Time-resolved coherent anti-Stokes Raman-scattering measurements of I2 in solid Kr: vibrational dephasing on the ground electronic state at 2.6-32 K

Time-resolved coherent anti-Stokes Raman-scattering (CARS) measurements are carried out for iodine (I2) in solid krypton matrices. The dependence of vibrational dephasing time on temperature and vibrational quantum number v is studied. The v dependence is approximately quadratic, while the temperature dependence of both vibrational dephasing and spectral shift, although weak, fits the exponential form characteristic of dephasing by pseudolocal phonons. The analysis of the data indicates that the frequency of the pseudolocal phonons is approximately 30 cm(-1). The longest dephasing times are observed for v = 2 being approximately 300 ps and limited by inhomogeneous broadening. An increase in the dephasing rate of v = 2 as the temperature is lowered to T = 2.6 K is taken as a clear indication of lattice-strain-induced inhomogeneity of the ensemble coherence.     

Electronic spectroscopy of I(2)-Xe complexes in solid Krypton

In the present work, we have studied ion-pair states of matrix-isolated I(2) with vacuum-UV absorption and UV-vis-NIR emission, where the matrix environment is systematically changed by mixing Kr with Xe, from pure Kr to a more polarizable Xe host. Particular emphasis is put on low doping levels of Xe that yield a binary complex I(2)-Xe, as verified by coherent anti-Stokes Raman scattering (CARS) measurements. Associated with interaction of I(2) with Xe we can observe strong new absorption in vacuum-UV, redshifted 2400 cm(-1) from the X → D transition of I(2). Observed redshift can be explained by symmetry breaking of ion-pair states within the I(2)-Xe complex. Systematic Xe doping of Kr matrices shows that at low doping levels, positions of I(2) ion-pair emissions are not significantly affected by complexation with Xe, but simultaneous increase of emissions from doubly spin-excited states indicates non-radiative relaxation to valence states. At intermediate doping levels ion-pair emissions shift systematically to red due to change in the average polarizability of the environment. We have conducted spectrally resolved ultrafast pump-probe ion-pair emission studies with pure and Xe doped Kr matrices, in order to reveal the influence of Xe to I(2) dynamics in solid Kr. Strikingly, relaxed emission from the ion-pair states shows no indication of complex presence. It further indicates that the complex escapes detection due to a non-radiative relaxation.     

Vibrational Dephasing in Ionic Liquids as a Signature of Hydrogen Bonding

Understanding both structure and dynamics is crucial for producing tailor‐made ionic liquids (ILs). We studied the vibrational and structural dynamics of medium versus weakly hydrogen‐bonded C?H groups of the imidazolium ring in ILs of the type [1‐alkyl‐3‐methylimidazolium][bis(trifluoromethanesulfonyl)imide] ([C_nmim][NTf₂]), with n=1, 2, and 8, by time‐resolved coherent anti‐Stokes Raman scattering (CARS) and quantum‐classical hybrid (QCH) simulations. From the time series of the CARS spectra, dephasing times were extracted by modeling the full nonlinear response. From the QCH calculations, pure dephasing times were obtained by analyzing the distribution of transition frequencies. Experiments and calculations reveal larger dephasing rates for the vibrational stretching modes of C(2)?H compared with the more weakly hydrogen‐bonded C(4,5)?H. This finding can be understood in terms of different H‐bonding motifs and the fast interconversion between them. Differences in population relaxation rates are attributed to Fermi resonance interactions.     

Complexes of acridine and 9-chloroacridine with I2: formation of unusual I6 chains through charge-transfer interactions involving amphoteric I2

Acridine and 9-chloroacridine form charge-transfer complexes with iodine in which the nitrogen-bound I2 molecule is amphoteric; one end serves as a Lewis acid to the heterocyclic donor, while the other end acts as a Lewis base to a second I2 molecule that bridges two acridine.I2 units. In the acridine derivative [(acridine.I2)2.I2, 1], the dimer has a "zigzag" conformation, while in the 9-chloroacridine derivative [(9-Cl-acridine.I2)2.I2, 2], the dimer is "C-shaped". The thermal decomposition of the two complexes is very different. Compound 1 loses one molecule of I2 to form an acridine.I2 intermediate, which has not been isolated. Further decomposition gives acridine as the form II polymorph, exclusively. Decomposition of 2 involves the loss of two molecules of I2 to form a relatively stable intermediate [(9-Cl-acridine)2.I2, 3]. Compound 3 consists of two 9-Cl-acridine molecules bridged through N...I charge-transfer interactions by a single I2 molecule. This compound represents the first known example, in which both ends of an I2 molecule form interactions in a complex that is not stabilized by the extended interactions of an infinite chain structure. The ability of the terminal iodine of an N-bound I2 to act either as an electron donor (complexes 1 and 2) or as an electron acceptor (complex 3) can be understood through a quantum mechanical analysis of the systems. Both electrostatic interactions and the overlap of frontier molecular orbitals contribute to the observed behavior.     

Probing the transition from hydrophilic to hydrophobic solvation with atomic scale resolution

Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L(1,3) edge EXAFS at 50 ps time delay points to the formation of an expanded water cavity around the iodine atom, in good agreement with classical and quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. These also show that while the hydrogen atoms pointed toward iodide, they predominantly point toward the bulk solvent in the case of iodine, suggesting a hydrophobic behavior. This is further confirmed by quantum chemical (QC) calculations of I(-)/I(0)(H(2)O)(n=1-4) clusters. The L(1) edge sub-picosecond spectra point to the existence of a transient species that is not present at 50 ps. The QC calculations and the QM/MM MD simulations identify this transient species as an I(0)(OH(2)) complex inside the cavity. The simulations show that upon electron abstraction most of the water molecules move away from iodine, while one comes closer to form the complex that lives for 3-4 ps. This time is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform an H-bond network. Only then is the interaction with the solvation shell strong enough to pull the water molecule of the complex toward the bulk solvent. Overall, much of the behavior at early times is determined by the reorientational dynamics of water molecules and the formation of a complete network of hydrogen bonded molecules in the first solvation shell.     

Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase

Despite extensive experimental and theoretical studies, the detailed catalytic mechanism of orotidine 5'-monophosphate decarboxylase (ODCase) remains controversial. In particular simulation studies using high level quantum mechanics have failed to reproduce experimental activation free energy. One common feature of many previous simulations is that there is a water molecule in the vicinity of the leaving CO2 group whose presence was only observed in the inhibitor bound complex of ODCase/BMP. Various roles have even been proposed for this water molecule from the perspective of stabilizing the transition state and/or intermediate state. We hypothesize that this water molecule is not present in the active ODCase/OMP complex. Based on QM/MM minimum free energy path simulations with accurate density functional methods, we show here that in the absence of this water molecule the enzyme functions through a simple direct decarboxylation mechanism. Analysis of the interactions in the active site indicates multiple factors contributing to the catalysis, including the fine-tuned electrostatic environment of the active site and multiple hydrogen-bonding interactions. To understand better the interactions between the enzyme and the inhibitor BMP molecule, simulations were also carried out to determine the binding free energy of this special water molecule in the ODCase/BMP complex. The results indicate that the water molecule in the active site plays a significant role in the binding of BMP by contributing approximately -3 kcal/mol to the binding free energy of the complex. Therefore, the complex of BMP plus a water molecule, instead of the BMP molecule alone, better represents the tight binding transition state analogue of ODCase. Our simulation results support the direct decarboxylation mechanism and highlight the importance of proper recognition of protein bound water molecules in the protein-ligand binding and the enzyme catalysis.     

Polarized pump-probe measurements of electronic motion via a conical intersection

Polarized femtosecond pump-probe spectroscopy is used to observe electronic wavepacket motion for vibrational wavepackets centered on a conical intersection. After excitation of a doubly degenerate electronic state in a square symmetric silicon naphthalocyanine molecule, electronic motions cause a approximately 100 fs drop in the polarization anisotropy that can be quantitatively predicted from vibrational quantum beat modulations of the pump-probe signal. Vibrational symmetries are determined from the polarization anisotropy of the vibrational quantum beats. The polarization anisotropy of the totally symmetric vibrational quantum beats shows that the electronic wavepackets equilibrate via the conical intersection within approximately 200 fs. The relationship used to predict the initial electronic polarization anisotropy decay from the asymmetric vibrational quantum beat amplitudes indicates that the initial width of the vibrational wavepacket determines the initial speed of electronic wavepacket motion. For chemically reactive conical intersections, which can have 1000 times greater stabilization energies than the one observed here, the same theory predicts electronic equilibration within 2 fs. Such electronic movements would be the fastest known chemical processes.     

Effect of interprotein polarization on protein–protein binding energy

Molecular dynamics simulation in explicit water for the binding of the benchmark barnase‐barstar complex was carried out to investigate the effect polarization of interprotein hydrogen bonds on its binding free energy. Our study is based on the AMBER force field but with polarized atomic charges derived from fragment quantum mechanical calculation for the protein complex. The quantum‐derived atomic charges include the effect of polarization of interprotein hydrogen bonds, which was absent in the standard force fields that were used in previous theoretical calculations of barnase‐barstar binding energy. This study shows that this polarization effect impacts both the static (electronic) and dynamic interprotein electrostatic interactions and significantly lowers the free energy of the barnase‐barstar complex. © 2012 Wiley Periodicals, Inc.     

Evidence for emergent chemical bonding in Au+-Rg complexes (Rg = Ne, Ar, Kr, and Xe)

Evidence is presented that there is a clear covalent component in the bonding of Au+ to Kr and Au+ to Xe, with some evidence that there may be such bonding between Au+ and Ar; for Au+ and Ne, there is no such evidence, and the bonding seems to be entirely physical. A model potential analysis shows that when all attractive inductive and dispersive terms out to R-8 are properly included in the Au+-Ne case, with an Ae(-bR) Born-Mayer repulsive term, essentially all the bonding in Au+-Ne can be rationalized by physical attraction alone. This is consistent with a natural bond order (NBO) analysis of the Au+-Ne ab initio wavefunctions, which shows the charge on Au+ to be very close to 1.0. In contrast, similar model potential and NBO analyses show quite clearly that physical interactions alone cannot account for the large bond energy values for the Au+-Kr and Au+-Xe complexes and are consistent with covalent contributions to the Au+-Kr and Au+-Xe interactions. Au+-Ar is seen to lie on the borderline between these two limits. In performing the model potential analyses, high-level ab initio calculations are employed [CCSD(T) energies, extrapolated to the complete basis set limit], to obtain reliable values of Re, De and omegae as input. A comparison of the gold-Xe bond distances in several solid-state Au(I, II and III) oxidation-state complex ions, containing "ligand" Xe atoms, prepared by Seppelt and co-workers, with that of the "free" Au+-Xe gas-phase ion is made, and a discussion of the trends is presented.     

Fewest switches adiabatic surface hopping as applied to vibrational energy relaxation

In this contribution quantum/classical surface hopping methodology is applied to vibrational energy relaxation of a quantum oscillator in a classical heat bath. The model of a linearly damped (harmonic) oscillator is chosen which can be mapped onto the Brownian motion (Caldeira-Leggett) Hamiltonian. In the simulations Tully's fewest switches surface hopping scheme is adopted with inclusion of dephasing in the adiabatic basis using a simple decoherence algorithm. The results are compared to the predictions of a Redfield-type quantum master equation modeling using the classical heat bath force correlation function as input. Thereby a link is established between both types of quantum/classical approaches. Viewed from the latter perspective, surface hopping with dephasing may be interpreted as "on-the-fly" stochastic realization of a quantum/classical Pauli master equation.     

Analysis on wetting and local dynamic properties of single water droplet on a polarized solid surface: a molecular dynamics study

Molecular dynamics simulations of single water droplets on a solid surface were carried out in order to investigate the effects that the Coulomb interaction between liquid and solid molecules has on wetting behavior by appending vertical electric polarization on a solid surface. The water droplet became more wettable both on upward and downward polarized surfaces, although structures of the adsorption layer appearing near the solid surface were clearly different, and the relation between droplet contact angle and surface polarization was also different for upward and downward polarization directions. The probability density distribution of molecular orientation around the adsorption layer indicated that preferable water molecule orientations varied largely by the surface polarization, and the rotational mobility around the preferable orientations was also affected. The dynamic property due to this rotational mobility was clearly captured by means of distribution of rotational diffusion coefficient, which potentially corresponded to local viscosity distribution.     

The solution of the inverse problem in polarization CARS-spectroscopy

An analysis of the solution of the ill-posed inverse problem in polarization CARS is carried out on the basis of mathematical experiments. Smoothing, determination of the number of components and the determination of parameters describing each component are considered. The use of all available experimental and theoretical information is shown to be necessary for correct solution of the problem. The efficiency of the proposed algorithm in the analysis of the complex inhomogeneously broadened lines of chlorocyclohexane is demonstrated.     

Towards homonuclear J solid-state NMR correlation experiments for half-integer quadrupolar nuclei: experimental and simulated 11B MAS spin-echo dephasing and calculated 2J(BB) coupling constants for lithium diborate

Magic-angle spinning (MAS) NMR spin-echo dephasing is systematically investigated for the spin I = 3/2 (11)B nucleus in lithium diborate, Li(2)O·2B(2)O(3). A clear dependence on the quadrupolar frequency (ω(Q)(PAS)/2π = 3C(Q)/[4I(2I- 1)]) is observed: the B3 (larger C(Q)) site dephases more slowly than the B4 site at all investigated MAS frequencies (5 to 20 kHz) at 14.1 T. Increasing the MAS frequency leads to markedly slower dephasing for the B3 site, while there is a much less evident effect for the B4 site. Considering samples at 5, 25, 80 (natural abundance) and 100% (11)B isotopic abundance, dephasing becomes faster for both sites as the (11)B isotopic abundance increases. The experimental behaviour is rationalised using density matrix simulations for two and three dipolar-coupled (11)B nuclei. The experimentally observed slower dephasing for the larger C(Q) (B3) site is reproduced in all simulations and is explained by the reintroduction of the dipolar coupling by the so-called "spontaneous quadrupolar-driven recoupling mechanism" having a different dependence on the MAS frequency for different quadrupolar frequencies. Specifically, isolated spin-pair simulations show that the spontaneous quadrupolar-driven recoupling mechanism is most efficient when the quadrupolar frequency is equal to twice the MAS frequency. While for isolated spin-pair simulations, increasing the MAS frequency leads to faster dephasing, agreement with experiment is observed for three-spin simulations which additionally include the homogeneous nature of the homonuclear dipolar coupling network. First-principles calculations, using the GIPAW approach, of the (2)J(11B-11B) couplings in lithium diborate, metaborate and triborate are presented: a clear trend is revealed whereby the (2)J(11B-11B) couplings increase with increasing B-O-B bond angle and B-B distance. However, the calculated (2)J(11B-11B) couplings are small (0.95, 1.20 and 2.65 Hz in lithium diborate), thus explaining why no zero crossing due to J modulation is observed experimentally, even for the sample at 25% (11)B where significant spin-echo intensity remains out to durations of ～200 ms.     

Theory of time-resolved level anticrossing experiment

The purpose of the present paper is to present a general treatment of steady state and time-resolved level-anticrossing (LAC) experiments using the generalized master equation approach in which both radiate and nonradiative decays and dephasing processes have been considered. Several models are treated to demonstrate the theoretical method. The theory is applicable to both atoms and molecules. It is shown that under appropriate conditions, as derived in this paper, quantum beats can be observed in the time-resolved LAC experiment. Numerical calculations have been performed to show the time-dependent behavior (build-up and decay) of the time-resolved LAC experiment. These quantum beats are then a direct measurement of the microscopic coupling parameters in intersystem crossing, etc. It will be shown that combining the steady state and the time-resolved LAC experiments one can determine not only the microscopic coupling parameters but also the relaxation and/or the dephasing rate constants. Hence the particular virtues of time dependent LAC experiments are seen in these model calculations.     

Effect of collision and magnetic field on quantum beat in biacetyl

Molecular quantum beats are shown for the case of biacetyl, to vary strongly under the influence of weak magnetic fields. Values for dephasing constants for a gas-phase molecular system were determined. Information on sub-Doppler level splittings in the intersystem-crossing process is obtained.     

Theoretical study of dynamic electron-spin-polarization via the doublet-quartet quantum-mixed state and time-resolved ESR spectra of the quartet high-spin state

The mechanism of the unique dynamic electron polarization of the quartet (S = 3/2) high-spin state via a doublet-quartet quantum-mixed state and detail theoretical calculations of the population transfer are reported. By the photo-induced electron transfer, the quantum-mixed charge-separate state is generated in acceptor-donor-radical triad (A-D-R). This mechanism explains well the unique dynamic electron polarization of the quartet state of A-D-R. The generation of the selectively populated quantum-mixed state and its transfer to the strongly coupled pure quartet and doublet states have been treated both by a perturbation approach and by exact numerical calculations. The analytical solutions show that generation of the quantum-mixed states with the selective populations after de-coherence and/or accompanying the (complete) dephasing during the charge-recombination are essential for the unique dynamic electron polarization. Thus, the elimination of the quantum coherence (loss of the quantum information) is the key process for the population transfer from the quantum-mixed state to the quartet state. The generation of high-field polarization on the strongly coupled quartet state by the charge-recombination process can be explained by a polarization transfer from the quantum-mixed charge-separate state. Typical time-resolved ESR patterns of the quantum-mixed state and of the strongly coupled quartet state are simulated based on the generation mechanism of the dynamic electron polarization. The dependence of the spectral pattern of the quartet high-spin state has been clarified for the fine-structure tensor and the exchange interaction of the quantum-mixed state. The spectral pattern of the quartet state is not sensitive towards the fine-structure tensor of the quantum-mixed state, because this tensor contributes only as a perturbation in the population transfer to the spin-sublevels of the quartet state. Based on the stochastic Liouville equation, it is also discussed why the selective population in the quantum-mixed state is generated for the "finite field" spin-sublevels. The numerical calculations of the elimination of the quantum coherence (de-coherence and/or dephasing) are demonstrated. A new possibility of the enhanced intersystem crossing pathway in solution is also proposed.     

Synthesis, structural characterization, and computational studies of novel diiodine adducts with the heterocyclic thioamides N-methylbenzothiazole-2-thione and benzimidazole-2-thione: implications with the mechanism of action of antithyroid drugs

Reaction of N-methylbenzothiazole-2-thione (C8H7NS2 or NMBZT) with diiodine produced the charge-transfer (ct) complex [(NMBZT).I2] (1). NMBZT reacts with diiodine in the presence of FeCl3 in a molar ratio of 3:6:1 and forms the ionic complex [[(NMBZT)2I+].[FeCl4]-] (2) together with [[(NMBZT)2I+].[I7]-] (2a) iodonium salt. The reaction of benzimidazole-2-thione (C7H6N2S or MBZIM) with diiodine on the other hand results in the formation of the ct [[(MBZIM)2I]+[I3]-].[(MBZIM).I2] (3) compound. The compounds have been characterized by elemental analyses, DTA-TG, FT-Raman, FT-IR, UV-vis, and 1H NMR spectroscopies, and X-ray crystal structure determinations. Compound 1, C8H7I2NS2, is orthorhombic with a space group Pna2(1) and a = 12.5147(13) angstroms, b = 22.536(3) angstroms, c = 4.2994(5) angstroms, and Z = 4. Compound 2, C16H14Cl4FeIN2S4, is monoclinic, space group C2/c, a = 35.781(2) angstroms, b = 7.4761(5) angstroms, c = 18.4677(12) angstroms, beta = 107.219(1) degrees, and Z = 8. Compound 3, C21H18I6N6S3, monoclinic, space group P2(1)/n, a = 14.0652(11) angstroms, b = 22.536(3) angstroms, c = 4.2994(5) angstroms, beta = 99.635(7) degrees, and Z = 4, consists of two component moieties cocrystallized, one neutral which contains the benzimidazole-2-thione (MBIZM) ligand bonded with an iodine atom through sulfur, forming a compound with a "spoke" structure [(MBZIM)I2] 3a, while the other is the ionic complex [[(MBZII)2I+].[I3]-] (3b). The X-ray crystal structure of 1 shows a bond between the thione-sulfur atom and one of the iodine atoms in an essentially planar arrangement. In the cation of 2, an iodine is coordinated by two thione-sulfur atoms in a linear arrangement but the molecule is not planar. For the first time in the solid state a spoke-ionic mixed complex has been characterized in 3. One component of the structure is a molecular diiodine adduct, i.e., [(MBZIM)I2] (3a), with a linear coordination geometry in a decidedly planar arrangement, and the other component is an ionic adduct [[(MBZIM)2I]+.[I3]-] (3b) with the cation having an arrangement similar to that found for 1. Theoretical calculations using density functional (DFT) and ab initio Hartree-Fock theory have been carried out for 1 and 3a,b. The results are consistent with the experimental data. Conclusions on the behavior of a thioamide, when used as an antithyroid drug, have also been made.     

Dynamics of electronic states and spin-flip for photodissociation of dihalogens in matrices: experiment and semiclassical surface-hopping and quantum model simulations for F2 and ClF in solid Ar

Three approaches are combined to study the electronic states' dynamics in the photodissociation of F(2) and ClF in solid argon. These include (a) semiclassical surface-hopping simulations of the nonadiabatic processes involved. These simulations are carried out for the F(2) molecule in a slab of 255 argon atoms with periodic boundary conditions at the ends. The full manifold of 36 electronic states relevant to the process is included. (b) The second approach involves quantum mechanical reduced-dimensionality models for the initial processes induced by a pump laser pulse, which involve wavepacket propagation for the preoriented ClF in the frozen argon lattice and incorporate the important electronic states. The focus is on the study of quantum coherence effects. (c) The final approach is femtosecond laser pump-probe experiments for ClF in Ar. The combined results for the different systems shed light on general properties of the nonadiabatic processes involved, including the singlet to triplet and intertriplet transition dynamics. The main findings are (1) that the system remains in the initially excited-state only for a very brief, subpicosecond, time period. Thereafter, most of the population is transferred by nonadiabatic transitions to other states, with different time constants depending on the systems. (2) Another finding is that the dynamics is selective with regard to the electronic quantum numbers, including the Lambda and Omega quantum numbers, and the spin of the states. (3) The semiclassical simulations show that prior to the first "collision" of the photodissociated F atom with an Ar atom, the argon atoms can be held frozen, without affecting the process. This justifies the rigid-lattice reduced-dimensionality quantum model for a brief initial time interval. (4) Finally, degeneracies between triplets and singlets are fairly localized, but intertriplet degeneracies and near degeneracies can span an extensive range. The importance of quantum effects in photochemistry of matrix-isolated molecules is discussed in light of the results.     

Quantum simulation of a hydrated noradrenaline analog with the torsional path integral method

An extended version of the torsional path integral Monte Carlo (TPIMC) method is presented and shown to be useful for studying the conformation of flexible molecules in solvated clusters. The new technique is applied to the hydrated clusters of the 2-amino-1-phenyl-ethanol (APE) molecule. APE + nH2O clusters with n = 0-4 are studied at 100 and 300 K using both classical and quantum simulations. Only at the lower temperature is the hydration number n found to impact the conformational distribution of the APE molecule. This is shown to be a result of the temperature-dependent balance between the internal energy and entropy contributions to the relative conformer free energies. Furthermore, at 100 K, large quantum effects are observed in the calculated conformer populations. A particularly large quantum shift of 30% of the total population is calculated for the APE + 2H2O cluster, which is explained in terms of the relative zero point energy of the lowest-energy hydrated structures for this cluster. Finally, qualitative agreement is found between the reported calculations and recent spectroscopy experiments on the hydrated clusters of APE, including an entropically driven preference for the formation of AG-type hydrated structures and the formation of a water "droplet" in the APE + 4H2O cluster.