Corrections in the CHARMM36 parametrization of chloride interactions with proteins, lipids, and alkali cations, and extension to other halide anions

The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of C

Computational investigation of the structure and antioxidant activity of some pyrazole and pyrazolone derivatives

Pyrazoles and pyrazolones constitute a group of organic compounds that have various medical applications such as antimicrobial, antipyretic, anti-inflammatory, antitumor and antioxidants. Pyrazolones can exist in different isomeric forms (CH, NH, OH) due to keto-enol, lactam-lactim and imine-enamine tautomerism. Determination of the most stable tautomeric form is thus important for understanding their biological roles at the molecular level. We performed a theoretical investigation of the structural and antioxidant properties of three synthetic pyrazolones (1–3), one synthetic pyrazole (4), one natural pyrazole (5) and two engineered hydroxyl derivatives of 1 (7, 8) and of 5 (9, 10) using the density functional theory at the B3LYP/6-311++G(d,p) level of theory in gas phase and in methanol (using the polarizable continuum model). It is found that substituents and solvents may influence the relative stability of pyrazolone isomers and that the CH tautomer is typically the least stable. Vertical ionization potentials, vertical electron affinities and X–H bond dissociation energies (X = C, N, O, S) are calculated for the global minimum structures and compared with those of the standard antioxidant flavonoid quercetin (6). Calculations predict that compounds 1 and 5 have antioxidant activity similar to 6 and that their mono and dihydroxyl derivatives (7–10) are more efficient antioxidants. Results also indicate that compounds 1–10 preferably interact with free radicals adopting the H atom transfer rather than the sequential electron transfer proton transfer mechanism. The study gives insight into the structural requirements for the design of highly efficient antioxidants. Keywords: Pyrazoles, Pyrazolones, Natural pyrazole, Tautomerism, DFT calculations, Antioxidants, Structural desig

Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia

A polarizable model for ammonia is optimized based on the ab initio properties of the NH₃ molecule and the NH₃–NH₃ and NH₃–H₂O dimers calculated at the MP2 level. For larger (NH₃)_<i>m</i>, NH₃(H₂O)_<i>n</i>, and H₂O­(NH₃)_<i>n</i> clusters (<i>m</i> = 2–7 and <i>n</i> = 1–4), the model yields structural and binding energies in good agreement with ab initio calculations without further adjustments. It also reproduces the structure, density, heat of vaporization, self-diffusion coefficient, heat capacity, and isothermal compressibility of liquid ammonia at the boiling point. The model is further validated by calculating some of these properties at various temperatures and pressures spanning the liquid and supercritical phases of the fluid (up to 700 K and 200 MPa). The excellent transferability of the model suggests that it can be used to investigate properties of fluid ammonia under conditions for which experiments are not easy to perform. For aqueous ammonia solutions, the model yields liquid structures and densities in good agreement with experimental data and allows the nonlinearity in the density-composition plot to be interpreted in terms of structural changes with composition. Finally, the model is used to investigate the solvation structure of ammonia in liquid water and of water in liquid ammonia and to calculate the solvation free energy of NH₃ and H₂O in aqueous ammonia as a function of solution composition and temperature. The simulation results suggest the presence of a transition around 50% molar NH₃/H₂O compositions, above which water molecules are preferably solvated by ammonia

Twisted Intramolecular Charge Transfer (TICT) Controlled by Dimerization : An Overlooked Piece of the TICT Puzzle

Organic dyes have shown high efficiencies in solar cells, which is mainly attributed to the push-pull strategy present in such dyes upon attaching to the semiconductor surfaces. We deeply studied the fundamental photophysical properties of cyanoacrylic dyes, mostly the L1 dye, and found unique emission properties that depend on many factors such as the solvent polarity and the concentration of the dye and could present a complete emission picture about this family of dyes. The L1 dye shows an intramolecular charge transfer (ICT) emission state at low concentrations (approximately nanomolar scale) and shows a twisted intramolecular charge transfer (TICT) emission state in specific solvents upon increasing the concentration to the micromolar scale. Moreover, the associated emission lifetimes of the ICT and TICT states of the L1 dye depend on solvent basicity, highlighting the role of hydrogen bond formation on controlling such states. Density functional theory calculations are performed to gain insight into the photophysical properties of the dye and revealed that H-bonding between the carboxylic groups triggers the dimerization at low concentrations. Using femtosecond transient absorption, we assigned the rate of TICT formation to be in the range (160-650 fs)(-1), depending on the size of the studied cyanoacrylic dye. Therefore, we add herein a new dimension for controlling the formation of the TICT state, in addition to the solvent polarity and acceptor strength parameters. These findings are not limited to the studied dyes, and we expect that numerous organic carboxylic acids dyes show similar properties

Mechanism of NH4(+) Recruitment and NH3 Transport in Rh Proteins

In human cells, membrane proteins of the rhesus (Rh) family excrete ammonium and play a role in pH regulation. Based on high-resolution structures, Rh proteins are generally understood to act as NH3 channels. Given that cell membranes are permeable to gases like NH3, the role of such proteins remains a paradox. Using molecular and quantum mechanical calculations, we show that a crystallographically identified site in the RhCG pore actually recruits NH4(+), which is found in higher concentration and binds with higher affinity than NH3, increasing the efficiency of the transport mechanism. A proton is transferred from NH4(+) to a signature histidine (the only moiety thermodynamically likely to accept a proton) followed by the diffusion of NH3 down the pore. The excess proton is circulated back to the extracellular vestibule through a hydrogen bond network, which involves a highly conserved and functionally important aspartic acid, resulting in the net transport of NH3

Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate

Proteins of the Amt/MEP family facilitate ammonium transport across the membranes of plants, fungi, and bacteria, and are essential for growth in nitrogen-poor environments. Some are known to facilitate the diffusion of the neutral NH3 while others, notably in plants, transport the positively charged NH4+. Based on the structural data for AmtB from Escherichia coli, we illustrate the mechanism by which proteins from the Amt family can sustain electrogenic transport. Free energy calculations show that NH4+ is stable in the AmtB pore, reaching a binding site from which it can spontaneously transfer a proton to a pore-lining histidine residue (His168). The substrate diffuses down the pore in the form of NH3 while the excess proton is co-transported through a highly conserved hydrogen-bonded His168-His318 pair. This constitutes a novel permeation mechanism that confers to the histidine dyad an essential mechanistic role that was so far unknown

New Megastigmane and Polyphenolic Components of Henna Leaves and Their Tumor-Specific Cytotoxicity on Human Oral Squamous Carcinoma Cell Lines

Polyphenols have a variety of phenolic hydroxyl and carbonyl functionalities that enable them to scavenge many oxidants, thereby preserving the human redox balance and preventing a number of oxidative stress-related chronic degenerative diseases. In our ongoing investigation of polyphenol-rich plants in search of novel molecules, we resumed the investigation of Lawsonia inermis L. (Lythraceae) or henna, a popular ancient plant with aesthetic and therapeutic benefits. The leaves’ 70% aq acetone extract was fractionated on a Diaion HP-20 column with different ratios of H2O/an organic solvent. Multistep gel chromatographic fractionation and HPLC purification of the Diaion 75% aq MeOH and MeOH fractions led to a new compound (1) along with tannin-related metabolites, benzoic acid (2), benzyl 6′-O-galloyl-β-D-glucopyranoside (3), and ellagic acid (4), which are first isolated from henna. Repeating the procedures on the Diaion 50% aq MeOH eluate led to the first-time isolation of two O-glucosidic ellagitannins, heterophylliin A (5), and gemin D (6), in addition to four known C-glycosidic ellagitannins, lythracin D (7), pedunculagin (8), flosin B (9), and lagerstroemin (10). The compound structures were determined through intensive spectroscopic investigations, including HRESIMS, 1D (1H and 13C) and 2D (1H–1H COSY, HSQC, HMBC, and NOESY) NMR, UV, [α]D, and CD experiments. The new structure of 1 was determined to be a megastigmane glucoside gallate; its biosynthesis from gallic acid and a β-ionone, a degradative product of the common metabolite β-carotin, was highlighted. Cytotoxicity investigations of the abundant ellagitannins revealed that lythracin D2 (7) and pedunculagin (8) are obviously more cytotoxic (tumor specificity = 2.3 and 2.8, respectively) toward oral squamous cell carcinoma cell lines (HSC-2, HSC-4, and Ca9-22) than normal human oral cells (HGF, HPC, and HPLF). In summary, Lawsonia inermis is a rich source of anti-oral cancer ellagitannins. Also, the several discovered polyphenolics highlighted here emphasize the numerous biological benefits of henna and encourage further clinical studies to profit from their antioxidant properties against oxidative stress-related disorders