Martin Cuma

A second generation multistate empirical valence bond model for proton transport in aqueous systems

Building on the previously developed multistate empirical valence bond model [U. W. Schmitt and G. A. Voth, J. Chem. Phys 111, 9361 (1999)] for the dynamics and energetics of an excess proton in bulk phase water, a second generation model is described. This model is shown to produce similar dynamic and structural properties to the previous model, while allowing for the use of the full hydronium charge. This characteristic of the model is required for its implementation in a host of realistic applications beyond bulk water. An improved state selection algorithm is also presented, resulting in a significantly reduced energy drift during microcanonical molecular dynamics simulations. The unusually high self diffusion constant of an excess proton in water due to the proton hopping (Grotthuss) process is observed in the simulation data and is found to be quantitatively in the same range as the experimental value if a quantum correction is taken into consideration. Importantly, a more complete analysis of proto...

Effect of Adjoining Aromatic Ring upon Excited State Proton Transfer. o-Hydroxybenzaldehyde

Abstract The ground and first few excited states of o-hydroxybenzaldehyde (oHBA) are computed at the CIS and MP2/CIS levels with a 6-31+G** basis set, with emphasis on its intramolecular H-bond. These results are compared with those for malonaldehyde, which differs from oHBA in that it lacks an adjoining benzene ring. In most respects, the addition of the latter aromatic system exerts surprisingly little influence upon the properties of malonaldehyde. With the exception of the 1ππ* state, electronic excitation weakens the H-bond and simultaneously raises the barrier to proton transfer in either system. Unlike the symmetric transfer potential in malonaldehyde, the enol and keto tautomers of oHBA are chemically distinct. π→π* excitation reverses the preference for the enol tautomer in the ground state. This reversal is connected with the changing degree of aromaticity in the benzene ring of oHBA. The asymmetric transfer potential in oHBA leads to forward and reverse barriers of different magnitude. When this factor is accounted for by an averaging procedure, the transfer barriers in oHBA are remarkably similar to those of the corresponding states of malonaldehyde.

Large-scale 3D inversion of marine magnetotelluric data: Case study from the Gemini prospect, Gulf of Mexico

Three-dimensional magnetotelluric MT inversion is an emerging technique for offshore hydrocarbon exploration. We have developed a new approach to the 3D inversion of MT data, based on the integral equation method. The Tikhonov regularization and physical constraint have been used to obtain a stable and reasonable solution of the inverse problem.Themethodisimplementedinafullyparallelcomputer code. We have applied the developed method and software for the inversion of marine MT data collected by the Scripps Institution of Oceanography SIO in the Gemini prospect, Gulf of Mexico. The inversion domain was discretized into 1.6 million cells. It took nine hours to complete 51 iterations on the 832-processor cluster with a final misfit between the observed and predicted data of 6.2%.The inversion results reveal a resistive salt structure, which is confirmed by a comparison with the seismic data. These inversion results demonstrate that resistive geoelectrical structures like salt domes can be mapped with reasonable accuracyusingthe3DinversionofmarineMTdata.

A multi-state empirical valence bond model for acid–base chemistry in aqueous solution

Abstract Classical molecular dynamics simulations in conjunction with a multi-state empirical valence bond (MS-EVB) model are used to study proton transport in strong and weak acid aqueous solutions. The strong acid, HCl, is modeled in its ionized state by inserting a chloride counter ion into the protonated water solution. Both equilibrium and dynamical properties differ only slightly from the previously studied isolated excess proton in water. The free-energy profile as a function of the separation between the excess charge and chlorine atom reveal minimal barrier for the anion-excess charge separation. To model the weak acid, protonated imidazole, the MS-EVB model was extended to include the protonated form of the acid in the EVB description, so that the dissociation step can be studied. Free energy profiles for the weak acid deprotonation show that several solvation shells around the weak acid molecule need to be included in the EVB model to correctly describe the stabilization of the solvated species. Structurally, one water molecule is coordinated to the proton donor in the protonated acid case, while two water molecules coordination is likely when the acid is deprotonated.

Massively parallel regularized 3D inversion of potential fields on CPUs and GPUs

We have recently introduced a massively parallel regularized 3D inversion of potential fields data. This program takes as an input gravity or magnetic vector, tensor and Total Magnetic Intensity (TMI) measurements and produces 3D volume of density, susceptibility, or three dimensional magnetization vector, the latest also including magnetic remanence information. The code uses combined MPI and OpenMP approach that maps well onto current multiprocessor multicore clusters and exhibits nearly linear strong and weak parallel scaling. It has been used to invert regional to continental size data sets with up to billion cells of the 3D Earths volume on large clusters for interpretation of large airborne gravity and magnetics surveys. In this paper we explain the features that made this massive parallelization feasible and extend the code to add GPU support in the form of the OpenACC directives. This implementation resulted in up to a 22x speedup as compared to the scalar multithreaded implementation on a 12 core Intel CPU based computer node. Furthermore, we also introduce a mixed single-double precision approach, which allows us to perform most of the calculation at a single floating point number precision while keeping the result as precise as if the double precision had been used. This approach provides an additional 40% speedup on the GPUs, as compared to the pure double precision implementation. It also has about half of the memory footprint of the fully double precision version. We describe implementation of scalable massively parallel potential fields modeling and inversion program.The code is capable of inverting gravity data for density and magnetics data for susceptibility or magnetization vector.Key features that allow scalability and good performance are use of the moving sensitivity domain around each data receiver and on-demand calculation of the sensitivity.Further improvement in performance is gained by use of mixed single-double precision arithmetic.The code is parallelized with MPI and OpenMP and alternatively the computation heavy kernels can be offloaded to GPUs using OpenACC.

Anisotropic 3D inversion of towed-streamer electromagnetic data: Case study from the Troll West Oil Province

One of the critical problems in the interpretation of marine controlled-source electromagnetic geophysical data is taking into account the anisotropy of the rock formations. We evaluated a 3D anisotropic inversion method based on the integral equation method. We applied this method to the full 3D anisotropic inversion of towed-streamer electromagnetic (EM) data. The towed-streamer EM system makes it possible to collect EM data with a high production rate and over very large survey areas. At the same time, 3D inversion of towed-streamer EM data has become a very challenging problem because of the huge number of transmitter positions of the moving towed-streamer EM system, and, correspondingly, the huge number of forward and inverse problems needed to be solved for every transmitter position over the large areas of the survey. We overcame this problem by exploiting the fact that a towed-streamer EM system’s sensitivity domain is significantly smaller than the area of the towed-streamer EM survey. This approach makes it possible to invert entire towed-streamer EM surveys with no approximations into high-resolution 3D geoelectrical sea-bottom models. We present an actual case study for the 3D anisotropic inversion of towed-streamer EM data from the Troll field in the North Sea.

Large-scale three-dimensional inversion of EarthScope MT data using the integral equation method

In this paper we apply 3D inversion to MT data collected in the Northwestern United States as a part of the EarthScope project. By the end of 2009 MT data had been collected from 262 stations located throughout Oregon, Washington, Idaho, and most of Montana and Wyoming. We used data from 139 MT stations in this analysis. We developed fully parallelized rigorous 3D MT inversion software based on the integral equation method with variable background conductivity. We also implemented a receiver footprint approach which considerably reduced the computational resources needed to invert the large volumes of data covering vast areas. The data set used in the inversion was obtained through the Incorporated Research Institutions for Seismology (IRIS). The inversion domain was divided into 2.7 M cells. The inverted electrical conductivity distribution agrees reasonably well with geological features of the region.

Regularized Focusing Inversion of Marine CSEM Data Using Minimum Vertical Support Stabilizer

Marine controlled-source electromagnetic (MCSEM) surveys have become an important part of off-shore petroleum exploration. In this paper we discuss new advances in the development of 3D inversion methods for the interpretation of MCSEM data. Our method is based on rigorous integral equation (IE) forward modeling and a new IE representation of the sensitivity (Frechet derivative matrix) of observed data to variations in sea-bottom conductivity. We use quasi-analytical approximation for models with variable background conductivity (QAVB) for more efficient Frechet derivative calculations. In our regularized focusing inversion algorithm we introduce a new stabilizing functional, a minimum vertical support stabilizer. This stabilizer helps generate a focused image of the relatively thin and flat resistive structure of a hydrocarbon (HC) reservoir. The methodology is tested on a 3D inversion of the synthetic EM data and the interpretation of an MCSEM survey conducted in the Troll West Gas Province (TWGP).

INFLUENCE OF ISOTOPIC SUBSTITUTION ON STRENGTH OF HYDROGEN BONDS OF COMMON ORGANIC GROUPS

Although the electronic contribution to the strength of a H–bond is unaffected by isotopic substitution, the heavier mass of deuterium compared with protium lowers some of the vibrational frequencies in the complex. The binding energy of the complex, which includes zero–point and thermal vibrational energies, can thus be altered by several tenths of a kcal mol−1 by H/D substitution. Ab initio calculations are used to analyze this phenomenon in a number of common organic functional groups that are prone to form H–bonds: hydroxyl, carboxyl and amide, both self–complexing as homodimers and with water molecules as partners. It is found that any site of D–substitution increases the complexation energy; however, the bridging sites show a stronger preference for D over H than do the non–bridging, or terminal, sites. Hence D–bonding can be considered to be stronger than H–bonding in these functional groups. Of the groups considered, the energetic preference for D over H is greater in the hydroxyl group, so deuterium would be expected to gravitate toward solvent water molecules in isotopic scrambling experiments. The increments in H–bonding energy resulting from each site of substitution are addititve in cases of multiple substitution.

Comparison of methods for calculating the properties of intramolecular hydrogen bonds. Excited state proton transfer

A series of molecules related to malonaldehyde, containing an intramolecular H-bond, are used as the testbed for a variety of levels of ab initio calculation. Of particular interest are the excitation energies of the first set of valence excited states, nπ* and ππ*, both singlet and triplet, as well as the energetics of proton transfer in each state. Taking coupled cluster results as a point of reference, configuration interaction-singles–second-order Moller–Plesset (CIS–MP2) excitation energies are too large, as are CIS to a lesser extent, although these approaches successfully reproduce the order of the various states. The same may be said of complete active space self-consistent-field (CASSCF), which is surprisingly sensitive to the particular choice of orbitals included in the active space. Complete active space–second-order perturbation theory (CASPT2) excitation energies are rather close to coupled cluster singles and doubles (CCSD), as are density functional theory (DFT) values. CASSCF proton trans...