Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster

Quantum Computation of Hydrogen Bond Dynamics and Vibrational Spectra

Calculating observable properties of chemical systems is often classically intractable and widely viewed as a promising application of quantum information processing. Here, we introduce a new framework for solving generic quantum chemical dynamics problems using quantum logic. We experimentally demonstrate a proof-of-principle instance of our method using the QSCOUT ion-trap quantum computer, where we experimentally drive the ion-trap system to emulate the quantum wavepacket dynamics corresponding to the shared-proton within an anharmonic hydrogen bonded system. Following the experimental creation and propagation of the shared-proton wavepacket on the ion-trap, we extract measurement observables such as its time-dependent spatial projection and its characteristic vibrational frequencies to spectroscopic accuracy (3.3 cm-1 wavenumbers, corresponding to >99.9% fidelity). Our approach introduces a new paradigm for studying the chemical dynamics and vibrational spectra of molecules and opens the possibility to describe the behavior of complex molecular processes with unprecedented accuracy.

Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol

Over a series of publications we have introduced a graph-theoretic description for molecular fragmentation. Here, a system is divided into a set of nodes, or vertices, that are then connected through edges, faces, and higher-order simplexes to represent a collection of spatially overlapping and locally interacting subsystems. Each such subsystem is treated at two levels of electronic structure theory, and the result is used to construct many-body expansions that are then embedded within an ONIOM-scheme. These expansions converge rapidly with many-body order (or graphical rank) of subsystems and have been previously used for ab initio molecular dynamics (AIMD) calculations and for computing multidimensional potential energy surfaces. Specifically, in all these cases we have shown that CCSD and MP2 level AIMD trajectories and potential surfaces may be obtained at density functional theory cost. The approach has been demonstrated for gas-phase studies, for condensed phase electronic structure, and also for basis set extrapolation-based AIMD. Recently, this approach has also been used to derive new quantum-computing algorithms that enormously reduce the quantum circuit depth in a circuit-based computation of correlated electronic structure. In this publication, we introduce (a) a family of neural networks that act in parallel to represent, efficiently, the post-Hartree-Fock electronic structure energy contributions for all simplexes (fragments), and (b) a new k-means-based tessellation strategy to glean training data for high-dimensional molecular spaces and minimize the extent of training needed to construct this family of neural networks. The approach is particularly useful when coupled cluster accuracy is desired and when fragment sizes grow in order to capture nonlocal interactions accurately. The unique multidimensional k-means tessellation/clustering algorithm used to determine our training data for all fragments is shown to be extremely efficient and reduces the needed training to only 10% of data for all fragments to obtain accurate neural networks for each fragment. These fully connected dense neural networks are then used to extrapolate the potential energy surface for all molecular fragments, and these are then combined as per our graph-theoretic procedure to transfer the learning process to a full system energy for the entire AIMD trajectory at less than one-tenth the cost as compared to a regular fragmentation-based AIMD calculation.

Mapping Quantum Chemical Dynamics Problems to Spin-Lattice Simulators

The accurate computational determination of chemical, materials, biological, and atmospheric properties has a critical impact on a wide range of health and environmental problems, but is deeply limited by the computational scaling of quantum mechanical methods. The complexity of quantum chemical studies arises from the steep algebraic scaling of electron correlation methods and the exponential scaling in studying nuclear dynamics and molecular flexibility. To date, efforts to apply quantum hardware to such quantum chemistry problems have focused primarily on electron correlation. Here, we provide a framework that allows for the solution of quantum chemical nuclear dynamics by mapping these to quantum spin-lattice simulators. Using the example case of a short-strong hydrogen-bonded system, we construct the Hamiltonian for the nuclear degrees of freedom on a single Born-Oppenheimer surface and show how it can be transformed to a generalized Ising model Hamiltonian. We then demonstrate a method to determine the local fields and spin-spin couplings needed to identically match the molecular and spin-lattice Hamiltonians. We describe a protocol to determine the on-site and intersite coupling parameters of this Ising Hamiltonian from the Born-Oppenheimer potential and nuclear kinetic energy operator. Our approach represents a paradigm shift in the methods used to study quantum nuclear dynamics, opening the possibility to solve both electronic structure and nuclear dynamics problems using quantum computing systems.

Weighted-Graph-Theoretic Methods for Many-Body Corrections within ONIOM: Smooth AIMD and the Role of High-Order Many-Body Terms

We present a weighted-graph-theoretic approach to adaptively compute contributions from many-body approximations for smooth and accurate post-Hartree-Fock (pHF) ab initio molecular dynamics (AIMD) of highly fluxional chemical systems. This approach is ONIOM-like, where the full system is treated at a computationally feasible quality of treatment (density functional theory (DFT) for the size of systems considered in this publication), which is then improved through a perturbative correction that captures local many-body interactions up to a certain order within a higher level of theory (post-Hartree-Fock in this publication) described through graph-theoretic techniques. Due to the fluxional and dynamical nature of the systems studied here, these graphical representations evolve during dynamics. As a result, energetic "hops" appear as the graphical representation deforms with the evolution of the chemical and physical properties of the system. In this paper, we introduce dynamically weighted, linear combinations of graphs, where the transition between graphical representations is smoothly achieved by considering a range of neighboring graphical representations at a given instant during dynamics. We compare these trajectories with those obtained from a set of trajectories where the range of local many-body interactions considered is increased, sometimes to the maximum available limit, which yields conservative trajectories as the order of interactions is increased. The weighted-graph approach presents improved dynamics trajectories while only using lower-order many-body interaction terms. The methods are compared by computing dynamical properties through time-correlation functions and structural distribution functions. In all cases, the weighted-graph approach provides accurate results at a lower cost.

Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis

Combining a computationally efficient and affordable molecular dynamics approach, based on atom-centered density matrix propagation scheme, with the density functional tight binding semiempirical quantum mechanics, we study the vibrational dynamics of a single molecule at series of finite temperatures, spanning quite wide range. Data generated by molecular dynamics simulations are further analyzed and processed using time series analytic methods, based on correlation functions formalism, leading to both vibrational density of states spectra and infrared absorption spectra at finite temperatures. The temperature-induced dynamics in structural intramolecular parameters is correlated to the observed changes in the spectral regions relevant to molecular detection. In particular, we consider a case when an intramolecular X-H stretching vibrational states are notably dependent on the intramolecular torsional degree of freedom, the dynamics of which is, on the other hand, strongly temperature-dependent.

IRMPD Spectra of Protonated Hydroxybenzaldehydes: Evidence of Torsional Barriers in Carboxonium Ions

Protonation at the formyl oxygen atom of benzaldehydes leading to the formation of carboxonium ions yields two distinct isomers, depending on the relative orientation of the proton either cis or trans with respect to the hydrogen atom on the adjacent carbon. In this context, the IR multiple photon dissociation (IRMPD) spectra of protonated ortho, meta, and para-hydroxybenzaldehydes (OH-BZH⁺ ), delivered into the gas phase by electrospray ionization of hydro-alcoholic solutions, are reported in the 3200-3700 cm^-1 spectral range. This range is characteristic of O-H stretching modes and thus able to differentiate cis and trans carboxonium isomers. Comparison between IRMPD spectra and DFT calculations at the B3LYP/6-311++G(2df2p) level suggests that for both p-OH-BZH⁺ and m-OH-BZH⁺ only cis conformers are present in the ion population analyzed. For o-OH-BZH⁺ , IRMPD spectroscopy points to a mixture comprising one trans and more than one cis conformers. The energy barrier for cis-trans isomerization calculated for each OH-BZH⁺ isomer is a measure of the degree of π-electron delocalization. Furthermore, IRMPD spectra of p-OH-BZH⁺ , m-OH-BZH⁺ and protonated phenol (this last used as reference) were recorded also in the fingerprint range. Both the observed C-O and O-H stretching vibrations appear to be a measure of π-electron delocalization in the ions.

Proton relays in anomalous carbocations dictate spectroscopy, stability, and mechanisms: case studies on C2H5+ and C3H3+

We present a detailed exposition of “Grothuss-like” proton shuttles in C₂H₅⁺ and C₃H₃⁺ that result in anomalous structural and spectral behavior.

A Grotthuss-like proton shuttle in the anomalous C2H3+ carbocation: energetic and vibrational properties for isotopologues

The proton shuttle in C₂H₃⁺ is reminiscent of the Grotthuss proton transfer mechanism.

Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions

Using ab initio molecular dynamics (AIMD) simulations that facilitate the treatment of rare events, we probe the active site participation in the rate-determining hydrogen transfer step in the catalytic oxidation of linoleic acid by soybean lipoxygenase-1 (SLO-1). The role of two different active site components is probed. (a) On the hydrogen atom acceptor side of the active site, the hydrogen bonding propensity between the acceptor side hydroxyl group, which is bound to the iron cofactor, and the backbone carboxyl group of isoleucine (residue number 839) is studied toward its role in promoting the hydrogen transfer event. Primary and secondary (H/D) isotope effects are also probed and a definite correlation with subtle secondary H/D isotope effects is found. With increasing average nuclear kinetic energy, the increase in transfer probability is enhanced due to the presence of the hydrogen bond between the backbone carbonyl of I839 and the acceptor oxygen. Further increase in average nuclear kinetic energy reduces the strength of this secondary hydrogen bond which leads to a deterioration in hydrogen transfer rates and finally embrances an Arrhenius-like behavior. (b) On the hydrogen atom donor side, the coupling between vibrational modes predominantly localized on the donor-side linoleic acid group and the reactive mode is probed. There appears to be a qualitative difference in the coupling between modes that belong to linoleic acid and the hydrogen transfer mode, for hydrogen and deuterium transfer. For example, the donor side secondary hydrogen atom is much more labile (by nearly a factor of 5) during deuterium transfer as compared to the case for hydrogen transfer. This appears to indicate a greater coupling between the modes belonging to the linoleic acid scaffold and the deuterium transfer mode and also provides a new rationalization for the abnormal (nonclassical) secondary isotope effect results obtained by Knapp, Rickert, and Klinman in J. Am. Chem. Soc. , 2002 , 124 , 3865 . To substantiate our findings noted in point a above, we have suggested an I839 → A839 or I839 → V839 mutation. This will modify the bulkiness of hydrogen the bonding residue, allowing greater flexibility in the secondary hydrogen bond formation highlighted above and adversely affecting the reaction rate.

Proton-bound dimers of 1-methylcytosine and its derivatives: vibrational and NMR spectroscopy

Vibrational spectroscopy and NMR demonstrate that the proton-bound dimer of 1-methylcytosine, 1, has an unsymmetrical structure at room temperature. In the gas phase, investigation of isolated homodimer 1 reveals five fundamental NH vibrations by IR Multiple Photon Dissociation (IRMPD) action spectroscopy. The NH···N stretching vibration between the two ring nitrogens exhibits a frequency of 1570 cm(-1), as confirmed by examination of the proton-bound homodimers of 5-fluoro-1-methycytosine, 2, and of 1,5-dimethylcytosine, 3, which display absorptions in the same region that disappear upon deuterium substitution. (13)C, and (15)N NMR of the solid iodide salt of 1 confirm the nonequivalence of the two rings in the anhydrous proton-bound homodimer at room temperature. IRMPD spectra of the three possible heterodimers also show NH···N stretches in the same domain, and at least one of the heterodimers, the proton-bound dimer of 1,5-dimethylcytosine with 1-methylcytosine, exhibits two bands suggestive of the presence of two tautomers close in energy.

Vibrational spectroscopy of bisulfate/sulfuric acid/water clusters: structure, stability, and infrared multiple-photon dissociation intensities

The structure and stability of mass-selected bisulfate, sulfuric acid, and water cluster anions, HSO4(-)(H2SO4)m(H2O)n, are studied by infrared photodissociation spectroscopy aided by electronic structure calculations. The triply hydrogen-bound HSO4(-)(H2SO4) configuration appears as a recurring motif in the bare clusters, while incorporation of water disrupts this stable motif for clusters with m > 1. Infrared-active vibrations predominantly involving distortions of the hydrogen-bound network are notably missing from the infrared multiple-photon dissociation (IRMPD) spectra of these ions but are fully recovered by messenger-tagging the clusters with H2. A simple model is used to explain the observed "IRMPD transparency".

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.

"Pump-probe" atom-centered density matrix propagation studies to gauge anharmonicity and energy repartitioning in atmospheric reactive adducts: case study of the OH + isoprene and OH + butadiene reaction intermediates

Time-resolved "pump-probe" ab initio molecular dynamics studies are constructed to probe the stability of reaction intermediates, the mechanism of energy transfer, and energy repartitioning, for moieties involved during the interaction of volatile organic compunds with hydroxyl radical. These systems are of prime importance in the atmosphere. Specifically, the stability of reaction intermediates of hydroxyl radical adducts to isoprene and butadiene molecules is used as a case study to develop novel computational techniques involving "pump-probe" ab initio molecular dynamics. Starting with the various possible hydroxyl radical adducts to isoprene and butadiene, select vibrational modes of each of the adducts are populated with excess energy to mimic the initial conditions of an experiment. The flow of energy into the remaining modes is then probed by subjecting the excited adducts to ab initio molecular dynamics simulations. It is found that the stability of the adducts arises directly due to the anhormonically driven coupling of the modes to facilitate repartitioning of the excess vibrational energy. This kind of vibrational repartitioning has a critical influence on the energy density.

Vibrational characterization of simple peptides using cryogenic infrared photodissociation of H2-tagged, mass-selected ions

We present infrared photodissociation spectra of two protonated peptides that are cooled in a ~10 K quadrupole ion trap and "tagged" with weakly bound H(2) molecules. Spectra are recorded over the range of 600-4300 cm(-1) using a table-top laser source, and are shown to result from one-photon absorption events. This arrangement is demonstrated to recover sharp (Δν ~6 cm(-1)) transitions throughout the fingerprint region, despite the very high density of vibrational states in this energy range. The fundamentals associated with all of the signature N-H and C=O stretching bands are completely resolved. To address the site-specificity of the C=O stretches near 1800 cm(-1), we incorporated one (13)C into the tripeptide. The labeling affects only one line in the complex spectrum, indicating that each C=O oscillator contributes a single distinct band, effectively "reporting" its local chemical environment. For both peptides, analysis of the resulting band patterns indicates that only one isomeric form is generated upon cooling the ions initially at room temperature into the H(2) tagging regime.

Quantum wavepacket ab initio molecular dynamics: generalizations using an extended Lagrangian treatment of diabatic states coupled through multireference electronic structure

We present a generalization to our previously developed quantum wavepacket ab initio molecular dynamics (QWAIMD) method by using multiple diabatic electronic reduced single particle density matrices, propagated within an extended Lagrangian paradigm. The Slater determinantal wavefunctions associated with the density matrices utilized may be orthogonal or nonorthogonal with respect to each other. This generalization directly results from an analysis of the variance in electronic structure with quantum nuclear degrees of freedom. The diabatic electronic states are treated here as classical parametric variables and propagated simultaneously along with the quantum wavepacket and classical nuclei. Each electronic density matrix is constrained to be N-representable. Consequently two sets of new methods are derived: extended Lagrangian-QWAIMD (xLag-QWAIMD) and diabatic extended Lagrangian-QWAIMD (DxLag-QWAIMD). In both cases, the instantaneous potential energy surface for the quantum nuclear degrees of freedom is constructed from the diabatic states using an on-the-fly nonorthogonal multireference formalism. By introducing generalized grid-based electronic basis functions, we eliminate the basis set dependence on the quantum nucleus. Subsequent reuse of the two-electron integrals during the on-the-fly potential energy surface computation stage yields a substantial reduction in computational costs. Specifically, both xLag-QWAIMD and DxLag-QWAIMD turn out to be about two orders of magnitude faster than our previously developed time-dependent deterministic sampling implementation of QWAIMD. Energy conservation properties, accuracy of the associated potential surfaces, and vibrational properties are analyzed for a family of hydrogen bonded systems.