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A density functional theory investigation of the chemical reactivity of the S=C=S...C1 complex toward 2,3-dimethylbutane (DMB) has been reported and compared to the related reaction of a C1 atom with DMB. The DFT calculations indicate that the reaction of C1 atom with DMB would have little tertiary selectivity toward chlorination consistent with experimental results for photochlorination of alkanes in invert solvents.

Density functional theory calculations for the cyclopropanation reactions of several mono zinc carbenoids and their corresponding gem-dizinc carbenoids with ethylene are reported. Results indicate that gem-dizinc carbenoids react with C=C bonds with significantly lower barriers to reaction and in a noticeably different manner than Simmons-Smith type mono zinc carbenoids.

Themechanisms of CO2insertion into the U–Nbond of a silylamido NHC (N-heterocyclic carbene) U(III) complex wereinvestigated theoretically. An earlier reported mechanism involvinga reversible NHC carboxylation was found to be energetically too demanding,and a novel four-step mechanism featuring a direct CO2insertioninto the U–N bond is proposed. [ABSTRACT FROM AUTHOR]

Indirect nitrous oxide (N 2 O) emissions from streams and rivers are a poorly constrained term in the global N 2 O budget. Current models of riverine N 2 O emissions place a strong focus on denitrification in groundwater and riverine environments as a dominant source of riverine N 2 O, but do not explicitly consider direct N 2 O input from terrestrial ecosystems. Here, we combine N 2 O isotope measurements and spatial stream network modeling to show that terrestrial-aquatic interactions, driven by changing hydrologic connectivity, control the sources and dynamics of riverine N 2 O in a mesoscale river network within the U.S. Corn Belt. We find that N 2 O produced from nitrification constituted a substantial fraction (i.e., >30%) of riverine N 2 O across the entire river network. The delivery of soil-produced N 2 O to streams was identified as a key mechanism for the high nitrification contribution and potentially accounted for more than 40% of the total riverine emission. This revealed large terrestrial N 2 O input implies an important climate-N 2 O feedback mechanism that may enhance riverine N 2 O emissions under a wetter and warmer climate. Inadequate representation of hydrologic connectivity in observations and modeling of riverine N 2 O emissions may result in significant underestimations.

Plain simulations and enhanced sampling unveil a novel siderocalin (Scn) recognition mode for An-Ent (where An = actinides and Ent = enterobactin) complexes and identify a "seesaw" relationship between actinide affinity to Ent and Scn recognition to an An-Ent complex. Electrostatic interactions predominantly govern competitive binding in both processes. Additionally, hydrolysis-induced negative charge, water expulsion-driven entropy, and Ent's conformational adaptability collectively enhance high-affinity recognition.

By means of molecular dynamics simulations, this work addresses the conformational flexibility and migration of trivalent neodymium (Nd 3+ ) coordinated with three or six titled (thio)phosphinic ligands and shows that the fluxionality of the complexes enables them to adapt to the solvent environment during the migration. Cyanex272 forms a more compact complex than the other two types of ligands and screens more significantly the interaction between the water solvent and the metal ion in the complex, which weakens the detainment of the aqueous environment. This results in faster motion of the Nd(C272) 3 complex both in its translation and rotation than the other complexes when migrating to the organic phase and wins over the other two ligands in transporting the metal ions from the aqueous phase to the organic phase. Depending on the solvent environment, these complexes may take two types of conformations to balance the forces from the environment benefited from their fluxionality. The migration of the M:L = 1:6 complexes, Nd[H(C272) 2 ] 3 and Nd[H(C301) 2 ] 3 , was also investigated. The rich presence of the alkyl groups in the complexes screens the influence of the aqueous environment and benefits the transportation of metal ions to the interface. This work is expected to contribute to the community of inorganic chemistry interested in the coordination chemistry of metal ions and their behaviors in the condensed phase.

Molecular dynamics (MD) simulations were performed to investigate the dynamics of humic acid (HA) in an aqueous solution and the influence of pH, temperature, and HA concentration. The HA model employed in MD simulations was chosen and validated using experimental chemical composition data and Fourier transform infrared (FTIR) spectra. The simulations showed that the HA molecule has a strong propensity to adopt a compact conformation in water independent of pH, while the aggregation of HA was found to be pH-dependent. At high pH, the ionized HAs assembled into a thread-like structure, maximizing contact with water. At low pH, the neutral HAs formed a droplet-like aggregate, minimizing contact with the solvent. The simulation results are consistent with experimental data from dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM) imaging. This work provides new insight into the folding and aggregation of HA as a function of pH and a molecular-level understanding of the relationship between the acidity and the structure, solubility, and aggregation of HA, with direct implications for HA-based remediation strategies of contaminated sites.

Boron-based catalysts show excellent performance in oxidative dehydrogenation (ODH) of light alkanes to alkenes with high selectivity and extremely good antioxidation properties. However, the anti-deep-oxidation mechanism remains unclear. Herein, we chose h -BN and B 2 O 3 as representative boron-based catalysts to investigate their reactions with two important intermediates in the light alkane ODH, Et· (evolving to ethene) and EtO· (evolving to ethene or CO x ), to elucidate the origin of the antioxidation of alkanes. The density functional theory calculations reveal that surface boron sites could eliminate alkoxy in their vicinity, resulting in exceptional inhibition of alkane deep-oxidation. The analysis of the electronic and geometric structures of key stationary points showed that the oxophilicity of B determined the low deep-oxidation of alkanes, and the homoleptic coordination of B with all three ligating atoms being O moderately enhanced its oxophilicity. This work represents a novel conceptual advance in the mechanistic understanding of alkane ODH.

Rivers and streams contribute significant quantities of methane (CH 4 ) to the atmosphere. However, there is a lack of CH 4 flux and ebullitive (bubble) emission data from urban rivers, which might lead to large underestimations of global aquatic CH 4 emissions. Here, we conducted high-frequency surveys using the boundary layer model (BLM) supplemented with floating chambers (FCs) and bubble traps to investigate the seasonal and diurnal variability in CH 4 emissions in a eutrophic urban river and to evaluate whether the contribution of bubbles is important. We found that ebullition contributed nearly 99% of CH 4 emissions and varied on hourly to seasonal time scales, ranging from 0.83 to 230 mmol m -2 d -1 , although diffusive emissions and CH 4 concentrations in bubbles did not exhibit temporal variability. Ebullitive CH 4 emissions presented high temperature sensitivity ( r = 0.6 and p < 0.01) in this urban river, and eutrophication might have triggered this high temperature sensitivity. The ebullitive CH 4 flux is more likely to be underestimated at low temperatures because capturing the bubble flux is more difficult, given the low frequency of ebullition events. This study suggests that future ebullition measurements on longer time scales are needed to accurately quantify the CH 4 budgets of eutrophic urban rivers.

The significance of understanding the interaction between actinide(III)/lanthanide(III) (An(III)/Ln(III)) and N-donor extractants lies in the importance of efficient An 3+ /Ln 3+ separation in advanced nuclear fuel cycles and the high expectation of the application of N-donor extractants. This work reports a density functional theory study aiming at a plausible explanation of the origin of the selectivity of the ligands in An 3+ /Ln 3+ separation and an evaluation of the influence of the bridging groups of typical N-donor extractants. Five bis(triazine) N-donor ligands were considered, differing in their denticity dictated by their bridging groups and in the flexibility of these bridging groups. The results showed much stronger hydration of Eu(III) in comparison to Am(III) in the ligand exchange of aqua ligands by N-donor ligands, while there was a moderate difference in their interaction strengths with the N-donor ligands. This implicated that the distinct difficulty in desolvating Eu(III) and Am(III) may govern their selectivity in liquid-liquid extraction. The analysis of the role of the bridging groups of the ligands confirmed the importance of a ligand to be equipped with preorganized binding sites to minimize the perturbation of entropy. We tentatively propose that this conclusion may hold in the explanation of the low selectivity of oxygenated extractants and the high selectivity of extractants with soft donors in An 3+ /Ln 3+ separation.

The functionalization of CO 2 mediated by a series of U(IV) mixed-sandwich compounds, (COT TIPS2 )Cp*UR (R = -CH 3 , -CH 2 Ph, -CH 2 TMS, -CH(TMS) 2 , -NHPh, -OPh, -SPh, -SePh; COT TIPS2 = C 8 H 6 (Si i Pr 3 -1,4) 2 ; Cp* = C 5 Me 5 ; TMS = SiMe 3 ), was investigated by the density functional theory method. A two-step mechanism was revealed, in which the insertion of CO 2 into the U-C bond was identified as the rate-determining step via a transition state featured by a four-membered ring with a free-energy barrier of 18.8 kcal/mol to the reaction of the (COT TIPS2 )Cp*UCH 3 system. The whole reaction was strongly exothermic by 45.0 kcal/mol. Substitution effect was discussed, including the bulkiness of the R group and the nature of the ligating atom, and steric hindrance and electrostatic interactions were found to be responsible for the observed variation in reactivity. The reactivity of U(III) and U(IV) complexes in CO 2 functionalization was also compared and discussed. The results were consistent with experimental studies and complemented with molecular level of understanding on the mechanisms of CO 2 functionalization promoted by tetravalent U complexes.

CyMe 4 -BTPhen (2,9-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin-3-yl)-1,10-phenanthroline, denoted as L) has been considered as a promising extractant in lanthanide(III)/actinide(III) separation. Vast endeavors in its application put forward a compelling need on the understanding of the underlying mechanism in the liquid-liquid extraction. To address the issue of its dynamics in biphasic systems, we carried out molecular dynamics (MD) simulations of L and its complexes with a heavy f-block metal ion, americium(III) (Am 3+ ) in "oil"/water binary solvents. Two types of organic phases have been considered, differing in the presence of octanol in the bulk n -dodecane or not, and the distribution of the solutes and their interfacial behaviors have been investigated. Two of the key factors that determine the efficiency of a liquid-liquid extraction protocol were delineated and discussed, that is, the appropriate ligand to enhance the lipophilicity of AmL complexes and appropriate way to form ion pairs to minimize the attraction between the complexes and aqueous phase. The simulations showed that the charge states of both ligand and AmL complexes were strongly correlated with their phase behavior, and the migration of neutral species was driven by van der Waals interactions while that of charged species by electrostatic interactions, indicating stronger lipophilicity of the former than the latter. The presence of octanol facilitated the migration of the ligand from the interface to the organic phase via hydrogen bond between its polar head and the ligand or the AmL complexes and constituted a polar core in the organic phase. This work bridged the widely used liquid-liquid extraction technique in chemistry to a fundamental chemical concept, that is, minimization of hydrophilicity and maximization of lipophilicity to facilitate phase transfer from the aqueous phase to the organic phase, and is expected to improve the understanding of dynamics of ligands and their complexes with metal ions and to contribute to the development of efficient protocols for phase transfer of target species.

The AMOEBA polarizable force field of ferric ion was optimized and applied to study the hydration of ferric ion and its complexation with porphine in the aqueous phase. The nonpolarizable force field was also optimized for comparison. The AMOEBA force field was found to give a more accurate hydration free energy than the nonpolarizable force field with respect to experimental data, and correctly predict the most stable electronic state of hydrated Fe 3+ , which is the sextet state, and of the Fe (III) -Por complex, which is the quartet state, consistent with the literature that was carried out using the DFT method. The explicit inclusion of charge transfer between Fe 3+ and ligand was found to be important in order to obtain a precise picture of polarization energy and van der Waals energy, which otherwise deviate from the corresponding energy components derived from ab initio calculations. The successful application of the AMOEBA force field in the characterization of aquo Fe (III) -Por complexes suggests that its use may be extended to the study of the dynamics of metalloenzyme containing highly charged metal ions in the condensed phase with reliable treatment of the interactions between metal atom and protein.

With the use of a commercially available chiral phosphine as the catalyst, the first catalytic enantioselective [4 + 3] annulation of allenoates with C,N-cyclic azomethine imines is developed. The reaction works efficiently under mild reaction conditions to afford seven-membered ring-fused quinazoline-based tricyclic heterocycles in high yields with good to excellent diastereo- and enantioselectivities.

This work targeted a molecular level of understanding on the dynamics of humic acid (HA) and its interaction with uranyl in the presence of hydrophobic surface mimicked by a carbon nanotube (CNT), which also represents a potential intruder in the environment accompanying with the development of nanotechnology. In aqueous phase, uranyl and HA were observed to build close contact spontaneously, driven by electrostatic interaction, leading to a more compact conformation of HA. The presence of CNT unfolds HA via π-π interactions with the aromatic rings of HA without significant perturbation on the interaction strength between HA and uranyl. These results show that the hydrophilic uranyl and the hydrophobic CNT influence the folding behavior of HA in distinct manners, which represents two fundamental mechanisms that the folding behavior of HA may be modulated in the environment, that is, uranyl enhances the folding of HA via electrostatic interactions, whereas CNT impedes its spontaneous folding via van der Waals (vdW) interactions. The work also provides molecular level of evidence on the transformation of a hydrophobic surface into a hydrophilic one via noncovalent functionalization by HA, which in turn affects the migration of HA and the cations it binds to.

1,3-Bis[3-(2-pyridyl)pyrazol-1-yl]propane (Bippp) and 1,2-bis[3-(2-pyridyl)pyrazyl-1-methyl]benzene (Dbnpp), the pyridylpyrazole based tetradentate ligands, were synthesized and characterized by MS, NMR, and FT-IR. The solvent extraction and complexation behaviors of Am(III) and Eu(III) with the ligands were investigated experimentally and theoretically. In the presence of 2-bromohexanoic acid, the two ligands can effectively extract Am(III) over Eu(III) and other rare earth(III) metals (RE(III)) in HNO3 solution with the separation factors (SFAm/RE) ranging from 15 to 60. Slope analyses showed that both Am(III) and Eu(III) were extracted as monosolvated species, which agrees well with the results observed from X-ray crystallography and MS analyses. The stability constants (log K) obtained from UV-vis titration for Eu(III) complexes with Bippp and Dbnpp are 4.75 ± 0.03 and 4.45 ± 0.04, respectively. Both UV-vis titration and solvent extraction studies indicated that Bippp had stronger affinity for Eu(III) than Dbnpp, which is confirmed by density functional theory (DFT) calculations. DFT calculations revealed that the AmL(NO3)3 (L = Bippp and Dbnpp) complexes are thermodynamically more stable in water than their Eu(III) analogues, which is caused by greater covalency of the Am-N than Eu-N bonds. Theoretical studies gave an insight into the nature of the M(III)-ligand bonding interactions.

The present theoretical study provides a realistic evaluation of the equilibrium structure, reaction modes, and bonding characteristics of a variety of neptunyl complexes formed with bis(triazinyl) N-donor extractants, which differ in their bridging groups such as pyridine, bipyridines, and orthophenanthroline, corresponding to the ligands (L) of tridentate bis(triazinyl)pyridines and tetradentate bis(triazinyl)bipyridines and bis(triazinyl)-1,10-phenanthrolines (BTPhens), respectively. Our calculations show that coordination of [NpO2](+) to tetradentate ligands is more favorable than that to tridentate ones no matter in a gas, aqueous, or organic phase. The presence of nitrate ions can enhance the coordination ability of neptunyl and stabilize the neutral NpO2L(NO3) complexes in thermodynamics. Our studies indicate that the complexation reaction mode [NpO2(H2O)n](+) + L + NO3(-) → NpO2L(NO3) + nH2O is the most probable at the interface between water and the organic phase. The contribution of an orthophenanthroline bridging group is relatively more pronounced compared to its pyridine counterpart in ligand-exchange reaction. Complexation reactions of hydrated neptunyl with C2-BTPhen and BTPhen assisted by a nitrate ion are favorable thermodynamically, resulting from the least deformation of the ligand and strong complexation stability. The quantum theory of atoms-in-molecules and charge decomposition analysis suggest that electron delocalization and charge transfer are the main reasons responsible for stabilization of the tetradentate complexes and reveal a strong ionic feature of the Np-ligand bonds. Inspection of the frontier molecular orbitals reveals a distinct 5f orbital (Np) interaction with ligand atoms, implying the extent of f-based covalency. Our study may facilitate the rational design of ligands toward the improvement of their binding ability with Np(V) and more efficient separation of Np in spent nuclear fuels.

NMR experiments have shown that water molecules in the crystal of the protein Crh are still mobile at temperatures well below 273 K. In order to investigate this water anomaly, a molecular dynamics (MD) simulation study of crystalline Crh was carried out to determine the mobility of water in this crystal. The simulations were carried out at three temperatures, 150, 200, and 291 K. Simulations of bulk water at these temperatures were also done to obtain the properties of the simple point charge (SPC) water model used at these temperatures and to allow a comparison of the properties of water in the Crh crystal with those of bulk water at the same temperatures. According to the simulations, water is immobilized at 150 K both in crystal and in bulk water. As expected, at 291 K it diffuses and rotates more slowly in the protein crystal than in bulk water. However, at 200 K, the translational and rotational mobility of the water molecules is larger in the crystal than in bulk water. The enhancement of water mobility in the crystal at 200 K was further investigated by MD simulations in which the backbone or all protein atoms were positionally restrained, and in which additionally the electrostatic protein-water interactions were removed. Of these changes in the environment of the water molecules, rigidifying the protein backbones slightly enhanced water diffusion, while it slowed down rotation. In contrast, removal of electrostatic protein-water interactions did not change water diffusion but enhanced rotational motion significantly. Further investigations are required to delineate particular features of the protein crystal that induce the anomalous behavior of water at 200 K.

Despite its experimental characterization, the detailed geometry and electronic structure of actinide metallofullerene U@C(82) have been rarely studied. We predict that (#5)C(82) and (#8)C(82) are the best cages for the encapsulation of monovalent and tetravalent U (i.e., U(+) and U(4+)), respectively; while (#9)C(82) is the best cage for divalent, trivalent, pentavalent, and hexavalent U cations (i.e., U(2+), U(3+), U(5+), and U(6+)). U@(#9)C(82) is the thermodynamically most stable one among all the isomers and thus corresponds to the most experimentally isolable isomer of U@C(82). The calculated spin density explicitly suggests that the endohedral metallofullerene U@(#9)C(82) is a trivalent ion-pair with an electronic configuration of U(3+)@C(82)(3-). The proposed geometry and electronic structure of U(3+)@(#9)C(82)(3-) are in good agreement with the experimental observation.

We report our recent DFT mechanistic study on the functionalization of CO2 and CS2 promoted by a trivalent uranium complex (Tp*)2UCH2Ph. In the calculations, the uranium atom is described by a quasi-relativistic 5f-in-core ECP basis set (LPP) developed for the trivalent uranium cation, which was qualified by the calculations with a quasi-relativistic small core ECP basis set (SPP) for uranium. According to our calculations, the functionalization proceeds in a stepwise manner, and the CO2 or CS2 does not interact with the central uranium atom to form a stable complex prior to the reaction due to the steric hindrance from the bulky ligands but directly cleaves the U-C (benzyl) bond by forming a C-C covalent bond. The released coordination site of uranium is concomitantly occupied by one chalcogen atom of the incoming molecule and gives an intermediate with the uranium atom interacting with the functionalized CO2 or CS2 in an η(1) fasion. This step is followed by a reorientation of the (dithio)carboxylate side chain of the newly formed PhCH2CE2(-) (E = O, S) ligand to give the corresponding product. Energetically, the first step is characterized as the rate-determining step with a barrier of 9.5 (CO2) or 25.0 (CS2) kcal/mol, and during the reaction, the chalcogen atoms are reduced, while the methylene of the benzyl group is oxidized. Comparison of the results from SPP and LPP calculations indicates that our calculations qualify the use of an LPP treatment of the uranium atom toward a reasonable description of the model systems in the present study.

GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular Simulation software for (bio)molecular simulation. It contains more than 70 programs that can be used to prepare data for the production of molecular simulation trajectories and to analyze these. These programs are reviewed and the various structural, dynamic, and thermodynamic quantities that can be analyzed using time series, correlation functions, and distributions are described together with technical aspects of their implementation in GROMOS. A few examples of the use of GROMOS++ for the analysis of MD trajectories are given. A full list of all GROMOS++ programs, together with an indication of their capabilities, is given in the Appendix .

Protonation of Compound 0 in the catalytic cycle of cytochrome P450cam may lead to the formation of either the reactive Compound I (coupling) or the ferric resting state (uncoupling). In this work, we investigate the effect of the D251N mutation on the coupling and uncoupling reaction by combined quantum mechanics/molecular mechanics (QM/MM) calculations. The mutated Asn251 residue has two possible orientations, i.e. directed toward the active site (no flip) or away from the active site (flip), with the latter one being preferred in classical molecular dynamics (MD) simulations. The possible proton transfer mechanisms in the coupling and uncoupling reaction were studied for three models of the D251N mutant, i.e. no flip (model I), flip (model II), and flip with an extra water (model III). According to the QM/MM calculations, the uncoupling reaction is always less favorable than the coupling reaction. The coupling reaction in the D251N mutant follows the same mechanism as in the wild-type enzyme, with initial O-O cleavage followed by proton transfer. The barrier for the initial step is similar in all D251N models, but the proton transfer is most facile in model III. The hydroxide anion formed in model III is not reprotonated easily by neighboring residues, while proton delivery from bulk solvent seems possible via a water network that remains intact during 2 ns classical MD simulation. The computational results are consistent with the experimental findings that the coupling reaction dominates the consumption of dioxygen in the D251N mutant, but with lower activity than in the wild-type enzyme.

We report a combined QM/MM study on the mechanism of the reductive half-reaction of aldehyde oxidoreductase. Five possible pathways are explored concerning the binding mode of acetaldehyde and the catalytic effect of the nearby glutamic acid (Glu869), taking both possible protonation states into account. In the most favorable pathway, Glu869 participates and acts as a Lewis base to deprotonate the labile hydroxide group. This proton transfer is essential for the high activity of the enzyme toward substrate because it increases the nucleophilicity of the migrating O atom and strengthens the electrophilicity of the target C atom in the substrate. The subsequent product-forming reactions occur in two discrete steps, first nucleophilic attack and then hydride transfer, which implies that the oxidation of aldehyde is a two-electron process. A variant of this mechanism, with an additional water molecule bridging the Glu869 side chain and the substrate, has similar barriers. Judging from previous gas phase calculations and our present QM/MM data, the catalytic effect of Glu869 mainly lowers the barrier of the nucleophilic attack so that the hydride transfer becomes the rate-determining step in the reductive half-reaction.

In the catalytic cycle of cytochrome P450cam, the hydroperoxo intermediate (Cpd 0) is formed by proton transfer from a reduced oxyheme complex (S5). This process is drastically slowed down when Asp251 is mutated to Asn (D251N). We report quantum mechanical/molecular mechanical (QM/MM) calculations that address this proton delivery in the doublet state through a hydrogen-bond network in the Asp251 channel, both for the wild-type enzyme and the D251N mutant, using four different active-site models. For the wild-type, we find a facile concerted mechanism for proton transfer from protonated Asp251 via Wat901 and Thr252 to the FeOO moiety, with a barrier of about 1 kcal/mol and a high exothermicity of more than 20 kcal/mol. In the D251N mutant with a neutral Asn251 residue, the proton transfer is almost thermoneutral or slightly exothermic in the three models considered. It is still very facile when the Asn251 residue adopts a conformation analogous to Asp251 in the wild-type enzyme, but the barrier increases significantly when the Asn251 side chain flips (as indicated by classical molecular dynamics simulations). This flip disrupts the hydrogen-bond network and hence the proton-transfer pathway, which causes a longer lifetime of S5 in the D251N mutant (consistent with experimental observations). The entry of an additional water molecule into the active site of D251N with flipped Asn251 regenerates the hydrogen-bond network and provides a viable mechanism for proton delivery in the mutant, with a moderate barrier of about 7 kcal/mol.