates its potential, but also its limitations for chemical cross‐linking applications utilizing the special features of open‐shell peptide ions on the basis of selective tandem MS analysis. Copyright © 2015 John Wiley & Sons, Ltd.     

Vibrational spectra of polyatomic molecules assisted by quantum thermal baths

We assess the performance of colored-noise thermostats to generate quantum mechanical initial conditions for molecular dynamics simulations, in the context of infrared spectra of large polyatomic molecules. Comparison with centroid molecular dynamics simulations taken as reference shows that the method is accurate in predicting line shifts and band widths in the ionic cluster (NaCl)(32) and in the naphthalene molecule. As illustrated on much larger polycyclic aromatic hydrocarbons, the method also allows fundamental spectra to be evaluated in the limit of T = 0, taking into account anharmonicities and vibrational delocalization.     

Improving anharmonic infrared spectra using semiclassically prepared molecular dynamics simulations

Classical molecular dynamics is a convenient method for computing anharmonic infrared spectra of polyatomic molecules and condensed phase systems. However it does not perform well for predicting accurate intensities and it lacks nuclear quantization, two deficiencies that are usually accounted for by empirical scaling factors. In this paper we show on the examples of the trans isomer of nitrous acid and naphthalene that both issues can be alleviated by preparing the initial conditions according to semiclassical quantization based on a normal mode representation. The method correctly reproduces fundamental frequencies obtained with quantum mechanical methods. At increasing temperatures, the effective frequencies are found to follow the same trends as path-integral based methods. In the low-temperature limit, the band intensities predicted by the method are also found to agree with quantum mechanical considerations.     

Vibron-polaron critical localization in a finite size molecular nanowire

The small polaron theory is applied to describe the vibron dynamics in an adsorbed nanowire with a special emphasis onto finite size effects. It is shown that the finite size of the nanowire discriminates between side molecules and core molecules which experience a different dressing mechanism. Moreover, the inhomogeneous behavior of the polaron hopping constant is established and it is shown that the core hopping constant depends on the lattice size. However, the property of a lattice with translational invariance is recovered when the size of the nanowire is greater than a critical value. Finally, it is pointed out that these features yield the occurrence of high energy localized states in which both the nature and the number are summarized in a phase diagram in terms of the relevant parameters of the problem (small polaron binding energy, temperature, lattice size).     

Vibron-polaron in alpha-helices. I. Single-vibron states

The vibron dynamics associated to amide-I vibrations in a three-dimensional alpha-helix is described according to a generalized Davydov model. The helix is modeled by three spines of hydrogen-bonded peptide units linked via covalent bonds. To remove the intramolecular anharmonicity of each amide-I mode and to renormalize the vibron-phonon coupling, two unitary transformations have been applied to reach the dressed anharmonic vibron point of view. It is shown that the vibron dynamics results from the competition between interspine and intraspine vibron hops and that the two kinds of hopping processes do not experience the same dressing mechanism. Therefore, at low temperature (or weak vibron-phonon coupling), the polaron behaves as an undressed vibron delocalized over all the spines whereas at biological temperature (or strong vibron-phonon coupling), the dressing effect strongly reduces the vibrational exchanges between different spines. As a result the polaron propagates along a single spine as in the one-dimensional Davydov model. Although the helix supports both acoustical and optical phonons, this feature originates in the coupling between the vibron and the acoustical phonons only. Finally, the lattice distortion which accompanies the polaron has been determined and it is shown that residues located on the excited spine are subjected to a stronger deformation than the other residues.     

Direct observation of self-trapped vibrational states in alpha-helices

Femtosecond infrared pump-probe spectroscopy of the N-H mode of a stable alpha-helix reveals two excited-state absorption bands, which disappear upon unfolding of the helix. A quantitative comparison with polaron theory shows that these two bands reflect two types of two-vibron bound states connected to the trapping of two vibrons at the same site and at nearest neighbor sites, respectively. The latter states originate from an acoustic phonon in the helix, which correlates adjacent sites.