Microbial carbon use efficiency promotes global soil carbon storage.

Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5-7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8-11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

Warming and elevated CO2 promote rapid incorporation and degradation of plant-derived organic matter in an ombrotrophic peatland.

Rising temperatures have the potential to directly affect carbon cycling in peatlands by enhancing organic matter (OM) decomposition, contributing to the release of CO2 and CH4 to the atmosphere. In turn, increasing atmospheric CO2 concentration may stimulate photosynthesis, potentially increasing plant litter inputs belowground and transferring carbon from the atmosphere into terrestrial ecosystems. Key questions remain about the magnitude and rate of these interacting and opposing environmental change drivers. Here, we assess the incorporation and degradation of plant- and microbe-derived OM in an ombrotrophic peatland after 4 years of whole-ecosystem warming (+0, +2.25, +4.5, +6.75 and +9°C) and two years of elevated CO2  manipulation (500 ppm above ambient). We show that OM molecular composition was substantially altered in the aerobic acrotelm, highlighting the sensitivity of acrotelm carbon to rising temperatures and atmospheric CO2 concentration. While warming accelerated OM decomposition under ambient CO2 , new carbon incorporation into peat increased in warming × elevated CO2 treatments for both plant- and microbe-derived OM. Using the isotopic signature of the applied CO2 enrichment as a label for recently photosynthesized OM, our data demonstrate that new plant inputs have been rapidly incorporated into peat carbon. Our results suggest that under current hydrological conditions, rising temperatures and atmospheric CO2  levels will likely offset each other in boreal peatlands.

Model protein excited states: MRCI calculations with large active spaces vs CC2 method.

Benchmarking calculations on excited states of models of phenylalanine protein chains are presented to assess the ability of alternative methods to the standard and most commonly used multiconfigurational wave function-based method, the complete active space self-consistent field (CASSCF), in recovering the non-dynamical correlation for systems that become not affordable by the CASSCF. The exploration of larger active spaces beyond the CASSCF limit is benchmarked through three strategies based on the reduction in the number of determinants: the restricted active space self-consistent field, the generalized active space self-consistent field (GASSCF), and the occupation-restricted multiple active space (ORMAS) schemes. The remaining dynamic correlation effects are then added by the complete active space second-order perturbation theory and by the multireference difference dedicated configuration interaction methods. In parallel, the approximate second-order coupled cluster (CC2), already proven to be successful for small building blocks of model proteins in one of our previous works [Ben Amor et al., J. Chem. Phys. 148, 184105 (2018)], is investigated to assess its performances for larger systems. Among the different alternative strategies to CASSCF, our results highlight the greatest efficiency of the GASSCF and ORMAS schemes in the systematic reduction of the configuration interaction expansion without loss of accuracy in both nature and excitation energies of both singlet ππ* and nπ* CO excited states with respect to the equivalent CASSCF calculations. Guidelines for an optimum applicability of this scheme to systems requiring active spaces beyond the complete active space limit are then proposed. Finally, the extension of the CC2 method to such large systems without loss of accuracy is demonstrated, highlighting the great potential of this method to treat accurately excited states, mainly single reference, of very large systems.

Recent developments in the general atomic and molecular electronic structure system.

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

Ab Initio Molecular Orbital Study of the First Four Si/C Alternately Substituted Annulenes.

The ground and low-lying excited states of four alternating Si/C annulenes, H nSi n/2C n/2 with n = 4, 6, 8, and 10, have been investigated by ab initio molecular orbital methods and compared to those of their all-carbon and all-silicon analogues. In the ground state, all of the Si/C-mixed annulenes, except for the largest 10-membered annulene (H10Si5C5), assume equal-bond-length structures by adopting a closed-shell electronic structure in the possible highest symmetry. For the largest H10Si5C5, the trend of the bond delocalization still remains but the circular structure is considerably distorted and nonplanar due to severe angle strain. In the low-lying singlet (S1) and triplet (T1) states, the geometry of the compounds tends to be nonplanar as the excitations produce silyl radical character. Relative energies of the T1 and S1 states of the 6-membered ring, compared to those of the respective ground states (S0), are higher than those of the 4- and 8-membered rings, suggesting a special stability for H6Si3C3. The planar rhombus shape of the formally antiaromatic H4Si2C2 suggests that a synthetic effort is merited. Bonding analyses are given to support the conclusions reached on the basis of geometric structures and excited-state energetics.

Quasi-Atomic Bond Analyses in the Sixth Period: II. Bond Analyses of Cerium Oxides.

The role of the 4f orbitals in bonding is examined for the molecules cerium monoxide and cerium dioxide that have cerium formally in the +2 and +4 oxidation states, respectively. It is shown that the 4f orbitals are used primarily for polarization of the 5d orbitals when cerium is in the lower oxidation state, while the 4f orbitals play a significant role in chemical bonding via 5d/4f hybridization when cerium is in the +4 oxidation state.

Spin-Orbit Coupling Constants in Atoms and Ions of Transition Elements: Comparison of Effective Core Potentials, Model Core Potentials, and All-Electron Methods.

The spin-orbit coupling constants (SOCC) in atoms and ions of the first- through third-row transition elements were calculated for the low-lying atomic states whose main electron configuration is [ nd] q ( q = 1-4 and 6-9, n = the principal quantum number), using four different approaches: (1) a nonrelativistic Hamiltonian used to construct multiconfiguration self-consistent field (MCSCF) wave functions utilizing effective core potentials and their associated basis sets within the framework of second-order configuration interaction (SOCI) to calculate spin-orbit couplings (SOC) using one-electron Breit-Pauli Hamiltonian (BPH), (2) a nonrelativistic Hamiltonian used to construct MCSCF wave functions utilizing model core potentials and their associated basis sets within the framework of SOCI to calculate SOC using the full BPH, (3) nonrelativistic and spin-independent relativistic Hamiltonians used to construct MCSCF wave functions utilizing all-electron (AE) basis sets within the framework of SOCI to calculate SOC using the full BPH, and (4) a relativistic Hamiltonian given by the exact two-component (X2C) transformation for construction of Kramers-restricted relativistic configuration interaction wave functions. In this investigation, these four approaches are referred to as ECP, MCP, AE, and X2C methods, respectively. The ECP, MCP, and AE methods are so-called two-step approaches (TSA), while the X2C method is a one-step approach (OSA). In the AE method, three different calculations-relativistic elimination of small components (RESC), third-order Douglas-Kroll-Hess (DKH3), and infinite-order two-component (IOTC) relativistic correction-were performed for the estimation of the scalar relativistic components in addition to those of the nonscalar relativistic (NSR) contributions. The calculated SOCC are compared to the available experimental data via the Landé interval rule. Although there are several exceptions, including states whose main configuration is [ nd]5, the average differences between the ECP and AE (IOTC) SOCC and between the ECP and the X2C SOCC are mostly less than 20%. The differences between the ECP and the experimental SOCC are even smaller. No serious discrepancy was found between the TSA and OSA predictions of SOCC for the first- and second-row transition elements in comparison to experiment. For atoms and ions of the third-row transition elements, the SOCC calculated through the Landé interval rule are not reliable. The low-energy spin-mixed (SM) states originating from a [5d] q configuration ( q = 2-4) have a larger energy lowering due to the SOC effects, in comparison with those for atoms and ions of the first- and second-row transition elements. For the spin-mixed (SM) states originating from a [5d] q configuration ( q = 6-8), the energy lowering of all 4F7/2, 5D1, and 5D3 states due to the SOC effects is smaller than those of the other SM states. This difficulty, which also arises for the MCP, AE, and X2C (OSA) approaches, suggests that the LS-coupling scheme is inappropriate.

Quasi-Atomic Bond Analyses in the Sixth Period: I. Relativistic Accurate Atomic Minimal Basis Sets for the Elements Cesium to Radon.

Full-valence relativistic accurate atomic minimal basis set (AAMBS) orbitals are developed for the sixth-row elements from cesium to radon, including the lanthanides. Saturated primitive atomic basis sets are developed and subsequently used to form the AAMBS orbitals. By virtue of the use of a saturated basis, properties computed based on the AAMBS orbitals are basis set independent. In molecules, the AAMBS orbitals can be used to construct valence virtual orbitals (VVOs) that provide chemically meaningful ab initio lowest unoccupied molecular orbitals (LUMOs) with basis set independent orbital energies. The optimized occupied molecular orbitals complemented with the VVOs form a set of full-valence molecular orbitals. They can be transformed into a set of oriented quasi-atomic orbitals (QUAOs) that provide information on intramolecular bonding via an intrinsic density analysis. In the present work, the development of the AAMBS for the sixth row is presented.

Hybrid Correlation Energy (HyCE): An Approach Based on Separate Evaluations of Internal and External Components.

A novel hybrid correlation energy (HyCE) approach is proposed that determines the total correlation energy via distinct computation of its internal and external components. This approach evolved from two related studies. First, rigorous assessment of the accuracies and size extensivities of a number of electron correlation methods, that include perturbation theory (PT2), coupled-cluster (CC), configuration interaction (CI), and coupled electron pair approximation (CEPA), shows that the CEPA(0) variant of the latter and triples-corrected CC methods consistently perform very similarly. These findings were obtained by comparison to near full CI results for four small molecules and by charting recovered correlation energies for six steadily growing chain systems. Second, by generating valence virtual orbitals (VVOs) and utilizing the CEPA(0) method, we were able to partition total correlation energies into internal (or nondynamic) and external (or dynamic) parts for the aforementioned six chain systems and a benchmark test bed of 36 molecules. When using triple-ζ basis sets it was found that per orbital internal correlation energies were appreciably larger than per orbital external energies and that the former showed far more chemical variation than the latter. Additionally, accumulations of external correlation energies were seen to proceed smoothly, and somewhat linearly, as the virtual space is gradually increased. Combination of these two studies led to development of the HyCE approach, whereby the internal and external correlation energies are determined separately by CEPA(0)/VVO and PT2/external calculations, respectively. When applied to the six chain systems and the 36-molecule benchmark test set it was found that HyCE energies followed closely those of triples-corrected CC and CEPA(0) while easily outperforming MP2 and CCSD. The success of the HyCE approach is more notable when considering that its cost is only slightly more than MP2 and significantly cheaper than the CC approaches.

What on Earth Have We Been Burning? Deciphering Sedimentary Records of Pyrogenic Carbon.

Humans have interacted with fire for thousands of years, yet the utilization of fossil fuels marked the beginning of a new era. Ubiquitous in the environment, pyrogenic carbon (PyC) arises from incomplete combustion of biomass and fossil fuels, forming a continuum of condensed aromatic structures. Here, we develop and evaluate 14C records for two complementary PyC molecular markers, benzene polycarboxylic acids (BPCAs) and polycyclic aromatic hydrocarbons (PAHs), preserved in aquatic sediments from a suburban and a remote catchment in the United States (U.S.) from the mid-1700s to 1998. Results show that the majority of PyC stems from local sources and is transferred to aquatic sedimentary archives on subdecadal to millennial time scales. Whereas a small portion stems from near-contemporaneous production and sedimentation, the majority of PyC (∼90%) experiences delayed transmission due to "preaging" on millennial time scales in catchment soils prior to its ultimate deposition. BPCAs (soot) and PAHs (precursors of soot) trace fossil fuel-derived PyC. Both markers parallel historical records of the consumption of fossil fuels in the U.S., yet never account for more than 19% total PyC. This study demonstrates that isotopic characterization of multiple tracers is necessary to constrain histories and inventories of PyC and that sequestration of PyC can markedly lag its production.

Effect of Boron Clusters on the Ignition Reaction of HNO3 and Dicynanamide-Based Ionic Liquids.

Many ionic liquids containing the dicynamide anion (DCA-, formula N(CN)2-) exhibit hypergolic ignition when exposed to the common oxidizer nitric acid. However, the ignition delay is often about 10 times longer than the desired 5 ms for rocket applications, so that improvements are desired. Experiments in the past decade have suggested both a mechanism for the early reaction steps and also that additives such as decaborane can reduce the ignition delay. The mechanisms for reactions of nitric acid with both DCA- and protonated DCAH are considered here, using accurate wave function methods. Complexation of DCA- or DCAH with borane clusters B10H14 or B9H14- is found to modify these mechanisms slightly by changing the nature of some of the intermediate saddle points and by small reductions in the reaction barriers.

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C2 molecule.

Relativistic ab Initio Accurate Atomic Minimal Basis Sets: Quantitative LUMOs and Oriented Quasi-Atomic Orbitals for the Elements Li-Xe.

Valence virtual orbitals (VVOs) are a quantitative and basis set independent method for extracting chemically meaningful lowest unoccupied molecular orbitals (LUMOs). The VVOs are formed based on a singular value decomposition (SVD) with respect to precomputed and internally stored ab initio accurate atomic minimal basis sets (AAMBS) for the atoms. The occupied molecular orbitals and VVOs together form a minimal basis set that can be transformed into orthogonal oriented quasi-atomic orbitals (OQUAOs) that provide a quantitative description of the bonding in a molecular environment. In the present work, relativistic AAMBS are developed that span the full valence orbital space. The impact of using full valence AAMBS for the formation of the VVOs and OQUAOs and the resulting bonding analysis is demonstrated with applications to the cuprous chloride, scandium monofluoride, and nickel silicide diatomic molecules.

Persistence of soil organic matter as an ecosystem property.

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily--and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

F-box-directed CRL complex assembly and regulation by the CSN and CAND1.

The COP9 signalosome (CSN) is thought to maintain the stability of cullin-RING ubiquitin ligases (CRL) by limiting the autocatalytic destruction of substrate adapters such as F box proteins (FBPs). CAND1, a protein associated with unneddylated CUL1, was proposed to assist in this role in an as yet unclear fashion. We found that only a subset of Schizosaccharomyces pombe FBPs, which feature a critical F box proline that promotes their interaction with CUL1, required CSN for stability. Unlike the CRL3 adaptor Btb3p, none of the CSN-sensitive FBPs were affected by deletion of ubp12. Contrary to current models, CAND1 does not control adaptor stability but maintains the cellular balance of CRL1 complexes by preventing rare FBPs from being outcompeted for binding to CUL1 by more ample adapters. These findings were integrated into a refined model of CRL control in which substrate availability toggles CRLs between independent CSN and CAND1 cycles.

Heavy Element Effects in the Diagonal Born-Oppenheimer Correction within a Relativistic Spin-Free Hamiltonian.

Methodologies beyond the Born-Oppenheimer (BO) approximation are nowadays important to explain high precision spectroscopic measurements. Most previous evaluations of the BO correction are, however, focused on light-element molecules and based on a nonrelativistic Hamiltonian, so no information about the BO approximation (BOA) breakdown in heavy-element molecules is available. The present work is the first to investigate the BOA breakdown for the entire periodic table, by considering scalar relativistic effects in the Diagonal BO correction (DBOC). In closed shell atoms, the relativistic EDBOC scales as Z(1.25) and the nonrelativistic EDBOC scales as Z(1.17), where Z is the atomic number. Hence, we found that EDBOC becomes larger in heavy element atoms and molecules, and the relativistic EDBOC increases faster than nonrelativistic EDBOC. We have further investigated the DBOC effects on properties such as potential energy curves, spectroscopic parameters, and various energetic properties. The DBOC effects for these properties are mostly affected by the lightest atom in the molecule. Hence, in X2 or XAt molecule (X = H, Li, Na, K, Rb, and Cs) the effect of DBOC systematically decreases when X becomes heavier but in HX molecules, the effect of DBOC seems relatively similar among all the molecules.

Threshold Ionization and Spin-Orbit Coupling of Ceracyclopropene Formed by Ethylene Dehydrogenation.

A Ce atom reaction with ethylene was carried out in a laser-vaporization metal cluster beam source. Ce(C2H2) formed by hydrogen elimination from ethylene was investigated by mass-analyzed threshold ionization (MATI) spectroscopy, isotopic substitutions, and relativistic quantum chemical computations. The theoretical calculations include a scalar relativistic correction, dynamic electron correlation, and spin-orbit coupling. The MATI spectrum exhibits two nearly identical band systems separated by 128 cm(-1). The separation is not affected by deuteration. The two-band systems are attributed to spin-orbit splitting and the vibrational bands to the symmetric metal-ligand stretching and in-plane carbon-hydrogen bending excitations. The spin-orbit splitting arises from interactions of a pair of nearly degenerate triplets and a pair of nearly degenerate singlets. The organolanthanide complex is a metallacyclopropene in C2v symmetry. The low-energy valence electron configurations of the neutral and ion species are Ce 4f(1)6s(1) and Ce 4f(1), respectively. The remaining two electrons that are associated with the isolated Ce atom or ion are spin paired in a molecular orbital that is a bonding combination between a 5d Ce orbital and a π* antibonding orbital of acetylene.

Infrared Spectroscopy and Structure of (NO)(n) Clusters.

Nitrogen oxide clusters (NO)n have been studied in He droplets via infrared depletion spectroscopy and by quantum chemical calculations. The ν1 and ν5 bands of cis-ON-NO dimer have been observed at 1868.2 and 1786.5 cm(-1), respectively. Furthermore, spectral bands of the trimer and tetramer have been located in the vicinity of the corresponding dimer bands in accord with computed frequencies that place NO-stretch bands of dimer, trimer, and tetramer within a few wavenumbers of each other. In addition, a new line at 1878.1 cm(-1) close to the band origin of single molecules was assigned to van der Waals bound dimers of (NO)2, which are stabilized due to the rapid cooling in He droplets. Spectra of larger clusters (n > 5), have broad unresolved features in the vicinity of the dimer bands. Experiments and calculations indicate that trimers consist of a dimer and a loosely bound third molecule, whereas the tetramer consists of two weakly bound dimers.

Electronic Polarization Effect of the Water Environment in Charge-Separated Donor-Acceptor Systems: An Effective Fragment Potential Model Study.

The electronic polarization (POL) of the surrounding environment plays a crucial role in the energetics of charge-separated systems. Here, the mechanism of POL in charge-separated systems is studied using a combined quantum mechanical and effective fragment potential (QM/EFP) method. In particular, the POL effect caused by charge separation (CS) is investigated at the atomic level by decomposition into the POL at each polarizability point. The relevance of the electric field generated by the CS is analyzed in detail. The model systems investigated are Na+-Cl- and guanine-thymine solvated in water. The dominant part of the POL arises from solvent molecules close to the donor (D) and acceptor (A) units. At short D-A distances, the electric field shows both positive and negative interferences. The former case enhances the POL energy. At longer distances, the interference is weakened, and the local electric field determines the POL energy.