Calculation of two-dimensional infrared spectra of ultrafast chemical exchange with numerical Langevin simulations

We combine numerical Langevin simulations with numerical integration of the Schrodinger equation to calculate two-dimensional infrared spectra of ultrafast chemical exchange. This provides a tool to model and interpret such spectra of molecules undergoing chemical processes, such as isomerization and solvent exchange reactions. Two-dimensional infrared spectroscopy has already been used to extract reaction rates for ultrafast chemical reactions. We demonstrate that these spectra are not only sensitive to the rates, but also to the finite duration of the exchange. This is emphasised by comparing with the popular Kubo two-state jump models, which do not account for finite exchange times.     

Diffusion-controlled formation of porous structures in ternary polymer systems

We propose a theory for the appearance of two-phase structures during the formation of polymer membranes from a casting solution immersed in a coagulant bath. Our model is based on diffusion induced phase separation at the spinodal in the ternary nonsolvent-solvent-polymer system. A simplified treatment of the interdiffusion process by the diffusion layer method permits the formulation of criteria for the formation of two-phase structures in the course of the solvent-coagulant exchange. Our criteria are expressed in terms of the composition dependence of the chemical potentials in the stable and metastable region of the ternary phase diagram. Comparison with experimental results shows qualitative similarities with theoretical predictions.     

Ultrafast two-dimensional infrared vibrational echo chemical exchange experiments and theory

Ultrafast two-dimensional (2D) infrared vibrational echo experiments and theory are used to examine chemical exchange between solute-solvent complexes and the free solute for the solute phenol and three solvent complex partners, p-xylene, benzene, and bromobenzene, in mixed solvents of the partner and CCl4. The experiments measure the time evolution of the 2D spectra of the hydroxyl (OD) stretching mode of the phenol. The time-dependent 2D spectra are analyzed using time-dependent diagrammatic perturbation theory with a model that includes the chemical exchange (formation and dissociation of the complexes), spectral diffusion of both the complex and the free phenol, orientational relaxation of the complexes and free phenol, and the vibrational lifetimes. The detailed calculations are able to reproduce the experimental results and demonstrate that a method employed previously that used a kinetic model for the volumes of the peaks is adequate to extract the exchange kinetics. The current analysis also yields the spectral diffusion (time evolution of the dynamic line widths) and shows that the spectral diffusion is significantly different for phenol complexes and free phenol.     

A microscopic model of chemical reactions with reorganization. High-energy approximation

A dynamical model of a chemical reaction, accompanied by reorganization of the immediate environment of the isolated chemical subsystem, is proposed. The model enables studying the emergence of nonequilibrium distribution functions as a combined result of the interaction within the dynamical subsystem and the energy exchange with a subsystem of inactive degrees of freedom (thermal bath). The study is based on the quasiclassical high-energy approximation for nonadiabatic effects in the energy exchange within the dynamical subsystem, for strong and weak coupling of the oscillator mode with the thermal bath. Such an approximation allows for the important statement that nonequilibrium effects in thermal reactions are absent if the initial translational distribution along the reaction coordinate and the initial vibrational distribution in transversal degrees of freedom are Boltzmann-like with the same temperature. The results obtained in the absence of the initial equilibrium distribution have been used for interpreting the kinetics of endothermic plasmochemical reactions proceeding under nonequilibrium conditions.     

Coherent control of cross-peaks in chirality-induced two-dimensional optical signals of excitons

Polarization tuning of the interference of chirality-induced tensor components is used to simulate the suppression of diagonal peaks and amplification of cross peaks in femtosecond two-dimensional photon echo signals of excitons in a chiral porphyrin dimer. Superpositions of various tensor components which generate the optimized signals are constructed using a genetic learning algorithm. Exciton couplings and bath correlations may be extracted from these highly resolved signals.     

Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy

The stochastic Liouville equations are employed to investigate the combined signatures of chemical exchange (two-state jump) and spectral diffusion (coupling to an overdamped Brownian oscillator) in the coherent response of an anharmonic vibration to three femtosecond infrared pulses. Simulations reproduce the main features recently observed in the OD stretch of phenol in benzene.     

Modelling of surface exchange reactions and diffusion in composites and polycrystalline materials

Abstract  Surface exchange reactions and chemical diffusion in composites, consisting of a dilute distribution of inclusions in a matrix, and polycrystalline materials have been modelled by application of both a square grain and a spherical grain model. The diffusion equations have been solved numerically by employing a finite element approach in the case of the square grain model and the Laplace transform method involving numerical Laplace inversion with respect to the spherical grain model. The boundary conditions refer to oxygen exchange reactions between a gas phase and a mixed ionically–electronically conducting ceramic sample within the linear response regime, i.e. small variations of the oxygen partial pressure. Diffusion profiles as well as the time dependence of the total amount of exchanged oxygen (relaxation curves) have been calculated. A necessary requirement for effective medium diffusion is proposed, and appropriate relations for the effective chemical surface exchange coefficient and the effective chemical diffusion coefficient are derived. On the contrary, when the time constant for diffusion from the matrix into the inclusions of a composite exceeds considerably the relaxation time for effective medium diffusion, relaxation curves with two separate time constants are observed. Analogously, in the case of polycrystalline materials the overall transport process is determined by slow (rate-limiting) bulk diffusion from the grain boundaries into the grains. Adequate formulae for the relaxation times are given based on analytical approximations of the solution functions to the diffusion equations. In addition, the spherical grain model is applied to interpret the re-oxidation kinetics of the positive temperature coefficient of resistivity (PTC) ceramics based on conductivity relaxation experiments. Graphical abstract        

A comparative high frequency EPR study of monomeric and dimeric Mn4 single-molecule magnets

We compare high frequency single crystal electron paramagnetic resonance (EPR) data for monomeric and dimeric Mn₄ complexes where, in the case of the latter, intra-dimer exchange interactions are known to significantly alter the low temperature quantum behavior. The monomeric system exhibits typical single-molecule S=9/2 EPR spectra; analysis of these data have enabled us to characterize the effective spin Hamiltonian parameters for this material. In the dimeric system, the ground state transition shows a splitting over a narrow range of fields and frequencies. The transfer of spectral weight between these split peaks is consistent with the exchange bias picture which has been developed to explain the absence of a zero-field tunneling resonance in low temperature hysteresis experiments. Indeed, these measurements provide the first independent confirmation for this exchange bias model. The absence of a significant intensity in excited state EPR transitions for the dimer contrasts the results for the monomer. This likely suggests important differences concerning the coherence of excited states of the dimer versus the monomer. No clear indications for intermolecular exchange interactions were observed in the EPR for the monomer.     

Cross‐Peaks in Simple Two‐Dimensional NMR Experiments from Chemical Exchange of Transverse Magnetisation

Two‐dimensional correlation measurements such as COSY, NOESY, HMQC, and HSQC experiments are central to small‐molecule and biomolecular NMR spectroscopy, and commonly form the basis of more complex experiments designed to study chemical exchange occurring during additional mixing periods. However, exchange occurring during chemical shift evolution periods can also influence the appearance of such spectra. While this is often exploited through one‐dimensional lineshape analysis (“dynamic NMR”), the analysis of exchange across multiple chemical shift evolution periods has received less attention. Here we report that chemical exchange‐induced cross‐peaks can arise in even the simplest two‐dimensional NMR experiments. These cross‐peaks can have highly distorted phases that contain rich information about the underlying exchange process. The quantitative analysis of such peaks, from a single 2D spectrum, can provide a highly accurate characterisation of underlying exchange processes.     

Dynamics of Cu monomer,dimer and trimer on Ag (110) (1 × 2) missing‐row reconstructed surface

The authors aimed to investigate the diffusion of Cu monomer, dimer and trimer on Ag (110) (1×2) missing‐row surface. This problem is addressed through molecular dynamic simulation based on semi‐empirical many‐body potential, derived from the embedded atom method. Within this approach, we have identified and calculated the activation energy of each microscopic mechanism. Thus, for Cu monomer, the diffusion process occurs essentially by simple hopping between nearest‐neighbor sites. While for the Cu dimer, three processes have been identified such as dissociation–reassociation (DR), concerted jump (CJ) and leapfrog mechanisms (LF) with a slight predominance of DR process and a dual competition between CJ and LF processes. But, in the case of small one‐dimensional cluster such as trimer on (110)(1×2) missing‐row reconstructed surface, the main diffusion mechanism is the LF process. These results shed light on the diffusion processes on missing‐row reconstructed surfaces, especially for heterogeneous systems. Copyright © 2013 John Wiley & Sons, Ltd.     

Orientational relaxation dynamics in aqueous ionic solution: polarization-selective two-dimensional infrared study of angular jump-exchange dynamics in aqueous 6M NaClO4

The dynamics of hydrogen bond (H-bond) formation and dissociation depend intimately on the dynamics of water rotation. We have used polarization resolved ultrafast two-dimensional infrared (2DIR) spectroscopy to investigate the rotational dynamics of deuterated hydroxyl groups (OD) in a solution of 6M NaClO(4) dissolved in isotopically mixed water. Aqueous 6M NaClO(4) has two peaks in the OD stretching region, one associated with hydroxyl groups that donate a H-bond to another water molecule (OD(W)) and one associated with hydroxyl groups that donate a H-bond to a perchlorate anion (OD(P)). Two-dimensional IR spectroscopy temporally resolves the equilibrium inter conversion of these spectrally distinct H-bond configurations, while polarization-selective 2DIR allows us to access the orientational motions associated with this chemical exchange. We have developed a general jump-exchange kinetic theory to model angular jumps associated with chemical exchange events. We use this to model polarization-selective 2DIR spectra and pump-probe anisotropy measurements. We determine the H-bond exchange induced jump angle to be 49 ± 5° and the H-bond exchange rate to be 6 ± 1 ps. Additionally, the separation of the 2DIR signal into contributions that have or have not undergone H-bond exchange allows us to directly determine the orientational dynamics of the OD(W) and the OD(P) configurations without contributions from the exchanged population. This proves to be important because the orientational relaxation dynamics of the populations that have undergone a H-bond exchange differ significantly from the populations that remain in one H-bond configuration. We have determined the slow orientational relaxation time constant to be 6.0 ± 1 ps for the OD(W) configuration and 8.3 ± 1 ps for the OD(P) configuration. We conclude from these measurements that the orientational dynamics of hydroxyl groups in distinct H-bond configurations do differ, but not significantly.     

Manipulating multidimensional electronic spectra of excitons by polarization pulse shaping

A simulation study demonstrates how coherent control, combined with adaptive polarization pulse shaping and a genetic algorithm, may be used to simplify femtosecond coherent nonlinear optical signals of excitons. Cross peaks are amplified and resolved, and diagonal peaks are suppressed in the heterodyne-detected two-pulse echo signal from the Soret band of a porphyrin dimer coupled to a Brownian oscillator bath. Various optimization strategies involving the spectral, temporal, and polarization profiles of the second pulse are compared.     

Comparative study of planar motion in monomeric and dimeric discotics

Deuterium NMR spectra are reported in powder samples of discotic monomer and dimer as a function of temperature in their column Col(ho) phases. To simulate the observed powder patterns, a threefold jump model is used in the monomer, while in the related dimer the libration motion of the monomeric core is described using the infinitesimal jump method under a restricting potential due to the spacer. By comparing the diffusive rates for the two samples, it is concluded that the planar motion in the dimer is at least 30 times smaller than that of the monomer. This could lead to an enhancement of charge and energy transport in discotic dimer systems.     

Electron spin resonance studies of spin-labeled polymers. IV. Slow-motional effects in solid polystyrene

Shape changes in the electron spin resonance spectrum of spin-labeled polystyrene have been studied as a function of temperature in the range 77–340°K. Rotational correlation times have been calculated by using recent theories of slow-motional effects on ESR spectra. Three models were used, namely, Brownian, moderate jump diffusion, and large jump diffusion. The moderate jump model gave correlation times in good accord with those found by other techniques for the δ relaxation in polystyrene. The relaxation was found to be independent of molecular weight.     

Aromaticity on the pancake-bonded dimer of neutral phenalenyl radical as studied by MS and NMR spectroscopies and NICS analysis

We have demonstrated the first MS and NMR observation of a face-to-face pi-bonded dimer of an organic radical (pancake-bonded dimer coined by R. S. Mulliken) in solution, using tri-tert-butylated phenalenyl radical 1, a 3-fold symmetric neutral hydrocarbon. In addition to the direct detection of the dimer signal by cold-spray ionization mass spectrometry (CSI-MS), 1H and 13C NMR spectra in solution gave definitive evidence of a well-defined D3d dimer structure with a 12-center-2-electron-long C-C bond formation, which is the same symmetry as seen in the crystalline state. On the basis of the NMR peaks of the dimer in the aromatic region (6.47 ppm for 1H NMR and 120-143 ppm for 13C NMR), we carried out nucleus-independent chemical shift (NICS) analysis, which showed that the ring center of the dimer became more aromatic (-7.1 ppm) than that of the monomer (-3.8 ppm). The trend of aromaticity generation was more pronounced in the interior of the dimer, which has been interpreted by the negative electron density induced in the bonding region as seen in the electrostatic potential surface.     

End-evaporation dynamics revisited

We present analytical results on the so-called end-evaporation kinetics in equilibrium polymeric systems following a temperature jump (T jump). A T jump prepares the system with a nonequilibrium length distribution, after which it relaxes back to its equilibrium state. Starting from a master equation, we develop a mean-field analytical theory based on a generating function approach, which allows explicit approximate expressions for the monomer and dimer concentrations to be derived in a discrete setting; the concentrations of the other chains as well as the average chain length were shown to be entirely expressible in terms of the monomer and dimer concentrations. We find that the calculated monomer and dimer concentrations as well as the average chain length are in good agreement with numerical simulation results and do not suffer from some of the defects of earlier continuum theories. Furthermore, the relaxation was shown to take place in three different stages. The first stage comprises the very fast relaxation of the monomers to almost their equilibrium concentration; the other polymer chains have hardly relaxed. During the second stage, which is highly nonlinear, a redistribution of material at practically constant monomer density takes place. Only in the final stage of the relaxation process the chain concentrations approach their true equilibrium values. In this stage there are only very small shifts in the concentrations of chains, which are governed by extremely slow "indirect" monomer-mediated processes.     

Solute-solvent complex kinetics and thermodynamics probed by 2D-IR vibrational echo chemical exchange spectroscopy

The formation and dissociation kinetics of a series of triethylsilanol/solvent weakly hydrogen bonding complexes with enthalpies of formation ranging from -1.4 to -3.3 kcal/mol are measured with ultrafast two-dimensional infrared (2D IR) chemical exchange spectroscopy in liquid solutions at room temperature. The correlation between the complex enthalpies of formation and dissociation rate constants can be expressed with an equation similar to the Arrhenius equation. The experimental results are in accord with previous observations on eight phenol/solvent complexes with enthalpies of formation from -0.6 to -2.5 kcal/mol. It was found that the inverse of the solute-solvent complex dissociation rate constant is linearly related to exp(-DeltaH0/RT) where DeltaH0 is the complex enthalpy of formation. It is shown here, that the triethylsilanol-solvent complexes obey the same relationship with the identical proportionality constant, that is, all 13 points, five silanol complexes and eight phenol complexes, fall on the same line. In addition, features of 2D IR chemical exchange spectra at long reaction times (spectral diffusion complete) are explicated using the triethylsilanol systems. It is shown that the off-diagonal chemical exchange peaks have shapes that are a combination (outer product) of the absorption line shapes of the species that give rise to the diagonal peaks.     

The Adsorption of CHF3 on NaY5.6 Zeolite and Microdynamic Behaviors in Small Pores

Adsorption of CHF₃ on a NaY5.6 zeolite has been studied by the measurement of H and F NMR of the CHF₃ molecule, focusing in particular on the measurements of a chemical shift and a longitudinal relaxation time, together with the adsorption isotherm measurements. A coordination structure of the adsorbed CHF₃ is determined from the relationship between a chemical shift and an adsorption amount. Relaxation times of H and F were measured at respective two resonance frequencies for various adsorption amounts and temperatures. These relaxation data have been analyzed by use of the thermally activated diffusion model proposed by Torrey. From these analyses, various microdynamic variables such as a mean life time of the trapped state and a mean jump distance in the diffusion were determined as functions of an adsorption amount and temperature.     

铵根离子在水溶液中的跳跃转动机理

铵根离子的动力学行为与生命体内的生物和化学过程密切相关.依据流体力学理论,由于铵根离子与水分子之间存在多个强氢键,其转动应较慢,但实验结果并非如此,其转动的微观机理尚不清晰.本文分子动力学模拟研究表明,水溶液中铵根离子主要以快速、大角度的跳跃方式进行转动,像水分子一样遵从扩展分子跳跃转动模型.通过微观转动模式的分解和两种转动弛豫时间的比较发现,相对其氢键骨架的扩散转动,跳跃转动对其转动速率贡献更大,并随浓度增大不断强化.与水分子氢键交换方式相比,铵根离子更倾向于在非氢键相连的水分子间发生交换.