Regioselective and solvent-dependent photoisomerization induced internal conversion in red fluorescent protein chromophore analogues.

Photophysical properties of three red fluorescent protein (RFP) chromophore analogues are reported here. The three RFP chromophore analogues differ in the additional conjugation present in the RFP chromophore. The three chromophores do not exhibit any solvent effect in both absorption and fluorescence spectra. The photoirradiation experiments and recording of 1H NMR before and after irradiation on one of the three RFP model chromophores show isomerization of the (Z,E) diastereomer to the (E,E) diastereomer. Calculation of S0 and S1 potential energy curves shows the preference for isomerization through the exocyclic C[double bond, length as m-dash]C bond with Z-stereochemistry, thus corroborating the experimental results. The computational studies also suggest that torsional motion along the exocyclic C[double bond, length as m-dash]C bond pushes the molecules to a conical intersection, thus paving the pathway for radiationless deactivation.

Revisiting fulgide photochromism: Mechanistic decoding and electron transport from computational exploration.

The photochromic behavior of the fulgide molecule relies on ring-closure and ring-opening processes involving conical intersections during excited state transformation between isomers. The precise location and topography of these conical intersections significantly shape the decay process and fluorescence phenomena inherent to the molecule. This work combines electronic structure theory calculations using the density functional theory and wavefunction methods, as well as surface hopping simulation to analyze the photochemical behavior of an experimentally synthesized fulgide molecule, (E)-p-methylacetophenylisopropylidenesuccinic anhydride (1E). Our study reveals the conical intersection between the first excited state (S1) and the ground electronic state (S0), which emerges beyond the S1 minimum of 1E to the ring-closing side. The distinctive topography of this conical intersection appears to be sloped. These findings suggest a reduced quantum yield for the formation of the closed isomer, indicating a higher likelihood of reformation of the open isomer(s). The surface hopping simulation further supports this observation, revealing a mere ∼8% quantum yield for the formation of the closed isomer. In addition, the photoisomerization of the fulgide molecule initiates a cascade of conduction switching and holds great potential for applications in molecular electronics. Delving into the realm of molecular electronics, we have further examined the electron transport properties, disclosing the higher conductivity of the closed isomer.

Efficiency Conceptualization Model: A Theoretical Method for Predicting the Turnover of Catalysts.

In recent times, the theoretical prediction of catalytic efficiency is of utmost urgency. With the advent of density functional theory (DFT), reliable computations can delineate a quantitative aspect of the study. To this state-of-the art approach, valuable incorporation would be a tool that can acknowledge the efficiency of a catalyst. In the current work, we developed the efficiency conceptualization model (ECM) method that utilizes the quantum mechanical tool to achieve efficiency in terms of turnover frequency (TOF). Twenty-six experimentally designed transition metal (TM) water oxidation catalysts were chosen under similar experimental conditions of temperature, pressure, and pH to execute the same. The computations conclude that the Fe based [Fe(OTf)2(Me2Pytacn)] (MWOC-17) is a highly active catalyst and, therefore, can endure for more time in the catalytic cycle. Our results conclude that the Ir-based catalysts [Cp∗Ir(κ2-N,O)X] with MWOC-23: X = Cl; and MWOC-24: X = NO3 report the highest computed turnover numbers (TONs), Γ0computed TON of 406 and 490 against the highest experimental TONs,  Γ0 experimental TON of 2000 and 1200 respectively, whereas the Co-based [Co(12-TMC)]2+ (MWOC-19) has the lowest TONs (Γ0computed TON = 19,  Γ0 experimental TON= 16) among the chosen catalysts and thereby successful in corroborating the previous experimental results.

Realization of efficient and selective NO and NO2 detection via surface functionalized h-B2S2 monolayer.

In the ever-growing field of two-dimensional (2D) materials, the boron-sulfide (B2S2) monolayer is a promising new addition to MoS2-like 2D materials, with the boron (a lighter element) pair (B2 pair) having similar valence electrons to Mo. Herein, we have functionalized the h-phase boron sulfide monolayer by introducing oxygen atoms (Oh-B2S2) to widen its application scope as a gas sensor. The charge carrier mobilities of this system were found to be 790 × 102 cm2 V-1 s-1 and 32 × 102 cm2 V-1 s-1 for electrons and holes, respectively, which are much higher than the mobilities of the MoS2 monolayer. The potential application of the 2D Oh-B2S2 monolayer in the realm of gas sensing was evaluated using a combination of density functional theory (DFT), ab initio molecular dynamics (AIMD), and non-equilibrium Green's function (NEGF) based simulations. Our results imply that the Oh-B2S2 monolayer outperforms graphene and MoS2 in NO and NO2 selective sensing with higher adsorption energies (-0.56 and -0.16 eV) and charge transfer values (0.34 and 0.13e). Furthermore, the current-voltage characteristics show that the Oh-B2S2 monolayer may selectively detect NO and NO2 gases after bias 1.4 V, providing a greater possibility for the development of boron-based gas-sensing devices for future nanoelectronics.

Deciphering the Internal Conversion Processes Involved in the Photochemical Ring-Opening of 1,3-Cyclohexadiene by Symmetric sp2-Carbon Substitutions.

Chemical substituents hold the potential to markedly influence the photochemical behavior in molecular systems and assist in gaining a comprehensive understanding of nonadiabatic phenomena. In this study, we have conducted a comparative analysis of the influence of chemical substituents on the photochemical ring-opening of 1,3-cyclohexadiene (CHD), considering four systems: CHD, 2,3-dimethylcyclohexadiene (CHD-Me2-1), 1,4-dimethylcyclohexadiene (CHD-Me2-2), and 1,2,3,4-tetramethylcyclohexadiene (CHD-Me4), using electronic structure theory calculations and nonadiabatic molecular dynamics simulations. Employing extended multistate complete active space second-order perturbation (XMS-CASPT2) theory, we optimized reactants, S1 states, conical intersections (CIns), and products, revealing structural and energetic variations consistent with prior research. Nonadiabatic molecular dynamics simulation was used to gain insights into photochemical dynamics at state-averaged complete active space self-consistent field (SA-CASSCF) theory. CHD-Me4 exhibited reduced carbon-carbon single bond rupture rates, responsible for ring-opening, due to substituent proximity. Further, CHD-Me2-2 and CHD-Me4 displayed prolonged excited-state relaxation times, highlighting notable substituents' impact. Analysis of kinetic energy profiles of specific carbon atoms also revealed restrained atomic displacements, particularly in CHD-Me2-2 and CHD-Me4. These findings advance our understanding of how substituents modulate photochemical reactions in cyclohexadiene derivatives, guiding new molecular design and future research.

Probing the dynamic behaviour and magnetic identification of seven coordinated Mn(II) complexes: a combined AIMD and multi-reference approach.

We present an in-depth solution phase dynamics of rare seven coordinated pentagonal bipyramidal Mn(II) complexes, together with their binding affinity anticipated using ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT). Moreover, the simulations at different temperatures (25 °C and 90 °C) interpret the rigidity and stability of the ligands with Mn(II) ions. An intuitive approach for modulating the easy plane magnetic anisotropy of the mononuclear Mn(II) complex has been revealed by this work. In this regard, we have performed an extensive theoretical study based on the ab initio CASSCF/NEVPT2 method, exhibiting the presence of an easy plane magnetic anisotropy with a positive value of axial zero-field splitting (ZFS) parameter D. The complex's magnetic properties and electronic relaxation reveal that the rhombic ZFS term (E) can be modulated as the symmetry around the Mn(II) ion varies. The magnitude of the D-value increased with a more symmetrical equatorial ligand as found in the order of [Mn(pydpa)(H2O)] > [Mn(cbda)(H2O)]- > [Mn(dpaaa)(H2O)]- > [Mn(dpasam)(H2O)]-. Furthermore, we found that substituting the equatorial oxygen atom with heavier S and Se-donor atoms switches the sign of magnetic anisotropy for the Mn(II) complexes. The magnitude of the D-value increased when the energy levels of the ground state (GS) and the first excited state (ES) decreased. The observed magneto-structural correlation reveals that shortening the distance of the axial water molecule (Mn-O(w)) increases the D-value by an order of magnitude for the symmetrical [Mn(pydpa)(H2O)] complex. Overall, the combined analysis of solution phase dynamics of Mn(II) complexes and their magnetic characterization opens up new avenues in coordination chemistry, molecular magnetism, spin-crossover materials, and catalysis.

Exploring π-π interactions and electron transport in complexes involving a hexacationic host and PAH guest: a promising avenue for molecular devices.

Single isolated molecules and supramolecular host-guest systems, which consist of π-π stacking interactions, are emerging as promising building blocks for creating molecular electronic devices. In this article, we have investigated the noncovalent π-π interaction and intermolecular electron charge transport involved in a series of host-guest complexes formed between a cage-like host (H6+) and polycyclic aromatic hydrocarbon (PAH) guests (G1-G7) using different quantum chemical approaches. The host (H6+) consists of two triscationic π-electron-deficient trispyridiniumtriazine (TPZ3+) units that are bridged face-to-face by three ethylene-triazole-ethylene. Our theoretical calculations show that the perylene and naphthalene inclusion complexes G7⊂H and G1⊂H have the highest and lowest interaction energies, respectively. In addition, energy decomposition analysis (EDA) indicated that the dispersion interaction term, ΔEdisp, significantly contributes to the host-guest interaction and is correlated with the existence of π-π van der Waals interaction. Using the nonequilibrium Greens function (NEGF) method in combination with density functional theory (DFT), the current-voltage (I-V) curves of the complexes were estimated. The conductance values increased when the guests were embedded inside the host cavity. Notably, the complex G7⊂H has the maximum conductance value. Overall, this study provided the electron transport of the PAH inclusion host-guest complex through π-π interaction and provided a direction for the fabrication of future supramolecular molecular devices.

Unveiling the Noncovalent Interaction of Thiazol-2-ylidene and Its Derivatives as N-heterocyclic Carbene with Different Proton Donor Molecules.

The importance of noncovalent interaction has gained attention in various domains covering drug and novel catalyst design. The present study mainly characterizes the role of hydrogen bond (H-bond) and other intermolecular interactions in different (1 : 1) complex analogues formed between the N-aryl-thiazol-2-ylidene (YR) and five proton donor (HX) molecules. The analysis of the singlet-triplet energy gap ( Δ E S - T ${{\rm{\Delta }}E_{\left( {S - T} \right)} }$ ) confirmed the stability of the singlet state for this class of N-aryl-thiazol-2-ylidenes than the triplet state. The interaction energy values of the YR-HX complexes follow the order: YR-NH3

The first HyDRA challenge for computational vibrational spectroscopy.

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane-cis-1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies.

Inhibition of amyloid ß1-42 peptide aggregation by newly designed cyclometallated palladium complexes.

Uncontrolled amyloid aggregation is a frequent cause of neurodegenerative disorders such as prions and Alzheimer's disease (AD). As a result, many drug development approaches focus on evaluating novel molecules that can alter self-recognition pathways. Herein, we designed and synthesized the cyclometallated pyrene (Pd-1 and Pd-3) and anthracene (Pd-2) based palladium complexes ([Pd((L1)Cl] Pd-1, [Pd(L2)Cl](Pd-2), and [Pd(L3)Cl] (Pd-3)). This study explores the effect of these complexes on the aggregation, fibrillation, and amyloid formation of bovine serum albumin (BSA) and Aß1-42 peptide. Several spectroscopic methods were used to characterize all the Pd-complexes, and the molecular structure of Pd-3 was determined by X-ray crystallography. The secondary structures were studied using circular dichroism (CD) and transmission electron microscopy (TEM), while amyloid aggregation and inhibitory activities were investigated using the Thioflavin-T (ThT) fluorescence assay. Molecular docking of the Pd-complex (Pd-3) was done using fibril (PDB: 2BEG) and monomeric (PDB: 1IYT) peptides using Auto-dock Vina. As a result, the hydrogen bonding and hydrophobic interaction between the aromatic rings of the Pd-complexes and the amino acids of amyloid-ß peptides significantly reduced the production of ordered ß-sheets of amyloid fibrils and protein aggregation in the presence of Pd-2 and Pd-3 complexes.

Room temperature exciton formation and robust optical properties of CVD-grown ultrathin Bi2O2Se crystals on arbitrary substrates.

The appealing success of non-van der Waals (non-VdW) two-dimensional (2D) bismuth oxyselenide (Bi2O2Se) crystals in optoelectronics provides an exciting avenue to investigate their fundamental physical properties. To date, the majority of efforts have focused on understanding the properties of 2D Bi2O2Se, usually grown on a mica substrate. However, a gap exists in realizing the origin of photoluminescence (PL) of new age non-VdW Bi2O2Se at visible and near-infrared (NIR) wavelengths and the effect of growth substrates on the structure and optical properties. Herein, we report that the formation of multiple excitons in momentum valleys is responsible for broadband absorption and visible PL from a few layer thick 2D Bi2O2Se. The effect of growth substrates on the structure and optical properties is investigated in detail. Our studies unfold that the growth substrates (mica, sapphire, quartz, SiO2, glass) introduce strain/doping in chemical vapor deposition (CVD)-grown Bi2O2Se crystals, and consequently, the morphology, lattice constant, absorption coefficient, optical bandgap, refractive index, and PL properties are modulated. In addition, the possible direct/indirect multiple exciton formation at the valence band to the conduction band at different symmetry points of Bi2O2Se is analyzed from experimental data on different growth substrates and corroborated with the density functional theory (DFT) calculation of the electronic band structure. Furthermore, temperature-dependent photo-carrier dynamics discloses an A/Γ-exciton activation energy of 209.6 meV in Bi2O2Se. These findings are significant for the futuristic optoelectronic applications of Bi2O2Se and the choice of growth substrates on directly fabricated nanodevices.

Design and synthesis of piano-stool ruthenium(II) complexes and their studies on the inhibition of amyloid ß (1-42) peptide aggregation.

Misfolding and protein aggregation have been linked to numerous human neurodegenerative disorders such as Alzheimer's, prion, and Parkinson's diseases. Ruthenium (Ru) complexes have received considerable attention in studying protein aggregation due to their interesting photophysical and photo properties. In this study, we have synthesized the novel Ru complexes ([Ru(p-cymene)Cl(L-1)][PF6](Ru-1), and [Ru(p-cymene)Cl(L-2)][PF6](Ru-2)) and investigated their inhibitory activity against the bovine serum albumin (BSA) aggregation and the Aß1-42 peptides amyloid formation. Several spectroscopic methods were used to characterize these complexes, and the molecular structure of the complex was determined by X-ray crystallography. Amyloid aggregation and inhibition activities were examined using the Thioflavin-T (ThT) assay, and the secondary structures of the protein were analyzed by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). The cell viability assay was carried out on the neuroblastoma cell line, revealing that the complex Ru-2 showed better protective effects against Aß1-42 peptide toxicity on neuro-2a cells than the complex Ru-1. Molecular docking studies elucidate the binding sites and interactions between the Ru-complexes and Aß1-42 peptides. The experimental studies revealed that these complexes significantly inhibited the BSA aggregation and Aß1-42 amyloid fibril formation at 1:3 and 1:1 molar concentrations, respectively. Antioxidant assays demonstrated that these complexes act as antioxidants, protecting from amyloid-induced oxidative stress. Molecular docking studies with the monomeric Aß1-42 (PDB: 1IYT) show hydrophobic interaction, and both complexes bind preferably in the central region of the peptide and coordinate with two binding sites of the peptide. Hence, we suggest that the Ru-based complexes could be applied as a potential agent in metallopharmaceutical research against Alzheimer's disease.

Torsional Rotation in Ditopic Receptor Host and its Complex Formation with Resorcinol Guest: A Computational Study.

Noncovalent interactions due to the presence of heteroatoms in supramolecular compounds have gained a lot of attention. These different heteroatom-based supramolecular compounds have inspired us to examine the noncovalent interaction in the isolated host and host-guest complexes. In view of this, in the current manuscript, we investigated the stability and torsional energy barrier of different conformers of the ditopic receptor host 1,6-bis(2,6-bis(benzothiazol-2-yl) pyridine-4-yloxy) hexane (bbh). The conformer that is accompanied by intramolecular C-H⋯N and C-H⋯S interactions is relatively more stable than the others. Due to torsional angle rotation within the host, the C-H⋯N and C-H⋯S interactions get disrupted and exhibit different binding sites for capturing guest molecules. In addition, we have extended the investigation to understand the interaction energy and nature of interaction in host-guest (1 : 1 and 1 : 2) complexes formed between the host (bbh) and guest (resorcinol) by using different DFT functionals. Extended transition state-natural orbital chemical valence (ETS-NOCV) analysis of complexes revealed that the electrostatic interaction significantly contributes to the host-guest interaction energy. The noncovalent (NCI) analysis provides the existence of intermolecular hydrogen bonding and other weak interactions within the complexes.

Computational insight into a mechanistic overview of water exchange kinetics and thermodynamic stabilities of bis and tris-aquated complexes of lanthanides.

A thorough investigation of Ln3+ complexes with more than one inner-sphere water molecule is crucial for designing high relaxivity contrast agents (CAs) used in magnetic resonance imaging (MRI). This study accomplished a comparative stability analysis of two hexadentate (H3cbda and H3dpaa) and two heptadentate (H4peada and H3tpaa) ligands with Ln3+ ions. The higher stability of the hexadentate H3cbda and heptadentate H4peada ligands has been confirmed by the binding affinity and Gibbs free energy analysis in aqueous solution. In addition, energy decomposition analysis (EDA) reveals the higher binding affinity of the peada4- ligand than the cbda3- ligand towards Ln3+ ions due to the higher charge density of the peada4- ligand. Moreover, a mechanistic overview of water exchange kinetics has been carried out based on the strength of the metal-water bond. The strength of the metal-water bond follows the trend Gd-O47 (w) > Gd-O39 (w) > Gd-O36 (w) in the case of the tris-aquated [Gd(cbda)(H2O)3] and Gd-O43 (w) > Gd-O40 (w) for the bis-aquated [Gd(peada)(H2O)2]- complex, which was confirmed by bond length, electron density (ρ), and electron localization function (ELF) at the corresponding bond critical points. Our analysis also predicts that the activation energy barrier decreases with the decrease in bond strength; hence k ex increases. The 17O and 1H hyperfine coupling constant values of all the coordinated water molecules were different, calculated by using the second-order Douglas-Kroll-Hess (DKH2) approach. Furthermore, the ionic nature of the bonding in the metal-ligand (M-L) bond was confirmed by the Quantum Theory of Atoms-In-Molecules (QTAIM) and ELF along with energy decomposition analysis (EDA). We hope that the results can be used as a basis for the design of highly efficient Gd(iii)-based high relaxivity MRI contrast agents for medical applications.

Pyridinic Dominance N-Doped Graphene: A Potential Material for SO2 Gas Detection.

The sensors based on graphene have shown great promise in the detection of toxic air pollutants that are detrimental to nature and create risks to human health. Many recent experimental and computational efforts have been dedicated to sensor concepts incorporating pure graphene, graphene oxide, and doped graphene. Herein, a combination of spin-polarized density functional theory (DFT) with van der Waals correction and ab initio molecular dynamics (AIMD) approaches are utilized to assess the gas sensing potential of pyridinic dominance N-doped graphene (PNG) toward SO2 detection. The potential of PNG systems as SO2 sensing can be explored through an in-depth analysis of adsorption energies, electronic parameters, charge transfer, selectivity, and thermal stability. It is further demonstrated that external strains and the modulation of external electric fields are two effective ways to modify the adsorption strength. In light of these findings, our studies suggest that PNG monolayers have the potential to be an essential substrate for the detection of SO2.

Perturbing π-clouds with Substituents to Study the Effects on Reaction Dynamics of gauche-1,3-Butadiene to Bicyclobutane Electrocyclization.

The conical intersection (CI) governs the ultra-fast relaxation of excited states in a radiationless manner and are observed mainly in photochemical processes. In the current work, we investigated the effects of substituents on the reaction dynamics for the conversion of gauche-1,3-butadiene to bicyclobutane via photochemical electrocyclization. We incorporated both electron withdrawing (-F) and donating (-CH3 ) groups in the conjugated system. In our study, we optimized the minimum energy conical intersection (MECI) geometries using the multi-configurational state-averaged CASSCF approach, whereas, to study the ground state reaction pathways for the substituted derivatives, dispersion corrected, B3LYP-D3 functional was used. The non-adiabatic surface hopping molecular dynamics simulations were performed to observe the behaviour of electronic states involved throughout the photoconversion process. The results obtained from the multi-reference second-order perturbation correction of energy at the XMS-CASPT2 level of theory, topography analysis, and non-adiabatic dynamics suggest that the -CH3 substituted derivatives can undergo faster thermal conversion to the product in the ground state with a smaller activation energy barrier compared to -F substituted derivative. Our study also reveals that the GBUT to BIBUT conversion follows both conrotatory and disrotatory pathways, whereas, on substitution with -F or -CH3 , the conversion proceeds via the conrotatory pathway.

Unraveling the Mechanistic Pathway for the Dual Fluorescence in Green Fluorescent Protein (GFP) Chromophore Analogue: A Detailed Theoretical Investigation.

The photophysical properties of the para-sulfonamide (p-TsABDI) analogue of the green fluorescent protein (GFP) chromophore with both proton donating and accepting sites have been exploited in polar solvents to understand the origin of the unusual dual fluorescence nature of the chromophore. In the polar solvents, the compound undergoes structural rearrangement upon photoexcitation, leading to the ultrafast excited-state intermolecular proton transfer (ESIPT) phenomenon at the S1 surface. In this work, we employed both the static electronic structure calculations and on-the-fly molecular dynamics simulation to unravel the underlying reason for this peculiar behavior of the p-TsABDI analogue in polar solvents. To represent this adequately and provide extensive information on the ESIPT mechanism mediated by the solvent molecules, we considered explicit solvent molecules using the integral equation formalism variant of polarizable continuum (IEFPCM) model. From the static calculation analysis, we can conclude that the dual emissive behavior of the compound is ascribed to the proton transfer (PT) phenomena in the excited-state. However, based on the static calculation exclusively, it is hard to ascertain the mechanistic pathway of the PT phenomena. Hence, to investigate the dynamics and reaction mechanism for the ESIPT process, we performed the on-the-fly dynamics simulation for p-TsABDI in solvent clusters. Dynamics simulation results reveal that, based on the time lag between all the proton transfer processes, the ESIPT mechanism occurs in a stepwise manner from the benzylidene moiety of the chromophore to its imidazolinone moiety. However, the nonexistence of crossings between the S1- and S0-states confirms the PT characteristics of the reactions.

Low-Energy Electron Interaction with the Phosphate Group in DNA Molecule and the Characteristics of Single-Strand Break Pathways.

We modeled the low-energy electron attachment to the sugar-phosphate-sugar (SPS) molecule for investigating the single-strand break (3' C-O and 5' C-O) at the DNA backbone. In particular, we predicted the electron capture at the phosphate center. We found that 0.6 eV electron can attach to the phosphate group, and the lifetime (∼40-55 fs) of the resulting temporary negative ion state is more than what we found for the lifetime of the metastable species (∼18-20 fs) formed at the cytosine base center. We treated the two competing dissociation channels in SPS molecule, that is, both the 3' C-O and 5' C-O lesions, separately. The activation energy barrier calculated for 5' C-O bond rupture is found to be less than that for 3' C-O bond dissociation. The overall low-energy electron transfer process is found to be mediated through a "shape resonance state" formed at the phosphate center.

The role of the shape resonance state in low energy electron induced single strand break in 2'-deoxycytidine-5'-monophosphate.

Low energy electron (LEE) induced single strand break (SSB) has been studied for 2'-deoxycytidine-5'-monophosphate (5'-dCMPH) molecules in the gas phase by means of ab initio electronic structure methods and local complex potential based time-dependent wavepacket quantum mechanical calculations. We have found that the LEE attachment to this cytidine nucleotide results in the formation of a transient metastable anion. The results obtained here show that the electron attachment takes place at the cytosine nucleobase center and within 18-20 fs, the LEE transfers to the σ* orbital of the sugar-phosphate 5' C-O bond. The characteristic electron attachment cross section spectrum is found at ∼1 eV, which is in good agreement with the available experimental observations. Quantum mechanical tunneling of the 5' C-O bound vibrational energy levels may contribute to SSB only above 1.5 eV energy regimes.

Low energy electron induced cytosine base release in 2'-deoxycytidine-3'-monophosphate via glycosidic bond cleavage: a time-dependent wavepacket study.

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2'-deoxycytidine-3'-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3' C-O bond cleavage from the lowest π* shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π* orbital of the base to the σ* orbital of the glycosidic N-C bond. In addition, the metastable state formed after impinging LEE (0-1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N-C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ~35-55 fs. Comparison of salient features of the two dissociation events, i.e., 3' C-O single strand break and glycosidic N-C bond cleavage in 3'-dCMPH molecule are also provided.