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Herpesviral protein kinases, such as the therapy-relevant pUL97 of human cytomegalovirus (HCMV), are important for viral replication efficiency as well as pathogenesis, and represent key antiviral drug targets. HCMV pUL97 is a viral cyclin-dependent kinase (CDK) ortholog, as it shares functional and structural properties with human CDKs. Recently, the formation of vCDK/pUL97–cyclin complexes and the phosphorylation of a variety of viral and cellular substrate proteins has been demonstrated. Genetic mapping and structural modeling approaches helped to define two pUL97 interfaces, IF1 and IF2, responsible for cyclin binding. In particular, the regulatory importance of interactions between vCDK/pUL97 and host cyclins as well as CDKs has been highlighted, both as determinants of virus replication and as a novel drug-targeting option. This aspect was substantiated by the finding that virus replication was impaired upon cyclin type H knock-down, and that such host-directed interference also affected viruses resistant to existing therapies. Beyond the formation of binary interactive complexes, a ternary pUL97–cyclin H–CDK7 complex has also been described, and in light of this, an experimental trans-stimulation of CDK7 activity by pUL97 appeared crucial for virus–host coregulation. In accordance with this understanding, several novel antiviral targeting options have emerged. These include kinase inhibitors directed to pUL97, to host CDKs, and to the pUL97–cyclin H interactive complexes. Importantly, a statistically significant drug synergy has recently been reported for antiviral treatment schemes using combinations of pharmacologically relevant CDK7 and vCDK/pUL97 inhibitors, including maribavir. Combined, such findings provide increased options for anti-HCMV control. This review focuses on regulatory interactions of vCDK/pUL97 with the host cyclin–CDK apparatus, and it addresses the functional relevance of these key effector complexes for viral replication and pathogenesis. On this basis, novel strategies of antiviral drug targeting are defined. [ABSTRACT FROM AUTHOR]

Human cytomegalovirus (CMV) infection is the leading non-genetic cause of congenital malformation in developed countries, causing significant fetal injury, and in some cases fetal death. The pathogenetic mechanisms through which this host-specific virus infects then damages both the placenta and the fetal brain are currently ill-defined. We investigated the CMV modulation of key signaling pathway proteins for these organs including dual-specificity tyrosine phosphorylation-regulated kinases (DYRK) and Sonic Hedgehog (SHH) pathway proteins using human first trimester placental trophoblast (TEV-1) cells, primary human astrocyte (NHA) brain cells, and CMV-infected human placental tissue. Immunofluorescence demonstrated the accumulation and re-localization of SHH proteins in CMV-infected TEV-1 cells with Gli2, Ulk3, and Shh re-localizing to the CMV cytoplasmic virion assembly complex (VAC). In CMV-infected NHA cells, DYRK1A re-localized to the VAC and DYRK1B re-localized to the CMV nuclear replication compartments, and the SHH proteins re-localized with a similar pattern as was observed in TEV-1 cells. Western blot analysis in CMV-infected TEV-1 cells showed the upregulated expression of Rb, Ulk3, and Shh, but not Gli2. In CMV-infected NHA cells, there was an upregulation of DYRK1A, DYRK1B, Gli2, Rb, Ulk3, and Shh. These in vitro monoculture findings are consistent with patterns of protein upregulation and re-localization observed in naturally infected placental tissue and CMV-infected ex vivo placental explant histocultures. This study reveals CMV-induced changes in proteins critical for fetal development, and identifies new potential targets for CMV therapeutic development. [ABSTRACT FROM AUTHOR]

The repertoire of currently available antiviral drugs spans therapeutic applications against a number of important human pathogens distributed worldwide. These include cases of the pandemic severe acute respiratory coronavirus type 2 (SARS-CoV-2 or COVID-19), human immunodeficiency virus type 1 (HIV-1 or AIDS), and the pregnancy- and posttransplant-relevant human cytomegalovirus (HCMV). In almost all cases, approved therapies are based on direct-acting antivirals (DAAs), but their benefit, particularly in long-term applications, is often limited by the induction of viral drug resistance or side effects. These issues might be addressed by the additional use of host-directed antivirals (HDAs). As a strong input from long-term experiences with cancer therapies, host protein kinases may serve as HDA targets of mechanistically new antiviral drugs. The study demonstrates such a novel antiviral strategy by targeting the major virus-supportive host kinase CDK7. Importantly, this strategy focuses on highly selective, 3D structure-derived CDK7 inhibitors carrying a warhead moiety that mediates covalent target binding. In summary, the main experimental findings of this study are as follows: (1) the in vitro verification of CDK7 inhibition and selectivity that confirms the warhead covalent-binding principle (by CDK-specific kinase assays), (2) the highly pronounced antiviral efficacies of the hit compounds (in cultured cell-based infection models) with half-maximal effective concentrations that reach down to picomolar levels, (3) a particularly strong potency of compounds against strains and reporter-expressing recombinants of HCMV (using infection assays in primary human fibroblasts), (4) additional activity against further herpesviruses such as animal CMVs and VZV, (5) unique mechanistic properties that include an immediate block of HCMV replication directed early (determined by Western blot detection of viral marker proteins), (6) a substantial drug synergism in combination with MBV (measured by a Loewe additivity fixed-dose assay), and (7) a strong sensitivity of clinically relevant HCMV mutants carrying MBV or ganciclovir resistance markers. Combined, the data highlight the huge developmental potential of this host-directed antiviral targeting concept utilizing covalently binding CDK7 inhibitors. [ABSTRACT FROM AUTHOR]

The infection of human cytomegalovirus (HCMV) is strongly determined by the host–cell interaction in a way that the efficiency of HCMV lytic replication is dependent on the regulatory interplay between viral and cellular proteins. In particular, the activities of protein kinases, such as cyclin-dependent kinases (CDKs) and the viral CDK ortholog (vCDK/pUL97), play an important role in both viral reproduction and virus–host interaction. Very recently, we reported on the complexes formed between vCDK/pUL97, human cyclin H, and CDK7. Major hallmarks of this interplay are the interaction between cyclin H and vCDK/pUL97, which is consistently detectable across various conditions and host cell types of infection, the decrease or increase in pUL97 kinase activity resulting from cyclin H knock-down or elevated levels, respectively, and significant trans-stimulation of human CDK7 activity by pUL97 in vitro. Due to the fact that even a ternary complex of vCDK/pUL97–cyclin H–CDK7 can be detected by coimmunoprecipitation and visualized by bioinformatic structural modeling, we postulated a putative impact of the respective kinase activities on the patterns of transcription in HCMV-infected cells. Here, we undertook a first vCDK/pUL97-specific transcriptomic analysis, which combined conditions of fully lytic HCMV replication with those under specific vCDK/pUL97 or CDK7 drug-mediated inhibition or transient cyclin H knockout. The novel results were further strengthened using bioinformatic modeling of the involved multi-protein complexes. Our data underline the importance of these kinase activities for the C-terminal domain (CTD) phosphorylation-driven activation of host RNA polymerase in HCMV-infected cells. The impact of the individual experimental conditions on differentially expressed gene profiles is described in detail and discussed. [ABSTRACT FROM AUTHOR]

Herpesviruses replicate their genomes and assemble their capsids in the host cell nucleus. To progress towards morphogenesis in the cytoplasm, herpesviruses evolved the strategy of nuclear egress as a highly regulated process of nucleo-cytoplasmic capsid transition. The process is conserved among α-, β- and γ-herpesviruses and involves the formation of a core and multicomponent nuclear egress complex (NEC). Core NEC is assembled by the interaction between the nucleoplasmic hook protein, i.e., pUL53 (human cytomegalovirus, HCMV), and the integral membrane-associated groove protein, i.e., pUL50. Our study aimed at the question of whether a panherpesviral NEC scaffold may enable hook-into-groove interaction across herpesviral subfamilies. For this purpose, NEC constructs were generated for members of all three subfamilies and analyzed for multi-ligand interaction using a yeast two-hybrid (Y2H) approach with randomized pUL53 mutagenesis libraries. The screening identified ten library clones displaying cross-viral shared hook-into-groove interaction. Interestingly, a slightly modified Y2H screening strategy provided thirteen further changed-hook pUL53 clones having lost parental pUL50 interaction but gained homolog interaction. In addition, we designed a sequence-predicted hybrid construct based on HCMV and Epstein-Barr virus (EBV) core NEC proteins and identified a cross-viral interaction phenotype. Confirmation was provided by applying protein–protein interaction analyses in human cells, such as coimmunoprecipitation settings, confocal nuclear rim colocalization assays, and HCMV ΔUL53 infection experiments with pUL53-complementing cells. Combined, the study provided the first examples of cross-viral NEC interaction patterns and revealed a higher yield of human cell-confirmed binding clones using a library exchange rate of 3.4 than 2.7. Thus, the study provides improved insights into herpesviral NEC protein binding specificities of core NEC formation. This novel information might be exploited to gain a potential target scaffold for the development of broadly acting NEC-directed inhibitory small molecules. [ABSTRACT FROM AUTHOR]

The complex host interaction network of human cytomegalovirus (HCMV) involves the regulatory protein kinase pUL97, which represents a viral cyclin-dependent kinase (CDK) ortholog. pUL97 interacts with the three human cyclin types T1, H, and B1, whereby the binding region of cyclin T1 and the pUL97 oligomerization region were both assigned to amino acids 231-280. We further addressed the question of whether HCMVs harboring mutations in ORF-UL97, i.e., short deletions or resistance-conferring point mutations, are affected in the interaction with human cyclins and viral replication. To this end, clinically relevant UL97 drug-resistance-conferring mutants were analyzed by whole-genome sequencing and used for genetic marker transfer experiments. The recombinant HCMVs indicated conservation of pUL97–cyclin interaction, since all viral UL97 point mutants continued to interact with the analyzed cyclin types and exerted wild-type-like replication fitness. In comparison, recombinant HCMVs UL97 Δ231-280 and also the smaller deletion Δ236-275, but not Δ241-270, lost interaction with cyclins T1 and H, showed impaired replication efficiency, and also exhibited reduced kinase activity. Moreover, a cellular knock-out of cyclins B1 or T1 did not alter HCMV replication phenotypes or pUL97 kinase activity, possibly indicating alternative, compensatory pUL97–cyclin interactions. In contrast, however, cyclin H knock-out, similar to virus deletion mutants in the pUL97–cyclin H binding region, exhibited strong defective phenotypes of HCMV replication, as supported by reduced pUL97 kinase activity in a cyclin H-dependent coexpression setting. Thus, cyclin H proved to be a very relevant determinant of pUL97 kinase activity and viral replication efficiency. As a conclusion, the results provide evidence for the functional importance of pUL97–cyclin interaction. High selective pressure on the formation of pUL97–cyclin complexes was identified by the use of clinically relevant mutants. [ABSTRACT FROM AUTHOR]

The human cytomegalovirus (HCMV) is a member of the beta-herpesvirus family and inflicts life-long latent infections in its hosts. HCMV has been shown to manipulate and dysregulate many cellular processes. One major interactor with the cellular host is the viral kinase pUL97. The UL97 gene is essential for viral replication, and kinase-deficient mutants of pUL97 display a severe replication defect. Recently, another group established an analog-sensitive version of the pUL97 protein. This mutant kinase can be treated with a non-hydrolysable ATP analog, thereby inhibiting its kinase function. This process is reversible by removing the ATP analog by media change. We introduced this mutant version of the pUL97 protein into the laboratory strain Ad169 of HCMV, BADwt, creating a BAD-UL97-as1 viral mutant. This mutant virus replicated normally in infected cells in the absence of the ATP analog and maintained its ability to phosphorylate its cellular substrates. However, when treated with the ATP analog, BAD-UL97-as1 displayed a defect in the production of intra- and extracellular viral DNA and in the production of viral progeny. Furthermore, in the presence of 3MB-PP1, a well-established substrate of pUL97 was no longer hyperphosphorylated. This effect was detectable as early as 4 h post treatment, which allows for studies on pUL97 without the complication of low viral titers. Nevertheless, we observed off-target effects of 3MB-PP1 on several cellular processes, which should be considered with this approach. [ABSTRACT FROM AUTHOR]

Background and aims: The amount of nitrogen (N) derived from symbiotic N2 fixation by legumes in grasslands might be affected by anthropogenic N and phosphorus (P) inputs, but the underlying mechanisms are not known. Methods: We evaluated symbiotic N2 fixation in 17 natural and semi-natural grasslands on four continents that are subjected to the same full-factorial N and P addition experiment, using the 15N natural abundance method. Results: N as well as combined N and P (NP) addition reduced aboveground legume biomass by 65% and 45%, respectively, compared to the control, whereas P addition had no significant impact. Addition of N and/or P had no significant effect on the symbiotic N2 fixation per unit legume biomass. In consequence, the amount of N fixed annually per grassland area was less than half in the N addition treatments compared to control and P addition, irrespective of whether the dominant legumes were annuals or perennials. Conclusion: Our results reveal that N addition mainly impacts symbiotic N2 fixation via reduced biomass of legumes rather than changes in N2 fixation per unit legume biomass. The results show that soil N enrichment by anthropogenic activities significantly reduces N2 fixation in grasslands, and these effects cannot be reversed by additional P amendment. [ABSTRACT FROM AUTHOR]

Evaluation of restoration activities is indispensable to assess the extent to which targets have been reached. Usually, the main goal of ecological restoration is to restore biodiversity and ecosystem functioning, but validation is often based on a single indicator, which may or may not cope with whole‐ecosystem dynamics. Network analyses are, however, powerful tools, allowing to examine both the recovery of various biotic and abiotic properties and the integrated response at community and ecosystem level.We used restoration sites where topsoil was removed from former intensively managed grassland and seeds were added. These sites were between 3 and 32 years old. We assessed how plants, soil biota, soil properties and correlation‐based interactions between biotic communities and their abiotic environment developed over time and compared the results with (i) intensively managed (not restored), and (ii) well‐preserved targeted semi‐natural grasslands.Plant, nematode, fungal and prokaryotic diversity and community structures of the restored grasslands revealed clear successional patterns and followed similar trajectories towards targeted semi‐natural grasslands. All biotic communities reached targeted diversity levels no later than 18 years post‐restoration.Ecological networks of intensively managed and short‐term (~4 years) restored grasslands were less tightly connected compared to those found in mid‐ and long‐term (~18–30 years) restored and target grasslands. Restoration specifically enhanced interactions among biotic communities, but reduced interactions between biotic communities and their abiotic environment as well as interactions among abiotic properties in the short‐ and mid‐term.Synthesis and applications: Overall, our study demonstrated that topsoil removal and seed addition were successful in restoring diverse, tightly coupled and well‐connected biotic communities above‐ and below‐ground similar to those found in the semi‐natural grasslands that were restoration targets. Network analyses proved to be powerful in examining the long‐term re‐establishment of functionally connected biotic communities in restored ecosystems. Thus, we provide an approach to holistically assess restoration activities by notably considering the complexity of ecosystems, much in contrast to most traditional approaches. [ABSTRACT FROM AUTHOR]

To evaluate how increased anthropogenic nutrient inputs alter carbon cycling in grasslands, we conducted a litter decomposition study across 20 temperate grasslands on three continents within the Nutrient Network, a globally distributed nutrient enrichment experimentWe determined the effects of addition of experimental nitrogen (N), phosphorus (P) and potassium plus micronutrient (Kμ) on decomposition of a common tree leaf litter in a long‐term study (maximum of 7 years; exact deployment period varied across sites). The use of higher order decomposition models allowed us to distinguish between the effects of nutrients on early‐ versus late‐stage decomposition.Across continents, the addition of N (but not other nutrients) accelerated early‐stage decomposition and slowed late‐stage decomposition, increasing the slowly decomposing fraction by 28% and the overall litter mean residence time by 58%.Synthesis. Using a novel, long‐term cross‐site experiment, we found widespread evidence that N enhances the early stages of above‐ground plant litter decomposition across diverse and widespread temperate grassland sites but slows late‐stage decomposition. These findings were corroborated by fitting the data to multiple decomposition models and have implications for N effects on soil organic matter formation. For example, following N enrichment, increased microbial processing of litter substrates early in decomposition could promote the production and transfer of low molecular weight compounds to soils and potentially enhance the stabilization of mineral‐associated organic matter. By contrast, by slowing late‐stage decomposition, N enrichment could promote particulate organic matter (POM) accumulation. Such hypotheses deserve further testing. [ABSTRACT FROM AUTHOR]

Increasing evidence suggests that remotely sensed spectral diversity is linked to plant species richness. However, a conflicting spectral diversity–biodiversity relationship in grasslands has been found in previous studies. In particular, it remains unclear how well the spectral diversity–biodiversity relationship holds in naturally assembled species‐rich grasslands. To address the linkage between spectral diversity and plant species richness in a species‐rich alpine grassland ecosystem, we investigated (i) the trade‐off between spectral and spatial resolution in remote sensing data; (ii) the suitability of three different spectral metrics to describe spectral diversity (coefficient of variation, convex hull volume and spectral species richness) and (iii) the importance of confounding effects of live plant biomass, dead plant biomass and plant life forms on the spectral diversity–biodiversity relationship. We addressed these questions using remote sensing data collected with consumer‐grade cameras with four spectral bands and 10 cm spatial resolution on an unmanned aerial vehicle (UAV), airborne imaging spectrometer data (AVIRIS‐NG) with 372 bands and 2.5 m spatial resolution, and a fused data product of both datasets. Our findings suggest that a fused dataset can cope with the requirement of both high spatial‐ and spectral resolution to remotely measure biodiversity. However, in contrast to several previous studies, we found a negative correlation between plant species richness and spectral metrics based on the spectral information content (i.e. spectral complexity). The spectral diversity calculated based on the spectral complexity was sensitive to live and dead plant biomass. Overall, our results suggest that remote sensing of plant species diversity requires a high spatial resolution, the use of classification‐based spectral metrics, such as spectral species richness, and awareness of confounding factors (e.g. plant biomass), which may be ecosystem specific. [ABSTRACT FROM AUTHOR]

Nutrients and herbivores are well‐known drivers of grassland diversity and stability in local communities. However, whether they interact to impact the stability of aboveground biomass and whether these effects depend on spatial scales remain unknown. It is also unclear whether nutrients and herbivores impact stability via different facets of plant diversity including species richness, evenness, and changes in community composition through time and space. We used a replicated experiment adding nutrients and excluding herbivores for 5 years in 34 global grasslands to explore these questions. We found that both nutrient addition and herbivore exclusion alone reduced stability at the larger spatial scale (aggregated local communities; gamma stability), but through different pathways. Nutrient addition reduced gamma stability primarily by increasing changes in local community composition over time, which was mainly driven by species replacement. Herbivore exclusion reduced gamma stability primarily by decreasing asynchronous dynamics among local communities (spatial asynchrony). Their interaction weakly increased gamma stability by increasing spatial asynchrony. Our findings indicate that disentangling the processes operating at different spatial scales may improve conservation and management aiming at maintaining the ability of ecosystems to reliably provide functions and services for humanity. [ABSTRACT FROM AUTHOR]

Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N2) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N2 is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene— nifH —was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2–4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes. [ABSTRACT FROM AUTHOR]

We present a hierarchy of local coupled cluster (CC) linear response (LR) methods to calculate ionization potentials (IPs), i.e., excited states with one electron annihilated relative to a ground state reference. The time-dependent perturbation operator V(t), as well as the operators related to the first-order (with respect to V(t)) amplitudes and multipliers, thus are not number conserving and have half-integer particle rank m. Apart from calculating IPs of neutral molecules, the method offers also the possibility to study ground and excited states of neutral radicals as ionized states of closed-shell anions. It turns out that for comparable accuracy IPs require a higher-order treatment than excitation energies; an IP-CC LR method corresponding to CC2 LR or the algebraic diagrammatic construction scheme through second order performs rather poorly. We therefore systematically extended the order with respect to the fluctuation potential of the IP-CC2 LR Jacobian up to IP-CCSD LR, keeping the excitation space of the first-order (with respect to V(t)) cluster operator restricted to the m = 1/2 ⊕ 3/2 subspace and the accuracy of the zero-order (ground-state) amplitudes at the level of CC2 or MP2. For the more expensive diagrams beyond the IP-CC2 LR Jacobian, we employ local approximations. The implemented methods are capable of treating large molecular systems with hundred atoms or more. [ABSTRACT FROM AUTHOR]

We introduce orbital specific virtuals (OSVs) to represent the truncated pair-specific virtual space in periodic local Møller-Plesset perturbation theory of second order (LMP2). The OSVs are constructed by diagonalization of the LMP2 amplitude matrices which correspond to diagonal Wannier-function (WF) pairs. Only a subset of these OSVs is adopted for the subsequent OSV-LMP2 calculation, namely, those with largest contribution to the diagonal pair correlation energy and with the accumulated value of these contributions reaching a certain accuracy. The virtual space for a general (non diagonal) pair is spanned by the union of the two OSV sets related to the individual WFs of the pair. In the periodic LMP2 method, the diagonal LMP2 amplitude matrices needed for the construction of the OSVs are calculated in the basis of projected atomic orbitals (PAOs), employing very large PAO domains. It turns out that the OSVs are excellent to describe short range correlation, yet less appropriate for long range van der Waals correlation. In order to compensate for this bias towards short range correlation, we augment the virtual space spanned by the OSVs by the most diffuse PAOs of the corresponding minimal PAO domain. The Fock and overlap matrices in OSV basis are constructed in the reciprocal space. The 4-index electron repulsion integrals are calculated by local density fitting and, for distant pairs, via multipole approximation. New procedures for determining the fit-domains and the distant-pair lists, leading to higher efficiency in the 4-index integral evaluation, have been implemented. Generally, and in contrast to our previous PAO based periodic LMP2 method, the OSV-LMP2 method does not require anymore great care in the specification of the individual domains (to get a balanced description when calculating energy differences) and is in that sense a black box procedure. Discontinuities in potential energy surfaces, which may occur for PAO-based calculations if one is not careful, virtually disappear for OSV-LMP2. Moreover, due to much increased compactness of the pair-specific virtual spaces, the OSV-LMP2 calculations are faster and require much less memory than PAO-LMP2 calculations, despite the noticeable overhead of the initial OSV construction procedure. [ABSTRACT FROM AUTHOR]

We describe theory and implementation of oscillator strengths, orbital-relaxed first-order properties, and nuclear gradients for the local algebraic diagrammatic construction scheme through second order. The formalism is derived via time-dependent linear response theory based on a second-order unitary coupled cluster model. The implementation presented here is a modification of our previously developed algorithms for Laplace transform based local time-dependent coupled cluster linear response (CC2LR); the local approximations thus are state specific and adaptive. The symmetry of the Jacobian leads to considerable simplifications relative to the local CC2LR method; as a result, a gradient evaluation is about four times less expensive. Test calculations show that in geometry optimizations, usually very similar geometries are obtained as with the local CC2LR method (provided that a second-order method is applicable). As an exemplary application, we performed geometry optimizations on the low-lying singlet states of chlorophyllide a. [ABSTRACT FROM AUTHOR]

It is generally assumed that restoring biodiversity will enhance diversity and ecosystem functioning. However, to date, it has rarely been evaluated whether and how restoration efforts manage to rebuild biodiversity and multiple ecosystem functions (ecosystem multifunctionality) simultaneously. Here, we quantified how three restoration methods of increasing intervention intensity (harvest only < topsoil removal < topsoil removal + propagule addition) affected grassland ecosystem multifunctionality 22 yr after the restoration event. We compared restored with intensively managed and targeted seminatural grasslands based on 13 biotic and abiotic, above‐ and belowground properties. We found that all three restoration methods improved ecosystem multifunctionality compared to intensively managed grasslands and developed toward the targeted seminatural grasslands. However, whereas higher levels of intervention intensity reached ecosystem multifunctionality of targeted seminatural grasslands after 22 yr, lower intervention missed this target. Moreover, we found that topsoil removal with and without seed addition accelerated the recovery of biotic and aboveground properties, and we found no negative long‐term effects on abiotic or belowground properties despite removing the top layer of the soil. We also evaluated which ecosystem properties were the best indicators for restoration success in terms of accuracy and cost efficiency. Overall, we demonstrated that low‐cost measures explained relatively more variation of ecosystem multifunctionality compared to high‐cost measures. Plant species richness was the most accurate individual property in describing ecosystem multifunctionality, as it accounted for 54% of ecosystem multifunctionality at only 4% of the costs of our comprehensive multifunctionality approach. Plant species richness is the property that typically is used in restoration monitoring by conservation agencies. Vegetation structure, soil carbon storage and water‐holding capacity together explained 70% of ecosystem multifunctionality at only twice the costs (8%) of plant species richness, which is, in our opinion, worth considering in future restoration monitoring projects. Hence, our findings provide a guideline for land managers how they could obtain an accurate estimate of aboveground‐belowground ecosystem multifunctionality and restoration success in a highly cost‐efficient way. [ABSTRACT FROM AUTHOR]

Human‐caused loss of vertebrate and invertebrate animals, defaunation, is increasing, and potentially affects plant community structure of diverse grassland ecosystems world‐wide.We experimentally simulated defaunation using size‐selective fences to progressively exclude large‐, medium‐ and small‐sized mammals, and invertebrates from two subalpine vegetation types in the Swiss National Park (SNP): intensively grazed short‐grass and moderately grazed tall‐grass vegetation. We assessed plant community properties yearly from 2009 to 2013, and examined treatment effects on plant community structure in the two grassland types.In the short‐grass vegetation, the exclusion of large mammals increased total plant biomass, while the exclusion of large and medium‐sized mammals increased total, grass and forb biomass compared to when all animals had access. These increases became stronger when invertebrates were also excluded. The exclusion of all mammals and invertebrates increased biomass of grasses by 205%, forbs by 100% and total plant biomass by 118% compared to when all animals had access, hence enhancing relative biomass of grasses from 43.6% to 60%, changing plant species composition and lowering richness of forbs by 16%, the number of plant families by 13% and family‐level Shannon diversity by 23%. In contrast to these significant community‐level responses found in the short‐grass vegetation, there was no evidence that the size‐selective exclusion of animals altered the plant community structure of the tall‐grass vegetation. The contrasting results were due to the difference in plant community composition prior to our experiment, which were related to differences in quantity and quality of forage and in grazing intensities of herbivores between the two grassland types.Synthesis. Our results showed that different‐sized animals, in particular large mammals and invertebrates, contributed to maintain the plant community structure in the short‐grass vegetation, highlighting the importance of multiple, functionally different animal groups for ecosystem functioning and stability. In contrast to the short‐grass vegetation, we could not detect such a top‐down control by animals in the tall‐grass vegetation. Our results suggest that potential defaunation effects on grassland plant community structure depend on the degree of grazing pressure release and grassland vegetation type. [ABSTRACT FROM AUTHOR]

In order to arrive at linear scaling of the computational cost with molecular size, local coupled cluster methods discriminate pairs of local molecular orbitals according to the spatial separation R of the latter. Only strong pairs are treated at the full coupled cluster level, whereas for weak pairs a lower level of theory (usually Møller-Plesset perturbation theory of second order,MP2) is used. Yet anMP2 treatment of weak pairs is inadequate in certain situations (for example, for describing p-stacking), which calls for an improved but still inexpensive method for dealing with the weak pairs. In a previous contribution, we proposed as a substituent for MP2 the LrCCD3 method, which is based on ring coupled cluster doubles (ring-CCD) and includes all third-order diagrams with energy contributions decaying not quicker than R-6. In the present work, we explore a still more accurate method, which is based on the same principles. It turned out to be essential to abandon the restriction to ring-CCD, i.e., to include further CCD diagrams beyond the ring approximation. The occurring intermediates turn out to be formally very similar to LMP2 density matrices, such that an efficient evaluation of these non-ring CCD diagrams is possible. Furthermore, a computationally cheap a posteriori estimate for the fourth-order singles contribution to the weak pair energy, which also exhibits a decay behavior of R-6, is introduced. The resulting method, denoted as LCCD[S]-R-6, indeed provides a substantial improvement in accuracy over the previous LrCCD3 method at a relatively modest additional computational cost. [ABSTRACT FROM AUTHOR]

A multistate local CC2 response method for the calculation of analytic energy gradients with respect to nuclear displacements is presented for ground and electronically excited states. The gradient enables the search for equilibrium geometries of extended molecular systems. Laplace transform is used to partition the eigenvalue problem in order to obtain an effective singles eigenvalue problem and adaptive, state-specific local approximations. This leads to an approximation in the energy Lagrangian, which however is shown (by comparison with the corresponding gradient method without Laplace transform) to be of no concern for geometry optimizations. The accuracy of the local approximation is tested and the efficiency of the new code is demonstrated by application calculations devoted to a photocatalytic decarboxylation process of present interest. [ABSTRACT FROM AUTHOR]

Soil nitrogen (N) availability is critical for grassland functioning. However, human activities have increased the supply of biologically limiting nutrients, and changed the density and identity of mammalian herbivores. These anthropogenic changes may alter net soil N mineralization (soil net Nmin), that is, the net balance between N mineralization and immobilization, which could severely impact grassland structure and functioning. Yet, to date, little is known about how fertilization and herbivore removal individually, or jointly, affect soil net Nmin across a wide range of grasslands that vary in soil and climatic properties. Here we collected data from 22 grasslands on five continents, all part of a globally replicated experiment, to assess how fertilization and herbivore removal affected potential (laboratory‐based) and realized (field‐based) soil net Nmin. Herbivore removal in the absence of fertilization did not alter potential and realized soil net Nmin. However, fertilization alone and in combination with herbivore removal consistently increased potential soil net Nmin. Realized soil net Nmin, in contrast, significantly decreased in fertilized plots where herbivores were removed. Treatment effects on potential and realized soil net Nmin were contingent on site‐specific soil and climatic properties. Fertilization effects on potential soil net Nmin were larger at sites with higher mean annual precipitation (MAP) and temperature of the wettest quarter (T.q.wet). Reciprocally, realized soil net Nmin declined most strongly with fertilization and herbivore removal at sites with lower MAP and higher T.q.wet. In summary, our findings show that anthropogenic nutrient enrichment, herbivore exclusion and alterations in future climatic conditions can negatively impact soil net Nmin across global grasslands under realistic field conditions. This is an important context‐dependent knowledge for grassland management worldwide. [ABSTRACT FROM AUTHOR]

A multistate local CC2 response method for the calculation of orbital-relaxed first order properties is presented for ground and electronically excited states. It enables the treatment of excited state properties including orbital relaxation for extended molecular systems and is a major step on the way towards analytic gradients with respect to nuclear displacements. The Laplace transform method is employed to partition the eigenvalue problem and the lambda equations, i.e., the doubles parts of these equations are inverted on-the-fly, leaving only the corresponding effective singles equations to be solved iteratively. Furthermore, the state specific local approximations are adaptive. Density-fitting is utilized to decompose the electron-repulsion integrals. The accuracy of the local approximation is tested and the efficiency of the new code is demonstrated on the example of an organic sensitizer for solar-cell applications, which consists of about 100 atoms. [ABSTRACT FROM AUTHOR]

A local method based on orbital specific virtuals (OSVs) for calculating the perturbative triples correction in local coupled cluster calculations is presented. In contrast to the previous approach based on projected atomic orbitals (PAOs), described by Schütz [J. Chem. Phys. 113, 9986 (2000)], the new scheme works without any ad hoc truncations of the virtual space to domains. A single threshold defines the pair and triple specific virtual spaces completely and automatically. It is demonstrated that the computational cost of the method scales linearly with molecular size. Employing the recommended threshold a similar fraction of the correlation energy is recovered as with the original PAO method at a somewhat lower cost. A benchmark for 52 reactions demonstrates that for reaction energies the intrinsic accuracy of the coupled cluster with singles and doubles excitations and a perturbative treatment of triples excitations method can be reached by OSV-local coupled cluster theory with singles and doubles and perturbative triples, provided a MP2 correction is applied that accounts for basis set incompleteness errors as well as for remaining domain errors. As an application example the interaction energies of the guanine-cytosine dimers in the Watson-Crick and stacked arrangements are investigated at the level of local coupled cluster theory with singles and doubles and perturbative triples. Based on these calculations we propose new complete-basis-set-limit estimates for these interaction energies at this level of theory. [ABSTRACT FROM AUTHOR]

We present a density fitted local configuration interaction singles (CIS) method for calculating optical bandgaps in 3D-periodic systems. We employ an Ewald technique to carry out infinite lattice summations for the exciton-exciton interaction, and robust product-density specific local density fitting in direct space for the electron-hole interaction. Moreover, we propose an alternative to the usual cyclic model with Born-von Karman periodic boundary conditions, the so called Wigner-Seitz supercell truncated infinite model, which exhibits much improved convergence of the CIS excitation energy with respect to the size of the supercell. Test calculations on a series of prototypical systems demonstrate that the method at the present stage can be used to calculate the excitonic bandgaps of 3D periodic systems with up to a dozen atoms in the unit cell, ranging from wide-gap insulators to semiconductors. [ABSTRACT FROM AUTHOR]

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Seminatural grasslands are important biodiversity hotspots, but they are increasingly degraded by intensive agriculture. Grassland restoration is considered to be promising in halting the ongoing loss of biodiversity, but this evaluation is mostly based on plant communities. Insect herbivores contribute substantially to grassland biodiversity and to the provisioning of a variety of ecosystem functions. However, it is unclear how they respond to different measures that are commonly used to restore seminatural grasslands from intensively used agricultural land. We studied the long‐term success of different restoration techniques, which were originally targeted at reestablishing seminatural grassland plant communities, for herbivorous insect communities on taxonomic as well as functional level. Therefore, we sampled insect communities 22 yr after the establishment of restoration measures. These measures ranged from harvest and removal of biomass to removal of the topsoil layer and subsequent seeding of plant propagules. We found that insect communities in restored grasslands had higher taxonomic and functional diversity compared to intensively managed agricultural grasslands and were more similar in composition to target grasslands. Restoration measures including topsoil removal proved to be more effective, in particular in restoring species characterized by functional traits susceptible to intensive agriculture (e.g., large‐bodied species). Our study shows that long‐term success in the restoration of herbivorous insect communities of seminatural grasslands can be achieved by different restoration measures and that more invasive approaches that involve the removal of the topsoil layer are more effective. We attribute these restoration successes to accompanying changes in the plant community, resulting in bottom‐up control of the herbivore community. Our results are of critical importance for management decisions aiming to restore multi‐trophic communities, their functional composition and consequently the proliferation of ecosystem functions. [ABSTRACT FROM AUTHOR]

An efficient method for the calculation of nuclear magnetic resonance (NMR) shielding tensors is presented, which treats electron correlation at the level of second-order Mo\ller-Plesset perturbation theory. It uses spatially localized functions to span occupied and virtual molecular orbital spaces, respectively, which are expanded in a basis of gauge including atomic orbitals (GIAOs or London atomic orbitals). Doubly excited determinants are restricted to local subsets of the virtual space and pair energies with an interorbital distance beyond a certain threshold are omitted. Furthermore, density fitting is employed to factorize the electron repulsion integrals. Ordinary Gaussians are employed as fitting functions. It is shown that the errors in the resulting NMR shielding constant, introduced (i) by the local approximation and (ii) by density fitting, are very small or even negligible. The capabilities of the new program are demonstrated by calculations on some extended molecular systems, such as the cyclobutane pyrimidine dimer photolesion with adjacent nucleobases in the native intrahelical DNA double strand (ATTA sequence). Systems of that size were not accessible to correlated ab initio calculations of NMR spectra before. The presented method thus opens the door to new and interesting applications in this area. [ABSTRACT FROM AUTHOR]

We extend the orbital-specific-virtual tensor factorization, introduced for local Mo\ller-Plesset perturbation theory in Ref. [J. Yang, Y. Kurashige, F. R. Manby and G. K. L. Chan, J. Chem. Phys. 134, 044123 (2011)], to local coupled cluster singles and doubles theory (OSV-LCCSD). The method is implemented by modifying an efficient projected-atomic-orbital local coupled cluster program (PAO-LCCSD) described recently, [H.-J. Werner and M. Schütz, J. Chem. Phys. 135, 144116 (2011)]. By comparison of both methods we find that the compact representation of the amplitudes in the OSV approach affords various advantages, including smaller computational time requirements (for comparable accuracy), as well as a more systematic control of the error through a single energy threshold. Overall, the OSV-LCCSD approach together with an MP2 correction yields small domain errors in practical calculations. The applicability of the OSV-LCCSD is demonstrated for molecules with up to 73 atoms and realistic basis sets (up to 2334 basis functions). [ABSTRACT FROM AUTHOR]

The atomic orbital basis set limit is approached in periodic correlated calculations for solid LiH. The valence correlation energy is evaluated at the level of the local periodic second order Mo\ller-Plesset perturbation theory (MP2), using basis sets of progressively increasing size, and also employing 'bond'-centered basis functions in addition to the standard atom-centered ones. Extended basis sets, which contain linear dependencies, are processed only at the MP2 stage via a dual basis set scheme. The local approximation (domain) error has been consistently eliminated by expanding the orbital excitation domains. As a final result, it is demonstrated that the complete basis set limit can be reached for both HF and local MP2 periodic calculations, and a general scheme is outlined for the definition of high-quality atomic-orbital basis sets for solids. [ABSTRACT FROM AUTHOR]

We present a density fitted local configuration interaction singles (CIS) method for calculating optical band gaps in 1D-periodic systems. The method is based on the Davidson diagonalization procedure, carried out in the reciprocal space. The one-electron part of the matrix-vector products is also evaluated in the reciprocal space, where the diagonality of the Fock matrix can be exploited. The contraction of the CIS vectors with the two electron integrals is performed in the direct space in the basis of localized occupied (Wannier) and virtual (projected atomic) orbitals. The direct space approach allows to utilize the sparsity of the integrals due to the local representation and locality of the exciton. The density fitting approximation employed for the two electron integrals reduces the nominal scaling with unit cell size to O(N4). Test calculations on a series of prototypical systems demonstrate that the method in its present stage can be used to calculate the excitonic band gaps of polymers with up to a few dozens of atoms in the cell. The computational cost depends on the locality of the exciton, but even relatively delocalized excitons occurring in the polybiphenyl in the parallel orientation, can be routinely treated with this method. [ABSTRACT FROM AUTHOR]

A new multistate local CC2 response method for calculating excitation energies and first-order properties of excited triplet states in extended molecular systems is presented. The Laplace transform technique is employed to partition the left/right local CC2 eigenvalue problems as well as the linear equations determining the Lagrange multipliers needed for the properties. The doubles part in the equations can then be inverted on-the-fly and only effective equations for the singles part must be solved iteratively. The local approximation presented here is adaptive and state-specific. The density-fitting method is utilized to approximate the electron-repulsion integrals. The accuracy of the new method is tested by comparison to canonical reference values for a set of 12 test molecules and 62 excited triplet states. As an illustrative application example, the lowest four triplet states of 3-(5-(5-(4-(bis(4-(hexyloxy)phenyl)amino)phenyl)thiophene-2-yl)thiophene-2-yl)-2-cyanoacrylic acid, an organic sensitizer for solar-cell applications, are computed in the present work. No triplet charge-transfer states are detected among these states. This situation contrasts with the singlet states of this molecule, where the lowest singlet state has been recently found to correspond to an excited state with a pronounced charge-transfer character having a large transition strength. [ABSTRACT FROM AUTHOR]

The lowest electronically excited states of the aniline dimer and trimer related to the lowest π*←π transition of the monomer are investigated by applying time-dependent coupled cluster theory, primarily at the level of the (spin-component-scaled) CC2 model. Minimum energy structures in the vicinity of the Franck-Condon points were determined on the individual potential energy surfaces. For the dimer we find an excimer and a head-to-tail configuration (with the monomers substantially displaced relative to the ground state minimum) for the lowest (dark) and second lowest (bright) states, respectively. The excitation is delocalized on both chromophores for both of these states. For the trimer three distinct minima with quite different hydrogen-bonding arrangements are found for the three lowest states. In strong contrast to the dimer the excitation here is clearly localized on the individual aniline chromophores for each of these three states. One of the three geometries is rather similar to the ground state minimum, while the two others are rather different and thus have presumably quite small Franck-Condon factors. It can be expected that only the electronic origin of the first conformer can eventually be detected in the absorption spectrum of the trimer, provided that it is separated by high-enough barriers from other, energetically lower configurations. [ABSTRACT FROM AUTHOR]

The aniline dimer and trimer are investigated in their electronic ground state. The potential energy surface was thoroughly searched for low lying minima by applying global optimizations on a model potential, which is recalibrated on-the-fly by ab initio calculations (spin-component-scaled LMP2) at relevant configurations. The most stable structure of the dimer corresponds to a head-to-tail arrangement with both aniline monomers being nearly equivalent. DFT-SAPT calculations reveal that the interaction energy is dominated by van der Waals dispersion, which is of comparable size as for the benzene dimer, but with a much larger total interaction energy than for the latter. The global minimum of the aniline trimer corresponds to a hydrogen bonding arrangement involving three directional NH–N hydrogen bonds, with the individual monomers being clearly distinguishable. Nonadditive three-body dispersion contributions appear to play a minor role for the trimer. [ABSTRACT FROM AUTHOR]

We have calculated the equilibrium geometry, formation energy, and bulk modulus of two molecular bulk crystals, NH3 and CO2, at the periodic post-Hartree–Fock correlated level. The dependence of the results on the basis set has been analyzed, by employing basis sets up to aug-cc-pVQZ quality. In the calculations, we used the periodic local Mo\ller–Plesset second order perturbation theory (LMP2), implemented in the CRYSCOR program. Multipolar expansion techniques, as well as density fitting, are employed in this code to reduce the number of and to factorize the required electron repulsion integrals; as a consequence of that, the computational cost for the correlation part of the calculations is comparable to that of the Hartree–Fock. Auxiliary calculations performed on molecular dimers are also reported to verify the accuracy of the LMP2 approach and of the basis sets used. Furthermore, the effect of spin-component scaling has been investigated for the two crystals. One intention of the present paper is also to lay out and specify the computational setup, which is generally applicable for accurate CRYSCOR calculations on molecular crystals. [ABSTRACT FROM AUTHOR]

A new Laplace transform based multistate local CC2 response method for calculating excitation energies of extended molecular systems is presented. By virtue of the Laplace transform trick, the eigenvalue problem involving the local CC2 Jacobian is partitioned along the doubles-doubles block (which is diagonal in the parental canonical method) without losing the sparsity in the integral, amplitude, and amplitude response supermatrices. Hence, only an effective eigenvalue problem involving singles vectors has to be solved, while the doubles part can be computed on-the-fly. Within this framework, a multistate treatment of excited states with state specific and adaptive local approximations imposed on the doubles part is straightforwardly possible. Furthermore, in the context of the density fitting approximation of the two-electron integrals, a procedure to specify the local approximation, i.e., the restricted pair lists and domains, on the basis of an analysis of the object to be approximated itself is proposed. Performance and accuracy of the new Laplace transformed density fitted local CC2 (LT-DF-LCC2) response method are tested for set of different test molecules and states. It turns out that LT-DF-LCC2 response is much more robust than the earlier local CC2 response method proposed before, which failed to find some excited states in difficult cases. [ABSTRACT FROM AUTHOR]

The potential energy surfaces of the S0 and S1(π*←π) states of the 2-naphthol(H2O)n, n∈{1,2} clusters were explored at the level of coupled cluster (CC2) response theory. In the electronic ground state two different types of hydrogen-bonding networks coexist for n=2, (i) a cyclic one [similar to those of the water trimer and phenol(H2O)2] where the hydroxy group of the aryl alcohol acts simultaneously as H donor for the first, and as H acceptor for the second water molecule, and (ii) a hydrogen-bonding arrangement where the aromatic π system is taking over the role as H acceptor. In the S1 state, on the other hand, the cyclic conformers are unstable. Consequently, the first group of cyclic ground state conformers gives rise to broad unstructured band shapes in the absorption spectrum, whereas the second group of conformers involving the aromatic π system gives rise to nicely structured band shapes. Based on these results the puzzling absorption spectrum of the n=2 cluster can properly be interpreted. [ABSTRACT FROM AUTHOR]

A hybrid scheme for the computation of reaction energies in large molecular systems is proposed. The approach is based on localized orbitals and allows for the treatment of different parts of a molecule at different computational levels. The localized orbitals are assigned to regions, and then different local correlation methods, such as local MP2 or local CCSD(T), can be applied to different regions. In contrast to previous hybrid schemes, the molecule does not have to be split into parts and, therefore, it is not necessary to saturate dangling bonds using link atoms. For fixed region sizes, the cost of the high-level calculation becomes independent of the molecular size, and it is demonstrated that O(1) scaling can be achieved. Illustrative applications are presented and the convergence of the results with respect to the size of the regions is investigated for reaction energies, barrier heights, and weakly bound complexes. [ABSTRACT FROM AUTHOR]

The S1(π*←π) state surfaces of the phenol-water1<=n<=3 clusters are reexplored at the level of coupled cluster response theory. The global minima for n=2 and n=3 so obtained are qualitatively different from those reported so far, which were obtained with methods such as configuration interaction singles or complete active space self-consistent field lacking dynamical electron correlation effects. Furthermore, the minimum-energy points on the conical intersection seams were located in this work. The results of these calculations offer a qualitative explanation for the anomalous photophysical behavior (broad congested absorption band structure, low quantum yield, short lifetime) of n=2 and the observed predissociation of n=3 at excess energies beyond ≈100 cm-1, resolving a disagreement between theory and experiment which persisted for almost a decade [ABSTRACT FROM AUTHOR]

A new ab initio method for calculating transition strengths and orbital-unrelaxed first-order properties of singlet ground and excited states of extended molecular systems is presented. It is based on coupled cluster response theory at the level of the CC2 model with local approximations introduced to the doubles-excitation part of the wave function. Density fitting is employed for the calculation of the electron repulsion integrals, so that—with the exception of doubles amplitudes—only three-indexed objects do occur in the formalism. The new method was tested by performing calculations for a set of various molecules and excited states and by comparing the results with corresponding canonical (nonlocal) calculations. It turned out that for calculating transition strengths and properties of excited states the ordinary Boughton-Pulay domains are insufficient in numerous cases. To circumvent this problem a new scheme for extending domains is proposed, which is based on the solution of the coupled perturbed localization and Hartree-Fock equations. When such extended domains are used, a satisfactory agreement between canonical and local results is achieved. [ABSTRACT FROM AUTHOR]

A new local method for the computation of electronic excitation energies of singlet states in extended molecular systems is presented. It is based on the CC2 model and local approximations to the wave functions. In the proposed method the singles excitations are treated nonlocally and local restrictions are imposed on doubles amplitudes only. The accuracy of the new method was tested by calculating several lowest excited states for 14 molecules and comparing them with canonical CC2 values. Deviations of the local excitation energies from the canonical reference values do not exceed 0.05 eV for all test molecules and all states in the lower energy range investigated in this work. The method uses the density-fitting approximation for all two-electron integrals, which considerably simplifies the computational complexity of the individual diagrams. A combination of the local approximations and the powerful density-fitting technique leads to a low-scaling method, capable to treat molecular systems comprised of 100 atoms and more in a basis of a polarized double zeta quality. A test calculation for a system consisting of 127 atoms and 370 active electrons without symmetry is presented to show the efficiency of the new method. [ABSTRACT FROM AUTHOR]

An efficient method to compute analytical energy derivatives for local second-order Møller–Plesset perturbation energy is presented. Density fitting approximations are employed for all 4-index integrals and their derivatives. Using local fitting approximations, quadratic scaling with molecular size and cubic scaling with basis set size for a given molecule is achieved. The density fitting approximations have a negligible effect on the accuracy of optimized equilibrium structures or computed energy differences. The method can be applied to much larger molecules and basis sets than any previous second-order Møller–Plesset gradient program. The efficiency and accuracy of the method is demonstrated for a number of organic molecules as well as for molecular clusters. Examples of geometry optimizations for molecules with 100 atoms and over 2000 basis functions without symmetry are presented. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Plant traits are commonly used to predict ecosystem-level processes, but the validity of such predictions is dependent on the assumption that trait variability between species is greater than trait variability within a species—the robustness assumption. Here, we compare leaf trait intraspecific and interspecific variability depending on geographical differences between sites and 5 years of experimental herbivore exclusion in two vegetation types of subalpine grasslands in Switzerland. Four leaf traits were measured from eight herbaceous species common to all 18 sites. Intraspecific trait variability differed significantly depending on site and herbivory. However, the amount and structure of variability depended on the trait measured and whether considering leaf traits separately or multiple leaf traits simultaneously. Leaf phosphorus concentration showed the highest intraspecific variability, while specific leaf area showed the highest interspecific variability and displayed intraspecific variability only in response to herbivore exclusion. Species identity based on multiple traits was not predictable. We find intraspecific variability is an essential consideration when using plant functional traits as a common currency not just species mean traits. This is particularly true for leaf nutrient concentrations, which showed high intraspecific variability in response to site differences and herbivore exclusion, a finding which suggests that the robustness assumption does not always hold. [ABSTRACT FROM AUTHOR]

Successful restoration of semi‐natural grasslands on grasslands previously subject to intensive management needs to overcome manifold barriers. These include high soil fertility, the dominance of a few fast‐growing plant species, degraded soil faunal communities and missing propagules of the targeted above‐ and below‐ground flora and fauna. A combination of removing the topsoil and introducing propagules of target plants has become one of the major tools for nature conservation agencies and practitioners to reduce soil fertility and restore former species‐rich grasslands in various European countries.Using topsoil removal as a restoration measure has provoked an ongoing debate between supporting nature conservation and rejecting soil protection agencies. Although it favours species‐rich plant communities, it strongly disturbs soil communities and affects physical and chemical soil properties and processes. Currently, there is a lack of long‐term data to assess how restored grassland ecosystems develop and recover after topsoil removal. Here, we used two well‐established bioindicators, soil nematodes and plants, to quantify restoration success of topsoil removal in comparison with alternative restoration measures and target communities 22 years after intervention.The nematode community composition indicated reduced nutrient availability in the restored systems, as was aimed at by topsoil removal. Nevertheless, after this 22‐year period following topsoil removal, nematode composition and structure revealed successful recovery.Plant communities benefitted from the reduction of soil nutrients after topsoil removal as indicated by higher numbers of plant species and higher Shannon diversity. Furthermore, topsoil removal strongly promoted the re‐establishment of plant species of the target plant community.Synthesis and applications. Overall, our study demonstrates how a massive intervention by topsoil removal proved successful in converting intensively managed into species‐rich grasslands. This contrasts with the mild intervention of repeated mowing and removing of the harvested plant material. We show that, in the long run, potential negative effects of topsoil removal on the soil fauna can be successfully overcome and plant communities can develop into targeted species‐rich grassland. Overall, our study demonstrates how a massive intervention by topsoil removal proved successful in converting intensively managed into species‐rich grasslands. This contrasts with the mild intervention of repeated mowing and removing of the harvested plant material. We show that, in the long run, potential negative effects of topsoil removal on the soil fauna can be successfully overcome and plant communities can develop into targeted species‐rich grassland. [ABSTRACT FROM AUTHOR]

The ground- and first excited state of s-tetrazine arising from a π*←n excitation (1Ag,1B3u) have been studied using the complete active space (CASSCF) and the second order multiconfiguration perturbation theory (CASPT2) ab initio methods. The focus of this study is on the effect of the electronic excitation on the molecular structure and on those electronic properties which are important to model the solvatochromatic behavior of the molecule in polymer matrices as used in permanent hole burning experiments. Since the accurate computation of excited state molecular properties represents a major challenge for today’s numerical quantum chemistry, some technical aspects are also considered. The present study shows that the change in geometry upon electronic excitation is small. This is in partial contradiction with the experimental studies which however disagree among themselves [see K. K. Innes, I. G. Ross, and W. R. Moomaw, J. Mol. Spectrosc. 132, 492 (1988), and R. E. Smalley, L. Wharton, and D. H. Levi, ibid. 66, 375 (1977)]. This study also confirms that the first excited state equilibrium structure is of D2h symmetry. In an earlier theoretical study it was found that the D2h symmetry structure may represent a saddle point rather than a minimum on the excited state potential surface [see A. C. Scheiner and H. F. Schaefer III, J. Chem. Phys. 87, 3539 (1987)]. In the first excited state, we observe an increase of the mean polarizability of s-tetrazine along with an enhanced anisotropy. The change in the polarizability is almost exclusively in the ‘‘in-plane’’ components of the tensor; the polarizability in the vertical direction is nearly unchanged. This observation questions recent experimental results reported for this molecule [see S. Heitz, D. Weidnauer, and A. Hese, J. Chem. Phys. 95, 7952 (1991)]. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We report a combined spectroscopic and theoretical investigation of the intermolecular vibrations of supersonic jet-cooled phenol·(H2O)3 and d1-phenol·(D2O)3 in the S0 and S1 electronic states. Two-color resonant two-photon ionization combined with time-of-flight mass spectrometry and dispersed fluorescence emission spectroscopy provided mass-selective vibronic spectra of both isotopomers in both electronic states. In the S0 state, eleven low-frequency intermolecular modes were observed for phenol·(H2O)3, and seven for the D isotopomer. For the S1 state, several intermolecular vibrational excitations were observed in addition to those previously reported. Ab initio calculations of the cyclic homodromic isomer of phenol·(H2O)3 were performed at the Hartree–Fock level. Calculations for the eight possible conformers differing in the position of the ‘‘free’’ O–H bonds with respect to the almost planar H-bonded ring predict that the ‘‘up–down–up–down’’ conformer is differentially most stable. The calculated structure, rotational constants, normal-mode eigenvectors, and harmonic frequencies are reported. Combination of theory and experiment allowed an analysis and interpretation of the experimental S0 state vibrational frequencies and isotope shifts. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The global and local minima, stationary points, and torsional rearrangement processes of cyclic homodromic (H2O)4 were studied on its four-dimensional torsional intermolecular potential energy surface. Eight different energetically low-lying torsional stationary point structures were found by ab initio theory, and fully structure-optimized at the second-order Mo\ller–Plesset level, using large basis sets. Second-order energies close to the one-particle basis set limit were obtained at these geometries using the explicitly correlated Mo\ller–Plesset method. The effects of higher-order correlation energy terms were investigated by coupled cluster theory, and terms beyond second order were found to cancel in good approximation. The S4 symmetric global minimum has a square and almost planar O...O...O...O arrangement with free O–H bonds alternating ‘‘up’’ and ‘‘down’’ relative to this plane, with two isometric versions of this structure. Another torsional conformer with two neighboring up O–H bonds followed by two neighboring down O–H bonds is a local minimum, 0.93 kcal/mol above the global minimum. The four versions of this structure are connected to the global minima via two distinct but almost degenerate first-order torsional saddle points, which occur as two sets of eight isometric versions each, both about 1.24 kcal/mol above the global minimum. Yet another set of eight second-order saddle points lies at 1.38 kcal/mol. The structure with three O–H bonds up and one down is not a stationary point, while the structure with all four O–H bonds on the same side of the plane is a first-order saddle point.The fully planar C4h symmetric structure is a fourth-order stationary point 2.8 kcal/mol above the minimum. The torsional interconversion paths between this multitude of points are complex, and are discussed in three-dimensional spaces of symmetry-adapted... [ABSTRACT FROM AUTHOR]

A torsional potential energy surface for the cyclic water trimer was calculated at the level of second-order Mo\ller–Plesset perturbation theory. For the construction of this ab initio surface, the first-order wave function was expanded in a many-electron basis which linearly depends on the interelectronic coordinates r12. The one-electron basis of Gaussian orbitals was calibrated on the water monomer and dimer to ensure that the ab initio surface computed represents the (near- ) basis set limit for the level of theory applied. The positions of the free O—H bonds are described by three torsional angles. The respective three-dimensional torsional space was investigated by 70 counterpoise corrected single-point calculations for various values of these angles, providing a grid to fit an analytical representation of the potential energy surface. The four symmetry unique stationary points previously found at the Hartree–Fock and conventional Mo\ller–Plesset levels [Schütz et al., J. Chem. Phys. 99, 5228 (1993)] were studied in detail: Relative energies of the structures were calculated by applying second-order Mo\ller–Plesset and coupled cluster methods; harmonic vibrational frequencies were calculated at the second-order Mo\ller–Plesset level with a 6-311++G(d,p) basis set at these stationary points. It is expected that the present torsional potential energy surface for the water trimer will play an important role in the understanding of the vibrational transitions observed by far-infrared vibration–rotation–tunneling spectroscopy in terms of a nearly free pseudorotational interconversion on a cyclic vibrational–tunneling path. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The minimum energy structure of the cyclic water trimer, its stationary points, and rearrangement processes at energies <1 kcal/mol above the global minimum are examined by ab initio molecular orbital theory. Structures corresponding to stationary points are fully optimized at the Hartree–Fock and second-order Mo\ller–Plesset levels, using the 6-311++G(d,p) basis; each stationary point is characterized by harmonic vibrational analyses. The lowest energy conformation has two free O–H bonds on one and the third O–H bond on the other side of an approximately equilateral hydrogen-bonded O...O...O (O3) triangle. The lowest energy rearrangement pathway corresponds to the flipping of one of the two free O–H bonds which are on the same side of the plane across this plane via a transition structure with this O–H bond almost within the O3 plane. Six distinguishable, but isometric transition structures of this type connect six isometric minimum energy structures along a cyclic vibrational-tunneling path; neighboring minima correspond to enantiomers. The potential energy along this path has C6 symmetry and a very low barrier V6=0.1±0.1 kcal/mol. This implies nearly free pseudorotational interconversion of the six equilibrium structures. The corresponding anharmonic level structure was modeled using an internal rotation Hamiltonian. Two further low-energy saddle points on the surface are of second and third order; they correspond to crown-type and planar geometries with C3 and C3h symmetries, respectively. Interconversion tunneling vibrations via these stationary points are also important for the water trimer dynamics. A unified and symmetry-adapted description of the intermolecular potential energy surface is given in terms of the three flipping coordinates of the O–H bonds. Implications of these results for the interpretation of spectroscopic data are discussed. [ABSTRACT FROM AUTHOR]