Superfluid helium droplet-mediated surface-deposition of neutral and charged silver atomic species.

Experimental and theoretical work has delivered evidence of the helium nanodroplet-mediated synthesis and soft-landing of metal nanoparticles, nanowires, clusters, and single atoms on solid supports. Recent experimental advances have allowed the formation of charged metal clusters into multiply charged helium nanodroplets. The impact of the charge of immersed metal species in helium nanodroplet-mediated surface deposition is proved by considering silver atoms and cations at zero-temperature graphene as the support. By combining high-level ab initio intermolecular interaction theory with a full quantum description of the superfluid helium nanodroplet motion, evidence is presented that the fundamental mechanism of soft-deposition is preserved in spite of the much stronger interaction of charged species with surfaces, with high-density fluctuations in the helium droplet playing an essential role in braking them. Corroboration is also presented that the soft-landing becomes favored as the helium nanodroplet size increases.

Functional group corrections to the GFN2-xTB and PM6 semiempirical methods for noncovalent interactions in alkanes and alkenes.

Analytical corrections were developed to improve the accuracy of the PM6 and GFN2-xTB semiempirical quantum mechanical methods for the evaluation of noncovalent interaction energies in alkanes and alkenes. We followed the approach of functional group corrections, wherein the atom-atom pair corrections depend on the nature of the interacting functional groups. The training set includes 21 alkane and 13 alkene complexes taken from the Donchev et al.'s database [Sci. Data 8, 55 (2021)], with interaction energies calculated at the CCSD(T)/CBS level, and our own data obtained for medium-size complexes (of 100 and 112 atoms). In general, for the systems included in the training and validation sets, the errors obtained with the PM6-FGC and xTB-FGC methods are within the chemical accuracy.

Meta-stability through intermolecular interactions protecting the identity of atomic metal clusters: ab initio evidences in (Cu5-Cu5)n (n < 3) cases.

Recent developments in new synthesis techniques have allowed the production of precise monodisperse metal clusters composed of a few atoms. These atomic metal clusters (AMCs) often feature a molecule-like electronic structure, which makes their physical and chemical properties particularly interesting in nanotechnology. Regarding potential applications, there is a major concern about the sintering of AMCs in nanoparticles due to the loss of their special properties. In this work, multireference ab initio theory is applied to demonstrate the formation of coupled AMC-AMC clusters in which the AMC partners maintain their 'identity' to a large extent in terms of their initial structures and atomic Mulliken charges, and their further oligomerization.

The PM6-FGC Method: Improved Corrections for Amines and Amides.

Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the -NH2 group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH3 molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set.

Dissymmetric Chiral Poly(diphenylacetylene)s: Secondary Structure Elucidation and Dynamic Luminescence.

The secondary structure of a dissymmetric and chiral poly(diphenylacetylene) (PDPA) is elucidated by combining the data from NMR experiments (regioregular head to tail structure), Raman and IR studies (E configuration of the polyene double bonds), and high-resolution AFM images (helical pitch, packing angle and orientation of the external helix). As a result, an E-transoidal polyene backbone describing three coaxial helices is obtained. Theoretical electronic circular dichroism (ECD) studies of the structure show a good correspondence between experimental and theoretical data and allow one to decipher that the first Cotton band is generated by the poly(diphenylacetylene) core and not only by the polyene backbone. The dynamic behavior of poly-(S)-2 is also demonstrated by a helix inversion effect produced by conformational changes at the pendant groups when annealed in solvents with different donor abilities. This phenomenon is accompanied by an inversion of the circular polarized luminescence of the PDPA (CPL switch).

Full Control of the Chiral Overpass Effect in Helical Polymers: P/M Screw Sense Induction by Remote Chiral Centers After Bypassing the First Chiral Residue.

In helical polymers, helical sense induction is usually commanded by teleinduction mechanism, where the largest substituent of the chiral residue directly attached to the main chain is the one that commands the helical sense. In this work, different helical structures with different helical senses are induced in a helical polymer [poly-(phenylacetylene)] when the conformational composition of two different dihedral angles of a pendant group with more than two chiral residues is tamed. Thus, while the dihedral angle at chiral residue 1 [(R)- or (S)-alanine], attached to the backbone, produces an extended or bent conformation in the pendant resulting in two scaffolds with different stretching degree, the second dihedral angle at chiral residue 2 [(R)- or (S)-methoxyphenylacetamide] places the substituents of this chiral center in a different spatial orientation, originating opposite helical senses at the polymer that are induced through a total control of the "chiral overpass effect".

Merging Supramolecular and Covalent Helical Polymers: Four Helices Within a Single Scaffold.

Supramolecular and covalent polymers share multiple structural effects such as chiral amplification, helical inversion, sergeants and soldiers, or majority rules, among others. These features are related to the axial helical structure found in both types of materials, which are responsible for their properties. Herein a novel material combining information and characteristics from both fields of helical polymers, supramolecular (oligo(p-phenyleneethynylene) (OPE)) and covalent (poly(acetylene) (PA)), is presented. To achieve this goal, the poly(acetylene) must adopt a dihedral angle between conjugated double bonds (ω1) higher than 165°. In such cases, the tilting degree (Θ) between the OPE units used as pendant groups is close to 11°, like that observed in supramolecular helical arrays of these molecules. Polymerization of oligo[(p-phenyleneethynylene)n]phenylacetylene monomers (n = 1, 2) bearing L-decyl alaninate as the pendant group yielded the desired scaffolds. These polymers adopt a stretched and almost planar polyene helix, where the OPE units are arranged describing a helical structure. As a result, a novel multihelix material was prepared, the ECD spectra of which are dominated by the OPE axial array.

Systematic Analysis of the Role of Substituents in Oxiranes, Oxetanes, and Oxathietanes Chemical Shifts.

The important role substituents play on proton chemical shifts in heterocyclic compounds was investigated in detail. For this purpose, a considerable number of model oxiranes, oxetanes, and oxathietanes with different substituents were studied in a systematic way. In addition, the oxygen and sulfur heteroatom influence on the chemical shift values was analyzed. The density functional theory (DFT) approximation was employed together with the M06 and the B3LYP functionals and the aug-pcS-1 and the 6-311++G** basis sets. We carried out a careful analysis of the shift values and the changes in the corresponding molecular electrostatic potential surfaces due to substitution. We observed that chemical shift values for the protons closest to the substituents are larger for the chloro and fluoro derivatives than those for the cyano and ethynyl ones. The presence of oxygen as well as sulfur in the ring causes an increase of the chemical shift values, most pronounced for the atom closest to the substituent. A large decrease of the proton shifts was observed when going from methylenecyclopropane to methyleneoxirane that can be attributed to π-electron resonance. Protons diagonal to the substituents behaved in a different way depending on their cis or trans disposition with respect to them. The conclusions of the present study will be useful in theoretical and experimental work on NMR spectra of heterocyclic compounds.

From Oligo(Phenyleneethynylene) Monomers to Supramolecular Helices: The Role of Intermolecular Interactions in Aggregation.

Supramolecular helices that arise from the self-assembly of small organic molecules via non-covalent interactions play an important role in the structure and properties of the corresponding materials. Here we study the supramolecular helical aggregation of oligo(phenyleneethynylene) monomers from a theoretical point of view, always guiding the studies with experimentally available data. In this way, by systematically increasing the number of monomer units, optimized n-mer geometries are obtained along with the corresponding absorption and circular dichroism spectra. For the geometry optimizations we use density functional theory together with the B3LYP-D3 functional and the 6-31G** basis set. For obtaining the spectra we resort to time-dependent density functional theory using the CAM-B3LYP functional and the 3-21G basis set. These combinations of density functional and basis set were selected after systematic convergence studies. The theoretical results are analyzed and compared to the experimentally available spectra, observing a good agreement.

The Competitive Aggregation Pathway of an Asymmetric Chiral Oligo(p-phenyleneethynylene) Towards the Formation of Individual P and M Supramolecular Helical Polymers.

A complex aggregation pathway towards two diastereomeric P and M supramolecular helices arises from the aggregation of a short, chiral, and rigid oligo(phenyleneethynylene) [OPE, (S)-1]. Thus, while AggI aggregate is obtained when a DCM solution of (S)-1 is diluted with MCH at room temperature, AggII aggregate is generated only after a slow heating (353 K)/cooling (273 K) process. Interestingly, during AggI formation (mechanism 1), short P chain oligomers are produced, which have a great tendency to aggregate in plane, yielding brick-like nanostructures that halt the aggregation process. On the other hand, after a heating/cooling cycle, long M type columnar helical aggregates (AggII ) are obtained, formed by individual supramolecular polymer chains (mechanism 2) easily visualized by AFM. The two different P/M orientations obtained for AggI and AggII reveal the dynamic character of the system and its ability to create diastereomeric helical structures under the right conditions. Different experimental protocols were explored to prepare long M type columnar helical aggregates, which are not obtained by using the previous MCH/DCM 99/1 (v/v) solvent mixture. The generation of the desired M oriented supramolecular polymer is achieved when toluene is added to the solvent mixture in a 97/2/1 MCH/Tol/DCM (v/v/v) ratio.

MMP1 and MMP11 Expression in Peripheral Blood Mononuclear Cells upon Their Interaction with Breast Cancer Cells and Fibroblasts.

Tumor-infiltrating immune cells phenotype is associated with tumor progression. However, little is known about the phenotype of the peripheral blood mononuclear cells (PBMC) from breast cancer patients. We investigated MMP1 and MMP11 expression in PBMC from breast cancer patients and we analyzed gene expression changes upon their interaction with cancer cells and cancer-associated fibroblasts (CAF). We measured the impact of PBMC on proinflammatory gene expression in breast cancer cells, normal fibroblast (NF), and CAF and the impact on proliferation and invasiveness capacity of breast cancer cells. Gene expression of MMP1 and MMP11 in PBMC from breast cancer patients (n = 54) and control (n = 28); expression of IL1A, IL6, IL17, IFNß, and NFĸB in breast cancer cell lines (MCF-7 and MDA-MB-231); and, additionally, IL10 and MMP11 in CAF and NF were analyzed by qRT-PCR before and after co-culture. Our results show the existence of a subpopulation of breast cancer patients (25.9%) with very high levels of MMP11 gene expression in PBMC. Also, gene expression of MMP1 and MMP11 increases in PBMC after co-culture with breast cancer cell lines, NF or CAF. PBMC from healthy or breast cancer patients induce an increased proliferation rate on MCF-7 and an increased invasiveness capacity of MDA-MB-231. Finally, we show a differential expression profile of inflammatory genes in NF and CAF when co-cultured with control or breast cancer PBMC. We have observed that MMPs' expression in PBMC is regulated by the microenvironment, while the expression of inflammatory genes in NF or CAF is differentially regulated by PBMC. These findings confirm the importance of the crosstalk between stromal cells and suggest that PBMC would play a role in promoting aggressive tumor behavior.

MMP11 expression in intratumoral inflammatory cells in breast cancer.

AIMS: It is known that matrix metalloproteinase (MMP)-11 has a role in tumour development and progression, and also that immune cells can influence cancer cells to increase their proliferative and invasive properties. The aim of the present study was to propose the evaluation of MMP11 expression by intratumoral mononuclear inflammatory cells (MICs) as a useful biological marker for breast cancer prognosis. METHODS AND RESULTS: This study comprised 246 women with invasive breast carcinoma, and a long follow-up period. Patients were stratified with regard to nodal status and to the development of metastatic disease. The median follow-up period in patients without metastasis was 146 months and in patients with metastatic disease 31 months. MMP11 was determined by immunohistochemistry. For relapse-free survival (RFS) and overall survival (OS) analysis we used the Cox's univariate method. Cox's regression model was used to examine the interactions between different prognostic factors in a multivariate analysis. CONCLUSIONS: Our results showed that MMP11 expression by stromal cells was significantly associated with prognosis. MMP11 expression by cancer-associated fibroblasts (CAFs) was associated with both shortened RFS and OS, but MMP11 expression by MICs showed a stronger association with both shortened RFS and OS, therefore being the most potent and independent factor to predict RFS and OS.

The Role of Substituents in Optical Rotation of Oxiranes, Oxetanes, and Oxathietanes.

Taking as examples a series of oxiranes, oxetanes, and oxathietanes with different substituents, we study in a systematic way the role that the latter play on the optical rotation of the molecules. For this, we use time-dependent density functional theory together with a hierarchy of Dunning's basis sets. The B3LYP and CAM-B3LYP exchange-correlation functionals are employed. We select results obtained with the CAM-B3LYP functional and the daug-cc-pVTZ basis set as our reference values. Additionally, specific rotation in all systems is calculated with the ORP basis set, specifically designed to carry out optical rotation calculations. The present study shows its good performance in CAM-B3LYP estimations of this property, providing results close to the reference values. The proper choice of the exchange-correlation functional proves to be much more important than that of the basis set. Considering the effect of the substituents, some of the presently investigated molecules show a behavior in line with earlier findings; however we have also found systems that do not match the conclusions previously available in the literature.

Dissecting the concave-convex π-π interaction in corannulene and sumanene dimers: SAPT(DFT) analysis and performance of DFT dispersion-corrected methods.

The characteristics of the concave-convex π-π interactions are evaluated in 32 buckybowl dimers formed by corannulene, sumanene, and two substituted sumanenes (with S and CO groups), using symmetry-adapted perturbation theory [SAPT(DFT)] and density functional theory (DFT). According to our results, the main stabilizing contribution is dispersion, followed by electrostatics. Regarding the ability of DFT methods to reproduce the results obtained with the most expensive and rigorous methods, TPSS-D seems to be the best option overall, although its results slightly tend to underestimate the interaction energies and to overestimate the equilibrium distances. The other two tested DFT-D methods, B97-D2 and B3LYP-D, supply rather reasonable results as well. M06-2X, although it is a good option from a geometrical point of view, leads to too weak interactions, with differences with respect to the reference values amounting to about 4 kcal/mol (25% of the total interaction energy). © 2017 Wiley Periodicals, Inc.

Accurate calculation of optically induced birefringences in chiral systems using efficient polarized basis sets.

Using state-of-the-art ab initio methodology, we evaluate universal molecular parameters entering the expressions for various optically induced birefringences in chiral fluids. For this, we use the single and double excitation coupled cluster (CCSD) theory together with Dunning's augmented correlation consistent polarized basis sets of increasing size. As this is the first time these parameters are evaluated for chiral molecules using the CCSD approach, we choose possibly small test systems: a model asymmetric methane molecule, and (R)-fluoro-oxirane. With this choice, the convergence of the molecular parameters with the increase of the basis set size is investigated in detail. The results are compared to those obtained with the LPol-n (n = ds, dl, fs) and the ORP basis sets, and to the corresponding Density Functional Theory (DFT) counterparts. We can conclude that the DFT medium constant values are considerably far from coupled cluster, and therefore, aware of the known excellent performance of the CCSD method in the evaluation of various dynamic responses, we do not recommend the former methodology for accurate evaluation of the present properties. Regarding basis set convergence, the performace of the LPol-ds basis set is more efficient than that of the d-aug-cc-pVDZ set, and therefore, the former basis set can be a good choice when dealing with the study of larger systems.

Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum.

A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials.

New Basis Set for the Evaluation of Specific Rotation in Flexible Biological Molecules in Solution.

A detailed theoretical investigation of specific rotation is carried out in solution for nine flexible molecules of biological importance. Systematic search for the main conformers is followed by time-dependent density functional theory (TD-DFT) calculations of specific rotation employing a wide range of basis sets. Due to conformational flexibility of the compounds under study, the possibility of basis set size reduction without deterioration of the results is investigated. The increasing size (d-)aug-cc-pVXZ (X = D, T, Q) bases of Dunning et al., and the ORP basis set, recently developed to efficiently provide molecular specific rotation, are used for this purpose. The polarizable continuum model is employed at all steps of the investigation. Comparison of the present results with the available data obtained in a vacuum reveals considerable differences, the values in solution being much closer to the experimental specific rotation data available. The ORP basis set proves to be competitive with the d-aug-cc-pVDZ set of Dunning in specific rotation calculations carried out in solution. While having the same number of functions, the former yields, in general, results considerably closer to the reference triple-ζ values. We can thus recommend the ORP basis set to study the optical rotation in conformationally flexible molecules in solution.

Influence of Multiple Conformations and Paths on Rate Constants and Product Branching Ratios. Thermal Decomposition of 1-Propanol Radicals.

The potential energy surface involved in the thermal decomposition of 1-propanol radicals was investigated in detail using automated codes (tsscds2018 and Q2DTor). From the predicted elementary reactions, a relevant reaction network was constructed to study the decomposition at temperatures in the range 1000-2000 K. Specifically, this relevant network comprises 18 conformational reaction channels (CRCs), which in general exhibit a large wealth of conformers of reactants and transition states. Rate constants for all the CRCs were calculated using two approaches within the formulation of variational transition-state theory (VTST), as incorporated in the TheRa program. The simplest, one-well (1W) approach considers only the most stable conformer of the reactant and that of the transition state. In the second, more accurate approach, contributions from all the reactant and transition-state conformers are taken into account using the multipath (MP) formulation of VTST. In addition, kinetic Monte Carlo (KMC) simulations were performed to compute product branching ratios. The results show significant differences between the values of the rate constants calculated with the two VTST approaches. In addition, the KMC simulations carried out with the two sets of rate constants indicate that, depending on the radical considered as reactant, the 1W and the MP approaches may display different qualitative pictures of the whole decomposition process.

Predicting the Helical Sense of Poly(phenylacetylene)s from their Electron Circular Dichroism Spectra.

The calculated ECD spectrum (time-dependent density functional theory TD-DFT) for small oligomers of polyphenylacetylenes (PPAs) show a very good match with the experimental spectra of the PPA polymers, particularly with the first Cotton band associated to the helical sense of the internal polyenic backbone. This has been proven with a series of PPAs representative of cis-cisoidal, cis-transoidal, compressed and stretched polyene backbones, with identical or opposite internal/external rotational senses and allows the prediction of the helical sense of the internal helix of a PPA directly from its CD spectra.

Fluorescence quenching of the N-methylquinolinium cation by pairs of water or alcohol molecules.

N-Methylquinolinium cation (MQ+) in its first-excited singlet state is a strong oxidant commonly used as a photosensitizer, whose fluorescence is therefore quenched by electron donors. Interestingly, the fluorescence of MQ+ is also quenched by hydroxy compounds such as water and alcohols, more difficult to oxidize. We investigated the quenching mechanism of MQ+ fluorescence by small amounts of water and alcohols in acetonitrile solution. The fluorescence intensities and lifetimes exhibited a nonlinear dependence on the quencher concentration. We found evidence that emissive exciplexes MQ+*-ROH are formed between the excited quinolinium and the hydroxy compounds. An accurate quantitative description of the results was obtained with a model in which the exciplex reacts with a second molecule of the hydroxy compound, which quenches the fluorescence. The rate constant of this process increased as the quencher ionization energy decreased. We showed also that a low basicity of the hydroxy compound inhibits the quenching process. These results are consistent with the existence of a concerted photoinduced proton-coupled electron transfer (PCET) involving an intermediate complex of the excited quinolinium with a H-bonded molecular pair of the hydroxy compounds. In these pairs, a water or an alcohol molecule is able to donate an electron to the photoexcited quinolinium cation and a proton to the second H-bonded hydroxy molecule, showing an enhanced reducing power in comparison with the isolated molecule. The structure of the intermediate complex was investigated using high-level quantum mechanical calculations. At high water concentrations in acetonitrile/water mixtures, the quenching process is slowed down, indicating that higher water aggregates are less effective for a PCET process. The results obtained may be relevant to the study of water oxidation and electron transfer in biological systems.