nan Vikas

Exploring Water Catalysis in the Reaction of Thioformic Acid with Hydroxyl Radical: A Global Reaction Route Mapping Perspective

Hydrogen abstraction pathways, in the gas-phase reaction of tautomers of thioformic acid (TFA), TFA(thiol), and TFA(thione), with hydroxyl radical in the presence and absence of single water molecule acting as a catalyst, is investigated with high-level quantum mechanical calculations at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p), CCSD(T)/6-311++G(d,p)//DFT/BHandHLYP/6-311++G(d,p), and DFT/B3LYP/6-311++G(2df,2p) levels of the theory. A systematic and automated search of the potential energy surface (PES) for the reaction pathways is performed using the global reaction route mapping (GRRM) method that employs an uphill walking technique to search prereaction complexes and transition states. The computations reveal significant lowering of the PES and substantial reduction in the activation energy for the hydrogen abstraction pathway in the presence of water, thereby proving water as an efficient catalyst in the reaction of both the TFA tautomers with OH radical. The hydrogen-bonding interactions are observed to be responsible for the large catalytic effect of water. Notably, in the case of TFA(thiol), formyl hydrogen abstraction is observed to be kinetically more favorable, while acidic hydrogen abstraction is observed to be thermodynamically more feasible. Interestingly, in the case of TFA(thione), reaction pathways involving only formyl hydrogen abstraction were observed to be feasible. The water-catalyzed hydrogen abstraction reaction of TFA with hydroxyl radical, investigated in this work, can provide significant insights into the corresponding reaction in the biological systems.

Electron-correlation based externally predictive QSARs for mutagenicity of nitrated-PAHs in Salmonella typhimurium TA100.

In quantitative modeling, there are two major aspects that decide reliability and real external predictivity of a structure-activity relationship (SAR) based on quantum chemical descriptors. First, the information encoded in employed molecular descriptors, computed through a quantum-mechanical method, should be precisely estimated. The accuracy of the quantum-mechanical method, however, is dependent upon the amount of electron-correlation it incorporates. Second, the real external predictivity of a developed quantitative SAR (QSAR) should be validated employing an external prediction set. In this work, to analyze the role of electron-correlation, QSAR models are developed for a set of 51 ubiquitous pollutants, namely, nitrated monocyclic and polycyclic aromatic hydrocarbons (nitrated-AHs and PAHs) having mutagenic activity in TA100 strain of Salmonella typhimurium. The quality of the models, through state-of-the-art external validation procedures employing an external prediction set, is compared to the best models known in the literature for mutagenicity. The molecular descriptors whose electron-correlation contribution is analyzed include total energy, energy of HOMO and LUMO, and commonly employed electron-density based descriptors such as chemical hardness, chemical softness, absolute electronegativity and electrophilicity index. The electron-correlation based QSARs are also compared with those developed using quantum-mechanical descriptors computed with advanced semi-empirical (SE) methods such as PM6, PM7, RM1, and ab initio methods, namely, the Hartree-Fock (HF) and the density functional theory (DFT). The models, developed using electron-correlation contribution of the quantum-mechanical descriptors, are found to be not only reliable but also satisfactorily predictive when compared to the existing robust models. The robustness of the models based on descriptors computed through advanced SE methods, is also observed to be comparable to those developed with the electron-correlation based descriptors. The work emphasizes that the correlation-energy can serve as a reliable descriptor to explore the origin of biological activities at the level of electron-dynamics.

Externally predictive quantitative modeling of supercooled liquid vapor pressure of polychlorinated-naphthalenes through electron-correlation based quantum-mechanical descriptors.

For predicting physico-chemical properties related to environmental fate of molecules, quantitative structure-property relationships (QSPRs) are valuable tools in environmental chemistry. For developing a QSPR, molecular descriptors computed through quantum-mechanical methods are generally employed. The accuracy of a quantum-mechanical method, however, rests on the amount of electron-correlation estimated by the method. In this work, single-descriptor QSPRs for supercooled liquid vapor pressure of chloronaphthalenes and polychlorinated-naphthalenes are developed using molecular descriptors based on the electron-correlation contribution of the quantum-mechanical descriptor. The quantum-mechanical descriptors for which the electron-correlation contribution is analyzed include total-energy, mean polarizability, dipole moment, frontier orbital (HOMO/LUMO) energy, and density-functional theory (DFT) based descriptors, namely, absolute electronegativity, chemical hardness, and electrophilicity index. A total of 40 single-descriptor QSPRs were developed using molecular descriptors computed with advanced semi-empirical (SE) methods, namely, RM1, PM7, and ab intio methods, namely, Hartree-Fock and DFT. The developed QSPRs are validated using state-of-the-art external validation procedures employing an external prediction set. From the comparison of external predictivity of the models, it is observed that the single-descriptor QSPRs developed using total energy and correlation energy are found to be far more robust and predictive than those developed using commonly employed descriptors such as HOMO/LUMO energy and dipole moment. The work proposes that if real external predictivity of a QSPR model is desired to be explored, particularly, in terms of intra-molecular interactions, correlation-energy serves as a more appropriate descriptor than the polarizability. However, for developing QSPRs, computationally inexpensive advanced SE methods such as PM7 can be more reliable than the expensive ab inito methods.

Global reaction route mapping of isomerization pathways of exotic C6H molecular species.

C6H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C6H is explored to search isomers of C6H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C6H. The reaction route search is performed through global reaction route mapping method, which utilizes an uphill walking technique based on an anharmonic downward distortion following approach to search intermediates and transition states. The computations performed at the CASSCF∕aug-cc-pVTZ, CCSD(T)∕6-311++G(d,p)∕∕DFT∕B3LYP∕6-311++G(d,p), and DFT∕B3LYP∕aug-cc-pVTZ levels of the theory identified 14 isomers (including 8 new isomeric forms of C6H) and 28 transition states. Most of the identified isomers are found to have significant multireference character. The kinetic stability and natural bond orbital analysis of the identified isomers is also investigated. The isomeric forms are further characterized using spectral analysis involving rotational constants, vibrational frequencies, and Raman scattering activities as well as analyzing the effect of isotopic substitution of hydrogen on the spectral features. This study proposes that the linear-C6H can readily isomerize to a six-member ring isomer.

Exploring the role of quantum chemical descriptors in modeling acute toxicity of diverse chemicals to Daphnia magna

Various quantum-mechanically computed molecular and thermodynamic descriptors along with physico-chemical, electrostatic and topological descriptors are compared while developing quantitative structure-activity relationships (QSARs) for the acute toxicity of 252 diverse organic chemicals towards Daphnia magna. QSAR models based on the quantum-chemical descriptors, computed with routinely employed advanced semi-empirical and ab-initio methods, along with the electron-correlation contribution (CORR) of the descriptors, are analyzed for the external predictivity of the acute toxicity. The models with reliable internal stability and external predictivity are found to be based on the HOMO energy along with the physico-chemical, electrostatic and topological descriptors. Besides this, the total energy and electron-correlation energy are also observed as highly reliable descriptors, suggesting that the intra-molecular interactions between the electrons play an important role in the origin of the acute toxicity, which is in fact an unexplored phenomenon. The models based on quantum-chemical descriptors such as chemical hardness, absolute electronegativity, standard Gibbs free energy and enthalpy are also observed to be reliable. A comparison of the robust models based on the quantum-chemical descriptors computed with various quantum-mechanical methods suggests that the advanced semi-empirical methods such as PM7 can be more reliable than the ab-initio methods which are computationally more expensive.

Does electron-correlation has any role in the quantitative structure-activity relationships?

For developing quantitative structure-activity relationships (QSARs), quantum-mechanical molecular descriptors based on the state-of-the-art quantum-mechanical methods such as Hartree-Fock (HF) method and density-functional theory (DFT), are now routinely employed. The validity of these quantum-mechanical methods, however, rests on the accurate estimation of electron-correlation energy. This work analyses the role of electron-correlation, using correlation energy as a molecular descriptor, in the QSARs. In particular, QSAR models, for the mutagenic activity of a set of nitrated polycyclic aromatic hydrocarbons (nitro-PAHs), are examined for the role of electron-correlation through state-of-the-art external validation parameters such as concordance correlation coefficient and recently proposed predictive squared correlation coefficients, namely, QF1(2), QF2(2), and QF3(2) etc. The electron-correlation contribution to the highest occupied and lowest unoccupied molecular orbital (HOMO/LUMO) energies is also analyzed. QSAR models based on the semi-empirical quantum-mechanical methods like PM6 and RM1 are also compared. It is found that the models, developed using electron-correlation contribution of the quantum-mechanical descriptors, are not only robust but also relatively more predictive than those developed with the HF and DFT descriptors. The latter are found to be even less reliable than PM6 and RM1 descriptors based models, which show comparable robustness and predictivity with those developed using electron correlation based descriptors. The external predictivity of model based on semi-empirical descriptors can be improved if electron-correlation contribution of the quantum-mechanical descriptors is explicitly included in the model. This work reports the first-ever use of electron-correlation energy and its contribution to the HOMO/LUMO energies as molecular descriptors.

Single-descriptor based quantum-chemical QSPRs for physico-chemical properties of polychlorinated-dibenzo-p-dioxins and -dibenzo-furans (PCDD/Fs): exploring the role of electron-correlation.

In this work, we propose and analyze single-descriptor based quantitative structure-property relationships (QSPRs) developed using quantum-chemical descriptors and their electron-correlation contribution, for various physico-chemical properties, namely, aqueous solubility, subcooled liquid vapour pressure, n-octanol/water and n-octanol/air partition coefficients of polychlorinated-dibenzo-p-dioxins (PCDDs) and -dibenzo-furans (PCDFs). The predictivity of the developed QSPRs is examined through external validation procedures employing an external prediction set of chemicals not used in the QSPR model development. From the comparison of different models, it is observed that the total energy and the mean polarizability of a molecule are highly significant in determining the predictivity of a QSPR, whereas dipole moment is found to be a poor descriptor in the models developed for all the properties analyzed. Besides these, the electron density based descriptors, namely, absolute electronegativity and electrophilicity index, were also observed to be highly influential in determining the external prediction for partition coefficients.

On the mechanism of intramolecular nitrogen‐atom hopping in the carbon chain of C6N radical: A Plausible 3c−4e crossover π̂ Long‐Bond

Linear isomers of C6N radical differ in the position of the nitrogen atom in the carbon chain of C6N. Reaction routes, involving intramolecular nitrogen atom insertion at varying position in the carbon chain of C6N, are analyzed for the isomerisation between linear isomers of C6N. Through an automated and systematic search performed with global reaction route mapping of the potential energy surface, thermal isomerisation pathways for C6N radical are proposed based on the computations carried out at CASSCF/aug‐cc‐pVTZ, and CCSD(T)/6‐311++G(d,p)//B3LYP/6‐311++G(d,p) levels of the theory. Notably, a high lying linear isomer, centrosymmetric with respect to the nitrogen atom, is observed to be stabilized by a unique crossover three center‐four electron π long bond between the carbon atoms that are spatially separated by a nitrogen atom in a natural bond orbital. This long bond is concluded to be responsible for the predicted thermal isomerisation to be more feasible than the dissociation during the isomerisation pathway of a linear isomer of C6N.

Electron in one-dimensional symmetric and asymmetric double-well potentials under intense/superintense laser fields: A numerical study based on time-dependent Schrödinger equation

The responses of an electron moving in one-dimensional symmetric and asymmetric double-well oscillator (DWO) potentials respectively are analyzed under intense and superintense laser fields by numerically solving the time-dependent Schrodinger equation and evolving the systems for 96 fs at λ=1064 nm as well as different laser intensities. Emphasis is placed on the study of only those features which can arise from the response of a single system. A detailed investigation of multiphoton processes such as high harmonics generation and the energy spectrum (obtained by fast fourier transform of the autocorrelation function) is made. The applicability of these DWOs as model systems for the generation of attosecond pulses is examined. Furthermore, a comparison is made with atoms and molecules under similar conditions, thereby establishing a qualitative parallelism in the behavior of real atoms/molecules and these model DWO systems.

Role of exchange and correlation in the real external prediction of mutagenicity: performance of hybrid and meta-hybrid exchange–correlation functionals

Quantum-mechanical exchange and correlation interactions between electrons are quite crucial in deciding molecular geometry and properties. Such electronic interactions can have a significant role in the reliability of a quantitative structure–activity relationship (QSAR) because the biological activities of the chemicals can be described as a function of the molecular structure through the QSARs which are routinely based on the quantum-mechanical molecular descriptors. In this work, we present a detailed analysis of the effect of the quantum-mechanical exchange and correlation on the internal stability and external predictivity of a QSAR model based on the quantum-mechanical molecular descriptors while modeling the mutagenic activity of a set of 51 nitrated-polycyclic aromatic hydrocarbons (PAHs). For this, various molecular descriptors are computed using electronic structure methods such as the Hartree–Fock (HF) method, and density functional theory (DFT) employing only the exchange functionals (HFX, B88), pure exchange and correlation functionals (HFX + LYP, BLYP), hybrid (B3LYP), meta (M06-L), and meta-hybrid (M06, M06-2X) exchange–correlation (XC) functionals. To further analyze the role of electron-correlation, QSAR models are also developed using the descriptors incorporating mainly the effect of electron-correlation. The external predictivity of the developed models is assessed through state-of-the-art external validation parameters employing an external prediction set of compounds. A comparison of the quality of the models developed with the descriptors computed using different electronic structure methods revealed that the exchange interactions are quite critical along with the electron-correlation in modeling the mutagenicity. Notably, for most of the models, electron-correlation based descriptors are found to be highly reliable when computed using the hybrid XC functionals, particularly B3LYP and M06-2X.