Method for assigning absorption bands in IR spectra of polyatomic molecules with respect to internal vibrational coordinates

A method is proposed for assigning absorption bands in IR spectra of polyatomic molecules. An algorithm is developed and a Fortran program is written based on this method. The method is illustrated for the example of the toluene molecule. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 2, pp. 169–173, March–April, 2007.     

The Static Modes: An alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility

We present a new competitive method for the atomic scale treatment of macromolecular flexibility called Static Mode method. This method is based on the “induced-fit” concept, i.e. it maps the intrinsic deformations of a macromolecule subject to diverse external excitations. The algorithm makes it possible to obtain a set of deformations, each one corresponding to a specific interaction on a specific molecular site, in terms of force constants contained in the energy model. In this frame, the docking problem can be expressed in terms of interaction sites between the two molecules, the molecular deformations being extracted from the pre-calculated Static Modes of each molecule. Some preliminary basic examples aimed at illustrating potential applications where macro- or bio-molecular flexibility is of key importance are given: flexibility inducing conformational changes in the case of furanose ring and flexibility for the characterization, including allostery, of poly(N-isopropylacrylamide)(P-NIPAM) active sites. We also discuss how this procedure allows “induced-fit” flexible molecular docking, beyond state-of-the-art semi-rigid methods.     

Semi-empirical method for analysis of electronic absorption spectra of 3,6-tetramethyldiaminophthalimide solutions

A new semi-empirical method (mωT or modified ω-technique adapted to thermosolvatochromic effect analysis) based on the first approximation by a self-consistent field procedure (ω-technique) is proposed to calculate solvatochromic effects of dyes in various solvents. The method relies on the direct dependence of the relative change of charge at a dye molecule atom influenced by an external solvent molecule on the atom/molecule interaction energy. The method was validated using the calculation of solvatochromic and thermosolvatochromic effects for 3,6-tetramethyldiaminophthalimide [4,7-tetramethyldiamino-1H-isoindole-1,3(2H)-dione] in inert solvents as an example.     

Linear optimal control for tracking a single fluorescent particle in a confocal microscope

We study the problem of localizing and tracking in a confocal laser scanning microscope a single fluorescent particle diffusing in three dimensions. The position of the particle is estimated from a collection of intensity measurements using a novel analytical algorithm. This estimator is then combined with a tracking algorithm based on a linear quadratic Gaussian controller to steer the detection volume of the microscope and follow the molecule. The feasibility of the approach is demonstrated through numerical simulations. These results indicate that, in such a system, tracking in three dimensions of a particle moving with a diffusion constant larger than 1 μm²/s is possible without the need for additional sensors or lasers.     

Rotational quasienergy states and alignment of molecules in a strong laser field

The interaction of a molecule with a strong laser field is investigated. Raman-type transitions between rotational levels of a fixed vibrational state of the ground-state term are taken into account in the “quantum rotator” approximation. An initial problem of the evolution of the state of a molecule interacting with a pulsed field is solved. The dynamics of the degree of alignment of a molecule with respect to the direction of polarization of the field during the pulse is investigated. It is shown that for sufficiently long pulses with a smooth envelope the axis of the molecule adiabatically follows the time-varying field amplitude, and alignment is maximum when the field intensity is maximum. It is shown that alignment of molecules can be substantial only if the second-order composite matrix elements, determining the probability amplitudes of transitions between rotational levels of a molecule, are much greater than the dissociation broadening of the levels. The angular distribution of the dissociation products of a molecule in a strong laser field is investigated. Zh. éksp. Teor. Fiz. 116, 1551–1564 (November 1999)     

Initial stage of the adsorption of fluorofullerene molecules on Si surface

Spatially resolved images of an individual C₆₀F₁₈ fluorofullerene molecule on Si(100) − 2 × 1 surface have been obtained using scanning tunneling microscopy. Scanning tunneling microscopy results and ab initio calculations show that the fluorofullerene molecules interact with the Si(100) − 2 × 1 surface with F atoms pointing down towards the surface. The adsorption energy of a C₆₀F₁₈ molecule on Si(100) − 2 × 1 surface is ∼12.1 eV, which is much higher than the adsorption energy of the same molecule on Si(111) − 7 × 7 surface (6.65 eV). C₆₀F₁₈ molecules are located in the troughs in-between the dimer rows occupying the four-dimer site on Si(100) − 2 × 1 surface.     

Radiative characteristics and kinetics of processes in low-pressure gas-discharge lamps based on a mixture of helium and iodine vapors

The UV radiation of glow- and capacitive-discharge lamps based on mixtures of inert gases with iodine vapors are optimized in the spectral range of 175–360 nm, in which working helium-iodine mixtures of different compositions are used. The most intense spectral lines in the bactericidal region of the spectrum were the atomic lines of iodine (183.0, 206.2 nm), and in the region of 320–360 nm, emission of the spectral band of an iodine molecule prevailed with a maximum at λ = 342 nm. For a capacitive lamp with a casing opaque in the spectral range λ < 250 nm, the main part of the plasma emission power is concentrated in the A′-D′ band of an iodine molecule with a maximum at 342 nm. The emission brightness of this lamp is optimized in iodine molecule transitions depending on the partial helium pressure. We present the results of simulating the kinetics of processes in a glow-discharge plasma in mixtures of He, Xe, and iodine vapors. We establish the dependence of the main part of the emission intensity of the 206.2 nm spectral line of an iodine atom and the 342 nm band of an iodine molecule on the helium pressure in a glow-discharge lamp operating on a He-I₂ mixture.     

Model of the photostimulated fragmentation of PETN molecules in selective photoinitiation

A model of the photostimulated fragmentation of the PETN molecule irradiated by the first harmonic of a neodymium laser (1060 nm) is proposed. Photoexcitation at 1060 nm leads to the n → π* transition of the 2p nonbinding electron of the oxygen to the π* antibonding orbital, a transition that causes the rupture of the O-N bond and the formation of NO₂^* radicals, thereby ensuring a further development of explosive decomposition. In the case of a free molecule or a molecule located on the surface of a microcrystal, the process does not require any thermal activation. In the case of a molecule at a regular lattice site, an additional activation energy (0.4 eV) is needed to overcome the potential barrier associated with the passage of through a bottleneck between the nearest-neighbor molecules.     

Localized excitation effects in (E,E)-2,5-<Emphasis Type="Italic">bis</Emphasis>[2-(4-N,N-dipropylaminophenyl) ethylenyl]-3,6-dimethylpyrazine and generation of its different forms in solution

Dipole moments of (E,E)-2,5-bis[2-(4-N,N-dipropylaminophenyl)ethylenyl]-3,6-dimethylpyrazine (VS365) quadrupolar dye in 1,4-dioxane and cyclohexane in addition to its instantaneous fluorescence spectra and fluorescence lifetimes in dichloromethane (pure and with added trifluoroacetic acid) were measured. Quantumchemical calculations show that the π − π conjugated system is localized in the flattest part of the molecule due to disorder in the ground-state geometry of the dye molecule and that this part is the one responsible for light absorption. The effect of localized excitation of the dye causes a considerable change in its dipole moment Δ^aμ. Various fluorescent forms of the dye that feature considerably spaced emission spectra and different fluorescence lifetimes originate by adding trifluoroacetic acid to the solution of oligophenylenevinylene in dichloromethane.     

A single molecule switch based on two Pd nanocrystals linked by a conjugated dithiol

Tunneling spectroscopy measurements have been carried out on a single molecule device formed by two Pd nanocrystals (dia. ∼5 nm) electronically coupled by a conducting molecule, dimercaptodiphenylacetylene. TheI-V data, obtained by positioning the tip over a nanocrystal electrode, exhibit negative differential resistance (NDR) on a background M-I-M characteristics. The NDR feature occurs at ∼0.67 V at 300 K and shifts to a higher bias of 1.93 V at 90 K. When the tip is held in the middle region of the device, a Coulomb blockade region is observed (±∼0.3 V)     

Vibrational spectra, normal coordinate analysis and thermodynamics of 2, 5-difluorobenzonitrile

The FTIR spectrum of 2, 5-difluorobenzonitrile has been recorded in the region 200–4000 cm⁻¹ (in liquid phase). The laser Raman spectrum in the range of 0–3500 cm⁻¹ (in liquid phase) has also been recorded. The spectra have been analyzed assuming C _s point group symmetry for the molecule. A zero-order normal coordinate analysis has been made for the molecule using force constants derived earlier. On the basis of potential energy distributions and eigen vectors unambiguous vibrational assignments have been made for all the fundamentals of the molecule. Thermodynamic functions have also been computed in the temperature range 200–1000 K by utilizing the observed fundamental frequencies assuming rigid-rotor harmonic oscillator approximation.     

Bistability of single 1,5 cyclooctadiene molecules on Si(001)

The adsorption and current-induced bistability of single 1,5 cyclooctadiene molecules on Si(001) were studied in ultrahigh vacuum by low-temperature scanning tunneling microscopy (STM). After a dosage of ≈0.05 L at room temperature followed by cooling to the measuring temperature of 7 K, we find that the cyclic alkene molecule preferably adsorbs in the bridge structure with both C=C double bonds reacting with two adjacent Si dimers via [2+2] cycloaddition reaction. The time-dependent current measured upon tunneling through the adsorbed molecule at fixed STM tip height displays a switching between two current levels with the same mean residence time in each level. Higher bias and/or reduced tip height—and therefore higher current—increase the switching rate, suggesting that the reversible switching is due to inelastic electron tunneling. The observed bistability is interpreted as a dynamic interconversion between two degenerate conformations of the adsorbed molecule.     

Conformal transitions of the laurdan molecule in the absorption and fluorescence spectra

The fluorescent probe molecule – laurdan (6-dodekanoil-2-dimetilamin naphthalene) – is investigated by experimental and quantum-chemical methods. The influence of the structure non-rigidity on the dipole moments, arrangement of energy levels, and distribution of charges in the laurdan molecule is studied. An optimized structure is obtained and analyzed by the molecular dynamics method. Several structures with different rotation angles of the dimethylamino group are investigated, for which energy, oscillator forces, and nature of electron states are calculated. Fluorescence spectra of the laurdan molecule in an inert solvent are interpreted. Centers of possible interaction of the molecule with a proton-donor solvent are established. Rate constants of radiative and nonradiative processes and quantum fluorescence yields of the examined probe are calculated.     

Observation of the Molecular Quenching of μp(2S) Atoms

Kinetic energy distributions of muonic hydrogen atoms μp(1S) have been obtained by means of a time-of-flight technique for hydrogen gas pressures between 4 and 64 hPa. A high energy component of ∼900 eV observed in the data is interpreted as the signature of long-lived μp(2S) atoms, which are quenched in a non-radiative process leading to the observed high energy: the collision of a thermalized μp(2S) atom with a hydrogen molecule H₂ results in the resonant formation of a {[(ppμ)⁺]^*pee}^* molecule. Then the (ppμ)⁺ complex undergoes Coulomb de-excitation and the ∼1.9 keV excitation energy is shared between a μp(1S) atom and one proton. The preliminary analysis of the time spectra gives a long-lived μp(2S) population of ∼1% of all stopped muons, and a quenching rate of ∼4⋅10¹¹ s⁻¹. This revised version was published online in August 2006 with corrections to the Cover Date.     

Spin-orbit coupling and the dynamic Jahn-Teller effect in the C 60 − system

The dynamic Jahn-Teller effect is studied for a charged fullerene molecule C ₆₀ ⁻ with allowance for spin-orbit coupling. The system of self-consistent equations describing the interaction of an electron and the molecular vibrations in the event of spin-orbit splitting of the electronic level is solved analytically. A novel type of nonlinear vibrations occurring in such a system is described. It is shown that with spin-orbit coupling taken into account, the static Jahn-Teller configurations in the C ₆₀ ⁻ molecule are unstable even in the limit of strong electron-vibronc coupling and that the symmetry of the atomic configuration of the unperturbed C ₆₀ ⁻ molecule is restored under time averaging. Zh. éksp. Teor. Fiz. 116, 194–203 (July 1999)     

Vibronic coupling effects in the C60 molecule

Many recent experiments have established that the Jahn-Teller (JT) effect plays a very important role in determining the properties of the C₆₀ molecule. A review of the underlying theory developed by the Nottingham group is presented for cases in which distinct minima in the potential energy surface occur. This relates directly to the C₆₀ molecule through the consideration of the T ⊗ h and H ⊗ h JT systems. When only linear coupling terms exist in the T ⊗ h system, the minima form a continuous trough of SO(3) symmetry and new methods must be used. Some details of these results are presented.     

Fragmentation of the POPOP molecule by electron-impact ionization

Single and dissociative ionizations of the POPOP molecule by electron impact in the gas phase are studied using mass spectroscopy. Fragmentation pathways of the molecule are proposed taking into account the common system of conjugated π-electrons and heteroatoms in the POPOP molecule. The appearance thresholds for certain fragments of the molecule are determined based on experimentally measured ionization cross sections as functions of the ionizing electron energy. An ion with m/z = 144 [C₉H₆ON]⁺ that is complementary to a fragment with m/z = 220 [C₁₃H₁₀ON]⁺ (present in the NIST mass spectrum database) is found for the first time in the mass spectrum of POPOP. Its appearance threshold is determined (E_ap = 9.48 eV). __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 75, No. 4, pp. 482–489, July–August, 2008.     

Single Molecule Genotyping by TIRF Microscopy

As part of a programme to develop a metrological framework for single molecule measurements in biology, we have investigated the applications of single molecule imaging to genomics. Specifically, we have developed a technique for measuring the frequencies of single nucleotide polymorphisms (SNPs) in complex or pooled samples of DNA. We believe that this technique has applications to statistical genotyping—the identification of correlations between SNP frequencies and particular phenotypes—and other areas where it is desirable to track the frequencies of SNPs in complex DNA populations.     

Kinetics of muon catalyzed fusion processes in solid H/D mixture

This paper presents the final results of an experimental study of the kinetics of the muon catalysed fusion (MCF) in solid hydrogen-deuterium mixtures (H/D) at a temperature of 3 K. The experiment E742 was carried out on a TRIUMF meson facility in Canada. Four exposures were performed at different deuterium concentrations in the H/D mixture: c_d = 0.0005, 0.02, 0.15 and 0.75. A simultaneous analysis of the measured time distributions of the 5.5 MeV γ-quanta and the 5.3 MeV conversion muons obtained from nuclear fusion in the pdμ molecule allowed to extract the values of MCF chain parameters in the H/D mixture: the fusion partial rates for different nuclear spin states of the pdμ molecule, and the pdμ molecule formation rate. The experimental data fitting procedure was conducted in two ways: using solely the analytical formulae describing the kinetics of the MCF processes in the H/D mixture, and the detailed Monte Carlo simulation of the entire experiment. The results obtained by these two methods are consistent with each other and confirm the existence of the Wolfenstein-Gerstein effect.     

IR spectrum of the closed form of indolinospironaphthooxazine

IR absorption spectra of indolinospironaphthooxazine (ISNO) are presented. The geometric structure and normal coordinates of the ISNO molecule have been calculated using a quantum mechanical DFT method. The IR spectrum of ISNO in its original spiro form has been interpreted for the first time. Four normal modes in the range 800–1200 cm^–1 with the largest amplitudes of C_spiro–O bond change are identified. The excited ISNO molecule spiro form may experience photoconversion to the merocyanine form through them.