The Raman vibrational frequency shifts of pure parahydrogen and orthodeuterium clusters of sizes N = 4-9 are calculated using the Langevin equation path integral ground state method. The shifts are calculated using three different methods; the results obtained from each are compared to experiment and variance properties are assessed. The first method requires the direct calculation of energies from two simulations: one when the cluster is in the v = 0 vibrational state and one when the cluster has v = 1 total quantum of vibration. The shift is directly calculated from the difference in those two energies. The second method requires only a v = 0 simulation to be performed. The ground state energy is calculated as usual and the excited state energy is calculated by using the distribution of the v = 0 simulation and the ratio of the density matrices between the v = 1 state and the v = 0 state. The shift is calculated from the difference in those two energies. These first two are both exact methods. The final method is based on perturbation theory where the shift is calculated by averaging the pairwise difference potential over the pair distribution function. However, this is an approximate approach. It is found that for large enough system sizes, despite the approximations, the perturbation theory method has the strongest balance between accuracy and precision when weighing against computational cost.

Clathrate hydrates, or cages comprised solely of water molecules, have long been investigated as a clean storage facility for hydrogen molecules. A breakthrough occurred when hydrogen molecules were experimentally placed within a structure-II clathrate hydrate, which sparked much interest to determine their feasibility for energy storage [Mao et al., Science 297, 2247-2249 (2002)]. We use Path Integral Molecular Dynamics (PIMD) and Langevin equation Path Integral Ground State (LePIGS) for finite temperature and zero-temperature studies, respectively, to determine parahydrogen occupancy properties in the small dodecahedral (512) and large hexakaidecahedral (51264) sized cages that comprise the structure-II unit cell. We look at energetic and structural properties of small clusters of hydrogen, treated as point-like particles, confined within each of the different sized clathrates, and treated as rigid, to determine energetic and structural properties in the zero-temperature limit. Our predicted hydrogen occupancy within these two cage sizes is consistent with previous literature values. We then calculate the energies as a function of temperature and merge the low temperature results calculated using finite temperature PIMD with the zero-temperature results using LePIGS, demonstrating that the two methods are compatible.

We extend the Langevin equation Path Integral Ground State (LePIGS), a ground state quantum molecular dynamics method, to simulate flexible molecular systems and calculate both energetic and structural properties. We test the approach with the H2O and D2O monomers and dimers. We systematically optimize all simulation parameters and use a unity trial wavefunction. We report ground state energies, dissociation energies, and structural properties using three different water models, two of which are empirically based, q-TIP4P/F and q-SPC/Fw, and one which is ab initio, MB-pol. We demonstrate that our energies calculated from LePIGS can be merged seamlessly with low temperature path integral molecular dynamics calculations and note the similarities between the two methods. We also benchmark our energies against previous diffusion Monte Carlo calculations using the same potentials and compare to experimental results. We further demonstrate that accurate vibrational energies of the H2O and D2O monomer can be calculated from imaginary time correlation functions generated from the LePIGS simulations using solely the unity trial wavefunction.

Raman vibrational shifts of small parahydrogen (pH2), orthodeuterium (oD2), and paratritium (pT2) clusters with respect to the free molecules are calculated by combining a first order perturbation theory approach with Langevin equation Path Integral Ground State (LePIGS) simulations [ J. Phys. Chem. A 2013 , 117 , 7461 ]. Our theoretical predictions are compared to existing cryogenic free jet expansion results for pure (pH2)N clusters [ Phys. Rev. Lett. 2004 , 92 , 223401 ] and to new measurements for (oD2)N clusters reported here. This method has been successfully used before to predict the Raman vibrational shifts of (pH2)N clusters [ J. Chem. Phys. 2014 , 141 , 014310 ]. The 6-D interaction potential of Hinde [ J. Chem. Phys. 2008 , 128 , 154308 ] is reduced to 1-D using the Adiabatic Hindered Rotor approximation to yield effective pair potentials for both molecules being in the ground vibrational state, and for one of them carrying one quantum of vibrational excitation. These reduced 1-D potentials are fitted to a Morse Long Range analytic form for later convenience. Good agreement between experiment and theory is found for the smaller clusters, but significant deviations remain for the larger ones.

We developed and studied the implementation of trial wavefunctions in the newly proposed Langevin equation Path Integral Ground State (LePIGS) method [S. Constable, M. Schmidt, C. Ing, T. Zeng, and P.-N. Roy, J. Phys. Chem. A 117, 7461 (2013)]. The LePIGS method is based on the Path Integral Ground State (PIGS) formalism combined with Path Integral Molecular Dynamics sampling using a Langevin equation based sampling of the canonical distribution. This LePIGS method originally incorporated a trivial trial wavefunction, ψT, equal to unity. The present paper assesses the effectiveness of three different trial wavefunctions on three isotopes of hydrogen for cluster sizes N = 4, 8, and 13. The trial wavefunctions of interest are the unity trial wavefunction used in the original LePIGS work, a Jastrow trial wavefunction that includes correlations due to hard-core repulsions, and a normal mode trial wavefunction that includes information on the equilibrium geometry. Based on this analysis, we opt for the Jastrow wavefunction to calculate energetic and structural properties for parahydrogen, orthodeuterium, and paratritium clusters of size N = 4 − 19, 33. Energetic and structural properties are obtained and compared to earlier work based on Monte Carlo PIGS simulations to study the accuracy of the proposed approach. The new results for paratritium clusters will serve as benchmark for future studies. This paper provides a detailed, yet general method for optimizing the necessary parameters required for the study of the ground state of a large variety of systems.

We report a first-principles prediction of the Raman shifts of parahydrogen (pH2) clusters of sizes N = 4-19 and 33, based on path integral ground-state simulations with an ab initio potential energy surface. The Raman shifts are calculated, using perturbation theory, as the average of the difference-potential energy surface between the potential energy surfaces for vibrationally excited and ground-state parahydrogen monomers. The radial distribution of the clusters is used as a weight function in this average. Very good overall agreement with experiment [G. Tejeda, J. M. Fernández, S. Montero, D. Blume, and J. P. Toennies, Phys. Rev. Lett. 92, 223401 (2004)] is achieved for p(H2)(2-8,13,33). A number of different pair potentials are employed for the calculation of the radial distribution functions. We find that the Raman shifts are sensitive to slight variations in the radial distribution functions.

We propose a Langevin equation path integral ground state (LePIGS) approach for the calculation of ground state (zero temperature) properties of molecular systems. The approach is based on a modification of the finite temperature path integral Langevin equation (PILE) method (J. Chem. Phys. 2010, 133, 124104) to the case of open Feynman paths. Such open paths are necessary for a ground state formulation. We illustrate the applicability of the method using model systems and the weakly bound water-parahydrogen dimer. We show that the method can lead to converged zero point energies and structural properties.

Author Institution: Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1; Department of Biochemistry, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1; Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1

Author Institution: Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada

For DNA single molecule sequencing, the complete detection of all dye-labeled monomers which are cleaved off during the sequencing reaction is an essential requirement. In this work we address the feasibility of single molecule detection in microstructures with a confocal multi element set-up. We present statistical data on single molecule recognition and explain a refined data evaluation technique for single molecule burst analysis. From these data the signal-to-noise ratio in microstructures is evaluated as well as the overall detection efficiency. So far, detection efficiencies of single molecule events of up to 60% have been shown in microstructures.