Molecule

About: Molecule is a research topic. Over the lifetime, 52462 publications have been published within this topic receiving 1234914 citations.

Infrared and Raman spectra of inorganic and coordination compounds

Abstract: Inorganic molecules (ions) and ligands are classified into diatomic, triatomic, four-atomic, five-atomic, six-atomic, and seven-atomic types, and their normal modes of vibration are illustrated and the corresponding vibrational frequencies are listed for each type. Molecules of other types are grouped into compounds of boron, carbon, silicon, nitrogen, phosphorus, and sulfur, and the structures and infrared (IR)/Raman spectra of select examples are shown for each group. Group frequency charts including band assignments are shown for phosphorus and sulfur compounds. Other group frequency charts include hydrogen stretching frequencies, halogen stretching frequencies, oxygen stretching and bending frequencies, inorganic ions, and metal complexes containing simple coordinating ligands. Keywords: inorganic compounds; coordination compounds; diatomic molecules (ligands); triatomic molecules (ligands); four-atomic molecules (ligands); five-atomic molecules (ligands); six-atomic molecules (ligands); seven-atomic molecules (ligands); boron compounds; carbon compounds; silicon compounds; nitrogen compounds; phosphorus compounds; sulfur compounds; group frequency charts

Understanding organofluorine chemistry. An introduction to the C–F bond

Abstract: Fluorine is the most electronegative element in the periodic table. When bound to carbon it forms the strongest bonds in organic chemistry and this makes fluorine substitution attractive for the development of pharmaceuticals and a wide range of speciality materials. Although highly polarised, the C–F bond gains stability from the resultant electrostatic attraction between the polarised Cδ+ and Fδ– atoms. This polarity suppresses lone pair donation from fluorine and in general fluorine is a weak coordinator. However, the C–F bond has interesting properties which can be understood either in terms of electrostatic/dipole interactions or by considering stereoelectronic interactions with neighbouring bonds or lone pairs. In this tutorial review these fundamental aspects of the C–F bond are explored to rationalise the geometry, conformation and reactivity of individual organofluorine compounds.

Characterization of c-h-o hydrogen-bonds on the basis of the charge-density

Abstract: It is shown that the total charge density is a valid source to confirm hydrogen bonding without invoking a reference charge density. A set of criteria are proposed based on the theory of “atoms in molecules” to establish hydrogen bonding, even for multiple interactions involving C-H-O hydrogen bonds. These criteria are applied to several van der Waals complexes. Finally a bifurcated intramolecular C-H-O hydrogen bond is predicted in the anti-AIDS drug AZT, which may highlight a crucial feature of the biological activity of a whole class of anti-AIDS drugs. Almost all the methods of physical chemistry, spectroscopy, and diffraction can be used to recognize and study hydrogen bonding.] Each technique focuses on specific properties in order to detect and characterize this phenomenon in its own way. This work is concerned with the manifestation of hydrogen bonding in the charge density obtained from ab initio calculations. Whereas crystallographers have concluded upon hydrogen bonding via purely geometrical criteria, recent deformation density2 studies allow one to observe hydrogen bonding beyond mere ge~metry.~ However, it is not necessary to subtract an arbitrary (promolecular) charge density from the total density to reveal hydrogen bonding, not even in the interpretation of X-ray experiment^.^ Boyd and Choi have shown in two important contribution^^^^ that the theory of “atoms in molecules’’ (AIM)7,8 can be used to characterize hydrogen bonding solely from the (total) charge density for a large set of acceptor molecules, involving HF and HC1 as donors. In a next stage Carroll and Bader performed a more extended analysis on a large set of BASE-HF comple~es.~ This theory has not only provided new insights in conventional intermolecular hydrogenI0.’ ] bonding but has also been successful in intramolecularI33l4 and x-type hydrogen bonds.I5 Drawing from earlier ob~ervations~~~~ ~.’~~~~ and the present work, we formulate eight concerted effects occurring in the charge density which are indicative of hydrogen bonding. All of these effects can be viewed as necessary criteria to conclude that hydrogen bonding is present. By observation one of these conditions has proven to be sufficient as well. This case study on C-H-O interactions shows that this less common type of hydrogen bonding obeys all of the proposed criteria. Moreover, the multiple interactions appearing in the present five examples do not impair the consistency of the global phenomenon of hydrogen bonding as it expresses itself in the charge density. In spite of an early affirmative infrared review,I6 the old controversy on whether C-H-O hydrogen bonds really exist continued for another decade,” but now the dust has settled’* (for an entertaining account of this controversy, see ref 19). The importance of these bonds has been recognized in crystal engineering’9,20 since C-H-O contacts have a determining influence on packing motifs.21

Crystal Structure and Hydrogen-Bonding System in Cellulose Iβ from Synchrotron X-ray and Neutron Fiber Diffraction

Abstract: The crystal and molecular structure together with the hydrogen-bonding system in cellulose Iβ has been determined using synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from tunicin. These samples diffracted both synchrotron X-rays and neutrons to better than 1 A resolution (>300 unique reflections; P21). The X-ray data were used to determine the C and O atom positions. The resulting structure consisted of two parallel chains having slightly different conformations and organized in sheets packed in a “parallel-up” fashion, with all hydroxymethyl groups adopting the tg conformation. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The hydrogen atoms involved in the intramolecular O3···O5 hydrogen bonds have well-defined positions, whereas those corresponding to O2 and O6 covered a wider v...

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

Abstract: Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within t...