A high resolving power multiple reflection matrix-assisted laser desorption/ionization time-of-flight mass spectrometer

Two electrostatic mirrors, mounted symmetrically on the same optical axis facing each other, are used to increase the time-of-flight of molecular ions produced in matrix-assisted laser desorption/ionization (MALDI). The mirrors, which are used in the non-compensating mode, are located between a MALDI ion source and a stop detector. The source is operated at 10.5 kV acceleration voltage using the delayed extraction technique. The high voltage for the mirror arrangement is switched on after the desorption event when the molecular ions have drifted into the region between the mirrors. The ions are trapped by successive reflections of the opposite electrostatic fields in the mirrors until the electric fields are switched off. The number of reflections depends on the speed of the ions when they enter the mirror trap and the ontime of the mirrors. When the electric fields are removed during the motion of the ions towards the stop detector, the ions penetrate the grids of the mirror and reach that detector. The extension of the flight path due to the number of reflections is used to increase the resolving power in time-of-flight spectra. Values of 55,000 for substance-P (MW 1346.7) and 31,000 for bovine insulin (MW 5734) were obtained for single laser shot spectra.     

Direct measurement of the angular dependence of the single-photon ionization of aligned N2 and CO2

By combining a state-of-the-art high-harmonic ultrafast soft X-ray source with field-free dynamic alignment, we map the angular dependence of molecular photoionization yields for the first time for a nondissociative molecule. The observed modulation in ion yield as a function of molecular alignment is attributed to the molecular frame transition dipole moment of single-photon ionization to the X, A and B states of N2(+) and CO2(+). Our data show that the transition dipoles for single-photon ionization of N2 and CO2 at 43 eV have larger perpendicular components than parallel ones. A direct comparison with published theoretical partial wave ionization cross-sections confirms these experimental observations, which are the first results to allow such comparison with theory for bound cation states. The results provide the first step toward a novel method for measuring molecular frame transition dipole matrix elements.     

Hard X-ray multilayer mirror round-robin on the wavefront preservation capabilities of W/B4C coatings

A round-robin between the multilayer deposition laboratories of the Advanced Photon Source, the European Synchrotron Radiation Facility and the National Synchrotron Light Source II has been initiated in order to study standard W/B₄C multilayer mirrors produced by the different facilities. The use of such multilayer mirrors for hard X-ray monochromatisation represents an important alternative to crystal-based devices when greater photon flux density is desirable for, e.g., X-ray imaging applications and other photon-intensive techniques. Currently, knowledge about the potential degradation of the wavefront in terms of beam profile distortion and coherence properties due to reflection on a multilayer mirror is limited. In order to address this issue, the beam profile and coherence properties of a monochromatic synchrotron beam reflected by the individual mirrors were studied at the Advanced Photon Source insertion device beamline 32-ID. The results indicate that by using the same coating material, commercially available high quality substrates and a similar coating technique, mirrors with comparable performance can be produced with quite different multilayer deposition facilities. Furthermore, no wave-optical formalism is available at this time which relates the influence of a multilayer reflection on the wavefront to the structural quality of the mirror. Hence, the experimental studies presented are highly targeted in order to identify parameters which have a potential influence on the wavefront preservation properties of a multilayer.     

LIGHT-INDUCED LINEAR ACTION DICHROISM IN PHOTOREVERSIBLY PHOTOCHROMIC SENSOR PIGMENTS—I. THEORY

Abstract— With a photoreversibly photochromic regulator pigment such as phytochrome, linear action dichroism could theoretically be obtained after photoselection even if the molecules are initially randomly oriented: If randomly oriented P_fr (fed-absorbing phytochrome) molecules are partially converted to P_fr (far-red absorbing phytochrome) molecules by plane-polarized red light, those molecules will preferentially be converted which have their 'red' transition moments nearly parallel to the electric vector of the red light. The effect of subsequent plane-polarized far-red light will depend on the plane of polarization. A general theory is developed for how this can be used to determine whether or not the transition moment changes direction during conversion. The pigment need not be isolated, since only physiological reactions (such as germination or chromatic adaptation) are measured.     

Biaxial nematics: computer simulation studies of a generic rod-disc dimer model

One possible route to the elusive biaxial nematic phase is through rod-disc dimers in which the rod and disc mesogenic units are linked via a flexible spacer. We have developed a continuous generic model of such rod-disc dimers in which neighbouring like groups tend to align parallel to each other while unlike groups tend to be orthogonal. A torsional potential controls the relative orientations of the groups within a single dimer; depending on the strength of the torsional potential, the groups may be orthogonal or parallel in the conformational ground state. Monte Carlo simulations show that a rigid rod-disc dimer is most likely to form a biaxial nematic phase if the anisotropies of the two groups are the same. Introduction of flexibility is found to have little effect on the qualitative behaviour of the dimer as the relative anisotropy of the two mesogenic groups is changed. However, when the torsional potential strongly favours the alignment of the rod and disc within a single molecule with their symmetry axes parallel there is a dramatic change. The system then exhibits a strong hysteresis in the molecular shape and biaxiality and the biaxial nematic-isotropic transition becomes strongly first order, in marked contrast to the second-order character usually found for this transition. This first-order transition is observed to occur for a range of relative anisotropies of the two groups rather than at a single point.     

Extended multi-configuration quasi-degenerate perturbation theory: the new approach to multi-state multi-reference perturbation theory

The distinctive desirable features, both mathematically and physically meaningful, for all partially contracted multi-state multi-reference perturbation theories (MS-MR-PT) are explicitly formulated. The original approach to MS-MR-PT theory, called extended multi-configuration quasi-degenerate perturbation theory (XMCQDPT), having most, if not all, of the desirable properties is introduced. The new method is applied at the second order of perturbation theory (XMCQDPT2) to the 1(1)A(')-2(1)A(') conical intersection in allene molecule, the avoided crossing in LiF molecule, and the 1(1)A(1) to 2(1)A(1) electronic transition in cis-1,3-butadiene. The new theory has several advantages compared to those of well-established approaches, such as second order multi-configuration quasi-degenerate perturbation theory and multi-state-second order complete active space perturbation theory. The analysis of the prevalent approaches to the MS-MR-PT theory performed within the framework of the XMCQDPT theory unveils the origin of their common inherent problems. We describe the efficient implementation strategy that makes XMCQDPT2 an especially useful general-purpose tool in the high-level modeling of small to large molecular systems.     

From local adsorption stresses to chiral surfaces: (R,R)-tartaric acid on Ni(110).

The chiral molecule (R,R)-tartaric acid adsorbed on nickel surfaces creates highly enantioselective heterogeneous catalysts, but the nature of chiral modification remains unknown. Here, we report on the behavior of this chiral molecule with a defined Ni(110) surface. A combination of reflection absorption infrared spectroscopy, scanning tunneling microscopy, and periodic density functional theory calculations reveals a new mode of chiral induction. At room temperatures and low coverages, (R,R)-tartaric acid is adsorbed in its bitartrate form with two-point bonding to the surface via both carboxylate groups. The molecule is preferentially located above the 4-fold hollow site with each carboxylate functionality adsorbed at the short bridge site via O atoms placed above adjacent Ni atoms. However, repulsive interactions between the chiral OH groups of the molecule and the metal atoms lead to severely strained adsorption on the bulk-truncation Ni(110) surface. As a result, the most stable adsorption structure is one in which this adsorption-induced stress is alleviated by significant relaxation of surface metal atoms so that a long distance of 7.47 A between pairs of Ni atoms can be accommodated at the surface. Interestingly, this leads the bonding Ni atoms to describe a chiral footprint at the surface for which all local mirror symmetry planes are destroyed. Calculations show only one chiral footprint to be favored by the (R,R)-tartaric acid, with the mirror adsorption site being unstable by 6 kJ mol(-1). This energy difference is sufficient to enable the same local chiral reconstruction and motif to be sustained over 90% of the system, leading to an overall highly chiral metal surface.     

Effects of wetting and anchoring on capillary phenomena in a confined liquid crystal

A fluid of hard spherocylinders of length-to-breadth ratio L/D=5 confined between two identical planar, parallel walls--forming a pore of slit geometry--has been studied using a version of the Onsager density-functional theory. The walls impose an exclusion boundary condition over the particle's centers of mass, while at the same time favoring a particular anchoring at the walls, either parallel or perpendicular to the substrate. We observe the occurrence of a capillary transition, i.e., a phase transition associated with the formation of a nematic film inside the pore at a chemical potential different from micro(b)-the chemical potential at the bulk isotropic-nematic transition. This transition terminates at an Ising-type surface critical point. In line with previous studies based on the macroscopic Kelvin equation and the mesoscopic Landau-de Gennes approach, our microscopic model indicates that the capillary transition is greatly affected by the wetting and anchoring properties of the semi-infinite system, i.e., when the fluid is in contact with a single wall or, equivalently, the walls are at a very large distance. Specifically, in a situation where the walls are preferentially wetted by the nematic phase in the semi-infinite system, one has the standard scenario with the capillary transition taking place at chemical potentials less than micro(b) (capillary nematization transition or capillary ordering transition). By contrast, if the walls tend to orientationally disorder the fluid, the capillary transition may occur at chemical potentials larger than micro(b), in what may be called a capillary isotropization transition or capillary disordering transition. Moreover, the anchoring transition that occurs in the semi-infinite system may affect very decisively the confinement properties of the liquid crystal and the capillary transitions may become considerably more complicated.     

Near—infrared SERS Study of the Adsorption of a PMMA Dip—coated onto Silver Mirror Substrate

The interface between a-PMMA thin film and silver mirror substrate was investigated using surface-enhanced Raman scattering (SERS). It is found that the molecular chain axis of a-PMMA tends to parallel the substrate in the interface. When the sample is annealed at different temperatures, some interesting changes appear in the SERS spectra. The spectra differences and their transition are due to the surface geometry change of the ester group.     

Control of 1,3-cyclohexadiene photoisomerization using light-induced conical intersections

We have studied the photoinduced isomerization from 1,3-cyclohexadiene to 1,3,5-hexatriene in the presence of an intense ultrafast laser pulse. We find that the laser field maximally suppresses isomerization if it is both polarized parallel to the excitation dipole and present 50 fs after the initial photoabsorption, at the time when the system is expected to be in the vicinity of a conical intersection that mediates this structural transition. A modified ab initio multiple spawning (AIMS) method shows that the laser induces a resonant coupling between the excited state and the ground state, i.e., a light-induced conical intersection. The theory accounts for the timing and direction of the effect.     

Separable unimolecular reaction rate theory

A new unimolecular reaction rate theory is derived on the basis of a classical model of the reaction. The fundamental assumptions are (i) instantaneous activation-deactivation events represented by a statistical transition probability, (ii) irreversible dissociation, and (iii) separability of internal and external dynamics. The third assumption is found to be satisfied when the statistical transition probability satisfies a generalized strong collision assumption and it leads to a rate theory which depends on internal molecular dynamics only through lifetime information for the isolated molecule. The new theory shows that the rate coefficient is non-Markoffian although the memory effects will not be apparent on the macroscopic time scales of traditional experiments. Thus Slater's “new approach to rate theory” is a special case of the separable rate theory when applied to slow reactions. New experimental techniques are predicted to have the capacity to resolve the memory effects in the rate coefficient and provide lifetime information which would then allow greatly improved accuracy in the prediction of rates for a wide range of unimolecular reactions.     

State-selective optimization of local excited electronic states in extended systems

Standard implementations of time-dependent density-functional theory (TDDFT) for the calculation of excitation energies give access to a number of the lowest-lying electronic excitations of a molecule under study. For extended systems, this can become cumbersome if a particular excited state is sought-after because many electronic transitions may be present. This often means that even for systems of moderate size, a multitude of excited states needs to be calculated to cover a certain energy range. Here, we present an algorithm for the selective determination of predefined excited electronic states in an extended system. A guess transition density in terms of orbital transitions has to be provided for the excitation that shall be optimized. The approach employs root-homing techniques together with iterative subspace diagonalization methods to optimize the electronic transition. We illustrate the advantages of this method for solvated molecules, core-excitations of metal complexes, and adsorbates at cluster surfaces. In particular, we study the local π→π(?) excitation of a pyridine molecule adsorbed at a silver cluster. It is shown that the method works very efficiently even for high-lying excited states. We demonstrate that the assumption of a single, well-defined local excitation is, in general, not justified for extended systems, which can lead to root-switching during optimization. In those cases, the method can give important information about the spectral distribution of the orbital transition employed as a guess.     

Theoretical analysis of correlation between ionization threshold fluence in IR‐MALDI and IR absorption spectrum of matrix molecules

To investigate the correlation between the wavelength dependence of ionization threshold fluence of target molecule in matrix‐assisted laser desorption/ionization by infrared (IR) laser and the IR absorption spectrum of matrix molecule, we have analyzed the IR absorption spectra of four matrix molecules using density functional theory and correlated ab initio molecular orbital method. The calculated IR absorption spectra of the isolated molecules showed more qualitative correlation with the wavelength dependence of ionization threshold fluence than those of the solid state structures. We can consider that a portion of matrix molecules lost the ordered crystal structure and that the transition to the diluted or isolated state occurred at the early process of IR laser irradiation. © 2012 Wiley Periodicals, Inc.     

Quantum fidelity for analyzing atoms and fragments in molecule: Application to similarity,chirality, and aromaticity

Quantum information theory is applied to formulate a new technique for dealing with molecular similarity problems. In this technique, the so‐called quantum fidelity appears to be a counterpart of the conventional similarity measure due to Carbo (Carbo, R.; Leyda, L.; Arnau, M. Int J Quantum Chem 1980, 17, 1185). We define many‐body spin‐free density matrices for atoms and fragments in molecule, and compute corresponding fidelity measures for molecular subsystems. It allows us to treat the problem from the beginning within a many‐electron setting. The approach is employed for analyzing similarity between free atoms and atoms in molecule. A new chirality index, as based on the fidelity between molecule and its mirror image, is suggested to be an approximately additive nonnegative quantity. We also examine a local aromaticity by computing the fidelity measures for benzenoid fragments in polyaromatic hydrocarbons. A detailed study of the proposed indices is reported at the ab initio or semiempirical levels. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Studies on the Mechanism for the Bimolecular Metathesis Reaction CH3 + HCI ⇔︁ CH4 + CI

The geometry optimization of the transition state, the precursor complex and the successor complex was performed at the 6–311G* basis set level. From the analysis of the vibrational frequency of the precursor complex, transition state, successor complex and the isolated state, the reaction mechanism was derived which was complicated with the bond‐rupture electron transfer theory. The atom H in molecule HCI attacks the atom C, forming a transition state via the precursor complex and the electron‐transfer happens in precursor complex. And the active energy, electronic coupling matrix element, the reorganization energy, and the reaction rate are obtained.     

Simple geometry gridless ion mirror

A gridless variation of the cylindrical ion mirror has been designed to create an electric field that is nonlinear in the axial direction and nearly homogeneous in the radial direction. The designs may include one or two chambers that consist of truncated cones. This new design concept yields ion mirrors with improved energy focusing over conventional single-field and multiple-field mirrors. Conventionally, ion mirrors with nonlinear field gradient use multiple diaphragm electrodes to which distinct voltages are applied. In this work, optimized nonlinear field distributions are achieved through shaping only two or three electrodes and applying only one or two voltages on the electrodes. The designs presented here offer high resolving power and low ion dispersion. SIMION simulations of performance from the ion source to the detector demonstrate resolving powers of 11,000 and 1,750 for ions with kinetic energy variations of 7.5% and 23.6%, respectively.     

Quantum chemical modeling of ethene epoxidation with hydrogen peroxide: the effect of microsolvation with water

Quantum chemical calculations were performed to study the mechanism of ethene epoxidation with hydrogen peroxide. The calculations were carried out at the B3LYP/6-311+G(d,p) level of theory. The applicability of this functional to the problem at hand, including basis set effects, was validated by CCSD(T) and CASSCF based multireference MP2 calculations. A mechanism was determined where hydrogen peroxide becomes polarized in the transition state upon binding to the ethene molecule. The distant hydroxide fragment of the attached hydrogen peroxide molecule becomes partly negatively charged, while the other part of the molecule involves a proton and becomes partly positively charged. In the absence of water an activation energy of 139.7 kJ mol(-1) was determined for the isolated H(2)O(2) + C(2)H(4) system. By microsolvating with water, the impact of a hydrogen-bonded network on the activation energy was addressed. A 43.7 kJ mol(-1) lowering of the activation energy, DeltaE(a), was observed when including up to 4 water molecules in the model. This effect results from the stabilization of the proton and hydroxide fragments in the transition state. The findings are discussed in the context of previous theoretical studies on similar systems. Effects of adding or removing a proton to mimic acidic and alkaline conditions are addressed and the limitations of the model in solvating the excess charge are discussed.     

Spin crossover transition of Fe(phen)2(NCS)2: periodic dispersion-corrected density-functional study

Periodic dispersion corrected DFT calculations have been performed to study the spin-crossover transition of Fe(phen)(2)(NCS)(2) in the molecular and in the crystalline state. We show that London dispersion interactions play a crucial role in the cohesion of the crystals. Based on calculations of vibrational eigenstates of the isolated molecule and of the crystalline phase in both the low- and high-spin states, the transition entropies and enthalpies have been calculated. We demonstrate that, due to the stabilization of the low-spin state by intermolecular dispersion forces, the transition enthalpy at the transition temperature is larger for the crystalline phase in comparison with an isolated molecule. The effective coordination number of the nitrogen atoms of the ligands around the iron atom has been identified as the order parameter driving the quasi-reversible low-spin to high-spin transition in the crystal. Finally, using constrained geometry relaxations at fixed values of the coordination number, we computed the energy barrier of the LS to HS transition and found it to be in a reasonable agreement with the experimental value.