DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations.

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman's path integral formalism of quantum mechanics. The flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.

Effects of Defects and Presence of Open-Metal Sites on the Structure and Dynamics of Water in Hydrophobic Zeolitic Imidazolate Frameworks.

Most of the chemistry in nanoporous materials with small pore sizes and windows takes place on the outer surface, which is in direct contact with the substrate/solvent, rather than within the pores and channels. Here, we report the results of our comprehensive atomistic molecular dynamics (MD) simulations to decipher the interaction of water with a realistic finite ∼5.1 nm nanoparticle (NP) model of ZIF-8, with edges containing undercoordinated Zn metal sites, vs a conventionally employed pristine crystalline bulk (CB) model. The hydrophobic interior surface of the CB model imparts significant dynamical behavior on water molecules with (i) increasing diffusivity from the surface toward the center of the pores and (ii) confined water, at low concentration, showing similar diffusivity to that of the bulk water. On the other hand, water molecules adsorbed on the surface of the NP model exhibit a range of characteristics, including "coordinated", "confined", and "bulk-like" behavior. Some of the water molecules form coordinative bonds with the undercoordinated Zn metal centers and act as nucleation sites for the water droplets to form, facilitating diffusion into the pores. However, diffusion of water molecules is limited to the areas near the surface and not all the way to the core of the NP model. Our atomistic MD simulations provide insights into the stability of ZIFs in aqueous solutions despite hydrolysis of their outer surface. Such insights are helpful in designing more robust nanoporous materials for applications in humid environments.

Real-Time Dynamics and Detailed Balance in Ring Polymer Surface Hopping: The Impact of Frustrated Hops.

Ring polymer surface hopping (RPSH) has been recently introduced as a well-tailored method for incorporating nuclear quantum effects, such as zero-point energy and tunneling, into nonadiabatic molecular dynamics simulations. The practical widespread usage of RPSH demands a comprehensive benchmarking of different reaction regimes and conditions with equal emphasis on demonstrating both the cons and the pros of the method. Here, we investigate the fundamental questions related to the conservation of energy and detailed balance in the context of RPSH. Using Tully's avoided crossing model as well as a 2-state quantum system coupled to a classical bath undergoing Langevin dynamics, we probe the critical problem of the proper treatment of the classically forbidden transitions stemming from the surface hopping algorithm. We show that proper treatment of these frustrated hops is key to the accurate description of real-time dynamics as well as reproducing the correct quantum Boltzmann populations.

In Silico High-Throughput Design and Prediction of Structural and Electronic Properties of Low-Dimensional Metal-Organic Frameworks.

The advent of π-stacked layered metal-organic frameworks (MOFs), which offer electrical conductivity on top of permanent porosity and high surface area, opened up new horizons for designing compact MOF-based devices such as battery electrodes, supercapacitors, and spintronics. Permutation of structural building blocks, including metal nodes and organic linkers, in these electrically conductive (EC) materials, results in new systems with unprecedented and unexplored physical and chemical properties. With the ultimate goal of providing a platform for accelerated material design and discovery, here we lay the foundations for the creation of the first comprehensive database of EC-MOFs with an experimentally guided approach. The first phase of this database, coined EC-MOF/Phase-I, is composed of 1,057 bulk and monolayer structures built by all possible combinations of experimentally reported organic linkers, functional groups, and metal nodes. A high-throughput screening (HTS) workflow is constructed to implement density functional theory calculations with periodic boundary conditions to optimize the structures and calculate some of their most relevant properties. Because research and development in the area of EC-MOFs has long been suffering from the lack of appropriate initial crystal structures, all of the geometries and property data have been made available for the use of the community through an online platform that was developed during the course of this work. This database provides comprehensive physical and chemical data of EC-MOFs as well as the convenience of selecting appropriate materials for specific applications, thus accelerating the design and discovery of EC-MOF-based compact devices.

Correction: Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites.

Correction for 'Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites' by Mohammad R. Momeni et al., Phys. Chem. Chem. Phys., 2021, 23, 3135-3143, https://doi.org/10.1039/D0CP05923D.

Modeling energy transfer and absorption spectra in layered metal-organic frameworks based on a Frenkel-Holstein Hamiltonian.

Optimizing energy and charge transfer is key in design and implementation of efficient layered conductive metal-organic frameworks (MOFs) for practical applications. In this work, for the first time, we investigate the role of both long-range excitonic and short-range charge transfer coupling as well as their dependency on reorganization energy on through-space charge transfer in layered MOFs. A π-stacked model system is built based on the archetypal Ni3(HITP)2, HITP = 2,3,6,7,10,11-hexaiminotriphenylene, layered MOF, and a Frenkel/charge transfer Holstein Hamiltonian is developed that takes into account both electronic coupling and intramolecular vibrations. The dependency of the long- and short-range couplings of secondary building units (SBUs) on the stacking geometry is evaluated, which predicts that photophysical properties of layered MOFs critically depend on the degree of ordering between layers. We show that the impact of the two coupling sources in these materials can be discerned or enhanced by the displacement of the SBUs along the long or short molecular axes. The effects of vibronic spectral signatures are examined in both perturbative and resonance regimes. Although, to the best of our knowledge, displacement engineering in layered MOFs currently remains beyond reach, the findings reported here offer new details on the photophysical structure-property relationships in layered MOFs and provide suggestions on how to combine elements of molecular design and engineering to achieve desirable properties and functions for nano- and mesoscale optoelectronic applications.

Metal-to-Semiconductor Transition in Two-Dimensional Metal-Organic Frameworks: An Ab Initio Dynamics Perspective.

Two-dimensional (2D) π-stacked layered metal-organic frameworks (MOFs) are permanently porous and electrically conductive materials with easily tunable crystal structures. Here, we provide an accurate examination of the correlation between structural features and electronic properties of Ni3(HITP)2, HITP = 2,3,6,7,10,11-hexaiminotriphenylene, as an archetypical 2D MOF. The main objective of this work is to unravel the responsive nature of the layered architecture to external stimuli such as temperature and show how the layer flexibility translates to different conductive behaviors. To this end, we employ a combination of quantum mechanical tools, ab initio molecular dynamics (AIMD) simulations, and electronic band structure calculations. We compare the band structure and projected density of states of equilibrated system at 293 K to that of the 0 K optimized structure. Effect of interlayer π-π and intralayer d-π interactions on charge mobility is disentangled and studied by increasing the distance between layers of Ni3(HITP)2 and comparison to an exemplary case of Zn3(HITP)2 2D MOF. Our findings show how a structural change, which can be deformations along the layers, slipping of layers, or change of the interlayer distance, can induce metal-to-semiconductor or indirect-to-direct semiconductor transition, suggesting a way to adjust or even switch between the intralayer vs interlayer conductive anisotropy in Ni3(HITP)2, in particular, and 2D MOFs in general.

Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites.

Molecular dynamics simulations combined with periodic electronic structure calculations are performed to decipher structural, thermodynamical and dynamical properties of the interfaced vs. confined water adsorbed in hexagonal 1D channels of the 2D layered electrically conductive Cu3(HHTP)2 and Cu3(HTTP)2 metal-organic frameworks (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene and HTTP = 2,3,6,7,10,11-hexathiotriphenylene). Comparing water adsorption in bulk vs. slab models of the studied 2D MOFs shows that water is preferentially adsorbed on the framework walls via forming hydrogen bonds to the organic linkers rather than by coordinating to the coordinatively unsaturated open-Cu2+ sites. Theory predicts that in Cu3(HTTP)2 the van der Waals interactions are stronger which helps the MOF maintain its layered morphology with allowing very little water molecules to diffuse into the interlayer space. Data presented in this work are general and helpful in implementing new strategies for preserving the integrity as well as electrical conductivity of porous materials in aqueous solutions.

Deterministic role of structural flexibility on catalytic activity of conductive 2D layered metal-organic frameworks.

A combined quantum mechanics and classical molecular dynamics approach is used to unravel the effects of structural deformations and heterogeneity on catalytic activity of 2D π-stacked layered metal-organic frameworks. Theory predicts that the flexible nature of these materials creates a complex array of catalytically active sites for oxidative dehydrogenation of propane. Using an ensemble approach and oxygen bond formation energy, as an excellent probe, we investigate the catalytic activity down to the single active site level.

Recent progress in approximate quantum dynamics methods for the study of proton-coupled electron transfer reactions.

Proton-coupled electron transfer (PCET) reactions are ubiquitous natural processes at the heart of energy conversion reactions in photosynthesis and respiration, DNA repair, and diverse enzymatic reactions. Theoretical formulation and computational method developments have eyed modeling of thermal and photoinduced PCET for the last three decades. The accumulation of these studies, collected in dozens of reviews, accounts, and perspectives, has firmly established the influence of quantum effects, including non-adiabatic electronic transitions, vibrational relaxation, zero-point energy, and proton tunneling, on the rate and mechanism of PCET reactions. Here, we focus on some recently-developed methods, spanning the last eight years, that can quantitatively capture these effects in the PCET context and provide efficient means for their qualitative description in complex systems. The theoretical background of each method and their accuracy with respect to exact results are discussed and the results of relevant PCET simulations based on each method are presented.

Adsorption based realistic molecular model of amorphous kerogen.

This paper reports the results of Grand Canonical Monte Carlo (GCMC)/molecular dynamics (MD) simulations of N2 and CO2 gas adsorption on three different organic geomacromolecule (kerogen) models. Molecular models of kerogen, although being continuously developed through various analytical and theoretical methods, still require further research due to the complexity and variability of the organic matter. In this joint theory and experiment study, three different kerogen models, with varying chemical compositions and structure from the Bakken, were constructed based on the acquired analytic data by Kelemen et al. in 2007: 13C nuclear magnetic resonance (13C-NMR), X-ray photoelectron spectroscopy (XPS), and X-ray absorption near-edge structure (XANES). N2 and CO2 gas adsorption isotherms obtained from GCMC/MD simulations are in very good agreement with the experimental isotherms of physical samples that had a similar geochemical composition and thermal maturity. The N2/CO2 uptake by the kerogen model at a range of pressure shows considerable similarity with our experimental data. The stronger interaction of CO2 molecules with the model leads to the penetration of CO2 molecules to the sub-surface levels in contrast to N2 molecules being concentrated on the surface of kerogen. These results suggest the important role of kerogen in the separation and transport of gas in organic-rich shale that are the target for sequestration of CO2 and/or enhanced oil recovery (EOR).

Quasi-Diabatic Propagation Scheme for Direct Simulation of Proton-Coupled Electron Transfer Reaction.

We apply a recently developed quasi-diabatic (QD) propagation scheme to simulate proton-coupled electron transfer (PCET) reactions. This scheme enables a direct interface between an accurate diabatic dynamics approach and the adiabatic vibronic states of the coupled electron-proton subsystem. It explicitly avoids theoretical efforts to preconstruct diabatic states for the transferring electron and proton or reformulate a diabatic dynamics method to the adiabatic representation, both of which are nontrivial tasks. Using a partial linearized path-integral approach and symmetrical quasi-classical approach as the diabatic dynamics methods, we demonstrate that the QD propagation scheme provides accurate vibronic dynamics of PCET reactions and reliably predicts the correct reaction mechanism without any a priori assumptions. This work demonstrates the possibility to directly simulate challenging PCET reactions by using accurate diabatic dynamics approaches and adiabatic vibronic information.

Disentangling Coupling Effects in the Infrared Spectra of Liquid Water.

A quantitative characterization of intermolecular and intramolecular couplings that modulate the OH-stretch vibrational band in liquid water has so far remained elusive. Here, we take up this challenge by combining the centroid molecular dynamics formalism, which accounts for nuclear quantum effects, with the MB-pol potential energy function, which accurately reproduces the properties of water across all phases, to model the infrared (IR) spectra of various isotopic water solutions with different levels of vibrational couplings, including those that cannot be probed experimentally. Analysis of the different IR OH-stretch line shapes provides direct evidence for the partially quantum-mechanical nature of hydrogen bonds in liquid water, which is emphasized by synergistic effects associated with intermolecular coupling and many-body electrostatic interactions. Furthermore, we quantitatively demonstrate that intramolecular coupling, which results in Fermi resonances due to the mixing between HOH-bend overtones and OH-stretch fundamentals, is responsible for the shoulder located at ∼3250 cm-1 of the IR OH-stretch band of liquid water.

Investigating photoinduced proton coupled electron transfer reaction using quasi diabatic dynamics propagation.

We investigate photoinduced proton-coupled electron transfer (PI-PCET) reactions through a recently developed quasi-diabatic (QD) quantum dynamics propagation scheme. This scheme enables interfacing accurate diabatic-based quantum dynamics approaches with adiabatic electronic structure calculations for on-the-fly simulations. Here, we use the QD scheme to directly propagate PI-PCET quantum dynamics with the diabatic partial linearized density matrix path-integral approach with the instantaneous adiabatic electron-proton vibronic states. Our numerical results demonstrate the importance of treating protons quantum mechanically in order to obtain accurate PI-PCET dynamics as well as the role of solvent fluctuation and vibrational relaxation on proton tunneling in various reaction regimes that exhibit different kinetic isotope effects. This work opens the possibility to study the challenging PI-PCET reactions through accurate diabatic quantum dynamics approaches combined with efficient adiabatic electronic structure calculations.

Ring Polymer Surface Hopping: Incorporating Nuclear Quantum Effects into Nonadiabatic Molecular Dynamics Simulations.

We apply a recently proposed ring polymer surface hopping (RPSH) approach to investigate the real-time nonadiabatic dynamics with explicit nuclear quantum effects. The nonadibatic electronic transitions are described through Tully's fewest-switches surface hopping algorithm and the motion of the nuclei are quantized through the ring polymer Hamiltonian in the extended phase space. Applying the RPSH method to simulate Tully's avoided crossing models, we demonstrate the critical role of the nuclear tunneling effect and zero-point energy for accurately describing the transmission and reflection probabilities with low initial momenta. In addition, in Tully's extended coupling model, we show that the ring polymer quantization effectively captures decoherence, yielding more accurate reflection probabilities. These promising results demonstrate the potential of using RPSH as an accurate and efficient method to incorporate nuclear quantum effects into nonadiabatic dynamics simulations.

New insights into the nonadiabatic state population dynamics of model proton-coupled electron transfer reactions from the mixed quantum-classical Liouville approach.

In a previous study [F. A. Shakib and G. Hanna, J. Chem. Phys. 141, 044122 (2014)], we investigated a model proton-coupled electron transfer (PCET) reaction via the mixed quantum-classical Liouville (MQCL) approach and found that the trajectories spend the majority of their time on the mean of two coherently coupled adiabatic potential energy surfaces. This suggested a need for mean surface evolution to accurately simulate observables related to ultrafast PCET processes. In this study, we simulate the time-dependent populations of the three lowest adiabatic states in the ET-PT (i.e., electron transfer preceding proton transfer) version of the same PCET model via the MQCL approach and compare them to the exact quantum results and those obtained via the fewest switches surface hopping (FSSH) approach. We find that the MQCL population profiles are in good agreement with the exact quantum results and show a significant improvement over the FSSH results. All of the mean surfaces are shown to play a direct role in the dynamics of the state populations. Interestingly, our results indicate that the population transfer to the second-excited state can be mediated by dynamics on the mean of the ground and second-excited state surfaces, as part of a sequence of nonadiabatic transitions that bypasses the first-excited state surface altogether. This is made possible through nonadiabatic transitions between different mean surfaces, which is the manifestation of coherence transfer in MQCL dynamics. We also investigate the effect of the strength of the coupling between the proton/electron and the solvent coordinate on the state population dynamics. Drastic changes in the population dynamics are observed, which can be understood in terms of the changes in the potential energy surfaces and the nonadiabatic couplings. Finally, we investigate the state population dynamics in the PT-ET (i.e., proton transfer preceding electron transfer) and concerted versions of the model. The PT-ET results confirm the participation of all of the mean surfaces, albeit in different proportions compared to the ET-PT case, while the concerted results indicate that the mean of the ground- and first-excited state surfaces only plays a role, due to the large energy gaps between the ground- and second-excited state surfaces.

An analysis of model proton-coupled electron transfer reactions via the mixed quantum-classical Liouville approach.

The nonadiabatic dynamics of model proton-coupled electron transfer (PCET) reactions is investigated for the first time using a surface-hopping algorithm based on the solution of the mixed quantum-classical Liouville equation (QCLE). This method provides a rigorous treatment of quantum coherence/decoherence effects in the dynamics of mixed quantum-classical systems, which is lacking in the molecular dynamics with quantum transitions surface-hopping approach commonly used for simulating PCET reactions. Within this approach, the protonic and electronic coordinates are treated quantum mechanically and the solvent coordinate evolves classically on both single adiabatic surfaces and on coherently coupled pairs of adiabatic surfaces. Both concerted and sequential PCET reactions are studied in detail under various subsystem-bath coupling conditions and insights into the dynamical principles underlying PCET reactions are gained. Notably, an examination of the trajectories reveals that the system spends the majority of its time on the average of two coherently coupled adiabatic surfaces, during which a phase enters into the calculation of an observable. In general, the results of this paper demonstrate the applicability of QCLE-based surface-hopping dynamics to the study of PCET and emphasize the importance of mean surface evolution and decoherence effects in the calculation of PCET rate constants.

New generation of dialkylsilylenes with stabilities comparable to diaminosilylenes: a theoretical study.

A new family of dialkylsilylenes is introduced which enjoys the stabilizing effect of α-cyclopropyl substituents. The singlet and triplet states of acyclic and saturated/unsaturated cyclic dicyclopropylsilylenes are fully optimized using MP2/6-31G(d) and B3LYP/6-31+G(d) levels. Their higher ΔE(S-T) values compared to the corresponding analogues which possess isopropyl groups instead of cyclopropyl represents the stabilizing interaction of the occupied Walsh orbital of the cyclopropyls with the vacant p-orbital of the silylene center. Appropriate isodesmic reactions clearly show that the stabilizing effect of this interaction on the singlet state is much more considerable than the corresponding triplet state. Cyclopropyls can serve as good sites for bulky substitution and, hence, provide steric protection for silylene.

[n]Imperilenes: stacked [n]trannulenes separated by planar cycloalkane rings.

Two trannulene moieties fused to each other by means of perfectly planar cycloalkane rings comprise an interesting class of molecules (above) named "imperilenes". Based on computed geometries and NICS(zz) values, only the [5], [7], and [9]imperilene singlet states as well as the 4+ charged [4], [6], and [8]imperilenes and their higher energy neutral quintet states are aromatic. The π electron systems of the individual trannulene rings, rather than the overall electron count, determine the behavior.