Proposed alteration of images of molecular orbitals obtained using a scanning tunnelling microscope as a probe of electron correlation

Scanning tunneling spectroscopy (STS) allows to image single molecules decoupled from the supporting substrate. The obtained images are routinely interpreted as the square moduli of molecular orbitals, dressed by the mean-field electron-electron interaction. Here we demonstrate that the effect of electron correlation beyond mean field qualitatively alters the uncorrelated STS images. Our evidence is based on the ab-initio many-body calculation of STS images of planar molecules with metal centers. We find that many-body correlations alter significantly the image spectral weight close to the metal center of the molecules. This change is large enough to be accessed experimentally, surviving to molecule-substrate interactions.Comment: 27 pages including Supplemental Information. To appear in Physical Review Letter

On the selection and design of proteins and peptide derivatives for the production of photoluminescent, red-emitting gold quantum clusters

Novel pathways of the synthesis of photoluminescent gold quantum clusters (AuQCs) using biomolecules as reactants provide biocompatible products for biological imaging techniques. In order to rationalize the rules for the preparation of red-emitting AuQCs in aqueous phase using proteins or peptides, the role of different organic structural units was investigated. Three systems were studied: proteins, peptides, and amino acid mixtures, respectively. We have found that cysteine and tyrosine are indispensable residues. The SH/S-S ratio in a single molecule is not a critical factor in the synthesis, but on the other hand, the stoichiometry of cysteine residues and the gold precursor is crucial. These observations indicate the importance of proper chemical behavior of all species in a wide size range extending from the atomic distances (in the AuI-S semi ring) to nanometer distances covering the larger sizes of proteins assuring the hierarchical structure of the whole self-assembled system

Visualizing electron correlation by means of ab-initio scanning tunneling spectroscopy images of single molecules

Scanning tunneling microscopy (STM) has been a fundamental tool to characterize many-body effects in condensed matter systems, from extended solids to quantum dots. STM of molecules decoupled from the supporting conductive substrate has the potential to extend STM characterization of many body effects to the molecular world as well. In this article, we describe a many-body tunneling theory for molecules decoupled from the STM substrate, and we report on the use of standard quantum chemical methods to calculate the quantities necessary to provide the 'correlated' STM molecular image. The developed approach has been applied to eighteen different molecules, to explore the effects of their chemical nature and of their substituents, as well as to verify the possible contribution by transition metal centers. Whereas the bulk of calculations have been performed with CISD because of the computational cost, some tests have been also performed with the more accurate CCSD method to quantify the importance of the computational level on many-body STM images. We have found that correlation induces a remarkable squeezing of the images, and that correlated images are not derived from Hartree-Fock HOMO or LUMO alone, but include contributions from other orbitals as well. Although correlation effects are too small to be resolved by present STM experiments for the studied molecules, our results provide hints for seeking out other species with larger, and possibly experimentally detectable, correlation effects.Comment: Main text + Supplemental materia

Computational screening of metalloporphyrin catalysts for the activation of carbon dioxide

Electrocatalytic CO2 reduction (eCO2R) to value-added chemicals offers a promising route for carbon capture and utilization. Metalloporphyrin (M-POR) is a class of catalysts for eCO2R that has drawn attention due to its tuneable electronic and structural properties. This work presents a computational screening, based on density functional theory calculations, of one of the key steps in the eCO2R: the adsorption of CO2 on 110 M-PORs with varying peripheral ligands, metal centres, and oxidation states, to understand how these factors can influence CO2 activation. A set of criteria was used to shortlist M-PORs based on their ability to lengthen the C–O bond, bend the O–C–O angle, bind CO2, and donate charge from the metal of the M-POR to the carbon of CO2. 16 systems were selected for their potential to activate CO2. These systems predominantly have the electron configuration of the metal centre in the d[6] and d[7] configurations. Natural bond orbital analysis revealed the impact of electron-withdrawing groups in the system, which increases orbital splitting and, consequently, lowers the ability of the M-POR to activate CO2. Second-order perturbation theory analysis confirms that the presence of electron-donating groups in the ligand structure enhances CO2 activation. This work demonstrates the interconnected effect of peripheral ligands, metal centres, and oxidation states in M-PORs on their ability to adsorb and activate CO2, thereby establishing structure-activity relationships within M-PORs

Computational screening of metalloporphyrin catalysts for the activation of carbon dioxide

Electrocatalytic CO2 reduction (eCO2R) to value-added chemicals offers a promising route for carbon capture and utilization. Metalloporphyrin (M-POR) is a class of catalysts for eCO2R that has drawn attention due to its tuneable electronic and structural properties. This work presents a computational screening, based on density functional theory calculations, of one of the key steps in the eCO2R: the adsorption of CO2 on 110 M-PORs with varying peripheral ligands, metal centres, and oxidation states, to understand how these factors can influence CO2 activation. A set of criteria was used to shortlist M-PORs based on their ability to lengthen the C–O bond, bend the O–C–O angle, bind CO2, and donate charge from the metal of the M-POR to the carbon of CO2. 16 systems were selected for their potential to activate CO2. These systems predominantly have the electron configuration of the metal centre in the d[6] and d[7] configurations. Natural bond orbital analysis revealed the impact of electron-withdrawing groups in the system, which increases orbital splitting and, consequently, lowers the ability of the M-POR to activate CO2. Second-order perturbation theory analysis confirms that the presence of electron-donating groups in the ligand structure enhances CO2 activation. This work demonstrates the interconnected effect of peripheral ligands, metal centres, and oxidation states in M-PORs on their ability to adsorb and activate CO2, thereby establishing structure-activity relationships within M-PORs

Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions

We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl- and SO42-. Simulations were conducted using different density functional theory methods (PBE, BLYP and revPBE), with and without the inclusion of dispersion interactions (-D3). Analysis of the ion-water structure and interaction strength, water exchange between the first and second hydration shell, and hydrogen bond network and low-frequency reorientation dynamics around the metal ions have been used to characterise the influence of solution composition on the ionic solvation shell. Counterions affect the properties of the hydration shell not only when they are directly coordinated to the metal ion, but also when they are at the second coordination shell. Chloride ions reduce the sodium hydration shell and expand the calcium hydration shell by stabilizing under-coordinated hydrated Na(H2O)5+ complexes and over-coordinated Ca(H2O)72+. The same behaviour is observed in CaSO4(aq), where Ca2+ and SO42- form almost exclusively solvent-shared ion pairs. Water exchange between the first and second hydration shell around Ca2+ in CaSO4(aq) is drastically decelerated compared with the simulations of the hydrated metal ion (single Ca2+, no counterions). Velocity autocorrelation function analysis, used to probe the strength of the local ion-water interaction, shows a smoother decay of Mg2+ in MgCl2(aq), which is a clear indication of a looser inter-hexahedral vibration in the presence of chloride ions located in the second coordination shell of Mg2+. The hydrogen bond statistics and orientational dynamics in the ionic solvation shell show that the influence on the water-water network cannot only be ascribed to the specific cation-water interaction, but also to the subtle interplay between the level of hydration of the ions, and the interactions between ions, especially those of opposite charge. As many reactive processes involving solvated metal ions occur in environments that are far from pure water but rich in ions, this computational study shows how the solution composition can result in significant differences in behaviour and function of the ionic solvation shell

Crystallisation route map

A route map for the assessment of crystallisation processes is presented. A theoretical background on solubility, meta-stable zone width, nucleation and crystal growth kinetics is presented with practical examples. The concepts of crystallisation hydrodynamics and the application of population balances and computational fluid dynamics for modelling crystallisation processes and their scaling up are also covered

Conformational and structural stability of the single molecule and hydrogen bonded clusters of para aminobenzoic acid in the gas and solution phases

The crystallographic structures of the α- and β- polymorphic forms of para aminobenzoic acid are deconstructed into their constituent hydrogen bonding molecular structural building blocks of monomers, dimers, tetramers and octamers, where they are analysed using ab initio quantum mechanical calculations of their conformation and cluster stability in solution. The molecular conformation found in the β-form is less stable than the same found in the α-form for both the gas and solution phases, suggesting that this causes a slight increase in the barrier to the crystallisation of the β-form in comparison to the α-form. The solution populations of the self-associated OH⋯O H-bonding ‘classic carboxylic acid dimer’, present in the α- and not the β-structure, is calculated to dominate in acetonitrile, dimethyl sulfoxide, ethanol, ethyl acetate, methanol, nitromethane and water. It is observed that this classic dimer is least stable in water, compared to the other PABA crystallisation solvents, with the OH⋯N H-bonding interaction present in the β-form being the second most stable dimeric interaction. These results are discussed in terms of the crystallisability and polymorphic behaviour of the α and β forms of PABA from the afore mentioned crystallisation solvents, whilst detailing how this approach could be reproducible for a range of polymorphic crystalline materials

Investigation of the chlorine dioxide disinfection in terms of disinfection by product (DBP) formation of Omerli raw water in Istanbul

Chlorine which is nowadays the most commonly used disinfectant, interacts aquatic organic matter and causes formation of harmful disinfection by products. For this reason, number of researches on chlorine dioxide as a disinfectant alternative to chlorine, increased in recent years. After disinfection via the chlorine dioxide, chlorite and chlorate which defines as inorganic by products are formed. Chlorite total maximum concentration in water is limited as 1 mg/L as by USEPA. WHO limits total maximum chlorite concentration as 0.7 mg/L in water. There is no detailed study has been conducted for determination of the limit value yet in our country. In this study; after 0.25; 0.50; 0.75; 1; 1.25 and 1.5 mg/L chlorine dioxide had been dosed to Omerli raw water samples taken in December, and February; disinfection by products: chlorite, chlorate, THMs, HAAs and water quality parameters such as TOC, chloride, floride, bromide, sulphate and nitrate were analyzed and effect of the pH and contact time also investigated

Desorption of rare earth elements (REEs) from schwertmannite under acid mine drainage (AMD) and AMD-seawater conditions

Schwertmannite as a sink for rare earth elements (REEs) in environments affected by acid mine drainage (AMD) plays a significant role in the fate of these elements. The conditions to precipitate schwertmannite (i.e., sulfate-rich water and pH between 2.5 and 3.5) are not suitable for this Fe-oxyhydroxysulfate (Fe8O8(OH)6SO4) to adsorb REEs. In estuaries where AMD-impacted rivers meet (e.g. the Odiel and the Tinto rivers in the Ría de Huelva estuary in SW Spain), AMD mixes with seawater raising the pH between 4.5 and 8, thereby enabling REE adsorption on schwertmannite at circumneutral pH. However, the estuarine tidal dynamics exposes REE-enriched schwertmannite to more acidic water, inducing REE desorption, which has yet to be studied. In the present work, batch experiments were performed to study the REE desorption from a REE-enriched schwertmannite within the pH range 4.5–7 in the presence of sulfate at room temperature. Solution-chemistry data were used to obtain the REE desorption surface constants from different surface complexation. Desorption of a Lu-enriched schwertmannite at different pH was investigated with High Energy X-Ray Diffraction (HEXD) and Extended X-ray Adsorption Fine Structure (EXAFS) to characterize the changes in the surface complexes during desorption. The results indicate that (1) REEs desorb from schwertmannite at pH < 6 and desorption is pH dependent, (2) desorption of light REEs is higher than that of heavy REEs, (3) REE sorption onto schwertmannite surface is not a totally reversible reaction, and that (4) both monodentate and bidentate surface complexes are involved in the Lu-desorption reaction. These observations indicate that (1) REE-enriched schwertmannite remains stable in the areas of the estuary nearer the sea and that (2) tidal fluctuations displace schwertmannite colloids towards areas that are more affected by AMD, inducing REE desorption from schwertmannite