Intrinsic Reaction Coordinate Research Articles

Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene.

We show herein that 1,10-dicyano substitution restricts the paragon fluxionality of bullvalene to just 14 isomers which isomerize along a single cycle. The restricted fluxionality of 1,10-dicyanobullvalene (DCB) is investigated by means of: (i) Bonding analyses of the isomer structures using the adaptive natural density partitioning (AdNDP). (ii) Quantum dynamical simulations of the isomerizations along the cyclic intrinsic reaction coordinate of the potential energy surface (PES). The PES possesses 14 equivalent potential wells supporting 14 isomers which are separated by 14 equivalent potential barriers supporting 14 transition states. Accordingly, at low temperatures, DCB appears as a hindered molecular rotor, without any delocalization of the wavefunction in the 14 potential wells, without any nuclear spin isomers, and with completely negligible tunneling. These results are compared and found to differ from those for molecular boron rotors. (iii) Born-Oppenheimer molecular dynamics (BOMD) simulations of thermally activated isomerizations. (iv) Calculations of the rate constants in the frame of transition state theory (TST) with reasonable agreement achieved with the BOMD results. (v) Simulations of the equilibration dynamics using rate equations for the isomerizations with TST rate coefficients. Accordingly, in the long-time limit, isomerizations of the 14 isomers, each with Cs symmetry, approach the "14 Cs → C7v" thermally averaged structure. This is a superposition of the 14 equally populated isomer structures with an overall C7v symmetry. By extrapolation, the results for DCB yield working hypotheses for so far un-explored properties e.g. for the equilibration dynamics of C10H10.

Concerning for the solvent-polarity-dependent conformational equilibrium and ESIPT mechanism in Pz3HC system: A novel insight

In this report, we propose a new insight into the interaction between the solvent-polarity-dependent conformational equilibrium and excited state intramolecular proton transfer (ESIPT) behavior of Pz3HC system in four different polar solvents (polarity order: ACN > THF > TOL > CYC). Using quantum chemistry method, we first announce a coexistence mechanism between Pz3HC-1 and Pz3HC-3 in the ground state in four solvents based on the Boltzmann distribution. In particular, Pz3HC-1 is the principal configuration in non-polar solvent, but Pz3HC-3 is the principal configuration in polar solvent. In addition, the simulated fluorescence spectra interprets the negative solvatochromism effect of Pz3HC-1 and Pz3HC-3 in four solvents. The evidence from intramolecular hydrogen bonding (IHB) parameters and electronic perspective collectively confirms the light-induced IHB enhancement and intramolecular charge transfer (ICT) properties in Pz3HC-1 and Pz3HC-3, which raises the likelihood of the ESIPT process. Combining the calculation of potential energy curve (PEC) and intrinsic reaction coordinate (IRC), we demonstrate that the ESIPT ease of Pz3HC-1 in different polar solvents obeys the order of CYC > TOL > THF > ACN, while the order of ESIPT ease in Pz3HC-3 is opposite. Notably, the ESIPT process of Pz3HC-3 in CYC solvent is accompanied by the twisted intramolecular charge transfer (TICT) process. In addition, we also reveal that the enol* and keto* fluorescence peaks of Pz3HC-3 in CYC solvent are quenched by ISC and TICT process, respectively. Our work not only provides a satisfactory explanation of the novel dynamics mechanism for Pz3HC system, but also brings light to the design and application of new sensing molecules in the future.

Investigating the catalytic activity of Mgn (n = 4–8) clusters for the hydrogen evolution reaction using density functional theory

AbstractTo efficiently desorb H2, pure Mgn (n = 4–8) clusters were chosen for the hydrogen evolution reaction with H2O. At the PBE0/def2‐TZVP level and the PBE0‐D3/def2‐TZVP level, the lowest energy structures of Mgn (n = 4–8) clusters and the most stable structures of Mgn@H2O (n = 4–8) complexes were searched in the local region. The transition state was predicted, and then the hydrogen evolution reaction channel was obtained by using the intrinsic reaction coordinate (IRC) to confirm the transition state. To better analyze the hydrogen reaction mechanism, the character of Mgn@H2O (n = 4–8) complexes and MgnO (n = 4–8) clusters, as well as the atomic charge change trend, were investigated using interaction region indicator function analysis (IRI) and natural population analysis (NPA). The reaction effect of Mg4 cluster and H2O is the worst. The energy barrier does, however, progressively lower as the cluster atom count rises, improving the reaction effect.

Intermolecular interaction of azide, cyano and alkyne-N-phenethylacetamide dimers: Experimental and quantum chemical approach

In this study, we present the synthesis and structure characterization by single-crystal X-ray Diffraction (SC-XRD), Ultraviolet Spectroscopy (UV), Fourier Transform Infrared Spectroscopy (FTIR), Nuclear Magnetic Resonance (NMR) and High-resolution Mass Spectrometry (HRMS) of 2-azido-N-phenethylacetamide (4) and 2-cyano-N-phenethylacetamide (6). Further, Density Functional Theory (DFT) was employed to get a better insight regarding the properties exhibited by the compounds. The computational chemistry has been used to explain and investigate the bimolecular nucleophilic substitution (SN2) and concerted acyl substitution mechanisms for the synthesis of compounds 4 and 6, respectively. Additionally, intrinsic reaction coordinate (IRC) calculations confirm the transition state for these reactions. The X-ray diffraction analysis showed that the compounds 4 and 6 crystallized as monoclinic systems, in space group P21/c and P21/n, respectively. The Hirshfeld Surface Analysis revealed that the main contributions in the crystal packing have H···H, H···N/N···H, H···C/C···H and H···O/O···H interactions. The frontier molecular orbital energies were calculated and the HOMO-LUMO energy gap of 4 and 6 were 10.011 and 10.278 eV, respectively. Theoretical values of electronic transitions, vibrational frequencies and NMR chemical shifts were calculated and compared with experimental results, they all showed good results.

Formic Acid-Ammonia Heterodimer: A New Δ-Machine Learning CCSD(T)-Level Potential Energy Surface Allows Investigation of the Double Proton Transfer.

The formic acid-ammonia dimer is an important example of a hydrogen-bonded complex in which a double proton transfer can occur. Its microwave spectrum has recently been reported and rotational constants and quadrupole coupling constants were determined. Calculated estimates of the double-well barrier and the internal barriers to rotation were also reported. Here, we report a full-dimensional potential energy surface (PES) for this complex, using two closely related Δ-machine learning methods to bring it to the CCSD(T) level of accuracy. The PES dissociates smoothly and accurately. Using a 2d quantum model the ground vibrational-state tunneling splitting is estimated to be less than 10-4 cm-1. The dipole moment along the intrinsic reaction coordinate is calculated along with a Mullikan charge analysis and supports the mildly ionic character of the minimum and strongly ionic character at the double-well barrier.

Synthesis, Characterization, Crystal Structure, and Theoretical Calculations of Novel 1,5-Benzodiazepine Derivatives Obtained via 1,3-Dipolar Cycloaddition Reactions

A series of triazolo-benzodiazepine derivatives were synthesized by the condensation of 2,2,4-trimethyl-2,3-dihydro-1H-1,5-benzodiazepine (BZD) 1 with nitrilimine analogs (N-aryl-C-ethoxycarbonyl-nitrilimines and diarylnitrilimines). The newly synthesized cycloadducts were well-characterized by various spectroscopic techniques (1H, 13C NMR, and HRMS). The structure of single-crystal was characterized using a single-crystal X-ray technique. A theoretical study of the chemo and regioselectivity has been performed by density functional theory at the B3LYP/6-311G(d,p) level of theory. A comprehensive theoretical study of the reaction mechanism was performed. The geometry of the different reactants and products were analyzed, the transition states were located and the corresponding reaction paths were determined and characterized by the intrinsic reaction coordinate. Computational results show that the reactions were completely chemo and regioselective, the mechanism of reactions was non-concerted and explained the effect of aryl groups on the reaction yield.

Test of the orbital-based LI3 index as a predictor of the height of the [formula omitted]MLCT [formula omitted][formula omitted]MC transition-state barrier for gas-phase [Ru(N[formula omitted]N)[formula omitted]][formula omitted] polypyridine complexes

Ruthenium(II) polypyridine compounds often luminesce, with ligand-dependant lifetimes. This is the third in a series of papers devoted to finding orbital-based luminescence indices (LI) for predicting luminescence lifetimes. The third attempt (LI3) was based upon a frontier molecular orbital (FMO) like estimate of the height of the barrier to conversion from an initial phosophorescent triplet metal-ligand charge transfer (3MLCT) state to a nonluminescent triplet metal-centered (3MC) state which decays nonradiatively. A linear correlation was found between LI3 and extracted empirical average 3MLCT →3MC transition state (TS) barrier heights (Eaves) which were not believed to be quantitative but which were believed to capture the trends in the true barrier heights correctly. As it is known that Eave is a large underestimate of the true 3MLCT →3MC TS barrier height in the case of the trisbipyridine ruthenium(II) cation { [Ru(bpy)3]2+ }, but accurate TS barrier heights are difficult to obtain experimentally, it was judged useful to verify the ideas used to derive the LI3 index in the present work by calculating the energetics of the gas-phase 3MLCT →3MC reaction for a series of ruthenium(II) tris bipyridine complexes using the same density functional and basis sets used in calculating LI3. Specifically, four closely-related bipyridine complexes { [Ru(N∧N)3]2+ with N∧N = bpy (6), 4,4’-dm-bpy (70), 4,4’-dph-bpy (73), and 4,4’-DTB-bpy (74) } were used for these calculations. In the process, we examined the gas-phase trans dissociation mechanism in greater detail than has been previously done and uncovered a two part mechanism. In the first part, the electron is transferred to a single ligand rather than symmetrically to all three ligands. It is the two Ru-N bonds to this ligand which are equally elongated in the transition state. The intrinsic reaction coordinate then continues down a ridge in hyperspace and bifurcates into one of two symmetry-equivalent 3MC structures with elongated trans bonds. Interestingly, no significant difference is found for the TS barriers for the four complexes treated here. Instead, LI3 is linearly correlated with the energy difference ΔE=E(3MLCT)−E(3MC), different from what was originally intended but still consistent with the FMO arguments underlying the derivation of LI3.

Investigations of the reaction mechanism of sodium with hydrogen fluoride to form sodium fluoride and the adsorption of hydrogen fluoride on sodium fluoride monomer and tetramer.

The reaction between Na and HF is a typical harpooning reaction which is of great interest due to its significance in understanding the elementary chemical reaction kinetics. This work aims to investigate the detailed reaction mechanisms of sodium with hydrogen fluoride and the adsorption of HF on the resultant NaF as well as the (NaF)4 tetramer. The results suggest that the reaction between Na and HF leads to the formation of sodium fluoride salt NaF and hydrogen gas. Na interacts with HF to form a complex HF···Na, and then the approaching of F atom of HF to Na results in a transition state H···F···Na. Accompanied by the broken of H-F bond, the bond forms between F and Na atoms as NaF, then the product NaF is yielded due to the removal of H atom. The resultant NaF can further form (NaF)4 tetramer. The interaction of NaF with HF leads to the complex NaF···HF; the form I as well as II of (NaF)4 can interact with HF to produce two complexes (i.e., (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF), but the form III of (NaF)4 can interact with HF to produce only one complex (NaF)4(III)···HF. These complexes were explored in terms of noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. NCI analyses confirm the existences of attractive interactions in the complexes HF···Na, NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF. QTAIM analyses suggest that the F···Na interaction forms in the HF···Na complex while the F···H hydrogen bonds form in NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF complexes. Natural bond orbital (NBO) analyses were also applied to analyze the intermolecular donor-acceptor orbital interactions in these complexes. These results would provide valuable insight into the chemical reaction of Na and HF and the adsorption interaction between sodium fluoride salt and HF. The calculations were carried out at the M06-L/6-311++G(2d,2p) level of theory which were performed using the Gaussian16 program. Intrinsic reaction coordinate (IRC) calculations were carried out at the same level of theory to confirm that the obtained transition state was true. The molecular surface electrostatic potential (MSEP) was employed to understand how the complex forms. Quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI) analysis was used to know the topology parameters at bond critical points (BCPs) and intermolecular interactions in the complex and intermediate. The topology parameters and the BCP plots were obtained by the Multiwfn software.

A 21st Century View of Allowed and Forbidden Electrocyclic Reactions.

In 1965, Woodward and Hoffmann proposed a theory to predict the stereochemistry of electrocyclic reactions, which, after expansion and generalization, became known as the Woodward-Hoffmann Rules. Subsequently, Longuet-Higgins and Abrahamson used correlation diagrams to propose that the stereoselectivity of electrocyclizations could be explained by the correlation of reactant and product orbitals with the same symmetry. Immediately thereafter, Hoffmann and Woodward applied correlation diagrams to explain the mechanism of cycloadditions. We describe these discoveries and their evolution. We now report an investigation of various electrocyclic reactions using DFT and CASSCF. We track the frontier molecular orbitals along the intrinsic reaction coordinate and modeled trajectories and examine the correlation between HOMO and LUMO for thermally forbidden systems. We also investigate the electrocyclizations of several highly polarized systems for which the Houk group had predicted that donor-acceptor substitution can induce zwitterionic character, thereby providing low-energy pathways for formally forbidden reactions. We conclude with perspectives on the field of pericyclic reactions, including a refinement as the meaning of Woodward and Hoffmann's "Violations. There are none!" Lastly, we comment on the burgeoning influence of computations on all fields of chemistry.

Experimental and kinetic study on 2-methoxyethanol part I: Molecular chemistry and pyrolysis investigation

Glycol ethers have been widely recognized as an alternative biofuels. 2-Methoxyethanol (ME2, HOCH2CH2OCH3) is the simplest and most representative glycol ether. Hence, the combustion chemistry of ME2 has aroused extensive interest. The ME2 pyrolysis has been investigated experimentally in a jet-stirred reactor (JSR) at atmospheric pressure within the temperature range of 650–1075 K for the first time. FTIR, GC–MS, and GC-FID were used to identify and quantify species profiles in ME2 pyrolysis. Sixteen intermediates were newly detected by the present work including acetaldehyde, hydroxyacetaldehyde, and methyl vinyl ether which are essential for mechanism development. The H abstraction reactions of ME2 by H, CH3, HO2, OH, O2, and the unimolecular reactions of four fuel-related radicals were first studied via high level ab initio calculations. The geometries optimization, vibrational frequencies, and intrinsic reaction coordinate (IRC) calculations were carried out at the M06–2X/6–311++G(d,p) level of theory. Conventional transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus/Master Equation (RRKM/ME) were used to calculate the temperature- and pressure-dependent rate constants from 300 to 2000 K and 0.01 to 100 atm for the first time. It is found that the H abstraction reactions at the two middle carbon atoms are the most favored pathways, and b-scissions for fuel-related radicals have the lowest energy barriers. The thermochemical properties of ME2 and its derived radicals have been obtained via the combination of composite methods. A mechanism involving 596 species and 3123 reactions was developed for the first time to predict the ME2 pyrolysis characteristics based on experimental and calculated results obtained by the present work. Good agreements were achieved between the measured and simulated results. Rate of production (ROP), as well as sensitivity analysis, were performed to get a deeper insight into the ME2 pyrolysis. It has been revealed that the major ME2 decomposition channels are the H abstractions by H, CH3, and OH radicals, and unimolecular reactions have scarce contributions to fuel decay. The results, in terms of the measured data and of the calculated results, and the newly developed kinetic model as well as findings obtained within this study will assist and contribute to a better understanding of combustion characteristics of ME2 and of glycol ethers as well.

Insight into acrolein activation by P/B intramolecular frustrated Lewis pairs

AbstractThe study investigates the reactivity of a cyclic five‐membered intramolecular P/B frustrated Lewis pair towards acrolein through a cycloaddition reaction. Intrinsic reaction coordinate (IRC) calculations suggest the single‐step mechanism. It has been observed that the cycloaddition reaction occurs through a concerted mechanism in both the presence and absence of the catalyst. Analysis of reaction force and reaction electronic flux provides valuable information about the total work required and electronic activity along the IRC. Additionally, natural bonding orbital (NBO) analyses enrich the understanding of the mechanism in terms of the electron transfer process during the chemical reaction.

DFT mechanistic study of [4+2] cycloaddition reactions of 1-methyl-1H-pyrrole-2,5-dione with furoic acid, anticancer Activity, molecular modeling and ADMET properties of new products from the Norcantharimide family substituted by a carboxylic acid

The [4+2] cycloaddition reactions of 1-methyl-1H-pyrrole-2,5-dione, with furan-2-carboxylic acid, 5-methylfuran-2-carboxylic acid and 5 -(hydroxymethyl)-furan-2-Carboxylic acid have been studied using various theoretical approaches at the M06/6–311++G(d,p) level of theory. Conceptual DFT (CDFT) analysis shows that 1-methyl-1H-pyrrole-2,5-dione behaves as an electrophile and furan-2-carboxylic acid, 5-methylfuran-2-carboxylic acid and 5 -(hydroxymethyl)-furan-2-Carboxylic acid act as nucleophiles. Furthermore, the regioselectivity has been explored from the Parr functions and Houk's rule. The studied DA reactions followed a one-step mechanism presenting a polar character where the formation of the new bonds takes place according to an asynchronous process. The activation and reaction energy values, extracted from the energetic profile plots, allow us to determine the most favorable reaction pathway. Moreover, the topology of the electronic localization function (ELF) in specific points of the intrinsic reaction coordinate profile (IRC) associated with the most favorable reaction pathway makes it possible to highlight a non-concerted two stages one-step molecular mechanism. The valorization of the anticancer activity of six products from the Norcantharimide family substituted by carboxylic acids has been carried out using molecular docking calculations. It has been shown, for the first time, that these products are efficient against breast cancer. Finally, the physicochemical properties and medicinal potential of these products were evaluated using the SwissADME online tool, revealing that they lack toxicity and their potential as promising drug candidates.

The increased Diels–Alder reactivity of umpolung tropone: analysis of individual atoms and bonds using QTAIM and IQA along complete IRC paths

AbstractA fruitful debate took place recently in literature, discussing the enhanced Diels–Alder reactivity of tropone derivatives for which the carbonyl polarity was reversed by means of umpolung. Karas et al. sustained that the umpolung increases the antiaromatic character of the ring, affecting the highest occupied molecular orbital (HOMO)/least unoccupied molecular orbital (LUMO) energies, speeding up the reaction. Tiekink et al. challenged this interpretation by sustaining that the asynchronicity of the reaction mechanisms, rather than orbital energy perturbation, was the main responsible for the smaller reaction barriers. We shed light on this dispute by computing full interaction quantum atom (IQA) and quantum theory of atoms in molecules (QTAIM) analyses over complete intrinsic reaction coordinate (IRC) paths for the Diels–Alder reaction of tropone and its umpolung derivatives, using the same systems studied by Karas et al. and Tiekink et al. Our results confirm that the asynchronicity is indeed very high for those reactions with smaller reaction barriers and offer an atom‐by‐atom and bond‐by‐bond analysis of the entire IRC pathways. Even though asynchronicity and lower reactions barriers seem to be related, antiaromaticity and lower barriers are related as well, but discussing both these interpretations does not necessarily require arguments on HOMO/LUMO energies to be invoked.

A TD‐DFT/DFT study on the ESIPT and photophysical properties of symmetrical 2‐hydroxybenzilidene1,3‐diamines derivatives

AbstractDensity functional theory (DFT) and Time dependent density functional theory (TD‐DFT) methods are used to simulate the photoexcitation and emission of the symmetrical 2‐hydroxybenzilidene1,3‐diamine (HBDA) Schiff base and some of its derivatives in the gas phase and solution. Our aim here is to explore the details of Excited‐State Intramolecular Proton Transfer (ESIPT) which underlies the activity of HBDA molecules as fluorescent probes. The structures of HBDA in S0 and the S1 states are optimized utilizing the DFT and TD‐DFT methods, respectively. Geometric configurations, electronic spectra, frontier molecular orbitals, and potential energy surfaces have all been computed and analyzed for the purpose of interpreting the mechanism of ESIPT. The geometries and relative stabilities of 15 tautomeric forms and the corresponding isomers of the studied molecules have been identified and their relative stabilities are investigated. The potential energy profiles and intrinsic reaction coordinates (IRC) calculations along the proton transfer coordinates both in the ground and in the excited state are monitored as well. The impact of the donating (OMe) and withdrawing (NO2) groups on the single and double proton transfers are investigated both in the gas phase and solution.

Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools.

The racemization of biomolecules in the active site can reduce the biological activity of drugs, and the mechanism involved in this process is still not fully comprehended. The present study investigates the impact of aromaticity on racemization using advanced theoretical techniques based on density functional theory. Calculations were performed at the ωb97xd/6-311++g(d,p) level of theory. A compelling explanation for the observed aromatic stabilization via resonance is put forward, involving a carbanion intermediate. The analysis, employing Hammett's parameters, convincingly supports the presence of a negative charge within the transition state of aromatic compounds. Moreover, the combined utilization of natural bond orbital (NBO) analysis and intrinsic reaction coordinate (IRC) calculations confirms the pronounced stabilization of electron distribution within the carbanion intermediate. To enhance our understanding of the racemization process, a thorough examination of the evolution of NBO charges and Wiberg bond indices (WBIs) at all points along the IRC profile is performed. This approach offers valuable insights into the synchronicity parameters governing the racemization reactions.

3D Information-Theoretic Analysis of the Simplest Hydrogen Abstraction Reaction.

We investigate the course of an elementary chemical reaction from the perspective of information theory in 3D space through the hypersurface of several information-theoretic (IT) functionals such as disequilibrium (D), Shannon entropy (S), Fisher information (I), and the complexity measures of Fisher-Shannon (FS) and López-Mancini-Calbet (LMC). The probe for the study is the hydrogenic identity abstraction reaction. In order to perform the analysis, the reactivity pattern of the reaction is examined by use of the aforementioned functionals of the single-particle density, which is analyzed in position (r) and momentum (p) spaces. The 3D analyses revealed interesting reactivity patterns in the neighborhood of the intrinsic reaction coordinate (IRC) path, which allow to interpret the reaction mechanism for this reaction in a novel manner. In addition, the chemically interesting regions that have been characterized through the information functionals and their complexity measures are depicted and analyzed in the framework of the three-dimensional structure of the information-theoretical data of a chemical reaction, that is, the reactant/product (R/P) complexes, the transition state (TS), and the ones that are only revealed through IT measures such as the bond-cleavage energy region (BCER), the bond-breaking/forming (B-B/F) region, and the spin-coupling (SC) process. Furthermore, focus has been placed on the diagonal part of the hypersurface of the IT functionals, aside from the IRC path itself, with the purpose of analyzing the dissociation process of the triatomic transition-state complex that has revealed other interesting features of the bond-breaking (B-B) process. In other respects, it is shown throughout the combined analyses of the 3D structure of the IT functionals in conjugated spaces that the chemically significant regions occurring at the onset of the TS are completely characterized by information-theoretic aspects of localizability (S), uniformity (D), and disorder. Further, novel regions of low complexity seem to indicate new boundaries for chemically stable complex molecules. Finally, the study reveals that the chemical reaction occurs at low-complexity regions, where the concurrent phenomena take place: bond-breaking/forming (B-B/F), bond-cleavage energy reservoirs (BCER), spin-coupling (SC), and transition state (TS).

Ortho-para interconversion of nuclear states of H2O through replica transition state: prospect of quantum entanglement at homodromic Bjerrum defect site

ContextFrom a nuclear spin prospective, water exists as para and ortho nuclear spin isomers (isotopomers). Spin interconversions in isolated molecules of water are forbidden, but many recent reports have shown them to happen in bulk, through dynamic proton exchanges happening between interconnected networks of a large array of water molecules. In this contribution, a possible explanation for an unexpected slow or delayed interconversion of ortho-para water in ice observed in an earlier reported experiment is provided. Using the results of quantum mechanical investigations, we have discussed the roles played by Bjerrum defects in the dynamic proton exchanges and ortho-para spin state interconversions. We guess that at the sites of the Bjerrum defects, there are possibilities of quantum entanglements of states, through pairwise interactions. Based on the perfectly correlated exchange happening via a replica transition state, we speculate that it can have significant influences on ortho-para interconversions of water. We also conjecture that the overall ortho-para interconversion is not a continuous process, rather can be imagined to be happening serendipitously, but within the boundary of the rules of quantum mechanics.MethodsAll computations were performed with Gaussian 09 program. B3LYP/6-31++G(d,p) methodology was used to compute all the stationary points. Further energy corrections were computed using CCSD(T)/aug-cc-pVTZ methodology. Intrinsic reaction coordinate (IRC) path computations were carried out for the transition states.

Characterizing Reaction Route Map of Realistic Molecular Reactions Based on Weight Rank Clique Filtration of Persistent Homology.

A reaction route map (RRM) constructed using the GRRM program is a collection of elementary reaction pathways, each of which comprises two equilibrium (EQ) geometries and one transition state (TS) geometry connected by an intrinsic reaction coordinate (IRC). An RRM can be mathematically represented by a graph with weights assigned to both vertices, corresponding to EQs, and edges, corresponding to TSs, representing the corresponding energies. In this study, we propose a method to extract topological descriptors of a weighted graph representing an RRM based on persistent homology (PH). The work of Mirth et al. [ J. Chem. Phys. 2021, 154, 114114], in which PH analysis was applied to the (3N - 6)-dimensional potential energy surface of an N atomic system, is related to the present method, but our method is practically applicable to realistic molecular reactions. Numerical assessments revealed that our method can extract the same information as the method proposed by Mirth et al. for the 0-th and 1-st PHs, except for the death of the 1-st PH. In addition, the information obtained from the 0-th PH corresponds to the analysis using the disconnectivity graph. The results of this study suggest that the descriptors obtained using the proposed method accurately reflect the characteristics of the chemical reactions and/or physicochemical properties of the system.

A Structure-Based Gaussian Expansion for Quantum Reaction Dynamics in Molecules: Application to Hydrogen Tunneling in Malonaldehyde.

We developed an approximate method for quantum reaction dynamics simulations, namely, a structure-based Gaussian (SBG) expansion approach, where SBG bases for the expansion of the wave function Ψ, expressed by a product of single-atom Cartesian Gaussians centered at the positions of respective nuclei, are mainly placed around critical structures on reaction pathways such as on the intrinsic reaction coordinate (IRC) through a transition state. In the present approach, the "pseudo-lattice points" at which SBGs are deployed are selected in a perturbative manner so as to make moderate the expansion length. We first applied the SBG idea to a two-dimensional quadruple-well model and obtained accurate tunneling splitting values between the lowest four states. We then applied it to hydrogen tunneling in malonaldehyde and achieved a tunneling splitting of 27.1 cm-1 with only 875 SBGs at the MP2/6-31G(d,p) level of theory, in good agreement with 25 cm-1 by the more elaborate multiconfiguration time-dependent Hartree method. Reasonable results were also obtained for singly and doubly deuterated malonaldehyde. We analyzed the tunneling states by utilizing expansion coefficients of individual SBGs and found that 40-45% of the SBGs in Ψ are nonplanar structures and SBGs away from the IRC contribute a little to hydrogen transfer.

The molecular level study of the fate of the CH3CH2C(O)OCH(O)CH3 radical derived from ethyl propionate

ABSTRACT A quantum chemical study has been presented on the decomposition of CH3CH2C(O)OCH(O • )CH3 which is derived from ethyl propionate (CH3CH2C(O)OCH2CH3) using the M06-2X/6-31 + G(d,p) level of theory. The thermal decomposition of CH3CH2C(O)OCH(O • )CH3 is essential to understand the chemistry of combustion of ethyl propionate. Here, the decomposition and oxidative pathways, bond fission and alpha ester rearrangement of CH3CH2C(O)OCH(O • )CH3 have been explored. We have obtained transition states for the different pathways and further verified each transition state by performing intrinsic reaction coordinate (IRC) calculations. The density of state spectra (DOS) was calculated using GaussSum software. The single-point energy calculations are performed at the same function but using larger basis sets such as 6-311++G(d,p) and 6-311++G(3df,2p). We have shown all stationary points and transition states involved in reaction pathways on the potential energy surface (PES) diagram and also discussed the thermochemistry of each reaction pathway. The thermal rate constants of various channels in the decomposition of CH3CH2C(O)OCH(O • )CH3 are determined using the Conventional Transition State Theory (CTST) in the temperature range of 250–450 K and 1atm. From PES, thermochemistry and kinetics analysis, we found that α-ester rearrangement produces propionic acid, which is dominant over the oxidative pathway for the decomposition of CH3CH2C(O)OCH(O • )CH3.