Is there a Covalent Au(I)-Au(I) Bond in the trans-(AuX)2 (X = F, Cl, Br, I) Structure? A Post-Hartree-Fock and Density Functional Theory Study.

We present an exhaustive exploration of the driving forces dominating the interaction between gold atoms in the trans-(AuX)2, where X is a halogen ligand. This work provides insights into the nature of the gold-gold contact in the trans-(AuX)2. The geometries and energies were calculated at the MP2, CCSD(T), and DFT-D3(BJ) (B3LYP, PBE, and TPSS) levels of theory. The results show a short Au-Au distance, typical of a covalent bond, but with a weak interaction energy associated with noncovalent interactions. It is established that the physical contributions from polarization and the electronic correlation forces are the most relevant at the post-Hartree-Fock level of theory. Also, the electrostatic term is attractive but with low contribution. Finally, the Wiberg indices and NBO analysis exposed a small covalent character between the gold atoms, revealing that this contribution is insufficient to explain the stability of the dimers. It is concluded that a sum of contributions makes it possible to establish an attraction between the gold atoms in the dimers studied beyond a classical aurophilic interaction.

Time-dependent density functional theory studies of the optical and electronic properties of the [M25(MPA)18]- (M = Au, Ag, MPA = SCH2CH2COOH) clusters.

Electronic absorption and emission spectra of [M25(MPA)18]- (M = Au, Ag; MPA = SCH2CH2COOH) clusters have been recorded for energies below 5 eV at the time-dependent density functional theory (TDDFT) level using B3LYP and TPSSh functionals and compared to the calculated ones using the computationally inexpensive simplified TDDFT (sTDDFT) approach. The results show a qualitative agreement between the TDDFT and sTDDFT approaches used here, which were also in line with the experimental and theoretical spectra previously reported. However, the sTDDFT calculations were several orders of magnitude faster than those obtained by TDDFT. Our results support that sTDDFT provides an excellent balance between accuracy and low computational cost, becoming a suitable approach for studying the absorption and emission spectra of noble-metal clusters of sizes that would be unaffordable by the traditional TDDFT methods. The main peaks of the experimental absorption spectrum of [Au25(MPA)18]- have been previously assigned, whereas [Ag25(MPA)18]- has not been synthesised. However, its absorption spectrum resulted in having similar features to the experimental spectrum of [Ag25(GSH)18]- (GSH = glutathione), used to validate our results. The emission spectra, which to date have not been reported either from experimental or theoretical means, were simulated by using the molecular structure of the first excited triplet state (T1). The emission spectra were obtained by comparing them to those of [M25(GSH)18]- since no experimental luminescence spectra have been reported for [M25(MPA)18]-. The calculations suggest that [Ag25(SR)18]- (SR = thiolate) clusters have a weak luminescence band in the NIR region. Finally, solvent shifts were found to be minor, whereas the absorption bands seem to be significantly redshifted in solid-state materials.

Unraveling the Role of the Tyrosine Tetrad from the Binding Site of the Epigenetic Writer MLL3 in the Catalytic Mechanism and Methylation Multiplicity.

MLL3, also known as KMT2C, is a lysine mono-methyltransferase in charge of the writing of an epigenetic mark on lysine 4 from histone 3. The catalytic site of MLL3 is composed of four tyrosines, namely, Y44, Y69, Y128, and Y130. Tyrosine residues are highly conserved among lysine methyltransferases' catalytic sites, although their complete function is still unclear. The exploration of how modifications on these residues from the enzymatic machinery impact the enzymatic activity of MLL3 could shed light transversally into the inner functioning of enzymes with similar characteristics. Through the use of QMMM calculations, we focus on the effect of the mutation of each tyrosine from the catalytic site on the enzymatic activity and the product specificity in the current study. While we found that the mutations of Y44 and Y128 by phenylalanine inactivated the enzyme, the mutation of Y128 by alanine reactivated the enzymatic activity of MLL3. Moreover, according to our models, the Y128A mutant was even found to be capable of di- and tri-methylate lysine 4 from histone 3, what would represent a gain of function mutation, and could be responsible for the development of diseases. Finally, we were able to establish the inactivation mechanism, which involved the use of Y130 as a water occlusion structure, whose conformation, once perturbed by its mutation or Y128 mutant, allows the access of water molecules that sequester the electron pair from lysine 4 avoiding its methylation process and, thus, increasing the barrier height.

Designing boron and metal complexes for fluoride recognition: a computational perspective.

Fluoride anions (F-) may have beneficial or harmful effects on the environment depending on their concentration. Here, we shed light on F- recognition by compounds containing boron, tellurium and antimony, which were experimentally demonstrated to be capable of interacting with the F- ion in a partially aqueous medium. Boron and metal complexes recognize F- anions primarily using electrostatic energy along with important contributions from orbital interaction energy. The natural orbitals for chemical valence (NOCV) methodology indicates that the main orbital interactions behind fluoride recognition are σ bonds between the receptors and the F- anions. The charged receptors, which provide (i) two B atoms, (ii) one B atom and one Sb atom, or (iii) one B atom and one Te atom to directly interact with the F- ions, appear to be some of the best structures for the recognition of F- anions. This is supported by the combination of favorable electrostatic and σ bond interactions. Overall, the presence of electron donor groups, such as -CH3 and -OH, in the receptor structure destabilizes the fluoride recognition because it decreases the attractive electrostatic energy and increases the Pauli repulsion energy in the receptor⋯F- bonds. Notably, electron acceptor groups, for example, -CN and -NO2, in the receptor structure favor the interaction with the F- ions, due to the improvement of the electrostatic and σ bond interactions. This study opens the way to find the main features of a receptor for F- recognition.

Calculations of the light absorption spectra of porphyrinoid chromophores for dye-sensitized solar cells.

Solar power is a strong alternative to the currently used fossil fuels in order to satisfy the world's energy needs. Among them, dye-sensitized solar cells (DSSC) represent a low-cost option. Efficient and cheap dyes are currently needed to make DSSCs competitive. Computational chemistry can be used to guide the design of new light-absorbing chromophores. Here, we have computationally studied the lowest excited states of ZnPBAT, which is a recently synthesized porphyrinoid chromophore with high light-absorption efficiency. The calculations have been performed at ab initio correlated levels of theory employing second-order coupled clusters (CC2) and algebraic diagrammatic construction using second order (ADC(2)) methods and by performing density functional theory (DFT) calculations using the time-dependent DFT (TDDFT) approach for excitation energies. The ultraviolet-visible (UV-vis) spectrum calculated at the ADC(2) and CC2 levels agrees well with the experimental one. The calculations show that ZnPBAT has six electronic transitions in the visible range of the absorption spectrum. The ab initio correlated calculations and previously reported experimental data have been used to assess the performance of several well-known density functionals that have been employed in the present TDDFT study. Solvent effects have been estimated by using the conductor-like screening model (COSMO). The influence of the addition of a TiO2 cluster to the chromophore systems has also been investigated. The results indicate that both CAM-B3LYP and Becke's "half-and-half" (BHLYP) density functionals are appropriate for the studies of excitation energies in the blue range of the visible spectrum for these kinds of porphyrinoid chromophores, whereas the excitation energies of the Q band calculated at the ab initio correlated level are more accurate than those obtained in the present TDDFT calculations. The inclusion of solvent effects has a modest influence on the spectrum of the protonated form of the studied chromophores, whereas solvent models are crucial when studying the absorption spectrum of the anionic chromophore. The calculated UV-vis spectrum for the chromophore anion is not significantly affected by attaching a TiO2 cluster to it.

Catalytic aspects of metallophthalocyanines adsorbed on gold-electrode. Theoretical exploration of the binding nature role.

The need of deeper insights regarding the inner working of catalysts represents a current challenge in the search of new ways to tune their activities towards new chemical transformations. Within this field, metallophthalocyanines-based (MPc) electrocatalysis has gained tremendous attention due to their versatility, low cost, great stability and excellent turn-over properties. In this concern, here we present a quantum chemical study of the formation of supramolecular complexes based on the adsorption of MPcs on gold substrates, and the effect of the substrate on their electrocatalytic properties. For this purpose, we used iron- (FePc), cobalt- (CoPc) and copper-phthalocyanines (CuPc). To model the gold surface we used two gold clusters of different sizes, given by Au26 and Au58 accounting for gold electrode Au(111) surface. Thus, both electronic and binding strength features of the adsorption process between the complexes were analyzed in detail in order to gain a deeper description of the nature of the MPc-Au(111) formation, by using Density Functional Theory (DFT) calculations, at the PBE and TPSS levels including the dispersive contribution according to the Grimme approach (D3). Our results show that dispersion forces rule the MPc-gold interaction, with binding strengths ranging between 61 and 153 kcal mol-1, in agreement to the reported experimental data. To provide a detailed picture of our findings we used the non-covalent interactions index (NCIs) analysis, which offers additional chemical insights regarding the forces that control their interaction strength. Finally, our calculations revealed that among the three MPcs, CuPc required less energy for its oxidation. However, the removal of the electron involves a tremendous decrease of the MPc-gold surface interaction strength thus suggesting its desorption, which would prevent the required reversibility of the redox reaction, explaining its low performance observed experimentally.

Theoretical study on interactions of fluorinated organomercurials with arene and gold fragments.

The electronic structure and spectroscopic properties of [Hg(C6F5)2]2-{L}, [Hg3(o-C6F4)3]2·{L} (L = naphthalene, biphenyl, fluorene) and [Hg3(o-C6F4)3]{Au3(µ-C(OEt)=NC6H4CH3)3}n (n = 1, 2) adducts were studied at the HF, MP2, SCS-MP2, DFT and DFT-D3 levels. The intermolecular interactions among the fragments were analyzed using the levels of calculations proposed. The energy decomposition analysis at the TPSS-D3 level was used to define the dominant components of the interaction. The van der Waals interactions between mercury and arene (Hg-arene) were found to be the main short-range stability contribution in the [Hg(C6F5)2]2-{L} and [Hg3(o-C6F4)3]2·{L} complexes. At the MP2, SCS-MP2 and DFT-D3 levels, equilibrium Hg-C distances are between 360 and 310 pm. The pair-wise energies were found to be between 18.0 and 6.0 kJ mol(-1). In the [Hg3(o-C6F4)3]{Au3(µ-C(OEt)=NC6H4CH3)3}n (n = 1, 2) complexes the metallophilic intermolecular interaction is Hg-Au. Pair-wise energies of 85.7, 39.4, 78.1 and 57.9 kJ mol(-1) were found at the MP2, SCS-MP2, TPSS-D3 and PBE-D3 levels using the [Hg3(o-C6F4)3]{Au3(µ-C(OEt)=NC6H4CH3)3} model. The same trend is maintained for the [Hg3(o-C6F4)3]{Au3(µ-C(OEt)=NC6H4CH3)3}2 model: 73.4, 29.3, 70.6 and 61.3 kJ mol(-1) by MP2, SCS-MP2, TPSS-D3 and PBE-D3, respectively. The absorption spectra of these complexes were calculated using the single excitation time-dependent method at the TPSS-D3 level to validate the models against the experimental data.

Closed-shell d10-d10 mechanochromic [AuPh(CNPh)]n complex: quantum chemistry electronic and optical properties.

The electronic structure, spectroscopic properties, and solid state chemistry of monomer and dimers of [AuPh(CNPh)] complex were studied at post-Hartree-Fock (MP2, SCS-MP2, and CC2) and density functional theory levels. The absorption spectra of these complexes were calculated using single excitation time-dependent (TD) methods at DFT, CC2, and SCS-CC2 levels. The influences of the bulk are accounted for at the PBE-D3 level, incorporating dispersion effects. The calculated values agree with the experimental range, where absorption and emission energies reproduce experimental trends with large Stokes shifts. The aurophilic interaction is identified as a key factor influencing the spectroscopic and structural properties of these complexes. The intermetallic interactions were found as the main factor responsible for MMCT electronic transitions in the models studied.

Theoretical insights into the adsorption of neutral, radical and anionic thiophenols on gold(111).

The interaction of thiol and thiolate containing molecules with gold (S-Au) has gained increasing interest because of its applications in molecular electronic devices and catalysis. In this context, the enhanced conductivity of thiophenol compared to alkanethiol represents an opportunity to develop more sensitive and selective gold-based devices by incorporating molecules with the aryl-thiol moiety into their structures. As has been proposed earlier, the thiol moiety is deprotonated after binding to gold, hence, we present here a comparative study of the S-Au bond strength between several neutral and deprotonated aromatic-sulfur systems in their anionic and radical forms with a detailed description of the nature of this interaction. The study was performed by means of computational chemistry methods, using a cluster of 42 Au atoms as a model of the Au(111) surface that allowed us to provide new chemical insights to control the S-Au interface interaction strength. Our results revealed that the thiophenols-gold interaction is mainly dispersive where the interaction energies range between 31 and 43 kcal mol(-1). The radical and anionic thiophenolates-gold interaction increases due to a strong charge transfer character, depicting interaction energies in the range of 50 to 55 kcal mol(-1) and 62 to 92 kcal mol(-1), respectively. These results suggest that for the anionic thiophenolate the binding strength can be tailored according to the electron-donor capabilities of the ligand which in turn can be finely tuned by several substituents. Our results are of possible impact for the design of new devices.

Computational studies of the metal-binding site of the wild-type and the H46R mutant of the copper, zinc superoxide dismutase.

Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general.

Closed-shell d10-d10 in [AuCl(CNR)] n and [AuCl(CO)] n (n = 1, 2; R = -H, -CH3, -Cy) complexes: quantum chemistry study of their electronic and optical properties.

The electronic structure and spectroscopic properties of [AuCl(CNR)] and [AuCl(CO)] (R = -H, -CH3, -Cy) complexes with d10-d10 type interactions were studied at the post-Hartree-Fock (MP2, SCS-MP2, CCSD(T)) and density functional theory levels. It was found that the nature of the intermetal interactions is consistent with the presence of an electrostatic (dipole-dipole) contribution and a dispersion-type interaction. The absorption spectra of these complexes were calculated using the single excitation time-dependent (TD) method at the DFT and SCS-CC2 levels. The calculated values are in agreement with the experimental range, where the absorption and emission energies reproduce the experimental trends, with large Stokes shifts. According to this, intermetallic interactions were found to be mainly responsible for the metal-metal charge transfer (MMCT) electronic transitions among the models studied.

A computationally efficient and reliable bond order measure.

Bond order indexes are useful measures that connect quantum mechanical results with chemical understanding. One of these measures, the natural bond order index, based on the natural resonance theory procedure and part of the natural bond orbital analysis tools, has been proved to yield reliable results for many systems. The procedure's computational requirements, nevertheless, scales so highly with the number of functions in the basis set and the delocalization of the system, that the calculation of this bond order is limited to small or medium size molecules. We present in this work a bond order index, the first order perturbation theory bond order (fopBO), which is based on and strongly connected to the natural bond orbital analysis tools. We present the methodology for the calculation of the fopBO index and a number of test calculations that shows that it is as reliable as the natural bond orbital index, with the same weak sensitivity to variations among commonly used basis sets and, as opposed to the natural bond order index, suitable for the study of large systems, such as most of those of biological interest.

Exploration of the Activation Mechanism of the Epigenetic Regulator MLL3: A QM/MM Study.

The mixed lineage leukemia 3 or MLL3 is the enzyme in charge of the writing of an epigenetic mark through the methylation of lysine 4 from the N-terminal domain of histone 3 and its deregulation has been related to several cancer lines. An interesting feature of this enzyme comes from its regulation mechanism, which involves its binding to an activating dimer before it can be catalytically functional. Once the trimer is formed, the reaction mechanism proceeds through the deprotonation of the lysine followed by the methyl-transfer reaction. Here we present a detailed exploration of the activation mechanism through a QM/MM approach focusing on both steps of the reaction, aiming to provide new insights into the deprotonation process and the role of the catalytic machinery in the methyl-transfer reaction. Our finding suggests that the source of the activation mechanism comes from conformational restriction mediated by the formation of a network of salt-bridges between MLL3 and one of the activating subunits, which restricts and stabilizes the positioning of several residues relevant for the catalysis. New insights into the deprotonation mechanism of lysine are provided, identifying a valine residue as crucial in the positioning of the water molecule in charge of the process. Finally, a tyrosine residue was found to assist the methyl transfer from SAM to the target lysine.

Electronic and optical properties of [Au(CH3CSS)]4 cluster. A quantum chemistry study.

The uses of the sulfur-gold bond in the design of new molecular clusters have gained increasing attention in recent years. Their size and shape are diverse providing a wide variety of optical and electronic properties. Here we present a computational study of the absorption and emission properties of a small [Au(dithioacetate)]4 cluster as a model for these systems. The electronic structure of the Au4S8 core of this cluster permits rationalization of the source of the optical properties and how these are connected with that specific structural scaffold. Due to the complex nature of the aurophilic intramolecular interactions taking place in this system, several methods were used, such as the MP2, SCS-MP2, PBE-D3, and TPSS-D3 levels; both in gas and solvent phases. The absorption spectra of the cluster were calculated by the single excitation time-dependent-DFT (TD-DFT) method, CC2, SCS-CC2, and ADC(2) levels. The ab initio correlated calculations and previously reported experimental data have been used to assess the performance of our calculations. Moreover, the emission T1-So transition was calculated, where the SCS-CC2 level showed an excellent agreement with the experimental results. The core Au4S8 was identified as mainly responsible for the absorption and emission transitions according to the theoretical model.

Exploration of the Interaction Strength at the Interface of Anionic Chalcogen Anchors and Gold (111)-Based Nanomaterials.

Nowadays, the use of sulfur-based ligands to modify gold-based materials has become a common trend. Here, we present a theoretical exploration of the modulation of the chalcogenides-gold interaction strength, using sulfur, selenium, and tellurium as anchor atoms. To characterize the chalcogenide-gold interaction, we designed a nanocluster of 42 gold atoms (Au42) to model a gold surface (111) and a series of 60 functionalized phenyl-chalcogenolate ligands to determine the ability of electron-donor and -withdrawing groups to modulate the interaction. The analysis of the interaction was performed by using energy decomposition analysis (EDA), non-covalent interactions index (NCI), and natural population analysis (NPA) to describe the charge transfer processes and to determine data correlation analyses. The results revealed that the magnitudes of the interaction energies increase following the order S < Se < Te, where this interaction strength can be augmented by electron-donor groups, under the donor-acceptor character the chalcogen-gold interaction. We also found that the functionalization in meta position leads to better control of the interaction strength than the ortho substitution due to the steric and inductive effects involved when functionalized in this position.

Theoretical exploration of the forces governing the interaction between gold-phthalocyanine and gold surface clusters.

Here we aim to explore the nature of the forces governing the adsorption of gold-phthalocyanine on gold substrates. For this, we designed computational models of metal-free phthalocyanine and gold-phthalocyanine deposited over a gold metallic surface represented by cluster models of different sizes and geometries. Thereby, we were able to determine the role of the metal center and of the size of the substrate in the interaction process. For this purpose, we worked within the framework provided by density functional theory, were the inclusion of the semi-empirical correction of the dispersion forces of Grimme's group was indispensable. It has been shown that the interaction between molecules and surfaces is ruled by van der Waals attractive forces, which determine the stabilization of the studied systems and their geometric properties. Their contribution was characterized by energy decomposition analysis and through the visualization of the dispersion interactions by means of the NCI methodology. Moreover, calculations of Density of States (DOS) showed that the molecule-surface system displays a metal-organic interface evidenced by changes in their electronic structure, in agreement with a charge transfer process found to take place between the interacting parts.

Further understanding of the Ru-centered [2+2] cycloreversion/cycloaddition involved into the interconversion of ruthenacyclobutane using the Grubbs catalysts from a reaction force analysis.

The chemical reactivity of the first- and second-generation Grubbs catalysts has always been a significant issue in olefin metathesis. In the present work, we study the [2+2] cycloreversion/cycloaddition and the alkylidene rotation involved into the interconversion of the ruthenacyclobutane intermediate, through the reaction force and reaction force constant analysis. It has been found that the structural contribution controls the barrier energy in the interconversion of ruthenacyclobutane via [2+2] cycloreversion/cycloaddition, which is slightly lower in the second generation of Grubbs catalysts while its electronic contribution is slightly higher, which unveils a major rigidity and donor/acceptor properties of the NHC. This finding explains a greater structural contribution in the rate constant. Moreover, on the basis of the reaction force constant, the process can be classified as "two-stage"-concerted reactions, noting a more asynchronous process when the first generation is used as a catalyst.Finally, a similar analysis into the alkylidene rotation was performed. It was determined that [2+2] cycloreversion and alkylidene rotations take place in a sequential manner, the energy barrier is again controlled by structural reorganization, and the pathway is less asynchronous.

Complexation of morin with three kinds of cyclodextrin. A thermodynamic and reactivity study.

Properties of inclusion complexes between morin (M) and beta-cyclodextrin (betaCD), 2-hydroxypropyl-beta-cyclodextrin (HPbetaCD) and Heptakis (2,6-O-di methyl) beta-cyclodextrin (DMbetaCD) such as aqueous solubility and the association constants of this complex have been determined. The water solubility of morin was increased by inclusion with cyclodextrins. The phase-solubility diagrams drawn from UV spectral measurements are of the A(L)-type. Also ORAC(FL) studies were done. An increase in the antioxidant reactivity is observed when morin form inclusion complex with the three cyclodextrin studied. Finally, thermodynamics studies of cyclodextrin complexes indicated that for DMbetaCD the inclusion is primarily enthalpy-driven process meanwhile betaCD and HPbetaCD are entropy-driven processes. This is corroborated by the different inclusion geometries obtained by 2D-NMR.

Improvement of photovoltaic performance by substituent effect of donor and acceptor structure of TPA-based dye-sensitized solar cells.

We report a computational study of a series of organic dyes built with triphenylamine (TPA) as an electron donor group. We designed a set of six dyes called (TPA-n, where n = 0-5). In order to enhance the electron-injection process, the electron-donor effect of some specific substituent was studied. Thus, we gave insights into the rational design of organic TPA-based chromophores for use in dye-sensitized solar cells (DSSCs). In addition, we report the HOMO, LUMO, the calculated excited state oxidized potential E(dye*)(eV) and the free energy change for electron-injection ΔGinject(eV), and the UV-visible absorption bands for TPA-n dyes by a time-dependent density functional theory (TDDFT) procedure at the B3LYP and CAM-B3LYP levels with solvent effect. The results demonstrate that the introduction of the electron-acceptor groups produces an intramolecular charge transfer showing a shift of the absorption wavelengths of TPA-n under studies. Graphical Abstract Several organic dyes TPA-n with different donors and acceptors are modeled. A strong conjugation acrros the donor and anchoring groips (TPA-n) bas been studied. Candidate TPA-3 shows a promising results.

Interfacial properties of poly(maleic acid-alt-1-alkene) disodium salts at water/hydrocarbon interfaces.

The interfacial properties of poly(maleic acid-alt-1-alkene) disodium salts at hydrocarbon/water interfaces are determined. In all the studied systems, the interfacial tension decreases markedly with the polyelectrolyte concentration as the side-chain length increases. The results of the standard free energy of adsorption, DeltaG(ads)(0), are a linear function of the number of carbon atoms in the polyelectrolyte side chain. The contribution to DeltaG(ads)(0) per mol of methylene group varies from -0.64 to -0.52 kJ/mol for the n-octane/water to n-dodecane/water interfaces. DeltaG(ads)(0) data also reveal that the adsorption process is mainly determined by adsorption efficiency. Comparatively, the adsorption effectiveness seems to play a less important role. The theoretical interaction energies calculated for the insertion of one hydrocarbon molecule into the space formed by two neighboring polyelectrolyte side chains are in good agreement with the experimental results. The latter results are consistent with van der Waals-type interactions between the hydrocarbon molecules and the polyelectrolyte side chains.