CN105718719A - Simulation method for optimizing molecular structure of biosurfactant - Google Patents
Simulation method for optimizing molecular structure of biosurfactant Download PDFInfo
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- CN105718719A CN105718719A CN201610024684.8A CN201610024684A CN105718719A CN 105718719 A CN105718719 A CN 105718719A CN 201610024684 A CN201610024684 A CN 201610024684A CN 105718719 A CN105718719 A CN 105718719A
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Abstract
The invention discloses a simulation method for optimizing molecular structure of biosurfactant. Through a specific quantum chemistry geometry optimization method, the molecular structure of the biosurfactant is optimized for making the stable configuration of a biosurfactant molecule in molecular dynamics simulation clear. The method comprises the following steps: firstly, through Materials Studio software, constructing an initial configuration of the biosurfactant molecule; secondly, utilizing Calculation in the DMol3Tools module of the Materials Studio software to carry out a molecular structure optimization process on the biosurfactant; and finally, through vibration frequency obtained by calculation, judging the stable configuration of the biosurfactant. The simulation method provides a stable and accurate molecular model for the molecular dynamics simulation of biosurfactant property, and guarantees the accuracy and the reliability of simulation.
Description
Technical field
The present invention relates to biological surface agent absorption and self assembly characteristic research field, be specifically related to a kind of analogy method optimizing biosurfactant molecular structure.
Background technology
The chemical surfactant displacement of reservoir oil is one of main method improving oil recovery factor in tertiary oil recovery, but after the displacement of reservoir oil, oil field exposes that anisotropism aggravation, channelling be serious and the problem such as formation contaminant gradually.Therefore, each elephant of China is all seeking a kind of oil production method improving oil recovery factor more preferably.Microbial Enhanced Oil Recovery is to act on oil reservoir Crude Oil and rock stratum by microorganism own metabolism effect (effect of cyton and microbiological deterioration etc.) and microbial metabolic products (biogas, small molecular weight acids, organic solvent, biopolymer and biosurfactant etc.), improve the characteristics such as the high and difficult flowing of Viscosity of Heavy Crude Oil, block high permeability zone, improve hypotonic district permeability, improve a biotechnology of oil recovery factor, have important meaning to improving oil recovery factor further.
Microorganism can improve oil recovery factor and depend primarily on microorganism self to the degraded of crude oil and the microbial metabolic products (biosurfactant, biogas, organic acid and biopolymer) the displacement two aspect effect to crude oil.Wherein, biosurfactant plays vital effect in microbe oil production.Biosurfactant is the surfactant with biological nature that a quasi-microorganism produces.Biotinylated biomolecule surfactant has the advantage not available for many chemical surfactants: biological surfactant can keep higher activity in very wide temperature range and when significantly high salinity, not easy in inactivation under acid and alkali condition；Easily being degraded by Institute of Micro-biology, toxicity is little or does not have toxicity, free from environmental pollution；There is specificity, selectivity；Raw material sources is extensive, cheap.
Mechanism of oil displacement for clear and definite biosurfactant, researcher adopts Evaluation on the experiment method, and it reduces the macroscopic properties such as surface tension, emulsified crude oil and change rock wettability, but the microscopic properties such as absorption and self assembly cannot adopt experimental technique to study completely, and molecule simulation method has greater advantage in explaining microcosmic interaction on molecule, atomic level, therefore the molecular simulation research of biosurfactant absorption and self assembly characteristic is arisen at the historic moment.In molecular simulation, the reasonability of model and accuracy are premise and the keys of whole simulation process, therefore, one accurately biosurfactant molecular configuration for its absorption and self assembly characteristic molecular simulation research it is critical that.
Summary of the invention
Structure for biosurfactant is more complicated than chemical surfactant, the problem that the molecular dynamics optimization method that chemical surfactant is conventional has not been suitable for biosurfactant structure optimization, the invention provides a kind of analogy method optimizing biosurfactant molecular structure, this analogy method is in order to the structural stability of biosurfactant molecule in optimization molecular simulation exactly, and the molecular simulation research for biological SURFACTANT ADSORPTION and self assembly characteristic lays a good foundation.
Its technical solution includes:
A kind of analogy method optimizing biosurfactant molecular structure, comprises 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.
As a preferred version of the present invention, described biosurfactant is rhamnolipid.
Optimization method provided by the invention has clear superiority compared with the molecular mechanics optimization method of biosurfactant: molecular mechanics optimization is interaction according to each atom of molecule and the optimization process that carries out on atomic scale, and the optimization method of the present invention is the process utilizing Schrodinger equation that molecule is optimized electronics aspect, biosurfactant molecular configuration hence with the inventive method optimization has more accurate, reasonable and stable feature, thereby further ensures that the result that biosurfactant nature is simulated has accuracy and reliability.
Accompanying drawing explanation
Below in conjunction with accompanying drawing, the present invention will be further described:
Fig. 1 is rhamnolipid molecule initial configuration；
Fig. 2 is the unstable configuration after adopting the inventive method to optimize；
Fig. 3 is the structural stability after adopting the inventive method to optimize；
Fig. 4 is rhamnolipid gas-liquid interface model；
Fig. 5 is rhamnolipid molecule hydrophilic-hydrophobic group division standard；Wherein rhamnose ring Ring, carboxy CO OH and ester group COO are hydrophilic group, and carbochain Line1 and Line2 is hydrophobic group；
Fig. 6 is the rhamnolipid hydrophilic-hydrophobic group interphase density curve adopting the inventive method to optimize；
Fig. 7 is the rhamnolipid hydrophilic-hydrophobic group interphase density curve adopting molecular mechanics to optimize.
Detailed description of the invention
Below in conjunction with specific embodiments and the drawings, the present invention is elaborated.
Embodiment 1:
It is optimized for example to be further appreciated by technical scheme and advantage below with rhanolipid as biosurfactant molecular structure.
The analogy method of rhanolipid as biosurfactant molecular structure, specifically includes following steps:
1, initial model builds
Related experiment according to rhamnolipid and theory literature, obtain the molecular structure of rhamnolipid, utilize the molecular structure of Sketch instrument manual construction rhamnolipid of MS software as basic molecular structural data file, and rhamnolipid initial configuration is as shown in Figure 1；
2, the optimization of biosurfactant structure
Determine the software parameter of structure optimization, GeometryOptimization method is adopted when optimizing biosurfactant structure, precision chooses Fine, calculating step number is 500 steps, adopt density functional theory (DFT) to carry out molecular structure and optimize process: the rotary setting optimizing process Middle molecule is unrestricted, adopt the method (GGA-PBE) that generalized gradient approximation (GGA) and PBE Density functional combine to calculate electron exchange correlation energy, adopt all-electronin to calculate all electronics of atom and adopt double; two basis set hyper polarization function (DNP) of numeric type to launch；Energy in quantum chemical method, gradient, displacement and self-consistent field (SCF) convergence be 1 × 10-5Hartree、With 1 × 10-6Hartree, maximum of which self-consistent field cycle-index is 300 times；
3, the judgement of 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, this 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.Optimizing after vibration frequency still has the rhamnolipid instability configuration of negative value to see Fig. 2, and the structural stability of rhamnolipid is shown in Fig. 3.Having carbochain on the right side of the rhamnolipid of arrow to be the molecular structure that negative frequency of vibration is corresponding in Fig. 2, this illustrates that this region energy is also not up to minimum.Again it is optimized after finely tuning along direction of vibration, obtains the structural stability of rhamnolipid shown in Fig. 3.Comparison diagram 2 and Fig. 3 are it can be seen that rhamnolipid instability configuration and structural stability there are differences.
4, the checking of biosurfactant structural stability
The structural stability utilizing rhamnolipid builds rhamnolipid gas-liquid interface model, model is carried out molecular mechanics optimization (DiscoverMinimizer), then again the model after optimizing is carried out molecular dynamics simulation (DiscoverMolecularDynamics), extract the hydrophilic density curve with hydrophobic group of rhamnolipid.Rhamnolipid gas-liquid interface model is shown in Fig. 4, rhamnolipid molecule hydrophilic-hydrophobic group division standard component Fig. 5, and the rhamnolipid hydrophilic-hydrophobic group interphase density curve after the inventive method optimization is shown in Fig. 6.As can be seen from Figure 6, in rhamnolipid, the density curve summit peak position of rhamnose ring, carboxyl and ester group (hydrophilic group) is at interfacial water layer region, the density curve summit peak position of carbochain (hydrophobic group) is in vapor phase areas, may determine that rhamnolipid molecule has amphiphilic, further illustrate the reasonability of rhamnolipid structural stability.
Rhamnolipid initial model is carried out molecular mechanics optimization, rhamnolipid structural stability after optimizing with molecular mechanics builds rhamnolipid gas-liquid interface, same model is carried out molecular mechanics optimization and molecular dynamics simulation, extract that rhamnolipid is hydrophilic and hydrophobic group density curve.Rhamnolipid hydrophilic-hydrophobic group interphase density curve after molecular mechanics optimization is shown in Fig. 7.As can be seen from Figure 7 the ester group of rhamnolipid and carboxyl (hydrophilic group) density curve summit peak position are in gas phase, and this illustrates that the rhamnolipid structural stability after molecular mechanics optimization exists irrationality.More accurate with the rhamnolipid structural stability comparative illustration optimization method provided by the invention optimized through the inventive method.
Rhamnolipid initial configuration and gas-liquid INTERFACE MODEL molecular mechanics parameters optimization: compass is selected in the field of force, Van der Waals interacts and adopts AtomBased method to calculate, Coulomb interactions adopts Ewald method to calculate, and optimization method selects SmartMinimization, and optimizing step number is 5000 steps；Gas-liquid interface Model Molecule dynamics simulation parameter: assemblage chooses NVT, and temperature chooses 298K, simulated time is 4000ps, and time step is 1fs, and every 1000 steps export a frame.
It should be noted that on the basis of above-mentioned rhamnolipid (as most representational Glycolipids Biosurfactants via), those skilled in the art can also optimize other biosurfactant molecular structure by the inventive method.
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.
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110875085A (en) * | 2018-09-03 | 2020-03-10 | 中国石油化工股份有限公司 | Method for efficiently optimizing molecular structures in batches |
| CN110880357A (en) * | 2019-11-21 | 2020-03-13 | 国网重庆市电力公司电力科学研究院 | Simulation analysis method for SF6 decomposition components based on carbon nano tube and readable storage medium |
| CN114242185A (en) * | 2021-12-23 | 2022-03-25 | 江汉大学 | Molecular self-assembly structure prediction method and device based on machine learning |
| CN114242185B (en) * | 2021-12-23 | 2024-10-25 | 江汉大学 | Molecular self-assembly structure prediction method and device based on machine learning |
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Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110875085A (en) * | 2018-09-03 | 2020-03-10 | 中国石油化工股份有限公司 | Method for efficiently optimizing molecular structures in batches |
| CN110875085B (en) * | 2018-09-03 | 2022-07-29 | 中国石油化工股份有限公司 | Method for efficiently optimizing molecular structure in batches |
| CN110880357A (en) * | 2019-11-21 | 2020-03-13 | 国网重庆市电力公司电力科学研究院 | Simulation analysis method for SF6 decomposition components based on carbon nano tube and readable storage medium |
| CN114242185A (en) * | 2021-12-23 | 2022-03-25 | 江汉大学 | Molecular self-assembly structure prediction method and device based on machine learning |
| CN114242185B (en) * | 2021-12-23 | 2024-10-25 | 江汉大学 | Molecular self-assembly structure prediction method and device based on machine learning |
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