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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Selective cleaving of both O–H and O–D bonds in HOD is achieved using reasonably simple UV pulses to excite the HOD molecule in its ground vibrational state to the repulsive first excited à (1B1) surface. Detailed theoretical analysis of population transfer and flux in theH+O–D/H–O+D channels reveals an important preparatory role for the cross-talk between the participating levels and a possible role for the beat structure of the population transfer oscillations in facilitating selective dissociation. Excitation using a 50 fs single color 67 169 cm-1 laserpulse achieves a branching ratio H+O–D/H–O+D=5.64 with 82% flux in theH+O–D channel and 15% in the H–O+D channel. A two color 50 fs laser pulse with frequencies of 54 920 and 52 303 cm-1 provides a branching ratio of H–O+D/H+O–D=2.83 and 52% flux in the H–O+D channel and 18% in the H+O–D channel. [ABSTRACT FROM AUTHOR]

Vibrational excitation (νf←νi) cross-sections σνf←νi(E) in resonant e-N2 and e-H2 scattering are calculated from transition matrix elements Tνf,νi(E) obtained using Fourier transform of the cross correlation function <[lowercase_phi_synonym]νf(R)|ψνi(R,t)>, where ψνi(R,t)≃e-iHA2-(R)t/h[lowercase_phi_synonym]νi(R) with time evolution under the influence of the resonance anionic Hamiltonian HA2-(A2-=N2-/H2-) implemented using Lanczos and fast Fourier transforms. The target (A2) vibrational eigenfunctions [lowercase_phi_synonym]νi(R) and [lowercase_phi_synonym]νf(R) are calculated using Fourier grid Hamiltonian method applied to potential energy (PE) curves of the neutral target. Application of this simple systematization to calculate vibrational structure in e-N2 and e-H2 scattering cross-sections provides mechanistic insights into features underlying presence/absence of structure in e-N2 and e-H2 scattering cross-sections. The results obtained with approximate PE curves are in reasonable agreement with experimental/calculated cross-section profiles, and cross correlation functions provide a simple demarcation between the boomerang and impulse models. [ABSTRACT FROM AUTHOR]

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Vibrational excitation cross-sections $\sigma_{\nu_f \leftarrow \nu_i } (E)$ in resonant e-F and HCl scattering are calculated from transition matrix elements $T_{\nu_f \leftarrow \nu_i } (E)$ obtained using Fourier transform of the cross correlation function $\left\langle {\phi_{\nu_f } \left( R \right)\vert \Psi_{\nu_i } \left( {R,t} \right)} \right\rangle $ where $\Psi_{\nu_i } \left( {R,t} \right)\approx e^{-i\hbar H_{AB^-} \left( R \right)t}\phi_{\nu { }_i} \left( R \right)$. Time evolution under the influence of the resonance anionic Hamiltonian H- (AB=F/HCl) is effected using Lanczos reduction technique followed by fast Fourier transform and the target (AB) vibrational eigenfunctions $\phi _{\nu_i } \left( R \right)$ and $\phi_{\nu_f } \left( R \right)$ are calculated using Fourier grid Hamiltonian method applied to potential energy (PE) curve of the neutral target. The resulting vibrational excitation cross-sections provide reasonable agreement with experimental and other theoretical results. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Quantum dynamical calculations on HOD subjected to different combinations of IR and UV pulses have been made to isolate field attributes which maximise selectivity and yield in the photodissociation of the desired O-H/O-D bond. Results from IR+UV pulse combinations which provide very high selectivity and/or yield are analysed in detail using population transfer, probability density flow, and flux variations to obtain microdynamic details favouring selectivity and yield. The expectation values for stretch and momentum in O-H and O-D bonds of the H-O-D molecule subjected to UV pulses effecting selective cleavage of these bonds have been analysed to decipher the mechanistic basis of selective dissociation. Fully quantum dynamical calculations using both the ground and excited potential energy surfaces with different initial states and UV pulses reveal that prior stretch in a bond before transferring it to the repulsive first excited state ensures preferential dissociation of this bond. The sampling of large stretch values and a quick downhill motion in the channel corresponding to dissociation of the prestretched bond on the upper surface are seen to underlie this preferential dissociation. [ABSTRACT FROM AUTHOR]

The structural features of vibrational excitation cross-sections in resonant e-H2 scattering have been investigated using a time dependent wave packet approach and a local complex potential to describe the 2Σu+ H2- anion. An analysis of the partial contributions to the vibrational excitation cross-sections reveals that all features of the excitation profile result from simple interference between bound vibrational levels of H2 and H2-. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [ABSTRACT FROM AUTHOR]

Selective control of HOD photodissociation (H--O + D ← HOD → H + O--D) has been theoretically investigated using CW lasers with appropriate carrier frequency and |0, 0>, |0, 1> and |0, 2> with zero quantum of excitation in the O-H bond and zero, one and two quanta of excitation in the O--D bond as the initial states. Results indicate that the O--H bond in HOD can be selectively dissociated with a maximum flux of 87% in the H + O--D channel from the ground vibrational state |0, 0>. For the O--D bond dissociation, it requires two quanta of excitation (|0, 2>) in the O--D mode to obtain 83% flux in the H--O + D channel. Use of a two colour laser set-up in conjunction with the field optimized initial state (FOIST) scheme to obtain an optimal linear combination of |0, 0> and |0, 1> vibrational states as the initial state provides an additional 7% improvement to flux in the H--O + D channel as compared to that from the pure |0, 1> state. [ABSTRACT FROM AUTHOR]

Results from application of a new implementation of the time-dependent wave packet (TDWP) approach to the calculation of vibrational excitation cross-sections in resonant e-CO scattering are presented to examine its applicability in the treatment of e-molecule resonances. The results show that the SCF level local complex potential (LCP) in conjunction with the TDWP approach can reproduce experimental features quite satisfactorily. [ABSTRACT FROM AUTHOR]

Abstract: Selective Control of HOD photodissociation has been investigated using simple field profiles. Initial results indicate that preferential dissociation of O–H bond may be achieved from the ground vibrational state and that the O–D bond can be selectively dissociated using only the fundamental excitation in this mode. Dissociation from 2 quanta of excitation in the O–D mode produces 82.8% products with O–D bond dissociation. Preferential maximization of O–D dissociation vis-à-vis O–H bond may also be achieved from the ground vibrational state using a combination of two lasers with carrier frequencies 54920cm−1 and 52203cm−1. The use of Field Optimized Initial STate (FOIST) based scheme to enhance selective control of HOD photodissociation provides additional 6−8% H–O+D products compared to those obtained without FOIST. [Copyright &y& Elsevier]

Effect of quantum mechanical tunneling on single strand breaks induced by low energy electron (LEE) has been investigated in a modeled gas phase system, 2′-deoxycytidine-3′-monophosphate (3′-dCMPH). The potential energy curves for the sugar-phosphate C-O (3′ C-O) bond cleavage have been generated using second order Mo\ller-Plesset perturbation theory at the 6-31+G(d) accuracy level. Results from the electronic structure theory calculations in conjunction with our time dependent calculations for the 3′ C-O bond rupture in 3′-dCMPH using local complex potential based time dependent wave packet approach show significant quantum tunneling of the 3′ C-O bond from the bound vibrational states above 1 eV of the anionic potential energy curve. A comparison of the fragmentation profile with that of our earlier gas phase investigations based on Hartree-Fock and density functional theory - Becke, 3-parameter, Lee-Yang-Parr methods with 6-31+G(d) basis set is also provided. Further, inspection of the singly occupied molecular orbitals generated at different 3′ C-O bond lengths clearly indicates the electron transfer from the low lying base-π* shape resonance state to the phosphate P = O π* orbital of the DNA backbone during the strand breaks. The decisive step during LEE induced strand breaks follows via 'charge induced dissociation' (CID) for the metastable anion formed below 1 eV, whereas quantum mechanical tunnel-ing is out-weighted the CID mechanism for the LEE above 1 eV. [ABSTRACT FROM AUTHOR]

The resonant low-energy electron (LEE) induced scattering off biomolecules is proposed to undergo dissociative electron attachment (DEA) as one of the favoured pathways. In the current work, we have considered the citric acid molecule due to its biological relevance in the Krebs cycle, in which LEEs may affect and lead to metabolic dysfunction. To investigate the DEA pathway of citric acid, we implemented the local complex potential-based time-dependent wavepacket (LCP-TDWP) approach. From our calculation, we observed that the vertical attachment energy (VAE) of the citric acid system is found to be −1.17 eV, and the electron attaches itself to the 2-carboxylic acid group to form a transient negative ion (TNI) which further dissociates into a free radical and a radical anion. The lifetime for the TNI is around 1000 fs, with a maximum cross-section seen at 1.09 eV. The interaction of low-energy electrons with citric acid can lead to dissociative electron attachment (DEA). In the current work, we used the local complex potential-based time-dependent wave packet (LCP-TDWP) approach to investigate DEA to citric acid. The time evolution of the probability density suggests the possibility of a boomerang model. [ABSTRACT FROM AUTHOR]

A new 3D fluorescent amide-functionalized Cd(II)-based metal-organic framework (MOF) with molecular formula [Cd5Cl6(L)(HL)2]·7H2O (1) was synthesized under solvothermal conditions using CdCl2·H2O and 4-(1H-tetrazol-5-yl)-N-[4-(1H-tetrazol-5-yl)phenyl]benzamide (H2L) in DMF/methanol in the presence of conc. HCl. Single-crystal X-diffraction analysis reveals that the 3D framework structure of 1 is constructed from octahedrally coordinated Cd2+ ions interconncted by chloride anions and ditopic tetrazolate-based ligand molecules. The phase-purity of the compound was confirmed by X-ray powder diffraction (XRPD) analysis, infrared spectroscopy, and elemental analysis. Thermogravimetric analysis suggests that 1 is thermally stable up to 300 °C. Steady-state fluorescence titration experiments reveal that activated 1' can selectively detect 2,4,6-trinitrophenol (TNP) in the presence of other competing nitroaromatic compounds with a detection limit of 42.84 ppb. Recyclability experiments reveal that 1' retains its initial fluorescence intensity even after several cycles, suggesting high photostability and reusability for long-term sensing applications. The extraordinarily selective fluorescence quenching is assigned to the presence of energy and electron transfer processes as well as the electrostatic interactions of the MOF with TNP. This new 3D amide-functionalized MOF is a potential candidate that can be developed into a highly selective and sensitive sensing device for the in-field detection of TNP. [ABSTRACT FROM AUTHOR]

A new 3D fluorescent amide-functionalized Cd(II)-based metal-organic framework (MOF) with molecular formula [Cd5Cl6(L)(HL)2]·7H2O (1) was synthesized under solvothermal conditions using CdCl2·H2O and 4-(1H-tetrazol-5-yl)-N-[4-(1H-tetrazol-5-yl)phenyl]benzamide (H2L) in DMF/methanol in the presence of conc. HCl. Single-crystal X-diffraction analysis reveals that the 3D framework structure of 1 is constructed from octahedrally coordinated Cd2+ ions interconncted by chloride anions and ditopic tetrazolate-based ligand molecules. The phase-purity of the compound was confirmed by X-ray powder diffraction (XRPD) analysis, infrared spectroscopy, and elemental analysis. Thermogravimetric analysis suggests that 1 is thermally stable up to 300 °C. Steady-state fluorescence titration experiments reveal that activated 1' can selectively detect 2,4,6-trinitrophenol (TNP) in the presence of other competing nitroaromatic compounds with a detection limit of 42.84 ppb. Recyclability experiments reveal that 1' retains its initial fluorescence intensity even after several cycles, suggesting high photostability and reusability for long-term sensing applications. The extraordinarily selective fluorescence quenching is assigned to the presence of energy and electron transfer processes as well as the electrostatic interactions of the MOF with TNP. This new 3D amide-functionalized MOF is a potential candidate that can be developed into a highly selective and sensitive sensing device for the in-field detection of TNP. [ABSTRACT FROM AUTHOR]

Three polycyclic chromeno[2,3-b]indolecontaining indole and naphthalene rings fused by a pyran ring were synthesized by metal-free C–H functionalization method and their photophysical studies were done. Steady state absorption spectra do not show solvent effect while fluorescence spectra exhibit solvatochromic shift. The molecules exhibit ultra-high Stokes shift of the order of 3.07 eV (24,696 cm−1) in acetonitrile and 2.12 eV (17,054 cm−1) in ethyl acetate. To corroborate experimental observation, we performed computational investigation both in gas and solvent phases. The computed results are in good agreement with the experimental observation. Analysis of the frontier molecular orbitals as well as natural transition orbitals depicts intramolecular charge transfer in the molecules. Further, gas phase as well as solvent phases optimized structures in the ground and excited states of all chosen molecules show increase in planarity in the excited state. An excited state intramolecular charge transfer accompanied by structural relaxation leading to planarity in the excited state has been suggested to cause large Stokes shifted fluorescence emission in these molecules. [ABSTRACT FROM AUTHOR]

Abstract: Bond dissociation in the deutereted water molecule HOD has been investigated to explore the possibility of selective control of dissociation of O–H and O–D bonds using simple field profiles and initial states that do not require high overtone excitations. Preliminary results indicate that considerable selectivity in dissociation of O–H and O–D bonds can be achieved using fundamental and first overtone excitations only and use of field optimized initial state (FOIST) based scheme with appropriate choice of field parameters and initial states may enhance both selectivity and yield. [Copyright &y& Elsevier]

Effect of electron correlation on single strand breaks (SSBs) induced by low energy electron (LEE) has been investigated in a fragment excised from a DNA, viz., 2′-deoxycytidine-3′-monophosphate [3′-dCMPH] molecule in gas phase at DFT-B3LYP/6-31+G(d) accuracy level and using local complex potential based time dependent wave packet (LCP-TDWP) approach. The results obtained, in conjunction with our earlier investigation, show the possibility of SSB at very low energy (0.15 eV) where the LEE transfers from π* to σ* resonance state which resembles a SN2 type mechanism. In addition, for the first time, an indication of quantum mechanical tunneling in strand breaking is seen from the highest anionic bound vibrational state (χ5), which may have a substantial role during DNA damage. [ABSTRACT FROM AUTHOR]

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 Aβ 1 – 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-β peptides significantly reduced the production of ordered β-sheets of amyloid fibrils and protein aggregation in the presence of Pd-2 and Pd-3 complexes. • Cyclometallated palladium complexes were designed and synthesized. • Molecular structure of representative complex was determined by X-ray crystallography. • In vitro and in silico anti-aggregation activities were performed against Aβ 1 – 42 peptide. • Palladium complexes interact with peptides and reduce amyloid-mediated cytotoxicity. [ABSTRACT FROM AUTHOR]

In the present work, we carried out a docking study of five aminothiazole-based Pd(II) complexes with B-DNA, followed by a noncovalent interaction analysis (hydrogen bonding, van der Waals, and repulsive interactions). The DNA-N 2 and DNA-N 4 show the best binding affinity supported by their corresponding Inhibition constant (k i). [Display omitted] In recent times, cancer has been reported as one of the largest growing deadly diseases in humankind. The use of cisplatin for oncological treatment has been known for a long time. However, no other suitable solutions have been extensively explored to substitute highly potent yet toxic cisplatin. In the current work, we have computationally investigated five experimentally synthesized Pd(II) complexes (N n , n = 1–5), along with their positively charged aqua derivatives (N n W, n = 1–5), having aminothiazole analogues that may act as a potent inhibitor(s) of cancer. The interaction of the Pd(II) complexes with the B-DNA (1BNA) and preformed intercalation site DNA (1XRW) was explored by implementing the molecular docking with clustering protocol to generate the most probable docked conformers. From the docking analyses, we found that the Pd(II) complexes bind to the minor groove of the DNA in a parallel fashion. Moreover, the results suggested that the minor groove binding moderately dominates the intercalation mode of binding besides having aromatic rings. The results also implied that the aqua derivatives of the Pd(II) complexes undergo strong binding (both minor groove and intercalation) due to the higher positive charge than their corresponding chloride derivatives. Furthermore, the aqua complexes with fluorinated aromatic rings (N 1 W and N 5 W) have a lower binding affinity for intercalation than for binding in the minor groove. Additionally, we performed the independent gradient model (IGM) analysis for the minor groove binding only from the first seed of the most probable docked conformers, for which our study confirmed the presence of hydrogen bonding and van der Waals interactions. Altogether, our results provide good insights into the fate of the chosen complexes and may act as a potent alternative(s) to cisplatin. [ABSTRACT FROM AUTHOR]

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)][PF 6 ](Ru-1), and [Ru(p-cymene)Cl(L-2)][PF 6 ](Ru-2)) and investigated their inhibitory activity against the bovine serum albumin (BSA) aggregation and the Aβ 1 – 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 A β 1 – 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 Aβ 1 – 42 peptides. The experimental studies revealed that these complexes significantly inhibited the BSA aggregation and Aβ 1 – 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 A β 1 – 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. The piano-stool imine-based ruthenium (II) complexes applied for in vitro anti-Alzheimer's activity against the amyoid β peptides. Both the complexes significantly inhibited the aggregation and amyloid fibril formation by interacting with amyloid fibrils. They have also possess antioxidant properties which protect amyloid-induced oxidative stress and restricted fibril formation. [Display omitted] • Piano-stool ruthenium (II) complexes were designed and synthesized. • Molecular structure of the complex was determined by X-ray crystallography. • In vitro and in silico anti-Alzheimer's activities were performed. • Ruthenium complexes interact with amyloid peptides and inhibit the Aβ-aggregation. • Antioxidant properties of the complexes reduced the amyloid-induced oxidative stress. [ABSTRACT FROM AUTHOR]

This section offers science-related news briefs as of September 10, 2017. Scientists from the Aligarh Muslim University and Saudi Arabia have isolated foodborne pathogens from burgers and shawarma to examine the inhibitory effect of rutin on biofilm formation. Researchers claim that an ethanolic extract from the medicinal plant Ashwagandha or Withania somnifera enhances the longevity of human cells. Researchers have found the different chemical and structural composition of gallstones.

Recent experimental and theoretical investigations on resonant electron scattering off DNA and DNA fragments using low-energy electrons (LEEs), to propose the mechanism for single strand breaks (SSBs) and double strand breaks (DSBs), have received considerable attention. It is our purpose here to understand theoretically the comprehensive route to SSB in a selected DNA fragment, namely, 2'-deoxycytidine-3'-monophosphate (3'-dCMPH), induced by LEE (0-3 eV) scattering using the local complex potential based time-dependent wave packet (LCP-TDWP) approach. To the best of our knowledge, there is no time-dependent quantum mechanical study that has been reported in the literature for this DNA fragment to date. Initial results obtained from our calculation in the gas phase provide a good agreement with experimental observation and show the plausibility of SSB at 0.75 eV, which is very close to the highest SSB yield reported from the experimental measurement (0.8 eV) on plasmid DNA in the condensed phase. [ABSTRACT FROM AUTHOR]