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.

Many-body Effects on Electronic Transport in Molecular Junctions: A Quantum Perspective.

This concept delves into quantum particle transport at the nanoscale, with a particular focus on how electrons move through molecular circuits. The thriving field of single molecular electronics benefits from the unique electrical and other properties of nanostructures. It concentrates on single molecular junctions that serve as bridges between electrodes. In this context, the electronic correlation-induced many-body effect gives rise to resonant states. These states, along with conductance, depend on electron spin. Thus, the field acts as a bridge between quantum and macroscopic worlds, unveiling unique behaviors of electrons. Additionally, external factors, such as magnetic fields and voltages, offer means to control the electron correlation in these junctions.

Strong Be-N Interaction Induced Complementary Chemical Tuning to Design a Dual-gated Single Molecule Junction.

The interaction between pyridines and the π-hole of BeH2 leads to the formation of strong beryllium-bonded complexes. Theoretical investigations demonstrate that the Be-N bonding interaction can effectively regulate the electronic current through a molecular junction. The electronic conductance exhibits distinct switching behavior depending on the substituent groups at the para position of pyridine, highlighting the role of Be-N interaction as a potent chemical gate in the proposed device. The complexes exhibit short intermolecular distances ranging from 1.724 to 1.752 Å, emphasizing their strong binding. Detailed analysis of electronic rearrangements and geometric perturbations upon complex formation provides insights into the underlying reasons for the formation of such strong Be-N bonds, with bond strengths varying from -116.25 to -92.96 kJ/mol. Moreover, the influence of chemical substituents on the local electronic transmission of the beryllium-bonded complex offers valuable insights for the implementation of a secondary chemical gate in single-molecule devices. This study paves the way for the development of chemically gateable, functional single-molecule transistors, advancing the design and fabrication of multifunctional single-molecule devices in the nanoscale regime.

Importance of water and intramolecular interaction governs substantial blue shift of Csp2 -H stretching frequency in complexes between chalcogenoaldehydes and water.

Geometrical structure, stability and cooperativity, and contribution of hydrogen bonds to the stability of complexes between chalcogenoaldehydes and water were thoroughly investigated using quantum chemical methods. The stability of the complexes increases significantly when one or more H2O molecules are added to the binary system, whereas it decreases sharply going from O to S, Se, or Te substitution. The O-H⋯O H-bond is twice as stable as Csp2 -H⋯O and O-H⋯S/Se/Te H-bonds. It is found that a considerable blue-shift of Csp2 -H stretching frequency in the Csp2 -H⋯O H-bond is mainly determined by an addition of water into the complexes along with the low polarity of the Csp2 -H covalent bond in formaldehyde and acetaldehyde. The Csp2 -H stretching frequency shift as a function of net second hyperconjugative energy for the σ*(Csp2 -H) antibonding orbital is observed. Remarkably, a considerable Csp2 -H blue shift of 109 cm-1 has been reported for the first time. Upon the addition of H2O into the binary systems, halogenated complexes witness a decreasing magnitude of the Csp2 -H stretching frequency blue-shift in the Csp2 -H⋯O H-bond, whereas CH3-substituted complexes experience the opposite trend.

Strongly Bound π-Hole Tetrel Bonded Complexes between H2 SiO and Substituted Pyridines. Influence of Substituents.

Ab initio calculation at the MP2/aug-cc-pVTZ level has been performed on the π-hole based N… Si tetrel bonded complexes between substituted pyridines and H2 SiO. The primary aim of the study is to find out the effect of substitution on the strength and nature of this tetrel bond, and its similarity/difference with the N… C tetrel bond. Correlation between the strength of the N… Si bond and several molecular properties of the Lewis acid (H2 SiO) and base (pyridines) are explored. The properties of the tetrel bond are analyzed using AIM, NBO, and symmetry-adapted perturbation theory calculations. The complexes are characterized with short N… Si intermolecular distances and high binding energies ranging between -142.72 and -115.37 kJ/mol. The high value of deformation energy indicates significant geometrical distortion of the monomer units. The AIM and NBO analysis reveal significant coordinate covalent bond character of the N⋅⋅⋅Si π-hole bond. Sharp differences are also noticed in the orbital interactions present in the N⋅⋅⋅Si and N⋅⋅⋅C tetrel bonds.

Auxiliary Therapeutic Role of Cholinergic Agents: Mechanistic Insights into the Antioxidant Behavior of Alzheimer's Disease Drugs.

Repurposing of existing drugs toward new therapeutic use(s) has become an emergent area of research in current times. In this context, the antioxidant behavior of eight cholinergic drugs used in the treatment of Alzheimer's disease (AD) was investigated theoretically. The low bond dissociation enthalpy values in all of the compounds advocated for the hydrogen atom transfer mechanism toward the observed antioxidant behavior. The kinetic study for the reaction of the drugs with hydroperoxyl radicals indicated an indirect reaction path owing to the presence of pre- and postreaction complexes. In some cases, the rate constant for the H-abstraction reaction (k = 2.8 × 103 L mol-1 s-1) is found to be close to that of a well-known non-phenolic antioxidant, α-terpinene (k = 4.3 × 103 L mol-1 s-1). Quantification of charge transfer character among the drugs with DNA bases and molecular docking calculations confirmed the groove binding model and predicted the drugs to be safe from DNA damage. A theoretical evaluation of the mechanistic details governing the antioxidant property along with the proven stress reversal ability of these AD drugs provided new insights to design and develop more efficient drugs with dual therapeutic potential.

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.

Generation, structures, relative energies, and isomerization reactions of C5H5+ cations.

The B3LYP, MP2, and CBS-QB3 quantum chemical methods are used to study the relative energy and isomerization reactions of C5H5+ cations. Ease of generation of 14 C5H5+ isomers by ionic dissociation of halide precursors does not correlate well with carbocation stability. The reaction profiles of concerted isomerization of various C5H5+ cations to six select cations are established along with the respective transition states. The rate coefficients of these processes are estimated by using transition state theory and activation energies computed. The transition states for these six reactions are characterized with regard to position along the isomerization pathway as per Hammond's postulate. The 6 isomerization reactions are combined to yield multi-step conversions of various C5H5+ species to the lowest energy vinylcyclopropenyl cation 1. Finally, three different routes for obtaining the select cations from C5H5Br precursors are profiled and the most favored pathways predicted.

Comparison between Chlorine-Shared and π-Halogen Bonds Involving Substituted Phosphabenzene and ClF Molecules.

Ab initio MP2/aug-cc-pVTZ calculations have been carried out in order to study the nature of P···Cl halogen bonding interaction between a phosphorus atom in an aromatic ring in para-substituted phosphabenzene (PPBZ) and ClF molecule. The interaction of PPBZ with ClF results in two different types of complexes: (i) complex formation through the chlorine-shared halogen bond (T1-X-PPBZ·ClF) and (ii) complex formation via halogen-π interaction (T2-X-PPBZ·ClF). T1-X-PPBZ·ClF complexes are found to be more stable than the T2-X-PPBZ·ClF complexes. This work also presents a general criterion to distinguish a chlorine-shared halogen bond from a traditional halogen bond and sheds light on the formation of the chlorine-shared halogen bond. The binding energy of T1-X-PPBZ·ClF complexes correlates well with the negative electrostatic potential of the P atom and PA value of the substituted PPBZ. The properties of both T1-X-PPBZ·ClF and T2-X-PPBZ·ClF complexes are analyzed using atom-in-molecule, natural bond orbital, and symmetry-adapted perturbation theory calculations. The variation of the Cl-F bond distances and the redshifts of the ν(ClF) vibration resulting from the interaction with PPBZs are discussed.

Nature of the Interaction of Pyridines with OCS. A Theoretical Investigation.

Ab initio calculations were carried out to investigate the interaction between para-substituted pyridines (X-C5H4N, X=NH2, CH3, H, CN, NO2) and OCS. Three stable structures of pyridine.OCS complexes were detected at the MP2=full/aug-cc-pVDZ level. The A structure is characterized by N…S chalcogen bonds and has binding energies between -9.58 and -12.24 kJ/mol. The B structure is bonded by N…C tetrel bond and has binding energies between -10.78 and -11.81 kJ/mol. The C structure is characterized by π-interaction and has binding energies between -10.76 and -13.33 kJ/mol. The properties of the systems were analyzed by AIM, NBO, and SAPT calculations. The role of the electrostatic potential of the pyridines on the properties of the systems is outlined. The frequency shift of relevant vibrational modes is analyzed.

Unusual Fluorine Substitution Effect on S···Cl Bonding between Sulfides and Atomic Chlorine.

A theoretical investigation on the interaction of various sulfides and their fluorinated counterparts (H2S, HSF, F2S, CH3SH, CH3SF, CH2FSH, CH2FSF, NH2SH, NH2SF) with atomic chlorine has been carried out using density functional theory (DFT) based LC-BLYP/aug-cc-pVTZ and sophisticated ab initio CCSD(T)/aug-cc-pVQZ methods. The present study is intended to discuss the influence of the substituents implanted at the sulfur atom on the bonding parameters. The optimized geometries reveal that intermolecular S···Cl distances are short and range between 2.423 and 2.561 Å. A strong contraction of the S-F bond is also predicted. Two-center-three-electron S···Cl bonds are formed; the interaction energies are large and range from -33.9 to -70.1 kJ mol-1. Very surprisingly, the interaction energies are greater and the intermolecular distances are shorter for F-substituted sulfides than for unsubstituted ones. This is in complete contrast with the lower proton affinities and less negative electrostatic potentials of fluorinated sulfides. AIM analysis, the charge transfer from the sulfur atom to the Cl atom, and the spin densities on the Cl and S atoms are considered to explain this unusual behavior. The hyperconjugation energies from the LP(F) to the σ*(S-Cl) antibonding orbital can be considered as one of the stabilizing factors for the greater stability of the fluorinated complexes over the nonfluorinated ones.

Theoretical investigation on gas-phase reaction of CF3CH2OCH3 with OH radicals and fate of alkoxy radicals (CF3CH(O•)OCH3/CF3CH2OCH2O•).

Detailed theoretical investigation has been performed on the mechanism, kinetics and thermochemistry of the gas phase reactions of CF3CH2OCH3 (HFE-263fb2) with OH radicals using ab-initio and DFT methods. Reaction profiles are modeled including the formation of pre-reactive and post-reactive complexes at entrance and exit channels, respectively. Our calculations reveal that hydrogen abstraction from the CH2 group is thermodynamically and kinetically more facile than that from the CH3 group. Using group-balanced isodesmic reactions, the standard enthalpies of formation for CF3CH2OCH3 and radicals (CF3CHOCH3 and CF3CH2OCH2) are also reported for the first time. The calculated bond dissociation energies for the CH bonds are in good agreement with experimental results. At 298K, the calculated total rate coefficient for CF3CH2OCH3+OH reactions is found to be in good agreement with the experimental results. The atmospheric fate of the alkoxy radicals, CF3CH(O)OCH3 and CF3CH2OCH2O are also investigated for the first time using the same level of theory. Out of three plausible decomposition channels, our results clearly point out that reaction with O2 is not the dominant path leading to the formation of CF3C(O)OCH3 for the decomposition of CF3CH(O)OCH3 radical in the atmosphere. This is in accord with the recent report of Osterstrom et al. [CPL 524 (2012) 32] but found to be in contradiction with experimental finding of Oyaro et al. [JPCA 109 (2005) 337].

A theoretical investigation on the conformation and the interaction of CHF2OCF2CHF2 (desflurane II) with one water molecule.

The conformation and the interaction of CHF2OCF2CHF2 (desflurane II) with one water molecule is investigated theoretically using the ab initio MP2/aug-cc-pvdz and DFT-based M062X/6-311++G(d,p) methods. The calculations include the optimized geometries, the harmonic frequencies of relevant vibrational modes along with a natural bond orbital (NBO) analysis including the NBO charges, the hybridization of the C atom and the intra- and intermolecular hyperconjugation energies. In the two most stable conformers, the CH bond of the F2HCO- group occupies the gauche position. The hyperconjugation energies are about the same for both conformers and the conformational preference depends on the interaction between the non-bonded F and H atoms. The deprotonation enthalpies of the CH bonds are about the same for both conformers, the proton affinity of the less stable conformer being 3 kcal mol−1 higher. Both conformers of desflurane II interact with water forming cyclic complexes characterized by CH…O and OH…F hydrogen bonds. The binding energies are moderate, ranging from −2.4 to −3.2 kcal mol−1 at the MP2 level. The origin of the blue shifts of the ν(CH) vibrations is analyzed. In three of the complexes, the water molecule acts as an electron donor. Interestingly, in these cases a charge transfer is also directed to the non bonded OH group of the water molecule. This effect seems to be a property of polyfluorinated ethers.

Theoretical study of the O···Cl interaction in fluorinated dimethyl ethers complexed with a Cl atom: is it through a two-center-three-electron bond?

Theoretical investigations are carried out on the interaction between fluorinated dimethyl ethers (FDME, nF = 0-4) and the Cl atom. Short intermolecular O···Cl distances between 2.401 and 2.938 Å reveal the formation of a new class of complexes. The interaction energies calculated with the G2(MP2) method range between -9.1 (nF = 4) and -26.0 (nF = 0) kJ/mol. The charge transfer occurring from the ethers to atomic Cl is moderate and ranges between 0.012 e (nF = 4) to 0.188 e (nF = 0). The binding energies are linearly related to the proton affinity, to the charge transfer (CT) occurring in the molecular system and inversely proportional to the ionization potential and electron affinity (IP-EA) values. The CT and spin density data indicate substantial two-center-three-electron O···Cl interaction in CH3OCH3···Cl and CH3OCH2F···Cl systems, whereas for highly fluorinated ethers the interaction is predominantly electrostatic in nature. The formation of the complex results in a contraction of the CH bonds, especially in the gauche position. The blue shifts of the C-H stretching vibrations calculated in the partially deuterated isotopomers range between 2 and 54 cm(-1) and are correlated to the variation of the CH distances.

Strong hyperconjugative interactions in isolated and water complexes of desflurane: a theoretical investigation.

Ab initio MP2/aug-cc-pvDZ and density functional B3LYP calculations with the 6-311++G(d,p) basis set are performed to investigate the conformation of desflurane (CHF2OCHFCF3), its acidity/basicity and its interaction with one water molecule. The calculations include the optimized geometries, the harmonic frequencies of relevant vibrational modes, the binding energies with water, and a detailed natural bond orbital (NBO) analysis Iincluding the NBO charges, the hybridization of the C atoms and the intra- and intermolecular hyperconjugations. The relative energies of the two most stable conformers are discussed as a function of the total hyperconjugative energies resulting from the interaction of lone pairs of the O and F atoms to the different antibonding orbitals of desflurane. The proton affinity is the same for both conformers but the acidity of the CH bond is larger for the less stable conformer. The binding energies of the complexes of two desflurane conformers with one water molecule range from -2.75 to -3.23 kcal mol(-1). Depending on the structure of the complexes, the CH bonds involved in the interaction are contracted or elongated. The σ*(CH) occupation predominates over the hybridization effect in determining the CH bond length. There is an unexpected charge transfer to the external OH bond of the water molecule. This effect is in good agreement with theoretical data on the complexes between fluorinated dimethyl ethers and water and seems to depend on the number of F atoms implanted on the ether molecule.

Exploring hydrogen bond in the excited state leading toward intramolecular proton transfer: detailed analysis of the structure and charge density topology along the reaction path using QTAIM.

Excited state intramolecular proton transfer (ESIPT) reaction along the O-H[Symbol: see text][Symbol: see text][Symbol: see text][Symbol: see text]O hydrogen bond of o-hydroxy benzaldehyde (OHBA), methyl salicylate (MS) and salicylic acid (SA) was investigated by ab-initio quantum chemical calculation and theory of atoms and molecules (QTAIM) for the first time. Variation in several geometric as well as QTAIM parameters along the reaction coordinate was monitored in the fully relaxed excited state potential energy curve (PEC) obtained from intrinsic reaction coordinate (IRC) analysis. Although, the excited state barrier height for the forward reaction (∆E (0) (#) ) reduces substantially in all the systems, MS and SA do not show any obvious asymmetry for proton transfer. For MS and SA, the crossover of the bond index as well as the lengths of the participating bonds at the saddle point is assigned due to this symmetry in accordance with bond energy - bond order (BEBO) model, which does not hold true in OHBA both in the ground and excited states. Bond ellipticity, covalent and metallic character were examined for different structures along the reaction path within the QTAIM framework. The QTAIM analysis was found to be able to uniquely distinguish between the ground and excited states of the OHBA molecule as well as both determining the effects on the bonding character of adding different substituent groups and differentiating between the ESIPT reactions in the SA and MS molecules.

Theoretical studies on the kinetics and mechanism of the gas-phase reactions of CHF(2)OCHF (2) with OH radicals.

The mechanism, kinetics and thermochemistry of the gas-phase reactions between CHF(2)OCHF(2) (HFE-134) and OH radical are investigated using the high level ab initio G2(MP2) and hybrid density functional model MPWB1K quantum chemical methods. Two relatively close in energy conformers are found for CHF(2)OCHF(2) molecule; both of them are likely to be important in the temperature range (250-1000 K) of our study. The hydrogen abstraction pathway for both the conformers with OH radical is studied and the rate constants are determined for the first time in a wide temperature range of 250 - 1000 K. The G2(MP2) calculated total rate constant value of 2.9 × 10(-15) cm(3) molecule(-1) s(-1) at 298 K is found to be in very good agreement with the reported experimental value of 2.4 × 10(-15) cm(3) molecule(-1) s(-1) at 298 K. The heats of reaction for CHF(2)OCHF(2) + OH reaction is computed to be -13.2 kcal mol(-1). The atmospheric lifetime of CHF(2)OCHF(2) is expected to be around 12 years.

A theoretical investigation of the interaction between substituted carbonyl derivatives and water: open or cyclic complexes?

The structures and binding energies of complexes between substituted carbonyl bases and water are the B3LYP/6-311++G(d,p) computational level. The calculations also include the proton affinity (PA) of the O of the C=O group, the deprotonation enthalpies (DPE) of the CH bonds along a natural bond orbital analysis. The calculations reveal that stable open C=O···H(w) O(w) as well as cyclic CH···O(w)H(w) ···O=C complexes are formed. The binding energies for the open complexes are linearly related to the PAs, whereas the binding energies for the cyclic complexes depend on both the PA and DPE. Different indicators of hydrogen bonds strength such as electron charge density, intramolecular and intermolecular hyperconjugation energy, occupation of orbitals, and charge transfer show significant differences between open and cyclic complexes. The contraction of the CH bond of the formyl group and the corresponding blue shift of the ν(CH) vibration are explained by the classical trans lone pair effect. In contrast, the elongation or contraction of the CH(3) group involved in the interaction with water results from the variation of the orbital interaction energies from the σ(CH) bonding orbital to the σ* and π* antibonding orbitals of the C=O group. The resulting blue or red shifts of the ν(CH(3)) vibrations are calculated in the partially deuterated isotopomers.

Theoretical investigation of the interaction between fluorinated dimethyl ethers (nF = 1-5) and water: role of the acidity and basicity on the competition between OH...O and CH...O hydrogen bonds.

Theoretical calculations have been carried out using ab initio MP2 and B3LYP density functional methods to investigate the interaction between fluorinated dimethyl ethers (nF = 1-5) and water. Depending on the number of F atoms implanted on the dimethyl ethers, linear structures stabilized by intermolecular O(w)H(w)...O or CH...O(w) hydrogen bonds or closed structures involving both hydrogen bonds are formed. Binding energies of the hydrogen-bonded complexes range between 4 and 12 kJ mol(-1). Blue shifts of the CH stretching vibrations are predicted even in the absence of a direct CH...O interaction. The red shifts of the OH stretching vibrations of water in the open and closed structures are analyzed as well. The natural bond orbital analysis includes the sigma*(O(w)H(w)) and sigma*(CH) occupation, the hybridization of the C atom, the atomic charges, and the intra- and intermolecular hyperconjugation energies. These parameters are discussed as a function of the proton affinity (PA) of the O atom and the deprotonation enthalpy (DPE) of the CH bonds of the fluorinated ethers calculated in a previous work. (16) Our results show that the effective PA in determining the intermolecular O --> sigma*(O(w)H(w)) hyperconjugation energies decreases with increasing acidity of the CH bond. In turn, the effective acidity of the CH bond in determining the intermolecular O(w) --> sigma*(CH) hyperconjugation energies decreases with increasing basicity of the O atom.

Theoretical studies on kinetics and reactivity of the gas-phase addition and H-abstraction reactions of pyridine with atomic chlorine.

Theoretical investigations are carried out on the mechanism, kinetics, and thermochemistry for the reaction between pyridine and atomic chlorine with use of the hybrid density functional model BB1K, BHandHLYP, and the ab initio MP2 method. Both addition to and hydrogen abstraction reaction from all the potential sites are considered. Barrier heights and thermochemistry for all the possible addition and abstraction processes are calculated for the first time. This helps to identify the most reactive reaction channels in different temperature ranges. The DFT-based reactivity descriptors are used to elucidate the site selectivity for the addition and abstraction reactions. The results obtained from the BB1K method are found to be in reasonably good agreement with the available experimental results.