Parallel Implementation of Semiclassical Transition State Theory

This paper presents the parsctst code, an efficient parallel implementation of the semiclassical transition state theory (SCTST) for reaction rate constant calculations. Parsctst is developed starting from a previously presented approach for the computation of the vibrational density of states of fully coupled anharmonic molecules (Nguyen et al. Chem. Phys. Lett. 2010, 499, 915). The parallel implementation makes it practical to tackle reactions involving more than 100 fully coupled anharmonic vibrational degrees of freedom and also includes multidimensional tunneling effects. After describing the pseudocode and demonstrating its computational efficiency, we apply the new code for estimating the rate constant of the proton transfer isomerization reaction of the 2,4,6-tri-tert-butylphenyl to 3,5-di-tert-butylneophyl. Comparison with both theoretical and experimental results is presented. Parsctst code is user-friendly and provides a significant computational time saving compared to serial calculations. We believe that parsctst can boost the application of SCTST as an alternative to the basic transition state theory for accurate kinetics modeling not only in combustion or atmospheric chemistry, but also in organic synthesis, where bigger reactive systems are encountered

A quantum method for thermal rate constant calculations from stationary phase approximation of the thermal flux-flux correlation function integral

This paper presents a quantum mechanical approximation to the calculation of thermal rate constants. The rate is derived from a suitable stationary phase approximation to the time integral of the thermal flux-flux correlation function. The goal is to obtain an expression that barely depends on the position of the flux operators, i.e., of the dividing surfaces, so that it can be applied also to complex systems by arbitrarily locating the dividing surfaces. The approach is tested on one and two dimensional systems where quantum effects are predominant over a wide range of temperatures. The results are quite accurate, i.e., within a few percent of the exact values for a reasonable range of dividing surface positions

Parallel Implementation of Semiclassical Transition State Theory and its application to high-dimensional tunneling reactions

Semiclassical Transition State Theory (SCTST) can incorporate the non-separable coupling between degrees of freedom (DOFs) of reactive systems and include the effects of reaction path curvature and anharmonicity, as well as quantum tunneling contributions in the rate constant. The rate expression is derived by relying on a perturbative expansion for the vibrational energy which makes it possible to express the semiclassical cumulative reaction probability in a convenient way, without any further assumptions about the separability of the DOFs.[1-4] The main goal of the talk is the extension of this semiclassical methodology to systems of increasing dimensionality upon computation of the densities of states for the reactants and the transition state by means of a convenient parallel implementation of the Wang-Landau algorithm.[5-6] The new strategy is implemented into two codes, \u201cparadensum\u201d and \u201cparsctst\u201d, which are currently distributed with the open source MultiWell program suite for chemical kinetics.[7] The needed input information is just the reaction barrier height, the normal mode frequencies, and the anharmonic force constants, which are routinely calculated by suitable electronic structure packages. After describing the codes and demonstrating their computational accuracy and efficiency, the new implementation is applied to estimate the rate constant of the proton transfer isomerization of the 2,4,6-tri-tert-butylphenyl to 3,5-di-tert-butylneophyl, a reaction involving 145 degrees of freedom and showing a clear tunneling regime below 250K.[6] References [1] Miller, W.H. J. Chem. Phys., 1975, 62, 1899 \u2013 1906. [2] Miller, W.H. Faraday Discuss. Chem. Soc. 1977, 62, 40 \u2013 46. [3] Miller, W.H.; Hernandez, R.; Handy, N.C.; Jayatilaka, D.; Willetts, A. Chem. Phys. Letters 1990, 172, 62 \u2013 68. [4] Hernandez, R.; Miller, W. H. Chem. Phys. Lett. 1993, 214 (2), 129 \u2013 136. [5] Aieta, C.; Gabas, F.; Ceotto, M. J. Phys. Chem. A 2016, 120 (27), 4853 \u2013 4862. [6] Aieta, C.; Gabas, F.; Ceotto, M. J. Chem. Theory Comput. 2019, 15, 2142 12 2153. [7] Barker, J.R.; Nguyen, T.L.; Stanton, J.F.; Aieta, C.; Ceotto, M.; Gabas, F.; Kumar, T.J.D.; Li, C.G.L.; Lohr, L.L.; Maranzana, A.; Ortiz, N.F.; Preses, J.M.; Simmie, J.M.; Sonk, J.A.; Stimac, P.J.; MultiWell-2017 Software Suite; J.R. Barker, University of Michigan, Ann Arbor, Michigan, USA, 2019; http://clasp-research.engin.umich.edu/multiwell/

Poor outcome for patients with gastric cancer and lung metastases treated with ramucirumab and paclitaxel

The aim of this report is to investigate the activity of ramucirumab in combination with paclitaxel in patients with metastatic gastric cancer (GC) and lung metastases. We retrospectively reviewed clinical data from patients with GC treated in second line with ramucirumab and paclitaxel according to the presence or not of lung metastases. Thirty-one patients were eligible. Five (16.1%) patients had lung metastases. The median progression-free survival was 156 days in patients without lung metastases compared with 54 days in patients with lung metastases. The median survival also showed a trend in favour of patients without lung metastases. Despite the small number of patients and the retrospective nature of the data, our analysis showed relatively poor efficacy of ramucirumab plus paclitaxel as a second-line treatment in patients with lung metastases from GC. Further studies are required to evaluate novel treatments in this subset of patients

Giant birefringence in optical antenna arrays with widely tailorable optical anisotropy

The manipulation of light by conventional optical components such as a lenses, prisms and wave plates involves engineering of the wavefront as it propagates through an optically-thick medium. A new class of ultra-flat optical components with high functionality can be designed by introducing abrupt phase shifts into the optical path, utilizing the resonant response of arrays of scatters with deeply-subwavelength thickness. As an application of this concept, we report a theoretical and experimental study of birefringent arrays of two-dimensional (V- and Y-shaped) optical antennas which support two orthogonal charge-oscillation modes and serve as broadband, anisotropic optical elements that can be used to locally tailor the amplitude, phase, and polarization of light. The degree of optical anisotropy can be designed by controlling the interference between the light scattered by the antenna modes; in particular, we observe a striking effect in which the anisotropy disappears as a result of destructive interference. These properties are captured by a simple, physical model in which the antenna modes are treated as independent, orthogonally-oriented harmonic oscillators

Aberration-free ultra-thin flat lenses and axicons at telecom wavelengths based on plasmonic metasurfaces

The concept of optical phase discontinuities is applied to the design and demonstration of aberration-free planar lenses and axicons, comprising a phased array of ultrathin subwavelength spaced optical antennas. The lenses and axicons consist of radial distributions of V-shaped nanoantennas that generate respectively spherical wavefronts and non-diffracting Bessel beams at telecom wavelengths. Simulations are also presented to show that our aberration-free designs are applicable to high numerical aperture lenses such as flat microscope objectives

Semiclassical molecular dynamics for spectroscopic calculations of high dimensional and condensed phase molecular systems

I will present some novel semiclassical methods designed for spectroscopic IR calculations of high dimensional and/or condensed phase systems. These methods are based on a \u201cdivide-and-conquer\u201d approach,[1-3] where the full dimensional spectra are obtained as a composition of several lower dimensional ones or exploit hierarchically the different levels of accuracy of different semiclassical propagators.[4-6] All methods are within 10-20 wavenumbers Mean Absolute Error average respect to the exact or experiments when available,[7,8] and are amenable to ab initio molecular dynamics simulations.[9-11

Semiclassical Molecular Dynamics : a useful Tool for Spectroscopic Interpretation

I will present some novel theoretical methods based on semiclassical molecular dynamics and designed for spectroscopy calculations (for example IR) of high dimensional and/or condensed phase systems. These approaches are predictive. They are either based on a \u201cdivide-and-conquer\u201d strategy, whereby the full dimensional spectra are obtained as a composition of several lower dimensional ones, or they exploit hierarchically the different levels of accuracy of different semiclassical propagators.[1-5] All methods provide frequency estimates whose Mean Absolute Error is generally within 10-20 wavenumbers of exact quantum mechanical results (when available), or experiments. The methods can be interfaced easily to ab initio molecular dynamics simulations allowing one to treat pretty large systems.[6-9] I will illustrate some applications involving several gas phase and some condensed phase systems