Single-point Energy Calculations Research Articles

QuanDB: a quantum chemical property database towards enhancing 3D molecular representation learning.

Previous studies have shown that the three-dimensional (3D) geometric and electronic structure of molecules play a crucial role in determining their key properties and intermolecular interactions. Therefore, it is necessary to establish a quantum chemical (QC) property database containing the most stable 3D geometric conformations and electronic structures of molecules. In this study, a high-quality QC property database, called QuanDB, was developed, which included structurally diverse molecular entities and featured a user-friendly interface. Currently, QuanDB contains 154,610 compounds sourced from public databases and scientific literature, with 10,125 scaffolds. The elemental composition comprises nine elements: H, C, O, N, P, S, F, Cl, and Br. For each molecule, QuanDB provides 53 global and 5 local QC properties and the most stable 3D conformation. These properties are divided into three categories: geometric structure, electronic structure, and thermodynamics. Geometric structure optimization and single point energy calculation at the theoretical level of B3LYP-D3(BJ)/6-311G(d)/SMD/water and B3LYP-D3(BJ)/def2-TZVP/SMD/water, respectively, were applied to ensure highly accurate calculations of QC properties, with the computational cost exceeding 107 core-hours. QuanDB provides high-value geometric and electronic structure information for use in molecular representation models, which are critical for machine-learning-based molecular design, thereby contributing to a comprehensive description of the chemical compound space. As a new high-quality dataset for QC properties, QuanDB is expected to become a benchmark tool for the training and optimization of machine learning models, thus further advancing the development of novel drugs and materials. QuanDB is freely available, without registration, at https://quandb.cmdrg.com/ .

DFT Struggles to Predict the Energy Landscape for Iron Pyridine Diimine-Catalyzed [2 + 2] Cycloaddition of Alkenes: Insights into the Problem and Alternative Solutions.

In recent years, noninnocent pyridine diimine (PDI) complexes featuring first-row transition metals have emerged as prominent catalysts, demonstrating efficacy in a diverse range of vital organometallic transformations. However, the inherent complexity of the fundamental reactivity paradigm in these systems arises from the presence of a noninnocent ligand and the multispin feasibility of 3d metals. While density functional theory (DFT) has been widely used to unravel mechanistic insights, its limitations as a single-reference method can potentially misrepresent spin-state energetics, compromising our understanding of these intricate systems. In this study, we employ extensive high-level ab initio state averaged-complete active space self-consistent field/N-electron valence state perturbation theory (SA-CASSCF/NEVPT2) calculations in combination with DFT to investigate an iron-PDI-catalyzed [2 + 2] cycloaddition reaction of alkenes. The transformation proceeds through two major steps: oxidative cyclization and reductive elimination. Contrary to the predictions of DFT calculations, which suggest two-state reactivity in the reaction and identify reductive elimination as the turnover-limiting step, SA-CASSCF/NEVPT2-corrected results unequivocally establish a single-state reactivity scenario with oxidative cyclization as the turnover-limiting step. SA-CASSCF/NEVPT2-based insights into electronic ground states and electron distribution elucidate the intriguing interactions between the PDI ligand and the iron center, revealing the highly multiconfigurational nature of these species and providing a precise depiction of metal-ligand cooperativity throughout the transformation. A comparative assessment of several widely recognized DFT functionals against SA-CASSCF/NEVPT2-corrected data indicates that single-point energy calculations using the modern density functional MN15 on TPSSh geometries offer the most reliable density functional methodology, in scenarios where SA-CASSCF/NEVPT2 computational cost is a consideration.

A Many-Body Perspective of Nuclear Quantum Effects in Aqueous Clusters.

Nuclear quantum effects play an important role in the structure and thermodynamics of aqueous systems. By performing a many-body expansion with nuclear-electronic orbital (NEO) theory, we show that proton quantization can give rise to significant energetic contributions for many-body interactions spanning several molecules in single-point energy calculations of water clusters. Although zero-point motion produces a large increase in energy at the one-body level, nuclear quantum effects serve to stabilize higher-order molecular interactions. These results are significant because they demonstrate that nuclear quantum effects play a nontrivial role in many-body interactions of aqueous systems. Our approach also provides a pathway for incorporating nuclear quantum effects into water potential energy surfaces. The NEO approach is advantageous for many-body expansion analyses because it includes nuclear quantum effects directly in the energies.

Structures and bonding characteristics of KCl(H2O)n clusters with n = 1-10 based on density functional theory.

Aqueous inorganic salt solutions play a prominent role in both physiological and chemical experiments, and significant attention has been directed toward understanding the mechanisms underlying salt dissolution. In our effort to elucidate the hydration process of potassium chloride, we employed a comprehensive genetic algorithm to explore the structures of KCl(H2O)n (n = 1-10). A series of stable structures were identified by high-level abinitio optimization and single-point energy calculations with a zero-point energy correction. An analysis of the probability distribution of KCl(H2O)1-10 revealed that clusters with high probability at low temperatures exhibit reduced probabilities at higher temperatures, while others become more prevalent. When n = 1-9, the contact ion pair configurations or partially dissociated structures dominate in the system, and the probability distribution plot shows that the proportion of the solvent-separated ion pair (SSIP) structures of KCl(H2O)n is very small, while the SSIP configuration in KCl(H2O)10 becomes a stable structure with increasing temperature. The results from natural bond orbital analysis reveal a stronger interaction between chloride ions and water molecules. These findings provide valuable insights for a more comprehensive understanding of the intricacies of potassium chloride dissolution in water.

Investigating Si (100) surface patterns as well as electrical states through integrating molecular dynamics simulations with density functional tight binding at atomic level

The present work performs molecular dynamics simulations within model potential’s framework to investigate surface atoms’ rearrangements, loading states, and stress distribution in Si (100) surface on heating, and then single point energy calculations for the obtained atomic packing structures of Si substrates are used to obtain electrical information through self-consistent charge density functional tight binding approach. From analysis of Lode-Nadai parameters, atomic stress, visually packing images, Mulliken charges of atoms, Mulliken electron populations on atomic orbitals, differential charge densities, and chemical potentials for substrates, the knowledge of surface patterns, micro-loading states on the atoms and electrical states are obtained. The simulation results show the positions of vacancies have a significant impact on the rearrangements of the surface atoms. The appropriate selection of vacancy positions could be helpful in designing patterns of Si (100) surface. The vacancies in the subsurface or deeper atomic layers present migrations, where the migrations are more likely to occur at higher temperatures. There are stress concentration area and apparent charge transfers for the atoms forming dimers and neighboring atoms around the vacancies, and the differential charge densities in the surface atoms also present significant differences. These substrates with different surface patterns have different chemical potentials.

Continuous-wave cavity ringdown for high-sensitivity polarimetry and magnetometry measurements.

We report the development of a novel variant of cavity ringdown polarimetry using a continuous-wave laser operating at 532nm for highly precise chiroptical activity and magnetometry measurements. The key methodology of the apparatus relies upon the external modulation of the laser frequency at the frequency splitting between non-degenerate left- and right-circularly polarized cavity modes. The method is demonstrated by the evaluation of the Verdet constants of crystalline CeF3 and fused silica, in addition to the observation of gas- and solution-phase optical rotations of selected chiral molecules. Specifically, optical rotations of (i) vapors of α-pinene and R-(+)-limonene, (ii) mutarotating D-glucose in water, and (iii) acidified L-histidine solutions are determined. The detection sensitivities for the gas- and solution-phase chiral activity measurements are ∼30 and ∼120μdeg over a 30s detection period per cavity round trip pass, respectively. Furthermore, the measured optical rotations for R-(+)-limonene are compared with computations performed using the TURBOMOLE quantum chemistry package. The experimentally observed optically rotatory dispersion of this cyclic monoterpene was thus rationalized via a consideration of its room temperature conformer distribution as determined by the aforementioned single-point energy calculations.

High-Pressure Limit and Pressure-Dependent Rate Rules for β-Scission Reaction Class of Hydroperoxyl Alkyl Hydroperoxyl Radicals (•P(OOH)2) in Normal-Alkyl Cyclohexanes Combustion.

Chemical kinetic studies of the β-scission reaction class of hydroperoxyl alkyl hydroperoxyl radicals (•P(OOH)2) from normal-alkyl cyclohexanes are carried out systematically through high-level ab initio calculations. Geometry optimizations and frequency calculations for all species involved in the reactions are performed at the B3LYP/CBSB7 level of theory. Electronic single-point energy calculations are calculated at the CBS-QB3 level of theory. Rate constants for the reactions of β-scission, in the temperature range of 500-1500 K and the pressure range of 0.01-100 atm, are calculated using transition state theory (TST) and Rice-Ramsberger-Kassel-Marcus/Master-Equation (RRKM/ME) theory taking asymmetric Eckart tunneling corrections and the one-dimensional hindered rotor approximation into consideration. The rate rules are obtained by averaging the rate constants of the representative reactions of this class. These rate rules can greatly assist in constructing more accurate low-temperature combustion mechanisms for normal-alkyl cyclohexanes.

Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study.

Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.

Oxidation pathways and kinetics of the 1,1,2,3-tetrafluoropropene (CF2CF-CH2F) reaction with Cl-atoms and subsequent aerial degradation of its product radicals in the presence of NO.

To give a comprehensive account of the environmental acceptability of 1,1,2,3-tetrafluoropropene (CF2CF-CH2F) in the troposphere, we have examined the oxidation reaction pathways and kinetics of CF2CF-CH2F initiated by Cl-atoms using the second-order Møller-Plesset perturbation (MP2) theory along with the 6-31+G(d,p) basis set. We also performed single-point energy calculations to further refine the energies at the CCSD(T) level along with the basis sets 6-31+G(d,p) and 6-311++G(d,p). The estimation of the relative energies and thermodynamic parameters of the CF2CF-CH2F + Cl reaction clearly shows that Cl-atom addition reaction pathways are more dominant compared to H-abstraction reaction pathways. The value of the rate coefficient for each reaction channel is calculated using the conventional transition state theory (TST) over the temperature range of 200-1000 K at 1 atm. The estimated overall rate coefficients for the title reaction are found to be 1.10 × 10-12, 1.21 × 10-10, and 1.13 × 10-8 cm3 per molecule per s via the respective calculation methods viz. MP2/6-31+G(d,p), CCSD(T)//MP2/6-31+G(d,p), and CCSD(T)/6-311++G(d,p)//MP2/6-31+G(d,p), at 298.15 K. Moreover, the calculated rate coefficients and percentage branching ratio values suggest that the Cl-atom addition reaction at the β-carbon atom is more preferable to that of the α-carbon addition to CF2CF-CH2F. Based on the rate coefficient values calculated by the three different methods, the atmospheric lifetime for the title reaction at 298.15 K is estimated. The radiative efficiency (RE) and Global Warming Potential (GWP) results of the title molecule show that its GWP would be negligible. Further, we have explored the degradation of its product radicals in the presence of O2 and NO. From the degradation results, we have found that CF2(Cl)COF, FCOCH2F, FCFO and FCOCl are formed as stable end products along with various radicals such as ˙CF2Cl and ˙CH2F. Therefore, these findings of kinetic and mechanistic data can be applied to the development and implementation of a novel CFC replacement.

Predicting Autoxidation of Sulfides in Drug-like Molecules Using Quantum Mechanical/Density Functional Theory Methods.

Autoxidation of drugs and drug-like molecules is a major concern in the development of safe and effective therapeutics. Because active pharmaceutical ingredients (APIs) that contain sulfur atoms can form sulfoxides under oxidative stress, predicting oxidative susceptibilities within an organic molecule can have a major impact in accelerating the compound's stability assessment. For investigation of a sulfur atom's oxidative stability, density functional theory (DFT) methods were applied to accurately predict S-O estimated bond dissociation enthalpies (BDEs) of sulfoxides. Our process employed B3LYP/6-31+G(d) for geometry optimization and frequency calculation, and we employed B3P86/6-311++G(2df,2p) to obtain electronic energies from single-point energy calculations. A total of 84 drug-like molecules containing 50 different sulfide scaffolds were used to develop a risk scale. Our results showed that when S-O BDE is less than 69 kcal/mol, the sulfur atom has low oxidative susceptibility. High oxidation risk occurs when the S-O BDE is greater than 75 kcal/mol. The risk scale was successful in predicting the relative propensities of sulfide oxidation among the small organic molecules and commercial drugs examined.

Utility of (MgO)12 nanocage as a chemical sensor for recognition of amphetamine drug: A computational inspection

DFT calculations on sensor-drug interactions are necessary for understanding binding mechanisms, predicting sensor performance, evaluating stability and reactivity, and rational design of sensor materials. We scrutinized the adsorption of amphetamine (AFE) on the pure magnesium oxide nano-cage (MgONC) by applying density functional theory. All geometries and single point energy computations were optimized at M06–2X/6–311 G (d, p). Furthermore, we performed an analysis of the natural bond orbital (NBO) and evaluated the values of partial natural charges. Additionally, we investigated donor-acceptor (D-A) interactions and examined the Wiberg bond index (WBI) in greater depth. The MgONC was capable of adsorbing AFE with greater strength with the energy of adsorption (Eads) of −48.19 kcal/mol (for stable configurations). Moreover, the NBO method demonstrated more effective D-A interactions between AFE and the MgONC. Based on the computations, for the most stable configuration, there was a substantial alteration in the HOMO-LUMO gap of the MgONC following the drug adsorption, thus increasing the electrical conductance (EC) of the MgONC. The sensing mechanism is related to the gap difference, which depends on the change in the EC. We adopted the conventional transition state theory for the prediction of recovery time. The computations indicated that the MgONC+ AFE configuration had a short recovery time for the desorption of AFE. Finally, based on our findings, we could conclude that the MgONC is an appropriate choice for the improvement of effective AFE sensors. DFT study of drug sensors will focus on enhancing sensitivity, selectivity, and stability while exploring novel materials and optimizing performance through theoretical simulations and analysis.

Understanding the binding interaction mechanism of i-motif with fluorophores: A biophysical approach

DNA exists in many canonical and non-canonical forms. i-motif: a non-canonical, tetraplex, antiparallel strand rich in cytosine, formed by hemi protonated cytosine- cytosine+ base pairs under slightly acidic pH levels, i-motifs are utilised in the study of numerous fields of applications. These i-motif tend to exhibit the property of switching the fluorescent nature of ligands such as thiazole orange, crystal violet and berberine upon interaction. This work is focussed on a basic overview of i-motif and its interactions with ligands to form fluorescence probes which could be useful in bio imaging. Herein, we are trying to find the electronic properties of small molecules upon interacting with i-motif. In order to find the active binding site in i-motif, Molecular Docking simulation was performed. The best docked pose obtained from the docking studies were subjected to molecular dynamics simulations. Further, DFT studies, optimization and single point energy calculations were carried out for freeligands and those bounded with the secondary DNA structures to understand the intermolecular interaction and to study their electronic properties.

A theoretical kinetic study of 1-butyne, 2-butyne, and 3-methyl-1-butyne combustion

Propargylic radicals are an essential component in molecular weight growth kinetics and can react to form polycyclic aromatic hydrocarbons and soot. To establish rate rules for propargylic radicals, a total of 16 H-atom abstraction reactions of three alkynes, namely 1-butyne (1-C4H6), 2-butyne (2-C4H6), and 3-methyl-1-butyne (C5H8), were calculated using high-level quantum chemistry, in which four active radicals including Ḣ, ȮH, ĊH3, and HȮ2 were involved. Considering the completeness of the establishment of rate rules, the H-atom abstraction sites have included the primary and secondary site of 1-C4H6, primary site of 2-C4H6, and tertiary site of C5H8. The M06–2X/6–311++G(d,p) level of density function theory was used for the geometry optimization, vibrational frequency, and dihedral scan calculations. Single point energy calculations were carried out at the CCSD/cc-pVXZ (X = T, Q) level of coupled cluster theory. The rate coefficients for all of the abstraction reactions and the thermochemical quantities of 1-C4H6, 2-C4H6, and C5H8 and their corresponding radical products were calculated. The results indicate that H-atom abstraction by ȮH radicals has the fastest reaction rates for all three species. Moreover, abstraction from the tertiary site on C5H8 is the fastest, followed by abstraction of secondary hydrogen atoms on 1-C4H6 and primary hydrogen atoms on 2-C4H6, while abstraction of primary hydrogen atoms on 1-C4H6 are the slowest. NUIGMech1.3 (mechanism of version 1.3 proposed by National University of Ireland, Galway) has been updated based on our calculations, and ignition delay times (IDTs) were predicted using the updated mechanism. The predicted IDTs gave better agreement with the experiment data at pressures of 1, 30 and 50 bar. Sensitivity analyses were performed to understand observed model predicted differences at low to intermediate temperatures (700–1000 K) at 10 bar. The results show that the reactions 1-C4H6/2-C4H6 + HȮ2 and HȮ2 + HȮ2<=> H2O2 + O2 have a significant effect on promoting and inhibiting reactivity, respectively. Further Flux analyses show that the H-atom abstraction from 1-C4H6 and 2-C4H6 by ȮH radical is a dominant channel in changing branching ratios.

Synthesis, structural characterizations and theoretical calculations of the Ni(II) complex based on a novel Salamo-Salen-Salamo-type hybrid ligand

The Salen compound is a typical Schiff base ligand, and by combining one Salen-structure unit with two Salamo-structure units, a novel hybrid Salamo-Salen-Salamo-type ligand H4L was synthesized. The synthesis of corresponding complexes based on the hybrid ligand was studied. Ni(II) ion participates in coordination and synthesizes a hybrid Salamo-Salen-Salamo-type mononuclear complex [Ni(LH2)]. X-ray single crystal diffraction analysis showed that Ni(II) ion has coordinated with Salen N2O2 structure, forming a planar geometry with tetracoordination. The Salamo structure units are not involved in coordination, and two Salamo long chains are spatially close to each other and there are N, O atoms that are easy to coordinate with metals, forming a potential coordination environment. The spectral properties of the complex was further discussed by IR and UV-vis spectroscopy, and the binding ratio of the ligand H4L to Ni(II) ion in solution was verified by UV-vis titration spectroscopy. Through the structural optimization of the ligand and single-point energy calculation of the complex, the HOMO-LUMO gaps of the ligand and the complex were analyzed to determine the softness of the ligand and the complex. TD-DFT analysis of the ligand and its complex was found to be consistent with experimental results, and the energy level transition sources of the main absorption peaks and their contributions were analyzed. The interaction force within the molecule of the Ni(II) complex was calculated, and finally the movable free region of the complex molecule in the unit cell was calculated and displayed.

Rational design of molecularly imprinted polymers for the recognition of geosmin: A computer-aided and experimental study

Dummy molecularly imprinted polymers (DMIPs) were prepared by combining the molecular imprinting technique with computer simulation for the selective adsorption of geosmin (GSM). The most stable geometric configuration and single-point energy calculations of the molecules were determined by the density functional theory (DFT) method at the M06–2X/6–31 + G (d, p) and the M06–2X/def2-TZVP level, respectively. Meanwhile, the binding energy at different monomer ratios (1:1, 1:2, 1:3 and 1:4) between dummy template with monomer was calculated. According to the theoretical studies, DMIPs materials were synthesized using methacrylic acid (MAA) as the functional monomer, forming a stable molecular/monomer complex in a 1:3 ratio. The DMIPs were characterized using infrared spectroscopy, scanning electron microscopy, and thermogravimetric analysis. The theoretical adsorption capacity (Qmax) of the obtained DMIPs was 1.23 mg g −1, it was approximately twice that of non-imprinted polymers (NIPs). Additionally, the results of the kinetic experiments showed that the DMIPs achieved adsorption equilibrium within 90 min. The combination of computational simulation and experimental approach can shorten the preparation cycle of DMIPs and improve their performance, enabling its efficient application in the analysis of actual samples.

Deciphering the non-covalent interactions in the furan⋯hexane complex using rotational spectroscopy and theoretical analyses.

The rotational spectrum of a binary complex formed between furan and n-hexane was investigated using a chirped pulse Fourier transform microwave spectrometer in the range of 2-6GHz. While furan has only one conformer, n-hexane exists in multiple conformations. The conformational landscape of the binary complex was systematically explored by using a semiempirical conformational search tool, namely CREST. The CREST conformational candidates were subjected to further geometry optimization and harmonic frequency calculations at the B3LYP-D3BJ/def2-TZVP level of theory, resulting in 34 minima within an energy window of 5 kJ mol-1. The three most stable furan⋯hexane minima all contain the most stable n-hexane conformer subunit and are separated by relatively low conformational conversion barriers. Additional calculations were carried out to support the conclusive identification of the global minimum structure responsible for the set of assigned rotational transitions. These include calculations at the B3LYP-D3BJ level with the aug-cc-pVTZ and 6-311++G(d,p) basis sets and the MP2/def2-TZVP level, as well as the single point energy calculations at the CCSD(T)-F12/cc-pVDZ level. Further non-covalent interaction and principal interacting orbital analyses show that the synergy of the πfuran → σ*hexane and σhexane → π*furan interactions plays an important role in stabilizing the observed furan-hexane conformer.

Investigation Of Spectroscopic And Electronic Properties Of Some Schiff Basesderived From 2-Hydroxy-3-Methoxy-5-Nitrobenzaldehyde By Dft Method

In this study, the theoretical spectroscopic and some electronic properties of MMP and FMP compounds were investigated and the obtained theoretical results were compared with some experimental values. For this purpose, firstly, MMP and FMP compounds were optimized by DFT method using the B3LYP functional and the 6-311G++(d,p) basis set. With the help of the optimized structure obtained, the chemical shift values of H-NMR and 13C-NMR were calculated in the gas phase by the Gaussian G09 (Linux) and Gauss View 5.0 programs according to the GIAO method. According to the results obtained, it was seen that the theoretical values were compatible with the experimental values. In the theoretical part of the study, the IR frequency values of the studied compounds were calculated using the same method and basis set, and vibration frequencies were marked. Finally, the nonlinear optical properties of the compounds of interest; Polarizability and hyperpolarizability values were calculated by making polar calculations in the single point energy calculation. As a result of the calculations, the energy band gaps between the HOMO and LUMO orbitals of MMP and FMP are 1.34 eV and 3.64 eV. First static hyperpolarizability of MMP and FMP were found as 29273.7 x10-33 and 26500.5 x10-33 esu, repectively.

Hydrogen production and storage through adsorption and dissociation of H2O on pristine and functionalized SWCNT: a DFT approach.

Adsorption of 1 and 2 H2O molecules for hydrogen production and storage on the surface of pristine, carbamic acid and 2-amino 3-acetylpyridine functionalized SWCNTs with the dimensionality of (2, 4), (5, 5), and (6, 0) at various positions, i.e., center and edges were investigated by using computational DFT calculations. Adsorption energies and structural and electronic parameters were determined for pristine and functionalized SWCNTs with four different H2O orientations. Functionalization of 2-amino 3-acetylpyridine resulted in more favorable adsorption energies for 1 and 2 H2O molecules splitting as compared to spitting on pristine and carbamic acid functionalized SWCNT. Calculated adsorption constant, Kad confirmed greater binding interactions of functionalized SWCNTs with 1 and 2 H2O molecules as compared to pristine SWCNT. Isosurface for the adsorption of 1 and 2 H2O molecules on pristine and functionalized SWCNTs elaborated altered electrophilic and nucleophilic character. Effect of H2O concentration was monitored to determine hydrogen storage capacity which was found to be 7.17 wt.% for thirty molecules. An important finding of study is production of Stone-Wales (SW) defect upon H2O adsorption leading to increase in hydrogen production and its storage capacity. The functionalization of topological defected SWCNTs provides distinctive applications of CNTs for gas storage purposes.t: METHODS: In the current study, First Principal Density Functional Theory (DFT) calculations were carried which provides greater computational efficiency as compared to many traditional quantum mechanical methods. SCME: ADF (2018) modeling suite software with in framework of DFT approach using exchange correlation (XC) LDA-GGA (Generalized Gradient Approximation) with PBE (Perdew, Burke and Ernzerhof) functional and DZ (Double beta) basis set was employed to investigate structural, energetic and electronic aspects of adsorption on the surface of pristine, carbamic acid and 2-amino 3-acetly pyridine functionalized SWCNTs. (2, 4), (5, 5) and (6, 0) SWCNTs were designed using Avogadro's software and were imported to SCM: ADF graphical interface and were optimized as adsorbent. Single point energy (SPE), geometry optimization and high accuracy frequency calculations were performed to determine energetic, electronic and thermodynamic characteristics and feasibility of adsorption using XC of GGA-PBE functional & DZ basis set.

Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input.

We implemented an ab initio CCS prediction workflow which incrementally refines generated structures using molecular mechanics, a deep learning potential, conformational clustering, and quantum mechanics (QM). Automating intermediate steps for a high performance computing (HPC) environment allows users to input the SMILES structure of small organic molecules and obtain a Boltzmann averaged collisional cross section (CCS) value as output. The CCS of a molecular species is a metric measured by ion mobility spectrometry (IMS) which can improve annotation of untargeted metabolomics experiments. We report only a minor drop in accuracy when we expedite the CCS calculation by replacing the QM geometry refinement step with a single-point energy calculation. Even though the workflow involves stochastic steps (i.e., conformation generation and clustering), the final CCS value was highly reproducible for multiple iterations on L-carnosine. Finally, we illustrate that the gas phase ensembles modeled for the workflow are intermediate files which can be used for the prediction of other properties such as aqueous phase nuclear magnetic resonance chemical shift prediction. The software is available at the following link: https://github.com/DasSusanta/snakemake_ccs.

Probing the combustion kinetics of dimethylformamide: A theoretical study of H-atom abstraction reactions

The DMF vapor in the exhaust gas is needed to be recovered and incinerated to eliminate NOx emissions. This process will also provide the required heat for the production process. To verify the combustion chemistry of DMF in control of its ignition in fuel-lean combustion, 16H-atom abstraction reactions of DMF were systematically studied by high-level quantum chemical calculation in this work. The reactions include abstracting two types of H-atom from DMF molecule: H-atom of aldehyde and methyl groups respectively. Moreover, eight abstractors: Ḣ, ȮH, O2, ĊH3, CH3Ȯ, CH3OȮ, NO2, and HȮ2 were involved. In ab initio calculation, the M06-2X/6–311++G(d,p) method was used for geometry optimization, vibration frequency, and dihedral scan calculation. CCSD/cc-pVXZ (X = T, Q) method was employed for the single point energy (SPE) calculation. The rate constants of all abstraction reactions and the thermochemical quantities of the DMF and corresponding two radical products were carried out simultaneously. The calculation results show that abstracting the H-atom of the aldehyde group is dominant over the methyl group H-atom abstraction. Moreover, for both the aldehyde and methyl groups, H-atom abstraction, ȮH, Ḣ, and CH3Ȯ abstractors produce the fastest rates. From the application point of view, one detailed kinetic model of DMF was developed by adopting our calculation results. The model accurately predicts the ignition delay times (IDTs) of DMF at a wide range of temperatures and equivalence ratios. The sensitivity analysis indicates that the branching ratio of abstracting aldehyde group H-atom and methyl group H-atom is crucial for the reactivity prediction of DMF.