Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections

In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the basis set superposition error and the inclusion of the deformation energies (for the S12L set) have been crucial for obtaining precise DLPNO-CCSD(T)/CBS interaction energies. Among the density functionals evaluated, the double-hybrid revPBE0-DH-NL and B2PLYP-NL with the three-body dispersion correction provide remarkably accurate association energies very close to the chemical accuracy. Overall, the NL van der Waals approach combined with proper density functionals can be seen as an accurate and affordable computational tool for the modeling of large weakly bonded supramolecular systems.Financial support by the “Ministerio de Economía y Competitividad” (MINECO) of Spain and European FEDER funds through projects CTQ2011-27253 and CTQ2012-31914 is acknowledged. The support of the Generalitat Valenciana (Prometeo/2012/053) is also acknowledged. J.A. thanks the EU for the FP7-PEOPLE-2012-IEF-329513 grant. J.C. acknowledges the “Ministerio de Educación, Cultura y Deporte” (MECD) of Spain for a predoctoral FPU grant

ENDOR Spectroscopy and DFT Calculations: Evidence for the Hydrogen-Bond Network Within α2 in the PCET of E. coli Ribonucleotide Reductase

Escherichia coli class I ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to deoxynucleotides and is composed of two subunits: α2 and β2. β2 contains a stable di-iron tyrosyl radical (Y[subscript 122]•) cofactor required to generate a thiyl radical (C[subscript 439]•) in α2 over a distance of 35 Å, which in turn initiates the chemistry of the reduction process. The radical transfer process is proposed to occur by proton-coupled electron transfer (PCET) via a specific pathway: Y[subscript 122] ⇆ W[subscript 48][?] ⇆ Y[subscript 356] in β2, across the subunit interface to Y[subscript 731] ⇆ Y[subscript 730] ⇆ C[subscript 439] in α2. Within α2 a colinear PCET model has been proposed. To obtain evidence for this model, 3-amino tyrosine (NH2Y) replaced Y[subscript 730] in α2, and this mutant was incubated with β2, cytidine 5′-diphosphate, and adenosine 5′-triphosphate to generate a NH2Y730• in D2O. [[superscript 2]H]-Electron–nuclear double resonance (ENDOR) spectra at 94 GHz of this intermediate were obtained, and together with DFT models of α2 and quantum chemical calculations allowed assignment of the prominent ENDOR features to two hydrogen bonds likely associated with C[subscript 439] and Y[subscript 731]. A third proton was assigned to a water molecule in close proximity (2.2 Å O–H···O distance) to residue 730. The calculations also suggest that the unusual g-values measured for NH[subscript 2]Y[subscript 730]• are consistent with the combined effect of the hydrogen bonds to Cys[subscript 439] and Tyr[subscript 731], both nearly perpendicular to the ring plane of NH[subscript 2]Y[subscript 730]. The results provide the first experimental evidence for the hydrogen-bond network between the pathway residues in α2 of the active RNR complex, for which no structural data are available.National Institutes of Health (U.S.) (NIH GM29595

Track D Social Science, Human Rights and Political Science

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138414/1/jia218442.pd

Plan de emerxencias. Fundación Pública Urxencias Sanitarias de Galicia-061

A Fundación Pública Urxencias Sanitarias de Galicia-061 é a encargada de proporcionar, desde o momento que ocorre a emerxencia, un control da situación, unha primeira avaliación e unha asistencia sanitaria que logre salvar o maior número de vidas e volver á normalidade o antes posible. Para isto, a actuación sanitaria debe seguir unha metodoloxía perfectamente establecida, xa que as actuacións organizadas son as mellores ferramentas de traballo. Así pois, é necesario posibilitar normas de actuación o máis protocolizadas posible, para poder traballar nas mellores condicións de seguridade e manter unhas directrices xerais, onde cada persoa coñeza tanto a súa función como a do resto dos componentes do equipo, procedendo, ademais, á súa identificación funcional mediante signos externos (uniformidade, carteis, identificación, etc.); para facilitar o entendemento e a coordinación de todos os implicados en resolver a situación acaecida. Con este fin, preséntase o Plan de emerxencias que a continuación se expón, nun afán de dar sempre a mellor e máis axeitada resposta; obxectivo primordial desde que a FPUS de Galicia–061 se instaura como responsable da medicina prehospitalaria na nosa comunidade autónoma.La Fundación Pública Urxencias Sanitarias de Galicia-061 es la encargada de proporcionar, desde el momento en que ocurre la emergencia, un control de la situación, una primera evaluación y una asistencia sanitaria que logre salvar el mayor número de vidas y volver a la normalidad lo antes posible. Para esto, la actuación sanitaria debe seguir una metodología perfectamente establecida, ya que las actuaciones organizadas son las mejores herramientas de trabajo. Así pues, es necesario posibilitar normas de actuación lo más protocolizadas posible, para poder trabajar en las mejores condiciones de seguridad y mantener unas directrices generales, donde cada persona conozca tanto su función como la del resto de los componentes del equipo, procediendo, además, a su identificación funcional mediante signos externos (uniformidad, carteles, identificación, etc.); para facilitar el entendimiento y la coordinación de todos los implicados en resolver la situación acaecidad. Con este fin, se presenta el Plan de emergencias que a continuación se expone, en un afán de dar siempre la respuesta mejor y más idónea; objetivo primordial desde que la FPUS de Galicia-061 se instaura como responsable de la medicina prehospitalaria en nuestra comunidad autónoma

An efficient and near linear scaling pair natural orbital based local coupled cluster method

In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009) https://doi.org/10.1063/1.3173827.]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 105–106 relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below 8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized

Mechanism of Olefin Asymmetric Hydrogenation Catalyzed by Iridium Phosphino-Oxazoline: A Pair Natural Orbital Coupled Cluster Study

Since the development of chiral phosphino-oxazoline iridium catalysts, which hydrogenate unfunctionalized alkenes enantioselectively, the asymmetric hydrogenation of prochiral olefins has become important in the production of chiral compounds. For the last 10 years, details of the mechanism, including formal oxidation state assignment of the metal center and the nature of intermediates and transition states have been debated. Various contributions have been given from a theoretical point of view, but due to the size of the structures, these have been forced to rely on density functional theory (DFT) methods. In our investigation of the catalytic cycle, we employ both DFT and a correlated ab initio method, namely, the newly implemented domain-based local pair natural orbital coupled-cluster theory with single and double excitations and the inclusion of perturbative triples correction (DLPNO-CCSD(T)). Our results show that the most likely active paths involve the formation of an intermediate IrV species. Furthermore, we have been able to predict the absolute configuration of the major products, and where comparison to experiment is possible, the results of our calculations agree with the enantiomeric excess obtained from hydrogenating five prochiral substrates. This work also shows that it is now possible to study catalytic reactions with untruncated models (having up to 88 atoms) at the CCSD(T) level of theory

Natural triple excitations in local coupled cluster calculations with pair natural orbitals

In this work, the extension of the previously developed domain based local pair-natural orbital (DLPNO) based singles- and doubles coupled cluster (DLPNO-CCSD) method to perturbatively include connected triple excitations is reported. The development is based on the concept of triples-natural orbitals that span the joint space of the three pair natural orbital (PNO) spaces of the three electron pairs that are involved in the calculation of a given triple-excitation contribution. The truncation error is very smooth and can be significantly reduced through extrapolation to the zero threshold. However, the extrapolation procedure does not improve relative energies. The overall computational effort of the method is asymptotically linear with the system size O(N). Actual linear scaling has been confirmed in test calculations on alkane chains. The accuracy of the DLPNO-CCSD(T) approximation relative to semicanonical CCSD(T0) is comparable to the previously developed DLPNO-CCSD method relative to canonical CCSD. Relative energies are predicted with an average error of approximately 0.5 kcal/mol for a challenging test set of medium sized organic molecules. The triples correction typically adds 30%–50% to the overall computation time. Thus, very large systems can be treated on the basis of the current implementation. In addition to the linear C150H302 (452 atoms, >8800 basis functions) we demonstrate the first CCSD(T) level calculation on an entire protein, Crambin with 644 atoms, and more than 6400 basis functions

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implements sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond