<i>Ab Initio</i> Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique

Here, we demonstrate the application of fragment-based electronic structure calculations in (a) <i>ab initio</i> molecular dynamics (AIMD) and (b) reduced dimensional potential calculations, for medium- and large-sized protonated water clusters. The specific fragmentation algorithm used here is derived from ONIOM, but includes multiple, overlapping “model” systems. The interaction between the various overlapping model systems is (a) approximated by invoking the principle of inclusion-exclusion at the chosen higher level of theory and (b) within a real calculation performed at the chosen lower level of theory. The fragmentation algorithm itself is written using bit-manipulation arithmetic, which will prove to be advantageous, since the number of fragments in such methods has the propensity to grow exponentially with system size. Benchmark calculations are performed for three different protonated water clusters: H₉O₄⁺, H₁₃O₆⁺ and H­(H₂O)₂₁⁺. For potential energy surface benchmarks, we sample the normal coordinates and compare our surface energies with full MP2 and CCSD­(T) calculations. The mean absolute error for the fragment-based algorithm is <0.05 kcal/mol, when compared with MP2 calculations, and <0.07 kcal/mol, when compared with CCSD­(T) calculations over 693 different geometries for the H₉O₄⁺ system. For the larger H­(H₂O)₂₁⁺ water cluster, the mean absolute error is on the order of a 0.1 kcal/mol, when compared with full MP2 calculations for 84 different geometries, at a fraction of the computational cost. <i>Ab initio</i> dynamics calculations were performed for H₉O₄⁺ and H₁₃O₆⁺, and the energy conservation was found to be of the order of 0.01 kcal/mol for short trajectories (on the order of a picosecond). The trajectories were kept short because our algorithm does not currently include dynamical fragmentation, which will be considered in future publications. Nevertheless, the velocity autocorrelation functions and their Fourier transforms computed from the fragment-based AIMD approaches were found to be in excellent agreement with those computed using the respective higher level of theory from the chosen hybrid calculation

A Multiwavelet Treatment of the Quantum Subsystem in Quantum Wavepacket <i>Ab Initio</i> Molecular Dynamics through an Hierarchical Partitioning of Momentum Space

We present an hierarchical scheme where the propagator in quantum dynamics is represented using a multiwavelet basis. The approach allows for a recursive refinement methodology, where the representation in momentum space can be adaptively improved through additional, decoupled layers of basis functions. The method is developed within the constructs of quantum-wavepacket ab initio molecular dynamics (QWAIMD), which is a quantum-classical method and involves the synergy between a time-dependent quantum wavepacket description and ab initio molecular dynamics. Specifically, the current development is embedded within an “on-the-fly” multireference electronic structural generalization of QWAIMD. The multiwavelet treatment is used to study the dynamics and spectroscopy in a small hydrogen bonded cluster. The results are in agreement with previous calculations and with experiment. The studies also allow an interpretation of the shared proton dynamics as one that can be modeled through the dynamics of dressed states

Constructing Periodic Phase Space Orbits from <i>ab Initio</i> Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H₅O₂⁺) Cation

A method of analysis is introduced to probe the spectral features obtained from <i>ab initio</i> molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of “modes” pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm^–1 in the vibrational spectrum of the H₅O₂⁺, Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water–water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted

Gauging the Flexibility of the Active Site in Soybean Lipoxygenase‑1 (SLO-1) through an Atom-Centered Density Matrix Propagation (ADMP) Treatment That Facilitates the Sampling of Rare Events

We present a computational methodology to sample rare events in large biological enzymes that may involve electronically polarizing, reactive processes. The approach includes simultaneous dynamical treatment of electronic and nuclear degrees of freedom, where contributions from the electronic portion are computed using hybrid density functional theory and the computational costs are reduced through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment. Thus, the paper involves a QM/MM dynamical treatment of rare events. The method is applied to probe the effect of the active site elements on the critical hydrogen transfer step in the soybean lipoxygenase-1 (SLO-1) catalyzed oxidation of linoleic acid. It is found that the dynamical fluctuations and associated flexibility of the active site are critical toward maintaining the electrostatics in the regime where the reactive process can occur smoothly. Physical constraints enforced to limit the active site flexibility are akin to mutations and, in the cases studied, have a detrimental effect on the electrostatic fluctuations, thus adversely affecting the hydrogen transfer process

Adaptive, Geometric Networks for Efficient Coarse-Grained <i>Ab Initio</i> Molecular Dynamics with Post-Hartree–Fock Accuracy

We introduce a new coarse-graining technique for <i>ab initio</i> molecular dynamics that is based on the adaptive generation of connected geometric networks or graphs specific to a given molecular geometry. The coarse-grained nodes depict a local chemical environment and are <i>networked</i> to create edges, triangles, tetrahedrons, and higher order simplexes based on (a) a Delaunay triangulation procedure and (b) a method that is based on molecular, bonded and nonbonded, local interactions. The geometric subentities thus created, that is nodes, edges, triangles, and tetrahedrons, each represent an energetic measure for a specific portion of the molecular system, capturing a specific set of interactions. The energetic measure is constructed in a manner consistent with ONIOM and allows assembling an overall molecular energy that is purely based on the geometric network derived from the molecular conformation. We use this approach to obtain accurate MP2 energies for polypeptide chains containing up to 12 amino-acid monomers (123 atoms) and DFT energies up to 26 amino-acid monomers (263 atoms). The energetic measures are obtained at much reduced computational costs; the approach currently yields MP2 energies at DFT cost and DFT energies at PM6 cost. Thus, in essence the method performs an efficient “coarse-graining” of the molecular system to accurately reproduce the electronic structure properties. The method is comparable in principle to several fragmentation procedures recently introduced in the literature, including previous procedures introduced by two of the authors here, but critically differs by overcoming the computational bottleneck associated with adaptive fragment creation without spatial cutoffs. The method is used to derive a new, efficient, ab initio molecular dynamics formalism (both Born–Oppenheimer and Car–Parrinello-style extended Lagrangian schemes are presented) a critical hallmark of which is that, at each dynamics time-step, multiple electronic structure packages can be simultaneously invoked to assemble the energy and forces for the full system. Indeed, in this paper, as an illustration, we use both Psi4 and Gaussian09 simultaneously at every time-step to perform AIMD simulations and also the energetic benchmarks. The approach works in parallel (currently over 100 processors), and the computational implementation is object oriented in C++. MP2 and DFT based on-the-fly dynamics results are recovered to good accuracy from the coarse-grained AIMD methods introduced here at reduced costs as highlighted above