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1.
ACS Nano ; 2020 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-32687321

RESUMO

Functionalization of surfaces with derivatives of Buckminsterfullerene fragment molecules seems to be a promising approach toward bottom-up fabrication of carbon nanotube modified electrode surfaces. The modification of a Cu(100) surface with molecules of the buckybowl pentaindenocorannulene has been studied by means of scanning tunneling microscopy, carbon monoxide-modified noncontact atomic force microscopy, time-of-flight secondary mass spectrometry, and quantum chemical calculations. Two different adsorbate modes are identified, in which the majority is oriented such that the bowl cavity points away from the surface and the convex side is partially immersed into a four-atom vacancy in the Cu(100) surface. A minority is oriented such that the convex side points away from the surface with the five benzo tabs oriented basically parallel to the surface. Thermal annealing leads to hydrogenation and planarization of the molecules in two steps under specific C-C bond cleavage. The benzo tabs of the convex side up species serve as a hydrogen source. The final product has an open-shell electron structure that is quenched on the surface.

2.
J Chem Theory Comput ; 16(5): 3028-3040, 2020 May 12.
Artigo em Inglês | MEDLINE | ID: mdl-32275424

RESUMO

We present a new implementation of density matrix renormalization group based tailored coupled clusters method (TCCSD), which employs the domain-based local pair natural orbital approach (DLPNO). Compared to the previous local pair natural orbital (LPNO) version of the method, the new implementation is more accurate, offers more favorable scaling, and provides more consistent behavior across the variety of systems. On top of the singles and doubles, we include the perturbative triples correction (T), which is able to retrieve even more dynamic correlation. The methods were tested on three systems: tetramethyleneethane, oxo-Mn(Salen), and iron(II)-porphyrin model. The first two were revisited to assess the performance with respect to LPNO-TCCSD. For oxo-Mn(Salen), we retrieved between 99.8 and 99.9% of the total canonical correlation energy which is an improvement of 0.2% over the LPNO version in less than 63% of the total LPNO runtime. Similar results were obtained for iron(II)-porphyrin. When the perturbative triples correction was employed, irrespective of the active space size or system, the obtained energy differences between two spin states were within the chemical accuracy of 1 kcal/mol using the default DLPNO settings.

3.
PLoS One ; 14(12): e0226487, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31856191

RESUMO

Bohemian gentian (Gentianella praecox subsp. bohemica) is an endemic taxon that occurs on the Czech Massif and together with the Sturmian gentian (Gentianella obtusifolia subsp. sturmiana) are the only autumnal species of Gentianella with large flowers in central Europe. Both species have declined dramatically in both population size and numbers of populations. The Bohemian gentian rescue programme, which recommended appropriate management measures, was adopted in 2011. Here we study the ecology of this species, results of the rescue programme and explore the possibilities of using the experience resulting from this programme for improving the viability of the second species. Long-term monitoring of populations of the Bohemian gentian has shown that regular mowing or grazing together with careful litter removal and gap creation are necessary for its survival in the current climatic conditions. We found some ecological differences between these two closely related species of Gentianella. However, our empirical experience of the largest population of the Sturmian gentian at a site where it thrives, and general evidence that gaps are crucial for the successful establishment of Gentianella seedlings, indicate that regular mowing or grazing together with careful litter removal and creation of gaps, should also be recommended as in the case of the Bohemian gentian rescue programme. Artificial gaps are especially crucial for successful seedling regeneration in oligotrophic meadows with dense vegetation, where the last Sturmian gentian populations survive.


Assuntos
Conservação dos Recursos Naturais/métodos , Fenômenos Ecológicos e Ambientais , Gentianella , Filogenia
4.
J Chem Phys ; 151(8): 084112, 2019 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-31470730

RESUMO

We introduce a new implementation of the coupled cluster method with single and double excitations tailored by the matrix product state wave functions (DMRG-TCCSD), which employs the local pair natural orbital (LPNO) approach. By exploiting locality in the coupled cluster stage of the calculation, we were able to remove some of the limitations that hindered the application of the canonical version of the method to larger systems and/or with larger basis sets. We assessed the accuracy of the approximation using two systems: tetramethyleneethane (TME) and oxo-Mn(Salen). Using the default cut-off parameters, we were able to recover over 99.7% and 99.8% of the canonical correlation energy for the triplet and singlet state of TME, respectively. In the case of oxo-Mn(Salen), we found that the amount of retrieved canonical correlation energy depends on the size of the complete active space (CAS)-we retrieved over 99.6% for the larger 27 orbital CAS and over 99.8% for the smaller 22 orbital CAS. The use of LPNO-TCCSD allowed us to perform these calculations up to quadruple-ζ basis set, amounting to 1178 basis functions. Moreover, we examined dependence of the ground state of oxo-Mn(Salen) on the CAS composition. We found that the inclusion of 4dxy orbital plays an important role in stabilizing the singlet state at the DMRG-CASSCF level via double-shell effect. However, by including dynamic correlation, the ground state was found to be triplet regardless of the size of the basis set or the composition of CAS, which is in agreement with previous findings by canonical DMRG-TCCSD in smaller basis.

5.
Phys Chem Chem Phys ; 21(9): 5022-5038, 2019 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-30762044

RESUMO

In this article we report an implementation of the perturbative triples correction to Mukherjee's state-specific multireference coupled cluster method based on the domain-based pair natural orbital approach (DLPNO-MkCC). We tested the performance of DLPNO-MkCCSD(T) in calculations involving tetramethyleneethane and isomers of naphthynes. These tests show that more than 97% of triples energy was recovered with respect to the canonical MkCCSD(T) method, which together with the DLPNO-MkCCSD part accounts for about 99.70-99.85% of the total correlation energy. The applicability of the method was demonstrated on calculations of singlet-triplet gaps for several large systems: triangulene, dynemicin A, and a beryllium complex.

6.
J Chem Theory Comput ; 15(4): 2206-2220, 2019 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-30802406

RESUMO

In this article, we investigate the numerical and theoretical aspects of the coupled-cluster method tailored by matrix-product states. We investigate formal properties of the used method, such as energy size consistency and the equivalence of linked and unlinked formulation. The existing mathematical analysis is here elaborated in a quantum chemical framework. In particular, we highlight the use of what we have defined as a complete active space-external space gap describing the basis splitting between the complete active space and the external part generalizing the concept of a HOMO-LUMO gap. Furthermore, the behavior of the energy error for an optimal basis splitting, i.e., an active space choice minimizing the density matrix renormalization group-tailored coupled-cluster singles doubles error, is discussed. We show numerical investigations on the robustness with respect to the bond dimensions of the single orbital entropy and the mutual information, which are quantities that are used to choose a complete active space. Moreover, the dependence of the ground-state energy error on the complete active space has been analyzed numerically in order to find an optimal split between the complete active space and external space by minimizing the density matrix renormalization group-tailored coupled-cluster error.

7.
Oecologia ; 187(3): 863-872, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29700631

RESUMO

Assessing genetic diversity within populations of rare species and understanding its determinants are crucial for effective species protection. While a lot is known about the relationships between genetic diversity, fitness, and current population size, very few studies explored the effects of past population size. Knowledge of past population size may, however, improve our ability to predict future population fates. We studied Gentianella praecox subsp. bohemica, a biennial species with extensive seed bank. We tested the effect of current, past minimal and maximal population size, and harmonic mean of population sizes within the last 15 years on genetic diversity and fitness. Maximum population size over the last 15 years was the best predictor of expected heterozygosity of the populations and was significantly related to current population size and management. Plant fitness was significantly related to current as well as maximum population size and expected heterozygosity. The results suggested that information on past population size may improve our understanding of contemporary genetic diversity across populations. They demonstrated that despite the strong fluctuations in population size, large reductions in population size do not result in immediate loss of genetic diversity and reduction of fitness within the populations. This is likely due to the seed bank of the species serving as reservoir of the genetic diversity of the populations. From a conservation point of view, this suggests that the restoration of small populations of short-lived species with permanent seed bank is possible as these populations may still be genetically diverse.


Assuntos
Espécies em Perigo de Extinção , Genética Populacional , Animais , Variação Genética , Densidade Demográfica
8.
J Chem Theory Comput ; 14(3): 1370-1382, 2018 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-29345924

RESUMO

This article reports development of a local variant of Mukherjee's state-specific multireference coupled cluster method based on the domain-based pair natural orbital approach (DLPNO-MkCC). The current implementation is restricted to connected single and double excitations and model space with up to biexcited references. The performance of the DLPNO-MkCCSD was tested on calculations of tetramethyleneethane. The results show that above 99.9% of the correlation energy was recovered, with respect to the conventional MkCC method. To demonstrate the applicability of the method to large systems, singlet-triplet gaps of triangulene and bis(1-(2,6-diisopropylphenyl)-3,3,5,5-tetramethylpyrrolidine-2-ylidene)beryllium complex were studied. For the last system (105 atoms), we were able to perform a calculation in cc-pVTZ with 2158 basis functions on a single CPU in less than 9 days.

9.
Nat Chem ; 9(9): 843-849, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28837177

RESUMO

Berkelium (Bk) has been predicted to be the only transplutonium element able to exhibit both +III and +IV oxidation states in solution, but evidence of a stable oxidized Bk chelate has so far remained elusive. Here we describe the stabilization of the heaviest 4+ ion of the periodic table, under mild aqueous conditions, using a siderophore derivative. The resulting Bk(IV) complex exhibits luminescence via sensitization through an intramolecular antenna effect. This neutral Bk(IV) coordination compound is not sequestered by the protein siderocalin-a mammalian metal transporter-in contrast to the negatively charged species obtained with neighbouring trivalent actinides americium, curium and californium (Cf). The corresponding Cf(III)-ligand-protein ternary adduct was characterized by X-ray diffraction analysis. Combined with theoretical predictions, these data add significant insight to the field of transplutonium chemistry, and may lead to innovative Bk separation and purification processes.

10.
Appl Plant Sci ; 5(1)2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-28090411

RESUMO

PREMISE OF THE STUDY: Polymorphic microsatellite loci were developed and used to genotype individuals of Gentianella praecox subsp. bohemica (Gentianaceae), a highly protected taxon in Europe, to study the genetic structure of the remaining populations. METHODS AND RESULTS: Thirty-eight primer pairs were successfully amplified; of these, 12 polymorphic microsatellite loci were developed using a 454 sequencing approach and used to genotype 180 individuals of G. praecox subsp. bohemica from six populations. Allelic richness ranged between one and nine alleles per locus. We detected a high frequency of polyploid individuals (77.8%). The highest average percentage of heterozygous genotypes was identified for samples from the Hroby population (75.5%). All loci can also be amplified in the congeneric species G. praecox subsp. praecox, G. amarella subsp. amarella, and G. obtusifolia subsp. sturmiana. CONCLUSIONS: These markers will provide knowledge on patterns of gene flow and population genetic structure, which is necessary for current protection actions and for effective conservation of this species in the future.

12.
J Chem Phys ; 145(16): 164106, 2016 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-27802607

RESUMO

In this work, we report an extension of our previous development of the universal state-selective (USS) multireference coupled-cluster (MRCC) formalism. It was shown [Brabec et al., J. Chem. Phys. 136, 124102 (2012)] and [Banik et al., J. Chem. Phys. 142, 114106 (2015)] that the USS(2) approach significantly improves the accuracy of Brillouin-Wigner and Mukherjee MRCC formulations, however, the numerical and storage costs associated with calculating highly excited intermediates pose a significant challenge, which can restrict the applicability of the USS(2) method. Therefore, we introduce a perturbative variant of the USS(2) approach (USS(pt)), which substantially reduces numerical overhead of the full USS(2) correction while preserving its accuracy. Since the new USS(pt) implementation calculates the triple and quadruple projections in on-the-fly manner, the memory bottleneck associated with the need of storing expensive recursive intermediates is entirely eliminated. On the example of several benchmark systems, we demonstrate accuracies of USS(pt) and USS(2) approaches and their efficiency in describing quasidegenerate electronic states. It is also shown that the USS(pt) method significantly alleviates problems associated with the lack of invariance of MRCC theories upon the rotation of active orbitals.

13.
J Phys Chem Lett ; 7(20): 4072-4078, 2016 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-27682626

RESUMO

In the past decade, the quantum chemical version of the density matrix renormalization group (DMRG) method has established itself as the method of choice for calculations of strongly correlated molecular systems. Despite its favorable scaling, it is in practice not suitable for computations of dynamic correlation. We present a novel method for accurate "post-DMRG" treatment of dynamic correlation based on the tailored coupled cluster (CC) theory in which the DMRG method is responsible for the proper description of nondynamic correlation, whereas dynamic correlation is incorporated through the framework of the CC theory. We illustrate the potential of this method on prominent multireference systems, in particular, N2 and Cr2 molecules and also oxo-Mn(Salen), for which we have performed the first post-DMRG computations in order to shed light on the energy ordering of the lowest spin states.

14.
J Comput Chem ; 37(12): 1059-67, 2016 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-26804120

RESUMO

We present an algorithm for reducing the computational work involved in coupled-cluster (CC) calculations by sparsifying the amplitude correction within a CC amplitude update procedure. We provide a theoretical justification for this approach, which is based on the convergence theory of inexact Newton iterations. We demonstrate by numerical examples that, in the simplest case of the CCD equations, we can sparsify the amplitude correction by setting, on average, roughly 90% nonzero elements to zeros without a major effect on the convergence of the inexact Newton iterations.

15.
J Phys Chem B ; 119(30): 9706-16, 2015 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-26146848

RESUMO

Several methods based on single- and two-photon fluorescence detected linear dichroism have recently been used to determine the orientational distributions of fluorescent dyes in lipid membranes. However, these determinations relied on simplified descriptions of nonlinear anisotropic properties of the dye molecules, using a transition dipole-moment-like vector instead of an absorptivity tensor. To investigate the validity of the vector approximation, we have now carried out a combination of computer simulations and polarization microscopy experiments on two representative fluorescent dyes (DiI and F2N12S) embedded in aqueous phosphatidylcholine bilayers. Our results indicate that a simplified vector-like treatment of the two-photon transition tensor is applicable for molecular geometries sampled in the membrane at ambient conditions. Furthermore, our results allow evaluation of several distinct polarization microscopy techniques. In combination, our results point to a robust and accurate experimental and computational treatment of orientational distributions of DiI, F2N12S, and related dyes (including Cy3, Cy5, and others), with implications to monitoring physiologically relevant processes in cellular membranes in a novel way.


Assuntos
Membrana Celular/química , Corantes Fluorescentes/química , Dinâmica não Linear , Fenômenos Ópticos , Fosfolipídeos , Conformação Molecular , Simulação de Dinâmica Molecular
16.
J Chem Phys ; 142(11): 114106, 2015 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-25796230

RESUMO

As a further development of the previously introduced a posteriori Universal State-Selective (USS) corrections [K. Kowalski, J. Chem. Phys. 134, 194107 (2011); J. Brabec et al., ibid. 136, 124102 (2012)], we suggest an iterative form of the USS correction by means of correcting effective Hamiltonian matrix elements. We also formulate USS corrections via the left Bloch equations. The convergence of the USS corrections with excitation level towards the full configuration interaction (FCI) limit is also investigated. Various forms of the USS and simplified diagonal USS corrections at the singles and doubles and perturbative triple levels are numerically assessed on several model systems and on the ozone and tetramethyleneethane molecules. It is shown that the iterative USS correction can successfully replace the previously developed a posteriori Brillouin-Wigner coupled cluster size-extensivity correction, while it is not sensitive to intruder states and performs well also in other cases when the a posteriori one fails, like, e.g., for the asymmetric vibration mode of ozone.

17.
J Chem Theory Comput ; 11(11): 5197-208, 2015 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-26894238

RESUMO

We present a special symmetric Lanczos algorithm and a kernel polynomial method (KPM) for approximating the absorption spectrum of molecules within the linear response time-dependent density functional theory (TDDFT) framework in the product form. In contrast to existing algorithms, the new algorithms are based on reformulating the original non-Hermitian eigenvalue problem as a product eigenvalue problem and the observation that the product eigenvalue problem is self-adjoint with respect to an appropriately chosen inner product. This allows a simple symmetric Lanczos algorithm to be used to compute the desired absorption spectrum. The use of a symmetric Lanczos algorithm only requires half of the memory compared with the nonsymmetric variant of the Lanczos algorithm. The symmetric Lanczos algorithm is also numerically more stable than the nonsymmetric version. The KPM algorithm is also presented as a low-memory alternative to the Lanczos approach, but the algorithm may require more matrix-vector multiplications in practice. We discuss the pros and cons of these methods in terms of their accuracy as well as their computational and storage cost. Applications to a set of small and medium-sized molecules are also presented.

18.
J Child Neurol ; 28(12): 1686-8, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23112246

RESUMO

Panayiotopoulos syndrome is an idiopathic epilepsy syndrome presenting with a large variety of autonomic symptoms. The mechanism of autonomic symptoms is still not well understood. A neurologically normal 13-month-old boy presented on 2 occasions with complex partial status epilepticus that included significant ictal priapism. Inpatient brain magnetic resonance imaging (MRI) scan showed restricted diffusion-weighted imaging within his left temporal lobe and electroencephalograms (EEGs) left temporal slowing only. An outpatient EEG 6 months later showed abundant multifocal, predominantly posterior, as well as irregular generalized spike-and-slow-wave discharges on normal background consistent with the diagnosis of Panayiotopoulos syndrome. Ictal priapism is a previously undescribed phenomenon that is consistent with parasympathetic manifestations noted in this young boy. Acute postictal MRI and EEG findings suggest that this undeniably fascinating seizure semiological sign may be localized to the left temporal region.


Assuntos
Doenças do Sistema Nervoso Autônomo/fisiopatologia , Encefalite/fisiopatologia , Epilepsia/fisiopatologia , Priapismo/diagnóstico , Imagem de Difusão por Ressonância Magnética , Eletroencefalografia , Hipocampo/patologia , Humanos , Lactente , Masculino
19.
J Chem Phys ; 137(17): 171101, 2012 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-23145708

RESUMO

The concept of the model space underlying multireference coupled-cluster (MRCC) formulations is a powerful tool to deal with complex correlation effects for various electronic states. Here, we demonstrate that iterative state-specific MRCC methods (SS-MRCC) based on properly defined model spaces can be used to describe core-level excited states even when Hartree-Fock orbitals are utilized. We show that the SS-MRCC models with single and double excitations are comparable in accuracy to high-level single reference equation-of-motion coupled cluster (EOMCC) formalism.

20.
J Chem Phys ; 137(9): 094112, 2012 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-22957560

RESUMO

In this paper we discuss the performance of the non-iterative state-specific multireference coupled cluster (SS-MRCC) methods accounting for the effect of triply excited cluster amplitudes. The corrections to the Brillouin-Wigner and Mukherjee's MRCC models based on the manifold of singly and doubly excited cluster amplitudes (BW-MRCCSD and Mk-MRCCSD, respectively) are tested and compared with exact full configuration interaction results for small systems (H(2)O, N(2), and Be(3)). For the larger systems (naphthyne isomers) the BW-MRCC and Mk-MRCC methods with iterative singles, doubles, and non-iterative triples (BW-MRCCSD(T) and Mk-MRCCSD(T)) are compared against the results obtained with single reference coupled cluster methods. We also report on the parallel performance of the non-iterative implementations based on the use of processor groups.

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