Revisiting van der Waals Radii: From Comprehensive Structural Analysis to Knowledge‐Based Classification of Interatomic Contacts
Weak noncovalent interactions are responsible for structure and properties of almost all supramolecular systems, such as nucleic acids, enzymes, and pharmaceutical crystals. However, the analysis of their significance and structural role is not straightforward and commonly requires model studies. Herein, we describe an efficient and universal approach for the analysis of noncovalent interactions and determination of van der Waals radii using the line-of-sight (LoS) concept. The LoS allows to unambiguously identify and classify the "direct" interatomic contacts in complex molecular systems. This approach not only provides an improved theoretical base to molecular "sizes" but also enables the quantitative analysis of specificity, anisotropy, and steric effects of intermolecular interactions.
We report the first high resolution spectroscopic study of the NH3–H2 van der Waals molecular complex. Three different experimental techniques, a molecular beam Fourier transform microwave spectrometer, a millimeter-wave intracavity jet OROTRON spectrometer, and a submillimeter-wave jet spectrometer with multipass cell, were used to detect pure rotational transitions of NH3–H2 in the wide frequency range from 39 to 230 GHz. Two nuclear spin species, (o)-NH3–(o)-H2 and (p)-NH3–(o)-H2, have been assigned as carriers of the observed lines on the basis of accompanying rovibrational calculations performed using the ab initio intermolecular potential energy surface (PES) of Maret et al. The experimental spectra were compared with the theoretical bound state results, thus providing a critical test of the quality of the NH3–H2 PES, which is a key issue for reliable computations of the collisional excitation and de-excitation of ammonia in the dense interstellar medium.
Toward the development of classical force fields for the accurate modeling of clay mineral-water systems, we have extended the use of metalâ€“Oâ€“H (Mâ€“Oâ€“H) angle bending terms to describe surface Siâ€“Oâ€“H bending for hydrated kaolinite edge structures. Kaolinite, comprising linked octahedral Al and tetrahedral Si sheets, provides a rigorous test by combining aluminol and silanol groups with water molecules in hydrated edge structures. Periodic density functional theory and classical force fields were used with molecular dynamics to evaluate the structure, dynamics, hydrogen bonding, and power spectra for deriving optimum bending force constants and optimal equilibrium angles. Cleavage energies derived from density functional theory molecular dynamics calculations indicate the relative stabilities of both AC1 and AC2 edge terminations of kaolinite where Siâ€“OH and Alâ€“(OH2) or Siâ€“OH, Alâ€“OH, and Alâ€“(OH2) groups exist, respectively. Although not examined in this study, the new Siâ€“Oâ€“H angle bending parameter should allow for improved modeling of hydroxylated surfaces of silica minerals such as quartz and cristobalite, as well as amorphous silica-based surfaces and potentially those of other silicate and aluminosilicate phases.
Ab initio calculations of the intermolecular potential energy surface (PES) of CO-N-2 have been carried out using the closed-shell single-and double-excitation coupled cluster approach with a non-iterative perturbative treatment of triple excitations method and the augmented correlation-consistent quadruple-zeta (aug-cc-pVQZ) basis set supplemented with midbond functions. The global minimum (D-e = 117.35 cm(-1)) of the four-dimensional PES corresponds to an approximately T-shaped structure with the N-2 subunit forming the leg and CO the top. The bound rovibrational levels of the CO-N-2 complex were calculated for total angular momenta J = 0-8 on this intermolecular potential surface. The calculated dissociation energies D-0 are 75.60 and 76.79 cm(-1) for the ortho-N-2 (A-symmetry) and para-N-2 (B-symmetry) nuclear spin modifications of CO-N-2, respectively. Guided by these bound state calculations, a new millimeter-wave survey for the CO-N-2 complex in the frequency range of 110-145 GHz was performed using the intracavity OROTRON jet spectrometer. Transitions not previously observed were detected and assigned to the subbands connecting the K = 0 and 1, (j(CO), j(N2)) = (1, 0) states with a new K = 1, (j(CO), j(N2)) = (2, 0) state. Finally, the measured rotational energy levels of the CO-N-2 complex were compared to the theoretical bound state results, thus providing a critical test of the quality of the PES presented. The computed rovibrational wave functions were analyzed to characterize the nature of the different bound states observed for the two nuclear spin species of CO-N2.
We have performed a comparative analysis of the bio-oil produced by thermal liquefaction of microalgae in different solvents using high-resolution Orbitrap mass spectrometry and GC-MS approach. Water, methanol, ethanol, butanol, isopropanol, acetonitrile, toluene, and hexane were used as solvents in which the liquefaction was performed. It was observed that all resulting oils demonstrate a considerable degree of similarity. For all samples, compounds containing 1 and 2 nitrogen atoms dominated in the positive ESI spectra, while a relative contribution of other compounds was small. In negative ESI mode, compounds having 2 to 7 oxygens were observed. Statistical analysis revealed that products can be combined in two groups depending on the solvent used for the liquefaction. To the first group, we can attribute the products obtained by using protic (alcohols) and to the second by using aprotic (acetonitrile, toluene) solvents. Nevertheless, based on our results, we concluded that solvent possesses a minor impact on molecular composition of bio-oil. We suggested that the driving force of the liquefaction reaction is the thermal dehydration of the carbohydrate in algae, resulting in water formation, which could be the trigger of the producing of bio-oil. To prove this hypothesis, we performed the reaction with the dry algae in the absence of the solvent and observed the formation of bio-oil.
The New Russian Encyclopedia is a fundamental reference publication in 18 volumes that characterizes nature, population, economy, history, science, art, technology and other important aspects. Contains about 60,000 articles, about 30,000 biographies, about 15,000 color illustrations, maps, charts, diagrams, tables. Leaves since 2003.
This volume, being the 55th of this Series, contains a wealth of information on bioactive natural products. In Chapter 1, Watson and colleagues have discussed the synthesis of monoterpene indole alkaloids, an important class of structurally diverse natural products, with respect to conventional and biomimetic synthetic approaches.
Titanocene(III) has been widely used in the synthesis of complex organic molecules and natural products including polyketides, phenylpropanoids, antibiotics, and alkaloids. Oltra and coworkers have provided a review on the stereoselective synthesis of natural products facilitated by titanocene(III) in Chapter 2.
About 70 biologically active macrocyclic bisbibenzyls (MBBs) have been isolated and structurally elucidated during the last 30 years. Song and Zhao, in Chapter 3, have provided a review on the synthesis of MBBs with diverse pharmacological properties.
Diabetes mellitus is the most common endocrine/metabolic disorder that poses a global health concern. Reyes and colleagues have discussed the hypoglycemic activity of some terrestrial and marine bioactive compounds with potential for treating type 2 diabetes in Chapter 4. In Chapter 5, Pietruszka and coworkers have highlighted the importance of some marine oxylipins that exhibit different bioactive properties.
Depression has become a psychiatric disorder, which leads to various disabilities. Natural compounds like polyphenols and terpenoids have antioxidant and neuroprotective properties and can be used for the treatment of depression. In Chapter 6, Rodrigues et al. review the clinical studies and trials on polyphenols and terpenoids for the treatment of various psychiatric disorders. The lipid A phosphate and their phosphorylated analogues found in Gram-negative bacteria are of major importance because they provide the host with defense against infections from various microorganisms. Paradies and Zimmermann have discussed physical characteristics, isolation, and bioactivity of lipopolysaccharides (lipid A) for developing new vaccines and therapeutics in Chapter 7.
Hydroxycinnamic acids (HCAs) are a group of phytonutrients with numerous beneficial effects on human health that are largely derived from plants. HCAs play important roles like defense against UV rays or pathogenic attack during growth and development of plants. In Chapter 8, El-Seedi and colleagues present a review focusing on the therapeutic effects of HCAs for the treatment of cancer, diabetes, pulmonary, hepatic, neuro-, and cardiovascular diseases. In Chapter 9, Pomilio and Mercader have presented the study of natural anthocyanins and other related flavonoids for the readers, highlighting their possible and preferable uses as health-protecting food dyes over synthetic ones. They have also discussed the anthocyanins isolated from Ipomoea cairica along with their QSAR studies.
Cardiovascular diseases are considered to be a major threat to health. Polyphenols and carotenoids are structurally diverse groups of bioactive compounds isolated from fruits and vegetables, carrying protective effects against endothelial dysfunction. These therapeutic effects have been explored by Yamagata in Chapter 10.
The roots of licorice and ivy leaves have been used in folk medicine and drugs since long. The biological activity of these complexes has been discussed by Yakovishin and Grishkovets in Chapter 11. In Chapter 12, the chemical and biological characteristics of amicoumacins and xenocoumacins are reviewed by Korshun et al. with reference to the preparation of antibiotics.
I hope that this volume will be received with the same enthusiasm as the earlier volumes of this long-standing series the first volume of which was published under my Editorship in 1988. I would like to express my gratitude to Ms. Taqdees Malik and Mr. Mahmood Alam for their assistance in the preparation of this volume.
The hydrogenation of diphenylacetylene (DPA) on palladium–silver catalysts with a single-atom structure was investigated. It has been shown experimentally that the reaction rate of alkene to alkane hydrogenation is substantially lower than the rate of DPA semi-hydrogenation. The kinetic barriers of all stages of hydrogenation were calculated by the DFT method.
The swelling of a poly (methyl methacrylate) in supercritical carbon dioxide was studied by means of full atomistic classical molecular dynamics simulation. In order to characterize the polymer swelling, we calculated various properties related to the density, structure, and dynamics of polymer chains as a function of the simulation time, temperature, and pressure. In addition, we compared the properties of the macromolecular chains in supercritical CO2 with the properties of the corresponding bulk system at the same temperature and atmospheric pressure. It was shown that diffusion of CO2 molecules into the polymer led to a significant increase in the chain mobility and distances between them. Analysis of diffusion coefficients of CO2 molecules inside and outside the poly(methyl methacrylate) sample has shown that carbon dioxide actively interacts with the functional groups of poly (methyl methacrylate). Joint analysis of the radial distribution functions obtained from classical molecular dynamics and of the averaging interatomic distances from Car-Parrinello molecular dynamics allows us to make a conclusion about the possibility of formation of weak hydrogen bonds between the carbon dioxide oxygen atom and the hydrogen atoms of the polymer methyl groups.