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Ichihara, O.; Barker, J.; Law, R.J.; Whittaker, M. Compound Design by Fragment-Linking. Mol. Inform. 2011, 30, 298–306. [ Google Scholar] [ CrossRef] Gupta, A.; Müller, A.T.; Huisman, B.J.H.; Fuchs, J.A.; Schneider, P.; Schneider, G. Generative Recurrent Networks for De Novo Drug Design. Mol. Inform. 2018, 37, 1700111. [ Google Scholar] [ CrossRef] [ PubMed][ Green Version] Popova, M.; Isayev, O.; Tropsha, A. Deep reinforcement learning for de novo drug design. Sci. Adv. 2018, 4, eaap7885. [ Google Scholar] [ CrossRef][ Green Version] Sánchez-Rodríguez, A.; Pérez-Castillo, Y.; Schürer, S.C.; Nicolotti, O.; Mangiatordi, G.F.; Borges, F.; Cordeiro, M.N.D.S.; Tejera, E.; Medina-Franco, J.L.; Cruz-Monteagudo, M. From flamingo dance to (desirable) drug discovery: A nature-inspired approach. Drug Discov. Today 2017, 22, 1489–1502. [ Google Scholar] [ CrossRef] All atoms (except hydrogen and helium with their single electron shells) are most stable when there are exactly eight electrons in their valence shell. This principle is referred to as the octet rule, and it states that an atom will give up, gain, or share electrons with another atom so that it ends up with eight electrons in its own valence shell. For example, oxygen, with six electrons in its valence shell, is likely to react with other atoms in a way that results in the addition of two electrons to oxygen’s valence shell, bringing the number to eight. When two hydrogen atoms each share their single electron with oxygen, covalent bonds are formed, resulting in a molecule of water, H 2O.

Pan, S.J.; Yang, Q. A Survey on Transfer Learning. IEEE Trans. Knowl. Data Eng. 2010, 22, 1345–1359. [ Google Scholar] [ CrossRef] Using an n 2 search over all LAEs in all GBs produces the set U of unique LAE classes, each with a representative LAE, for the GB system. For a sufficiently small ε each GB will be characterized by a unique fingerprint in terms of the LAEs it contains. As ε gets smaller, the number of unique LAEs that characterize a GB increases exponentially. When an LAE is sufficiently dissimilar to all others in the set, it is added and becomes the representative LAE for the class of all other LAEs that are similar to it. Any of the LAEs in the class could be the representative LAE since they are all similar. As additional data becomes available, this set of U LAEs may increase in size if new LAE classes are discovered. Section III in the Supplementary Information presents additional details. Figure 2.6 The water molecule (left) depicts a polar bond with a slightly positive charge on the hydrogen atoms and a slightly negative charge on the oxygen. Examples of nonpolar bonds include methane (middle) and oxygen (right). Hydrogen BondsBöhm, H.-J. LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput.-Aided Mol. Des. 1992, 6, 593–606. [ Google Scholar] [ CrossRef] [ PubMed] The conditions under which two atoms will bond together depend on the atoms’ electron configurations, which completely determine their chemical reactivity. The more stable the electron configuration, the less reactive the atom; the extremes of stability are the ‘inert gases’, such as argon, helium and neon, which are almost totally non-reactive. Their near-inertness is caused by their having complete outermost electron orbitals, with no opportunity for more electrons to ‘join’ the atom, and no ‘spare’ or ‘loose’ electrons to leave the atom.

Ionic and covalent bonds are strong bonds that require considerable energy to break. However, not all bonds between elements are ionic or covalent bonds. Weaker bonds can also form. These are attractions that occur between positive and negative charges that do not require much energy to break. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. These bonds give rise to the unique properties of water and the unique structures of DNA and proteins.Nishibata, Y.; Itai, A. Automatic creation of drug candidate structures based on receptor structure. Starting point for artificial lead generation. Tetrahedron 1991, 47, 8985–8990. [ Google Scholar] [ CrossRef] The nucleus is held together by the strong force, one of the four basic forces in nature. This force between the protons and neutrons overcomes the repulsive electrical force that would otherwise push the protons apart, according to the rules of electricity. Some atomic nuclei are unstable because the binding force varies for different atoms based on the size of the nucleus. These atoms will then decay into other elements, such as carbon-14 decaying into nitrogen-14. What are protons? Shimada, M., Kokawa, H., Wang, Z. J., Sato, Y. S. & Karibe, I. Optimization of grain boundary character distribution for intergranular corrosion resistant 304 stainless steel by twin-induced grain boundary engineering. Acta Mater. 50, 2331–2341 (2002).

The interplay between grain boundary structure and defect sink/annealing behavior IOP Conference Series: Materials Science and Engineering 89, 012004 (2015). When two atoms are brought together, they may link to form a molecule; any bonds that form are called primary bonds. Alternatively, they may move apart and so retain their individual identity. Depending on the degree of interaction between the atoms, one of three states can form, these being gases, liquids or solids. These are referred to as the three main phases of matter, where a phase is defined as a structurally homogeneous part of the system and each phase will have its own distinct structure and associated properties. In the gaseous state there is little or no resistance to the relative movement of atoms or molecules, while in the liquid state the resistance to movement is considerably greater, but molecules can still flow past each other with great ease. In solids the movement of atoms and molecules is restricted to a local vibration, although some movement at the atomic level is possible through diffusion. Gillet, V.J.; Newell, W.; Mata, P.; Myatt, G.; Sike, S.; Zsoldos, Z.; Johnson, A.P. SPROUT: Recent developments in the de novo design of molecules. J. Chem. Inf. Comput. Sci. 1994, 34, 207–217. [ Google Scholar] [ CrossRef]Nicolaou, C.A.; Kannas, C.; Loizidou, E. Multi-Objective Optimization Methods in De Novo Drug Design. Mini-Rev. Med. Chem. 2012, 12, 979–987. [ Google Scholar] [ CrossRef] [ PubMed] Barigye, S.J.; García de la Vega, J.M.; Perez-Castillo, Y. Generative Adversarial Networks (GANs) Based Synthetic Sampling for Predictive Modeling. Mol. Inform. 2020, 39, 2000086. [ Google Scholar] [ CrossRef] [ PubMed] Looking at the periodic table again ( Figure 2.3), you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C), nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.

The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed. that is sensitive to the norm of each SOAP vector. Normally, SOAP similarity uses a dot product on normalized SOAP vectors; however, in our experience this reduces the discriminative ability of the representation. Lenselink, E.B.; ten Dijke, N.; Bongers, B.; Papadatos, G.; van Vlijmen, H.W.T.; Kowalczyk, W.; Ijzerman, A.P.; van Westen, G.J.P. Beyond the hype: Deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. J. Cheminform. 2017, 9, 45. [ Google Scholar] [ CrossRef][ Green Version] Figure 2.7 Electron Shells Electrons orbit the atomic nucleus at distinct levels of energy called electron shells. (a) With one electron, hydrogen only half-fills its electron shell. Helium also has a single shell, but its two electrons completely fill it. (b) The electrons of carbon completely fill its first electron shell, but only half-fills its second. (c) Neon, an element that does not occur in the body, has 10 electrons, filling both of its electron shells.Figure 2.2 Elements of the Human Body The main elements that compose the human body are shown from most abundant to least abundant. The next scientist to further modify and advance the atomic model was Rutherford, who studied under Thomson, according to the chemistry department at Purdue University. In 1911, Rutherford published his version of the atom, which included a positively charged nucleus orbited by electrons. This model arose when Rutherford and his assistants fired alpha particles at thin sheets of gold. An alpha particle is made up of two protons and two neutrons, all held together by the same strong nuclear force that binds the nucleus, according to the Jefferson Lab. Bandaki, A. D. & Patala, S. A three-dimensional polyhedral unit model for grain boundary structure in fcc metals. Npj Comput. Mater. 3, 13 (2017). Schneider, P.; Schneider, G. De Novo Design at the Edge of Chaos. J. Med. Chem. 2016, 59, 4077–4086. [ Google Scholar] [ CrossRef] [ PubMed] There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell. Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH 4) molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds ( Figure 2.6).