Steepest descent reaction path integration using a first-order predictor–corrector method

Atmospheric oxidation pathways of CF3CH2CFCl2 (HCFC-234fb) with OH-radicals and Cl-atoms: insights into the mechanism, thermodynamics, and kinetics

The atmospheric oxidation of 1,1-dichloro-1,3,3,3-tetrafluoropropane, HCFC-234fb (DTP), leads to the formation of harmful radicals, contributing to stratospheric ozone depletion. Thus, a detailed study of the gas-phase oxidation of the first-generation chlorofluorocarbon alternative HCFC-234fb by a reaction with hydroxyl radicals and chlorine atoms is important to understand its harmful effects on the environment. In this work, we have performed quantum chemical calculations to investigate the thermodynamic and kinetic aspects of the titled reaction. The potential energy profile calculated at the CCSD(T)/aug-cc-pVTZ//MP2/cc-pVTZ level of theory shows that the major reaction pathway involves the abstraction of the H-atom from the central carbon atom, C2, giving rise to the product radical CF3C˙HCCl2F. The calculated rate-coefficients for the reaction with ˙OH and Cl-atoms are 3.89 × 10-15 and 2.54 × 10-17 cm3 molecule-1 s-1, respectively, at 298 K and are in accordance with the experimental rate coefficients. The results suggest that the rate-coefficient for the reaction of DTP with ˙OH is two orders of magnitude higher than that with Cl-atoms, indicating greater significance of the former reaction in the atmosphere. With the rate-coefficient values, the lifetime and the radiative efficiency were calculated to be 8.2 years and 0.246 W m-2 ppb-1, respectively. A 100-year global warming potential (GWP) of 712 was also estimated using the lifetime corrected radiative efficiency value.

Investigating the Atmospheric Fate and Kinetics of OH Radical-Initiated Oxidation Reactions for Epoxybutane Isomers: Theoretical Insight

Epoxides, which belong to the category of oxygenated volatile organic compounds (OVOCs), are emitted into the atmosphere by an array of sources and can impact both human and environmental well-being significantly. This study involves comprehensive computational analyses aimed at investigating the mechanism, thermodynamic aspects, and reaction kinetics associated with hydrogen abstraction reactions of cis-2,3-epoxybutane, trans-2,3-epoxybutane, and 1,2-epoxybutane by OH radicals. The potential energy diagrams involving all of the species for each specific pathway were constructed at the CCSD(T)/aug-cc-pVTZ//M06-2X/cc-pVTZ level of theory. The rate coefficients for all possible pathways were calculated using the Rice-Ramsperger-Kassel-Marcus master equation (RRKM-ME) corrected by Eckart tunneling within the 200-350 K temperature range and 1 atm pressure. The overall rate coefficients of the reaction of cis-2,3-epoxybutane, trans-2,3-epoxybutane, and 1,2-epoxybutane with OH radicals at 298.15 K were found to be 0.32 × 10-12, 0.33 × 10-12, and 0.66 × 10-12 cm3 molecule-1 s-1, respectively. We also studied the atmospheric lifetime and photochemical ozone creation potential (POCP) of all three compounds. In addition, we have provided extensive degradation pathways for the product radicals formed from the initial reaction with OH radicals in the presence of O2 and NO. The study showed that the product radicals can result in various harmful end products, including grade 1 and grade 2 carcinogens, as listed by the World Health Organization (WHO).

New insights into the mechanism and kinetics of the addition reaction of unsaturated Criegee intermediates to CF3COOH and tropospheric implications

In this work, we have investigated the mechanism, thermochemistry and kinetics of the reaction of syn-cis-CH2RzCRyCO+O- (where Rz, Ry = H, CH3-) unsaturated Criegee intermediates (CIs) with CF3COOH using quantum chemical methods. The rate coefficients for the barrierless reactions were calculated using variable reaction coordinate variational transition state theory (VRC-VTST). For the syn-cis-CH2RzCRyCO+O- conformation in which conjugated CC and CO double bonds are aligned with each other, we propose a new pathway for the unidirectional addition of an OC-OH molecule (CF3COOH) to the CC double bond of syn-cis-CH2RzCRyCO+O-. The rate coefficient for the 1,4-CC addition reaction at 298 K is ∼10-10 to 10-11 cm3 s-1, resulting in the formation of CF3C(O)OCH2CRzRyCOOH trifluoroacetate alkyl allyl hydroperoxide (TFAAAH) as a new transitory adduct. It can act as a precursor for the formation of secondary organic aerosols (SOAs). This novel TFAAAH hydroperoxide was identified through a detailed quantum chemical study of the 1,4-addition mechanism and will provide new insights into the significance of the 1,4-addition reaction of unsaturated Cls with trace tropospheric gases on -CRzCH2 vinyl carbon atoms.

Laser induced fluorescence and computational studies on the tropospheric photooxidation reactions of methyl secondary butyl ether initiated by OH radicals

The kinetics of the reaction of methyl secondary butyl ether with OH radicals was investigated experimentally using the pulsed laser photolysis-laser induced fluorescence technique (PLP-LIF) over temperatures ranging from 268 to 363 K. The rate coefficient value at 298 K was measured to be (1.09 ± 0.02) × 10-11 cm3 molecule-1 s-1 and the deduced Arrhenius expression is [Formula: see text]= (2.21 ± 0.29) × 10-12 exp ((471.71 ± 38.50)/T) cm3 molecule-1 s-1. To complement the experimental data, the kinetic study of the title reaction was performed computationally at CCSD(T)/cc-pVTZ//M06-2X/6-311 + G(d,p) level of theory with the incorporation of tunnelling correction from 200 to 400 K. The end products formed were qualitatively analyzed by using gas chromatography equipped with mass spectrometry (GC-MS) as detection technique and the mechanism for degradation was proposed. Thermochemical parameters were evaluated to determine the feasibility of individual reaction pathways. Atmospheric implications were evaluated and discussed in this manuscript.

Biocomputational characterisation of MBO_200107 protein of Mycobacterium tuberculosis variant caprae: a molecular docking and simulation study

The principal objective of this study was to delineate the potentiality of the MBO_200107 protein from the Mycobacterium tuberculosis variant caprae in cancer research. It is a cytoplasmic protein, comprised of a 354-long amino acid chain, alkaline, had a molecular weight of 39089.37 Da, an isoelectric point of 9.62 and a grand average of hydropathicity of -0.345. One of the functional domains was predicted as Gammaglutamylcyclotransferase (GGCT). Among tertiary structures, the Modeller and Phyre2 model satisfied all the quality parameters, though they are truncated; contrarily, the I-TASSER model is full length and contains the sequence for the GGCT domain, though it did not meet all the quality parameters. It also has significant sequence similarities (47.5% by EMBOSS Water and 72.4% by EMBOSS Matcher) with a human GGCT, and the conserved sequences are confined to the GGCT domain of the MBO_200107. According to molecular docking analyses, the protein has a binding affinity of -4.8 kcal/mol by Autodock Vina and -56.465 kcal/mol by HPEPDOCK to the human glutathione (GSH), an essential metabolite for GGCT metabolism. The Molecular dynamic simulation of the docked complex showed the binding efficiency of the GSH to MBO_200107 with a minimal structural alteration. The in silico findings mentioned above revealed that the protein could be used as a supplementary tool in cancer research, such as designing vaccines or drugs where the role of GGCT has been implicated. Further, we recommend fully characterising the protein and conducting essential in vitro and in vivo experiments to determine its detailed usefulness.Communicated by Ramaswamy H. Sarma.

In Silico Functional Characterization of a Hypothetical Protein From Pasteurella Multocida Reveals a Novel S-Adenosylmethionine-Dependent Methyltransferase Activity

Genomes may now be sequenced in a matter of weeks, leading to an influx of "hypothetical" proteins (HP) whose activities remain a mystery in GenBank. The information included inside these genes has quickly grown in prominence. Thus, we selected to look closely at the structure and function of an HP (AFF25514.1; 246 residues) from Pasteurella multocida (PM) subsp. multocida str. HN06. Possible insights into bacterial adaptation to new environments and metabolic changes might be gained by studying the functions of this protein. The PM HN06 2293 gene encodes an alkaline cytoplasmic protein with a molecular weight of 28352.60 Da, an isoelectric point (pI) of 9.18, and an overall average hydropathicity of around -0.565. One of its functional domains, tRNA (adenine (37)-N6)-methyltransferase TrmO, is a S-adenosylmethionine (SAM)-dependent methyltransferase (MTase), suggesting that it belongs to the Class VIII SAM-dependent MTase family. The tertiary structures represented by HHpred and I-TASSER models were found to be flawless. We predicted the model's active site using the Computed Atlas of Surface Topography of Proteins (CASTp) and FTSite servers, and then displayed it in 3 dimensional (3D) using PyMOL and BIOVIA Discovery Studio. Based on molecular docking (MD) results, we know that HP interacts with SAM and S-adenosylhomocysteine (SAH), 2 crucial metabolites in the tRNA methylation process, with binding affinities of 7.4 and 7.5 kcal/mol, respectively. Molecular dynamic simulations (MDS) of the docked complex, which included only modest structural adjustments, corroborated the strong binding affinity of SAM and SAH to the HP. Evidence for HP's possible role as an SAM-dependent MTase was therefore given by the findings of Multiple sequence alignment (MSA), MD, and molecular dynamic modeling. These in silico data suggest that the investigated HP might be used as a useful adjunct in the investigation of Pasteurella infections and the development of drugs to treat zoonotic pasteurellosis.

Multiple evaluations of atmospheric behavior between Criegee intermediates and HCHO: Gas-phase and air-water interface reaction

Given the high abundance of water in the atmosphere, the reaction of Criegee intermediates (CIs) with (H₂O)₂ is considered to be the predominant removal pathway for CIs. However, recent experimental findings reported that the reactions of CIs with organic acids and carbonyls are faster than expected. At the same time, the interface behavior between CIs and carbonyls has not been reported so far. Here, the gas-phase and air-water interface behavior between Criegee intermediates and HCHO were explored by adopting high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations. Quantum chemical calculations evidence that the gas-phase reactions of CIs + HCHO are submerged energy or low energy barriers processes. The rate ratios speculate that the HCHO could be not only a significant tropospheric scavenger of CIs, but also an inhibitor in the oxidizing ability of CIs on SO_x in dry and highly polluted areas with abundant HCHO concentration. The reactions of CH₂OO with HCHO at the droplet's surface follow a loop structure mechanism to produce i) SOZ (), ii) BHMP (HOCH₂OOCH₂OH), and iii) HMHP (HOCH₂OOH). Considering the harsh reaction conditions between CIs and HCHO at the interface (i.e., the two molecules must be sufficiently close to each other), the hydration of CIs is still their main atmospheric loss pathway. These results could help us get a better interpretation of the underlying CIs-aldehydes chemical processes in the global polluted urban atmospheres.

Photo-oxidation reaction of tert-butyl chloride with OH radicals and Cl atoms in the troposphere and its implications

In the present work, the temperature-dependent kinetics for the reaction of tert-butyl chloride (TBC) with OH radicals and Cl atoms were determined experimentally between 268 and 363 K, and theoretically between 200 and 400 K. Pulsed laser photolysis-laser induced fluorescence (PLP-LIF) and relative rate (RR) methods were used to obtain the rate coefficients for the reaction of TBC with OH radicals and Cl atoms, respectively. The Arrhenius equations and were obtained for both reactions based on the experimentally measured rate coefficients. The theoretical rate coefficients were determined at the CCSD(T)/aug-cc-pVTZ//M06-2X/6-31+G(d,p) level for the reaction of TBC with OH radicals and at the CCSD(T)/cc-pVDZ//MP2/6-311+G(d,p) level for the reaction with Cl atoms with incorporated tunnelling corrections. The product analysis of both reactions in the presence of oxygen (O₂) was carried out, and a degradation pathway for TBC was proposed. The potential implications of these reactions in the atmosphere were discussed using the obtained kinetic parameters.

Unraveling photo-induced proton transfer mechanism and proposing solvent regulation manner for the two intramolecular proton-transfer-site BH-BA fluorophore

To expound specific excited state processes of the novel excitation wavelength dependent emission BH-BA fluorophore for better subsequent applications, this wok mainly focus on exploring photo-induced hydrogen bonding geometrical changes, excited state intramolecular proton transfer (ESIPT) mechanism and related regulated behavior via solvent polarity. The differences of structural parameters, infrared (IR) vibrational spectra, core-valence bifurcation (CVB) index as well as electronic densities ρ(r) between S₀ and S₁ states related to dual hydrogen bonds (O₁-H₂···N₃ and O₄-H₅···N₆) reveal S₁-state hydrogen bonding strength facilitate ESIPT behaviors for BH-BA system. Of particular note, O₄-H₅···N₆ plays a more dominant role. Photo-induced intramolecular charge transfer (ICT) and variations of Hirshfled and NPA charges over atoms related to hydrogen bonding moieties promote the ESIPT tendency for BH-BA. Combined potential energy surfaces (PESs), transition state (TS) and intrinsic reaction coordinate (IRC) paths, we illustrate the excited state intramolecular single proton transfer (ESISPT) mechanism of BH-BA should occur along with O₄-H₅···N₆ hydrogen bonding wire, which could be adjusted by surrounding solvent polarity.

A comparable DFT study on reaction of CHCl•- with O3 and S2O

CONTEXT

In this discussion, we began building two model, S₂O + CHCl^•- and O₃ + CHCl^•-, using DFT-BHandHLYP method, to study their reactions mechanisms on singlet PES. For this purpose, we hope to explore the effects of the difference between sulfur and oxygen atoms on the CHCl^•- anion. Experimentalists and computer scientists may utilize the collected data to generate a wide range of hypotheses for experimental phenomena and predictions, allowing them to realize their full potential.

METHODS

The ion-molecule reaction mechanism of CHCl^•- with S₂O and O₃ was studied using the DFT-BHandHLYP level of theory with the aug-cc-pVDZ basis set. Our theoretical findings show that Path 6 is the favored reaction pathway for CHCl^•- + O₃ reaction as identified by the O-abstraction reaction pattern. Comparing to the direct H- and Cl-abstraction mechanisms, the reaction (CHCl^•- + S₂O) prefers the intramolecular S_N2 reaction pattern. Moreover, the calculated results demonstrated that the CHCl^•- + S₂O reaction is thermodynamically more favorable than the CHCl^•- + O₃ reaction, which is kinetically more advantageous. As a result, if the required reaction condition in the atmospheric process is met, the O₃ reaction will happen more effectively. In terms of kinetics and thermodynamics viewpoints, the CHCl^•- anion was very effective in eliminating S₂O and O₃.

Kinetics of IO radicals with C1, C2 aliphatic alcohols in tropospherically relevant conditions

Kinetics of the reaction of IO radicals with methanol (MeOH) and ethanol (EtOH) were experimentally studied in the gas phase using pulsed laser photolysis-cavity ring-down spectroscopy (PLP-CRDS). IO radicals were produced in situ at the reaction zone by photolysing a mixture of precursors (CH₃I + O₃ + N₂) at 248 nm and thereby electronically excited at 445.04 nm. The rate coefficients for the reactions of (IO + MeOH) and (IO + EtOH) were measured at a total pressure of 60 Torr/N₂ in the range of 258-360 K. At room temperature, the experimental rate coefficients of the title reactions were measured to be [Formula: see text] and [Formula: see text]. Dependencies of the kinetics with photolysis laser fluence and experimental pressures were verified. Effects of pressure over the kinetic behaviour of the studied systems were observed to be insignificant within the statistical uncertainties when studied in the range of ~ 30-150 Torr/N₂, whereas a minor and linear fluence dependency was observed within the studied limit. From the measured kinetic parameters, the atmospheric lifetimes of MeOH and EtOH were calculated in the tropospherically relevant conditions regarding their reactions with important atmospheric oxidants like Cl atom, OH and IO radicals. To complement experimental results, kinetics and thermochemistry for the title reactions were investigated theoretically via canonical variational transition state (CVT) theory in combination with small curvature tunnelling (SCT) corrections with a dual-level Interpolated Single Point Energy (ISPE) approach at the CCSD(T)/def2-QZVPP//M06-2X/def2-TZVPP level of theory/basis set in the temperatures between 200 and 400 K. Good degree of agreement was encountered between experimentally measured and theoretically calculated rate coefficients. This article also discusses the thermochemical parameters and kinetic branching ratios (BRs) of all the pathways involved in the title reactions.

Identification of potential inhibitors of omicron variant of SARS-Cov-2 RBD based virtual screening, MD simulation, and DFT

Emergence of the SARS-CoV-2 Omicron variant of concern (VOC; B.1.1.529) resulted in a new peak of the COVID-19 pandemic, which called for development of effective therapeutics against the Omicron VOC. The receptor binding domain (RBD) of the spike protein, which is responsible for recognition and binding of the human ACE2 receptor protein, is a potential drug target. Mutations in receptor binding domain of the S-protein have been postulated to enhance the binding strength of the Omicron VOC to host proteins. In this study, bioinformatic analyses were performed to screen for potential therapeutic compounds targeting the omicron VOC. A total of 92,699 compounds were screened from different libraries based on receptor binding domain of the S-protein via docking and binding free energy analysis, yielding the top 5 best hits. Dynamic simulation trajectory analysis and binding free energy decomposition were used to determine the inhibitory mechanism of candidate molecules by focusing on their interactions with recognized residues on receptor binding domain. The ADMET prediction and DFT calculations were conducted to determine the pharmacokinetic parameters and precise chemical properties of the identified molecules. The molecular properties of the identified molecules and their ability to interfere with recognition of the human ACE2 receptors by receptor binding domain suggest that they are potential therapeutic agents for SARS-CoV-2 Omicron VOC.

Experimental and Theoretical Investigation of Reactions of Formyl (HCO) Radicals in the Gas Phase: (I) Kinetics of HCO Radicals with Ethyl Formate and Ethyl Acetate in Tropospherically Relevant Conditions

Formyl (HCO) radicals were generated in situ in the gas phase via the photolysis of glyoxal in N₂ at 248 nm using the pulsed laser photolysis-cavity ring-down spectrometry technique, and the absorption cross-section of the radical was measured to be σ_HCO = (5.3 ± 0.9) × 10^-19 cm² molecule^-1 at 298 K and 615.75 nm, which was the probing wavelength. The kinetics of the reactions of HCO radicals with ethyl formate (EF) and ethyl acetate (EA) were investigated experimentally in the temperature range of 260-360 (±2) K at a pressure of 60 Torr/N₂. The absolute rate coefficient for the reaction between HCO and EF was measured to be kHCO+EFExpt(298 K) = (1.39 ± 0.30) × 10^-14 cm³ molecule^-1 s^-1 at ambient temperature, whereas that for the reaction of HCO with EA was measured tobe kHCO+EATheory(298 K) = (2.05 ± 0.43) × 10^-14 cm³ molecule^-1 s^-1. The reaction of HCO with EA was faster than that with EF, which might be due to the greater stability of the formed radical intermediate due to hyperconjugative and inductive effects. The dependency of the measured kinetics on experimental pressures and laser fluences was examined within a certain range. To complement the experiments, kinetics of the title reactions in the temperature range of 200-400 K were deciphered theoretically via the canonical variational transition-state theory with small-curvature tunneling and interpolated single-point energy (CVT/SCT/ISPE) method using a dual-level approach at the CCSD(T)/cc-pVTZ//MP2/6-311++G(d,p) level of theory/basis set. A good degree of agreement was detected between the rate coefficients measured experimentally and those calculated theoretically both at room temperature and throughout the range of temperatures studied. The kinetic branching ratios and thermochemistry of the reactions were investigated to understand the thermodynamic feasibility and kinetic lability of each pathway throughout the studied temperatures. Atmospheric implications of these reactions of HCO radicals are also discussed.

Interplay of Steric Effects and Aromaticity Reversals to Expand the Structural/Electronic Responses of Dihydrophenazines

To gain insights into the coupling of conformational and electronic variables, we exploited steric hindrance to modulate a polycyclic skeleton with a bent conformation in the S₀ state and a twisted conformation in the S₁ state under the guidance of photoexcited aromaticity reversals. Polycyclic 5,10-dihydrophenazine (DHP) adopted a bent structure in S₀ but involved a bent-to-planar transformation in S₁ due to the excited-state aromaticity of the 8π-electron central ring. The N,N'-locations and 1,4,6,9-sites of the DHP skeleton provided a versatile chemical handle for fine-tuning intramolecular steric hindrance. Specifically, N,N'-diphenyl-5,10-dihydrophenazine (DPP-00) and its derivatives DPP-10-DPP-22 were synthesized with different numbers of methyl groups on the 1,4,6,9-sites. X-ray crystal analyses suggested that the DHP skeletons of DPP-00-DPP-22 had more bending configurations along the N···N axis with an increase in the number of methyl groups. Following the bending-promoted interruption of π-conjugation, the absorption spectra of DPP-00-DPP-22 significantly blue-shifted from 416 to 324 nm. By contrast, the emission bands exhibited a reverse shift to longer wavelengths from 459 to 584 nm as the number of methyl substituents increased. Theoretical calculations revealed that introducing methyl groups caused the planar DHP skeleton in S₁ to further twist along the N···N axis, resulting in a twisted high-strain conformation. The greater Stokes shift of the more steric-hindered structure can be attributed to the release of larger strain and aromatic stabilization energy. This research highlighted the potential promise associated with the interplay of steric effects and aromaticity reversals in a single fluorophore.

Assessing and rationalizing the performance of Hessian update schemes for reaction path Hamiltonian rate calculations

The reaction path Hamiltonian (RPH) can be used to calculate chemical reaction rate constants, going beyond transition-state theory in taking account of recrossing by providing an approximation to the dynamic transmission coefficient. However, the RPH necessitates the calculation of the Hessian matrix at a number of points along the minimum energy path; the associated computational cost stands as a bottleneck in RPH calculations, especially if one is interested in using high-accuracy electronic structure methods. In this work, four different Hessian update schemes (symmetric rank-1, Powell-symmetric Broyden, Bofill, and TS-BFGS updates) are assessed to see whether or not they reliably reproduce calculated transmission coefficients for three different chemical reactions. Based on the reactions investigated, the symmetric rank-1 Hessian update was the least appropriate for RPH construction, giving different transmission coefficients from the standard analytical Hessian approach, as well as inconsistent frequencies and coupling properties. The Bofill scheme, the Powell-symmetric Broyden scheme, and the TS-BFGS scheme were the most reliable Hessian update methods, with transmission coefficients that were in good agreement with those calculated by the standard RPH calculations. The relative accuracy of the different Hessian update schemes is further rationalized by investigating the approximated Coriolis and curvature coupling terms along the reaction-path, providing insight into when these schemes would be expected to work well. Furthermore, the associated computational cost associated with the RPH calculations was substantially reduced by the tested update schemes. Together, these results provide useful rules-of-thumb for using Hessian update schemes in RPH simulations.

Kinetics of IO radicals with ethyl formate and ethyl acetate: a study using cavity ring-down spectroscopy and theoretical methods

The gas-phase kinetics of the reactions of IO radicals with ethyl formate (EF) and ethyl acetate (EA) were investigated experimentally using cavity ring-down spectroscopy (CRDS). IO radicals were generated in situ in the CRD reaction zone by photolyzing a mixture of (CH₃I + O₃ + N₂) at 248 nm and thereby probed at 445.04 nm. The rate coefficients for the reactions (IO + EF) and (IO + EA) were measured at a total pressure of 65 Torr of N₂ in the temperature range of 258-358 and 260-360 K, respectively. The rate coefficients for the reactions (IO + EF) and (IO + EA) were measured experimentally at room temperature to be kExpt,298KIO+EF = (3.38 ± 0.67) × 10^-14 and kExpt,298KIO+EA = (1.56 ± 0.30) × 10^-13 cm³ molecule^-1 s^-1, respectively. The effects of pressure and photolysis laser fluence on the kinetics of test reactions were found to be negligible within the experimental uncertainties for the studied range. To complement our experimental findings, the kinetics of the title reactions were investigated theoretically using canonical variational transition state theory (CVT) with small curvature tunnelling (SCT) at the CCSD(T)//M06-2X/def2-SV(P) level of theory in temperatures between 200 and 400 K. Very good agreement was observed between the experimentally measured and theoretically calculated rate coefficients for both the reactions at 298 K. The thermochemical parameters as well as the branching ratios for the title reactions are also discussed in this study.

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this "on-the-fly" approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. This approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH₂O → H₂ + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

A Combined Experimental and Theoretical Study to Determine the Kinetics of 2-Ethoxy Ethanol with OH Radical in the Gas Phase

The reactivity of 2-ethoxy ethanol with OH radicals was experimentally measured in the temperature range of 278-363 K using the pulsed laser photolysis-laser-induced fluorescence (PLP-LIF) technique. The rate coefficient at room temperature was measured to be (1.14 ± 0.03) × 10^-11 cm³ molecule^-1 s^-1, and the Arrhenius expression was derived to be k_expt^278-363K = (1.61 ± 0.35) × 10^-13 exp{(1256 ± 236)/T} cm³ molecule^-1 s^-1. Computational calculations were performed to compute the kinetics of the titled reaction in the temperature range of 200-400 K using advanced methods incorporated with tunneling correction at the CCSD(T)/aug-cc-pVTZ//M06-2X/6-31+G(d,p) level of theory. The Arrhenius expression derived from the computationally calculated rate coefficients is k_theo^200-400K = (1.59 ± 0.35) × 10^-13exp{(1389 ± 62)/T} cm³ molecule^-1 s^-1. The feasibility of each reaction pathway was also determined using the calculated thermochemical parameters. Atmospheric implication parameters such as cumulative atmospheric lifetime and photochemical ozone creation potential were calculated and are discussed in this paper.

Computational investigations on kinetics of reaction between t-butanol and OH radical and ozone formation potential

The kinetics of the gas-phase atmospheric reaction of t-butanol with OH radicals is computationally studied using the CCSD(T)/aug-cc-pVTZ//M06-2X/6-311++G(d,p) level of calculation. The rate coefficients are evaluated for a wide temperature range of 250-1200 K and the calculated rate coefficient value of 0.83×10^-12cm³molecule^-1s^-1 at 298K is in close agreement with experimental results. The H-abstraction from the -CH₃ group is predicted to be the main reaction channel. A weak negative temperature dependence of rate coefficient is observed in 250-300 K. The study also highlighted the possibility of re-generation of OH radicals at higher temperature. The ozone formation potential of t-butanol in the troposphere has also been estimated and discussed.

Investigation of kinetics of phenyl radicals with ethyl formate in the gas phase using cavity ring-down spectroscopy and theoretical methodologies

The gas-phase kinetics of phenyl radical (^·C₆H₅) with ethyl formate (HCO₂Et, EF) was investigated experimentally using ultrasensitive laser-based cavity ring-down spectroscopy (CRDS). Phenyl radicals were generated by photolyzing nitrosobenzene (C₆H₅NO) at 248 nm and thereby probed at 504.8 nm. The rate coefficients for the (phenyl radical + EF) reaction were investigated between the temperatures of 260 and 361 K and at a pressure of 61 Torr with nitrogen (N₂) as diluent. The temperature-dependent Arrhenius expression for the test reaction was obtained as: [Formula: see text]=(1.20  ±  0.16) × 10^-13 exp[-(435.6  ±  50.0)/T] cm³ molecule^-1 s^-1 and the rate coefficient at room temperature was measured out to be: [Formula: see text]=(4.54  ±  0.42) × 10^-14 cm³ molecule^-1 s^-1. The effects of pressure and laser fluence on the kinetics of the test reaction were found to be negligible within the experimental uncertainties. To complement the experimental findings, kinetics for the reaction of phenyl radicals with EF was investigated theoretically using Canonical Variational Transition State Theory (CVT) with Small Curvature Tunnelling (SCT) at CCSD(T)/cc-pVDZ//B3LYP/6-31 + G(d,p) level of theory in the temperatures between 200 and 400 K. The theoretically calculated rate coefficients for the title reaction were expressed in the Arrhenius form as: [Formula: see text]= (1.48  ±  0.56) × 10^-38 × T^8.47 × exp[(2431.3  ±  322.0)/T] cm³ molecule^-1 s^-1 and the corresponding rate coefficient at room temperature was calculated to be: [Formula: see text]= 4.91 × 10^-14 cm³ molecule^-1 s^-1. A very good agreement was observed between the experimentally measured and theoretically calculated rate coefficients at 298 K. Thermochemical parameters as well as branching ratios for the reaction of (phenyl radical + EF) are also discussed in this manuscript.

Experimental and Computational Investigations of the Tropospheric Photooxidation Reactions of 1,1,1,3,3,3-Hexafluoro-2-Methyl-2-Propanol Initiated by OH Radicals and Cl Atoms

The gas-phase kinetics for the reactions of OH radicals and Cl atoms with 1,1,1,3,3,3-hexafluoro-2-methyl-2-propanol (HF2M2P) were measured at temperatures between 268 and 363 K using the relative rate experimental technique. Methane and acetonitrile were used as reference compounds to measure the rate coefficients of the title reactions. For the reactions of HF2M2P with OH radicals and Cl atoms, the rate coefficients were measured to be (7.07 ± 1.21) × 10^-15 and (2.85 ± 0.54) × 10^-14 cm³ molecule^-1 s^-1, respectively, at 298 K. The obtained Arrhenius expressions for the reactions of HF2M2P with OH radicals and Cl atoms are k_{HF2M2P + OH}^{Exp - (268 - 363 K)} = (7.84 ± 0.75) × 10^-14 exp [-(717 ± 59)/T] and k_{HF2M2P + Cl}^{Exp - (268 - 363 K)} = (3.21 ± 0.45) × 10^-12 exp [-(1395 ± 83)/T] cm³ molecule^-1 s^-1. In addition to the experimental measurements, computational kinetic calculations were also performed for the title reactions at the M06-2X/MG3S//M06-2X/6-31 + G(d,p) level of theory using advanced methods such as the canonical variational transition-state theory coupled with small curvature tunneling corrections at temperatures between 200 and 400 K. Theoretical calculations reveal that the H-abstraction from the CH₃ group is a more favorable reaction channel than that from the OH group. Thermochemistry, branching ratios, cumulative atmospheric lifetime, global warming potential, acidification potential, and photochemical ozone creation potential of HF2M2P were calculated in the present investigation.

Kinetic Investigations of the Reaction of Phenyl Radicals with Ethyl Acetate in the Gas Phase: An Experimental and Computational Study

Cavity ring-down spectroscopy (CRDS) was employed to investigate the kinetics of the reaction between phenyl radicals (C₆H₅^•) and ethyl acetate (EtOAc) in the gas phase. Nitrosobenzene (C₆H₅NO) was used as the radical precursor to generate C₆H₅^• at 248 nm, and the generated radicals were subsequently probed at 504.8 nm. The rate coefficients were investigated experimentally in the temperature range of 258-358 K with an interval of 20 K and at a total pressure of 55 Torr in the nitrogen atmosphere. The obtained Arrhenius expression for the title reaction (C₆H₅^• + EtOAc) in the temperature range of 258-358 K was k_{phenyl + EtOAc}^{Expt - (258 - 358 K)} = (9.33 ± 0.11) × 10^-16 exp[(883.7 ± 181.0)/T] cm³ molecule^-1 s^-1, and the rate coefficient at room temperature (298 K) was k_{phenyl + EtOAc}^{Expt - 298 K} = (2.20 ± 0.12) × 10^-14 cm³ molecule^-1 s^-1. Negligible effects of pressure and photolysis laser fluence were found on the experimentally measured rate coefficients. To complement our experimental findings, rate coefficients of the title reaction were computationally investigated employing the canonical variational transition-state theory with small curvature tunnelling (CVT/SCT) at the CCSD(T)/cc-pVDZ//B3LYP/6-31+G(d,p) level of theory in the temperature range of 200-400 K. The temperature-dependent rate coefficient in the studied temperature range was obtained to be k_{phenyl + EtOAc}^{Theory - (200 - 400 K)} = (7.68 ± 0.12) × 10^-17 exp[(1731.6 ± 216.0)/T] cm³ molecule^-1 s^-1, and the rate coefficient at 298 K was obtained as k_{phenyl + EtOAc}^{Theory - 298 K} = 2.45 × 10^-14 cm³ molecule^-1 s^-1. Both the experimentally measured and computed rate coefficients show good agreement at 298 K. A negative temperature dependency was observed for both the experimentally measured and computed rate coefficients. A detailed discussion of the thermochemical parameters and branching ratios of the title reaction are also presented in this Article.

Kinetic and Mechanistic Investigation for the Gas-Phase Tropospheric Photo-oxidation Reactions of 2,2,2-Trifluoroethyl Acrylate with OH Radicals and Cl Atoms

The photo-oxidation of 2,2,2-trifluoroethyl acrylate (TFEA) (CH₂CHC(O)OCH₂CF₃) initiated by OH radicals and Cl atoms was investigated in tropospheric conditions using both experimental and computational methods. The kinetic measurements were carried out in the temperature range of 268-363 K using the relative rate method. The rate coefficients for the reaction of OH radicals with TFEA were measured relative to diethyl ether, ethylene, and acetaldehyde. The rate coefficients for the reaction of Cl atoms with TFEA were measured relative to propylene and ethylene. The rate coefficients for the reaction of TFEA with OH radicals and Cl atoms at 298 K were experimentally measured to be k_R1^{exp - 298 K} = (1.41 ± 0.31) × 10^-11 cm³ molecule^-1 s^-1 and k_R2^{exp - 298 K} = (2.37 ± 0.50) × 10^-10 cm³ molecule^-1 s^-1, respectively. The deduced temperature-dependent Arrhenius expressions for the reactions of OH radicals and Cl atoms with TFEA are k_R1^{exp - (268 - 363 K)} = (9.82 ± 1.37) × 10^-12 exp. [(812 ± 152)/T] cm³ molecule^-1 s^-1 and k_R2^{exp - (268 - 363 K)} = (1.25 ± 0.17) × 10^-11 exp. [(862 ± 85)/T] cm³ molecule^-1 s^-1, respectively. To complement our experimental results, computational calculations were performed at CCSD(T)/cc-pVDZ//M062X/6-31+G(d,p) and CCSD(T)/cc-pVDZ//MP2/6-311+G(d,p) levels of theory, respectively, in combination with canonical variational transition-state theory (CVT) with small curvature tunneling (SCT) over the temperature range of 200-400 K. Furthermore, the degradation mechanisms initiated by OH radicals and Cl atoms were proposed for the titled reactions based on the qualitative analysis of the products in gas chromatography-mass spectrometry (GC-MS) and gas chromatography-infrared spectroscopy (GC-IR). Atmospheric implications, thermochemistry, and branching ratios for the titled reactions are discussed in detail in the paper.

CHF2CF2OCHF2: conformational analysis and direct dynamics study of its reaction with Cl atoms and atmospheric fate

Conformers of CHF₂CF₂OCHF₂ are identified, and the kinetics of its reaction with Cl atoms and final atmospheric degradation products are studied to assess atmospheric impact.

Atmospheric oxidation mechanism and kinetics of 2-bromo-4,6-dinitroaniline by OH radicals - a theoretical study

2-Bromo-4,6-dinitroaniline (BNA) is identified as a domestic-dust pollutant in urban environments, with deleterious atmospheric effects. In the present work, we studied the reaction pathways and kinetics for BNA oxidation by the OH radical using quantum-chemical methods and canonical-variational transition-state theory with small-curvature tunneling correction (CVT/SCT). OH-radial-mediated BNA oxidation was studied by considering OH addition to carbon atoms (C1 to C6) of BNA and H-atom abstraction at the -NH₂ group and carbon atoms (C3 and C5) of BNA by OH radicals. It is observed that an OH-addition reaction is energetically more favorable. In addition, the rate constant was calculated for the favorable initial OH-addition reactions over the temperature range of 278 to 1000 K. The subsequent reactions for the favorable BNA-OH adduct intermediate with O₂, HO₂ and NO radicals are studied. We have identified the following possible end products from this BNA-oxidation reaction: (i) 2-amino-3-bromo-6-hydroperoxy-5-methyl-1-nitro-cyclohexa-2,4 dienol, (ii) 2-amino-1-bromo-6-hydroperoxy-5-methyl-3-nitro-cyclohexa-2,4-dienol, (iii) 2-amino-1-bromo-6-hydroperoxy-5-methyl-3-nitro-cyclohexa-2,4-dienol, (iv) 3-amino-4-bromo-4-hydroperoxy-8-methyl-2-nitro-6,7-dioxa-bicyclo oct-2-en-8-ol, (v) 2-amino-1-bromo-6-hydroperoxy-5-methyl-3-nitro-cyclohexa-2,4-dienol, and (vi) 3-amino-2-bromo-8-methyl-4-nitro-6,7-dioxa-bicyclo oct-3-ene-2,8-diol.

Simulation of Vibronic Spectra of Flexible Systems: Hybrid DVR-Harmonic Approaches

Our general framework for the simulation of vibrational signatures in electronic spectra has been extended to treat one large-amplitude motion (LAM) at the anharmonic level, coupled to the other small-amplitude motions (SAM) treated as harmonic. The coupling between LAM and SAM is minimized thanks to the use of delocalized internal coordinates, which are built automatically from the molecular topology. General LAMs can be employed, ranging from intrinsic reaction coordinates to rigid or flexible paths based on the distinguished coordinate approach. The anharmonic model is based on a fully numerical method based on the discrete variable representation (DVR) theory, supporting different types of boundary conditions. The inclusion of this model in a general-purpose electronic structure code makes available to the user a large panel of quantum chemistry models, for both isolated and condensed phases. The flexibility and reliability of the new framework are illustrated by some case studies, covering various types of LAMs, ranging from a small test case, the photoelectron spectrum of ammonia, to larger systems, such as phenylanthracene and cyclobutanone.

Comparison of classical reaction paths and tunneling paths studied with the semiclassical instanton theory

Comparison of classical reaction paths and semiclassical instanton paths for a proton transfer reaction mechanism.

Heuristic control of kinetic energy in dynamic reaction coordinate calculations

For the understanding and prediction of chemical reactions, detailed knowledge of the minimum energy path between reactants and transition state is of utmost importance. Stewart et al. (J. Comput. Chem. 1987, 8, 1117) proposed the usage of molecular trajectories calculated from Newton's equations of motion for an efficient reaction path following. Two operational modes are possible thereby: intrinsic (IRC) and dynamic reaction coordinate calculations (DRC). The technical difference between these modes is that in an IRC calculation the kinetic energy of the nuclei is quenched while the total energy is conserved in DRC calculations. In this work, a heuristic control methodology of atomic kinetic energies in DRC calculations using fuzzy logic is proposed. A diversified test set of 10 reactions has been collected to examine the performance of this approach. Fuzzy rule-based models are found to be a convenient way to make the determination of accessible paths of chemical reactions computationally efficient.