Theoretical Chemistry

In this paper, we associate an applicability domain (AD) of QSAR/QSPR models with the area in the input (descriptor) space in which the density of training data points exceeds a certain threshold. It could be proved that the predictive performance of the models (built on the training set) is larger for the test compounds inside the high density area, than for those outside this area. Instead of searching a decision surface separating high and low density areas in the input space, the one-class classification 1-SVM approach looks for a hyperplane in the associated feature space. Unlike other reported in the literature AD definitions, this approach: (i) is purely “data-based”, i.e. it assigns the same AD to all models built on the same training set, (ii) provides results that depend only on the initial descriptors pool generated for the training set, (iii) can be used for the huge number of descriptors, as well as in the framework of structured kernel-based approaches, e.g., chemical graph kernels. The developed approach has been applied to improve the performance of QSPR models for stability constants of the complexes of organic ligands with alkaline-earth metals in water.

Here, chemoinformatics is considered as a theoretical chemistry discipline complementary to quantum chemistry and force-field molecular modeling. These three fields are compared with respect to molecular representation, inference mechanisms, basic concepts and application areas. A chemical space, a fundamental concept of chemoinformatics, is considered with respect to complex relations between chemical objects (graphs or descriptor vectors). Statistical Learning Theory, one of the main mathematical approaches in structure-property modeling, is briefly reviewed. Links between chemoinformatics and its “sister” fields – machine learning, chemometrics and bioinformatics are discussed.

We have analyzed the effect of external electric field on the aziridinium ion intermediate of mustine drug molecule using conceptual density functional theory based reactivity descriptors. The aziridinium ion intermediate is formed during the alkylation of DNA by mustine, a member of the nitrogen mustard family. This species experiences a field exerted by polarity of the solvent and metal ions present in body fluids (in extra- and intra-cellular fluids, blood etc.). The stability and reactivity of the aziridinium ion is monitored by studying some density based reactivity descriptors in the presence of external electric fields. Further, shifting of the reactive center (i.e., the LUMO) of the drug intermediate with variation in the electric field was observed. In addition, the maximum hardness and minimum electrophilicity principles were analyzed.► In this article, effect of external electric field on a drug intermediate is studied. ► Variation of shape of LUMO and DFT based reactivity descriptors in presence of external electric fields are observed. ► Further, the maximum hardness and minimum electrophilicity principles are analyzed.

Platinum-based heterogeneous catalysts are critical to many important commercial chemical processes, but their efficiency is extremely low on a per metal atom basis, because only the surface active-site atoms are used. Catalysts with single-atom dispersions are thus highly desirable to maximize atom efficiency, but making them is challenging. Here we report the synthesis of a single-atom catalyst that consists of only isolated single Pt atoms anchored to the surfaces of iron oxide nanocrystallites. This single-atom catalyst has extremely high atom efficiency and shows excellent stability and high activity for both CO oxidation and preferential oxidation of CO in H2. Density functional theory calculations show that the high catalytic activity correlates with the partially vacant 5d orbitals of the positively charged, high-valent Pt atoms, which help to reduce both the CO adsorption energy and the activation barriers for CO oxidation.

Il segno del chimico è il testo di una lettura scenica costruita con brani di Primo Levi, realizzata per incarico del Centro Internazionale di Studi Primo Levi e del Teatro Stabile di Torino. Lo spettacolo è stato allestito nel luglio 2010, per la regia e l’interpretazione di Valter MALOSTI, in occasione del convegno internazionale ESOF, EuroScience Open Forum. Nel novembre 2011 è stato portato in scena a New York da John Turturro.

In the present account we investigate a theoretical link between bond length, electron sharing, and bond energy within the context of quantum chemical topology theories. The aromatic stabilization energy, ASE, was estimated from this theoretical link without using isodesmic reactions for the first time. The ASE values obtained from our method show a meaningful correlation with the number of electrons contributing in the aromaticity. This theoretical link demonstrates that structural, electronic, and energetic criteria of aromaticity –ground-state aromaticity– belong to the same class and guarantees that they assess the same property as aromaticity. Theory suggests that interatomic exchange-correlation potential, obtained from the theory of Interacting Quantum Atoms (IQA), is linearly connected to the delocalization index of Quantum Theory of Atoms in Molecules (QTAIM) and bond length through a first order approximation. Our study shows that the relationship between energy-structure-electron sharing marginally deviates from the ideal linear form expected from the first order approximation. The observed deviation from linearity was attributed to a different contribution of exchange-correlation into the bond energy for the σ- and π-frameworks. Finally, we proposed two-dimensional energy-structure-based aromaticity indices in analogy to the electron sharing indices of aromaticity.

The electronic spectrum of alizarin (AZ) in methanol solution was measured and used as reference data for color prediction. The visible part of the spectrum was modelled by different DFT functionals within the TD-DFT framework. The results of a broad range of functionals applied for theoretical spectrum prediction were compared against experimental data by a direct color comparison. The tristimulus model of color expressed in terms of CIE XYZ and CIE Lab parameters was applied both to experimental and predicted spectra. It was found that the HSE03 method along with the 6-31G(d,p) basis set provides the most accurate color prediction, much better than other commonly used functionals such as B3LYP, CAM-B3LYP or PBE0. Besides, the influence of potential errors, introduced by theoretical predictions on color estimation, was examined for different wavelengths. The obtained results showed that color prediction is significantly dependent on the type of basis set and functional applied. The proposed methodology provides a simple, straightforward and more reliable way of theoretical protocols validation than just a comparison of experimental and estimated values of maximum absorbance wavelength.

The work Anatomia Magna is a research work and books research created by JoanCarles Testagorda Garcia. I explain the relation of the weather  state of mind functions of the hair, thermogenesis, production of climate, mathematical union humidity, quantum physics, neurotransmitters, electricity etc.

Quantum chemical calculations using density functional theory and correlated ab initio methods of the 10 p-electron systems (N 6 H 6) 2 + and C 2 N 4 H 6 show that the planar forms are no minima on the potential energy surfaces. The twisted ring structures of the two species are energy minima, but acyclic isomers are much lower in energy. The planar geometries sustain strong diamagnetic ring current comparable with that of benzene. In contrast, the calculated multicenter normalized Giambiagi electron delocalization index I NG suggests that p-delocalization in planar (N 6 H 6) 2 + and C 2 N 4 H 6 is much weaker than in benzene. Since aromaticity is synonymous for a particular stability of cyclic delocalized systems, it may be stated that calculation or measurement of magnetic chemical shifts due to induced ring currents is not a reliable method to ascertain the aromatic character of a molecule. Aromatic compounds exhibit ring current induced magnetic shielding, but the reverse conclusion that ring current induced magnetic shielding identifies aroma-ticity is not justified. Furthermore, the 4n + 2 rule as indicator of aromatic stabilization should only be used in conjunction with the ring size; the nature of the occupied p orbitals must always be examined.

In physics, as a branch of science that studies energy and matter, the central problem has always been the question of the mechanisms of energy interactions and the formation of material structures. There is a growing consensus that this may be the same mechanism as matter is a form of energy. But from this point, the disagreements start. Thus, the unified model of fundamental interactions (‘theory of everything’) remains out of reach.

The two currently leading theories, the Standard Model of elementary particle physics and the General Theory of Relativity, separately cover only part of the interactions. Moreover, they are incompatible since they proceed from hypotheses about different mechanisms. However, as they are considered impeccable dogmas that are both right, generations of physicists tried to unify them without any success. The thought that they may be both wrong is alien to the current mainstream of theoretical physics.

The author of the book breaks this taboo. He shows the fallacy of both models and suggests that trying to unify them is a meaningless pursuit. But criticism alone is not enough, and we need to find a way out. Instead of unifying old theories, we can build a new theory that unifies physical phenomena. In the first volume of the “Symphony of Matter and Mind” series, the author begins to develop a model of a universal mechanism operating at all levels of matter and in all types of energy interactions, thus indicating a way out of the impasse of theoretical physics.

This paper is focused on modern approaches to machine learning, most of which are as yet used infrequently or not at all in chemoinformatics. Machine learning methods are characterized in terms of the “modes of statistical inference” and “modeling levels” nomenclature and by considering different facets of the modeling with respect to input/ouput matching, data types, models duality, and models inference. Particular attention is paid to new approaches and concepts that may provide efficient solutions of common problems in chemoinformatics: improvement of predictive performance of structure–property (activity) models, generation of structures possessing desirable properties, model applicability domain, modeling of properties with functional endpoints (e.g., phase diagrams and dose–response curves), and accounting for multiple molecular species (e.g., conformers or tautomers).

This document is a Persian translation of the following papers:
PCCP 2010, 12, 12630
PCCP, 2011, 13, 4576
PCCP, 2011, 13, 12655
JCC, 2011, 32, 2422
JPC A, 2011, 115, 12708

For more information also see:
JPC A, 2011, 115, 12555
JCTC, 2013, 9, 4789

Interatomic magnetizability provides insight into the
extent of electronic current density between two adjacent atomic
basins. By studying a number of well-known aromatic, nonaromatic,
and antiaromatic molecules, it is demonstrated that interatomic
magnetizability (bond magnetizability) not only is able to verify the
exact nature of aromaticity/antiaromaticity among different molecules,
but also can distinguish the correct aromaticity order among
sets of aromatic/antiaromatic molecules. The interatomic magnetizability
is a direct measure of the current flux between two adjacent
atomic basins and is the first QTAIM-derived index that evaluates
aromaticity based on a response property, that is, magnetizability. Bond magnetizability is easy to compute, straightforward to
interpret, and can be employed to evaluate the pure π- or σ-orbital contributions to magnetic aromaticity.

Developing a comprehensive method to compute bond orders is a problem that has eluded chemists since Lewis's pioneering work on chemical bonding a century ago. Here, a computationally efficient method solving this problem is introduced and demonstrated for diverse materials including elements from each chemical group and period. The method is applied to non-magnetic, collinear magnetic, and non-collinear magnetic materials with localized or delocalized bonding electrons. Examples studied include the stretched O 2 molecule, 26 diatomic molecules, 3d and 5d transition metal solids, periodic materials with 1 to 8748 atoms per unit cell, a biomolecule, a hypercoordinate molecule, an electron deficient molecule, hydrogen bound systems, transition states, Lewis acid–base complexes, aromatic compounds, magnetic systems, ionic materials, dispersion bound systems, nanostructures, and other materials. From near-zero to high-order bonds were studied. Both the bond orders and the sum of bond orders for each atom are accurate across various bonding types: metallic, covalent, polar-covalent, ionic, aromatic, dative, hypercoordinate, electron deficient multi-centered, agostic, and hydrogen bonding. The method yields similar results for correlated wavefunction and density functional theory inputs and for different S Z values of a spin multiplet. The method requires only the electron and spin magnetization density distributions as input and has a computational cost scaling linearly with increasing number of atoms in the unit cell. No prior approach is as general. The method does not apply to electrides, highly time-dependent states, some extremely high-energy excited states, and nuclear reactions.

The influence of electron density on the magnitude of non-nuclear magnetic shielding, NICS, is
studied in detail by scanning the electron density vs. NICSzz (the out-of-plane component of
NICS). This study sheds new light on the role of electron density on the magnitude of NICS.
Scanning the electron density vs. NICSzz not only helps to discriminate the electronic ring
currents operative in aromatic, nonaromatic and antiaromatic species, but also yields a measure
to compare the strength of diatropic/paratropic currents in molecules with different ring sizes or
different number of p electrons without relying on the methods of sigma–pi separation.

The potential enzyme evaluation of the acidophilic, chemolitotrophic and heterotrophic bacteria specific to the mining biotope is of high interest in the solubilization, recovery and / or removal of platinum metals from industrial waste car tires. The obtained data show that the formation of extracellular polymeric substances plays an important role in the attachment of the chemolithotrophic bacteria on the surface of minerals, as well as sulphur. In this sense, a direct interaction between the bacterial cells and the solid surface is mandatory for an efficient mobilization of platinum metals from waste car tires. These occur at two levels: (a) physical sorption due to electrostatic forces with low pH in the leaching media; (b) chemical sorption is carried out only in the type of chemical bonds between the bacterial cell disulphide bond and minerals. The optimization of the technological process such as solubilization and the recovery of platinum metal ions contained in ferrous and non-ferrous industrial waste was materialized through a series of laboratory experiments based mainly on the affinity of bacterial cells for certain organic and / or inorganic surfaces. It is based on the results of the physical-chemical characterization of the liquid samples taken. This study deals with the optimization of the solubilization process of metal ions contained in such samples.

This research was funded by, and implemented within, a UK national research organisation, while the author was the KE and Impact Evaluation Manager responsible for assessing impact on a £15m UK government-funded research programme.

This work was also submitted as the authors MBA dissertation which was accepted and awarded in 2009.

ABSTRACT: A methodology and methods ‘toolbox’ is proposed for conducting impact research and assessment from within research programmes. The emphasis is upon how to clarify and assess the wider impacts from the early stages onwards.

The approach explicitly acknowledges, and attempts to address, the known issues and challenges of impact assessment while drawing upon the resources and opportunities available to research managers and researchers within such programmes.

The study has two triangulating foundations. Firstly, it examines the academic literature to help identify and design the pilot methodology and methods. Secondly it trials these in a real programme to both test and improve them.

The study was conducted over one year within one leading UK research organisation, where two research programmes (and around 60 research projects of £15m total value) were being assessed for their impacts. The study draws upon actual impact management experience and reflection, prospective (ex ante) and retrospective (ex post) assessments, participatory contributions from leading researchers undergoing assessment, and consultation with external users. The findings of this study outline the pilot and its first iteration. Recommendations are made for improvement to the methodology and methods.

A subsequent follow-on bid to UK government incorporating the impacts identified from implementing this methodology, successfully led to a further £15m of government funding.

It is expected the pilot methodology and methods will be applicable to other organisations, conducting and funding such research programmes, required to research and assess the wider research impacts.

Although primary focus of implemetation trials was upon research in physical sciences, technology, high-tech engineering, computing/IT, and environment, the wider literature study, the methodology design and justification, the methods proposed and used, and the resulting general recommendations and lessons are expected to apply more broadly to many other research areas, where the impact is to be found more widely in the society, economy, government or public sector or within organizations, policies, professions or the public.

Interest in this work is expected from research programme managers, impact managers and assessors, management consultants advising in this area, and government funding managers, all seeking to embed a developing approach to understand, capture, and enhance wider impact.

Evaluarea potentialului enzimatic al bacteriilor acidofile, chemolitotrofe si heterotrofe, specifice biotopului minier este de mare interes in solubilizarea, recuperarea si/sau indepartarea metalelor platinice din deseuri industriale auto uzate. Datele obtinute au evidentiat faptul ca formarea substantelor polimerice extracelulare joaca un rol important in atasarea bacteriilor chemolitotrofe pe suprafata mineralelor, precum si de sulf. In acest sens, interactiunea directa intre celula bacteriana si suprafata solida este obligatorie pentru o mobilizare eficienta a metalelor platinice din deseuri auto uzate. Acestea au loc la doua niveluri: (a) sorbtia fizica din cauza fortelor electrostatice datorita pH-ului scazut din mediile de lesiere; (b) sorbtia chimica in care se realizeaza numai legaturi chimice de tip legaturi bisulfide intre celula bacteriana si minerale. Activitatea de optimizare a procesului tehnologic de solubilizare si recuperare a ionilor metalici platimici continuti in deseuri industriale feroase si neferoase s-a concretizat printr-o serie de experimente de laborator care se bazeaza in principal pe afinitatea unor celule bacteriene pentru anumite suprafete de natura organica si/sau anorganica. Pe baza rezultatelor caracterizarii fizico-chmice a probelor lichide prelevate s-a considerat important studiul de fata privind optimizarea procesului de solubilizare a ionilor metalici continuti in acestea. Cercetarile in domeniul ecologiei microbiene a mediilor extreme de acide s-au intensificat in ultimii ani pe linia cercetarilor fundamentale cat si applicative. Datele din literature de specialitate reflecta faptul ca rolul bacteriilor chemolitotrofe, cat si a celor heterotrofe, este si continua sa fie de mare interes practic pentru procesele de solubilizare a metalelor sau de sorbtie a acestora din efluenti lichizi. Metodele de mobilizare bacteriana a metalelor platinice sunt urmatoarele: (1) includerea in materiale inerte de natura organica si anorganica; (2) absorbtia pe un material solid; (3) mobilizarea prin legaturi de afinitate intre molecule biologice; (4) mobilizarea metalelor platinice si celulelor prin legaturi covalente sau coordinative cu alte materiale decat cele inerte. Rezumatul reprezinta o contributie la cercetarea si dezvoltarea proceselor tehnologice bazate pe activitatea bacteriilor chemolitotrofe acidofile cu aplicatii eficiente in bioremedierea mediilor poluate cu substante anorganice reziduale cat si pentru recuperarea unor cantitati de ioni metalici.

A series of 2-hydroxy-5-bromo-4-methoxy-N-(substituted phenyl) chalconeimine was synthesized, characterized and tested for their antimicrobial activity. These new derivative was achieved by treating 2-hydroxy-5-bromo-4-methoxy chalcone with substituted aniline at reflux temperature using ethanol as solvent in presence of H2SO4. Structures of the synthesized compounds were characterized using IR, 1H-NMR and mass spectroscopy. The synthesized compounds were screened for their in vitro antibacterial activity against bacteria S. aureus, E. coli, P. aeruginosa and S. Pyogenes. And antifungal activity against C. Albicans and A.Clavatus some of these compounds exhibited moderate to good activity.