Muneerah Al Mogren

Vibrationally Resolved Photoelectron Spectroscopy of Electronic Excited States of DNA Bases: Application to the à State of Thymine Cation

For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules. While ground state investigations are currently straightforward, those of electronic excited states are not. Here, we characterized the à electronic state of ionic thymine (T(+)) DNA base using explicitly correlated coupled cluster ab initio methods and state-of-the-art synchrotron-based electron/ion coincidence techniques. The experimental spectrum is composed of rich and long vibrational progressions corresponding to the population of the low frequency modes of T(+)(Ã). This work challenges previous numerous works carried out on DNA bases using common synchrotron and VUV-based photoelectron spectroscopies. We provide hence a powerful theoretical and experimental framework to study the electronic structure of ionized DNA bases that could be generalized to other medium-sized biologically relevant systems.

A G3 study of the structure of carbon-nitrogen nanoclusters.

Possible structures of the carbon-nitrogen clusters of the form C(m)N(n) (m = 1-4, n = 1-4, m + n = 2-5) were predicted for the neutral, anion, and cation species in the singlet, doublet, and triplet states, whenever appropriate. The calculations were performed at the G3, MP2(fc)/6-311+G*, and B3LYP/6-311+G* levels of theory. Several molecular properties related to the experimental data--such as the electronic energy, equilibrium geometry, binding energy, HOMO-LUMO gap (HLG), and spin contamination --were calculated. In addition the vertical electron attachment, the adiabatic electron affinity, and vertical ionization energy, of the neutral clusters were calculated. Most of the predicted lowest energy structures were linear, whereas bent structures became more stable with the increase of the cluster size and increase of the number of the N atoms. In most of the predicted lowest energy structures, the N atom prefers the terminal position with acetylenic bond. The calculated BE of the predicted clusters increases with the increase of the cluster size for the neutral and cation clusters but decreases with the increase of the cluster size for the anion clusters. The predicted clusters are characterized by high HLG of about 11 eV on the average, with that of the anion clusters is smaller than that for the neutral and cation clusters. It is concluded then that the anion clusters are less stable than the corresponding neutral and cation clusters. Finally, the N(2) loss reaction is treated.

Electronic and spectroscopic characterizations of SNP isomers

High-level ab initio electronic structure calculations were performed to characterize SNP isomers. In addition to the known linear SNP, cyc-PSN, and linear SPN isomers, we identified a fourth isomer, linear PSN, which is located ∼2.4 eV above the linear SNP isomer. The low-lying singlet and triplet electronic states of the linear SNP and SPN isomers were investigated using a multi-reference configuration interaction method and large basis set. Several bound electronic states were identified. However, their upper rovibrational levels were predicted to pre-dissociate, leading to S + PN, P + NS products, and multi-step pathways were discovered. For the ground states, a set of spectroscopic parameters were derived using standard and explicitly correlated coupled-cluster methods in conjunction with augmented correlation-consistent basis sets extrapolated to the complete basis set limit. We also considered scalar and core-valence effects. For linear isomers, the rovibrational spectra were deduced after generation of their 3D-potential energy surfaces along the stretching and bending coordinates and variational treatments of the nuclear motions.

Toward the laboratory identification of [O,N,S,S] isomers: Implications for biological NO chemistry

Benchmark ab initio calculations are performed to investigate the stable isomers of [O,N,S,S]. These computations are carried out using coupled cluster (RCCSD(T)) and explicitly correlated coupled cluster methods (RCCSD(T)-F12). In addition to the already known cis isomer of SSNO, nine other stable forms are predicted. The most stable isomer is cis-OSNS. Nine structures are chain bent-bent with relatively large dipole moments which make them detectable, as cis-SSNO, by infrared, far-infrared, and microwave spectroscopies. We found also a C2v isomer (NS2O). Since these species are strongly suggested to play an important role as intermediates during the bioactive reaction products of the NO/H2S interaction, the rotational and vibrational spectroscopic parameters are presented to help aid the in vivo identification and assignment of these spectra. Results from this work show that [O,N,S,S] may play key roles during nitric oxide transport and deliver in biological media, as well as, provide an explanation for the weak characteristic of disulfide bridges within proteins.

HNS(+) and HSN(+) cations: Electronic states, spin-rovibronic spectroscopy with planetary and biological implications.

Ab initio methods in conjunction with a large basis set are used to compute the potential energy surfaces of the 12 lowest electronic states of the HNS(+) and HSN(+) isomeric forms. These potentials are used in discussions of the metastability of these cations and plausible mechanisms for the H(+)/H + SN(+)/SN, S/S(+) + NH(+)/NH, N/N(+) + SH(+)/SH ion-molecule reactions. Interestingly, the low rovibrational levels of HSN(+)(1(2)A″) and HNS(+)(1(2)A″) electronically excited ions are predicted to be long-lived. Both ions are suggested to be a suitable candidate for light-sensitive NO(⋅) donor in vivo and as a possible marker for the detection of intermediates in nitrites + H2S reactions at the cellular level. The full spin rovibronic levels of HNS(+) are presented, which may assist in the experimental identification of HNS(+) and HSN(+) ions and in elucidating their roles in astrophysical and biological media.

Electronic structure and properties of neutral, anionic and cationic silicon-nitrogen nanoclusters.

We performed a G3 investigation of the possible stable structures of silicon–nitrogen SinNm clusters where m = 1–4, n = 1–4, m + n = 2–5. We considered the neutral, anionic and cationic molecular species in the singlet, doublet and triplet states, as appropriate. For neutral clusters, our data confirm previous DFT and post Hartree-Fock findings. For charged clusters, our results represent predictions. Several molecular properties related to the experimental data, such as the electronic energy, equilibrium geometry, binding energy (BE), HOMO–LUMO gap (HLG), and spin contamination

Prediction of metastable AlS2+ dications in the gas phase

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Benchmark study of the structural and spectroscopic parameters of the hydroxymethyl peroxy (HOCH2OO) radical and its decomposition reaction to HO2 and H2CO

were computed. We also derived the vertical electron attachment (VEA), the adiabatic electron affinity (AEA), and the vertical ionization energy (VIE), of the neutral clusters. Similar to their carbon–nitrogen counterparts, the lowest energy structures for neutral and cationic silicon–nitrogen clusters are found to be linear or quasilinear. In contrast, anionic silicon–nitrogen clusters tend to form 3D structures as the size of the cluster increases.