Quantum Chemical Research Articles

ModelHamiltonian: A Python-scriptable library for generating 0-, 1-, and 2-electron integrals.

ModelHamiltonian is a free, open source, and cross-platform Python library designed to express model Hamiltonians, including spin-based Hamiltonians (Heisenberg and Ising models) and occupation-based Hamiltonians (Pariser-Parr-Pople, Hubbard, and Hückel models) in terms of 1- and 2-electron integrals, so that these systems can be easily treated by traditional quantum chemistry software programs. ModelHamiltonian was originally intended to facilitate the testing of new electronic structure methods using HORTON but emerged as a stand-alone research tool that we recognize has wide utility, even in an educational context. ModelHamiltonian is written in Python and adheres to modern principles of software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. While we anticipate that most users will use ModelHamiltonian as a Python library, we include a graphical user interface so that models can be built without programming, based on connectivity/parameters inferred from, for example, a SMILES string. We also include an interface to ChatGPT so that users can specify a Hamiltonian in plain language (without learning ModelHamiltonian's vocabulary and syntax). This article marks the official release of the ModelHamiltonian library, showcasing its functionality and scope.

Theoretical Study of the Halogen Concentration Effect on the 1,3-Butadiene Polymerization Catalyzed by the Neodymium-Based Ziegler–Natta System

In this work, an attempt is made to theoretically substantiate the experimentally known facts of the influence of halogen concentration on the catalytic properties of the neodymium-based Ziegler–Natta system. Based on the structural and thermochemical data obtained using modern methods of quantum chemistry, the process of the 1,3-butadiene cis-1,4-polymerization under the model active centers of the neodymium Ziegler–Natta catalysts with different contents of chloride ions was studied. Results are presented that explain the increase in the cis-stereospecificity and activity of the polymerization system with an increase in the content of the chloride ions in the neodymium catalytic system. Reasons were established for the decrease in the concentration of active centers relative to the introduced Nd(III) with an excess of chloride ions and the occurrence of the anti-syn isomerization as a source of the formation of the trans-1,4-structures in the cis-1,4-polybutadiene.

PyCI: A Python-scriptable library for arbitrary determinant CI.

PyCI is a free and open-source Python library for setting up and running arbitrary determinant-driven configuration interaction (CI) computations, as well as their generalizations to cases where the coefficients of the determinant are nonlinear functions of optimizable parameters. PyCI also includes functionality for computing the residual correlation energy, along with the ability to compute spin-polarized one- and two-electron (transition) reduced density matrices. PyCI was originally intended to replace the abinitio quantum chemistry functionality in the HORTON library but emerged as a standalone research tool, primarily intended to aid in method development, while maintaining high performance so that it is suitable for practical calculations. To this end, PyCI is written in Python, adopting principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. Computationally intensive steps, notably operations related to generating Slater determinants and computing their expectation values, are delegated to low-level C++ code. This article marks the official release of the PyCI library, showcasing its functionality and scope.

Tunable Charge Transport Using Heterocycles-Flanked Alkoxyphenanthrenes for High-Performing OFETs.

A series of new heterocycles-flanked alkoxyphenanthrenes with D'-D-D' and A-D-A architecture was synthesized for high-performance solution-processable p-channel, n-channel, and ambipolar organic field-effect transistors. The impact of electron-donating and -accepting abilities of the sulfur- and nitrogen-containing heteroaromatics on photophysical, electrochemical, and semiconducting properties was analyzed. The presence of heteroaryl rings improves the extended conjugation, two-dimensional lattices of π-π stacks, and increased molecular interaction of the functionalized phenanthrenes (PN) to allow better self-assembly. The electronically dynamic PN self-assembles into continuous microdomains, forming percolation channels for holes, electrons, or both reliant on functionalization. The low-lying LUMO levels of the compounds enabled ambipolar transport and reduced energy levels for charge injections. Spin-coated devices fabricated using functionalized PN with sulfur-containing heteroaryl substituted PN exhibited the highest hole mobility of 0.85 cm2/(V s) with 108 on/off current ratio. Compounds with A-D-A architecture showed n-channel/ambipolar charge transport, especially napthalimide acceptor substituted PN exhibited n-channel electron mobility of 0.78 cm2/(V s) and an on/off ratio of 106. X-ray diffraction and scanning electron microscopy studies further delineate the impact of efficient packing in the film. Quantum chemistry calculations combined with Marcus-Hush electron transfer theory interpret the transport parameters, and heteroatoms are established to impact the charge mobility intensely.

Synthesis, Crystal Structure and Antifungal Activity of (E)-1-(4-Methylbenzylidene)-4-(3-Isopropylphenyl) Thiosemicarbazone: Quantum Chemical and Experimental Studies.

A novel (E)-1-(4-methylbenzylidene)-4-(3-isopropylphenyl) thiosemicarbazone was synthesized in a one-pot four-step synthetic route. Fourier transform infrared spectroscopy (FTIR), 1H and 13C nuclear magnetic resonances (NMR), single-crystal X-ray diffraction, and UV-visible absorption spectroscopy were utilized to confirm the successful preparation of the title compound. Single-crystal data indicated that the intramolecular hydrogen bond N(3)-H(3)···N(1) and intermolecular hydrogen bond N(2)-H(2)···S(1) (1 - x, 1 - y, 1 - z) existed in the crystal structure and packing of the title compound. Besides the covalent interaction, the non-covalent weak intramolecular hydrogen bond N(3)-H(3)···N(1) discussed by atoms in molecules (AIM) theory also functioned in maintaining the title compound's crystal structure. The strong intermolecular hydrogen bond N(2)-H(2)···S(1) (1 - x, 1 - y, 1 - z) discussed by Hirshfeld surface analysis played a major role in maintaining the title compound's crystal packing. The local maximum and minimum electrostatic potential of the title compound was predicted by electrostatic potential (ESP) analysis. The UV-visible spectra and HOMO-LUMO analysis revealed that the title compound has a low ΔEHOMO-LUMO energy gap (3.86 eV), which implied its high chemical reactivity due to the easy occurrence of charge transfer interactions within the molecule. Molecular docking and in vitro antifungal assays evidenced that its antifungal activity is comparable to the reported pyrimethanil, indicating its usage as a potential candidate for future antifungal drugs.

Quantum Chemical (QC) Calculations and Linear Solvation Energy Relationships (LSER): Hydrogen-Bonding Calculations with New QC-LSER Molecular Descriptors

Quantum Chemical (QC) Calculations and Linear Solvation Energy Relationships (LSER): Hydrogen-Bonding Calculations with New QC-LSER Molecular Descriptors

Dynamic Jahn-Teller effect in the strong spin-orbit coupling regime

Exotic quantum phases, arising from a complex interplay of charge, spin, lattice and orbital degrees of freedom, are of immense interest to a wide research community. A well-known example of such an entangled behavior is the Jahn-Teller effect, where the lifting of orbital degeneracy proceeds through lattice distortions. Here we demonstrate that a highly-symmetrical 5d1 double perovskite Ba2MgReO6, comprising a 3D array of isolated ReO6 octahedra, represents a rare example of a dynamic Jahn-Teller system in the strong spin-orbit coupling regime. Thermodynamic and resonant inelastic x-ray scattering experiments, supported by quantum chemistry calculations, undoubtedly show that the Jahn-Teller instability leads to a ground-state doublet, resolving a long-standing puzzle in this family of compounds. The dynamic state of ReO6 octahedra persists down to the lowest temperatures, where a multipolar order sets in, allowing for investigations of the interplay between a dynamic JT effect and strongly correlated electron behavior.

A paradigm for natural eutectic solvents based on fatty acids: Molecular interactions and toxicological considerations

In this work, we present experimental and molecular modeling results on archetypal hydrophobic natural deep eutectic solvents (NADES) based on fatty acids (octanoic and dodecanoic acid) and menthol, a representative monoterpenoid. Our goal is to provide a multiscale characterization to enhance the understanding of this field by studying these selected archetypical mixtures. We examine their liquid state properties, intermolecular forces, nanoscopic arrangements, toxicity, and environmental impact.The computational study integrates quantum chemistry, molecular dynamics (both all-atom and coarse-grained approaches), and thermodynamic modeling (COSMO-RS approach) to analyze the fluids and their interactions with biological entities, such as proteins and plasma membranes. The experimental characterization focuses on elucidating intermolecular interactions and liquid phase dynamics using NMR spectroscopy, visible and UV Resonance Raman spectroscopy (UVRR). Notably, this is the first report of UVRR data on NADES.Additionally, we simulate the effect of the molecular moieties forming the solvents on biological targets—specifically, protein and cell membrane models –. This in silico analysis aims to rationalize and predict their potential toxicity.Overall, our experimental findings and in silico simulations contribute to a deeper understanding of these novel solvents in terms of their network of interactions. Additionally, they highlight the potential impact on biological targets, providing new data to accurately define the eco-friendliness of type V DES and their suitability as sustainable alternatives to traditional molecular solvents.

Liquid-Liquid equilibrium Behavior and intermolecular interactions of Levulinic acid and water with isopropyl ether and methyl Tert-Butyl ether

Levulinic acid (LA) is a crucial bio-based chemical with extensive industrial applications. Due to its significant share in the cost of production, the development of efficient techniques for the separation of LA is essential. Traditional separation using sulphuric acid raises environmental and cost concerns, making liquid–liquid extraction a more sustainable and cost-effective alternative. liquid–liquid equilibrium (LLE) investigation was carried out for two ternary mixtures of water + LA + isopropyl ether / methyl tert-butyl ether (MTBE) at two temperatures and 101.3 kPa. The results indicated that the solvent MTBE, as an extractant, showed a higher partition coefficient and selectivity for LA than isopropyl ether, demonstrating its superior effectiveness in recovering LA. The interaction insights between LA and the extractants were explored using quantum chemistry calculations, which aligned well with the collected results. The ascertained LLE data was modeled using the NRTL equation, achieving the RMSD values below 0.01, demonstrating a good concordance between the collected data and computed values. The fitted NRTL model parameters are conducive to the designing and optimizing the LA separation process.

Modulating Electrostatic Properties and Noncovalent Interactions via Structural Isomerism: The Microwave Spectra and Molecular Structures of (E)- and (Z)-1,2,3,3,3-Pentafluoropropene and Their Gas-Phase Heterodimers with the Argon Atom.

Microwave spectra of both the E and Z isomers of 1,2,3,3,3-pentafluoropropene along with all three of the singly substituted 13C isotopologues for each are obtained using broadband chirped-pulse Fourier transform microwave spectroscopy from 2.0-18.1 GHz. Associated quantum chemistry calculations show that the barrier to internal rotation of the CF3 group is significantly higher for the Z isomer, which is stabilized by an intramolecular hydrogen bond, although the barriers in both isomers are sufficiently high to prevent the observation of any effects due to internal rotation. The normal isotopologues of the argon heterodimers for both isomers are also observed in the broadband spectrum and a Balle-Flygare cavity Fourier transform microwave spectrometer is used to obtain the 5.0-20.6 GHz spectra of the corresponding 13C isotopologues. In each case, the argon atom locates so as to maximize its interactions with areas of significant electron density. However, mapped electrostatic potential surfaces indicate that the areas of greatest nucleophilicity are different for the two isomers, suggesting that they may interact differently in forming heterodimers with protic acids.

Photodegradation Pathways of Aliphatic Polyamide through Conical Intersection between Ground and Excited States.

Time-dependent density functional theory studies were performed to investigate the photochemistry properties of the widely used aliphatic polyamide (APA), alias nylon, under ultraviolet radiation with N-ethylacetamide (NEA) being the model molecule. The characteristics of the transition molecular orbitals for the low-order excited states (ESs) of NEA were clarified, and the ES geometries related to the transition worthy of study were optimized. Our research proved that there is a conical intersection between the ground and excited states featured by the transition from the lone pair orbital to the σ antibonding orbital on the C-N bond within the peptide group or the N-C bond adjacent to the carbonyl group, and the C-N or N-C bond has the probability to be disrupted after internal conversion. These original quantum chemistry discoveries depict the C-N and N-C bond cleavage scheme that initiates the primary and secondary paths in the scission processes of the APA chain, respectively, which is helpful for giving new insight into the overall photodissociation mechanism of APA and designing advanced polyamide-based synthetic fibers.

Mechanism of dust suppressant by sodium carboxymethyl cellulose grafted acrylic copolymer

In order to inhibit dust, a substance C-PAA was synthesized by free radical polymerization using sodium carboxymethyl cellulose and acrylic acid as raw materials and ammonium persulfate as an initiator. The optimal synthesis process was determined by using a single factor experimental method. Quantum chemistry and experiments were used to investigate the chemical synthesis of C-PAA. The results indicate that the active centers of the reaction were at the OH bond of sodium carboxymethyl cellulose, where H was seized by ·SO4-, produced by ammonium persulfate, to form an alkoxyl radical. Concurrently, ·SO4- attacked acrylic acid, resulting in the breakage of the CC bond, creating a CC bond, and combining with the alkoxyl group to create a new ether group that produced the compound C-PAA. The enthalpy change and activation energy of the reaction were −178.40 KJ/mol and −22.59 KJ/mol, respectively, and the infrared absorption peaks of the newly generated fatty ether and the increase in the relative content of the ether group in the final product proved that the preparation of C-PAA was successful. In order to further improve the wetting performance of the dust suppressant, pyrene fluorescence spectrometry was used to determine the critical micelle concentration of the surfactant sodium dodecyl sulfate as 1.5 g/L, and 1.5 g/L sodium dodecyl sulfate was mixed with C-PAA to obtain the dust suppressant SC-PAA. In comparison to the H2O-lignite system, the total number of hydrogen bonds in the SC-PAA-lignite system increased from 2023 to 2405, according to the molecular dynamics results. The rationale is that C-PAA in SC-PAA has a plethora of oxygen-containing functional groups, which enable it to create more hydrogen bonds with H2O as well as amino and hydroxyl groups on the surface of lignite. Due to hydrogen bonding, the dust suppressant is able to gather more water molecules adsorbed on the surface of the lignite. It then utilizes the capillary force of the coal pores to penetrate deeply into the fissures within the coal particles, thereby enhancing the wetting impact on the lignite.

Solvation and its influence on the electronic structure and pharmacological activity of 2-fluoro-6-trifluromethyl acetophenone

The molecular framework and vibrational spectra of 2′-Fluoro-6′-Trifluoromethyl Acetophenone (MA3) in diverse solvent environments are being studied using quantum chemistry methods like DFT. The structure was successfully optimized using gas phase and solvent phases such as ethanol, diethyl sulfoxide, chloroform, and diethyl ether. Using FT-Raman and FT-IR techniques, both theoretical and experimental scenarios were examined. The IEFPCM model was used to explore the electronic properties, including HOMO-LUMO gaps, UV–Vis spectra, NBO, Mulliken analysis, and MEP, in various solvents. The TD-DFT approach and IEFPCM model were utilized to replicate the UV spectra. The Fukui function helped locate reactive sites and understand chemical interactions. Comprehensive topological analysis using Multiwfn – 3.8 suite integrated RDG, ALIE, ELF, and LOL to identify key binding sites and weak interactions. The molecular docking studies highlighted the compound’s binding affinities with target proteins, showcasing its potential pharmacological applications. This research underscores the critical role of solvation in determining the electronic and structural properties of MA3, paving the way for its application in drug development and other fields.

Highly-efficient separation of pyromellitic acid and trimellitic acid mixtures via forming deep eutectic solvents: Experiment and calculation

Pyromellitic acid (PMA) and trimellitic acid (TMA) are significant chemical raw materials and intermediates. They simultaneously exist in the industry processes of synthesis and are difficult to be separated. In this work, several kinds of biodegradable compounds were chosen as hydrogen bond acceptors (HBAs) to separate PMA and TMA mixtures from acetone solutions via forming deep eutectic solvent (DES). It has been found that all these compounds can separate PMA and TMA mixtures to obtain pure PMA or TMA. However, the interaction between HBAs and PMA or TMA is quite different. Choline chloride cannot extract TMA but can form a DES with PMA in acetone. Hexamethylenetetramine (HA) and L-carnitine (L-car) can form DESs with both PMA and TMA in acetone solution. But when L-car or HA is added, the extraction rate of PMA is larger than that of TMA until the extraction rate of PMA reach 100%, and pure TMA is left in the acetone solution. The selective separation mechanism was explored by infrared spectroscopy combined with quantum chemistry calculation, and the strength and site of the interaction between extractants with PMA and TMA were calculated.

Influence of the Fe(II) Spin State on Iron-Ligand Bonds in Heme Model Iron-PorphyrinComplexes with 4, 5 and 6 Ligands.

In this work heme models with four [Fe(II)(P)], five [Fe(II)(P)Im], [Fe(II)(P)(Im)O2] and six ligands [Fe(II)(P)(Im)O2], where P = porphyrin, with different spin states (ms =5, 3 and 1) of the iron atom were investigated using relativistic-corrected quantum chemistry methods (PW6B95-D3-DKH/jorge-TZP-DKH). Dependence of the iron-ligand bond properties on (i) spin state and (ii) number of ligands were analyzed using natural bond orbital analysis, electron density topology, electrostatic potential and electron localization function. It is shown that reversible binding of O2 is possible in case of formation of semicoordination bond between Fe(II) and imidazole. Binding of the fifth and sixth ligand from the energetic and orbital points of view is more favorable for the triplet Fe(II) state. At the same time for the six-coordinated complex [Fe(II)(P)(Im)O2] interconversion of Fe(II) electrons of valent 3d orbital from quintet to triplet and vice versa is possible under thermal fluctuations (energy barriers less than 2 kcal/mol).

Comparative Assessment between Glowing Family Elements of Metal and Graphene Quantum Dots Based on their Properties: A Theoretical and Experimental Study

The quantum dots (QDs) have wide range of applications in the field of biology and energy due to exceptionally photo-physical properties and highly active larger surface area. Both metal quantum dots (MQDs) and graphene quantum dots (GQDs) have created a new platform for quantum chemistry not only theoretical point of view but also open various real applications. The photo-physical properties arise due to tunable band gap and active functional groups adhere to the surface. Both MQDs and GQDs have very good properties such as solubility in wide range of solvent, good stability in photo-physical and chemical environment, less poisoning in animal body, small size and tunable photoluminescence is favourable for cell dynamics and imaging, up-conversion and down conversion photoluminescence nature, good electrochemical activity. The functionalization of QDs with micro and macromolecules in all direction are possible as results we find different shape of QDs due to very small size of QDs just like few atoms. Some theoretical studies have been observed to evaluate the origin of these properties. This review focused on the comparative studies including advantage and disadvantage between GQDs and MQDs based on their properties and also give significant imminent to motivate more encouraging development. Moreover, this review study offers significant insights for enhancing the characteristics of quantum dots.

Determination of Calcium Isotopes Using Inductive Coupled Plasma-Tandem Mass Spectrometry with Ozone-Induced Oxidation.

In this study, we propose a new method for determination of calcium (Ca) isotopes using inductive coupled plasma-tandem mass spectrometry (ICP-MS/MS). The most abundant isotope of Ca, 40Ca, has a spectrum identical with that of argon (Ar), which is often used as the carrier gas in ICP-MS analysis. The detection capability for 40Ca is thus significantly reduced in the presence of 40Ar. To avoid interference from 40Ar during the 40Ca measurements, ozone (O3) was used as the reaction gas in the ICP-MS/MS analysis. The reaction of Ca+ with O3 in the collision cell preferentially produced CaO3+. In contrast, the reaction between Ar+ and O3 produced ArO+, which further reacted with the oxidized O3 to produce Ar+. Because Ar+ does not produced ArO3+ as the main product of the reaction with O3, the measurement of Ca+ as CaO3 via O3-induced oxidation resulted in considerably less interference from Ar+. The detailed mechanism of CaO3+ formation was investigated via quantum chemistry calculations by using density functional theory. The interaction between Ca+ and O3 yielded CaO3+, which immediately dissociated into either Ca+ and O3 or CaO+ and O2 because the pressure in the collision cell was approximately 1 Pa in the MS/MS experiments. Consequently, CaO3+ was formed by the consecutive reaction of Ca+ with O3, with CaO+ and CaO2+ as intermediates. The present method achieved the detection of less abundant Ca isotopes in certified reference materials such as 43Ca, 44Ca, 46Ca, and 48Ca, thereby allowing the determination of Ca isotopes with high sensitivity.

Quantum chemistry − guided design of luminescent Triphenylene − based co-crystals: Unveiling heavy atom for enhanced fluorescence lifetime

This study employed quantum chemical methods to predict and synthesize three luminescent cocrystals. Utilizing Triphenylene as the electron donor and 1,2,4,5-tetracyanobenzene (TCNB), 2,3,5,6-tetrafluoroterephthalonitrile (TFP), and 2,3,5,6-tetrachloroterephthalonitrile (TCP) as acceptors, the structures and internal interactions of these cocrystals were analyzed. The predominant interactions observed were charge transfer, hydrogen bonding, and π-π interactions. Notably, the Triphenylene-TCP cocrystal exhibited a significantly extended fluorescence lifetime compared to the other two. Further investigations, employing time-dependent density functional theory (TD-DFT) on Triphenylene-TCP, suggested that intersystem crossing (ISC) and reverse intersystem crossing (RISC) mechanisms contribute to the prolonged fluorescence lifetime. This study offers valuable insights into the design of supramolecular cocrystals to enhance the performance of organic fluorescent materials.

OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors.

Non-Markovian dynamics arising from the strong coupling of a system to a structured environment is essential in many applications of quantum mechanics and emerging technologies. Deriving an accurate description of general quantum dynamics including memory effects is, however, a demanding task, prohibitive to standard analytical or direct numerical approaches. We present a major release of our open source software package, OQuPy (Open Quantum System in Python), which provides several recently developed numerical methods that address this challenging task. It utilizes the process tensor approach to open quantum systems (OQS) in which a single map, the process tensor, captures all possible effects of an environment on the system. The representation of the process tensor in a tensor network form allows for an exact yet highly efficient description of non-Markovian OQS (NM-OQS). The OQuPy package provides methods to (1) compute the dynamics and multi-time correlations of quantum systems coupled to single and multiple environments, (2) optimize control protocols for NM-OQS, (3) simulate interacting chains of NM-OQS, and (4) compute the mean-field dynamics of an ensemble of NM-OQS coupled to a common central system. Our aim is to provide an easily accessible and extensible tool for researchers of OQS in fields such as quantum chemistry, quantum sensing, and quantum information.

Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics.

Compound identification is at the center of metabolomics, usually by comparing experimental mass spectra against library spectra. However, most compounds are not commercially available to generate library spectra. Hence, for such compounds, MS/MS spectra need to be predicted. Machine learning and heuristic models have largely failed except for lipids. Here, quantum chemistry software can be used to predict mass spectra. However, quantum chemistry predictions for collision induced dissociation (CID) mass spectra in LC-MS/MS are rare. We present the CIDMD (Collision-Induced Dissociation via Molecular Dynamics) framework to model CID-based MS/MS spectra. It uses first-principles molecular dynamics (MD) to simulate the physical process of molecular collisions in CID tandem mass spectrometry. First, molecular ions are constructed at specific protonation sites. Using density functional theory, these protonated ions are targeted by argon collider gas atoms at user-specified velocities. Subsequent bond breakages are simulated over time for at least 1,000 fs. Each simulation is repeated multiple times from various collisional directions. Fragmentations are accumulated over those repeated collisions to generate CIDMD in silico mass spectra. Twelve small metabolites (<205 Da) were selected to test the accuracy of this framework in comparison to experimental MS/MS spectra. When testing different protomers, collider velocities, number of simulations, simulation time and impact factor b cutoffs, we yielded 261 predicted mass spectra. These in silico spectra resulted in entropy similarity scores of an average 624 ± 189 for all 261 spectra compared to their corresponding experimental spectra, which improved to 828 ± 77 when using optimal parameters of the most probable protomers for 12 molecules. With increasing molecular mass, higher velocities achieved better results. Similarly, different protomers showed large differences in fragmentation; hence, with increasing numbers of protomers and tautomers, the average CIDMD prediction accuracy decreased. Mechanistic details showed that specific fragment ions can be produced from different protomers via multiple fragmentation pathways. We propose that CIDMD is a suitable tool to predict mass spectra of small metabolites like produced by the gut microbiome.