Prediction of photodynamics of 200 nm excited cyclobutanone with linear response electronic structure and ab initio multiple spawning.

Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S2). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. We use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations.

Efficient analytical gradients of property-based diabatic states: Geometry optimizations for localized holes.

We present efficient analytical gradients of property-based diabatic states and couplings using a Lagrangian formalism. Unlike previous formulations, the method achieves a computational scaling that is independent of the number of adiabatic states used to construct the diabats. The approach is generalizable to other property-based diabatization schemes and electronic structure methods as long as analytical energy gradients are available and integral derivatives with the property operator can be formed. We also introduce a scheme to phase and reorder diabats to ensure their continuity between molecular configurations. We demonstrate this for the specific case of Boys diabatic states obtained from state-averaged complete active space self-consistent field electronic structure calculations with GPU acceleration in the TeraChem package. The method is used to test the Condon approximation for the hole transfer in an explicitly solvated model DNA oligomer.

Evidence for Water Antibonding Orbital Mixing in the Hydrated Electron from Its Oxygen 1s X-ray Absorption Spectrum.

The X-ray absorption spectrum (XAS) of the hydrated electron (e(aq)-) has been simulated using time-dependent density functional theory with a quantum mechanics/molecular mechanics description. A unique XAS peak at 533 eV is observed with an energy and intensity in quantitative agreement with recent time-resolved experiments, allowing its assignment as arising from water O1s transitions to the singly occupied molecular orbital (SOMO) in which the excess electron resides. The transitions acquire oscillator strength due to the SOMO comprising an admixture of a cavity-localized orbital and water 4a1 and 2b2 antibonding orbitals. The mixing of antibonding orbitals has implications for the strength of couplings between e(aq)- and intramolecular modes of water.

Active orbital preservation for multiconfigurational self-consistent field.

We introduce Active Orbital Preservation for Multiconfigurational Self-Consistent Field (AOP-MCSCF), an automated approach to improving the consistency of active space orbitals over multiple molecular configurations. Our approach is based on maximum overlap with a reference set of active space orbitals taken from a single geometry of a chromophore in the gas phase and can be used to automatically preserve the appropriate orbitals of the chromophore across multiple thermally sampled configurations, even when the chromophore is solvated by quantum-mechanically treated water molecules. In particular, using the singular value decomposition of a Molecular Orbital (MO) overlap matrix between the system and reference, we rotate the MOs of the system to align with the reference active space orbitals and use the resulting rotated orbitals as an initial guess to a MCSCF calculation. We demonstrate the approach on aqueous p-hydroxybenzylidene-imidazolinone (HBI) and find that AOP-MCSCF converges to the "correct" orbitals for over 90% of 3000 thermally sampled configurations. In addition, we compute the linear absorption spectrum and find excellent agreement with new experimental measurements up to 5.4 eV (230 nm). We show that electrostatic contributions to the solvation energy of HBI largely explain the observed state-dependent solvatochromism.

Diabatic Many-Body Expansion: Development and Application to Charge-Transfer Reactions.

We explore the convergence of the many-body expansion for a prototypical hole-transfer reaction between Zn(0) and Zn(I) in a condensed-phase environment. Poor convergence of state energies is seen when the adiabatic representation is used, which can be understood from the fragment single-point calculations at low orders of the many-body expansion incorrectly localizing charges compared to the full system, thus leading to qualitative errors in the electronic structure of the adiabatic states between fragments. Using a charge-localized representation of the electronic Hamiltonian, we introduce a diabatic many-body expansion method with quantitative accuracy for ground- and excited-state potential energy surfaces of a charge-transfer reaction. Combining with a multiconfigurational self-consistent field affords a fragmentation approach that scales quadratically with system size while retaining chemical accuracy (<1 kcal/mol) in total energies compared to full system calculations.

Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library.

BACKGROUND: We re-evaluate our RNA-As-Graphs clustering approach, using our expanded graph library and new RNA structures, to identify potential RNA-like topologies for design. Our coarse-grained approach represents RNA secondary structures as tree and dual graphs, with vertices and edges corresponding to RNA helices and loops. The graph theoretical framework facilitates graph enumeration, partitioning, and clustering approaches to study RNA structure and its applications. METHODS: Clustering graph topologies based on features derived from graph Laplacian matrices and known RNA structures allows us to classify topologies into 'existing' or hypothetical, and the latter into, 'RNA-like' or 'non RNA-like' topologies. Here we update our list of existing tree graph topologies and RAG-3D database of atomic fragments to include newly determined RNA structures. We then use linear and quadratic regression, optionally with dimensionality reduction, to derive graph features and apply several clustering algorithms on our tree-graph library and recently expanded dual-graph library to classify them into the three groups. RESULTS: The unsupervised PAM and K-means clustering approaches correctly classify 72-77% of all existing graph topologies and 75-82% of newly added ones as RNA-like. For supervised k-NN clustering, the cross-validation accuracy ranges from 57 to 81%. CONCLUSIONS: Using linear regression with unsupervised clustering, or quadratic regression with supervised clustering, provides better accuracies than supervised/linear clustering. All accuracies are better than random, especially for newly added existing topologies, thus lending credibility to our approach. GENERAL SIGNIFICANCE: Our updated RAG-3D database and motif classification by clustering present new RNA substructures and RNA-like motifs as novel design candidates.