The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-spiral conformation in which every backbone N−H group donates a hydrogen bond to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence.
A hydrogen bond is a partially electrostatic force of attraction between a hydrogen (H) atom which is bound to a more electronegative atom or group, such as nitrogen (N), oxygen (O), or fluorine (F)—the hydrogen bond donor—and another adjacent atom bearing a lone pair of electrons—the hydrogen bond acceptor.
A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge. However, in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions.
Molybdenum disulfide is an inorganic compound composed of molybdenum and sulfur. Its chemical formula is MoS
2.
The hydrophobic effect is the observed tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules. The word hydrophobic literally means "water-fearing", and it describes the segregation of water and nonpolar substances, which maximizes hydrogen bonding between molecules of water and minimizes the area of contact between water and nonpolar molecules.
Supramolecular chemistry is the domain of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. Whereas traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects.
Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary. The scaffold for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecule's various hydrogen bonds. This leads to several recognizable domains of protein structure and nucleic acid structure, including such secondary-structure features as alpha helixes and beta sheets for proteins, and hairpin loops, bulges, and internal loops for nucleic acids. The terms primary, secondary, tertiary, and quaternary structure were introduced by Kaj Ulrik Linderstrøm-Lang in his 1951 Lane Medical Lectures at Stanford University.
Thermostability is the quality of a substance to resist irreversible change in its chemical or physical structure, often by resisting decomposition or polymerization, at a high relative temperature.
Supramolecular polymers are a kind of polymers whose monomeric units hold together via highly directional and reversible non-covalent interactions. Unlike conventional bonded polymers, supramolecular polymers engage in a variety of non-covalent interactions that define their properties. These interactions include hydrogen bonding, π-π interaction, metal coordination, and host–guest interaction. Owing to the presence of these reversible noncovalent interactions, supramolecular polymers exhibit dynamic properties such as self-healing.
Molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. There are two types of self-assembly. These are intramolecular self-assembly and intermolecular self-assembly. Commonly, the term molecular self-assembly refers to intermolecular self-assembly, while the intramolecular analog is more commonly called folding.
Low-frequency collective motion in proteins and DNA refers to the application of statistical thermodynamics to understand low-frequency vibrations in biomolecules.
The term macromolecular assembly (MA) refers to massive chemical structures such as viruses and non-biologic nanoparticles, cellular organelles and membranes and ribosomes, etc. that are complex mixtures of polypeptide, polynucleotide, polysaccharide or other polymeric macromolecules. They are generally of more than one of these types, and the mixtures are defined spatially, and with regard to their underlying chemical composition and structure. Macromolecules are found in living and nonliving things, and are composed of many hundreds or thousands of atoms held together by covalent bonds; they are often characterized by repeating units. Assemblies of these can likewise be biologic or non-biologic, though the MA term is more commonly applied in biology, and the term supramolecular assembly is more often applied in non-biologic contexts. MAs of macromolecules are held in their defined forms by non-covalent intermolecular interactions, and can be in either non-repeating structures, or in repeating linear, circular, spiral, or other patterns. The process by which MAs are formed has been termed molecular self-assembly, a term especially applied in non-biologic contexts. A wide variety of physical/biophysical, chemical/biochemical, and computational methods exist for the study of MA; given the scale of MAs, efforts to elaborate their composition and structure and discern mechanisms underlying their functions are at the forefront of modern structure science.
A two-dimensional polymer (2DP) is a sheet-like monomolecular macromolecule consisting of laterally connected repeat units with end groups along all edges. This recent definition of 2DP is based on Hermann Staudinger's polymer concept from the 1920s. According to this, covalent long chain molecules ("Makromoleküle") do exist and are composed of a sequence of linearly connected repeat units and end groups at both termini.
The empirical definition of self-assembly is typically given as a phenomenon where the components of a system assemble themselves to form a larger functional unit. This spontaneous organization can be due to direct specific interaction, collective effects, and/or occur indirectly through their environment. This definition mirrors the one provided by Nature.com and is applicable to a variety of components regardless of their dimensions. The thermodynamics-based definition of self-assembly was introduced by Nicholas A. Kotov and describes self-assembly as a process where components of the system acquire non-random spatial distribution with respect to each other and the boundaries of the system. This definition allows one to account for mass and energy fluxes taking place in the self-assembly processes and is specifically applicable to the processes of spontaneous organization of nanoparticles with each other and with the boundaries of the system.
Tungsten diselenide is an inorganic compound with the formula WSe2. The compound adopts a hexagonal crystalline structure similar to molybdenum disulfide. Every tungsten atom is covalently bonded to six selenium ligands in a trigonal prismatic coordination sphere while each selenium is bonded to three tungsten atoms in a pyramidal geometry. The tungsten–selenium bond has a length of 0.2526 nm, and the distance between selenium atoms is 0.334 nm. Layers stack together via van der Waals interactions. WSe2 is a very stable semiconductor in the group-VI transition metal dichalcogenides.
Baruch Barzel is an Israeli physicist and applied mathematician at Bar-Ilan University . His main research areas are statistical physics, complex systems, nonlinear dynamics and network science. Barzel completed his Ph.D. in physics at the Hebrew University of Jerusalem, Israel as a Hoffman Fellow. He then pursued his postdoctoral training at the Center for Complex Network Research at Northeastern University and at the Channing Division of Network Medicine, Harvard Medical School. Barzel is also an active public lecturer on science and on Judaism, and presents a weekly corner on Jewish thought on Israel National Radio .
Naphthalenetetracarboxylic diimide (NTCDI) is a solid organic compound and one of the simplest naphthalenediimides (NDIs). NTCDI is produced from the parent naphthalene via an intermediate compound naphthalenetetracarboxylic dianhydride.
