Extensive ab initio calculations were employed to characterize stable conformers of gaseous arginine, both the canonical and zwitterionic tautomers. Step-by-step geometry optimizations of possible single-bond rotamers at the B3LYP/6-31G(d), B3LYP/6-31++G(d,p), and MP2/6-31++G(d,p) levels yield numerous structures that are more stable than any known ones. The final electronic energies of the conformers were determined at the CCSD/6-31++G(d,p) level. The lowest energies of the canonical and zwitterionic structures are lower than the existing values by 2.0 and 2.3 kcal/mol, respectively. The relative energies, rotational constants, dipole moments, and harmonic frequencies of the stable conformers remain for future experimental verification. The conformational distributions at various temperatures, estimated according to thermodynamic principles, consist almost exclusively of the newly found structures. One striking feature is the occurrence of blue-shifting hydrogen bonds in all six of the most stable conformers. A unique feature of important conformations is the coexistence of dihydrogen and blue- and red-shifting hydrogen bonds. In addition to the hydrogen bonds, the stereoelectronic effects were also found to be important stabilization factors. The calculated and measured proton affinities agree within the theoretical and experimental uncertainties, affirming the high quality of our conformational search. The theoretical gas-phase basicity of 245.9 kcal/mol is also in good agreement with the experimental value of 240.6 kcal/mol. The extensive searches establish firmly that gaseous arginine exists primarily in the canonical and not the zwitterionic form.

Glutamate transporters (GluTs) are the primary regulators of extracellular concentration of the neurotransmitter glutamate in the central nervous system. In this study, we have investigated the dynamics and coupling of the substrate and Na(+) binding sites, and the mechanism of cotransport of Na(+) ions, using molecular dynamics simulations of a membrane-embedded model of GluT in its apo (empty form) and various Na(+)- and/or substrate-bound states. The results shed light on the mechanism of the extracellular gate and on the sequence of binding of the substrate and Na(+) ions to GluT during the transport cycle. The results suggest that the helical hairpin HP2 plays the key role of the extracellular gate for the substrate binding site, and that the opening and closure of the gate is controlled by substrate binding. GluT adopts an open conformation in the absence of the substrate exposing the binding sites of the substrate and Na(+) ions to the extracellular solution. Based on the calculated trajectories, we propose that Na1 is the first element to bind GluT, as it is found to be important for the completion of the substrate binding site. The subsequent binding of the substrate, in turn, is shown to result in an almost complete closure of the extracellular gate and the formation of the Na2 binding site. Finally, binding of Na2 locks the extracellular gate and completes the formation of the occluded state of GluT.

Selective photoreduction of carbon dioxide (CO2) into carbon‐neutral fuels such as methane (CH4) is extremely desirable but remains a challenge since sluggish multiple proton–electron coupling transfer and various C1 intermediates are involved. Herein, a synergistic function between single Pd atoms (Pd1) and Pd nanoparticles (PdNPs) on graphitic carbon nitride (C3N4) for photocatalytic CO2 methanation is presented. The catalyst achieves a high selectivity of 97.8% for CH4 production with a yield of 20.3 µmol gcat.−1 h−1 in pure water. Mechanistic studies revealed that Pd1 sites activated CO2, while PdNPs sites boosted water (H2O) dissociation for increased H* coverage. The H* produced by PdNPs migrate to the Pd1 sites to promote multiple proton–electron coupling transfer via hydrogen spillover. Moreover, the adjacent Pd1 and PdNPs effectively stabilized intermediates such as *CHO, thereby favoring the pathway for CH4 production. This work provides a new perspective into the development of selective photocatalytic CO2 conversion through the artful design of synergistic catalytic sites.

The transport cycle in the glutamate transporter (GlT) is catalyzed by the cotransport of three Na(+) ions. However, the positions of only two of these ions (Na1 and Na2 sites) along with the substrate have been captured in the crystal structures reported for both the outward-facing and the inward-facing states of Glt(ph). Characterizing the third ion binding site (Na3) is necessary for structure-function studies attempting to investigate the mechanism of transport in GlTs at an atomic level, particularly for the determination of the sequence of the binding events during the transport cycle. In this study, we report a series of molecular dynamics simulations performed on various bound states of Glt(ph) (the apo state, as well as in the presence of Na(+), the substrate, or both), which have been used to identify a putative Na3 site. The calculated trajectories have been used to determine the water accessibility of potential ion-binding residues in the protein, as a prerequisite for their ion binding. Combined with conformational analysis of the key regions in the protein in different bound states and several additional independent simulations in which a Na(+) ion was randomly introduced to the interior of the transporter, we have been able to characterize a putative Na3 site and propose a plausible binding sequence for the substrate and the three Na(+) ions to the transporter during the extracellular half of the transport cycle. The proposed Na3 site is formed by a set of highly conserved residues, namely, Asp(312), Thr(92), and Asn(310), along with a water molecule. Simulation of a fully bound state, including the substrate and the three Na(+) ions, reveals a stable structure--showing closer agreement to the crystal structure when compared to previous models lacking an ion in the putative Na3 site. The proposed sequence of binding events is in agreement with recent experimental models suggesting that two Na(+) ions bind before the substrate, and one after that. Our results, however, provide additional information about the sites involved in these binding events.

Membrane transporters rely on highly coordinated structural transitions between major conformational states for their function, to prevent simultaneous access of the substrate binding site to both sides of the membrane-a mode of operation known as the alternating access model. Although this mechanism successfully accounts for the efficient exchange of the primary substrate across the membrane, accruing evidence on significant water transport and even uncoupled ion transport mediated by transporters has challenged the concept of perfect mechanical coupling and coordination of the gating mechanism in transporters, which might be expected from the alternating access model. Here, we present a large set of extended equilibrium molecular dynamics simulations performed on several classes of membrane transporters in different conformational states, to test the presence of the phenomenon in diverse transporter classes and to investigate the underlying molecular mechanism of water transport through membrane transporters. The simulations reveal spontaneous formation of transient water-conducting (channel-like) states allowing passive water diffusion through the lumen of the transporters. These channel-like states are permeable to water but occluded to substrate, thereby not hindering the uphill transport of the primary substrate, i.e., the alternating access model remains applicable to the substrate. The rise of such water-conducting states during the large-scale structural transitions of the transporter protein is indicative of imperfections in the coordinated closing and opening motions of the cytoplasmic and extracellular gates. We propose that the observed water-conducting states likely represent a universal phenomenon in membrane transporters, which is consistent with their reliance on large-scale motion for function.major facilitator superfamily | LeuT-fold transporters | ABC transporters | neurotransmitter transporters

A full structural assignment of the neutral, protonated, and deprotonated histidine conformers in the gas phase is presented. A total of 3024 unique trial structures were generated by all combinations of internal single-bond rotamers of these species and optimized at the B3LYP/6-311G* level and further optimized at the B3LYP/6-311++G** level. A set of unique conformers is found, and their relative energies, free energies, dipole moments, rotational constants, electron affinities, ionization energies, and harmonic frequencies are determined. The population ratio of histidine and its tautomer is 1:0.16 at 298 K. Massive conformational changes are observed due to protonation and deprotonation, and the intramolecular H-bonds are characterized with the atoms in molecules theory. The calculated proton dissociation energy, gas-phase acidity, proton affinity, and gas-phase basicity are in excellent agreement with the experiments. The deprotonation and protonation of gaseous histidine both occur on the imidazole ring, explaining the versatile biofunctions of histidine in large biomolecules. The UV spectra of neutral and singly and doubly protonated histidine are investigated with the TDDFT/B3LYP/6-311+G(2df,p) calculations. The S0-S1, S0-S2, and S0-S3 excitations of histidine are mixed pipi*/npi* transitions at 5.37, 5.44, and 5.69 eV, respectively. The three excitation energies for histidine tautomer are 4.85, 5.47, and 5.52 eV, respectively. The three excitations for protonated histidine are mainly npi* transitions at 5.45, 5.67, and 5.82 eV, respectively. The S0-S1 excitation of protonated histidine produces ImH-CbetaH2-CalphaH(COOH)-NH2+, while the S0-S2 and S0-S3 transitions produce ImH-CbetaH2-CalphaH(NH2)-(COOH)+. These data may help to understand the mechanisms of the UV fragmentation of biomolecules.

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An N-heterocyclic carbene-catalyzed β-hydroxylation of enals is developed. The reaction goes through a pathway involving multiple radical intermediates, as supported by experimental observations. This oxidative single-electron-transfer reaction allows for highly enantioselective access to β-hydroxyl esters that are widely found in natural products and bioactive molecules.