Solid-state Density Functional Theory Research Articles

Revisiting the OH + H2 → H2O + H reaction at the molecular level: the plausible catalytic role of ice in its own reconstruction

Context. In spite of the permanent damage suffered from the radiation field (cosmic rays, X-rays, and intense UV-visible radiations), interstellar grains are still covered by ices mantles whose role in interstellar chemistry is well beyond any doubt. This clearly means that the destruction of the ice cover has to be counterbalanced by efficient reconstruction mechanisms. Aims. Our goal is to determine whether the ice, which is still present after irradiation, has a catalytic role in the OH + H2 → H2O + H reaction for its own reconstruction. We focus on the three plausible reaction paths depending on the way reactants OH or H2 are adsorbed at the ice surface. Methods. Calculations were performed in both cluster and solid state approaches, using ab-initio post Hartree-Fock methods for small systems, standard density functional theory (DFT) for larger clusters, and periodic solid state DFT with specific formalisms accounting for weak interactions in systems of infinite dimensions. Results. Although the end product is the same, that is namely the reconstruction of one H2O on the subjacent ice, three different reaction paths are found depending on whether H2 reacts with adsorbed OH(ads), wether OH reacts with adsorbed H2(ads) or wether both OH(ads) and H2(ads) are adsorbed on the ice before reacting. In the first case, there is an activation barrier of ~6 kcal mol−1, requiring the tunneling effect for the reaction to proceed, which is in agreement with preceding studies. In the second case, the reaction is a barrierless process leading to the direct reconstruction of the ice. In the third case, the double adsorption increases the activation barrier due to the lowering of the starting energy. This is found regardless of the dimension of the supporting ice aggregates. Conclusions. Icy grain surfaces play a critical role for their own reconstruction in cold, dense interstellar clouds. The prevalence of tunneling over the direct mechanism should strongly depend on the temperature and local environment.

Structural Origin of the Optical Properties of Ag-Doped Fluorophosphate and Sulfophosphate Glasses.

Given the ubiquity of glass formulations that are functionalized with silver compounds, the electronic interaction between isolated silver cations and the glass network deserves more attention. Here, we report the structural origin of the optical properties that result from silver doping in fluorophosphate (PF) and sulfophosphate (PS) glasses. To achieve this, solid-state nuclear magnetic resonance (NMR) spectroscopy and density functional theory (DFT) are combined with optical spectroscopic analysis and physical property measurements. Comparing the 31P NMR, 27Al 1d NMR, and 27Al multi-quantum magic-angle spinning NMR of doped glasses and glasses with large amounts of Ag+ added, we deduce silver's bonding preference in these mixed-anion aluminophosphate glasses. We show that such understanding provides an explanation for the large Stokes shift observed for Ag+ in PF and PS glasses, which is related to absorption by the ionic Ag+···-O-P species and transfer of the excitation energy within more covalently bonded Ag2O-like clusters. This is corroborated by DFT calculations, which show that the Ag+···-O-P and Ag+···-O-S bonds in corresponding crystals are mostly ionic. The introduction of more silver ions into the crystal structure results in more covalent bonding between Ag+ and the phosphate matrix.

Extending Solid-State Calculations to Ultra-Long-Range Length Scales.

We present a method that enables solid-state density functional theory calculations to be applied to systems of almost unlimited size. Computations of physical effects up to the micron length scale but which nevertheless depend on the microscopic details of the electronic structure, are made possible. Our approach is based on a generalization of the Bloch state, which involves an additional sum over a finer grid in reciprocal space around each k point. We show that this allows for modulations in the density and magnetization of arbitrary length on top of a lattice-periodic solution. Based on this, we derive a set of ultra-long-range Kohn-Sham equations. We demonstrate our method with a sample calculation of bulk LiF subjected to an arbitrary external potential containing nearly 3500atoms. We also confirm the accuracy of the method by comparing the spin density wave state of bcc Cr against a direct supercell calculation starting from a random magnetization density. Furthermore, the spin spiral state of γ-Fe is correctly reproduced.

Cataloguing the Energetic Contributions to the Supramolecular Assembly of para-Substituted N,N′-Diphenylureas and Their Organometallic Derivatives in the Solid State: A Density Functional Theory Approach

Crystal engineering relies on the predictability of the elaborate interplay of cohesive and conformational energies driven by both intra- and intermolecular interactions of the constituent molecules. In an effort to better understand these influences on the crystal packing of para-substituted N,N′-diphenylureas (pDPUs) and organometallic derivatives, we present a detailed computational investigation of pDPU species utilizing solid-state density functional theory (DFT) and demonstrate the applicability of predictive supramolecular synthons applied toward the growth of related organometallic complexes. Dominant noncovalent interactions of pDPUs can be tuned by altering the electron-withdrawing character of the para substituents. The strength of this electron-withdrawing nature governs the inclination of the molecules to form either dominant electrostatic or π-stacking intermolecular interactions in the crystal structure due to potential molecular conformational stabilization through intramolecular C–H···O electrostatic interactions between ortho phenyl hydrogens and the urea oxygen atoms. This propensity is also influenced by the symmetry of para substitutions in mono- and disubstituted DPUs. The results of the holistic DFT investigation show a relationship between gas-phase and solid-state conformations and also present evidence of mechanisms leading to deviations in predicted crystallization behaviors on the basis of the balance of intra- and intermolecular interactions. The foundational computational study was expanded to build on previous experimental and theoretical work involving zerovalent transition-metal complexes in which p-isocyanophenyl DPUs were appended with group IV metal carbonyl fragments. In this study, we synthesized an asymmetric analogue of the latter in which N-(p-isocyanophenyl)-N′-phenylurea (pCNHDPU) was appended to a Mo(CO)5 metal carbonyl fragment, allowing us to associate the crystallization behaviors and interactions of organometallic DPU derivatives with those of simpler pDPUs. It was observed that the supramolecular assembly of the organometallic complexes display similar predictive patterns as well as additional complexities to molecular packing arising from the bulkier metal carbonyl substituents. An inclusive computational categorization of DPU-based systems in complement to experimental data will aid in the advancement of design rules for the patterned crystal growth of DPU and related systems for the development of innovative materials having unique solid-state properties.

Simulation and Assignment of the Terahertz Vibrational Spectra of Enalapril Maleate Cocrystal Polymorphs.

The identification of crystalline drug polymorphs using terahertz vibrational spectroscopy is a powerful approach for the nondestructive and noninvasive characterization of solid-state pharmaceuticals. However, a complete understanding of the terahertz spectra of molecular solids is challenging to obtain because of the complex nature of the low-frequency vibrational motions found in the sub-3 THz (sub-100 cm-1) range. Unambiguous assignments of the observed spectral features can be achieved through quantum mechanical solid-state simulations of crystal structures and lattice vibrations utilizing the periodic boundary condition approach. The terahertz spectra of two polymorphs of enalapril maleate are presented here to demonstrate that even large pharmaceuticals can be successfully modeled using solid-state density functional theory, including cocrystalline solids comprised of multiple distinct species. These simulations enable spectral assignments to be made, but also provide insights into the conformational and cohesion energies that contribute to the polymorph stabilities. The results reveal that the Form II polymorph of enalapril maleate is the more stable of the two under ambient conditions, and that this stability is driven by a greater intermolecular cohesion energy as compared to Form I.

Crown Ether Modulation Enables over 23% Efficient Formamidinium-Based Perovskite Solar Cells.

The use of molecular modulators to reduce the defect density at the surface and grain boundaries of perovskite materials has been demonstrated to be an effective approach to enhance the photovoltaic performance and device stability of perovskite solar cells. Herein, we employ crown ethers to modulate perovskite films, affording passivation of undercoordinated surface defects. This interaction has been elucidated by solid-state nuclear magnetic resonance and density functional theory calculations. The crown ether hosts induce the formation of host-guest complexes on the surface of the perovskite films, which reduces the concentration of surface electronic defects and suppresses nonradiative recombination by 40%, while minimizing moisture permeation. As a result, we achieved substantially improved photovoltaic performance with power conversion efficiencies exceeding 23%, accompanied by enhanced stability under ambient and operational conditions. This work opens a new avenue to improve the performance and stability of perovskite-based optoelectronic devices through supramolecular chemistry.

Isolable Dibenzo[a,e]disilapentalene with a Dichotomic Reactivity toward CO2.

The first dibenzo[a,e]disilapentalene with two Si═C moieties in the heteropentalene core has been prepared. Its solid-state structure and density functional theory (DFT) calculations revealed that the Si═C bonds are involved in an expanded π-conjugated system. The Si═C bonds show a distinguished reactivity toward CO2, depending on the reaction conditions. While one product results from fixation of two CO2 molecules across one Si═C bond, two different products could be isolated from the reaction of three CO2 molecules with both Si═C bonds. The mechanism has been uncovered by DFT calculations.

Conformations in Solution and in Solid-State Polymorphs: Correlating Experimental and Calculated Nuclear Magnetic Resonance Chemical Shifts for Tolfenamic Acid

A new approach for quantitively assessing putative crystal structures with applications in crystal structure prediction (CSP) is introduced that is based upon experimental solution- and magic-angle spinning (MAS) solid-state NMR data and density functional theory (DFT) calculation. For the specific case of tolfenamic acid (TFA), we consider experimental solution-state NMR for a range of solvents, experimental MAS NMR of polymorphs I and II, and DFT calculations for four polymorphs. The change in NMR chemical shift observed in passing from the solution state to the solid state (ΔδExperimental) is calculated as the difference between 1H and 13C experimental solid-state chemical shifts for each polymorphic form (δSolidexpt) and the corresponding solution-state NMR chemical shifts (δSolutionexpt). Separately, we use the gauge-included projector augmented wave (GIPAW) method to calculate the NMR chemical shifts for each form (δSolidcalc) and for TFA in solution (δSolutioncalc) using the dynamic 3D solution conformational ensemble determined from NMR spectroscopy. The calculated change in passing from the solution state to the solid state (ΔδCalculated) is then calculated as the difference of δSolidcalc and δSolutioncalc. Regression analysis for ΔδCalculated against ΔδExperimental followed by a t-test for statistical significance provides a robust quantitative assessment. We show that this assessment clearly identifies the correct polymorph, i.e., when comparing ΔδExperimental based on the experimental MAS NMR chemical shifts of form I or II with ΔδCalculated based on calculated chemical shifts for polymorphs I, II, III, and IV. Complementarity to the established approach of comparing δSolidexpt to δSolidcalc is explored. We further show that our approach is applicable if there are no solid-state crystal structure data. Specifically, δSolidcalc in ΔδCalculated is replaced by the chemical shift for an isolated molecule with a specific conformation. Sampling conformations at specific 15° angle values and comparing them against experimental 13C chemical shift data for forms I and II identifies matching narrow ranges of conformations, successfully predicting the conformation of tolfenamic acid in each form. This methodology can therefore be used in crystal structure prediction to both reduce the initial conformational search space and also quantitatively assess subsequent putative structures to reliably and unambiguously identify the correct structure.

Multifidelity Statistical Machine Learning for Molecular Crystal Structure Prediction.

The prediction of crystal structures from first-principles requires highly accurate energies for large numbers of putative crystal structures. High accuracy of solid state density functional theory (DFT) calculations is often required, but hundreds or more structures can be present in the low energy region of interest, so that the associated computational costs are prohibitive. Here, we apply statistical machine learning to predict expensive hybrid functional DFT (PBE0) calculations using a multifidelity approach to re-evaluate the energies of crystal structures predicted with an inexpensive force field. The method uses an autoregressive Gaussian process, making use of less expensive GGA DFT (PBE) calculations to bridge the gap between the force field and PBE0 energies. The method is benchmarked on the crystal structure landscapes of three small, hydrogen-bonded organic molecules and shown to produce accurate predictions of energies and crystal structure ranking using small numbers of the most expensive calculations; the PBE0 energies can be predicted with errors of less than 1 kJ mol-1 with between 4.2 and 6.8% of the cost of the full calculations. As the model that we have developed is probabilistic, we discuss how the uncertainties in predicted energies impact the assessment of the energetic ranking of crystal structures.

Hydrogen-Bonded Crystalline Molecular Machines with Ultrafast Rotation and Displacive Phase Transitions.

Two new crystalline rotors 1 and 2 assembled through N-H⋅⋅⋅N hydrogen bonds by using halogenated carbazole as stators and 1,4-diaza[2.2.2]bicyclooctane (DABCO) as the rotator, are described. The dynamic characterization through 1 H T1 relaxometry experiments indicate very low rotational activation barriers (Ea ) of 0.67 kcal mol-1 for 1 and 0.26 kcal mol-1 for 2, indicating that DABCO can reach a THz frequency at room temperature in the latter. These Ea values are supported by solid-state density functional theory computations. Interestingly, both supramolecular rotors show a phase transition between 298 and 250 K, revealed by differential scanning calorimetry and single-crystal X-ray diffraction. The subtle changes in the crystalline environment of these rotors that can alter the motion of an almost barrierless DABCO are discussed here.

Structure and Dynamics of Perylene Bisimide Pigments for “Cool” Organic Coatings by Solid-State NMR: A Combined Experimental and DFT Study

In this work, a combination of high-resolution solid-state nuclear magnetic resonance (SSNMR) experiments and density functional theory calculations has been exploited for obtaining a detailed characterization of the structural and dynamic properties of the perylene bisimide derivative (PBI) Paliogen Black L0086 (P-black). This “cool” organic pigment is characterized by unusual transparent, reflective, and cooling features in the near-infrared (NIR) spectrum. A full assignment of the 13C SSNMR spectrum was achieved, highlighting correlations between 13C isotropic chemical shifts and specific supramolecular features. The π-flip motion of the phenyl rings of the methoxybenzyl side groups bonded to the imide nitrogen atoms was characterized in the 310–386 K temperature range, determining activation energy and correlation times. This motion showed a strong dependence on the supramolecular order of P-black and the length of the alkyl linker between the side group and the perylene bisimide core. The results obtained in this work open the way to investigations on similar PBI pigments, aiming at achieving a collection of molecular, supramolecular, and NIR data that could allow the identification of the main factors determining the NIR performance.

Crystalline Molecular Standards for Low-Frequency Vibrational Spectroscopies

The sub-200 cm−1 (sub-6 THz) vibrations of molecular crystals provide identifying features that are characteristic of each solid sample under study. These distinctive vibrational spectra have driven the development of new techniques and instrumentation in analytical spectroscopy. As terahertz time-domain spectroscopy and low-frequency Raman spectroscopy become increasingly prevalent in non-specialist laboratories, the need for a common set of spectral standards for use across these techniques becomes imperative. To meet this need, α-lactose monohydrate, biotin, and L-cystine are proposed here as molecular standards to evaluate instrument performance with both terahertz and Raman spectroscopies, as well serve as benchmarks for quantum mechanical simulations and analyses of these spectra. These substances all reveal a series of readily discernable peaks across the low-frequency region and also over a range of temperatures (295–50 K) making them even more useful. The often overlooked aspect of detailed spectral interpretation and assignment is directly addressed with rigorous solid-state density functional theory simulations of the three compounds based on a standard computational framework. By investigating these proposed molecular crystal standards with commonly available experimental and theoretical approaches, a set of realistic performance expectations can be achieved for both commercial instrumentation and software being used in low-frequency vibrational spectroscopy.

Assessing the Performance of Density Functional Theory Methods on the Prediction of Low-Frequency Vibrational Spectra

The low-frequency (terahertz) dynamics of condensed phase materials provide valuable insight into numerous bulk phenomena. However, the assignment and interpretation of experimental results require computational methods due to the complex mode types that depend on weak intermolecular forces. Solid-state density functional theory has been used in this regard with great success, yet the selection of specific computational parameters, namely the chosen basis set and density functional, has a profound influence on the accuracy of predicted spectra. In this work, the role of these two parameters is investigated in a series of organic molecular crystals, in order to assess the ability of various methods to reproduce intermolecular forces, and subsequently experimental terahertz spectra. Specifically, naphthalene, oxalic acid, and thymine were chosen based on the varied intermolecular interactions present in each material. The results highlight that unconstrained geometry optimizations can be used as an initial proxy for the accuracy of interatomic forces, with errors in the calculated geometries indicative of subsequent errors in the calculated low-frequency vibrational spectra, providing a powerful metric for the validation of theoretical results. Finally, the origins of the observed shortcomings are analyzed, providing a basic framework for further studies on related materials.

Combined X-ray Crystallographic, IR/Raman Spectroscopic, and Periodic DFT Investigations of New Multicomponent Crystalline Forms of Anthelmintic Drugs: A Case Study of Carbendazim Maleate.

Synthesis of multicomponent solid forms is an important method of modifying and fine-tuning the most critical physicochemical properties of drug compounds. The design of new multicomponent pharmaceutical materials requires reliable information about the supramolecular arrangement of molecules and detailed description of the intermolecular interactions in the crystal structure. It implies the use of a combination of different experimental and theoretical investigation methods. Organic salts present new challenges for those who develop theoretical approaches describing the structure, spectral properties, and lattice energy Elatt. These crystals consist of closed-shell organic ions interacting through relatively strong hydrogen bonds, which leads to Elatt > 200 kJ/mol. Some technical problems that a user of periodic (solid-state) density functional theory (DFT) programs encounters when calculating the properties of these crystals still remain unsolved, for example, the influence of cell parameter optimization on the Elatt value, wave numbers, relative intensity of Raman-active vibrations in the low-frequency region, etc. In this work, various properties of a new two-component carbendazim maleate crystal were experimentally investigated, and the applicability of different DFT functionals and empirical Grimme corrections to the description of the obtained structural and spectroscopic properties was tested. Based on this, practical recommendations were developed for further theoretical studies of multicomponent organic pharmaceutical crystals.

Nature of the Surface Intermediates Formed from Methane on Cu-ZSM-5 Zeolite: A Combined Solid-State Nuclear Magnetic Resonance and Density Functional Theory Study

The intermediates formed upon the interaction of methane with Cu-modified ZSM-5 zeolites (Cu/H-ZSM-5) have been analyzed with solid-state NMR spectroscopy and DFT methods. Methane activation by Cu/...

Dirac's equation and its implications for density functional theory based calculations of materials containing heavy elements

Electronic structure calculations based on density functional theory (DFT) give quantitatively accurate predictions of properties of most materials containing light elements. For heavy materials, and in particular for $f$-electron systems, DFT based methods can fail both qualitatively and quantitatively for two distinct reasons: their failure to describe confinement effects arising from localized $f$-electron behavior and their incomplete or approximate treatment of relativity. In addition, different methods for incorporating relativistic effects, which give identical results in most light materials, can give different predictions in heavy elements. In order to develop a quantitative capability for calculating the properties of these materials, it is essential to separate the predictions of the underlying equations from the uncertainty introduced in approximations used in computation. Working toward that goal, we have developed a code, called dirac-fp, which is based directly on solving the Dirac-Kohn-Sham equations and uses the full-potential linear muffin-tin orbital (FP-LMTO) approach to electronic structure. In order to assess the performance of dirac-fp, we perform calculations on three different face-centered cubic materials using different approximate treatments of relativity: the scalar relativistic (SR) approach commonly used in most solid-state DFT codes, the scalar relativistic plus spin-orbit coupling corrections (SR+SO) approach which includes spin-orbit coupling self-consistently using the SR states inside the muffin tins, and the Dirac-Kohn-Sham (Dirac) approach implemented in dirac-fp. Performing calculations on thorium, in which relativistic effects should be strong, aluminum, in which relativistic effects should be negligible, and gold, in which relativistic effects play an intermediate role, we find that the Dirac approach is able to provide theoretically consistent results in the electronic structure and ground-state properties across all three materials.

Werner-Type Complexes of Uranium(III) and (IV).

Transmetalation of the β-diketiminate salt [M][MenacnacPh] (M+ = Na or K; MenacnacPh- = {PhNC(CH3)}2CH-) with UI3(THF)4 resulted in the formation of the homoleptic, octahedral complex [U(MenacnacPh)3] (1). Green colored 1 was fully characterized by a solid-state X-ray diffraction analysis and a combination of UV/vis/NIR, NMR, and EPR spectroscopic studies as well as solid-state SQUID magnetization studies and density functional theory calculations. Electrochemical studies of 1 revealed this species to possess two anodic waves for the U(III/IV) and U(IV/V) redox couples, with the former being chemically accessible. Using mild oxidants, such as [CoCp2][PF6] or [FeCp2][Al{OC(CF3)3}4], yields the discrete salts [1][A] (A = PF6-, Al{OC(CF3)3}4-), whereas the anion exchange of [1][PF6] with NaBPh4 yields [1][BPh4].

Investigation of the cis-trans structures and isomerization of oligoprolines by using Raman spectroscopy and density functional theory calculations: solute-solvent interactions and effects of terminal positively charged amino acid residues.

Using low-wavenumber Raman spectroscopy in combination with theoretical calculations via solid-state density functional theory (DFT)-D3, we studied the vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series. The P12 series includes P12, the positively charged amino acid residue (arginine and lysine) N-terminus proline oligomers RP11 and KP11, and the C-terminus P11R and P11K. We assigned the spring-type phonon mode to 74–76 cm−1 bands for the PPI and PPII conformers and the carbonyl group ring-opening mode 122 cm−1 in the PPI conformer of poly-l-proline. Amide I and II were assigned based on the results of mode analysis for O, N, and C atom displacements. The broad band feature of the H-bond transverse mode in the Raman spectra indicates that the positively charged proline oligomers PPII form H-bonds with water in the solid phase, whereas P12 is relatively more hydrophobic. In propanol, the PPI conformer of the P12 series forms less H-bond network with the solvent. The PPII conformer exhibits a distinct Raman band at 310 cm−1, whereas the PPI has bands at 365, 660, and 960 cm−1 with reasonable intensity that can be used to quantitatively determine these two conformational forms. The 365 cm−1 mode comprising the motion of a C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O group turning to the helix axis was used to monitor the isomerization reaction PPI ↔ PPII. In pure propanol, RP11 and KP11 were found to have mostly PPI present, but P11R and P11K preferred PPII. After adding 20% water, the PPI in P11R and P11K was completely converted to PPII, whereas a small fraction of PPI remained in RP11 and KP11. The substituted positively charged amino acid affected the balance of the PPI/PPII population ratio.

Identifying and explaining vibrational modes of quinacridones via temperature-resolved terahertz spectroscopy: absorption experiments and solid-state density functional theory simulations.

Quinacridone and its substituted analogs are pigments widely used in art and industry. The temperature dependence of the crystal structures of two quinacridone polymorphs (β and γ), along with the common variant 2,9-dimethylquinacridone, were investigated using powder X-ray diffraction and terahertz spectroscopy. These were then compared with solid-state density functional theory simulations of both structures and vibrations. X-ray patterns were collected at eight temperatures in the range 13-298 K and terahertz spectra at fifteen temperatures in the range 20-300 K. Simulations were at absolute zero and at appropriate expansions to model room temperature. It was found that some of the powder X-ray diffraction features in only β-quinacridone (15.7°, 19.7° and 31.2° at 13 K) underwent anomalous shifting with temperature change. We attribute this to the unique coplanar hydrogen bonding pattern of β-quinacridone compared to the other solids, with the unusual diffraction peaks originating from crystallographic planes perpendicular to the a axis intermolecular hydrogen bonds. This observation coincides with a contraction of the a axis with heating and results from its relatively weak N-HO hydrogen bonds and significant C-HH-C repulsions. Associated with this anomalous contraction, for β-quinacridone only spectral peaks are seen to increase in energy with temperature.

Exploring the Dynamics of Bound Water in Nylon Polymers with Terahertz Spectroscopy.

Terahertz (THz) spectroscopy was used to observe adsorbed water structure and dynamics within polymer films, ultimately providing a strong rationale for the observed rates of water desorption. The THz absorption spectra of nylon-6 films undergo drastic changes during the hydration and drying processes. Additionally, the structural change from γ to α crystals, induced by the hydration, was observed by the characteristic band of α-nylon-6 at 6.5 THz. Importantly, the THz spectra of adsorbed water, as well as deuterated water, within in the nylon films were observed by the continuous measurement of α-nylon during dehydration. The difference spectra clearly show three absorption bands of water molecules named Peaks I-III, which behave differently between the H2O and D2O materials. The spectra were assigned using a combination of ab initio molecular dynamics simulations and solid-state density functional theory calculations and were compared to previous spectral assignments of bulk water. The results show that the inclusion of H2O and D2O into polymer films results in a distinct set of spectral features that, while similar in frequencies to the dynamics of bulk water, represent significantly different motions owing to the unique chemical environment within the material. These results highlight the significant utility of using THz spectroscopy to study the hydration dynamics and spectral signatures of bound water in this important class of materials.