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

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

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

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

Morphological population balance modelling of the effect of crystallisation environment on the evolution of crystal size and shape of para-aminobenzoic acid

A current morphological population balance (MPB) modelling methodology, which integrates crystal morphology, facet growth kinetics with multi-dimensional population balance, is overviewed and demonstrated, hence providing an attractive approach for modelling crystallisation processes. MPB modelling is applied to simulate the batch crystallisation of the alpha-form of para-aminobenzoic acid from ethanolic solutions as a function of the crystallisation environment including cooling rate, seeding temperature and seed conditions (loading, size and shape). The evolution of crystal shape/size and their distributions revealed that higher loading led to smaller and less needle-like crystals with similar yields, hence potentially being an important parameter for process control. Examination of the development of the fracture surface for broken seeds, mimicking the seed conditions after milling in practice in the simulated processes, demonstrated that these faces grew fast and then rapidly disappeared from the external crystal morphology. Restriction and challenges inherent in the current model are also highlighted

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

The thermal expansion coefficients of the alpha and beta polymorphic forms of p-aminobenzoic acid in relation to their bulk crystal chemistry

The thermal expansion behaviour of the alpha and beta polymorphs of para-aminobenzoic acid are presented and discussed in terms of the bulk crystal chemistry and the associated strengths of the constituent intermolecular synthons for these two materials. Analysis of temperature dependant powder diffraction data over the temperature range 298.15–403.15 K facilitates calculation of the linear thermal expansion coefficients: αa = 8.36 × 10−06 K−1, αb = 94.5 × 10−06 K−1 and αc = 9.91 × 10−06 K−1 for the alpha polymorph and αa = 21.5 × 10−06 K−1, αb = 48.5 × 10−06 K−1 and αc = 2.22 × 10−06 K−1 for the beta polymorph. The exceptionally large increase in the thermal expansion of the b axis for the alpha form reflects the weak dispersive interactions which propagate along this axis. In contrast, the a and c axes contain relatively strong hydrogen bonds which stabilise the lattice and limit thermal expansion. The thermal expansion of the beta form reflects the more isotropic nature of the intermolecular synthons for this polymorph in comparison to the alpha form. The thermal expansion of the b axis of the beta form is larger than that of the a and c axes but to a much lesser extent than that observed for the alpha form. This is rationalised through identification of a hydrogen bonding component which contributes to the stabilisation of the b axis in comparison to the almost fully dispersive nature found in the alpha structure

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

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed