Quantum Mechanical Calculations Research Articles

HessFit: A Toolkit to Derive Automated Force Fields from Quantum Mechanical Information.

In this study, we introduce a novel approach to enhance the accuracy of molecular dynamics simulations by refining the force fields (FFs) through a combination of transferable parameters and molecule-specific characteristics derived from quantum mechanical (QM) calculations. Traditional FFs often prioritize generality over precision, leading to limitations in the accuracy of accurately capturing intra- and intermolecular interactions. To address this, we present an open-source toolkit, called HessFit, designed to integrate QM-derived bonded parameters and atomic charges into existing FFs. In combination with bond, angle, torsional, and nonbonded parameters derivation, HessFit can easily extract multiple barrier terms of dihedrals from QM Hessian and gradient or return all terms through a fitting procedure scheme of QM potential energy surface. We showcase the effectiveness of HessFit through comprehensive evaluations of vibrational properties across a diverse set of small molecules and demonstrate that experimental results support its ability in predicting thermodynamic properties of organic molecules compared to previous state-of-the-art approaches. We further explore its application to Zn2+ metalloprotein models, which are hard systems to treat with automatic approaches. Our results demonstrate that HessFit parameters compete with GAFF2 and OPLS parameters to describing small organic molecules, and its feasibility is also comparable to current FFs used to modeling nonstandard residues in Zn proteins for molecular dynamics simulations. The effectiveness of the HessFit protocol makes it a valuable tool for deriving or extending force field parameters for novel compounds in several molecular modeling applications.

Computationally Assisted Analysis of NMR Chemical Shifts as a Tool in Conformational Analysis.

A key to understanding the properties of functional molecules is to determine their conformation in solution. A conformational analysis procedure that relies on quantum mechanical calculations and the widely used DP4+ probability was evaluated to decipher the structural information encoded in NMR chemical shifts. The results underscore the potential utility of using NMR chemical shifts in advancing conformational analysis studies of complex molecules in solution.

Unveiling the Multifaceted Nature of 4‐(4‐Methylphenyl Thio)benzophenone: Electronic Structure and Excited States in Gas Phase and Solvents

AbstractBenzophenone and its derivatives are widely used as UV filters and UV‐ink photoinitiators. The photoinitiating properties of benzophenones depend on their degree of conjugation and delocalization within the molecule. By understanding how conjugation, delocalization, and different substituents affect these properties, benzophenone derivatives can be customized for specific applications. Using quantum mechanical calculations based on B3LYP/6‐311++G(d, p) density functional theory (DFT), chemical reactivity, stability, and photoinitiating capabilities of 4‐(4‐methylphenylthio)benzophenone are analyzed. This includes studying its physical and chemical properties in the gas phase, as well as its excited state electronic transitions, vibrational characteristics, and spectroscopic properties both in gas phase and in various solvents. The DFT‐computed infrared spectra match experimental results. The UV/Visible spectra shows absorption towards longer wavelengths due to extended delocalization of π‐electrons. In different solvents with varying polarity, the absorption spectra exhibit high‐intensity peaks, shift in excitation energy and wavelengths based on the polarity of the solvent. This knowledge allows for the development of novel initiators with customized light absorption, excited state lifetimes, and reaction selectivities, which can enhance processes like UV‐curing, photopolymerization, and other light‐driven reactions.

Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency

Rhomboid intramembrane serine proteases have been implicated in several pathologies, and emerge as attractive pharmacological target candidates. The most potent and selective rhomboid inhibitors available to date are peptidyl α-ketoamides, but their selectivity for diverse rhomboid proteases and strategies to modulate it in relevant contexts are poorly understood. This gap, together with the lack of suitable in vitro models, hinders ketoamide development for relevant eukaryotic rhomboid enzymes. Here we explore the structure-activity relationship principles of rhomboid inhibiting ketoamides by medicinal chemistry and enzymatic in vitro and in-cell assays with recombinant rhomboid proteases GlpG, human mitochondrial rhomboid PARL and human RHBDL2. We use X-ray crystallography in lipidic cubic phase to understand the binding mode of one of the best ketoamide inhibitors synthesized here containing a branched terminal substituent bound to GlpG. In addition, to extend the interpretation of the co-crystal structure, we use quantum mechanical calculations and quantify the relative importance of interactions along the inhibitor molecule. These combined experimental analyses implicates that more extensive exploration of chemical space at the prime side is unexpectedly powerful for the selectivity of rhomboid inhibiting ketoamides. Together with variations in the peptide sequence at the non-prime side, or its non-peptidic alternatives, this strategy enables targeted tailoring of potent and selective ketoamides towards diverse rhomboid proteases including disease-relevant ones such as PARL and RHBDL2.

The Structural Basis of the Activity Cliff in Modafinil-Based Dopamine Transporter Inhibitors.

Modafinil analogs with either a sulfoxide or sulfide moiety have improved binding affinities at the human dopamine transporter (hDAT) compared to modafinil, with lead sulfoxide-substituted analogs showing characteristics of atypical inhibition (e.g., JJC8-091). Interestingly, the only distinction between sulfoxide and sulfide substitution is the presence of one additional oxygen atom. To elucidate why such a subtle difference in ligand structure can result in different typical or atypical profiles, we investigated two pairs of analogs. Our quantum mechanical calculations revealed a more negatively charged distribution of the electrostatic potential surface of the sulfoxide substitution. Using molecular dynamics simulations, we demonstrated that sulfoxide-substituted modafinil analogs have a propensity to attract more water into the binding pocket. They also exhibited a tendency to dissociate from Asp79 and form a new interaction with Asp421, consequently promoting an inward-facing conformation of hDAT. In contrast, sulfide-substituted analogs did not display these effects. These findings elucidate the structural basis of the activity cliff observed with modafinil analogs and also enhance our understanding of the functionally relevant conformational spectrum of hDAT.

Studying the capability of graphene, BC3, and NC3 nanoflakes as Busulfan drug carriers in the presence of static electric field and solvent effects: quantum mechanical calculations

Studying the capability of graphene, BC3, and NC3 nanoflakes as Busulfan drug carriers in the presence of static electric field and solvent effects: quantum mechanical calculations

Mechanism of 7H-Dibenzo[c,g]carbazole metabolism in cytochrome P450 1A1: Insights from computational studies

7H-Dibenzo[c,g]carbazole (DBC) is a prevalent environmental contaminant that induces tumorigenesis in several experimental animals. Recently, it has been utilized to develop high-performance solar cells and organic phosphorescent materials. It is imperative to strengthen investigations of DBC metabolism to understand its potential risks to human health. In this study, human CYP1A1 was employed as the metabolic enzyme to investigate the metabolic mechanism of DBC by molecular docking, molecular dynamics (MD) simulation, and quantum mechanical (QM) calculation. The results indicate that DBC binds to CYP1A1 in two modes (mode 1 and mode 2) mainly through nonpolar solvation energies (ΔGnonpolar). The formation of the two binding modes is attributed to the anchoring effect of the hydrogen bond formed by DBC with Asp320 (mode 1) or Ser116 (mode 2). Mode 1 is a "reactive" conformation, while mode 2 is not considered a "reactive" conformation. C5 is identified as the dominant site, and the pyrrole nitrogen cannot participate in the metabolism. DBC is metabolized mainly by a distinct electrophilic addition-rearrangement mechanism, with an energy barrier of 21.74 kcal/mol. The results provide meaningful insights into the biometabolic process of DBC and contribute to understanding its environmental effects and health risks.

The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations.

Femtosecond fluorescence upconversion experiments were combined with CASPT2 and time dependent DFT calculations to characterize the excited state dynamics of the mutagenic etheno adduct 1,N2-etheno-2'-deoxyguanosine (ϵdG). This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The ϵdG fluorescence is strongly modified with respect to that of the canonical nucleoside dG, notably by an about 6-fold increase in fluorescence lifetime and quantum yield at neutral pH. In addition, femtosecond fluorescence upconversion experiments reveal the presence of two emission bands with maxima at 335 nm for the shorter-lived and 425 nm for the longer-lived. Quantum mechanical calculations rationalize these findings and provide absorption and fluorescence spectral shapes similar to the experimental ones. Two different bright minima are located on the potential energy surface of the lowest energy singlet excited state. One planar minimum, slightly more stable, is associated with the emission at 335 nm, whereas the other one, with a bent etheno ring, is associated with the red-shifted emission.

Unraveling the role of boron dimers in the electrical anisotropy and superconductivity in boron-doped diamond

We use quantum mechanics (QM) to determine the states formed by B dopants in diamond. We find that isolated B sites prefer to form BB dimers and that the dimers pair up to form tetramers (BBCBB) that prefer to aggregate parallel to the (111) surface in the <110> direction, one double layer below the H-terminated surface double layer. These tetramers lead to metallic character (Mott metal Insulator Transition) with holes in the valence band near the Γ point and electrons in the BBCBB tetramer promoted band along the X direction. Our experiments find very significant anisotropy in the superconductivity for boron-doped diamond thin films prepared with Microwave Plasma Assisted Chemical Vapor Deposition using deuterium-rich plasma. This leads to much higher conductivity in the X direction than the Y direction, as predicted by the QM. This phase transition to the anomalous phase is linked with the emergence of boson quantum entanglement states behaving as a bosonic insulating state. These anisotropic superconducting properties of the diamond film might enable applications such as single-photon detectors. We expect that this formation of a dirty superconductivity state is related to the BBCBB tetramers found in our QM calculations.

ScaleLat: A chemical structure matching algorithm for mapping atomic structure of multi-phase system and high entropy alloys

ScaleLat (Scale Lattice) is a computer program written in C for performing the atomic structure analysis of multi-phase system or high entropy alloys (HEAs). The program implements an atomic cluster cell extraction algorithm to obtain all symmetry independent characteristic atomic cluster cells for the complex atomic configurations which are usually obtained from molecular dynamics or kinetic Monte-Carlo simulations at nanoscale or mesoscopic scale. ScaleLat implements an efficient and unique chemical structure matching algorithm to match all extracted atomic clusters from a large supercell (>104 atoms) to a representative small one (∼ 103 or less), providing the possibility to directly use the highly accurate quantum mechanical methods to study the electronic, magnetic, and mechanical properties of multi-component alloys for complex microstructures. We demonstrate the capability of ScaleLat code by conducting both the atomic structure matching analysis for Fe-12.8 at.% Cr binary alloy and equiatomic CrFeCoNiCu high entropy alloy, successfully obtaining the representative supercells containing 102∼103 atoms for two systems. The reliability of the proposed chemical structure matching scheme is tested and confirmed by calculating the electronic structures of both examples using trial supercells with various sizes. Overall, ScaleLat program provides a universal platform to efficiently map all essential chemical structures of large complex atomic structures to a relatively easy-handling small supercell for quantum mechanical calculations of various user interested properties. Program SummaryProgram Title: ScaleLatCPC Library link to program files: https://doi.org/10.17632/cv6wsxy938.1Developer's repository link: https://github.com/NanLi-xjtu/ScaleLat.gitLicensing provisions: MITProgramming language: CNature of Problem: Very large supercells containing more than 104 atoms must be used to describe the atomic structure of multi-phase materials or high entropy alloys, and their electronic and mechanical properties are almost not possible to be investigated using quantum mechanical calculations within conventional computational hardware. Decreasing the total number of atoms in a smaller representative supercell which preserves all essential chemical structures of the original large supercell is the key to tackling the problem.Solution to the Problem: An atomic cluster cell extraction algorithm is realized to thoroughly obtain all symmetry independent characteristic chemical structures of multi-phase system or high entropy alloys. Utilizing the direct atom swapping method, the efficient chemical structure matching procedure is developed to map all extracted characteristic atomic cluster cells of benchmark structure to the small supercell by minimizing their differences in both the types and relative fractions of atomic cluster cell sets.

Separation of isotopologues of amphetamine with various degree of deuteration on achiral and polysaccharide-based chiral columns in high-performance liquid chromatography

Hydrogen/deuterium (H/D) isotope effects are not unusual in chromatography and such phenomena have been observed in both gas- and liquid-phase separations. Despite the numerous reports on this topic, the understanding of mechanisms and the underlying noncovalent interactions at play remains rather challenging. In our recent study, we reported baseline separation of isotopologoues of some amphetamine (AMP) derivatives on achiral and polysaccharide-based chiral columns, as well as some correlations between the degree of separation of enantiomers and isotopologues on (the same) polysaccharide-based chiral column(s). Following our previous findings on isotope effects in high-performance liquid chromatography, we report herein a comparative study on the isotope effects observed with AMP and methamphetamine (MET). The impact of some pivotal factors such as the number of deuterium atoms part of AMP isotopologues, the structure of its isotopomers, the chemical structure of the achiral and chiral stationary phases used in this study, and the use of methanol- vs acetonitrile-containing mobile phases on the isotope effects was examined and discussed. Quantitative correlations between the observed isotope effects and the enantioselectivity of the chiral columns used are also shortly discussed. Furthermore, considering the chromatographic results as benchmark experimental data, we attempted to elucidate the molecular bases of the observed phenomena using quantum mechanics calculations.

Substitution-Induced Mechanistic Switching in SNAr-Warheads for Cysteine Proteases.

The aim of this study was to investigate the transition from non-covalent reversible over covalent reversible to covalent irreversible inhibition of cysteine proteases by making delicate structural changes to the warhead scaffold. To this end, dipeptidic rhodesain inhibitors with different N-terminal electrophilic arenes as warheads relying on the SNAr mechanism were synthesized and investigated. Strong structure-activity relationships of the inhibition potency, the degree of covalency, and the reversibility of binding on the arene substitution pattern were found. The studies were complemented and substantiated by molecular docking and quantum-mechanical calculations of model systems. Furthermore, the improvement in the membrane permeability of peptide esters in comparison to their corresponding carboxylic acids was exemplified.

Agglomeration in dimethyl sulfoxide and water binary System: A comprehensive study through thermodynamics, vibrational spectroscopy, quantum mechanical calculations and morphology

Some nano- or micro-sized agglomerates with different morphologies in the dimethyl sulfoxide (DMSO) and water binary system at different molar fractions were characterized using Scanning Electron Microscope (SEM) and Dynamic Light Scattering (DLS) for the first time. Four fundamental clusters with the composition of [(DMSO)2], [(DMSO)3], [(DMSO)2∙ H2O] and [(DMSO)3∙ H2O] were identified through the combination of quantum mechanical calculations and vibrational spectroscopy. These clusters act as seeds for the growth of agglomerates both in pure DMSO and in DMSO-water binary mixtures. According to SEM images, the morphology of the agglomerates varies with the molar fraction, wherein two main kinds were observed, viz. one growing from the center and spreading out to the surrounding, and the other growing into a chain-like structure. Inter-cluster and/or inter-agglomerate interactions are responsible for the molar fraction dependence of density, viscosity and other related thermodynamic properties. The present work is the first to study the morphology of agglomerates in the DMSO-water binary system and the first to propose the essential roles played by four dominant clusters in the agglomerating process.

Synthesis of isoprene from 1-butanol and from diethyl ether in the presence of 3d-metal oxides nano-clusters acting as catalysts

The conformational equilibria of 1-butanol (1-BuOH) and diethyl ether (DEE) molecules were investigated in gas and liquid phases. The geometry of the molecules of all stable isomers of 1-BuOH and DEE was fully optimised and the thermochemical quantities’ values (ΔH, ΔG and ΔS) were computed in the temperature range from close to 0 K to 1000 K at the Density Functional Theory (DFT) level. DEE shows two rotamers (namely, Tt and Tg), whereas five different rotamers were identified for 1-BuOH (namely, Tt, Tg, Gt, Gg and Gg’) with different stability, due to the presence of intramolecular interactions. Electrostatic properties of 1-BuOH, ethanol (EtOH), and DEE were also evaluated. Calculated vibration spectra of 1-BuOH and DEE were compared with the experimental FT-IR and Raman spectra recorded in neat phase and diluted in cyclohexane (CHX). The experimental vibrational spectra found the best match with the sum of calculated spectra using the Boltzmann coefficients based on the thermal stability of each conformer. The frequency shift observed for some peaks as a function of the concentration of 1-BuOH in CHX reveals the impact of hydrogen bonds between 1-BuOH molecules, in particular in the case of conformer Gg’. In contrast, very weak interactions among molecules of DEE were spectroscopically detected. The transformation reactions of {1-BuOH+EtOH} and {DEE+EtOH} mixtures at different temperatures were studied using the method of quantum mechanical calculations. The mechanism of isoprene formation from these mixtures was determined taking into account the chemisorption of 1-BuOH and DEE onto metal oxide nano-clusters M4O4 (M = Sc to Zn) and its effect on the vibrations of BuOH and DEE at the interface for M = Zn, Cu and Ti using Raman microscopic spectroscopy.

Exploratory data science on supercomputers for quantum mechanical calculations

Literate programming—the bringing together of program code and natural language narratives—has become a ubiquitous approach in the realm of data science. This methodology is appealing as well for the domain of Density Functional Theory (DFT) calculations, particularly for interactively developing new methodologies and workflows. However, effective use of literate programming is hampered by old programming paradigms and the difficulties associated with using high performance computing (HPC) resources. Here we present two Python libraries that aim to remove these hurdles. First, we describe the PyBigDFT library, which can be used to setup materials or molecular systems and provides high-level access to the wavelet based BigDFT code. We then present the related remotemanager library, which is able to serialize and execute arbitrary Python functions on remote supercomputers. We show how together these libraries enable transparent access to HPC based DFT calculations and can serve as building blocks for rapid prototyping and data exploration.

Toward Accurate Quantum Mechanical Thermochemistry: (1) Extensible Implementation and Comparison of Bond Additivity Corrections and Isodesmic Reactions.

Obtaining accurate enthalpies of formation of chemical species, ΔHf, often requires empirical corrections that connect the results of quantum mechanical (QM) calculations with the experimental enthalpies of elements in their standard state. One approach is to use atomization energy corrections followed by bond additivity corrections (BACs), such as those defined by Petersson et al. or Anantharaman and Melius. Another approach is to utilize isodesmic reactions (IDRs) as shown by Buerger et al. We implement both approaches in Arkane, an open-source software that can calculate species thermochemistry using results from various QM software packages. In this work, we collect 421 reference species from the literature to derive ΔHf corrections and fit atomization energy corrections and BACs for 15 commonly used model chemistries. We find that both types of BACs yield similar accuracy, although Anantharaman- and Melius-type BACs appear to generalize better. Furthermore, BACs tend to achieve better accuracy than IDRs for commonly used model chemistries, and IDRs can be less robust because of the sensitivity to the chosen reference species and reactions. Overall, Anantharaman- and Melius-type BACs are our recommended approach for achieving accurate QM corrections for enthalpies.

Crystal violet degradation by visible light-driven AgNP/TiO2 hybrid photocatalyst tracked by SERRS spectroscopy

Dyes are important concerns regarding aquatic environmental contamination given their extensive industrial use and the occurrence of highly toxic and carcinogenic effects on the biota. In this work, photodegradation processes of the organic dye crystal violet (CV) by a hybrid plasmonic photocatalyst involving titanium dioxide (TiO2) and silver nanoparticles (AgNP), through irradiation with low-power visible light were studied, and the experiments were tracked by ultraviolet-visible absorption (UV–VIS) and surface-enhanced resonance Raman scattering (SERRS) spectroscopies. Enhanced photocatalytic activity was observed, reaching about 71, 80 and 87 % of CV removal with only 100 minutes of irradiation, depending on the Ag loading used. The high photocatalytic efficiency is further highlighted by the low energy consumption in the process, requiring only ca. 1.46 kW h L-1 in the best reaction condition. Quantum-mechanical calculations were used to the assignment of electronic spectra, as well as to the prediction of frontier molecular orbitals and atomic charges, aiming to propose mechanisms for radical attacks. Such results allow suggesting degradation processes involved mainly N-demethylation and bond breaking of central carbon. The presence of CV protonated species was also supported through Density Functional Theory (DFT) investigation. The integration of theoretical and experimental results allows proposing the formation of pararosaniline, phenol and benzophenone derivatives, which may have highest ecotoxicity than the original contaminant, outstanding the remarkable relevance of SERRS spectroscopy in monitoring such recalcitrant substances.

17-β-Estradiol—β-Cyclodextrin complex as an aqueous solution: Structural and physicochemical characterization supported by MM and QM calculations

17-β-estradiol (EST) is an Active Pharmaceutical Ingredient characterized by a low water solubility. Complexation with β-cyclodextrin (βCD) enhances its bioavailability, hence such complex is an interesting research object from pharmaceutical point of view. However, basic facts like description of complex's structure and definition of its molar ratio, were debatable already for decades. This work for the first time justifies the EST:βCD molar ratio as 1:2 using the HRMS (high-resolution mass spectrometry) and phase solubility studies. The latter are used to define complex stability constant, as well. The structure and stability is analyzed using a variety of computational approaches: Quantum Mechanics (QM) based methods (DFT, semiempirical approaches) and MD/MMGBSA approach. In case of the QM, for the first time in the computational analysis of cyclodextrin complexes, a thorough benchmarking test is presented. Different computational parameters (solvent model, presence/absence of dispersion correction etc.) are used. Obtained results are compared with the experimental data.

A Combined Experimental, DFT and Molecular Dynamics Simulation Study of Binary Mixture of Ethylbenzene and Aniline

AbstractDensity and viscosity values of the binary mixture of ethylbenzene and aniline have been experimentally measured in different mole fractions at temperatures of 293.15 to 313.15 K and at an absolute pressure of 86.7 kPa. Based on the obtained experimental data, the excess molar volume and viscosity deviations have been reported, which can interpret the interactions in this mixture. The obtained data were fitted with the Redlich‐Kister equation. In addition, the viscosity results are discussed using the equation proposed by Gruenberg‐Nissan. After experimental studies, in order to investigate the interactions of these two components and their mixture, quantum mechanical calculations and molecular dynamics simulation have been used. In this way, the structures of the desired molecules have been optimized. Then Atoms in Molecules (AIM) and frontier molecular orbital (FMO) techniques have been used for a more detailed investigation. Finally, by plotting radial distribution functions (RDFs) obtained from molecular dynamics, these interactions have been investigated in a more comprehensive way. In addition, the simulated densities at 298.15 K have been reported. At the end, clear pictures of the interactions of molecules in mixtures were obtained by comparing the achievements of experimental measurements, quantum chemical and calculations MD simulation.

Reaction mechanisms for methyl isocyanate (CH3NCO) gas-phase degradation

Methyl isocyanate (MIC) is a toxic chemical found in many commercial, industrial, and agricultural processes, and was the primary chemical involved in the Bhopal, India disaster of 1984. The atmospheric environmental chemical reactivity of MIC is relatively unknown with only proposed reaction channels, mainly involving OH-initiated reactions. The gas-phase degradation reaction pathways of MIC and its primary product, formyl isocyanate (FIC), were investigated with quantum mechanical (QM) calculations to assess the fate of the toxic chemical and its primary transformation products. Transition state energy barriers and reaction energetics were evaluated for thermolysis/pyrolysis-like reactions and bimolecular reactions initiated by relevant radicals (•OH and Cl•) to evaluate the potential energy surfaces and identify the primary reaction pathways and products. Thermolysis/pyrolysis of MIC requires high energy to initiate N-CH3 and C-H bond dissociation and is unlikely to dissociate except under extreme conditions. Bimolecular radical addition and H-abstraction reaction pathways are deemed the most kinetically and thermodynamically favorable mechanisms. The primary transformation products of MIC were identified as FIC, methylcarbamic acid, isocyanic acid (isocyanate radical), and carbon dioxide. The results of this work inform the gas-phase reaction channels of MIC and FIC reactivity and identify transformation products under various reaction conditions.