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Many computational models have been developed to predict the rates of atomic displacements in two-dimensional (2D) materials under electron beam irradiation. However, these models often drastically underestimate the displacement rates in 2D insulators, in which beam-induced electronic excitations can reduce the binding energies of the irradiated atoms. This bond softening leads to a qualitative disagreement between theory and experiment, in that substantial sputtering is experimentally observed at beam energies deemed far too small to drive atomic dislocation by many current models. To address these theoretical shortcomings, this paper develops a first-principles method to calculate the probability of beam-induced electronic excitations by coupling quantum electrodynamics (QED) scattering amplitudes to density functional theory (DFT) single-particle orbitals. The presented theory then explicitly considers the effect of these electronic excitations on the sputtering cross section. Applying this method to 2D hexagonal BN and MoS

Explicit time-dependent electronic structure theory methods are increasingly prevalent in the areas of condensed matter physics and quantum chemistry, with the broad-band optical absorptivity of molecular and small condensed-phase systems nowadays routinely studied with such approaches. In this paper, it is demonstrated that electronic dynamics simulations can similarly be employed to study cross sections for the scattering-induced electronic excitations probed in nonresonant inelastic X-ray scattering and momentum-resolved electron energy loss spectroscopies. A method is put forth for evaluating the electronic dynamic structure factor, which involves the application of a momentum boost-type perturbation and transformation of the resulting reciprocal space density fluctuations into the frequency domain. Good agreement is first demonstrated between the dynamic structure factor extracted from these electronic dynamics simulations and the corresponding transition matrix elements from linear response theory. The method is then applied to some extended (quasi)one-dimensional systems, for which the wave vector becomes a good quantum number in the thermodynamic limit. Finally, the dispersion of many-body excitations in a series of hydrogen-terminated graphene flakes (and twisted bilayers thereof) is investigated to highlight the utility of the presented approach for capturing morphology-dependent effects in the inelastic scattering cross sections of nanostructured and/or noncrystalline materials.

Abstract Autocatalysis and its relevance to various polymeric systems are discussed by taking inspiration from biology. A number of research directions related to synthesis, characterization, and multi-scale modeling are discussed in order to harness autocatalytic reactions in a useful manner for different applications ranging from chemical upcycling of polymers (depolymerization and reconstruction after depolymerization), self-generating micelles and vesicles, and polymer membranes. Overall, a concerted effort involving in situ experiments, multi-scale modeling, and machine learning algorithms is proposed to understand the mechanisms of physical and chemical autocatalysis. It is argued that a control of the autocatalytic behavior in polymeric systems can revolutionize areas such as kinetic control of the self-assembly of polymeric materials, synthesis of self-healing and self-immolative polymers, as next generation of materials for a sustainable circular economy. Graphic Abstract

Deuterium, a stable hydrogen isotope, has been playing important roles in many scientific areas, including polymer science. The developments of deuteration science and polymer science have been int...

We investigate (1) electron-beam-induced plasmon absorption spectra of Ag molecular nanowire dimers and (2) electron-beam-induced energy transfer between two nanowires. We employ linear-response time-dependent density functional theory (TDDFT) and real-time TDDFT methods to simulate the electron-beam-induced plasmonic excitations, dynamics, and corresponding electron energy loss spectrum for small models of a single molecular nanowire with four Ag atoms and for two Ag nanowires. An array of different relative orientations of nanowires and of different initial excitation conditions resulting from applying an electron beam at different positions with respect to the Ag nanowires is investigated. The results demonstrate (1) an electron beam can induce plasmonic excitations from the molecular Ag nanowire ground state to the excited states that are both optically allowed and forbidden, (2) a tunability for selective excitations that can be controlled by the position of a focused electron beam, and (3) kinetic and dynamic behaviors of time-dependent electron-beam-induced energy transfer between two Ag molecular nanowires depend on the position of the beam source and nanowire separation distance, providing insights into the spatial dependences of plasmonic couplings in nanowire arrays.

Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1–6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1–2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters.

Single atom impurities in graphene, substitutional silicon defects in particular, have been observed to diffuse under electron beam irradiation. However, the relative importance of elastic and inelastic scattering in facilitating their mobility remains unclear. Here, we employ excited-state electronic structure calculations to explore potential inelastic effects, and find an electronically nonadiabatic excited-state silicon diffusion pathway involving "softened" Si-C bonding that presents an ∼2 eV lower diffusion barrier than the ground-state pathway. Beam-induced transition rates to this state indicate that the excited-state pathway is accessible through irradiation of the defect site. However, even in the limit of fully elastic scattering, upward nonadiabatic transitions are also possible along the diffusion coordinate, increasing the diffusion barrier and further demonstrating the potential for electronic nonadiabaticity to influence beam-induced atomic transformations in materials. We also propose some experimentally testable signatures of such excited-state pathways.

Selective deuteration is an important tool for many analytical techniques including neutron scattering and spectroscopies. However, the availability of deuterated materials is limited because of the challenges in their synthesis. Here, we report the synthesis of partially and fully deuterated e-caprolactone monomers and their corresponding polymers, poly(e-caprolactone)s (PCLs), and the investigation of isotope effects on their crystalline structures and physical properties. Deuteration of PCLs leads to smaller crystal lattices and volumes compared to protiated PCLs by the amount proportional to the deuteration levels. The linear trend suggests that the volume isotope effect in PCL is primarily governed by the vibrations of C–D and C–H bonds. The large intrachain contraction of deuterated PCLs compared to that of polyethylene reported in the literature can be ascribed to the presence of polar ester groups in PCLs. Deuterated PCLs also display lower melting temperatures than protiated PCLs proportional to ...

Graphene, with unique mechanical and electrical properties, offers diverse application opportunities from beyond Moore’s nano-electronics to water filtration. However, accomplishing these relies on cleaning and processing large areas of supported and suspended graphene sheets. Here, we demonstrate the use of an Ar cluster ion beam as a versatile tool for graphene cleaning, defect engineering, and nanopore fabrication. In-situ and ex-situ characterization techniques were utilized in combination with first principles molecular dynamics, to highlight the differences in processing of the supported and suspended graphene samples. In this work, we monitor interaction of the Ar cluster ion beam with graphene as a function of ion dose with in-situ secondary ion mass spectrometry (SIMS), as well as ex-situ Raman spectroscopy measurements. Scanning transmission electron microscopy (STEM) results confirm that the Ar cluster ion beam can form nanopores in the suspended graphene; while the basal plane of graphene remains intact maintaining the lattice structure. Finally, Scanning Electron Microscopy (SEM) image analysis of the irradiated samples allows quantitative tracking of pore areas and their distribution as a function of ion dose. This study highlights the flexibility of the Ar cluster ion beam in 2D material processing, and offers insights into Ar beam interaction with graphene.

The prevalent catalysts for natural and artificial N2 fixation are known to hinge upon transition-metal (TM) elements. Herein, we demonstrate by density functional theory that Al-doped graphene is a potential non-TM catalyst to convert N2 to NH3 in the presence of relatively mild proton/electron sources. In the integrated structure of the catalyst, the Al atom serves as a binding site and catalytic center while the graphene framework serves as an electron buffer during the successive proton/electron additions to N2 and its various downstream NxHy intermediates. The initial hydrogenation of N2 can readily take place via an internal H-transfer process with the assistance of a Li+ ion as an additive. In view of the recurrence of H transfer in the first step of N2 reduction observed in biological nitrogenases and other synthetic catalysts, this finding highlights the significance of heteroatom-assisted H transfer in the design of synthetic catalysts for N2 fixation.

According to recent experiments, atomically thin hexagonal boron nitride and graphene are permeable to protons and deuterons (and not to other atomic species), and the experimental estimates of the activation energy are lower than the theoretical values by about 0.5 eV for the isolated proton–membrane transfer model. Our analysis of the electronic potential energy surfaces along the normal to the transmission direction, obtained using correlated electronic structure methods, suggests that the aqueous environment is essential to stabilize the proton transmission, as opposed to the hydrogen atom. Therefore, the process is examined within a molecular model of H2O–H(D)+–material–H2O. Exact quantum-mechanical scattering calculations are performed to assess the relevance of the nuclear quantum effects, such as tunneling factors and the kinetic isotope effect (KIE). Deuteration is found to affect the thermal reaction rate constants (KIE of 3–4 for hexagonal boron nitride and 20–30 for the graphene) and to effect...

The effects of deuterium isotope substitution on conjugated polymer chain stacking of poly(3-hexylthiophene) is studied experimentally by X-ray diffraction (XRD) in combination with gel permeation chromatography and theoretically using density functional theory and quantum molecular dynamics. For four P3HT materials with different levels of deuteration (pristine, main-chain deuterated, side-chain deuterated, and fully deuterated), the XRD measurements show that main-chain thiophene deuteration significantly reduces crystallinity, regardless of the side-chain deuteration. The reduction of crystallinity due to the main-chain deuteration is a quantum nuclear effect resulting from a static zero-point vibrational energy combined with a dynamic correlation of the dipole fluctuations. The quantum molecular dynamics simulations confirm the interchain correlation of the proton-proton and deuteron-deuteron motions but not of the proton-deuteron motion. Thus, isotopic purity is an important factor affecting stability and properties of conjugated polymer crystals, which should be considered in the design of electronic and spintronic devices.

A time dependent self consistent field based method for determining the rates of electronic excitations induced in materials by the presence of external point charges is presented. The method utilizes the full scalar potential of the external point charge in the interaction Hamiltonian instead of relying on multipolar expansions thereof. A general method is presented for determining the conditions under which dipole selection rules are adequate to describe the electronic response of the material to perturbation by external point charges. The position dependence of point charge induced transition rates between the ground and lowest few excited electronic states was resolved for a small polybenzoid. Notably, electronic excitations that are optically forbidden can be strongly allowed for particular positions of the perturbing point charge. Application of the methods detailed here can lead to an improved understanding of the electronic response of materials under irradiation by beams of charged particles.

A time dependent self consistent field based method for determining the rates of electronic excitations induced in materials by the presence of external point charges is presented. The method utilizes the full scalar potential of the external point charge in the interaction Hamiltonian instead of relying on multipolar expansions thereof. A general method is presented for determining the conditions under which dipole selection rules are adequate to describe the electronic response of the material to perturbation by external point charges. The position dependence of point charge induced transition rates between the ground and lowest few excited electronic states was resolved for a small polybenzoid. Notably, electronic excitations that are optically forbidden can be strongly allowed for particular positions of the perturbing point charge. Application of the methods detailed here can lead to an improved understanding of the electronic response of materials under irradiation by beams of charged particles.

A time dependent self consistent field based method for determining the rates of electronic excitations induced in materials by the presence of external point charges is presented. The method utilizes the full scalar potential of the external point charge in the interaction Hamiltonian instead of relying on multipolar expansions thereof. A general method is presented for determining the conditions under which dipole selection rules are adequate to describe the electronic response of the material to perturbation by external point charges. The position dependence of point charge induced transition rates between the ground and lowest few excited electronic states was resolved for a small polybenzoid. Notably, electronic excitations that are optically forbidden can be strongly allowed for particular positions of the perturbing point charge. Application of the methods detailed here can lead to an improved understanding of the electronic response of materials under irradiation by beams of charged particles.

The rapid progress of noisy intermediate-scale quantum (NISQ) computing underscores the need to test and evaluate new devices and applications. Quantum chemistry is a key application area for these devices, and therefore serves as an important benchmark for current and future quantum computer performance. Previous benchmarks in this field have focused on variational methods for computing ground and excited states of various molecules, including a benchmarking suite focused on performance of computing ground states for alkali-hydrides under an array of error mitigation methods. Here, we outline state of the art methods to reach chemical accuracy in hybrid quantum-classical electronic structure calculations of alkali hydride molecules on NISQ devices from IBM. We demonstrate how to extend the reach of variational eigensolvers with new symmetry preserving Ans\"atze. Next, we outline how to use quantum imaginary time evolution and Lanczos as a complementary method to variational techniques, highlighting the advantages of each approach. Finally, we demonstrate a new error mitigation method which uses systematic error cancellation via hidden inverse gate constructions, improving the performance of typical variational algorithms. These results show that electronic structure calculations have advanced rapidly, to routine chemical accuracy for simple molecules, from their inception on quantum computers a few short years ago, and they point to further rapid progress to larger molecules as the power of NISQ devices grows.

Direct write with a liquid precursor using an ion beam in situ, allows fabrication of nanostructures with higher purity than using gas phase deposition. Specifically, positively charged helium ions, when compared to electrons, localize the reaction zone to a single-digit nanometer scale. However, to control the interaction of the ion beam with the liquid precursor, as well as enable single digit fabrication, a comprehensive understanding of the radiolytic process, and the role of secondary electrons has to be developed. Here, we demonstrate an approach for directly writing platinum nanostructures from aqueous solution using a helium ion microscope, and discuss possible mechanisms for the beam-induced particle growth in the framework of Born-Oppenheimer and real-time electron dynamics models. We illustrate the nanoparticle nucleation and growth parameters through data analysis of in situ acquired movie data, and correlate these results to a fully encompassing, time-dependent, quantum dynamical simulation that takes into account both quantum and classical interactions. Finally, sub-15 nm resolution platinum structures generated in liquid are demonstrated.

The identification of isotopic labels by conventional macroscopic techniques lacks spatial resolution and requires relatively large quantities of material for measurements. We recorded the vibrational spectra of an α amino acid, l-alanine, with damage-free “aloof” electron energy-loss spectroscopy in a scanning transmission electron microscope to directly resolve carbon-site–specific isotopic labels in real space with nanoscale spatial resolution. An isotopic red shift of 4.8 ± 0.4 milli–electron volts in C–O asymmetric stretching modes was observed for 13C-labeled l-alanine at the carboxylate carbon site, which was confirmed by macroscopic infrared spectroscopy and theoretical calculations. The accurate measurement of this shift opens the door to nondestructive, site-specific, spatially resolved identification of isotopically labeled molecules with the electron microscope.

We propose a fast and accurate calculation method to compute the electronic couplings between molecular units in a thiophene-ring-based polymer chain mimicking a real organic semiconducting polymer, poly(3-hexylthiophene). Through a unit block diabatization scheme, the method employed minimal number of diabatic orbitals to compute the site energies and electronic couplings, which were validated by comparing with benchmark density functional theory calculations. In addition, by using the obtained electronic couplings, a quantum dynamics simulation was carried out to propagate a hole initially localized in a thiophene-ring unit of the polymer chain. This work establishes a simple, efficient, and robust means for the simulation of electron or hole transfer processes in organic semiconducting materials, an important capability for study and understanding of the class of organic optoelectronic and photovoltaic materials. © 2018 Wiley Periodicals, Inc.

The prevalent catalysts for natural and artificial N

Over the past decade, the open frame (``cagey'') structure of $\mathrm{CoS}{\mathrm{b}}_{3}$ skutterudite has invited intensive filling studies with various rare-earth elements for delivering state-of-the-art midtemperature thermoelectric performance. To rationalize previously reported experimental results and provide new insight into the underexplored roles of La fillers and Sb vacancies, ab initio density functional theory studies, along with semiclassical Boltzmann transport theory calculations, are performed for pristine $\mathrm{CoS}{\mathrm{b}}_{3}$ of different lattice settings and La-filled $\mathrm{CoS}{\mathrm{b}}_{3}$ with and without Sb's mono- and divacancy defects. The effects of spin-orbit coupling (SOC), partial La filling, Sb vacancy defects, and spin polarization on the electronic and thermoelectric properties are systematically examined. The SOC shows minor effects on the electronic and thermoelectric properties of $\mathrm{CoS}{\mathrm{b}}_{3}$. The peculiar quasi-Dirac band in the pristine $\mathrm{CoS}{\mathrm{b}}_{3}$ largely survives La filling but not Sb vacancies, which instead introduce dispersive bands in the band gap region. The non-spin-polarized and spin-polarized solutions of La-filled $\mathrm{CoS}{\mathrm{b}}_{3}$ are nearly degenerate. Importantly, the band structure, density of states, and Fermi surface of the latter are significantly spin polarized, giving rise to spin-dependent thermoelectric properties. Seebeck coefficients directly calculated as a function of chemical potential are interpreted in connection with the electronic structures. Temperature-dependent Seebeck coefficients derived for the experimentally studied materials agree well with available experimental data. Seebeck coefficients obtained as a function of charge carrier concentration corroborate the thermoelectrically favorable role at high filling fractions played by the Fermi electron pockets associated with the degenerate valleys in the conduction bands, and also point toward a similar role of the Fermi hole pockets associated with the degenerate hills in the valence bands. These results serve to advance the understanding of $\mathrm{CoS}{\mathrm{b}}_{3}$ skutterudite, a class of materials with important fundamental and application implications for thermoelectrics and spintronics.

The motion of local substrate nuclei is incorporated into the quantum hydrogen transfer reaction which occurs in the active site of soybean lipoxygenase-1, modeled within a quantum trajectory (QT) framework. Interactions within the active site are obtained from on-the-fly electronic structure (ES) calculations at the density-functional tight-binding (DFTB) level. By selectively constraining substrate nuclei, changes in the rate constants and kinetic isotope effect are computed over a 100 K temperature range. Substrate motion, occurring on the time-scale of the hydrogen transfer, enhances both the rate constants and isotope effect, but does not change trends captured in a constrained substrate environment.

Adsorption of atomic hydrogen colliding with C37H15, a planar “flake” of graphene, is examined using a hybrid quantum trajectory/electronic structure (QTES) dynamics for the values of the collision energies below 2.0 eV. The entire system of 53 atoms is represented by a quantum trajectory ensemble. The quantum correction on dynamics is included for the adsorbing hydrogen. The electronic structure is computed on-the-fly using the density functional tight binding (DFTB) method. The highest probability of adsorption is obtained for the kinetic energy of incident hydrogen in the range from 0.1 to 0.9 eV. Adsorption mechanism involves transfer of the collision energy to the graphene flake and projection of the carbon atom of the forming CH bond, accompanying sp3 hybridization of orbitals. The QTES–DFTB simulations with and without the quantum correction show that localization of the proton wave function and details of the mixed quantum/classical description of light and heavy nuclei greatly influence the adsor...

A method of molecular dynamics with quantum corrections, practical for studies of large molecular systems, is reviewed. The approach is based on the Bohmian formulation of the time-dependent Schrod...

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum computational chemistry calculations with electrostatic field solvers to perform detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. The resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices., 21 pages, 8 figures; A smart model is a good model

The experimentally observed effect of selective deuterium substitution on the open circuit voltage for a blend of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM; Nat. Commun. 2014, 5, 3180) is explored using a 221-atom model of a polymer-wrapped PCBM molecule. The protonic and deuteronic wave functions for the H/D isotopologues of the hexyl side chains are described within a quantum trajectory/electronic structure approach where the dynamics is performed with newly developed nonlinear corrections to the quantum forces, necessary to describe the nuclear wave functions; the classical forces are generated with a density functional tight binding method. The resulting protonic and deuteronic time-dependent wave functions are used to assess the effects of isotopic substitution (deuteration) on the energy gaps relevant to the charge transfer for the donor and acceptor electronic states. While the isotope effect on the electronic energy levels is found negligible, the quantum-induced fluctuations of the energy gap between the charge transfer and charge separated states due to nuclear wave functions may account for experimental trends by promoting charge transfer in P3HT:PCBM and increasing charge recombination on the donor in the deuterium substituted P3HT:PCBM.

Chemistry as well as sputtering and reflection dynamics of lithiated carbon material, bombarded by slow hydrogen atoms are studied. We present a realistic method for computational simulation of the dynamics of the polar Li–C–O–H material dynamics. It is based on an approximate, semi-empirical quantum mechanics of electrons and classical mechanics of nuclei. Results are validated qualitatively by comparison with experiments and with a first principle DFT computations. In particular, we explain observed details of the hydrogen bonding chemistry in lithiated carbon, showing that incoming hydrogen interacts preferably with Li-C rather than C structures.

An approximate dynamics method, based on donor and acceptor quantum trajectory ensembles, is employed to model hydrogen tunneling and the kinetic isotope effect (KIE) in soybean lipoxygenase-1. The proton is treated as a three-dimensional quantum-mechanical particle moving between the donor and acceptor wells for multiple configurations of the active site. Substitution of the proton with a deuteron reduces the transmission probability, integrated over enzyme configurations, by a factor of 51, which is in reasonable agreement with the experimental value of KIE equal to 81, validating the applicability of the current approach in biological systems.

An approach for performing real-time dynamics of electron transfer in a prototype redox reaction that occurs in reactive collisions between neutral and ionic fullerenes is discussed. The quantum dynamical simulations show that the electron transfer occurs within 60 fs directly preceding the collision of the fullerenes, followed by structural changes and relaxation of electron charge. The consequences of real-time electron dynamics are fully elucidated for the far from equilibrium processes of collisions between neutral and multiply charged fullerenes.

We report theoretical studies of the initial phase of bulk C(2) condensation into carbon nano-structures by means of Born-Oppenheimer and time-dependent quantum mechanical Liouville-von Neumann molecular dynamics based on the density-functional tight-binding (DFTB) framework for electrons. We observe that the time-dependent quantum mechanical approach leads to faster formation of carbon nanostructures than analogous Born-Oppenheimer simulations. Our results suggest that the condensation of bulk carbon is nonadiabatic in nature, with the critical role of electronic stopping as in ion-irradiation of materials. Contrary to time-dependent quantum mechanical simulations, Born-Oppenheimer dynamics incorrectly predict that the short carbon chains obtained from initial reactive collisions between C(2) quickly evaporate, leading to much lower probability of secondary collisions and condensation. We also discuss some deficiencies in Born-Oppenheimer dynamics that lead to unphysical charge polarization and electron transfer.

We study the hydrogen tunneling problem in a model system that represents the active site of the biological enzyme, soybean lipoxygenase-1. Toward this, we utilize quantum wavepacket dynamics performed on potential surfaces obtained by using hybrid density functional theory under the influence of a dynamical active site. The kinetic isotope effect is computed by using the transmission amplitude of the wavepacket, and the experimental value is reproduced. By computing the hydrogen nuclear orbitals (eigenstates) along the reaction coordinate, we note that tunneling for both hydrogen and deuterium occurs through the existence of distorted, spherical s-type proton wave functions and p-type polarized proton wave functions for transfer along the donor-acceptor axis. In addition, there is also a significant population transfer through distorted p-type proton wave functions directed perpendicular to the donor-acceptor axis (via intervening pi-type proton eigenstate interactions) which underlines the three-dimensional nature of the tunneling process. The quantum dynamical evolution indicates a significant contribution from tunneling processes both along the donor-acceptor axis and along directions perpendicular to the donor-acceptor axis. Furthermore, the tunneling process is facilitated by the occurrence of curve crossings and avoided crossings along the proton eigenstate adiabats.

13C CP MAS NMR spectra of the flavonoids: morin, kaempferol, 3,7-dihydroxyflavone, tricin and isoflavones: genistein and formononetin were recorded to characterize solid-state conformations. Intramolecular hydrogen bonds forming five-, six- and seven-membered rings are present in the two morin molecules in the crystals – their 13C resonances have been assigned with the aid of the calculated shielding constants. Linear relationships between the calculated shielding constants σDFT (ppm) and chemical shifts (δCPMAS, ppm) were obtained for all studied compounds. Higher correlation coefficients suggest that the conformation with “clockwise” orientation of both OH groups is more probable in the solid 3,7-dihydroxyflavone, whereas in the solid formononetin the OH and OCH3 substituents are directed “anticlockwise”. The barrier to the rotation of phenyl ring B decreases in the order: morin (2′-OH, 3-OH) > kaempferol (3-OH) > tricin.

Ab initio electronic structure simulations are carried out on small alanine-based peptide fragments with an excess electron added to a Coulomb-stabilized amide OCN π* orbital that forms a C O − radical anion center. A focus of the study is to determine to what extent and by what means helix-involved N C α bonds are “protected” against cleavage compared to similar bonds in non-helical peptides. The primary findings, many of which support earlier suggestions, include: (1) There is little or no increase in the energy barriers for N C α bond cleavage caused by an amino acid being in a helix where its carbonyl oxygen is involved in a hydrogen bond to an H N bond of an amino acid displaced by one helix turn. (2) When an electron attaches to a helix-involved Coulomb-stabilized OCN π* orbital and the N C α bond cleaves, three hydrogen bonds act to bind together the c and z fragment ions. One of these hydrogen bonds is especially strong (ca. 16 kcal mol −1 ) because it involves a negatively charged oxygen center. This suggests that the “protection” against N C α cleavage of helix-involved amino acids may, as others suggested earlier, result from the strong hydrogen bonding that binds the c and z fragment ions. (3) When an electron attaches to a helix-involved OCN π* orbital, an electron can migrate to the π* orbital of another amino acid one turn down the helix, but only by overcoming a barrier. After migrating to a new amino acid, N C α cleavage can occur at the latter site, also in line with what earlier workers have suggested. Suggestions of experiments that might test the hypotheses treated here are also put forth.

In a recent publication, we introduced a computational approach to treat the simultaneous dynamics of electrons and nuclei. The method is based on a synergy between quantum wave packet dynamics and ab initio molecular dynamics. Atom-centered density-matrix propagation or Born-Oppenheimer dynamics can be used to perform ab initio dynamics. In this paper, wave packet dynamics is conducted using a three-dimensional direct product implementation of the distributed approximating functional free-propagator. A fundamental computational difficulty in this approach is that the interaction potential between the two components of the methodology needs to be calculated frequently. Here, we overcome this problem through the use of a time-dependent deterministic sampling measure that predicts, at every step of the dynamics, regions of the potential which are important. The algorithm, when combined with an on-the-fly interpolation scheme, allows us to determine the quantum dynamical interaction potential and gradients at every dynamics step in an extremely efficient manner. Numerical demonstrations of our sampling algorithm are provided through several examples arranged in a cascading level of complexity. Starting from a simple one-dimensional quantum dynamical treatment of the shared proton in [Cl-H-Cl](-) and [CH3-H-Cl](-) along with simultaneous dynamical treatment of the electrons and classical nuclei, through a complete three-dimensional treatment of the shared proton in [Cl-H-Cl](-) as well as treatment of a hydrogen atom undergoing donor-acceptor transitions in the biological enzyme, soybean lipoxygenase-1 (SLO-1), we benchmark the algorithm thoroughly. Apart from computing various error estimates, we also compare vibrational density of states, inclusive of full quantum effects from the shared proton, using a novel unified velocity-velocity, flux-flux autocorrelation function. In all cases, the potential-adapted, time-dependent sampling procedure is seen to improve the computational scheme tremendously (by orders of magnitude) with minimal loss of accuracy.