*J Phys Chem A ; 2020 Jul 24.*

##### RESUMO

We present a workflow to aid the discovery of new dyes for the role of a photosensitive unit in the dye-sensitized photo-electrochemical cells (DS-PECs). New structures are generated in a fully automated way using the Compound Attachment Tool (CAT) introduced in this work. These structures are characterized with efficient approximate density functional theory (DFT) methods, and molecules with favorable optical properties are suggested for possible further use in DS-PECs. As around 2500 structures are generated in this work, and as we aim for still larger volumes of compounds to screen in subsequent applications, we have assessed the reliability of low-cost screening methods and show that simplified time-dependent density functional theory (sTDDFT) provides a satisfying accuracy/cost ratio. From the dyes considered, we propose a set that can be suitable for panchromatic sensitization of the photoelectrode in DS-PECs to further increase DS-PEC efficiency.

*J Comput Chem ; 2020 Apr 16.*

##### RESUMO

On a comprehensive database with 1,644 datapoints, covering several aspects of main-group as well as of transition metal chemistry, we assess the performance of 60 density functional approximations (DFA), among them 36 double hybrids (DH). All calculations are performed using a Slater type orbital (STO) basis set of triple-Î¶ (TZ) quality and the highly efficient pair atomic resolution of the identity approach for the exchange- and Coulomb-term of the KS matrix (PARI-K and PARI-J, respectively) and for the evaluation of the MP2 energy correction (PARI-MP2). Employing the quadratic scaling SOS-AO-PARI-MP2 algorithm, DHs based on the spin-opposite-scaled (SOS) MP2 approximation are benchmarked against a database of large molecules. We evaluate the accuracy of STO/PARI calculations for B3LYP as well as for the DH B2GP-PLYP and show that the combined basis set and PARI-error is comparable to the one obtained using the well-known def2-TZVPP Gaussian-type basis set in conjunction with global density fitting. While quadruple-Î¶ (QZ) calculations are currently not feasible for PARI-MP2 due to numerical issues, we show that, on the TZ level, Jacob's ladder for classifying DFAs is reproduced. However, while the best DHs are more accurate than the best hybrids, the improvements are less pronounced than the ones commonly found on the QZ level. For conformers of organic molecules and noncovalent interactions where very high accuracy is required for qualitatively correct results, DHs provide only small improvements over hybrids, while they still excel in thermochemistry, kinetics, transition metal chemistry and the description of strained organic systems.

*J Phys Chem B ; 124(9): 1665-1677, 2020 Mar 05.*

##### RESUMO

Vibrational circular dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work, we study the origin of these VCD signals using the general coupled oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and ß-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the through-space coupling of electric dipoles. The crucial role played by intramolecular hydrogen bonds in determining VCD intensities is also illustrated. Moreover, we find that the contributions to the rotational strengths, considered to be insignificant in standard VCD models, may have sizable magnitudes and can thus not always be neglected. In addition, the VCD robustness of the amide I and II modes has been investigated by monitoring the variation of the rotational strength and its contributing terms during linear transit scans and by performing calculations with different computational parameters. From these studies-and in particular, the decomposition of the rotational strength made possible by the GCO analysis-it becomes clear that one should be cautious when employing measures of robustness as proposed previously.

*J Chem Theory Comput ; 2020 Jan 24.*

##### RESUMO

We report a production level implementation of pair atomic resolution of the identity (PARI) based second-order Møller-Plesset perturbation theory (MP2) in the Slater type orbital (STO) based Amsterdam Density Functional (ADF) code. As demonstrated by systematic benchmarks, dimerization and isomerization energies obtained with our code using STO basis sets of triple-Î¶-quality show mean absolute deviations from Gaussian type orbital, canonical, basis set limit extrapolated, global density fitting (DF)-MP2 results of less than 1 kcal/mol. Furthermore, we introduce a quadratic scaling atomic orbital based spin-opposite-scaled (SOS)-MP2 approach with a very small prefactor. Due to a worst-case scaling of [Formula: see text], our implementation is very fast already for small systems and shows an exceptionally early crossover to canonical SOS-PARI-MP2. We report computational wall time results for linear as well as for realistic three-dimensional molecules and show that triple-Î¶ quality calculations on molecules of several hundreds of atoms are only a matter of a few hours on a single compute node, the bottleneck of the computations being the SCF rather than the post-SCF energy correction.

*J Chem Inf Model ; 60(1): 259-267, 2020 Jan 27.*

##### RESUMO

As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments.

*J Am Chem Soc ; 142(2): 1020-1028, 2020 01 15.*

##### RESUMO

The self-assembly of chiral supramolecular polymers is an intricate process that spans a wide range of length scales. Circular dichroism techniques are ideal to study this process as they provide information on the molecular scale but are at the same time also sensitive probes of the long-range interactions that control the growth and morphology of these polymers. As yet, Electronic Circular Dichroism that uses electronic transitions as a probe has by far been the method of choice while Vibrational Circular Dichroism, which uses vibrational transitions to probe structure, is much less employed. Here, we report experimental and theoretical studies of the self-assembly of helical supramolecular polymers of (S)-triarylamine tris-amides ((S)-TATA) in which both techniques are applied in concert. Theoretical studies based on quantum chemical calculations and on simplified models that allow for extrapolation to "infinitely" long polymers provide a solid basis for interpreting results from each of the two techniques that on their own would appear to be contradictory. In the particular case of (S)-TATA it is shown that upon equilibration the initially formed fibers undergo a conformational transition that becomes only "visible" by the combination of the two techniques. Our studies thus show that combining electronic and vibrational domains offers a unique and complementary means to probe these polymers, precisely because they are sensitive to different aspects of molecular and polymeric structure.

*Chem Sci ; 10(33): 7680-7689, 2019 Sep 07.*

##### RESUMO

The flexibility of a molecule has important consequences on its function and application. Vibrational Circular Dichroism (VCD) is intrinsically an excellent experimental technique to get a hold on this flexibility as it is highly sensitive to key conformational details and able to distinguish rapidly interconverting conformers. One of the major challenges in analyzing the spectra by comparison to theoretical predictions is the uncertainty in the computed energies of the multitude of conformations. This uncertainty also affects the reliability of the stereochemical assignment it is normally used for. We present here a novel approach that explicitly takes the energy uncertainties into account in a genetic algorithm based method that fits calculated to the experimental spectra. We show that this approach leads to significant improvements over previously used methodologies. Importantly, statistical validation studies provide quantitative measures for the reliability of relevant parameters used such as the energy uncertainty and the extent to which conformational heterogeneity can be determined. Similarly, quantitative measures can be obtained for the possibility that the flexibility that is introduced in the fit might lead to an incorrect assignment of the stereochemistry. These results break new ground for different techniques based on VCD to elucidate conformational flexibility.

*Anal Chim Acta ; 1090: 100-105, 2019 Dec 20.*

##### RESUMO

The absolute configuration of a chiral molecule is key to its biological activity. Being able to find out what this configuration is, is thus crucial for a wide range of applications. The difficulties associated with such a determination steeply rise as the number of chiral centers in a given compound becomes larger. Concurrently, it becomes increasingly more challenging to determine the levels and identity of potential stereochemical contaminants in a given sample with one and the same technique, leading in practice to extensive and laborious efforts employing multiple analytical techniques. Here, experimental and theoretical studies based on Vibrational Circular Dichroism (VCD) are presented for dydrogesterone, a synthetic drug employed in reproductive medicine that is a prototypical example of such a multi-center chiral compound. We show that our approach allows us to distinguish and assign its absolute configuration without prior knowledge to one of the 64 possible stereoisomers associated with the six chiral centers. Studies on mixtures of dydrogesterone and 6-dehydroprogesterone, one of the diastereomers of dydrogesterone and generally the dominant impurity of dehydrogesterone, show that we can identify the presence of both compounds from one single VCD spectrum. Moreover, we find that we can determine diastereomeric contamination levels as low as 5% from the experimental VCD spectra.

*J Chem Inf Model ; 59(7): 3191-3197, 2019 07 22.*

##### RESUMO

We present the QMflows Python package for quantum chemistry workflow automatization. QMflows allows users to write complex workflows in terms of simple Python scripts. It supports the development of interoperable workflows involving multiple quantum chemistry codes and executes them efficiently on large scale parallel computers. This open source library provides standardized interfaces to a number of quantum chemistry packages and can be easily extended to accommodate additional codes. QMflows features are described and illustrated with a number of representative applications.

*J Chem Phys ; 151(3): 034302, 2019 Jul 21.*

##### RESUMO

The NL-eEDM collaboration is building an experimental setup to search for the permanent electric dipole moment of the electron in a slow beam of cold barium fluoride molecules [NL-eEDM Collaboration, Eur. Phys. J. D 72, 197 (2018)]. Knowledge of the molecular properties of BaF is thus needed to plan the measurements and, in particular, to determine the optimal laser-cooling scheme. Accurate and reliable theoretical predictions of these properties require the incorporation of both high-order correlation and relativistic effects in the calculations. In this work, theoretical investigations of the ground and lowest excited states of BaF and its lighter homologs, CaF and SrF, are carried out in the framework of the relativistic Fock-space coupled cluster and multireference configuration interaction methods. Using the calculated molecular properties, we determine the Franck-Condon factors (FCFs) for the A2Π1/2âX2Σ1/2 + transition, which was successfully used for cooling CaF and SrF and is now considered for BaF. For all three species, the FCFs are found to be highly diagonal. Calculations are also performed for the B2Σ1/2 +âX2Σ1/2 + transition recently exploited for laser-cooling of CaF; it is shown that this transition is not suitable for laser-cooling of BaF, due to the nondiagonal nature of the FCFs in this system. Special attention is given to the properties of the A'2Δ state, which in the case of BaF causes a leak channel, in contrast to CaF and SrF species where this state is energetically above the excited states used in laser-cooling. We also present the dipole moments of the ground and excited states of the three molecules and the transition dipole moments (TDMs) between the different states. Finally, using the calculated FCFs and TDMs, we determine that the A2Π1/2âX2Σ1/2 + transition is suitable for transverse cooling in BaF.

*J Phys Chem Lett ; 10(9): 2151-2155, 2019 May 02.*

##### RESUMO

Coinage metal clusters are of great importance for a wide range of scientific fields, ranging from microscopy to catalysis. Despite their clear fundamental and technological importance, the experimental structural determination of copper clusters has attracted little attention. We fill this gap by elucidating the structure of cationic copper clusters through infrared (IR) photodissociation spectroscopy of Cu n+-Ar m complexes. Structures of Cu n+ ( n = 3-10) are unambiguously assigned based on the comparison of experimental IR spectra in the 70-280 cm-1 spectral range with spectra calculated using density functional theory. Whereas Cu3+ and Cu4+ are planar, starting from n = 5, Cu n+ clusters adopt 3D structures. Each successive cluster size is composed of its predecessor with a single atom adsorbed onto the face, giving evidence of a stepwise growth.

*Inorg Chem ; 57(24): 15350-15360, 2018 Dec 17.*

##### RESUMO

Because of its sensitivity to the atomic scale environment, solid-state NMR offers new perspectives in terms of structural characterization, especially when applied jointly with first-principles calculations. Particularly, challenging is the study of actinide-based materials because of the electronic complexity of the actinide cations and to the hazards due to their radioactivity. Consequently, very few studies have been published in this subfield. In the present paper, we report a joint experimental-theoretical analysis of thorium tetrafluoride, ThF4, containing a closed-shell actinide (5f0) cation. Its crystalline structure has been revisited in the present work using powder neutron diffraction experiments. The 19F NMR parameters of the seven F crystallographic sites have been modeled using an empirical superposition model, periodic first-principles calculations, and a cluster-based all-electron approach. On the basis of the atomic position optimized structure, a complete and unambiguous assignment of the 19F NMR resonances to the F sites has been obtained.

*J Chem Phys ; 149(17): 174113, 2018 Nov 07.*

##### RESUMO

We report in this paper an implementation of a 4-component relativistic Hamiltonian based Equation-of-Motion Coupled-Cluster with singles and doubles (EOM-CCSD) theory for the calculation of ionization potential, electron affinity, and excitation energy. In this work, we utilize the previously developed double group symmetry-based generalized tensor contraction scheme and also extend it in order to carry out tensor contractions involving non-totally symmetric and odd-ranked tensors. Several approximated spin-free and two-component Hamiltonians can also be accessed in this implementation. We have applied this method to the halogen monoxide (XO, X = Cl, Br, I, At, Ts) species, in order to assess the quality of a few other recent EOM-CCSD implementations, where spin-orbit coupling contribution has been approximated in different degrees. Besides, we have also studied various excited states of CH2IBr, CH2I2, and I 3 - (as well as single electron attachment and detachment electronic states of the same species) where comparison has been made with a closely related multi-reference coupled-cluster method, namely, Intermediate Hamiltonian Fock Space Coupled-Cluster singles and doubles theory.

*J Chem Theory Comput ; 14(3): 1510-1522, 2018 Mar 13.*

##### RESUMO

A complete implementation of the polarization propagator based on the Dirac-Coulomb Hamiltonian is presented and applied to excitation spectra of various systems. Hereby the effect of spin-orbit coupling on excitation energies and transition moments is investigated in detail. The individual perturbational contributions to the transition moments could now be separately analyzed for the first time and show the relevance of one- and two-particle terms. In some systems different contributions to the transition moments partially cancel each other and do not allow for simple predictions. For the outer valence spectrum of the H2Os(CO)4 complex a detailed final state analysis is performed explaining the sensitivity of the excitation spectrum to spin-orbit effects. Finally, technical issues of handling double group symmetry in the relativistic framework and methodological aspects of our parallel implementation are discussed.

*Chemphyschem ; 19(5): 561-565, 2018 03 05.*

##### RESUMO

Experimental and theoretical studies of the vibrational circular dichroism (VCD) spectrum of 3-methyl-1-(methyldiphenlsilyl)-1-phenylbutan-1-ol, whose absolute configuration is key to elucidating the Brook rearrangement of tertiary benzylic α-hydroxylsilanes, are presented. It is found that the entire OH-bending region in this spectrum-a region that provides important marker bands-cannot be reproduced at all by standard theoretical approaches even though other regions are well described. Using a novel approach to disentangle contributions to the rotational strength of these bands, internal coordinates are identified that critically influence the appearance of this part of the spectrum. We show that the agreement between experiment and theory is greatly improved when structural dynamics along these coordinates are explicitly taken into account. The general applicability of the approach underlines its usefulness for structurally flexible chiral systems, a situation that is more the rule rather than the exception.

*Phys Chem Chem Phys ; 19(40): 27892-27894, 2017 Oct 18.*

##### RESUMO

We appreciate Aranda's comments on our recent work entitled ''Elucidation of charge-transfer SERS selection rules by considering the excited state properties and the role of electrode potential''. We would also like to thank the editor of Physical Chemistry Chemical Physics for giving us an opportunity to specify more details of our work in this reply. An important part of our article concerns the role of the electrode potential in charge-transfer SERS spectra and we would like to first address the questions that Aranda et al. posed about our labeling.

*Phys Chem Chem Phys ; 19(28): 18311-18320, 2017 Jul 19.*

##### RESUMO

The light harvesting complex II (LHCII), is a pigment-protein complex responsible for most of the light harvesting in plants. LHCII harvests sunlight and transfers excitation energy to the reaction centre of the photo-system, where the water oxidation process takes place. The energetics of LHCII can be modulated by means of conformational changes allowing a switch from a harvesting to a quenched state. In this state, the excitation energy is no longer transferred but converted into thermal energy to prevent photooxidation. Based on molecular dynamics simulations at the microsecond time scale, we have recently proposed that the switch between different fluorescent states can be probed by correlating shifts in the chromophore-chromophore Coulomb interactions to particular protein movements. However, these findings are based upon calculations in the ideal point dipole approximation (IDA) where the Coulomb couplings are simplified as first order dipole-dipole interactions, also assuming that the chromophore transition dipole moments lay in particular directions of space with constant moduli (FIX-IDA). In this work, we challenge this approximation using the time-dependent density functional theory (TDDFT) combined with the frozen density embedding (FDE) approach. Our aim is to establish up to which limit FIX-IDA can be applied and which chromophore types are better described under this approximation. For that purpose, we use the classical trajectories of solubilised light harvesting complex II (LHCII) we have recently reported [Liguori et al., Sci. Rep., 2015, 5, 15661] and selected three pairs of chromophores containing chlorophyll and carotenoids (Chl and Car): Chla611-Chla612, Chlb606-Chlb607 and Chla612-Lut620. Using the FDE in the Tamm-Dancoff approximation (FDEc-TDA), we show that IDA is accurate enough for predicting Chl-Chl Coulomb couplings. However, the FIX-IDA largely overestimates Chl-Car interactions mainly because the transition dipole for the Cars is not trivially oriented on the polyene chain.

##### Assuntos

Complexos de Proteínas Captadores de Luz/química , Carotenoides/química , Clorofila/química , Complexos de Proteínas Captadores de Luz/metabolismo , Simulação de Dinâmica Molecular , Estrutura Terciária de Proteína , Solubilidade , Termodinâmica*Phys Chem Chem Phys ; 19(11): 7833-7843, 2017 Mar 15.*

##### RESUMO

The goal of this study is to shed light on the charge-transfer (CT) mechanism of surface-enhanced Raman scattering (SERS) by considering the properties of CT excited states. The calculations have been done by means of an excited-state gradient approximation for a pyridine molecule interacting with a silver cluster, and provided a satisfactory improvement in comparison to previous work. The effect of electrode potential on the SERS-CT spectra has been modelled theoretically by applying an external electric field for selected CT transitions and the enhancement of the ν6a and ν9a modes and a decline in the intensity of the ν8a mode under a negative electric field (which is directed toward the cluster) have been observed. These results match well with the experimental studies and also explain the effect of electrode potentials on the patterns of spectra, as experimental evidence of the CT mechanism. Finally, this study demonstrated that the excited state vector gradient can be used as a distinguishing factor to explain the SERS selection rules.

*J Chem Theory Comput ; 13(3): 1094-1101, 2017 Mar 14.*

##### RESUMO

The f-block elements are addressed in this third part of a series of prolapse-free basis sets of quadruple-Î¶ quality (RPF-4Z). Relativistic adapted Gaussian basis sets (RAGBSs) are used as primitive sets of functions while correlating/polarization (C/P) functions are chosen by analyzing energy lowerings upon basis set increments in Dirac-Coulomb multireference configuration interaction calculations with single and double excitations of the valence spinors. These function exponents are obtained by applying the RAGBS parameters in a polynomial expression. Moreover, through the choice of C/P characteristic exponents from functions of lower angular momentum spaces, a reduction in the computational demand is attained in relativistic calculations based on the kinetic balance condition. The present study thus complements the RPF-4Z sets for the whole periodic table (Z ≤ 118). The sets are available as Supporting Information and can also be found at http://basis-sets.iqsc.usp.br .