Ensemble modelling, uncertainty and robust predictions of organic carbon in long-term bare-fallow soils.

Simulation models represent soil organic carbon (SOC) dynamics in global carbon (C) cycle scenarios to support climate-change studies. It is imperative to increase confidence in long-term predictions of SOC dynamics by reducing the uncertainty in model estimates. We evaluated SOC simulated from an ensemble of 26 process-based C models by comparing simulations to experimental data from seven long-term bare-fallow (vegetation-free) plots at six sites: Denmark (two sites), France, Russia, Sweden and the United Kingdom. The decay of SOC in these plots has been monitored for decades since the last inputs of plant material, providing the opportunity to test decomposition without the continuous input of new organic material. The models were run independently over multi-year simulation periods (from 28 to 80 years) in a blind test with no calibration (Bln) and with the following three calibration scenarios, each providing different levels of information and/or allowing different levels of model fitting: (a) calibrating decomposition parameters separately at each experimental site (Spe); (b) using a generic, knowledge-based, parameterization applicable in the Central European region (Gen); and (c) using a combination of both (a) and (b) strategies (Mix). We addressed uncertainties from different modelling approaches with or without spin-up initialization of SOC. Changes in the multi-model median (MMM) of SOC were used as descriptors of the ensemble performance. On average across sites, Gen proved adequate in describing changes in SOC, with MMM equal to average SOC (and standard deviation) of 39.2 (±15.5) Mg C/ha compared to the observed mean of 36.0 (±19.7) Mg C/ha (last observed year), indicating sufficiently reliable SOC estimates. Moving to Mix (37.5 ± 16.7 Mg C/ha) and Spe (36.8 ± 19.8 Mg C/ha) provided only marginal gains in accuracy, but modellers would need to apply more knowledge and a greater calibration effort than in Gen, thereby limiting the wider applicability of models.

Author Correction: Trade-offs in using European forests to meet climate objectives.

In this Letter, in "About 75% of this reduction is expected to come from emission reductions and the remaining 25% from land use, land-use change and forestry", '25%' should read '1%' and '75%' should read '99%'. In the sentence "The carbon-sink-maximizing portfolio has a small negative effect on annual precipitation (-2 mm) and no effect on air temperature (Table 1)" the word 'precipitation' was omitted. Denmark was accidentally deleted during the conversion of Fig. 1. The original Letter has been corrected online.

Trade-offs in using European forests to meet climate objectives.

The Paris Agreement promotes forest management as a pathway towards halting climate warming through the reduction of carbon dioxide (CO2) emissions1. However, the climate benefits from carbon sequestration through forest management may be reinforced, counteracted or even offset by concurrent management-induced changes in surface albedo, land-surface roughness, emissions of biogenic volatile organic compounds, transpiration and sensible heat flux2-4. Consequently, forest management could offset CO2 emissions without halting global temperature rise. It therefore remains to be confirmed whether commonly proposed sustainable European forest-management portfolios would comply with the Paris Agreement-that is, whether they can reduce the growth rate of atmospheric CO2, reduce the radiative imbalance at the top of the atmosphere, and neither increase the near-surface air temperature nor decrease precipitation by the end of the twenty-first century. Here we show that the portfolio made up of management systems that locally maximize the carbon sink through carbon sequestration, wood use and product and energy substitution reduces the growth rate of atmospheric CO2, but does not meet any of the other criteria. The portfolios that maximize the carbon sink or forest albedo pass only one-different in each case-criterion. Managing the European forests with the objective of reducing near-surface air temperature, on the other hand, will also reduce the atmospheric CO2 growth rate, thus meeting two of the four criteria. Trade-off are thus unavoidable when using European forests to meet climate objectives. Furthermore, our results demonstrate that if present-day forest cover is sustained, the additional climate benefits achieved through forest management would be modest and local, rather than global. On the basis of these findings, we argue that Europe should not rely on forest management to mitigate climate change. The modest climate effects from changes in forest management imply, however, that if adaptation to future climate were to require large-scale changes in species composition and silvicultural systems over Europe5,6, the forests could be adapted to climate change with neither positive nor negative  climate effects.

Europe's forest management did not mitigate climate warming.

Afforestation and forest management are considered to be key instruments in mitigating climate change. Here we show that since 1750, in spite of considerable afforestation, wood extraction has led to Europe's forests accumulating a carbon debt of 3.1 petagrams of carbon. We found that afforestation is responsible for an increase of 0.12 watts per square meter in the radiative imbalance at the top of the atmosphere, whereas an increase of 0.12 kelvin in summertime atmospheric boundary layer temperature was mainly caused by species conversion. Thus, two and a half centuries of forest management in Europe have not cooled the climate. The political imperative to mitigate climate change through afforestation and forest management therefore risks failure, unless it is recognized that not all forestry contributes to climate change mitigation.

Molecular understanding of sulphuric acid-amine particle nucleation in the atmosphere.

Nucleation of aerosol particles from trace atmospheric vapours is thought to provide up to half of global cloud condensation nuclei. Aerosols can cause a net cooling of climate by scattering sunlight and by leading to smaller but more numerous cloud droplets, which makes clouds brighter and extends their lifetimes. Atmospheric aerosols derived from human activities are thought to have compensated for a large fraction of the warming caused by greenhouse gases. However, despite its importance for climate, atmospheric nucleation is poorly understood. Recently, it has been shown that sulphuric acid and ammonia cannot explain particle formation rates observed in the lower atmosphere. It is thought that amines may enhance nucleation, but until now there has been no direct evidence for amine ternary nucleation under atmospheric conditions. Here we use the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN and find that dimethylamine above three parts per trillion by volume can enhance particle formation rates more than 1,000-fold compared with ammonia, sufficient to account for the particle formation rates observed in the atmosphere. Molecular analysis of the clusters reveals that the faster nucleation is explained by a base-stabilization mechanism involving acid-amine pairs, which strongly decrease evaporation. The ion-induced contribution is generally small, reflecting the high stability of sulphuric acid-dimethylamine clusters and indicating that galactic cosmic rays exert only a small influence on their formation, except at low overall formation rates. Our experimental measurements are well reproduced by a dynamical model based on quantum chemical calculations of binding energies of molecular clusters, without any fitted parameters. These results show that, in regions of the atmosphere near amine sources, both amines and sulphur dioxide should be considered when assessing the impact of anthropogenic activities on particle formation.

Calculation of the Gibbs free energy of solvation and dissociation of HCl in water via Monte Carlo simulations and continuum solvation models.

The Gibbs free energy of solvation and dissociation of hydrogen chloride in water is calculated through a combined molecular simulation/quantum chemical approach at four temperatures between T = 300 and 450 K. The Gibbs free energy is first decomposed into the sum of two components: the Gibbs free energy of transfer of molecular HCl from the vapor to the aqueous liquid phase and the standard-state Gibbs free energy of acid dissociation of HCl in aqueous solution. The former quantity is calculated using Gibbs ensemble Monte Carlo simulations using either Kohn-Sham density functional theory or a molecular mechanics force field to determine the system's potential energy. The latter Gibbs free energy contribution is computed using a continuum solvation model utilizing either experimental reference data or micro-solvated clusters. The predicted combined solvation and dissociation Gibbs free energies agree very well with available experimental data.

Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations.

Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ~0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the Pγ-Oß dissociation concerted with approach of the lytic water to PγO3-. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO(4)2- via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F1-ATPase, raising the possibility of a common mechanism.

Structural rearrangements and magic numbers in reactions between pyridine-containing water clusters and ammonia.

Molecular cluster ions H(+)(H(2)O)(n), H(+)(pyridine)(H(2)O)(n), H(+)(pyridine)(2)(H(2)O)(n), and H(+)(NH(3))(pyridine)(H(2)O)(n) (n = 16-27) and their reactions with ammonia have been studied experimentally using a quadrupole-time-of-flight mass spectrometer. Abundance spectra, evaporation spectra, and reaction branching ratios display magic numbers for H(+)(NH(3))(pyridine)(H(2)O)(n) and H(+)(NH(3))(pyridine)(2)(H(2)O)(n) at n = 18, 20, and 27. The reactions between H(+)(pyridine)(m)(H(2)O)(n) and ammonia all seem to involve intracluster proton transfer to ammonia, thus giving clusters of high stability as evident from the loss of several water molecules from the reacting cluster. The pattern of the observed magic numbers suggest that H(+)(NH(3))(pyridine)(H(2)O)(n) have structures consisting of a NH(4)(+)(H(2)O)(n) core with the pyridine molecule hydrogen-bonded to the surface of the core. This is consistent with the results of high-level ab initio calculations of small protonated pyridine/ammonia/water clusters.

Rethinking the application of the first nucleation theorem to particle formation.

The critical cluster is the threshold size above which a cluster will be more likely to grow than to evaporate. In field and laboratory measurements of new particle formation, the number of molecules of a given species in the critical cluster is commonly taken to be the slope of the log-log plot of the formation rate versus the concentration of the species. This analysis is based on an approximate form of the first nucleation theorem, which is derived with the assumption that there are no minima in the free energy surface prior to the maximum at the critical size. However, many atmospherically relevant systems are likely to exhibit such minima, for example, ions surrounded by condensable vapour molecules or certain combinations of acids and bases. We have solved numerically the birth-death equations for both an electrically neutral one-component model system with a local minimum at pre-critical sizes and an ion-induced case. For the ion-induced case, it is verified that the log-log slope of the nucleation rate versus particle concentration plot gives accurately the difference between the cluster sizes at the free energy maximum and minimum, as is expected from the classical form of the ion-induced nucleation rate. However, the results show that applying the nucleation theorem to neutral systems with stable pre-nucleation clusters may lead to erroneous interpretations about the nature of the critical cluster.

Re-examining the properties of the aqueous vapor-liquid interface using dispersion corrected density functional theory.

First-principles molecular dynamics simulations, in which the forces are computed from electronic structure calculations, have great potential to provide unique insight into structure, dynamics, electronic properties, and chemistry of interfacial systems that is not available from empirical force fields. The majority of current first-principles simulations are driven by forces derived from density functional theory with generalized gradient approximations to the exchange-correlation energy, which do not capture dispersion interactions. We have carried out first-principles molecular dynamics simulations of air-water interfaces employing a particular generalized gradient approximation to the exchange-correlation functional (BLYP), with and without empirical dispersion corrections. We assess the utility of the dispersion corrections by comparison of a variety of structural, dynamic, and thermodynamic properties of bulk and interfacial water with experimental data, as well as other first-principles and force field-based simulations.

Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional.

Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.

Vapor-liquid coexistence curves for methanol and methane using dispersion-corrected density functional theory.

First principles Monte Carlo simulations in the Gibbs and isobaric-isothermal ensembles were performed to map the vapor-liquid coexistence curves of methanol and methane described by Kohn-Sham density functional theory using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation functionals with the Grimme correction term for dispersive (D2) interactions. The simulations indicate that the BLYP-D2 description with the TZV2P basis set underpredicts the saturated vapor densities and overpredicts the saturated liquid densities and critical and boiling temperatures for both compounds. Although the deviations are quite large, these results present a significant improvement over the BLYP functional without the correction term, which misses the experimental results by a larger extent in the opposite direction. Simulations at one temperature indicate that use of the larger QZV3P basis set may lead to improved saturated vapor densities, but not to significant changes in the liquid density.

Vapor-liquid nucleation of argon: exploration of various intermolecular potentials.

The homogeneous vapor-liquid nucleation of argon has been explored at T=70 and 90 K using classical nucleation theory, semiempirical density functional theory, and Monte Carlo simulations using the aggregation-volume-bias algorithm with umbrella sampling and histogram-reweighting. In contrast with previous simulation studies, which employed only the Lennard-Jones intermolecular potential, the current studies were carried out using various pair potentials including the Lennard-Jones potential, a modified Buckingham exponential-six potential, the Barker-Fisher-Watts pair potential, and a recent ab initio potential developed using the method of effective diameters. It was found that the differences in the free energy of formation of the critical nuclei between the potentials cannot be explained solely in terms of the difference in macroscopic properties of the potentials, which gives a possible reason for the failure of classical nucleation theory.

First principles Monte Carlo simulations of aggregation in the vapor phase of hydrogen fluoride.

The aggregation of hydrogen fluoride vapor is explored through the use of Monte Carlo simulations employing Kohn-Sham density functional theory with the exchange/correlation functional of Becke-Lee-Yang-Parr to describe the molecular interactions. Canonical ensemble simulations sampling the classical phase space were carried out for a system consisting of ten molecules at constant density (2700 A(3)/molecule) and at three different temperatures (T = 310, 350, and 390 K). Aggregation-volume-bias and configurational-bias Monte Carlo approaches (along with pre-sampling with an approximate potential) were employed to increase the sampling efficiency of cluster formation and destruction. A hydrogen-bond analysis shows that about two thirds of the HF molecules are part of small aggregates at 310 K, whereas only about 10% of the molecules are clustered at 390 K. As for other hydrogen-bonding systems, the size distribution exhibits some sensitivity to the criteria used to define a hydrogen bond, but the qualitative features are not affected by these differences. From the temperature dependence of the equilibrium constants, the dimer and trimer aggregation energies (not corrected for nuclear quantum effects) are estimated using a simple distance-based hydrogen-bonding criterion as -13 +/- 3 and -65 +/- 16 kJ mol(-1), respectively, whereas these binding energies are found to be somewhat different for a combined distance-angular criterion with values of -17 +/- 6 and -63 +/- 11 kJ mol(-1), respectively. The strictness of the hydrogen-bonding criterion plays a significant role for the assignment of clusters to linear, cyclic, and branched architectures with the fraction of the latter being drastically reduced for the distance-angular criterion. The average molecular dipole moment increases from 1.85 Debye for isolated molecules to about 2.0 D for dimers to about 2.75 D for larger aggregates, and the H-F bond length shows a concomitant, but smaller increase from about 0.94 to 0.98 A.

Excited state hydrogen bond dynamics: coumarin 102 in acetonitrile-water binary mixtures.

The time dependent change in the intermolecular response of solvent molecules following photoexcitation of Coumarin 102 (C102) has been measured in acetonitrile-water binary mixtures. Experiments were performed on mixtures of composition x(CH3CN) = 0.25, 0.50, 0.75, and 1.00. At low water concentrations (x(H2O) < or = 0.25) the solvent response is consistent with previous measurements probing dipolar solvation. With increasing water concentration (x(H2O) > or = 0.50) an additional response is found subsequent to dipolar solvation, exhibited as a rapid gain in the solvent's polarizability on a approximately 250 fs time scale. Monte Carlo simulations of the C102:binary mixture system were performed to quantify the number of hydrogen-bonding interactions between C102 and water. These simulations indicate that the probability of the C102 solute being hydrogen bound with two water molecules, both as donors at the carbonyl site, increases in a correlated fashion with the amplitude of the additional response in the measurements. We conclude that excitation of C102 simultaneously weakens and strengthens hydrogen bonding in complexes with two inequivalently bound waters.

Stereocontrolled synthesis and alkylation of cyclic beta-amino esters: asymmetric synthesis of a (-)-sparteine surrogate.

A convenient method for the stereoselective synthesis of cyclic beta-amino esters from an iodo alphabeta-unsaturated ester and alpha-methylbenzylamine is described. Subsequent enolate generation and alkylation proceeds with complete stereocontrol, with the two stereogenic centres working together. In this way, a functionalised piperidine suitable for alkaloid natural product synthesis was prepared. The usefulness of the methodology is exemplified with the concise synthesis of a (-)-sparteine surrogate.

The use of chiral lithium amides in the desymmetrisation of N-trialkylsilyl dimethyl sulfoximines.

BACKGROUND: Chiral base desymmetrisation of dimethyl sulfoximines could provide a general route to chiral, enantioenriched dialkyl sulfoximines with potential for use in asymmetric catalysis. RESULTS: Asymmetric deprotonation of N-trialkylsilyl dimethyl sulfoximines with either enantiomer of lithium N,N-bis(1-phenylethyl)amide in the presence of lithium chloride affords enantioenriched sulfoximines on electrophilic trapping. Ketones, ketimines, trialkylsilyl chlorides and activated alkyl halides may be used as electrophiles in the reaction. Furthermore, a modified Horner-Emmons methodology was investigated. CONCLUSION: Simple chiral lithium amides afford products with enantiomeric excesses of up to 70%, illustrating that chiral base desymmetrisation of dimethyl sulfoximines is possible.

Reactivity series for s-BuLi/diamine-mediated lithiation of N-Boc pyrrolidine: applications in catalysis and lithiation of N-Boc piperidine.

Using competition experiments between a range of ligands and (-)-sparteine, a reactivity series for N-Boc pyrrolidine lithiation using s-BuLi/diamines has been constructed; the results indicate that the s-BuLi/(+)-sparteine surrogate complex is more reactive than s-BuLi/(-)-sparteine and this has been exploited in the selection of ligand pairs for ligand exchange catalytic asymmetric lithiation of N-Boc pyrrolidine and lithiation of N-Boc piperidine.

Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study.

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of water utilizing both ab initio (based on density functional theory) and empirical (fixed charge and polarizable) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times will be characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for interfacial water. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the ab initio interaction potential predicts a significant decrease in the molecular dipole moment and expansion in the oxygen-oxygen distance as one approaches the interface in accordance with recent experiments. All classical polarizable interaction potentials show a less dramatic drop in the molecular dipole moment, and all empirical interaction potentials studied yield an oxygen-oxygen contraction as the interface is approached.