CN105718719A - Simulation method for optimizing molecular structure of biosurfactant - Google Patents

Abstract

The invention discloses a simulation method for optimizing the molecular structure of a biosurfactant, which optimizes the molecular structure of a biosurfactant through a specific quantum chemical geometry optimization method to clarify the biosurfactant molecule in molecular dynamics simulation stable configuration. In this method, the initial configuration of the biosurfactant molecule is constructed first through the Materials Studio software, and secondly, the molecular structure optimization process of the biosurfactant is carried out by using the Calculation in the DMol ³ Tools module of the Materials Studio software, and finally, the vibration frequency obtained by calculation is used to judge Stable conformation of biosurfactant molecules. The simulation method of the invention provides an accurate and stable molecular model for the molecular dynamics simulation of the biosurfactant properties, and ensures the accuracy and reliability of the simulation.

Description

A Simulation Method for Optimizing the Molecular Structure of Biosurfactants

technical field

The invention relates to the field of research on the adsorption and self-assembly characteristics of biosurfactants, in particular to a simulation method for optimizing the molecular structure of biosurfactants.

Background technique

Chemical surfactant flooding is one of the main methods to enhance oil recovery in tertiary oil recovery, but after oil flooding, the oil field gradually exposed problems such as increased heterogeneity, serious channeling and formation pollution. Therefore, all major oil fields in my country are looking for a better oil recovery method to enhance oil recovery. Microbial oil recovery technology is to act on the oil reservoir through the metabolism of microorganisms (the function of cell body and microbial degradation, etc.) Crude oil and rock formations, improving the characteristics of high viscosity and difficult flow of heavy oil, sealing high permeability zones, increasing permeability of low permeability areas, and improving oil recovery are a biotechnology that is of great significance to further enhance oil recovery .

The ability of microorganisms to enhance oil recovery mainly depends on the degradation of crude oil by microorganisms and the displacement of crude oil by microbial metabolites (biosurfactants, biogas, organic acids and biopolymers). Among them, biosurfactants play a vital role in microbial oil recovery. Biosurfactants are a class of surfactants produced by microorganisms with biological properties. Bio-surfactants have advantages that many chemical surfactants do not have: bio-surfactants can maintain relatively high activity in a wide temperature range and high salinity It is not easy to be inactivated under harsh conditions; it is easily degraded by microorganisms, has little or no toxicity, and does not pollute the environment; it has specificity and selectivity; it has a wide range of raw materials and low prices.

In order to clarify the oil displacement mechanism of biosurfactants, researchers have used experimental methods to evaluate their macroscopic properties such as reducing surface tension, emulsifying crude oil, and changing rock wettability, but microscopic properties such as adsorption and self-assembly cannot be completely determined by experimental methods. However, molecular simulation methods have great advantages in explaining microscopic interactions at the molecular and atomic levels. Therefore, molecular simulation research on the adsorption and self-assembly properties of biosurfactants came into being. In molecular simulation, the rationality and accuracy of the model are the premise and key of the whole simulation process. Therefore, an accurate biosurfactant molecular configuration is crucial for the molecular simulation research of its adsorption and self-assembly properties.

Contents of the invention

Aiming at that the structure of biosurfactant is more complicated than that of chemical surfactant, the molecular dynamics optimization method commonly used for chemical surfactant is not applicable to the problem of structure optimization of biosurfactant. The present invention provides an optimized biosurfactant The simulation method of molecular structure, which is used to accurately optimize the stable configuration of biosurfactant molecules in molecular simulation, lays a good foundation for the molecular simulation research of biosurfactant adsorption and self-assembly characteristics.

Its technical solutions include:

A simulation method for optimizing the molecular structure of a biosurfactant, comprising the following steps in sequence:

Step 1: Build an initial model,

Use the Sketch tool in the MaterialsStudio software to construct the biosurfactant molecule to be calculated as the basic molecular structure data file;

Step 2, optimizing the molecular structure of the biosurfactant,

Use the Calculation in the DMol ³ module to carry out energy minimization processing on the structure data file in step 1, and obtain the molecular structure data file after energy minimization processing;

Step 3, determine the stable configuration of the biosurfactant,

Use VibrationalAnalysis to extract the vibration frequency parameters of the molecular structure data file after energy minimization processing. If the extracted vibration frequency parameters are all positive values, the molecular structure after energy minimization processing is the stable configuration of the biosurfactant; If the vibration frequency parameter has a negative value, fine-tune the molecular structure corresponding to the negative value along the vibration direction, repeat step 2, and then judge according to the vibration frequency parameter until the vibration frequency parameters are all positive values.

As a preferred solution of the present invention, the biosurfactant is rhamnolipid.

Compared with the molecular mechanics optimization method of biosurfactant, the optimization method provided by the present invention has obvious advantages: molecular mechanics optimization is an optimization process carried out according to the interaction of each atom of the molecule on the atomic level, and the optimization method of the present invention is The process of optimizing molecules using the Schrödinger equation from the electronic level, so the biosurfactant molecular configuration optimized by the method of the present invention has more accurate, reasonable and stable characteristics, thereby further ensuring the results of biosurfactant property simulation With accuracy and reliability.

Description of drawings

The present invention will be further described below in conjunction with accompanying drawing:

Fig. 1 is the initial configuration of rhamnolipid molecule;

Fig. 2 is the unstable configuration after adopting the method of the present invention to optimize;

Fig. 3 adopts the stable configuration after the method optimization of the present invention;

Fig. 4 is a rhamnolipid gas-liquid interface model;

Figure 5 is the standard for dividing the hydrophilic and hydrophobic groups of rhamnolipid molecules; wherein the rhamnose ring Ring, carboxyl COOH and ester group COO are hydrophilic groups, and the carbon chains Line1 and Line2 are hydrophobic groups;

Fig. 6 is the rhamnolipid hydrophilic-hydrophobic group interface density curve optimized by the method of the present invention;

Fig. 7 is the interface density curve of rhamnolipid hydrophilic and hydrophobic groups optimized by molecular mechanics.

detailed description

The present invention will be described in detail below in conjunction with specific embodiments and accompanying drawings.

Example 1:

In the following, the optimization of the molecular structure of biosurfactant rhamnolipid is taken as an example to further understand the technical solutions and advantages of the present invention.

The method for simulating the molecular structure of biosurfactant rhamnolipid specifically comprises the following steps:

1. Initial Model Construction

According to the relevant experimental and theoretical literature of rhamnolipids, the molecular structure of rhamnolipids was obtained, and the molecular structure of rhamnolipids was manually constructed using the Sketch tool of MS software as the basic molecular structure data file. The initial structure of rhamnolipids The type is shown in Figure 1;

2. Optimization of biosurfactant structure

Determine the software parameters for structure optimization, use the GeometryOptimization method when optimizing the structure of biosurfactants, select Fine as the precision, and calculate the number of steps as 500 steps, and use density functional theory (DFT) to optimize the molecular structure: the rotation setting of molecules during the optimization process In order not to be restricted, the method of combining generalized gradient approximation (GGA) and PBE density functional (GGA-PBE) is used to calculate the electron exchange correlation energy, and all electrons of the atom are calculated using the double-valued basis set addition. function (DNP) expansion; the convergence criteria of energy, gradient, displacement and self-consistent field (SCF) in quantitative calculations are 1×10 ^-5 Hartree, and 1×10 ^-6 Hartree, where the maximum number of self-consistent field cycles is 300;

3. Judgment of stable configuration of biosurfactant

Use VibrationalAnalysis to extract the vibration frequency parameters of the molecular structure data file after energy minimization processing. If the extracted vibration frequency parameters are all positive, the molecular structure after energy minimization is the stable configuration of the biosurfactant; if the vibration frequency parameters have negative values, the molecular structure corresponding to the negative value will vibrate along the Fine-tune the direction, repeat step 2, and then judge according to the vibration frequency parameters until the vibration frequency parameters are all positive values. The unstable configuration of rhamnolipid with negative vibration frequency after optimization is shown in Figure 2, and the stable configuration of rhamnolipid is shown in Figure 3. The carbon chain on the right side of the rhamnolipid with an arrow in Figure 2 is the molecular structure corresponding to the negative vibration frequency, which shows that the energy in this region has not yet reached the minimum. After fine-tuning along the vibration direction, optimization was performed again to obtain the stable configuration of the rhamnolipid shown in Figure 3. Comparing Figure 2 and Figure 3, it can be seen that there are differences between the unstable and stable configurations of rhamnolipids.

4. Verification of the stable configuration of biosurfactants

Using the stable configuration of rhamnolipids to build a rhamnolipid gas-liquid interface model, perform molecular mechanics optimization (DiscoverMinimizer) on the model, and then perform molecular dynamics simulation (DiscoverMolecularDynamics) on the optimized model to extract rhamnolipids Density curves of hydrophilic and hydrophobic groups. The rhamnolipid gas-liquid interface model is shown in Figure 4, the standard part of the rhamnolipid molecular hydrophilic and hydrophobic group division is shown in Figure 5, and the rhamnolipid hydrophilic and hydrophobic group interface density curve optimized by the method of the present invention is shown in Figure 6 . As can be seen from Figure 6, the highest peak position of the density curve of the rhamnose ring, carboxyl group and ester group (hydrophilic group) in the rhamnolipid is in the interfacial water layer region, and the density of the carbon chain (hydrophobic group) The highest peak of the curve is in the gas phase region, it can be judged that the rhamnolipid molecule has amphipathicity, which further illustrates the rationality of the stable configuration of the rhamnolipid.

Molecular mechanics optimization was carried out on the initial model of rhamnolipid, and the gas-liquid interface of rhamnolipid was constructed with the stable configuration of rhamnolipid after molecular mechanics optimization. The model was also optimized by molecular mechanics and molecular dynamics simulation, and rhamnolipid was extracted Glycolipid hydrophilic and hydrophobic group density curves. The interface density curve of the rhamnolipid hydrophilic and hydrophobic groups after molecular mechanics optimization is shown in Figure 7. It can be seen from Figure 7 that the highest peak of the density curve of the ester group and carboxyl group (hydrophilic group) of the rhamnolipid is in the gas phase, which shows that the stable configuration of the rhamnolipid after molecular mechanics optimization is unreasonable . Compared with the rhamnolipid stable configuration optimized by the method of the present invention, it shows that the optimization method provided by the present invention is more accurate.

The initial configuration of the rhamnolipid and the molecular mechanics optimization parameters of the gas-liquid interface model: Compass is used for the force field, the AtomBased method is used for the calculation of the Van der Waals interaction, the Ewald method is used for the calculation of the Coulomb interaction, and SmartMinimization is used for the optimization method, and the number of optimization steps is 5000 steps; Molecular dynamics simulation parameters of the liquid interface model: NVT is selected for the ensemble, 298K is selected for the temperature, the simulation time is 4000ps, the time step is 1fs, and one frame is output every 1000 steps.

It should be noted that, on the basis of the above-mentioned rhamnolipid (as the most representative glycolipid biosurfactant), those skilled in the art can also use the method of the present invention to optimize the molecular structure of other biosurfactants.

Claims (2)

1. the analogy method optimizing biosurfactant molecular structure, it is characterised in that comprise the following steps successively:

Step one, structure initial model,

Utilize the biosurfactant molecule to be calculated of the Sketch tools build in MaterialsStudio software as basic molecular structural data file；

Step 2, biosurfactant molecular structure is optimized,

Utilize DMol³Structured data document in step one is carried out energy minimization process by the Calculation in module, obtains the molecular structural data file after energy minimization processes；

Step 3, judge biosurfactant structural stability,

VibrationalAnalysis is utilized to extract the frequency of vibration parameter of molecular structural data file after energy minimization processes, if the frequency of vibration parameter extracted be on the occasion of, then the molecular structure after energy minimization processes is the structural stability of biosurfactant；If frequency of vibration parameter has negative value, then the molecular structure that negative value is corresponding is finely tuned along direction of vibration, repeats after step 2, judge further according to frequency of vibration parameter, until its frequency of vibration parameter be on the occasion of.

2. the analogy method of optimization biosurfactant molecular structure according to claim 1, it is characterised in that: described biosurfactant is rhamnolipid.