Molecular Electronic Structure Calculations Research Articles

Simultaneous Intra- and Intermolecular Singlet Fission in Bipentacene Macrocycle Aggregates.

Singlet fission (SF) is a process where a singlet state splits into two triplet states, which is essential for enhancing optoelectronic devices. Macrocyclic structures allow for precise control of chromophore orientation and facilitate singlet fission in solutions. However, the behavior of these structures in thin films, crucial for solid-state device optimization, remains underexplored. This study examines the aggregation and singlet fission processes of bipentacene macrocycles (BPc) in thin films using molecular dynamics simulations and electronic structure calculations. Findings indicate that BPc aggregates more rapidly with less chloroform, aligning parallel to the substrate. Intramolecular singlet fission (iSF) rates are rarely changed during evaporation, but the efficiency of intermolecular singlet fission (xSF) improves due to the increase in packing domains, suggesting that orderly crystal domains are not necessary for device efficiency. This opens avenues for varied device designs and traditional solution-based methods for optimal device development.

Nuclear structure and Breit interaction effects in relativistic molecular electronic structure calculations

We examine the effects of nuclear structure and the self-consistent treatment of the Breit interaction on the calculation of properties associated with PT-odd interactions in TlF. We also demonstrate that 99.9999% of the Breit energy in TlF is recovered from the one-centre contributions to the interaction energy in the self-consistent field approximation. The formulation of our electronic structure code, BERTHA, facilitates the evaluation of all one-centre effects using efficient methods borrowed from relativistic atomic physics at negligible computational cost. A further analysis of this behaviour is provided for the homonuclear mean-field system, At, in the Dirac–Hartree–Fock–Breit approximation. For closed-shell systems, a formal analysis of the origin of this behaviour suggests that this computational economy may be of general applicability in relativistic molecular electronic structure theory.

Electron impact scattering and electronic excitation in glycolaldehyde: The first ever detected sugar in space

Detailed theoretical investigations on structural, spectroscopic and electron scattering cross sections of glycolaldehyde, the first ever detected sugar in space are reported in this work. Spectroscopic calculations are performed on the ground and excited states of glycolaldehyde using density functional theory (DFT) and time-dependent density functional theory (TDDFT), respectively. The optimized geometrical parameters and vibrational spectrum are in good agreement with the earlier reported work. Vertical excited state (VES) energies at the TDDFT/B3LYP/aug-cc-PVQZ level of theory along with detailed assignments are reported up to 30 transitions. The TDDFT predicted Rydberg series energies are compared with the Rydberg series of glycolaldehyde converging to its first IP, computed using the standard Rydberg formula and are found to be in good agreement. In the absence of sufficient experimental data on excited states of glycolaldehyde, the theoretical results are validated by comparison of VES calculations performed at the same level of theory with the available experimental data for an analogous molecule viz. acetaldehyde. Triplet excited-state energies for glycolaldehyde are reported here for the first time. Electron impact cross section calculations in the energy range 0.1 to 20 eV are carried out using ab-initio R-matrix method. We have detected one π* shape resonance in all the three models viz. SE, SEP and CC, which may also lead to a possible fragmentation channel wherein a hydrogen atom is removed from the molecule forming a glycolaldehyde dehydrogenated anionic radical (C2H3O2−). The π* shape resonance is correlated with the corresponding molecular orbital electronic structure calculations. Additionally, differential, electronic excitation, ionization and total cross sections are reported here for the first time.

A Multi-target Study of Natural Compounds in Preventing Neurodegenerative Disease Progression: A Computational Modeling Study

This work reveals how two natural multi-target compounds (Carnosine and Homocarnosine) can prevent the oligomerization of beta-amyloid peptides (A[Formula: see text]. Properly combining molecular dynamics, docking and electronic structure calculations it was possible to investigate how Carnosine/Homocarnosine strongly interact with the amino acids of the A[Formula: see text](1-42) peptide responsible for the complexation with metallic ions (metallic hypothesis). This discovery may prevent the formation of harmful protein deposits, thereby preventing the progression of, for example, Alzheimer’s disease (AD). These important results suggest that Carnosine/Homocarnosine can interact with, at least, two of the amino acids responsible for the complexation of the A[Formula: see text](1-42) peptide with the metallic ion copper(II). These findings open a new perspective on the inhibitory potential of these molecules in the treatment of AD and other neurodegenerative diseases.

Hydrogen Bonds in Lead Halide Perovskites: Insights from Ab Initio Molecular Dynamics.

Hydrogen bonds (HBs) play an important role in the rotational dynamics of organic cations in hybrid organic/inorganic halide perovskites, thus affecting the structural and electronic properties of the perovskites. However, the properties and even the existence of HBs in these perovskites are not well established. In this study, we investigate HBs in perovskites MAPbBr3 (MA+ = CH3NH3+), FAPbI3 (FA+ = CH(NH2)2+), and their solid solution with composition (FAPbI3)7/8(MAPbBr3)1/8, using ab initio molecular dynamics and electronic structure calculations. We consider HBs donated by X-H fragments (X = N and C) of the organic cations and accepted by the halides (Y = Br and I) and characterize their properties based on pair distribution functions and on a combined distribution function of the hydrogen-acceptor distance with the donor-hydrogen-acceptor angle. By analyzing these functions, we establish geometrical criteria for HB existence based on the hydrogen-acceptor (H-Y) distance and donor-hydrogen-acceptor angle (X-H-Y). The distance condition is defined as d(H - Y) < 3 Å for N-H-donated HBs and d(H - Y) < 4 Å for C-H-donated HBs. The angular condition is 135° < (X - H - Y) < 180° for both types of HBs. A HB is considered to be formed when both angular and distance conditions are simultaneously satisfied. At the simulated temperature (350 K), the HBs dynamically break and form. We compute the time correlation functions of HB existence and HB lifetimes, which range between 0.1 and 0.3 ps at that temperature. The analysis of HB lifetimes indicates that N-H-Br bonds are relatively stronger than N-H-I bonds, while C-H-Y bonds are weaker, with a minimal influence from the halide and cation. To evaluate the impact of HBs on the vibrational spectra, we present the power spectrum in the region of N-H and C-H stretching modes, comparing them with the normal mode frequencies of isolated cations. We show that the peaks associated with N-H stretching modes in perovskites are redshifted and asymmetrically deformed, while the C-H peaks do not exhibit these effects.

The Catalytic Mechanism of Acetoacetate Decarboxylase: A Detailed Study of Schiff Base Formation, Protonation States, and Their Impact on Catalysis.

The enzyme acetoacetate decarboxylase (AAD) has a crucial function in the process of decarboxylating the substrate acetoacetate (AA). It has been extensively studied over the years, but its exact catalytic mechanism has remained partly unsolved due to the difficulty in assessing reaction intermediates. In this study, we combine molecular dynamics and electronic structure calculations to rediscover its catalytic mechanism. Our results show that the presence of the substrate, the acetoacetate, significantly influences the electrostatic potential of the active site. Furthermore, our simulations show that the decarboxylation reaction can take place by means of a direct proton transfer instead of via an enamine intermediate, which is thought to be strictly necessary. This work provides new insights into the role of the electrostatic interactions on the catalytic activity of AAD and for the first time connects it to the catalytic mechanism of other decarboxylases.

Liquid structures of chloroethenes from molecular simulations and electronic structure calculations

The structures of six liquid chloroethenes viz., chloroethene, 1,1-Dichloroethene, cis- and trans-1,2-Dichloroethene, trichloro- and tetrachloroethene, are explored using the all-atom molecular dynamics simulations, molecular simulations with the 3D-reference interaction site model and the Kovalenko-Hirata closure relation (3D-RISM-KH), and dispersion corrected density functional theory. The liquid structures have different local orientations stabilized by possible π-stacking, π⋅⋅⋅Cl, and H⋅⋅⋅Cl intermolecular interactions. The RISM computations and MD simulations are in good agreement with each other, and provided important structural details. The electronic structure calculations support the presence of dimeric structures in the liquid form as well as the findings from the molecular simulations.

Electronic structures of zwitterionic and protonated forms of glycine betaine in water: Insights into solvent effects from ab initio simulations

Glycine betaine (GB), a naturally occurring osmolyte, has many biological functions and is used in food supplements, pharmaceuticals, and animal feed. GB usually exists as a zwitterion in aqueous solutions. Due to the hygroscopic property of GB, protonated form of GB, GBH+ (noted as GBH) is often used. In order to understand the hydration structures of GB and GBH at the atomic and electronic-structure level, a combination of ab initio molecular dynamics simulations and electronic structure calculations based on density functional theory (DFT), single-excitation configuration interaction method, and coupled-cluster ansatz was utilized. A hybrid explicit–implicit solvation model was used to elucidate solvent effects. Within the hybrid scheme, microsolvated structures of GB and GBH with up to 100 water molecules were obtained, showing that water molecules bind to GB and GBH in a dramatically different manner. By calculating the molecular electron-density distributions at PBE0-D4/def2-TZVP level, it shows that the variation of electron density for GB is more significant than GBH, suggesting that GB can interact with more water molecules than GBH. The interaction energies of GB–(H2O)n and GBH–(H2O)n systems (n = 1–6) at DLPNO-CCSD(T)/cc-pVQZ level highlight the difference from an energy point of view. Using the microsolvated structures of GB and GBH, the features of experimental K-edge spectra can be reproduced using the efficient PNO-ROCIS/B3LYP method, implying the reliability of the hybrid explicit–implicit solvation approach. The results suggest that complementary insights into the geometries and electronic structures of GB and GBH could be obtained through combined methods, which provides a methodological approach for understanding the hydration structures of zwitterionic and charged molecules.

MRChem Multiresolution Analysis Code for Molecular Electronic Structure Calculations: Performance and Scaling Properties.

MRChem is a code for molecular electronic structure calculations, based on a multiwavelet adaptive basis representation. We provide a description of our implementation strategy and several benchmark calculations. Systems comprising more than a thousand orbitals are investigated at the Hartree-Fock level of theory, with an emphasis on scaling properties. With our design, terms that formally scale quadratically with the system size in effect have a better scaling because of the implicit screening introduced by the inherent adaptivity of the method: all operations are performed to the requested precision, which serves the dual purpose of minimizing the computational cost and controlling the final error precisely. Comparisons with traditional Gaussian-type orbitals-based software show that MRChem can be competitive with respect to performance.

Experimental and Computational Description of the Interaction of H and H- with U.

The results of ab initio correlated molecular orbital theory electronic structure calculations for low-lying electronic states are presented for UH and UH- and compared to photoelectron spectroscopy measurements. The calculations were performed at the CCSD(T)/CBS and multireference CASPT2 including spin-orbit effects by the state interacting approach levels. The ground states of UH and UH- are predicted to be 4Ι9/2 and 5Λ6, respectively. The spectroscopic parameters Te, re, ωe, ωexe, and Be were obtained, and potential energy curves were calculated for the low energy Ω states of UH. The calculated adiabatic electron affinity is 0.468 eV in excellent agreement with an experimental value of 0.462 ± 0.013 eV. The lowest vertical detachment energy was predicted to be 0.506 eV for the ground state, and the adiabatic ionization energy (IE) is predicted to be 6.116 eV. The bond dissociation energy (BDE) and heat of formation values of UH were obtained using the IE calculated at the Feller-Peterson-Dixon level. For UH, UH-, and UH+, the BDEs were predicted to be 225.5, 197.9, and 235.5 kJ/mol, respectively. The BDE for UH is predicted to be ∼20% lower in energy than that for ThH. The analysis of the natural bond orbitals shows a significant U+H- ionic component in the bond of UH.

Gas-phase formation of silicon monoxide via non-adiabatic reaction dynamics and its role as a building block of interstellar silicates.

Silicon monoxide (SiO) is classified as a key precursor and fundamental molecular building block to interstellar silicate nanoparticles, which play an essential role in the synthesis of molecular building blocks connected to the Origins of Life. In the cold interstellar medium, silicon monoxide is of critical importance in initiating a series of elementary chemical reactions leading to larger silicon oxides and eventually to silicates. To date, the fundamental formation mechanisms and chemical dynamics leading to gas phase silicon monoxide have remained largely elusive. Here, through a concerted effort between crossed molecular beam experiments and electronic structure calculations, it is revealed that instead of forming highly-stable silicon dioxide (SiO2), silicon monoxide can be formed via a barrierless, exoergic, single-collision event between ground state molecular oxygen and atomic silicon involving non-adiabatic reaction dynamics through various intersystem crossings. Our research affords persuasive evidence for a likely source of highly rovibrationally excited silicon monoxide in cold molecular clouds thus initiating the complex chain of exoergic reactions leading ultimately to a population of silicates at low temperatures in our Galaxy.

Cluster Assembled Silicon-Lithium Nanostructures: A Nanowire Confined Inside a Carbon Nanotube.

We computationally explore an alternative to stabilize one-dimensional (1D) silicon-lithium nanowires (NWs). The Li12Si9 Zintl phase exhibits the NW , combined with Y-shaped Si4 structures. Interestingly, this NW could be assembled from the stacking of the Li6Si5 aromatic cluster. The @CNT nanocomposite has been investigated with density functional theory (DFT), including molecular dynamics simulations and electronic structure calculations. We found that van der Waals interaction between Li’s and CNT’s walls is relevant for stabilizing this hybrid nanocomposite. This work suggests that nanostructured confinement (within CNTs) may be an alternative to stabilize this free NW, cleaning its properties regarding Li12Si9 solid phase, i.e., metallic character, concerning the perturbation provided by their environment in the Li12Si7 compound.

Molecular structural, vibrational assignments, electronic structure and DFT calculations, and molecular docking of N-benzylideneaniline and N-salicylidene-o-aminoaphenol Schiff bases

Two Schiff bases N-benzylidenaniline (BZA) and N-salicylidene-o-aminoaphenol (SAP) were synthesized. Structure of SAP was determined by Xrd analysis. It was found that SAP crystallized with two molecules perpendicular to each other and connected by inter- and intramolecular hydrogen bonding. The compound crystallized in the triclinic space group P-1 with a Z value of 2. Geometry optimization of BZA and SAP were investigated by DFT (Gaussian 09W) and REDF2 (Spartan 14). The optimized structure of SAP is consistent with that obtained from the Xrd analysis. Quantum global reactivity descriptors of the two compounds were calculated using the HOMO and LUMO energy values. IR, Raman and theoretical calculations (DFT method) of the vibrational modes of the two derivatives in the wavenumber range 1700–200 cm−1 using Gaussian 09W and Spartan 14 software were carried out. Molecular docking of the two reported compounds with either B-DNA (1ZEW) or protein (4MZI) were studied.

Investigation of γ-irradiated polyvinylidene fluoride and its acute toxicity

Polyvinylidene fluoride (PVDF) is an industrial polymer with many applications. The EPR spectrum of polyvinylidene fluoride (PVDF) irradiated by γ-rays at low temperature (-196°C) provides evidence for the presence of radicals formed by loss of a fluorine atom from PVDF, and polyenyl radicals. Polyenyl radicals dominate in the polymer irradiated at room temperature. Peroxide radicals formed as a result of oxidation of primary free radicals by atmospheric oxygen are observed in the EPR spectrum of a polymer irradiated in air, or when air is introduced to a polymer irradiated in a vacuum. Carbonization and oxidation of γ-irradiated PVDF were observed in the XPS spectrum. A model for polymer degradation based on correlated G3(MP2) molecular orbital theory electronic structure calculations is described. The presence of HF in the products and a low yield of products with the composition CxFyHz indicate the absence of noticeable thermal destruction of the main polymer chain upon heating to 220°C of both the initial and γ-irradiated PVDF. Although any HF released during the PVDF dehydrofluorination would be toxic, a study of the acute toxicity of γ-irradiated PVDF showed that the polymer does not exhibit toxicity after a single intragastric route of administration to mice.

Computational Prediction of All Lanthanide Aqua Ion Acidity Constants.

The protonation state of lanthanide-ligand complexes, or lanthanide-containing porous materials, with many Brønsted acid sites can change due to proton loss/gain reactions with water or other heteroatom-containing compounds. Consequently, variations in the protonation state of lanthanide-containing species affect their molecular structure and desired properties. Lanthanide(III) aqua ions undergo hydrolysis and form hydroxides; they are the best characterized lanthanide-containing species with multiple Brønsted acid sites. We employed constrained ab initio molecular dynamics simulations and electronic structure calculations to determine all acidity constants of the lanthanide(III) aqua ions solely from computation. The first, second, and third acidity constants of lanthanide(III) aqua ions were predicted, on average, within 1.2, 2.5, and 4.7 absolute pKa units from experiment, respectively. A table includes our predicted pKa values alongside most experimentally measured pKa values known to date. The approach presented is particularly suitable to determine the Brønsted acidity of lanthanide-containing systems with multiple acidic sites, including those whose measured acidity constants cannot be linked to specific acid sites.

Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion-Water Hydrogen Bonding at the Air/Water Interface.

Liquid microjet photoelectron spectroscopy is an increasingly common technique to measure vertical ionization energies (VIEs) of aqueous solutes, but the interpretation of these experiments is subject to questions regarding sensitivity to bulk versus interfacial solvation environments. We have computed aqueous-phase VIEs for a set of inorganic anions, using a combination of molecular dynamics simulations and electronic structure calculations, with results that are in excellent agreement with experiment regardless of whether the simulation data are restricted to ions at the air/water interface or to those in bulk aqueous solution. Although the computed VIEs are sensitive to ion-water hydrogen bonding, we find that the short-range solvation structure is sufficiently similar in both environments that it proves impossible to discriminate between the two on the basis of the VIE, a conclusion that has important implications for the interpretation of liquid-phase photoelectron spectroscopy. More generally, analysis of the simulation data suggests that the surface activity of soft anions is largely a second or third solvation shell effect, arising from disruption of water-water hydrogen bonds and not from significant changes in first-shell anion-water hydrogen bonding.

Conformer-dependent vacuum ultraviolet photodynamics and chiral asymmetries in pure enantiomers of gas phase proline

Proline is a unique amino-acid, with a secondary amine fixed within a pyrrolidine ring providing specific structural properties to proline-rich biopolymers. Gas-phase proline possesses four main H-bond stabilized conformers differing by the ring puckering and carboxylic acid orientation. The latter defines two classes of conformation, whose large ionization energy difference allows a unique conformer-class tagging via electron spectroscopy. Photoelectron circular dichroism (PECD) is an intense chiroptical effect sensitive to molecular structures, hence theorized to be highly conformation-dependent. Here, we present experimental evidence of an intense and striking conformer-specific PECD, measured in the vacuum ultraviolet (VUV) photoionization of proline, as well as a conformer-dependent cation fragmentation behavior. This finding, combined with theoretical modeling, allows a refinement of the conformational landscape and energetic ordering, that proves inaccessible to current molecular electronic structure calculations. Additionally, astrochemical implications regarding a possible link of PECD to the origin of life’s homochirality are considered in terms of plausible temperature constraints.

Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex.

The cytochrome bc1 complex is a transmembrane enzymatic protein complex that plays a central role in cellular energy production and is present in both photosynthetic and respiratory chain organelles. Its reaction mechanism is initiated by the binding of a quinol molecule to an active site, followed by a series of charge transfer reactions between the quinol and protein subunits. Previous work hypothesized that the primary reaction was a concerted proton-coupled electron transfer (PCET) reaction because of the apparent absence of intermediate states associated with single proton or electron transfer reactions. In the present study, the kinetics of the primary bc1 complex PCET reaction is investigated with a vibronically nonadiabatic PCET theory in conjunction with all-atom molecular dynamics simulations and electronic structure calculations. The computed rate constants and relatively high kinetic isotope effects are consistent with experimental measurements on related biomimetic systems. The analysis implicates a concerted PCET mechanism with significant hydrogen tunneling and nonadiabatic effects in the bc1 complex. Moreover, the employed theoretical framework is shown to serve as a general strategy for describing PCET reactions in bioenergetic systems.

Interfacial interaction and prenucleation at liquid-Al/γ-Al2O3{1 1 1} interfaces

Alumina (α- and γ-Al2O3) particles are formed in liquid Al-Mg alloys during the liquid dealing and cast processes. These native oxide particles have non-trivial influences on the microstructures and properties of the solidified parts, and may act as potential heterogenous nucleation sites during solidification. At present there is still a lack of understanding about the interaction and atomic arrangements at the interfaces between liquid-Al and γ-Al2O3 substrates. Here we investigate the liquid-Al/γ-Al2O3{1 1 1} interfaces by means of ab initio molecular dynamics simulations and electronic structure calculations. We found that the interfacial interaction at the interfaces leads to formation of an ordered terminating Al layer. This newly formed terminating Al layer is positively charged and chemically bonded to the substrate and thus, becomes part of the substrate. Analysis showed that the terminating Al layer contains vacancies and displacements, being atomically rough. The newly-formed Al layer is also structurally coupled with the substrates. These γ-Al2O3 particles are weak templates for nearby liquid to nucleate. The present study sheds some light on the role of alumina particles in grain refinement of Al-based alloys during solidification processing.

Micro-solvation and counter ion effects on ionic reactions: Activation of potassium fluoride with 18-crown-6 and tert-butanol in aprotic solvents

Ionic reactions have an important solvent effect and the first solvation shell makes the most important contribution for determining the reactivity. In the case of nucleophilic fluorination with potassium fluoride, the solubilization of the salt is another aspect which needs be considered. In the present work, the effect of adding stoichiometric quantity of 18-crown-6 and the bulky alcohol tert-butanol to the reaction of potassium fluoride with alkyl bromide in toluene and acetonitrile solvents was investigated by theoretical methods as molecular dynamics and electronic structure calculations, as well as by experiments. The calculations indicate that the fluoride ion in the KF (18-crown-6) complex interacts with tert-butanol molecules forming aggregates with one (acetonitrile solvent) and three (toluene solvent) tert-butanol molecules. The calculations predict that formation of these aggregates increase the solubilization of KF and produces and important rate acceleration effect in both acetonitrile and toluene solvents, which is experimentally observed. In the concentration around 0.75 mol L−1 of the tert-butanol, the reaction rate is proportional to the alcohol concentration and the rate of alkyl halide decay becomes 10 times higher than the rate without this alcohol. The present results point out that both the interactions of KF with crown ether and tert-butanol molecules have a synergic effect, increasing its reactivity towards SN2 reactions.