Double Hybrid Functionals and the Π-System Bond Length Alternation Challenge: Rivaling Accuracy of Post-HF Methods

Predicting accurate bond length alternations (BLAs) in long conjugated oligomers has been a significant challenge for electronic-structure methods for many decades, made particularly important by the close relationships between BLA and the rich optoelectronic properties of π-delocalized systems. Here, we test the accuracy of recently developed, and increasingly popular, double hybrid (DH) functionals, positioned at the top of Jacobs Ladder of DFT methods of increasing sophistication, computational cost, and accuracy, due to incorporation of MP2 correlation energy. Our test systems comprise oligomeric series of polyacetylene, polymethineimine, and polysilaacetylene up to six units long. MP2 calculations reveal a pronounced shift in BLAs between the 6-31G(d) basis set used in many studies of BLA to date and the larger cc-pVTZ basis set, but only modest shifts between cc-pVTZ and aug-cc-pVQZ results. We hence perform new reference CCSD(T)/cc-pVTZ calculations for all three series of oligomers against which we assess the performance of several families of DH functionals based on BLYP, PBE, and TPSS, along with lower-rung relatives including global- and range-separated hybrids. Our results show that DH functionals systematically improve the accuracy of BLAs relative to single hybrid functionals. xDH-PBE0 (N4 scaling using SOS-MP2) emerges as a DH functional rivaling the BLA accuracy of SCS-MP2 (N5 scaling), which was found to offer the best compromise between computational cost and accuracy the last time the BLA accuracy of DFT- and wave function-based methods was systematically investigated. Interestingly, xDH-PBE0 (XYG3), which differs to other DHs in that its MP2 term uses PBE0 (B3LYP) orbitals that are not self-consistent with the DH functional, is an outlier of trends of decreasing average BLA errors with increasing fractions of MP2 correlation and HF exchange.

Uso da técnica de análise de componentes principais na redefinição do parâmetro BLA

Dissertação (mestrado)—Universidade de Brasília, Instituto de Física, Programa de Pós-Graduação em Física, 2016.

Dimerization of polyacetylene treated as a spin-Peierls distortion of the Heisenberg Hamiltonian

Extracting a bond-length-dependent Heisenberg-like Hamiltonian from the potential-energy surfaces of the two lowest states of ethylene, it is possible to study the geometry of polyacetylene by minimization of the cohesive energy, using both variational-cluster and Rayleigh-Schrödinger perturbative expansions. The dimerization amplitude is satisfactorily reproduced. Optimizing the variational-cluster-expansion total energy with the equal-bond-length constraint, the barrier to reversal of alternation is obtained. The alternating-to-regular phase transition is treated from the Néel-state starting function and appears to be of second order.

Spin current in the Mobius cyclacene belts

We report on density functional theory studies of the electronic structure and magnetic properties of Mobius-[n]cyclacenes. The geometry of Mobius bands presents a modulation of bond lengths that is needed to accommodate the twist. This modulation takes the form of bond alternation defects analogous to those of solitons in polyacetylene. The ground state of all Mobius bands is a triplet, with a spin density distribution that follows the bond length modulation. A molecular dynamics simulation of the Mobius cyclacene at 300 K shows that the twist travels around the belt inducing a magnetic current. (C) 2009 Elsevier B. V. All rights reserved.

Calibration of the length of a chain of single gold atoms

Using a scanning tunnelling microscope or mechanically controllable break junction it has been shown that it is possible to control the formation of a wire made of single gold atoms. In these experiments an interatomic distance between atoms in the chain of ∼3.6 Å was reported which is not consistent with recent theoretical calculations. Here, using precise calibration procedures for both techniques, we measure the length of the atomic chains. Based on the distance between the peaks observed in the chain length histogram we find the mean value of the interatomic distance before chain rupture to be 2.5±0.2 Å. This value agrees with the theoretical calculations for the bond length. The discrepancy with the previous experimental measurements was due to the presence of He gas, that was used to promote the thermal contact, and which affects the value of the work function that is commonly used to calibrate distances in scanning tunnelling microscopy and mechanically controllable break junctions at low temperatures.

Immunological synapse: a mathematical model of the bond formation process:mathematical modelling of the immature synapse

The cell:cell bond between an immune cell and an antigen presenting cell is a necessary event in the activation of the adaptive immune response. At the juncture between the cells, cell surface molecules on the opposing cells form non-covalent bonds and a distinct patterning is observed that is termed the immunological synapse. An important binding molecule in the synapse is the T-cell receptor (TCR), that is responsible for antigen recognition through its binding with a major-histocompatibility complex with bound peptide (pMHC). This bond leads to intracellular signalling events that culminate in the activation of the T-cell, and ultimately leads to the expression of the immune eector function. The temporal analysis of the TCR bonds during the formation of the immunological synapse presents a problem to biologists, due to the spatio-temporal scales (nanometers and picoseconds) that compare with experimental uncertainty limits. In this study, a linear stochastic model, derived from a nonlinear model of the synapse, is used to analyse the temporal dynamics of the bond attachments for the TCR. Mathematical analysis and numerical methods are employed to analyse the qualitative dynamics of the nonequilibrium membrane dynamics, with the specic aim of calculating the average persistence time for the TCR:pMHC bond. A single-threshold method, that has been previously used to successfully calculate the TCR:pMHC contact path sizes in the synapse, is applied to produce results for the average contact times of the TCR:pMHC bonds. This method is extended through the development of a two-threshold method, that produces results suggesting the average time persistence for the TCR:pMHC bond is in the order of 2-4 seconds, values that agree with experimental evidence for TCR signalling. The study reveals two distinct scaling regimes in the time persistent survival probability density prole of these bonds, one dominated by thermal uctuations and the other associated with the TCR signalling. Analysis of the thermal fluctuation regime reveals a minimal contribution to the average time persistence calculation, that has an important biological implication when comparing the probabilistic models to experimental evidence. In cases where only a few statistics can be gathered from experimental conditions, the results are unlikely to match the probabilistic predictions. The results also identify a rescaling relationship between the thermal noise and the bond length, suggesting a recalibration of the experimental conditions, to adhere to this scaling relationship, will enable biologists to identify the start of the signalling regime for previously unobserved receptor:ligand bonds. Also, the regime associated with TCR signalling exhibits a universal decay rate for the persistence probability, that is independent of the bond length.

Reactivity, photolability, and computational studies of the ruthenium nitrosyl complex with a substituted cyclam fac-[Ru(NO)Cl(2)(kappa(3)N(4),N(8),N(11)(1-carboxypropyl)cyclam)]Cl center dot H(2)O

Chemical reactivity, photolability, and computational studies of the ruthenium nitrosyl complex with a substituted cyclam, fac-[Ru(NO)Cl(2)(kappa(3)N(4),N(8),N(11)(1-carboxypropyl)cyclam)]Cl center dot H(2)O ((1-carboxypropyl) cyclam = 3-(1,4,8,11-tetraazacyclotetradecan-1-yl) propionic acid)), (I) are described. Chloride ligands do not undergo aquation reactions (at 25 degrees C, pH 3). The rate of nitric oxide (NO) dissociation (k(obs-NO)) upon reduction of I is 2.8 s(-1) at 25 +/- 1 degrees C (in 0.5 mol L(-1) HCl), which is close to the highest value found for related complexes. The uncoordinated carboxyl of I has a pK(a) of similar to 3.3, which is close to that of the carboxyl of the non coordinated (1-carboxypropyl) cyclam (pK(a) = 3.4). Two additional pK(a) values were found for I at similar to 8.0 and similar to 11.5. Upon electrochemical reduction or under irradiation with light (lambda(irr) = 350 or 520 nm; pH 7.4), I releases NO in aqueous solution. The cyclam ring N bound to the carboxypropyl group is not coordinated, resulting in a fac configuration that affects the properties and chemical reactivities of I, especially as NO donor, compared with analogous trans complexes. Among the computational models tested, the B3LYP/ECP28MDF, cc-pVDZ resulted in smaller errors for the geometry of I. The computational data helped clarify the experimental acid-base equilibria and indicated the most favourable site for the second deprotonation, which follows that of the carboxyl group. Furthermore, it showed that by changing the pH it is possible to modulate the electron density of I with deprotonation. The calculated NO bond length and the Ru/NO charge ratio indicated that the predominant canonical structure is [Ru(III)NO], but the Ru-NO bond angles and bond index (b.i.) values were less clear; the angles suggested that [Ru(II)NO(+)] could contribute to the electronic structure of I and b.i. values indicated a contribution from [Ru(IV)NO(-)]. Considering that some experimental data are consistent with a [Ru(II)NO(+)] description, while others are in agreement with [Ru(III)NO], the best description for I would be a linear combination of the three canonical forms, with a higher weight for [Ru(II)NO(+)] and [Ru(III)NO].

XAS characterization of the RuO(2)-Ta(2)O(5) system local (crystal) structure

The influence of the preparation method on the structural properties of the RuO(2)-Ta(2)O(5) system was investigated. Both thin films on Ti substrates and powder samples of nominal composition Ti/RuO(2)-Ta(2)O(5) (Ru:Ta = 100:0, 90:10, 80:20, 30:70, and 0:100 at.%) were prepared through thermal decomposition of polymeric precursors (DPP). The thin films and powder samples were investigated using X-ray absorption spectroscopy (XAS). XANES analyses showed that Ru and Ta are present in the Ru(IV) and Ta(V) oxidation states. EXAFS signals of all the samples were analyzed, to obtain the average bond length (r), coordination number, and the Debye-Waller factor (sigma(2)) for each Ru-O, Ru-Ru, Ta-O nearest-neighbor. The first shell Ru-O distance was found at 1.91-1.92 angstrom with coordination number of 1.8-2.1, and at 2.01-2.02 angstrom with coordination number of 3.9-4.1. The Ta-O distance obtained for all the samples and in both modes (transmission and fluorescence) had significantly different values from the theoretical ones. The results revealed that the local structure around both the Ru and Ta sites are similar, and that they consist of distorted M-O(6) octahedra (where M = Ru or Ta). (C) 2010 Elsevier B.V. All rights reserved.

Cyanocobalt(III) complexes of penta- and tetradentate-coordinated macrocyclic hexaamines

The pendent-arm macrocyclic hexaamine trans-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane-6,13-diamine (L) may coordinate in tetra-, penta- or hexadentate modes, depending on the metal ion and the synthetic procedure. We report here the crystal structures of two pseudo-octahedral cobalt(III) complexes of L, namely sodium trans-cyano(trans-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane-6,13-diamine)cobalt(III) triperchlorate, Na[Co(CN)(C13H30N6)](ClO4)(3) or Na{trans-[CoL(CN)]}(ClO4)(3), (I), where L is coordinated as a pentadentate ligand, and trans-dicyano(trans-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane-6,13-diamine) cobalt (III) trans-dicyano (trans-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane-6,13-diaminium)cobalt(III) tetraperchlorate tetrahydrate, [Co(CN)(2)(Cl4H32N6)][Co(CN)(2)(Cl4H30N6)](ClO4)(4)•-4H(2)O or trans-[CoL(CN)(2)]trans-[Co(H2L)(CN)(2)] (ClO4)(4)•-4H(2)O, (II), where the ligand binds in a tetradentate mode, with the remaining coordination sites being filled by C-bound cyano ligands. In (I), the secondary amine Co-N bond lengths lie within the range 1.944 (3)-1.969 (3) &ANGS;, while the trans influence of the cyano ligand lengthens the Co-N bond length of the coordinated primary amine [Co-N = 1.986 (3) &ANGS;]. The Co-CN bond length is 1.899 (3) &ANGS;. The complex cations in (11) are each located on centres of symmetry. The Co-N bond lengths in both cations are somewhat longer than in (I) and span a narrow range [1.972 (3)-1.982 (3) &ANGS;]. The two independent Co-CN bond lengths are similar [1.918 (4) and 1.926 (4) &ANGS;] but significantly longer than in the structure of (1), again a consequence of the trans influence of each cyano ligand.

Strength improvement of adhesively-bonded scarf repairs in aluminium structures with external reinforcements

Adhesively bonded techniques are an attractive option to repair aluminium structures, compared to more traditional methods. Actually, as a result of the improvement in the mechanical characteristics of adhesives, adhesive bonding has progressively replaced the traditional joining methods. There are several bonded repair configurations, as single-strap, double-strap and scarf. Compared with strap repairs, scarf repairs have the advantages of a higher efficiency and the absence of aerodynamic disturbance. The higher efficiency is caused by the elimination of the significant joint eccentricities of strap repairs. Moreover, stress distributions along the bond length are more uniform, due to tapering of the scarf edges. The main disadvantages of this technique are the difficult machining of the surfaces, associated costs and requirement of specialised labour. This work reports on an experimental and numerical study of the tensile behaviour of two-dimensional (2D) scarf repairs of aluminium structures bonded with the ductile epoxy adhesive Araldite® 2015. The numerical analysis, by Finite Elements (FE), was performed in Abaqus® and used cohesive zone models (CZM) for the simulation of damage onset and growth in the adhesive layer, thus enabling the strength prediction of the repairs. A parametric study was performed on the scarf angle (α) and different configurations of external reinforcement (applied on one or two sides of the repair, and also different reinforcement lengths). The obtained results allowed the establishment of design guidelines for repairing, showing that the use of external reinforcements enables increasing α for equal strength recovery, which makes the repair procedure easier. The numerical technique was accurate in predicting the repairs’ strength, enabling its use for design and optimisation purposes.

Development of hybrid composite plate (HCP) for strengthening and repair of RC structures

Tese de Doutoramento em Engenharia Civil

Influência do tipo de adesivo no comportamento de elementos de betão reforçados com laminados de CFRP de acordo com a técnica NSM

Dissertação de mestrado integrado em Engenharia Civil

Systematic study of the static electrical properties of the CO molecule: influence of the basis set size and correlation energy

The influence of the basis set size and the correlation energy in the static electrical properties of the CO molecule is assessed. In particular, we have studied both the nuclear relaxation and the vibrational contributions to the static molecular electrical properties, the vibrational Stark effect (VSE) and the vibrational intensity effect (VIE). From a mathematical point of view, when a static and uniform electric field is applied to a molecule, the energy of this system can be expressed in terms of a double power series with respect to the bond length and to the field strength. From the power series expansion of the potential energy, field-dependent expressions for the equilibrium geometry, for the potential energy and for the force constant are obtained. The nuclear relaxation and vibrational contributions to the molecular electrical properties are analyzed in terms of the derivatives of the electronic molecular properties. In general, the results presented show that accurate inclusion of the correlation energy and large basis sets are needed to calculate the molecular electrical properties and their derivatives with respect to either nuclear displacements or/and field strength. With respect to experimental data, the calculated power series coefficients are overestimated by the SCF, CISD, and QCISD methods. On the contrary, perturbation methods (MP2 and MP4) tend to underestimate them. In average and using the 6-311 + G(3df) basis set and for the CO molecule, the nuclear relaxation and the vibrational contributions to the molecular electrical properties amount to 11.7%, 3.3%, and 69.7% of the purely electronic μ, α, and β values, respectively

Platinum (II) and palladium (II) complexes with (N,N') and (C,N,N') ligands derived from pyrazole as anticancer and antimalarial agents: synthesis, characterization and in vitro activities

The study of the reactivity of three 1-(2-dimethylaminoethyl)-1H-pyrazole derivatives of general formula [1-(CH2)2NMe2}-3,5-R2-pzol] {where pzol represents pyrazole and Rdouble bond; length as m-dashH (1a), Me (1b) or Ph (1c)} with [MCl2(DMSO)2] (Mdouble bond; length as m-dashPt or Pd) under different experimental conditions allowed us to isolate and characterize cis-[M{κ2-N,N′-{[1-(CH2)2NMe2}-3,5-R2-pzol])}Cl2] {MMdouble bond; length as m-dashPtPt (2a-2c) or Pd (3a-3c)} and two cyclometallated complexes [M{κ3-C,N,N′-{[1-(CH2)2NMe2}-3-(C5H4)-5-Ph-pzol])}Cl] {Mdouble bond; length as m-dashPt(II) (4c) or Pd(II) (5c)}. Compounds 4c and 5c arise from the orthometallation of the 3-phenyl ring of ligand 1c. Complex 2a has been further characterized by X-ray crystallography. Ligands and complexes were evaluated for their in vitro antimalarial against Plasmodium falciparum and cytotoxic activities against lung (A549) and breast (MDA MB231 and MCF7) cancer cellular lines. Complexes 2a-2c and 5c exhibited only moderate antimalarial activities against two P. falciparum strains (3D7 and W2). Interestingly, cytotoxicity assays revealed that the platinacycle 4c exhibits a higher toxicity than cisplatin in the three human cell lines and that the complex 2a presents a remarkable cytotoxicity and selectivity in lung (IC50 = 3 μM) versus breast cancer cell lines (IC50 > 20 μM). Thus, complexes 2c and 4c appear to be promising leads, creating a novel family of anticancer agents. Electrophoretic DNA migration studies in presence of the synthesized compounds have been performed, in order to get further insights into their mechanism of action.

O ESTADO DA ARTE DA LIGAÇÃO DE HIDROGÊNIO

Along the historical background of science, the hydrogen bond became widely known as the universal interaction, thus playing a key role in many molecular processes. Through the available theoretical approaches, many of these processes can be unveiled on the basis of the molecular parameters of the subject intermolecular system, such as the variation of bond length and mainly the frequency shift observed in the proton donor. Supported by the natural bond analysis (NBO) with the quantification of the hybridization contributions, the structural deformations and vibrational effects cited above are also attributed to the outcome of the intermolecular interaction strength, which consequently can be estimated by means of the quantum theory of atoms in molecules (QTAIM) as well as evaluated by the symmetry-adapted perturbation theory (SAPT). Moreover, to identify the preferential interaction sites for proton donors and acceptors, the molecular electrostatic potential (MEP) is useful in this regard.