Intrinsic Reaction Coordinate Research Articles

A computational perspective on mechanism and kinetics of the reactions of CF3C(O)OCH2CF3 with OH radicals and Cl atoms at 298 K

Theoretical investigations are carried out on the gas-phase reactions of CF3C(O)OCH2CF3, 2,2,2-trifluoroethyl trifluoroacetate (TFETFA) with OH radicals and Cl atoms by means of modern DFT methods. Two conformers relatively close in energy have been identified for TFETFA, both of them are likely to be important in the temperature range of our study. Reaction profiles are modeled including the formation of two pre-reactive and post-reactive complexes. The optimized geometries, frequencies and minimum energy path are obtained at hybrid density functional model, M06-2X level using 6-31+G(d,p) basis set. The single point energy calculation was further refined by using 6-311++G(d,p) and Aug-cc-pVTZ basis sets. The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation. Theoretically calculated rate constants at 298K and using the canonical transition state theory (CTST) are found to be in good agreement with the experimentally measured ones. Using group-balanced isodesmic reactions, the standard enthalpies of formation for CF3C(O)OCH2CF3 and radical generated by hydrogen abstraction, CF3C(O)OCHCF3, are also reported for the first time. The estimated atmospheric lifetime of TFETFA is expected to be 0.15 years.

Polarizability, hardness and electrophilicity as global descriptors for intramolecular proton transfer reaction path

Potential energy (PE) curves for intramolecular proton transfer in the ground (GSIPT) and excited (ESIPT) states of 1-hydroxy-2-acetonaphthone (1H2AN) is studied using DFT-B3LYP/6-31+G(d,p) and TD-DFT/6-31+G(d,p) level of theory respectively. Our calculations suggest the non-viability of ground state intramolecular proton transfer in 1H2AN. Excited states PE calculations support the viability of ESIPT process in 1H2AN. Here, for the first time, polarizability, chemical hardness and electrophilicity are being used as global reactivity descriptors to locate the transition state for intermolecular proton transfer process. Both the minimum polarizability principle (MPP) and maximum hardness principle (MHP) are being obeyed along the intrinsic reaction co-ordinate (IRC) for intramolecular proton transfer process. We have also raised the decade old issue i.e. the use of O–H distance of enol tautomer as proton transfer co-ordinate instead of IRC. Our computation of these global reactivity descriptors along the proton transfer co-ordinate support intrinsic reaction coordinate (IRC) as the effective proton transfer co-ordinate, instead of variation of O–H distance of enol tautomer.

A QM/QTAIM microstructural analysis of the tautomerisation via the DPT of the hypoxanthine·adenine nucleobase pair

We provide a pathway for the tautomerisation of the biologically important hypoxanthine·adenine (Hyp·Ade) nucleobase pair (Cs) formed by the keto tautomer of the Hyp and the amino tautomer of the Ade into the Hyp*·Ade* base pair (Cs) formed by the enol tautomer of the Hyp and the imino tautomer of the Ade by applying quantum-mechanical calculations and Bader's Quantum Theory of Atoms in Molecules analysis. It was found out that the dipole active Hyp·Ade↔Hyp*·Ade* tautomerisation occurs via the asynchronous concerted double proton transfer (DPT) through the TSHyp·Ade↔Hyp*·Ade* (Cs). Based on the sweeps of the energies of the intermolecular H-bonds along the intrinsic reaction coordinate, it was established that the N6H···O6 H-bond (5.40) is cooperative with the N1H···N1 H-bond (6.99) in the Hyp·Ade base pair, as well as the O6H···N6 H-bond (11.50) is cooperative with the N1H···N1 H-bond (7.28 kcal·mol−1) in the Hyp*·Ade* base pair, mutually strengthening each other. The Hyp*·Ade* base pair possesses an extremely short lifetime 2.68·10−14 s, which is predetermined by the negative value of the Gibbs free energy of the reverse barrier of its tautomerisation, and all of the six low-frequency intermolecular vibrations cannot develop during this period of time. Consequently, the Hyp·Ade→Hyp*·Ade* DPT tautomerisation cannot serve as a source of the rare tautomers of the bases.

How does the long G·G* Watson-Crick DNA base mispair comprising keto and enol tautomers of the guanine tautomerise? The results of a QM/QTAIM investigation.

The double proton transfer (DPT) in the long G·G* Watson-Crick base mispair (|C6N1(G*)N1C6(G)| = 36.4°; C1 symmetry), involving keto and enol tautomers of the guanine (G) nucleobase, along two intermolecular neighboring O6H···O6 (8.39) and N1···HN1 (6.14 kcal mol(-1)) H-bonds that were established to be slightly anti-cooperative, leads to its transformation into the G*·G base mispair through a single transition state (|C6N1N1C6| = 37.1°; C1), namely to the interconversion into itself. It was shown that the G·G* ↔ G*·G tautomerisation via the DPT is assisted by the third specific contact, that sequentially switches along the intrinsic reaction coordinate (IRC) in an original way: (G)N2H···N2(G*) H-bond (-25.13 to -10.37) → N2···N2 van der Waals contact (-10.37 to -9.23) → (G)N2···HN2(G*) H-bond (-9.23 to 0.79) → (G*)N2···HN2(G) H-bond (0.79 to 7.35 Bohr). The DPT tautomerisation was found to proceed through the asynchronous concerted mechanism by employing the QM/QTAIM approach and the methodology of the scans of the geometric, electron-topological, energetic, polar and NBO properties along the IRC. Nine key points, that can be considered as part of the tautomerisation repertoire, have been established and analyzed in detail. Furthermore, it was shown that the G·G* or G*·G base mispair is a thermodynamically and dynamically stable structure with a lifetime of 8.22 × 10(-10) s and all 6 low-frequency intermolecular vibrations are able to develop during this time span. Lastly, our results highlight the importance of the G·G* ↔ G*·G DPT tautomerisation, which can have implications for biological and chemical sensing applications.

Dissociation of Cyclopropanone Molecule and Ion

Investigate the dissociation and ionization process of cyclopropanone molecules by using the Density functional method. Find the transition states of cyclopropanone molecule and ion, and get the products from transition state to isomer. In the same time, calculate frequency and energy. Confirm their transition states between the reactants and resultants through the Intrinsic Reaction Coordinates (IRC) calculation. PACS: 07.77.Gx

DFT study of the mechanism and stereoselectivity of the 1,3-dipolar cycloaddition between pyrroline-1-oxide and methyl crotonate

A theoretical study of the regio- and stereoselectivities of the 1,3-dipolar cycloaddition reaction between methyl crotonate and pyrroline-1-oxide has been carried out using density functional theory (DFT) at the B3LYP/6-31G(d) level of theory. The reaction has been followed by performing transition state optimization, calculations of intrinsic reaction coordinate and activation energies; the molecular mechanism of the reactions is concerted and asynchronous. The regio- and exo/endo-selectivity have been explained in terms of frontier molecular orbital interactions, local and global electrophilicity and nucleophilicity indices and an analysis of the Wiberg bond indices in the transition state. The FMO analysis and DFT-based reactivity indices showed that the regioselectivity of this reaction is controlled by the HOMOdipole–LUMOdipolarophile interaction. The activation parameters indicated favoured endo approach along the meta-pathway in agreement with the experimental results. The molecular mechanism of the 1,3-dipolar cycloaddition reaction between pyrroline-1-oxide and methyl crotonate is theoretically investigated by DFT method at the B3LYP/6-31G* level. The transition states corresponding to the possible stereoisomeric pathways along regioisomeric reaction channels were searched, localized and optimized. The cycloaddition is favored along the reaction channel with the meta-endo adduct as major diastereomer in agreement with experiment.

Structural, energetic and tautomeric properties of the T·T∗/T∗·T DNA mismatch involving mutagenic tautomer of thymine: A QM and QTAIM insight

It was revealed by thorough study of the T·T∗ (C1)↔T∗·T (C1) tautomerisation via the synchronous concerted double proton transfer (DPT) through the TS (C2v) that the T·T∗/T∗·T H-bonded mismatch is dynamically stable non-planar complex with a lifetime 1.6×10−10s. The 5 key points were firstly detected and completely investigated along the intrinsic reaction coordinate of the DPT tautomerisation. The reported data allow us to suggest that the T∗ mutagenic tautomer of the thymine (T) is shared with approximately equal probability between two DNA strands during the dissociation of the mispair by DNA polymerase.

Computational study on the kinetics of OH initiated oxidation of methyl difluoroacetate (CF2HCOOCH3)

The kinetics of hydrogen atom abstraction reactions of methyl difluoroacetate (CF2HCOOCH3) by OH radical has been studied by quantum mechanical method. The geometry optimisation and frequency calculation of the titled compound was performed with density functional theory using hybrid meta density functional MPWB1K with 6-31+G(d,p) basis set. Transition states have been determined and intrinsic reaction coordinate (IRC) calculation has been performed to ascertain that the transition from reactants to products was smooth through the corresponding transition state. Energy values are refined by making single point energy calculation at G3B3 level of theory and an energy level diagram is constructed. The standard enthalpies of formation of reactants and other species formed during the reaction were calculated using isodesmic method. The rate constants are calculated using canonical transition state theory and the overall rate constant is determined to be 1.35×10−13 cm3 molecule−1 s−1 at 298 K and 1 atmospheric pressure. Tunnelling has been taken into account in the determination of the rate constant because it plays a critical role at low temperature especially when transfer of hydrogen takes place. The calculated value is found to be in good agreement with the experimentally determined value of 1.48×10−13 cm3 molecule−1 s−1.

The physicochemical essence of the purine·pyrimidine transition mismatches with Watson-Crick geometry in DNA: A·C* versa A*·C. A QM and QTAIM atomistic understanding

It was established for the first time by DFT and MP2 quantum-mechanical (QM) methods either in vacuum, so in the continuum with a low dielectric constant (ε = 4), typical for hydrophobic interfaces of specific protein-nucleic acid interactions, that the repertoire for the tautomerisation of the biologically important adenine·cytosine* (A·C*) mismatched DNA base pair, formed by the amino tautomer of the A and the imino mutagenic tautomer of the C, into the A*·C base mispair (∆G = 2.72 kcal mol−1 obtained at the MP2 level of QM theory in the continuum with ε = 4), formed by the imino mutagenic tautomer of the A and the amino tautomer of the C, proceeds via the asynchronous concerted double proton transfer along two antiparallel H-bonds through the transition state (TSA·C*↔A*·C). The limiting stage of the A·C*→A*·C tautomerisation is the final proton transfer along the intermolecular N6H···N4 H-bond. It was found that the A·C*/A*·C DNA base mispairs with Watson–Crick geometry are associated by the N6H⋯N4/N4H⋯N6, N3H⋯N1/N1H⋯N3 and C2H⋯O2 H-bonds, respectively, while the TSA·C*↔A*·C is joined by the N6–H–N4 covalent bridge and the N1H⋯N3 and C2H⋯O2 H-bonds. It was revealed that the A·C*↔A*·C tautomerisation is assisted by the true C2H⋯O2 H-bond, that in contrast to the two others conventional H-bonds exists along the entire intrinsic reaction coordinate (IRC) range herewith becoming stronger at the transition from vacuum to the continuum with ε = 4. To better understand the behavior of the intermolecular H-bonds and base mispairs along the IRC of the A·C*↔A*·C tautomerisation, the profiles of their electron-topological, energetical, geometrical, polar and charge characteristics are reported in this study. It was established based on the profiles of the H-bond energies that all three H-bonds are cooperative, mutually strengthening each other. The nine key points, providing a detailed physicochemical picture of the A·C*↔A*·C tautomerisation, were revealed and thoroughly examined along the IRC. It was shown that the A*·C base mispair with the population ~1 % obtained at the MP2 level of QM theory in the continuum with ε = 4 is thermodynamically and dynamically stable structure. Its lifetime was calculated to be 5.76·10−10 s at the MP2 level of QM theory in the continuum with ε = 4. This lifetime, from the one side, enables all six low-frequency intermolecular vibrations to develop, but, from the other side, it is by order less than the time (several ns) required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication. This means that the A*·C base mispair “slips away from the hands” of the replication machinery into the A·C* mismatched base pair. Consequently, the authors came to the conclusion that exactly the A·C* base mispair is an active player of the point mutational events and is effectively dissociated by the replication machinery into the A and C* monomers in contrast to the A*·C base mispair, playing the mediated role of a provider of the A·C* base mispair in DNA that is synthesised.

Theoretical Study of Topographical Features around the Conical Intersections of 9-(2-Cyclopenten-1-ylidene)-9H-fluorene

Ab initio molecular orbital calculations have been performed to examine the topographical features around the conical intersections (CIXs) for the photoisomerization of 9-(2-cyclopenten-1-ylidene)-9H-fluorene (CPF). The present study is motivated by the computational findings of the topographical features in the CIX region of a fluorene-based light-driven molecular motor with smooth rotation (denoted by M5-PCPF). CPF is a parent molecule of M5-PCPF but exhibits neither helicity nor unidirectionality. A stable geometry in S1 (S1-geometry) is located in the region where the ethylenic rotary axis is perpendicularly twisted, but the fluorene part wags little against the rotary axis, as is the case of M5-PCPF. However, the topographical features around the CIXs of CPF are different from those of M5-PCPF. The wagging motion of the fluorene stator to the negative direction from S1-geometry leads straight to a CIX which implements forward and backward rotations. On the other hand, only the wagging motion to the positive direction does not lead to a CIX, and additional geometrical deformations are needed. Depending on the directions of additional geometrical deformations, two CIXs, which play the roles of respective exit channels for forward and backward rotations, are located in the positive wagging region. The difference in the topographical features in the CIX region between CPF and M5-PCPF is ascribed to the effect of the pentamethylene chain. By virtue of much less computational labor of CPF as well as the electronic structures being similar to those of M5-PCPF, the intrinsic reaction coordinate was followed from the ethylenic ππ* state at the stable geometry in S0 into S1-geometry. Thereby, it was confirmed that a spectroscopically dark state due to the π(fluorene)π*(ethylene) excitation contributes less to the photochemical process of the ethylenic bond torsion, as is the case of M5-PCPF.

MOLECULAR STRUCTURE, VIBRATIONAL ASSIGNMENTS, CONFORMATIONAL STABILITY, GROUND AND EXCITED STATE HYDROGEN-BONDING ANALYSIS OF 2-NITROSO VINYL AMINE

In the present work, a detailed conformational study is performed using several computational methods, including density functional theory (DFT) (B3LYP), MP2 and G2MP2 on 2-Nitroso vinyl amine (NVA) in order to determine the stability order of conformers and the various possibilities of intramolecular hydrogen bonding (HB) formation. Four conformers exhibit HB . This feature, although not being the dominant factor in energetic terms, appears to be of foremost importance to define the geometry of the molecule. According to our theoretical results, oximimine conformers are more stable than the corresponding nitrosoamine and nitrosoimine analogues. Theoretical calculations show the following order for intramolecular HB strength in the conformers of title compound: [Formula: see text]The nature of intramolecular HB has been investigated by means of the Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis. Also, Harmonic Oscillator Model of Aromaticity (HOMA) index as a geometrical indicator of a local aromaticity are investigated. The influence of the solvent on the stability order of conformers and the strength of intramolecular HB is considered using the Onsager reaction field model. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies confirm that charge transfer occur within the molecule. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the1H NMR chemical shift at GIAO/B3LYP/6–311++G** levels of theory are also presented. The excited-state properties of intramolecular HB in H -bonded systems have been investigated theoretically using the time-dependent density functional theory (TD-DFT) method. The complete vibrational assignment for three H -bonded conformers has been made on the basis of the calculated potential energy distribution (PED).

Mechanism of Formation of Trans Fatty Acids under Heating Conditions in Triolein

To elucidate the relationship between heat-induced cis/trans isomerization and reaction temperature and energy in unsaturated lipids, we investigated the molecular mechanism of the heat-induced cis/trans isomerization of 18:1 isomers. Triolein (18:1,9c) was heated at two range temperatures (130, 160, 190, 220 °C and 135, 140, 145, 150, 155 °C) and analyzed by the gas chromatography (GC) method. When the heating temperature increased to 150 °C, the amount of trans 18:1n-9 changed from 0.0897 mg/g oil (1 h) to 0.1700 mg/g oil (3 h). This study shows that the cis to trans isomerization may occur at 150 °C. The formation of fatty acid isomers followed a proton transfer route. All key geometries, transition states, intermediates, and bond dissociation energies (BDE) were optimized at the B3LYP/6-31G* level for the density functional theory (DFT). The zero-point energy corrections of the isomers were carried out using calculations at the B3LYP/6-311++G** level. The calculated energy difference between the cis and trans oleic acid was equal to 7.6 kJ/mol, and the energy barriers of the transition from cis 18:1n-9 to trans 18:1n-9 were 294.5 kJ/mol. The intrinsic reaction coordinates (IRCs) were obtained to be used as an expression of the reaction route and to analyze the transition states and intermediates. The study results suggest that the heating temperature should be kept under 150 °C, to avoid the risk of trans fatty acid (TFA) intake in daily food.

Theoretical investigation on the kinetics and branching ratio of the gas phase reaction of sevoflurane with Cl atom

The present work deals with the theoretical investigation on the Cl initiated H-atom abstraction reaction of sevoflurane, (CF3)2CHOCH2F. A dual-level procedure has been adopted for studying the kinetics of the reaction. Geometrical optimization and frequency calculation were performed at DFT(BHandHLYP)/6-311G(d,p) while single-point energy calculation was made at CCSD(T)/6-311G(d,p) level of theory. The intrinsic reaction coordinate (IRC) calculation has also been performed to confirm the smooth transition from the reactant to product through the respective transition state. The rate constants were calculated using conventional transition state theory (TST). It has been found that 99 % of the reaction proceeded via the H-atom abstraction from the –CH2F end of the sevoflurane. The rate constant of the dominant path is found to be 1.13 × 10⁻¹³ cm³ molecule⁻¹ s⁻¹. This is in excellent agreement with the reported experimental rate constant of 1.10 × 10⁻¹³ cm³ molecule⁻¹ s⁻¹ obtained by relative rate method using FTIR/Smog chamber and LP/LIF techniques.

Insights into the Mechanism of the Benzoannelated Thieno[3,2-b]furan Halogenation. Importance of HOMO–HOMO Interaction

In this paper the mechanism of the benzoannelated thieno[3,2-b]furan halogenation reaction has been characterized using density functional theory calculations. The solvent effect on the studied reaction is taken into account. A variation in charge, bond length, and bond order in the transformation of the π-complex to the σ-complex and final products along the reaction minimal energy path given as the intrinsic reaction coordinate has been investigated. Particular attention was focused on the evolution of π MOs along the reaction coordinate. The importance of HOMO-HOMO interaction between the lone pair electrons of the bromine molecule and π MOs of thieno[3,2-b]benzofuran has been emphasized.

Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches

It was established that the cytosine·thymine (C·T) mismatched DNA base pair with cis-oriented N1H glycosidic bonds has propeller-like structure (|N3C4C4N3| = 38.4°), which is stabilized by three specific intermolecular interactions-two antiparallel N4H…O4 (5.19 kcal mol(-1)) and N3H…N3 (6.33 kcal mol(-1)) H-bonds and a van der Waals (vdW) contact O2…O2 (0.32 kcal mol(-1)). The C·T base mispair is thermodynamically stable structure (ΔG(int) = -1.54 kcal mol(-1) ) and even slightly more stable than the A·T Watson-Crick DNA base pair (ΔG(int) = -1.43 kcal mol(-1)) at the room temperature. It was shown that the C·T ↔ C*·T* tautomerization via the double proton transfer (DPT) is assisted by the O2…O2 vdW contact along the entire range of the intrinsic reaction coordinate (IRC). The positive value of the Grunenberg's compliance constants (31.186, 30.265, and 22.166 Å/mdyn for the C·T, C*·T*, and TS(C·T ↔ C*·T*), respectively) proves that the O2…O2 vdW contact is a stabilizing interaction. Based on the sweeps of the H-bond energies, it was found that the N4H…O4/O4H…N4, and N3H…N3 H-bonds in the C·T and C*·T* base pairs are anticooperative and weaken each other, whereas the middle N3H…N3 H-bond and the O2…O2 vdW contact are cooperative and mutually reinforce each other. It was found that the tautomerization of the C·T base mispair through the DPT is concerted and asynchronous reaction that proceeds via the TS(C·T ↔ C*·T*) stabilized by the loosened N4-H-O4 covalent bridge, N3H…N3 H-bond (9.67 kcal mol(-1) ) and O2…O2 vdW contact (0.41 kcal mol(-1) ). The nine key points, describing the evolution of the C·T ↔ C*·T* tautomerization via the DPT, were detected and completely investigated along the IRC. The C*·T* mispair was revealed to be the dynamically unstable structure with a lifetime 2.13·× 10(-13) s. In this case, as for the A·T Watson-Crick DNA base pair, activates the mechanism of the quantum protection of the C·T DNA base mispair from its spontaneous mutagenic tautomerization through the DPT.

Mechanisms on electrical breakdown strength increment of polyethylene by acetophenone and its analogues addition: a theoretical study

A theoretical investigation is completed on the mechanism of electrical breakdown strength increment of polyethylene. It is shown that it is one of the most important factors for increasing electrical breakdown strength of polyethylene through keto-enol isomerization of acetophenone and its analogues at the ground state S0 and the lowest triplet state T1. The minimum structures and transition states of the keto- and the enol-tautomer of acetophenone and its analogues at the S0 and T1 states are obtained at the B3LYP/6-311+G(d,p) level, as well as the harmonic vibration frequencies of the equilibrium geometries and the minimum energy path (MEP) by the intrinsic reaction coordinate (IRC) theory at the same level. The two C-C bond cleavage reaction channels have been identified in acetophenone. The calculated results show that the energy barriers of keto-enol isomerization of acetophenone and its analogues at S0 and T1 states are much smaller than the average C-C bond energy of polyethylene, and the acetophenone doping or bond linked into polyethylene can increase the electrical breakdown strength and inhibit polyethylene electrical tree initiation and aging.

Revisiting the seemingly straightforward hydrogen cyanide/hydrogen isocyanide isomerisation

Both HCN and HNC are prominent in the interstellar medium and may have significant roles in prebiotic chemistry. Considerable attention has, therefore, been accorded to the HCN ↔ CNH isomerisation, sometimes viewed as a prototypical unimolecular process. However, detailed analysis of the potential energy of the HCN/CNH system along its intrinsic reaction coordinate, in terms of the first and second derivatives of the energy, shows that this is not a straightforward proton transfer. It appears to involve two distinct transition regions, one in which the C–H bond breaks and the other in which the N–H forms. Between these regions is a transitory state, with all vibrational frequencies being real, in which the hydrogen is situated above the C–N bond and not directly associated with either the carbon or the nitrogen. In this state, the vibrational modes of the hydrogen are, respectively, approximately parallel and perpendicular to the C–N bond.

Effects of Lewis Acids on the Thermal Rearrangements of Chloromethylsilane: A Density Functional Theory Study

Understanding the thermal rearrangement mechanism of chloromethylsilane in the presence of Lewis acids is particularly important in industrial applications. In this study, the thermal rearrangements of chloromethylsilane under the catalysis of AlCl3 and BF3 were studied on the basis of density functional theory (DFT) at the B3LYP/6-311G (d, p) level. The structures of the reactants, transition states and products were located and fully optimized. The geometries of various stationary points and the harmonic vibrational frequencies were calculated at the same levels. The reaction paths were investigated and confirmed by intrinsic reaction coordinate (IRC) calculations. The results showed that the thermal rearrangement of chloromethylsilane in the presence of a Lewis acid occurred via two pathways (MX3-1 and MX3-2). Only pathway MX3-1 had a catalytic effect. The determining factor of the reaction activation energies and rates was the formation of the transition state in each reaction. Among all the reactions, the Al atom could form an approximate tetrahedral coordination with four Cl atoms, resulting in the lowest energy barrier. The kinetic and thermodynamic calculations also proved this result.

Why the tautomerization of the G·C Watson–Crick base pair via the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis

The ground-state tautomerization of the G·C Watson–Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4), corresponding to a hydrophobic interface of protein–nucleic acid interactions, using DFT and MP2 levels of quantum-mechanical (QM) theory and quantum theory “Atoms in molecules” (QTAIM). Based on the sweeps of the electron-topological, geometric, polar, and energetic parameters, which describe the course of the G·C ↔ G∗·C∗ tautomerization (mutagenic tautomers of the G and C bases are marked with an asterisk) through the DPT along the intrinsic reaction coordinate (IRC), it was proved that it is, strictly speaking, a concerted asynchronous process both at the DFT and MP2 levels of theory, in which protons move with a small time gap in vacuum, while this time delay noticeably increases in the continuum with ϵ = 4. It was demonstrated using the conductor-like polarizable continuum model (CPCM) that the continuum with ϵ = 4 does not qualitatively affect the course of the tautomerization reaction. The DPT in the G·C Watson–Crick base pair occurs without any intermediates both in vacuum and in the continuum with ϵ = 4 at the DFT/MP2 levels of theory. The nine key points along the IRC of the G·C base pair tautomerization, which could be considered as electron-topological “fingerprints” of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These key points have been used to define the reactant, transition state, and product regions of the DPT reaction in the G·C base pair. Analysis of the energetic characteristics of the H-bonds allows us to arrive at a definite conclusion that the middle N1H⋯N3/N3H⋯N1 and the lower N2H⋯O2/N2H⋯O2 parallel H-bonds in the G·C/G∗·C∗ base pairs, respectively, are anticooperative, that is, the strengthening of the middle H-bond is accompanied by the weakening of the lower H-bond. At that point, the upper N4H⋯O6 and O6H⋯N4 H-bonds in the G·C and G∗·C∗ base pairs, respectively, remain constant at the changes of the middle and the lower H-bonds at the beginning and at the ending of the G·C ↔ G∗·C∗ tautomerization. Aiming to answer the question posed in the title of the article, we established that the G∗·C∗ Löwdin’s base pair satisfies all the requirements necessary to cause point mutations in DNA except its lifetime, which is much less than the period of time required for the replication machinery to forcibly dissociate a base pair into the monomers (several ns) during DNA replication. So, from the physicochemical point of view, the G∗·C∗ Löwdin’s base pair cannot be considered as a source of point mutations arising during DNA replication.

Depletion of atmospheric ozone by nitrogen dioxide: a bifurcated reaction pathway

Theoretical investigation on the reaction of NO2 with O3 in the context of ozone depletion is reported in this study. The progress of this reaction in single or concrete steps is an open and highly challenging question for both experimentalists and theoreticians. The reaction is studied through DFT methods, M06-2X, BH and HLYP and MPW1K with 6-311++G(2df,2p) basis set and also at UCCSD and CASPT2 methods with 6-31G(d,p) basis set. The single-point energies of the reactive species are calculated at CASSCF, UCCSD(T), UQCISD(T) and MRCI methods with 6-311++G(2df,2p) basis set. The reaction proceeds along an intermediate through a rate-limiting first transition state. This intermediate is followed by a second transition state, and the intrinsic reaction coordinate (IRC) calculations from this transition state show that the reaction path follows a product channel and another transition state. Two sequential transition states are calculated and the potential energy surface bifurcation is observed through a valley-ridge inflection point. The IRC calculations from third transition state lead to second product channel in which NO and O2 are formed. The energy barrier calculated for the formation of NO3 and O2 in the first product channel is 33.96 kcal/mol, and an energy barrier of 34.07 kcal/mol is calculated for the formation of NO + 2O2 product channel. The rate constant calculated at 298 K for the two product channels is 2.31 × 10−7 cm3 molecule−1 s−1. These results show that the formation of the two product channels is equally probable. The photodissociation wavelength of the reactive species involved in the reaction system is calculated using equation of motion coupled cluster (EOMCC) method. The calculated photodissociation wavelength shows that a significant amount of NO2 photofragment enters into the stratosphere and potentially involves in the depletion of ozone. The photodissociation wavelength of the reactive species calculated using EOMCC method is in good agreement with the available experimental data.