Single-point Energy Calculations Research Articles

An ANI-2 enabled open-source protocol to estimate ligand strain after docking.

In protein-ligand docking, the score assigned to a protein-ligand complex is approximate. Especially, the internal energy of the ligand is difficult to compute precisely using a molecular mechanics based force-field, introducing significant noise in the rank-ordering of ligands. We propose an open-source protocol (https://github.com/UnixJunkie/MMO), using two quantum mechanics (QM) single point energy calculations, plus a Monte Carlo (Monte Carlo) based ligand minimization procedure in-between, to estimate ligand strain after docking. The MC simulation uses the ANI-2x (QM approximating) force field and is performed in the dihedral space. On some protein targets, using strain filtering after docking allows to significantly improve hit rates. We performed a structure-based virtual screening campaign on nine protein targets from the Laboratoire d'Innovation Thérapeutique-PubChem assays dataset using Cambridge crystallographic data centre genetic optimization for ligand docking. Then, docked ligands were submitted to the strain estimation protocol and the impact on hit rate was analyzed. As for docking, the method does not always work. However, if sufficient active and inactive molecules are known for a given protein target, its efficiency can be evaluated.

Atmospheric Degradation Mechanism of Isoamyl Acetate Initiated by OH Radicals and Cl Atoms Revealed by Quantum Chemical Calculations and Kinetic Modeling.

Isoamyl acetate is one of the volatile organic compound class molecules relevant to agricultural and industrial applications. With the growing interest in isoamyl acetate applications in industry, the atmospheric fate of isoamyl acetate must be considered. Reaction mechanisms, potential energy profiles, and rate constants of isoamyl acetate reaction with atmospheric relevant oxidant OH radicals and Cl atoms have been obtained from the quantum chemical calculations and kinetic modeling. The geometry optimizations were conducted using M06-2X/6-311++G(3df,3pd) followed by single point-energy calculations at the DLPNO-CCSD(T) method with an extrapolated complete basis set. The rate constants were calculated by solving the master equation. A hydrogen-abstraction reaction dominates the first step of isoamyl acetate degradation, while the addition-substitution reaction plays a small role in the degradation products. The kinetic study was conducted to evaluate the rate constants within a temperature range of 200-400 K. The total rate constants for the isoamyl acetate degradation reactions initiated by the OH radical and Cl atom were determined to be 6.96 × 10-12 and 1.27 × 10-10 cm3 molecule-1 s-1, respectively, under standard temperature and pressure conditions. The product degradation mechanism, ozone formation potential, and atmospheric impacts were discussed.

Molecular interaction studies of L-proline in water and ethanol at different temperatures using dielectric relaxation, refractive index and DFT methods

The complex dielectric permittivity of L-Proline in water and ethanol solutions with molar concentrations ranging from 0.025 M to 0.15 M was measured by open-ended coaxial probe technique. The measurements were carried out across a frequency span of 0.02 < ν/GHz < 20 and temperatures varying from 298.15 K to 323.15 K. The densities (ρ) and refractive index (nD ) of the L-proline in aqueous and ethanol solutions were also determined to provide insights into the solute-solvent interactions in the system. The Havriliak-Negami equation was employed to compute the dielectric relaxation time of the mixtures. The relaxation time of L-Proline in an ethanol medium was found to be higher than that of L-Proline in an aqueous medium due to the greater degree of self-association of ethanol molecules. Additionally, the relaxation time of the mixtures lengthened with rising molar concentration, which is attributed to the presence of hydrogen bonds among L-Proline and aqueous/ethanol molecules. The strength of the hydrogen bond interaction of L-Proline in both mediums was calculated using single-point energy calculations employing IEFPCM/PCM solvation models through DFT/B3LYP and MP2 approaches with a 6-311 G ++ (d, p) basis set. The results were correlated with the hydrogen bond strength, Gibbs’ free energy of activation parameter, and dipole-dipole interactions. Communicated by Ramaswamy H. Sarma

Density functional theory guide for copolymerization mechanism between allyl radical with radicalophile: photo-driven radical mediated [3 + 2] cyclization.

The challenge of activating inert allyl monomers for polymerization has persisted, prompting our proposal of the photo-driven radical mediated [3 + 2] cyclization reaction (PRMC). This innovative approach significantly expedites the homopolymerization of multi-allyl monomers, enabling the synthesis of embolic microspheres for hepatocellular carcinoma interventions. PRMC involves allyl monomers to form allylic radicals and then radicals participating in a cycloaddition reaction with unsaturated olefins as radicalophiles to form cyclopentane-based radical products. While extensively studied in the theoretical and experimental homopolymerization, PRMC's application in copolymerization remains unexplored. To address this knowledge gap, we explored the elementary reaction, selecting allyl methyl ether radicals (AMER) and α,β-unsaturated ketones as radicalophiles for copolymerization investigations by density functional theory (DFT) analysis. We quantified energy differences between ground and excited states of reactants, elucidated frontier molecular orbitals, and assessed thermodynamic data for copolymerization feasibility. We also evaluated the electronic properties of reactants, predicting the reactivity of radicalophiles and the interactions of intermolecular reactions. Additionally, we applied transition state theory and interaction/deformation models and conducted a local orbital analysis to comprehensively study excess electron distribution and gyration radius of cyclic radical product. Our findings offer vital insights into PRMC's potential in copolymerization. This research provides a robust theoretical foundation for practical application, enhancing the polymerization field. Based on density functional theory (DFT), the calculations were performed at the M06-2X/6-311 + + G(d,p) level in/by Gaussian 16 package. Subsequently, our analytical results apply time-dependent density-functional theory (TD-DFT) and solvent modeling (SMD). Single-point energy calculations determine the driving force behind the radicals' reaction with radicalophiles. Furthermore, we assessed the electrostatic potential (ESP) of the reactants. The results of the calculations were visualized by the Multiwfn 3.6 and VMD 1.9 programs.

Theoretical kinetics study of key reactions between ammonia and fuel molecules, part II: H-atom abstraction from alcohols and ethers by ṄH2 radicals

Ammonia, as a carbon-free fuel, is expected to be a carbon-neutral alternative fuel to control pollution emissions. However, with lower reactivity, pure ammonia needs to be blended with highly reactive biofuels including alcohols and ethers, for a better combustion performance. Alcohols and ethers can be produced from various sources, including renewable materials and fossil fuels. Therefore, the combination of ammonia with alcohols/ethers is a promising choice for developing carbon-neutral energy solutions. As an important intermediate, ṄH2 radicals can easily be formed during the pyrolysis or oxidation processes for ammonia combustion. The H-atom abstraction reaction between ṄH2 radicals and fuel molecules is vital in determining the blending fuel reactivity. High-level ab initio calculations have been carried out in this study to perform a systematic theoretical chemical kinetic investigation of H-atom abstraction by ṄH2 radicals from C1–C5 alcohols, 2,3-dimethyl-2-butanol, C1–C4 ethers and methyl isobutyl ether with a total of 61 H-atom abstraction reaction channels. The QCISD(T)/CBS//M06–2X/6–311++G(d, p) level of theory was employed to investigate the potential energy surfaces of the title reactions involved. Electronic geometry optimization, frequency analysis, and zero-point energy correction were performed for reactants, transition states and products related to 61 reaction channels at the M06–2X/6–311++G(d, p) level of theory. Single-point energy calculations were performed at the QCISD(T)/cc-pVXZ (X = D, T) and MP2/cc-pVYZ (Y = D, T, Q) level of theory and then extrapolated to the complete basis set. Conventional transition state theory was used to calculate the rate constants for different channels in the temperature range from 500 to 2000 K. The calculated individual and average rate constants for H-atom abstraction from different sites of alcohols and ethers were also obtained to explore the kinetic influence from the functional group. This is the first systematic study providing the rate constants for the title reactions which can be used to develop the combustion kinetic models for ammonia/alcohols and ammonia/ethers blends.

Insight into the interaction between amino acids and SO2: Detailed bonding modes.

Amino acids are a highly effective and environmentally friendly adsorbent for SO2. However, there has been no comprehensive study of the binding modes between amino acids and SO2 at the molecular level. In this paper, the binding modes of three amino acids (Asp, Lys, and Val) with SO2 are studied comprehensively and in detail using quantum chemical calculations. The results indicate that each amino acid has multiple binding modes: 22 for Asp, 49 for Lys, and 10 for Val. Both the amino and carboxyl groups in amino acids, as well as those in side chains, can serve as binding sites for chalcogen bonds. The binding energies range from - 6.42 to - 1.06kcal/mol for Asp, - 12.43 to - 1.63kcal/mol for Lys, and - 7.42 to - 0.60kcal/mol for Val. Chalcogen and hydrogen bonds play a crucial role in the stronger binding modes. The chalcogen bond is the strongest when interacting with an amino group, with an adiabatic force constant of 0.475 mDyn/Å. Energy decomposition analysis indicates that the interaction is primarily electrostatic attraction, with the orbital and dispersive interactions dependent on the binding mode. Amino acids and complexes of amino acids with SO2 were used to do semi-empirical MD using Molclus combined with xtb at the GFN2 level. Optimization and frequency calculations of the structures were conducted using density-functional theory (DFT) B3LYP/6-311G* (with DFT-D3 correction). Single-point energy calculations were performed for all structures using DLPNO-CCSD(T)/aug-cc-pVTZ with tightPNO. Further analysis of the structures was conducted using ESP, AIM, IGMH, and sob-EDA to gain a deeper understanding of the interactions between amino acids and SO2.

Theoretical insights into enantioselective [2 + 1] cyclopropanation reactions of diazo compounds with electron-deficient olefins.

The cyclopropane skeleton plays a significant role in bioactive molecules due to its distinctive structural properties. This has sparked keen interest and in-depth exploration in the field of stereoselective synthesis of cyclopropane derivatives. In the present study, the mechanism and the origin of stereoselectivity of diastereodivergent synthesis of cyclopropane derivatives via the catalyst-free [2 + 1]-cyclopropanation reactions of 3-diazo-N-methylindole (R1) with two types of electron-deficient olefins (R2 and R3) in both aqueous and toluene media have been studied using the DFT calculations. The findings indicate that these [2 + 1] cycloaddition reactions proceed in two stages, where the first step is not only the rate-determining step but also critically dictates the stereoselectivity of the product. The calculated diastereomeric ratios are in agreement with the experimental results. Furthermore, by utilizing non-covalent interaction (NCI) analysis and energy decomposition analysis based on molecular force fields (EDA-FF), we elucidated that the electrostatic interactions between reactant fragments in the transition state TS1s for the first step are the predominant factors determining the stereoselectivity, as opposed to the experimentally hypothesized steric hindrance and π-π stacking interactions. The geometrical structures of all minima and transition states on the potential energy surface (PES) in solvents water and toluene were fully optimized using the DFT method at the M06-2X(D3)/SMD/6-31 + G(d,p) level of theory. Single-point energy calculations were carried out based on the optimized geometries in the solution at the M06-2X(D3)/6-311 + G(d,p) level. All the DFT calculations were performed using the Gaussian 09 software. The optimized molecular structures were visualized using CYLview software. NCI analysis was performed using the Multiwfn and VMD softwares. The Multiwfn program was also used for CDFT and EDA-FF analyses.

Exploration of Free Energy Surface of the Au10 Nanocluster at Finite Temperature.

The first step in comprehending the properties of Au10 clusters is understanding the lowest energy structure at low and high temperatures. Functional materials operate at finite temperatures; however, energy computations employing density functional theory (DFT) methodology are typically carried out at zero temperature, leaving many properties unexplored. This study explored the potential and free energy surface of the neutral Au10 nanocluster at a finite temperature, employing a genetic algorithm coupled with DFT and nanothermodynamics. Furthermore, we computed the thermal population and infrared Boltzmann spectrum at a finite temperature and compared it with the validated experimental data. Moreover, we performed the chemical bonding analysis using the quantum theory of atoms in molecules (QTAIM) approach and the adaptive natural density partitioning method (AdNDP) to shed light on the bonding of Au atoms in the low-energy structures. In the calculations, we take into consideration the relativistic effects through the zero-order regular approximation (ZORA), the dispersion through Grimme's dispersion with Becke-Johnson damping (D3BJ), and we employed nanothermodynamics to consider temperature contributions. Small Au clusters prefer the planar shape, and the transition from 2D to 3D could take place at atomic clusters consisting of ten atoms, which could be affected by temperature, relativistic effects, and dispersion. We analyzed the energetic ordering of structures calculated using DFT with ZORA and single-point energy calculation employing the DLPNO-CCSD(T) methodology. Our findings indicate that the planar lowest energy structure computed with DFT is not the lowest energy structure computed at the DLPN0-CCSD(T) level of theory. The computed thermal population indicates that the 2D elongated hexagon configuration strongly dominates at a temperature range of 50-800 K. Based on the thermal population, at a temperature of 100 K, the computed IR Boltzmann spectrum agrees with the experimental IR spectrum. The chemical bonding analysis on the lowest energy structure indicates that the cluster bond is due only to the electrons of the 6 s orbital, and the Au d orbitals do not participate in the bonding of this system.

Structural characterizations of histidine-containing tripeptides complexed with zinc and cadmium dications using IRMPD spectroscopy and theoretical calculations

Metalated gas-phase complexes, M2+(HisAlaAla), M2+(AlaHisAla), and M2+(AlaAlaHis), where M = Zn and Cd, were examined using infrared multiple photon dissociation (IRMPD) spectroscopy with light from a free-electron laser (FEL). These complexes were chosen because they provide model systems for metal binding to proteins. Complementary simulated annealing calculations were performed to determine energetically low-lying conformers and isomers of these structures. Quantum chemical calculations were used to optimize the structures at the B3LYP level of theory using 6-311+G(d,p) and def2-TZVP basis sets for zinc and cadmium complexes, respectively. IRMPD and calculated linear absorption spectra were compared to evaluate which structures are present. Relative energies of the various species were evaluated using single-point energy calculations for low-lying structures at the B3LYP, B3P86, and MP2(full) levels using 6-311+G(2d,2p) and def2-TZVPP basis sets. For species with histidine at a terminal position (AAH or HAA), the conformations that best reproduce the IRMPD spectra are charge-solvated (CS) conformers, where the metal dication binds to the amine and carbonyl groups of the peptide backbone and to the nitrogen of the histidine side chain, along with contributions from an iminol structure for AAH. The species with the histidine in the center position (AHA) adopt an iminol structure, where the metal dication binds to the backbone iminol nitrogens, the α-amine, π-imine, and the carbonyl of the C-terminus.

Quantum chemical pathways for the formation of 2,3,7,8-tetrachloro dibenzo-p-dioxin (TCDD) from 2,4,5-trichlorophenol: a mechanistic and thermo-kinetic study.

Dioxins, specifically 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (TCDD), are highly toxic dioxins known for their severe health impacts and persistent environmental pollutants. This study focuses on understanding the formation pathways of TCDD from its precursor molecule 2,4,5-trichlorophenol (2,4,5-TCP). In our exploration of reaction pathways from 2,4,5-trichlorophenol (TCP), we delve into three reaction mechanisms: free-radical, direct condensation, and anionic. Our findings highlight the significance of the radical mechanism, particularly propagated by H radicals, with a notable increase in dioxin formation around 900K. These results are consistent with experimental observations indicating an increase in the conversion of trichlorophenol from 600 to 900K in the non-catalytic gas phase reaction. Thermodynamic parameters (∆H, ∆S, and ∆G), reaction barriers, and rate constants (k) were calculated across a temperature range of 300-1200K to support the findings and provide insights into the optimal temperature range for controlling dioxins during the incineration process. In this study, quantum chemical calculations were conducted using density functional theory (DFT) with the B3LYP functional and the 6-311 + + G(d,p) basis set in Gaussian 16 software. Stationary points, including transition states (TS), were confirmed with frequency calculations. Intrinsic reaction coordinate (IRC) calculations ensured minimum energy paths between TS and products, visualized in GaussView 6.0 Program. Single-point energy calculations utilized a more precise basis set, 6-311 + + G(3df,2p), for enhanced energy accuracy, incorporating zero-point vibrational energy (ZPE) and other energy corrections. These calculations were repeated over a temperature range of 298.15-1200K at 1atm pressure. Finally, rate constant (k) expressions associated with TCDD formation were determined using transition state theory (TST).

On the fate of protonated chloroformates in the gas phase: a competition between forming HCl and chloroformic acid.

Chloroformates are prevalent in the atmosphere due to their utilization as fuel additives and industrial solvents. These species may undergo interactions with atmospheric water resulting in protonated chloroformates. This study delves into the gas-phase dissociation of these protonated species. Tandem mass spectrometry was employed to scrutinize the unimolecular dissociation of protonated methyl (1), ethyl (2), neopentyl (3), and phenyl chloroformate (4). Notably, 1 and 4 exhibited HCl loss, yielding CH3OCO+ and C6H5OCO+, respectively, with 1 additionally generating neutral methanol and ClCO+. 4 additionally loses CO and CO2. In contrast, 2 and 3 each only exhibit a single fragmentation channel, with 2 losing C2H4 to generate protonated chloroformic acid and 3 generating protonated 2-methylbutene by losing neutral chloroformic acid. Density functional theory at the B3LYP/6-311+G(d,p) level of theory was employed to explore minimum energy reaction pathways for each ion, and CBS-QB3 single-point energy calculations were added to provide reliable energetics. The Rice-Ramsperger-Kassel-Marcus (RRKM) calculations of the rate constants for selected competing processes were carried out to link theory and experiment. One common unimolecular process observed was the 1,3-H shift of the proton from the carbonyl oxygen to the ester oxygen before dissociation.

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.

Theoretical and kinetic study of the H-atom abstraction reactions by Ḣ atom from alkyl cyclohexanes.

Reaction kinetics of hydrogen atom abstraction from six alkyl cyclohexanes, methyl cyclohexane (MCH), ethyl cyclohexane (ECH), n-propyl cyclohexane (nPCH), iso-propyl cyclohexane (iPCH), sec-butyl cyclohexane (sBCH) and iso-butyl cyclohexane (iBCH), by the Ḣ atom are systematically studied in this work. The M06-2X method combined with the 6-311++G(d,p) basis set is used to perform geometry optimization, frequency analysis and zero-point energy calculations for all species. The intrinsic reaction coordinate (IRC) calculations are performed to confirm the transition states connecting the reactants and products correctly. One-dimensional hindered rotors are used to treat the low frequency torsional models with potentials scanned at the M06-2X/6-31G level of theory. Electronic single-point energy calculations for all reactants, transition states, and products are performed at the QCISD(T)/CBS level of theory. High-pressure limiting rate constants of 39 reaction channels are obtained using conventional transition state theory with asymmetric Eckart tunneling corrections in the temperature range 298.15-2000 K. Reaction rate rules for H-atom abstraction by the Ḣ atom from alkyl cyclohexanes on primary, secondary and tertiary carbon sites on both the side chain and ring are provided. The obtained rate constants are given by the Arrhenius expression in the temperature range 500-2000 K, which can be used for the combustion kinetics model development for alkyl cyclohexanes.