Inhibitory effects of Ephedra alte on IL-6, hybrid TLR4, TNF-α, IL-1ß, and extracted TLR4 receptors: in silico molecular docking.

Inflammation is a physiological reaction of the immune system required to remove the presence of pathogenic germs. Many herbal-derived extracts and phytoconstituents show anti-inflammatory effects. Among these natural phytoconstituents is Ephedra alte (E. alte), which shows pepsin enzyme inhibitory, antibacterial, and antioxidant activities. In this work, molecular docking study is conducted on five major human anti-inflammatory cytokines receptors (IL-6, hybrid TLR4, TNF-α, IL-1ß, and extracted TLR4) to explore the molecular recognition process and complex ligand-receptor interactions of E. alte phytoconstituents. Human TLR4 receptor has been computationally extracted, for the first time, from the hybrid TLR4 human and VLRB inshore hagfish. Among E. alte phytoconstituents, only ß-Sitosterol and Androstan-3-one have better LBE (Lowest Binding Energy) scores with inhibition constant (K i) values than those of other tested compounds. The ß-Sitosterol and Androstan-3-one results indicate that these compounds could be efficient inhibitors of inflammation and reduce the oxidative stress by interfering with the activity of the five studied proteins.

Spectroscopic detection of the stannylidene (H2C=Sn and D2C=Sn) molecule in the gas phase.

The H2CSn and D2CSn molecules have been detected for the first time by laser-induced fluorescence (LIF) and emission spectroscopic techniques through the B̃1B2-X̃1A1 electronic transition in the 425-400 nm region. These reactive species were prepared in a pulsed electric discharge jet using (CH3)4Sn or (CD3)4Sn diluted in high-pressure argon. Transitions to the electronic excited state of the jet-cooled molecules were probed with LIF, and the ground state and low-lying Ã1A2 state energy levels were measured from single vibronic level emission spectra. We supported the experimental studies by a variety of ab initio calculations that predicted the energies, geometries, and vibrational frequencies of the ground and lower excited electronic states. The spectroscopy of stannylidene (H2CSn) is in many aspects similar to that of silylidene (H2CSi) and germylidene (H2CGe).

Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations.

p53, a tumor suppressor protein, is essential for preventing cancer development. Enhancing our understanding of the human p53 function and its modifications in carcinogenesis will aid in developing more highly effective strategies for cancer prevention and treatment. In this study, we have modeled five human p53 forms, namely, inactive, distal-active, proximal-active, distal-Arg175His mutant, and proximal-Arg175His mutant forms. These forms have been investigated using Gaussian accelerated molecular dynamics (GaMD) simulations in OPC water model at physiological temperature and pH. Our observations, obtained throughout [Formula: see text] of production run, are in good agreement with the relevant results in the classical molecular dynamics (MD) studies. Therefore, GaMD method is more economic and efficient method than the classical MD method for studying biomolecular systems. The featured dynamics of the five human p53-DBD forms include noticeable conformational changes of L1 and [Formula: see text]-[Formula: see text] loops as well as [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] turns. We have identified two clusters that represent two distinct conformational states in each p53-DBD form. The free-energy profiles of these clusters demonstrate the flexibility of the protein to undergo a conformational transition between the two clusters. We have predicted two out of seven possible druggability pockets on the clusters of the Arg175His forms. These two druggability pockets are near the mutation site and are expected to be actual pockets, which will be helpful for the compound clinical progression studies.

An experimental and theoretical study of the Ã(2)A(″)Π-X̃(2)A(') band system of the jet-cooled HBBr/DBBr free radical.

The electronic spectra of the HBBr and DBBr free radicals have been studied in depth. These species were prepared in a pulsed electric discharge jet using a precursor mixture of BBr3 vapor and H2 or D2 in high pressure argon. Transitions to the electronic excited state of the jet-cooled radicals were probed with laser-induced fluorescence and the ground state energy levels were measured from the single vibronic level emission spectra. HBBr has an extensive band system in the red which involves a linear-bent transition between the two Renner-Teller components of what would be a (2)Π state at linearity. We have used high level ab initio theory to calculate potential energy surfaces for the bent (2)A' ground state and the linear Ã(2)A(″)Π excited state and we have determined the ro-vibronic energy levels variationally, including spin orbit effects. The correspondence between the computed and experimentally observed transition frequencies, upper state level symmetries, and H and B isotope shifts was used to make reliable assignments. We have shown that the ground state barriers to linearity, which range from 10 000 cm(-1) in HBF to 2700 cm(-1) in BH2, are inversely related to the energy of the first excited (2)Σ ((2)A') electronic state. This suggests that a vibronic coupling mechanism is responsible for the nonlinear equilibrium geometries of the ground states of the HBX free radicals.

BH2 revisited: New, extensive measurements of laser-induced fluorescence transitions and ab initio calculations of near-spectroscopic accuracy.

The spectroscopy of gas phase BH2 has not been explored experimentally since the pioneering study of Herzberg and Johns in 1967. In the present work, laser-induced fluorescence (LIF) spectra of the Ã(2)B1(Πu)-X̃ (2)A1 band system of (11)BH2, (10)BH2, (11)BD2, and (10)BD2 have been observed for the first time. The free radicals were "synthesized" by an electric discharge through a precursor mixture of 0.5% diborane (B2H6 or B2D6) in high pressure argon at the exit of a pulsed valve. A total of 67 LIF bands have been measured and rotationally analyzed, 62 of them previously unobserved. These include transitions to a wide variety of excited state bending levels, to several stretch-bend combination levels, and to three ground state levels which gain intensity through Renner-Teller coupling to nearby excited state levels. As an aid to vibronic assignment of the spectra, very high level hybrid ab initio potential energy surfaces were built starting from the coupled cluster singles and doubles with perturbative triples (CCSD(T))/aug-cc-pV5Z level of theory for this seven-electron system. In an effort to obtain the highest possible accuracy, the potentials were corrected for core correlation, extrapolation to the complete basis set limit, electron correlation beyond CCSD(T), and diagonal Born-Oppenheimer effects. The spin-rovibronic states of the various isotopologues of BH2 were calculated for energies up to 22 000 cm(-1) above the X̃ (000) level without any empirical adjustment of the potentials or fitting to experimental data. The agreement with the new LIF data is excellent, approaching near-spectroscopic accuracy (a few cm(-1)) and has allowed us to understand the complicated spin-rovibronic energy level structure even in the region of strong Renner-Teller resonances.

An experimental and theoretical study of the electronic spectrum of the HBCl free radical.

Following our previous discovery of the spectra of the HBX (X = F, Cl, and Br) free radicals [S.-G. He, F. X. Sunahori, and D. J. Clouthier, J. Am. Chem. Soc. 127, 10814 (2005)], the Ã(2)A(″)Π-X̃(2)A(') band systems of the HBCl and DBCl free radicals have been studied in detail. The radicals have been prepared in a pulsed electric discharge jet using a precursor mixture of BCl3 and H2 or D2 in high pressure argon. Laser-induced fluorescence (LIF) and single vibronic level emission spectra have been recorded to map out the ground and excited state vibrational energy levels. The band system involves a linear-bent transition between the two Renner-Teller components of what would be a (2)Π electronic state at linearity. We have used high level ab initio theory to calculate the ground and excited state potential energy surfaces and have determined the vibronic energy levels variationally. The theory results were used to assign the LIF spectra which involve transitions from the ground state zero-point level to high vibrational levels of the excited state. The correspondence between theory and experiment, including the transition frequencies, upper state band symmetries, and H, B, and Cl isotope shifts, was used to validate the assignments.

A new, definitive analysis of a very old spectrum: the highly perturbed A2Πu-X2Πg band system of the chlorine cation (Cl2+).

The laser-induced fluorescence spectrum of jet-cooled chlorine cation has been recorded in the 500-312 nm region with high sensitivity and rigorous vibrational and spin-orbit cooling. More than 80 bands of the highly vibrationally perturbed A (2)Π(u)-X (2)Π(g) electronic transition have been detected and shown to originate from the Ω = 3/2 spin-orbit component of v = 0 of the ground state. The spectrum extends some 3700 cm(-1) to the red of any previously published report and the 0-0 band has been identified for the first time. The bands have regular rotational structure but exhibit irregular vibrational intervals and isotope splittings. Our ab initio studies show that the perturbations are due to a ΔΩ = 0 spin-orbit interaction between the A(2)Π(3/2u) and B(2)Δ(3/2u) states which have an avoided crossing at ~2.5 Å, which corresponds to v ≈ 4 of the A state. The nonadiabatic coupled equations have been solved for this two-state interaction after constructing the diabatic potentials including only the diagonal (ΔΛ = 0) spin-orbit coupling, yielding low-lying vibrational energy levels, isotope splittings, and rotational constants in good agreement with experiment. The calculations show that many of the observed bands are actually transitions to predominantly B state vibrational levels, which borrow oscillator strength from the A-X transition through spin-orbit mixing. Starting from the coupled equations solutions, we have fitted the experimental data using an effective Hamiltonian matrix that includes the vibrational energy levels of the A and B states and a single electronic spin-orbit coupling term H(SO)(AB) which has a value of 240 cm(-1). Transitions up to v' = 32 in both states have been satisfactorily fitted for all three chlorine isotopologues, providing a quantitative description of the perturbations. Transitions to higher levels are complicated by interactions with other electronic states.

A laser-induced fluorescence study of the jet-cooled nitrous oxide cation (N2O+).

Laser-induced fluorescence and wavelength resolved emission spectra of the à (2)Σ(+) - X̃ (2)Π(i) electronic transition of the jet-cooled nitrous oxide cation have been recorded. The ions were produced in a pulsed electric discharge at the exit of a supersonic expansion using a precursor mixture of N(2)O in high pressure argon. Both spin-orbit components of the 0(0) (0) band were studied at high resolution and rotationally analyzed to provide precise molecular constants for the combining states. Emission spectra were obtained by laser excitation of the 0(0) (0), 2(0) (1), 3(0) (1), and 2(0) (2) absorption bands, providing extensive data on the ground state bending, stretching, and combination vibrational levels. These data were fitted to a Renner-Teller model including spin-orbit, anharmonic, and Fermi resonance terms. The observed energy levels and fitted parameters were found to be comparable to those in the literature predicted from an ab initio potential energy surface.

Heavy atom nitroxyl radicals. VI. The electronic spectrum of jet-cooled H2PO, the prototypical phosphoryl free radical.

The previously unknown electronic spectrum of the H(2)PO free radical has been identified in the 407-337 nm region using a combination of laser-induced fluorescence and single vibronic level emission spectroscopy. High level ab initio predictions of the properties of the ground and first two excited doublet states were used to identify the spectral region in which to search for the electronic transition and were used to aid in the analysis of the data. The band system is assigned as the B̃(2)A(')-X̃(2)A(') electronic transition which involves promotion of an electron from the π to the π∗ molecular orbital. The excited state r(0) molecular structure was determined by rotational analysis of high resolution LIF spectra to be r(PO) = 1.6710(2) Å, r(PH) = 1.4280(6) Å, θ(HPO) = 105.68(7)°, θ(HPH) = 93.3(2)°, and the out-of-plane angle = 66.8(2)°. The structural changes on electronic excitation, which include substantial increases in the PO bond length and out-of-plane angle, are as expected based on molecular orbital theory and our previous studies of the isoelectronic H(2)AsO, Cl(2)PS, and F(2)PS free radicals.

Laser induced fluorescence spectroscopy of the jet-cooled carbon dioxide cation (12CO2(+) and 13CO2(+)).

The A (2)Pi(u)-X (2)Pi(g) band systems of jet-cooled (12)CO(2)(+) and (13)CO(2)(+) have been recorded by laser-induced fluorescence (LIF) techniques. Very intense, vibrationally cold expansions of these cations have been obtained using a pulsed electric discharge jet with a precursor mixture of carbon dioxide or (13)C labeled CO(2) in high pressure argon. The LIF bands have been partially rotationally analyzed to obtain band origins which yielded an accurate measure of the excited state vibronic energy levels. The energy levels of both isotopologues were fitted with a Renner-Teller model that included spin-orbit coupling, Fermi resonance and anharmonic terms. Single vibronic level emission spectra were also recorded for the (13)CO(2)(+) ion and the ground state energy levels fitted using the same Renner-Teller model. The isotope relations have been used to test the validity of the derived parameters. The results give a through description of the vibronic energy levels in the ground and first excited electronic states of the carbon dioxide cation.