Letteratura scientifica selezionata sul tema "Sigma-Hole interactions"

S-Nitrosothiols, ubiquitous biological derivatives of nitric oxide, can engage in σ-hole/bonding with Lewis bases, which, in combination with hydrogen bonding with Lewis acids, could be the basis of enzymatic control of S-nitrosothiol reactions.

Intermolecular bonding attraction at π-bonded centers is often described as “electrostatically driven” and given quasi-classical rationalization in terms of a “pi hole” depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO−, CN−) with simple atomic anions (H−, F−) or with one another. Such “anti-electrostatic” anion–anion attractions are shown to lead to robust metastable binding wells (ranging up to 20–30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi–Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that “deletion” of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi–Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency (“charge transfer”) rather than envisioned Coulombic properties of unperturbed monomers.

We employ a variety of natural bond orbital (NBO) and natural resonance theory (NRT) tools to comprehensively investigate the nature of halogen and pnicogen bonding interactions in RPH2···IF/FI binary complexes (R = CH3, OH, CF3, CN, and NO2) and the tuning effects of R-substituents. Though such interactions are commonly attributed to “sigma-hole”-type electrostatic effects, we show that they exhibit profound similarities and analogies to the resonance-type 3-center, 4-electron (3c/4e) donor-acceptor interactions of hydrogen bonding, where classical-type “electrostatics” are known to play only a secondary modulating role. The general 3c/4e resonance perspective corresponds to a continuous range of interatomic A···B bond orders (bAB), spanning both the stronger “covalent” interactions of the molecular domain (say, bAB ≥ ½) and the weaker interactions (bAB ˂ ½, often misleadingly termed “noncovalent”) that underlie supramolecular complexation phenomena. We show how a unified NBO/NRT-based description of hydrogen, halogen, pnicogen, and related bonding yields an improved predictive utility and intuitive understanding of empirical trends in binding energies, structural geometry, and other measurable properties that are expected to be manifested in all such supramolecular interaction phenomena.

Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several “sigma-hole” interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14–17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.

Comprendre la formation et la stabilisation des interactions non-covalentes est de grande importance dans le domaine de l'ingénierie cristalline. Dans cette perspective, les travaux réalisés se focalisent sur l’étude d'une sous-classe d'interactions non-covalentes connues sous le nom d'interactions à trou-sigma. Ces interactions sont définies comme celles impliquant des sites électrophiles appelés trou-sigma, qui sont associés à un atome lié de manière covalente et appartenant soit au bloc p (groupes 13-18) soit au bloc d (groupes 8, 11 et 12) du tableau périodique, et des sites nucléophiles provenant soit de la même molécule soit d'une molécule différente. Selon le groupe de l'atome sur lequel se trouve le trou-sigma, l'interaction peut être classée en plusieurs sous-classes. Parmi celles-ci, nous nous sommes concentrés sur les cas d'interactions de type liaison halogène (HaB) et liaison chalcogène (ChB). Comparé au cas bien établi des liaisons hydrogène (HB), la formation et la stabilisation des interactions HaB et ChB sont encore peu explorées. Cette thèse vise précisément à fournir des informations approfondies sur les caractéristiques de ce type d’interactions, principalement à travers de l’analyse de la distribution de la densité électronique entre la paire d'atomes en interaction et comment celle-ci influence l'organisation moléculaire à l'état solide. Deux thèmes principaux de la cristallographie sont couverts au cours de cette thèse : (i) les études de diffraction des rayons X sur monocristal à haute pression et (ii) l'analyse de la distribution de charge électronique. Les recherches structurelles et électroniques sont effectuées sur la base des données dérivées des expériences de diffraction des rayons X sur monocristal (SCXRD) réalisées dans des conditions ambiantes ou extrêmes. Les structures cristallines ainsi obtenues ont été utilisées pour obtenir la distribution de la densité électronique dans les phases périodiques. Les distributions électroniques des systèmes moléculaires extraits de leurs environnements cristallins ont été utilisées pour calculer le potentiel électrostatique dans les surfaces moléculaires et pour effectuer les analyses topologiques de la densité électronique et de sa fonction laplacienne dans le cadre de la Théorie Quantique des Atomes dans les Molécules (QTAIM). L'effet de l'environnement cristallin dans les propriétés d’interaction associées aux trous-sigma a été exploré également en détail. Les informations recueillies à partir de ces analyses sont non seulement utiles pour mieux comprendre les molécules avec lesquelles nous avons travaillé, mais aussi pour concevoir de nouveaux modèles moléculaires dans le but de viser le contrôle de la relation structure-propriétés dans les cristaux moléculaires issus de cette approche
Understanding the fundamentals of the formation and stabilization of non-covalent interactions is of paramount importance in the field of crystal engineering. In this direction, this thesis reports the crystallographic investigation of a sub-class of non-covalent interactions known as sigma-hole interactions. sigma-hole interactions are defined as those involving electrophilic sites (also called sigma-holes) associated to a covalently bonded atom belonging to either p-block (groups 13-18) or d-block (groups 8,11 and 12) of the periodic table, and nucleophilic sites coming from either the same or a different molecule. Depending upon the group of the atom on which the sigma-hole is present, the interaction can be further classified into various sub-classes. Out of these, we have focused on the cases of halogen bond (HaB) and chalcogen bond (ChB) interactions. As compared to the well-established case of hydrogen bonds (HB), the rationale behind the formation and stabilization of HaB and ChB are still less explored. This thesis is aimed exactly in such a direction, to provide a deeper insight into the characteristics of HaB and ChB interactions, mainly by understanding how the electron density is distributed among the interacting pair of atoms and how it eventually influences the molecular organization in solid-state. Two main stream topics of crystallography are covered during the course of this thesis: (i) high-pressure X-ray diffraction studies and (ii) charge density analysis. Structural and electronic investigations are carried out based on the data derived from single-crystal X-ray diffraction (SCXRD) experiments performed either at ambient or extreme conditions. The so-obtained crystal structures were used to derive the electron density distribution in the periodic phases. The electron distributions of the molecular systems extracted from their crystalline environments were used to calculate the electrostatic potential in molecular surfaces and to carry out the topological analyses of the electron density and its laplacian function within the framework of the Quantum Theory of Atoms in Molecules (QTAIM) methodology. The effect of crystalline environments in tuning the properties of sigma-hole interactions is also explored in detail. The information gathered from such analyses is not only helpful to better understand the molecules in hands, but also to design new molecular patterns with the aim to control the structure-properties relationship in molecular crystals

Non-covalent bonds are an important class of intermolecular interactions, which result in the ordering of atoms and molecules on the supramolecular scale. One such type of interaction is brought about by the bond formation between a region of positive electrostatic potential (σ-hole) interacts and a Lewis base. Previously, the halogen bond has been extensively studied as an example of a σ-hole interaction, where the halogen atom acts as the bond donor. Similarly, carbon, and the other tetrel elements can participate in σ-hole bonds. This thesis explores the nature of the carbon tetrel bond through the use of computational chemistry and solid state nuclear magnetic resonance (NMR) spectroscopy. The results of calculations of interaction energies and NMR parameters are reported for a series of model compounds exhibiting tetrel bonding from a methyl carbon to the oxygen and nitrogen atoms in a range of functional groups. The ¹³C chemical shift (𝛿iso) and the ¹ᶜ𝐽(¹³C,¹⁷O/¹⁵N) coupling across the tetrel bond are recorded as a function of geometry. The sensitivity of the NMR parameters to the non-covalent interaction is demonstrated via an increase in 𝛿iso and in |¹ᶜ𝐽(¹³C,¹⁷O/¹⁵N)| as the tetrel bond strengthens. There is no direct correlation between the NMR trends and the interaction energy curves; the energy minimum does not appear to correspond to a maximum or minimum chemical shift or J-coupling value. Gauge-including projector-augmented wave density functional theory (DFT) calculations of 𝛿iso are reported for crystals which exhibit tetrel bonding in the solid state. Experimental 𝛿iso values for sarcosine, betaine and caffeine and their tetrel-bonded salts generally corroborate the computational findings. This work offers new insights into tetrel bonding and facilitates the incorporation of tetrel bonds as restraints in NMR crystallographic structure refinement.

Noncovalent interactions are of great importance in studies on crystal design and drug discovery. One such noncovalent interaction, halogen bonding, is present between a covalently bound halogen atom and a Lewis base. A halogen bond is a directional interaction caused by the anisotropic distribution of charge on a halogen atom X covalently bound to A, which in turn forms a positive region called σ-hole on the A–X axis. Utilization of halogen bonds in lead optimization have been rarely considered in drug discovery until recently and yet more than 50% of the drug candidates are halogenated. To date, the halogen bond has not been subjected to practical molecular mechanical-molecular dynamics (MM-MD) study, where this noncovalent interaction cannot be described by conventional force fields because they do not account for the anisotropic distribution of the charge density on the halogen atoms. This problem was solved by the author and, for the first time, an extra-point of positive charge was used to represent the σ-hole on the halogen atom. This approach is called positive extra-point (PEP) approach. Interestingly, it was found that the performance of the PEP approach in describing halogen bond was better than the semiempirical methods including the recent halogen-bond corrected PM6 (PM6-DH2X) method. The PEP approach also gave promising results in describing other noncovalent halogen interactions, such as C–X···H and C–X···π-systems. The PEP resulted in an improvement in the accuracy of the electrostatic-potential derived charges of halogen-containing molecules, giving in turn better dipole moments and solvation free energies compared to high-level quantum mechanical and experimental data.With the aid of our PEP approach, the first MM-molecular dynamics (MM-MD) study of inhibitors that form a halogen bond with a receptor was performed for tetrahalobenzotriazole inhibitors complexed to cyclin-dependent protein kinase (CDK2). When the PEP approach was used, the calculated MM-generalized Born surface area (MM-GBSA)//MM-MD binding energies for halobenzimidazole and halobenzotriazole inhibitors complexed with protein kinase CK2 were found to correlate well with the corresponding experimental data, with correlation coefficients R2 of greater than 0.90. The nature and strength of halogen bonding in halo molecule···Lewis base complexes were studied in terms of molecular mechanics using our PEP approach. The contributions of the σ-hole (i.e., positively charged extra-point) and the halogen atom to the strength of this noncovalent interaction were clarified using the atomic parameter contribution to the molecular interaction approach. The molecular mechanical results revealed that the halogen bond is electrostatic and van der Waals in nature. The strength of the halogen bond increases with increasing the magnitude of the extra-point charge. The van der Waals interaction’s contribution to the halogen bond strength is most favorable in chloro complexes, whereas the electrostatic interaction is dominant in iodo complexes.The failure of the PM6 semiempirical method in describing noncovalent halogen interactions —not only halogen bonds, but also hydrogen bonds involving halogen atoms— was reported and corrected by the introduction of a second and third generation of noncovalent halogen interactions correction. The developed correction yielded promising results for the four examined noncovalent halogen interactions, namely: C–X···O, C–X···N, C–X···π-system, and C–X···H interactions.

The aim of this thesis is to investigate strength and origin of the stabilization for various types of noncovalent interactions. As this knowledge could lead to a deeper understand- ing and rationalization of the binding phenomena. Further, to participate on the de- velopment of new noncovalent data sets, which are nowadays inevitable in the process of parametrization and validation of new computational methods. In all the studies, different binding motifs of model complexes, which represent usually crystal structures, structures from unrelaxed scans or the local minima, were investi- gated. The calculations of the reference stabilization energies were carried out at ab initio level (e.g. CCSD(T)/CBS, QCISD(T)/CBS). Further, the accuracy of more ap- proximate methods (e.g. MP2.5, DFT-D or SQM methods) toward reference method, was tested. In order to obtain the nature of the stabilization the DFT-SAPT decompo- sition was frequently utilized. In the first part of the thesis, the importance and basic characteristics of different types of noncovalent interactions (e.g. halogen bond, hydrogen bond, π· · · π interaction etc.), are discussed. The second part provides the description of computational methods which were essential for our investigation. The third part of the thesis provides an overview for part...

Nitric oxide is an important compound for inter and intra cellular signal processing during various physiological conditions and it helps to increase the flow of blood inside human tissues. S-nitrosothiol is the major component during nitric oxide production under biological conditions. The interaction of -SNO group of S-nitrosothiol with amino acids is important in biological context. The interaction can occur through two σ-holes/ chalcogen bonding formed close to Sulphur along S-N and S-C bonding. Some relevant examples show here that ionic state of -SNO group plays a pivotal role during this interaction. Ionized and neutral Lewis bases with S-nitrosothiol through σ-hole/ chalcogen bonding along SN bonding forms more stable complex than that along S-C bonding

Abstract Ukraine ranks the third largest gas reserves in Europe. Gas production is carried out mainly from the Dnieper-Donets Basin (DDB). A gradual decline in reserves is forcing Ukraine to actively search for possible sources to increase reserves by finding bypassed gas intervals in existing wells or exploration of new prospects. This paper describes 3 case studies, where advanced pulsed neutron logging technology has shown exceptional value in gas-bearing layer identification in different scenarios. The logging technology was applied for formation evaluation. The technology is based on the neutron interaction with the minerals and the fluids contained in the pore space. The logging tool combines measurements from multiple detectors and spacing for self-compensated neutron cross-capture section (sigma) and hydrogen index (HI), and the Fast Neutron Cross Section (FNXS) high-energy neutron elastic cross section rock property. Comprehensive capture and inelastic elemental spectroscopy are simultaneously recorded and processed to describe the elemental composition and the matrix properties, reducing the uncertainties related to drilling cuttings analysis, and overall, the petrophysical evaluation combined with other log outputs. The proposed methodology was tested in several wells, both in open hole and behind casing. In the study we present its application in three wells from different fields of the DDB. The log data acquisition and analysis were performed across several sandstone beds and carbonates formation with low porosities (<10%), in various combinations of casing and holes sizes. The results showed the robustness and effectiveness of using the advanced pulsed neutron logging (PNL) technologies in multiple cases: Case Study A: Enabling a standalone cased hole evaluation and highlighting new potential reservoir zones otherwise overlooked due to absence of open hole logs. Case Study B: Finding by-passed hydrocarbon intervals that were missed from log analysis based on conventional open hole logs for current field operator. Case Study C: Identifying gas saturated reservoirs and providing solid lithology identification that previously was questioned from drilling cuttings in an unconventional reservoir.

Abstract Field A is located in the center of the Dnieper-Donets basin (DDB), producing gas from clastic reservoirs from several deep horizons in the Upper Visean sediments. The case study highlights the application of advanced pulsed neutron logging technologies and high-resolution data processing to unlock the sedimentary layers’ characteristics and the gas potential behind the casing. Multiple rock measurements are simultaneously recorded for continuous lithology identification, porosity quantification, and differentiating gas-filled porosity from low porosity formations. Dedicated log data acquisition and processing techniques enable investigating the effect of thin laminations on reservoir quality and producibility. The use of advanced pulsed neutron logging and interpretation method reduces the operational risks while securing critical reservoir parameters. A pulsed neutron spectroscopy tool provided a rich dataset including a self-compensated sigma and neutron porosity logs, fast neutron cross section (FNXS) together with capture and inelastic elemental spectroscopy. The logs interpretation was performed integrating FNXS and very high-resolution neutron porosity with mineral dry weight fractions and matrix properties from elemental spectroscopy processing. The comparison between the pulsed neutron measurements with standard open hole logs highlights the critical role of advanced fit-to-purpose logging techniques to accurately describe the underlying complexity of the formation and obtain improved net reservoir and net pay thicknesses in laminated and heterogeneous sequences. The logging objectives were successfully met, and additional valuable information related to the reservoir were determined in an efficient manner. The study also shows the critical value of FNXS as confident gas measurement. The FNXS measures the ability of the formation interacting with fast neutrons which are highly dependent on atomic density and not dominated by particular isotopes such as traditional sigma and porosity measurements. It is highly sensitive to gas-filled porosity, but it is independent of hydrogen index, acting like a cased-hole density measurement. Moreover, it demonstrates the importance of accurate knowledge of the mineralogy and matrix as well as the ability to measure at very high resolution to unravel the highly layered nature of the formation and its implication on completion and production strategy. Pulsed neutron logging has evolved over a half century, but the intrinsic physical measurements remain unchanged. With the advent and introduction of the new FNXS measurement and a high-quality spectroscopy elemental concentration, a higher quality measurement and interpretation can be obtained from standalone pulsed neutron logging. The advanced technology and log data analysis interpretation module can be considered as an effective and comprehensive methodology for robust formation evaluation in similar and complex setting.