Structural chemistry

Structural chemistry is a part of chemistry and deals with spatial structures of molecules (in the gaseous, liquid or solid state) and solids (with extended structures that cannot be subdivided into molecules). The main tasks are: The formulation of general laws for structure-property relationships; and The derivation of general rules on how the chemical and physical properties of the constituents of matter determine the resulting structures (e.g. the relationship between the electron configuration of the crystal building blocks and the symmetry of the resulting crystal lattice). For structure elucidation a range of different methods are used. One has to distinguish between methods that elucidate solely the connectivity between atoms (constitution) and such that provide precise three dimensional information such as atom coordinates, bond lengths and angles and torsional angles. The latter methods include (mainly): for the gaseous state: gas electron diffraction and microwave spectroscopy for the liquid state: NMR spectroscopy (note, obtaining precise structural information from liquids and solutions is still rather difficult compared to gases and crystalline solids) for the solid state: X-ray, electron and neutron diffraction To identify connectivity and the presence of functional groups a variety of methods of molecular spectroscopy and solid state spectroscopy can be used.

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Organic compounds

Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the α-amino acids, from which proteins are composed. Only 22 α-amino acids appear in the genetic code of all life. Amino acids can be classified according to the locations of the core structural functional groups, as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, ionization, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.

Chemical substances

A chemical substance is a form of matter having constant chemical composition and characteristic properties. Chemical substances can be simple substances (substances consisting of a single chemical element), chemical compounds, or alloys. Chemical substances that cannot be separated into their simpler constituent elements by physical means are said to be 'pure'; this notion intended to set them apart from mixtures.

Stereochemistry

Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation. The study of stereochemistry focuses on the relationships between stereoisomers, which by definition have the same molecular formula and sequence of bonded atoms (constitution), but differ in the geometric positioning of the atoms in space. For this reason, it is also known as 3D chemistry—the prefix "stereo-" means "three-dimensionality".

Steric effects arise from the spatial arrangement of atoms. When atoms come close together there is generally a rise in the energy of the molecule. Steric effects are nonbonding interactions that influence the shape (conformation) and reactivity of ions and molecules. Steric effects complement electronic effects, which dictate the shape and reactivity of molecules. Steric repulsive forces between overlapping electron clouds result in structured groupings of molecules stabilized by the way that opposites attract and like charges repel.

In organic chemistry, a homologous series is a sequence of compounds with the same functional group and similar chemical properties in which the members of the series can be branched or unbranched, or differ by molecular formula of and molecular mass of 14u. This can be the length of a carbon chain, for example in the straight-chained alkanes (paraffins), or it could be the number of monomers in a homopolymer such as amylose. Compounds within a homologous series typically have a fixed set of functional groups that gives them similar chemical and physical properties.

The structural formula of a chemical compound is a graphic representation of the molecular structure (determined by structural chemistry methods), showing how the atoms are possibly arranged in the real three-dimensional space. The chemical bonding within the molecule is also shown, either explicitly or implicitly. Unlike other chemical formula types, which have a limited number of symbols and are capable of only limited descriptive power, structural formulas provide a more complete geometric representation of the molecular structure.

Identification of N-glycan positional isomers by combining IMS and vibrational fingerprinting of structurally determinant CID fragments

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Priyanka Bansal

While glycans are present on the surface of cells in all living organisms and play key roles in most biological processes, their isomeric complexity makes their structural characterization challenging

ROYAL SOC CHEMISTRY2022

A new approach for identifying positional isomers of glycans cleaved from monoclonal antibodies

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Priyanka Bansal, Vasyl Yatsyna, Natalia Yalovenko

Glycosylation patterns in monoclonal antibodies (mAbs) can vary significantly between different host cell types, and these differences may affect mAbs safety, efficacy, and immunogenicity. Recent stud

ROYAL SOC CHEMISTRY2021

Studies on the sp-sp intermolecular coupling reactions with the palladium water-soluble catalyst prepared in situ from palladium(II) acetate and sulfonated triphenylphosphine P(C6H4-m-SO3Na)(3) (TPPTS

1995