Search

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]

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]

A combined experimental and theoretical study of the 2-naphthol·H2O/D2O system was performed. Two different rotamers of 2-naphthol (2-hydroxynaphthalene, 2HN) exist with the O–H bond in cis- and trans-position relative to the naphthalene frame. Using Hartree–Fock (HF) calculations with the 6-31G(d,p) basis set, fully energy-minimized geometries were computed for both cis- and trans-2HN·H2O of (a) the equilibrium structures with trans-linear H-bond arrangement and Cs symmetry and (b) the lowest-energy transition states for H atom exchange on the H2O subunit, which have a nonplanar C1 symmetry. Both equilibrium and transition state structures are similar to the corresponding phenol·H2O geometries. The H-bond stabilization energies with zero point energy corrections included are ≊5.7 kcal/mol for both rotamers, ≊2.3 kcal/mol stronger than for the water dimer, and correspond closely to the binding energy calculated for phenol·H2O at the same level of theory. Extension of the aromatic π-system therefore hardly affects the H-bonding conditions. The barrier height to internal rotation around the H-bond only amounts to 0.5 kcal/mol. Harmonic vibrational analysis was carried out at these stationary points on the HF/6-31G(d,p) potential energy surface with focus on the six intermolecular modes. The potential energy distributions and M-matrices reflect considerable mode scrambling for the deuterated isotopomers. For the a’ intermolecular modes anharmonic corrections to the harmonic frequencies were evaluated. The β2 wag mode shows the largest anharmonic contributions. For the torsional mode τ (H2O H-atom exchange coordinate) the vibrational level structure in an appropriate periodic potential was calculated. On the experimental side resonant-two-photon ionization and dispersed fluorescence emission spectra of 2HN·H2O and d-2HN·D2O were measured. A detailed assignment of the bands in... [ABSTRACT FROM AUTHOR]

Extensive ab initio calculations of the phenol·H2O complex were performed at the Hartree–Fock level, using the 6-31G(d,p) and 6-311++G(d,p) basis sets. Fully energy-minimized geometries were obtained for (a) the equilibrium structure, which has a translinear H bond and the H2O plane orthogonal to the phenol plane, similar to (H2O)2; (b) the lowest-energy transition state structure, which is nonplanar (C1 symmetry) and has the H2O moiety rotated by ±90°. The calculated MP2/6-311G++(d,p) binding energy including basis set superposition error corrections is 6.08 kcal/mol; the barrier for internal rotation around the H bond is only 0.4 kcal/mol. Intra- and intermolecular harmonic vibrational frequencies were calculated for a number of different isotopomers of phenol·H2O. Anharmonic intermolecular vibrational frequencies were computed for several intermolecular vibrations; anharmonic corrections are very large for the β2 intermolecular wag. Furthermore, the H2O torsion τ around the H-bond axis, and the β2 mode are strongly anharmonically coupled, and a two-dimensional τ/β2 potential energy surface was explored. The role of tunneling splitting due to the torsional mode is discussed and tunnel splittings are estimated for the calculated range of barriers. The theoretical studies were complemented by a detailed spectroscopic study of h-phenol·H2O and d-phenol·D2O employing two-color resonance-two-photon ionization and dispersed fluorescence emission techniques, which extends earlier spectroscopic studies of this system. The β1 and β2 wags of both isotopomers in the S0 and S1 electronic states are newly assigned, as well as several other weaker transitions. Tunneling splittings due to the torsional mode may be important in the S0 state in conjunction with the excitation of the intermolecular σ and β2 modes. [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]

Abstract: Plant stoichiometry, the relative concentration of elements, is a key regulator of ecosystem functioning and is also being altered by human activities. In this paper we sought to understand the global drivers of plant stoichiometry and compare the relative contribution of climatic vs. anthropogenic effects. We addressed this goal by measuring plant elemental (C, N, P and K) responses to eutrophication and vertebrate herbivore exclusion at eighteen sites on six continents. Across sites, climate and atmospheric N deposition emerged as strong predictors of plot‐level tissue nutrients, mediated by biomass and plant chemistry. Within sites, fertilization increased total plant nutrient pools, but results were contingent on soil fertility and the proportion of grass biomass relative to other functional types. Total plant nutrient pools diverged strongly in response to herbivore exclusion when fertilized; responses were largest in ungrazed plots at low rainfall, whereas herbivore grazing dampened the plant community nutrient responses to fertilization. Our study highlights (1) the importance of climate in determining plant nutrient concentrations mediated through effects on plant biomass, (2) that eutrophication affects grassland nutrient pools via both soil and atmospheric pathways and (3) that interactions among soils, herbivores and eutrophication drive plant nutrient responses at small scales, especially at water‐limited sites. [ABSTRACT FROM AUTHOR]

Many studies report that mountain plant species are shifting upward in elevation. However, the majority of these reports focus on shifts of upper limits. Here, we expand the focus and simultaneously analyze changes of both range limits, optima, and abundances of 183 mountain plant species. We therefore resurveyed 1,576 vegetation plots first recorded before 1970 in the European Alps. We found that both range limits and optima shifted upward in elevation, but the most pronounced trend was a mean increase in species abundance. Despite huge species-specific variation, range dynamics showed a consistent trend along the elevational gradient: Both range limits and optima shifted upslope faster the lower they were situated historically, and specie's abundance increased more for species from lower elevations. Traits affecting the specie's dispersal and persistence capacity were not related to their range dynamics. Using indicator values to stratify species by their thermal and nutrient demands revealed that elevational ranges of thermophilic species tended to expand, while those of cold-adapted species tended to contract. Abundance increases were strongest for nutriphilous species. These results suggest that recent climate warming interacted with airborne nitrogen deposition in driving the observed dynamics. So far, the majority of species appear as "winners" of recent changes, yet "losers" are overrepresented among high-elevation, coldadapted species with low nutrient demands. In the decades to come, high-alpine species may hence face the double pressure of climatic changes and novel, superior competitors that move up faster than they themselves can escape to even higher elevations [ABSTRACT FROM AUTHOR]

Abstract: Theory predicts that mammalian herbivores affect the quantity and quality of plants on which they preferentially feed in the short term. In the longer term, they can promote either preferred or less preferred plants, depending on whether preferred plants are adapted or sensitive to grazing. Less clear are the short‐ and long‐term responses of herbivorous insects to mammalian herbivory, and how these responses depend on the specific plants or plant functional types on which the insects feed. We progressively excluded large, medium and small mammals for five growing seasons in two subalpine vegetation types with long‐term differences in mammalian grazing intensity. Short‐grass vegetation has a history of intensive grazing, while tall‐grass vegetation has been grazed less intensively. We tested whether mammals altered the abundance and body size of leafhoppers specialized on specific plant functional types (grasses, sedges, forbs, or legumes/forbs), distinguishing between short‐term (exclosures) and long‐term (vegetation types) differences in mammalian grazing pressure. Furthermore, we assessed whether leafhoppers’ responses were explained by changes in biomass or quality of the plant functional types on which they feed. In the short term, mammal exclosures increased the abundance of grass‐ and forb‐feeding leafhoppers via increases in the biomass of grasses and forbs, regardless of vegetation type. Both grasses and forbs are preferred food plants of mammals. In the long term, the biomass of sedges, which are less preferred by mammals, increased in the less intensively grazed tall‐grass vegetation. This resulted in a higher abundance of sedge‐feeding leafhoppers. The small size of these sedge feeders lowered the average leafhopper body size in the tall‐grass vegetation. Plant nutritional quality did not explain any effects of exclusions or vegetation types. Our results demonstrate that both short‐ and long‐term effects of mammalian herbivores on the biomass of specific plant functional types caused concurrent changes in the abundance of specialized herbivorous insects, which scaled up to community‐wide shifts in insect body size, a key life‐history trait. A plant‐functional‐type approach can thus help to predict how overabundance or extinction of mammalian herbivores impacts on other components of the food web at various timescales. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]

Even though mammalian herbivores can exert strong indirect effects on other animals by altering the vegetation, the study of trophic cascades retains a focus on apex predators and their top-down forces. Bottom-up trophic interaction chains induced by mammalian herbivores, particularly in invertebrate food webs, remain largely unexplored., We tested whether effects of mammalian herbivores on the vegetation ricochet back up several trophic levels of the invertebrate food web. We further tested two alternative hypotheses: the strength of herbivore-induced indirect interactions either increases with plant productivity because of a concurrent higher grazing intensity, or it decreases because of a higher plant tolerance to grazing., We progressively excluded large, medium and small herbivorous mammals from replicated plots of 6 m2 in productive, intensively grazed short-grass vegetation and less productive, less intensively grazed tall-grass vegetation of subalpine grasslands. We measured vegetation quantity, quality, structure and composition, and determined the abundance of invertebrate herbivores, detritivores, omnivores and predators. We used structural equation modelling to test vegetation-mediated cascading effects of the different mammalian herbivores across different trophic groups of invertebrates., In the short-grass vegetation, mammals caused changes in vegetation quantity and thickness. These changes directly affected detritivorous and predatory invertebrate abundance, yet indirectly affected predatory and omnivorous invertebrates through a bottom-up trophic cascade via changes in herbivorous invertebrate abundance. In the tall-grass vegetation, mammal-induced changes in vegetation quality and composition affected detritivorous invertebrates and in turn omnivorous invertebrates, but these cascading effects were weaker than those in the short-grass vegetation. Smaller mammals were at least as important as large mammals in structuring the invertebrate food web., Our results demonstrate that differently sized mammalian herbivores can trigger trophic cascades in the local invertebrate food web. Our findings further support the hypothesis that herbivore-induced indirect interactions are stronger in more productive systems because of higher foraging intensity, as opposed to the hypothesis that a higher grazing tolerance of plants should dampen herbivore-induced indirect interactions in productive systems. [ABSTRACT FROM AUTHOR]