Leslie Vogt

Report on the sixth blind test of organic crystal structure prediction methods

The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.

Accelerating Resolution-of-the-Identity Second-Order Møller−Plesset Quantum Chemistry Calculations with Graphical Processing Units†

The modification of a general purpose code for quantum mechanical calculations of molecular properties (Q-Chem) to use a graphical processing unit (GPU) is reported. A 4.3x speedup of the resolution-of-the-identity second-order Møller-Plesset perturbation theory (RI-MP2) execution time is observed in single point energy calculations of linear alkanes. The code modification is accomplished using the compute unified basic linear algebra subprograms (CUBLAS) library for an NVIDIA Quadro FX 5600 graphics card. Furthermore, speedups of other matrix algebra based electronic structure calculations are anticipated as a result of using a similar approach.

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library

Two new tools for the acceleration of computational chemistry codes using graphical processing units (GPUs) are presented. First, we propose a general black-box approach for the efficient GPU acceleration of matrix-matrix multiplications where the matrix size is too large for the whole computation to be held in the GPUs onboard memory. Second, we show how to improve the accuracy of matrix multiplications when using only single-precision GPU devices by proposing a heterogeneous computing model, whereby single- and double-precision operations are evaluated in a mixed fashion on the GPU and central processing unit, respectively. The utility of the library is illustrated for quantum chemistry with application to the acceleration of resolution-of-the-identity second-order Møller-Plesset perturbation theory calculations for molecules, which we were previously unable to treat. In particular, for the 168-atom valinomycin molecule in a cc-pVDZ basis set, we observed speedups of 13.8, 7.8, and 10.1 times for single-, double- and mixed-precision general matrix multiply (SGEMM, DGEMM, and MGEMM), respectively. The corresponding errors in the correlation energy were reduced from -10.0 to -1.2 kcal mol(-1) for SGEMM and MGEMM, respectively, while higher accuracy can be easily achieved with a different choice of cutoff parameter.

S0-State Model of the Oxygen-Evolving Complex of Photosystem II

The S0 → S1 transition of the oxygen-evolving complex (OEC) of photosystem II is one of the least understood steps in the Kok cycle of water splitting. We introduce a quantum mechanics/molecular mechanics (QM/MM) model of the S0 state that is consistent with extended X-ray absorption fine structure spectroscopy and X-ray diffraction data. In conjunction with the QM/MM model of the S1 state, we address the proton-coupled electron-transfer (PCET) process that occurs during the S0 → S1 transition, where oxidation of a Mn center and deprotonation of a μ-oxo bridge lead to a significant rearrangement in the OEC. A hydrogen bonding network, linking the D1-D61 residue to a Mn-bound water molecule, is proposed to facilitate the PCET mechanism.

Bypassing the Kohn-Sham equations with machine learning

Last year, at least 30,000 scientific papers used the Kohn–Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn–Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative. The present work overcomes this difficulty by directly learning the density-potential and energy-density maps for test systems and various molecules. We perform the first molecular dynamics simulation with a machine-learned density functional on malonaldehyde and are able to capture the intramolecular proton transfer process. Learning density models now allows the construction of accurate density functionals for realistic molecular systems.Machine learning allows electronic structure calculations to access larger system sizes and, in dynamical simulations, longer time scales. Here, the authors perform such a simulation using a machine-learned density functional that avoids direct solution of the Kohn-Sham equations.

Oxygen-evolving complex of Photosystem II: an analysis of second-shell residues and hydrogen-bonding networks.

The oxygen-evolving complex (OEC) is a Mn4O5Ca cluster embedded in the Photosystem II (PSII) protein complex. As the site of water oxidation, the OEC is connected to the lumen by channels that conduct water, oxygen, and/or protons during the catalytic cycle. The hydrogen-bond networks found in these channels also serve to stabilize the oxidized intermediates, known as the S states. We review recent developments in characterizing these networks via protein mutations, molecular inhibitors, and computational modeling. On the basis of these results, we highlight regions of the PSII protein in which changes have indirect effects on the S1, S2, and S3 oxidation states of the OEC while still allowing photosynthetic activity.

Computational insights on crystal structures of the oxygen-evolving complex of photosystem II with either Ca2+ or Ca2+ substituted by Sr2+

The oxygen-evolving complex of photosystem II can function with either Ca(2+) or Sr(2+) as the heterocation, but the reason for different turnover rates remains unresolved despite reported X-ray crystal structures for both forms. Using quantum mechanics/molecular mechanics (QM/MM) calculations, we optimize structures with each cation in both the resting state (S1) and in a series of reduced states (S0, S-1, and S-2). Through comparison with experimental data, we determine that the X-ray crystal structures with either Ca(2+) or Sr(2+) are most consistent with the S-2 state (i.e., Mn4[III,III,III,II] with O4 and O5 protonated). As expected, the QM/MM models show that Ca(2+)/Sr(2+) substitution results in the elongation of the heterocation bonds and the displacement of terminal waters W3 and W4. The optimized structures also show that hydrogen-bonded W5 is displaced in all S states with Sr(2+) as the heterocation, suggesting that this water may play a critical role during water oxidation.

Engineering directed excitonic energy transfer

We provide an intuitive platform for engineering exciton transfer dynamics. We show that careful consideration of the spectral density, which describes the system-bath interaction, leads to opportunities to engineer exciton transfer. Since excitons in nanostructures are proposed for use in quantum information processing and artificial photosynthetic designs, our approach paves the way for engineering a wide range of desired exciton dynamics. We carefully describe the validity of the model and use experimentally relevant material parameters to show counter-intuitive examples of directed exciton transfer in a linear chain of quantum dots.

Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II

The oxygen-evolving complex (OEC) of photosystem II (PSII) is a unique Mn4O5Ca cluster that catalyzes water oxidation via four photoactivated electron transfer steps. As the protein influence on the redox and protonation chemistry of the OEC remains an open question, we present a classical valence model of the OEC that allows the redox state of each Mn and the protonation state of bridging μ-oxos and terminal waters to remain in equilibrium with the PSII protein throughout the redox cycle. We find that the last bridging oxygen loses its proton during the transition from S0 to S1. Two possible S2 states are found depending on the OEC geometry: S2 has Mn4(IV) with a proton lost from a terminal water (W1) trapped by the nearby D1-D61 if O5 is closer to Mn4, or Mn1(IV), with partial deprotonation of D1-H337 and D1-E329 if O5 is closer to Mn1. In S3, the OEC is Mn4(IV) with W2 deprotonated. The estimated OEC Ems range from +0.7 to +1.3 V, enabling oxidation by P680(+), the primary electron donor in PSII. In chloride-depleted PSII, the proton release increases during the S1 to S2 transition, leaving the OEC unable to properly advance through the water-splitting cycle.

Single Molecule Rectification Induced by the Asymmetry of a Single Frontier Orbital

A mechanism for electronic rectification under low bias potentials is elucidated for the prototype molecule HS-phenyl-amide-phenyl-SH. We apply density functional theory (DFT) combined with the nonequilibrium Greens function formalism (NEGF), as implemented in the TranSIESTA computational code to calculate transport properties. We find that a single frontier orbital, the closest to the Fermi level, provides the dominant contribution to the overall transmission and determines the current. The asymmetric distribution of electron density in that orbital leads to rectification in charge transport due to its asymmetric response, shifting toward (or away from) the Fermi level under forward (or reverse) applied bias voltage. These findings provide a simple design principle to suppress recombination in molecular assemblies of dye-sensitized solar cells (DSSCs) where interfacial electron transfer is mediated by frontier orbitals with asymmetric character.