**1. Introduction**

Antimicrobial resistance against available antibiotics has been acknowledged as one of the most serious problems in medicine nowadays. This resulted in a surge of new research works related to the synthesis of novel compounds that could serve as a potential modern-generation groups of antimicrobial particles. One of these groups are Gemini surfactants (initially referred to as bis-surfactants), which are heavily reported for their antimicrobial effect [1]. In recent years, Gemini surfactants have been heavily addressed in the world of science. Over the past five years, more than 130 articles dealing with the subject of Gemini surfactants have been published, among which researchers determined the methods of synthesis of new compounds, their physicochemical properties and even their potential use or application.

Gemini surfactants have unique structural properties. They consist of two amphiphilic groups connected by a spacer at the head level, which can be both hydrophilic and hydrophobic [2,3]. They have at least two hydrophobic chains and two ionic or polar groups. There is a grea<sup>t</sup> variety in their structure e.g., short and long methylene groups can be used as a linker, stiff (stilbene), polar (polyether) and nonpolar (aliphatic) groups can be used as a linker [2,3]. The ionic group can be positive (ammonium) or negative (phosphorus,

**Citation:** Rzycki, M.; Kaczorowska, A.; Kraszewski, S.; Drabik, D. A Systematic Approach: Molecular Dynamics Study and Parametrisation of Gemini Type Cationic Surfactants. *Int. J. Mol. Sci.* **2021**, *22*, 10939. https://doi.org/10.3390/ijms222010939

Academic Editor: Małgorzata Borówko

Received: 27 August 2021 Accepted: 8 October 2021 Published: 10 October 2021

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**Copyright:** © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

sulfur, carboxylase), while the polar non-ionic groups can be polyether or sugar. Most Gemini surfactants have a symmetrical structure with two identical polar groups and two identical chains (but there are also Gemini that are asymmetrical or with three polar groups or chains) [4]. A universal scheme of Gemini is presented in Figure 1.

**Figure 1.** General scheme of Gemini structure classification presented on QAS-type spacer Gemini molecule.

A major part of synthesised Gemini surfactants has performed exquisite antibacterial properties against both Gram-positive and Gram-negative bacteria [5–7]. The most common antibacterial particles of this group are based on quaternary ammonium salts (QAS). Such salts prevent the development of bacteria and fungi; therefore, they are used on a large scale for cleaning, maintenance and disinfection. There were several attempts to evaluate the effectiveness of antibacterial activity of Gemini surfactants. However, these are usually limited to the compound structure—it is directly associated with the type and length of spacer in the molecule and/or the length of hydrophobic chains [8–10]. Numerous scientists proved that number of carbon atoms is correlated with the antimicrobial activity [11,12]. It has been established that a greater number of carbons in the molecule's structure increases its antibacterial activity, and the presence of 12 carbon atoms cause the greatest antibacterial response. It was proposed that the shorter chains might not interact with the hydrophobic region of the bilayer as smoothly and immediately as the longer ones [13]. However, very long tails might curve and twist disqualifying the interactions with negatively charged membrane surfaces by covering cationic head groups. Although it is believed that the major element in the surfactant antimicrobial properties is connected to the hydrophobic chain. It was confirmed that the head group type and structure are also essential factors of biological activity as in the case of QAS molecules [14]. Moreover, Moran et al. revealed that the structure of the hydrophilic core also plays an important role in antimicrobial effects [15,16].

Nevertheless, as mentioned earlier, all works focus only on the structural differences of Gemini surfactants. Furthermore, the conclusions are usually limited to one subgroup of Gemini compounds, hence when analysed more globally, are often mutually contradictory. The reported antimicrobial activity is based on minimum inhibitory concentration (MIC), which strongly depends on the protocol used [17]. The studies reporting the interactions and the effect of Gemini on membranes—with particular emphasis on their properties and potential rupture—are scarce in the literature. There are only available few studies on commercially available Gemini surfactants such as octenidine (OCT) [18–20]. This is quite surprising as membrane destruction was emphasised as one of the potential targets for antimicrobial effect [21,22]. To this end, in our work we have focused on systematic theoretical studies of Gemini agents. Specifically, we have reviewed available literature and

recreated the structure of the synthesised Gemini particle groups. This was followed by the classification of molecules into subgroups and the parametrisation of the compounds to create force fields for molecular dynamics studies. As a result, we obtained 250 valid force fields of Gemini class surfactants. Finally, we have selected valid representatives of the subgroups and investigated their interaction with lipid membranes. The selection of representatives was partially determined by the conclusions of structural studies. We ended with 25 selected particles used in molecular dynamics studies. The model membrane system was based on the inner membrane of *E. coli*. In this work we report the theoretical effect of Gemini class surfactants on properties and behaviour of the membrane. Additionally, the incorporation and behaviour of the molecules were also assessed. Based on our systematic characterisation of membrane system, we selected four parameters that were strongly affected by Gemini agents' incorporation. Those were: area compressibility, bending rigidity, lateral diffusion coefficient and surface tension. This selection of impactful parameters allowed us to make a preliminary selection of Gemini molecules groups that could show strong antimicrobial effect from those analysed. This work could provide a means for more detailed studies of Gemini class surfactants and their interaction with lipid membrane models. Such systematic computational analysis provides in silico method to select, from the group of molecules, the ones that are most likely candidates for antimicrobial compounds. It can result in decreasing the amount of expensive synthesis work, which can restrain this type of studies. In a further perspective, it could help in initial scanning of the molecules and facilitate comparison between different MIC studies to determine valid candidates for next-generation antimicrobial substances.

#### **2. Results and Discussion**
