Introduction to the scientific language

A SMILES (Simplified Molecular-Input Line-Entry System) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. For instance, the SMILES for the ethanol is CCO, for the benzene ring is c1ccccc1, for the dinitrogen is N#N. Official documentation for SMILES notation can be found at OpenSMILES and Daylight Chemical Information Systems.
A molecular unit is a molecular construction that can react, together with other units to form a larger molecule or three-dimensional networks. In the polymer builder, it is always represented by a single SMILES, that can also include the * ASCII character to indicate possible available connections. In our notation, the open connections must always be labeled with a 1 or a 2 using the notation [*:N] (with N that is 1 or 2). The [*:1] indicates the connection that attaches to an already constructed unit, while [*:2] will connect to the following unit. This distinction is necessary since the building process always follows a growth vector. Starting from a seeding molecular unit, one or more branches are created always following the process to connect a [*:1] to a [*:2]. A molecular unit can also be defined (or edited), using the structure editor integreted in the web interface (see picture below). In the editor, the open connection [*:1] is indicated with R1, the open connection [*:2] corresponds to R2.
A building block is the smallest block to construct polymers. It is constituted by few molecular units, each one with a very specific role. Building blocks can be composed to create segments, that, in turn, are used to create polymers. Building blocks are stored and created in the corresponding catalog. Two types of building blocks are defined, the linear one and the dendrimeric one.
- A linear building block is a building block defined by three molecular units: the repeating unit, the head and the tail. The repeating unit is a molecular unit with two open connections and constitutes the unit that repeats itself during the construction of a polymer. One connection must have label 2 and the other label 1. The head is a molecular unit whose aim is to close the connection of the repeating unit with label 1. It can be something as simple as a hydrogen atom or a more complex group of atoms forming in the polymerization process (e.g. ([*:2])OC for polyhydroxyalcanoates). A head always has one open connection with label 1. Contrary to the repeating unit, the head is not used in the growth of a polymer, but it is used to close a connection any time this is necessary. For instance, it is used at the beginning of a polymer chain whose first building block is the corresponding repeating unit. The tail is a form to close the connection of the repeating unit with label 2. The same considerations for the head can be applied to the tail, with the difference that the tail has a connection labelled with 1, that connects to the 2 of the repeating unit. An example of linear building block is in the picture below.
- A dendrimeric building block is an entity formed by five molecular units: the central unit, the repeating unit, the central-unit capping, the repeating-unit head and the repeating-unit tail. The central unit can have many open connections, but they are always of the same type. In particular, they are all connections where to grow from. Following the notation introduced in the liner building blocks, they will always be of type [*:2]. The central unit represents the seed unit in case of a dendrimeric growth. The repeating unit is the unit that repeats itself in the process of dendrimeric growth. It can have many open connections, one will always connect to a previous unit (type [*:1]), all the others must be equivalent and allow the repetition process (type [*:2]). The central-unit capping is the way one can close the opened connections of the central unit. It must contain a connection with label 1. The repeating-unit tail is the way one can close the [*:2] connections of the repeating unit. It must contain a connection with label 1. The repeating-unit head that is the way one can close the [*:1] of the repeating unit. It must contain a connection with label 2. An example of dendrimeric building block is in the picture below.
A segment is an ordering pattern constructed using one or more building blocks. It is the second level for the description of the polymer construction. One or several segments can be combined to form a polymer. We have four types of segments: linear block, linear random, dendrimeric from central unit, dendrimeric from repeating unit.
- A linear block segment is a segment defined by a list of linear building blocks and their correspondent occurrence. Each building block in the list, multiplied by its occurrence, represent a block in the polymer construction. Following the order in the list, the blocks are connected to each other. Even though the repeating unit of each building block is the one that is used in the construction, it is important for the segment to maintain knowledge of the head and tail of all the involved building blocks, in case there will be the need to close connections.
- A linear random segment is a segment defined by a set of building blocks that are placed randomly when constructing the polymer, respecting a ratio among them. The ratio is specified as input in the definition of this segment. The random nature of the connection among blocks is an important aspect of the polymer construction and the random segment is the only level where randomisation can be introduced.
- A dendrimeric segment from central unit is a dendrimer construction that uses the constituting elements of a SINGLE dendrimeric building block. The specification “from central unit” indicates here to use the more standard way to construct dendrimers, meaning using the central unit of the building block as seed for the construction. Two more inputs define the dendrimeric segments: the number of generations for the construction and the connections to use for the growth. The number of generations is the number of times the dendrimer growth step should be performed. We call generation zero (G0) the construction with only the central unit, generation one (G1) the construction with one iteration of the dendrimer repeating unit, and so on. The connections to use in the growth are instead defined selecting, among all the available connections of the building-block central unit, the one that should be used for the growth and the one that should instead be closed. The one that are closed, will be terminated with the corresponding capping.
- A dendrimeric segment from repeating unit is, similarly to the “from central unit” one, a dendrimer construction that uses the constituting elements of a SINGLE dendrimeric building block. In this case, however, the central unit of the building block is ignored and the growth starts directly from a repeating unit. This is not the standard way to construct dendrimer components, however we found it very useful because it leaves the possibility to have an open connection of type [*:1] that can connect to a previously constructed building block. The quantity that defines this dendrimeric segments are the same of the dendrimeric segment from central unit, with the only difference that now GO represent the case of one single repeating unit and that the connections available to open/close are only the one with label 1. The connection with label 0, as already mentioned, is not an available connection to grow from, but a connection to connect to a previous block.
We define polymer in the context of the polymer builder as a SINGLE POLYMER CHAIN. This might not be the unique definition that can be found in literature. In some contexts, the term polymer might refer to the macroscopic object that therefore is composed by several polymeric chains. However, we prefer here to separate what we call polymer (the single chain) and a polymer melt, that is a system containing various polymers. In technical terms, a polymer is a sequence of segments connected among them and for which all the cappings have been applied in order to guarantee that all the connections have been closed. Importantly, every atom in a polymer will be considered as part of the same entity for the generation of the topology: inter-component potentials are non-bonded interaction, while intra-component interactions are bonded interactions.

The GUI does not support the creation of a dendrimer yet, although the desired structure may be provided to you by our team. If this was the case, please contact support@nextmol.com .