CN104021265A - Complex system reaction access calculating system and implementing method thereof - Google Patents
Complex system reaction access calculating system and implementing method thereof Download PDFInfo
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Abstract
The invention belongs to the technical field of chemical and molecular structure information, and provides a complex system reaction access calculating system and an implementing method thereof. The calculating system comprises a molecular simulation and quantum chemistry calculating module, a molecular conformation searching module and a refined calculation and application module. A molecular structure simplified pattern reaction system is constructed, a characteristic reaction path is analyzed, and relevant key structures comprising ground states and transient states of reactions of a target reaction system are searched for. Based on a low-dimensional characteristic potential energy surface in a pattern system, a reaction network access is set up, and reaction coordinates of local minimum points and saddle points of a potential energy surface in a network are recorded; based on information of the reaction coordinates, molecule grafting restoring the pattern system (simple) to the target system (complex) is achieved. Through the molecular conformation searching technology, under the condition of characteristic coordinate restraint, a conformation set of reaction objects of the target system is searched for, and molecules in the conformation set are structurally optimized; effective ground state and transient state molecular structures of the reaction objects are collected according to the reaction characteristics of the characteristic coordinates on the reaction path.
Description
Technical field
What the present invention relates to is the system and method for a kind of chemistry and molecular structure information technical field, specifically quick location and prediction chemical reaction path, a reactant key structure, and calculate complex system reaction path computing system and its implementation of reaction activity.
Background technology
Chemical reaction is the restructuring of the chemical bond of molecular structure from reactant state to product state, and chemical reaction potential barrier is the key factor that determines chemical reaction rate, chemical production efficiency.In theory, can to a Chemical Kinetics, carry out complete description by building multidimensional potential energy surface.Yet the complete traversal search of multidimensional reaction potential energy surface need to consume huge calculated amount, current Computing level can not meet this demand, so the actual computation of multidimensional reaction potential energy surface scanning is still difficult to realize.During transition state theory calculates as a theory that theoretical model is widely used in reaction kinetics accurately and effectively.In multidimensional reaction potential energy surface, orienting response transition state structures will contribute to understand better chemical reaction generating process accurately and fast, calculate reaction rate.At present,, chemical constitution simple reaction system clear and definite for mechanism, according to transition state theory, can take the computation schema of conjecture-optimization to obtain possible reaction transition state, and under measured response coordinate approximate description key reaction path, judgement reaction rate determines the reaction path that step is pointed, calculates reaction activity.On mathematics, the transition state instructing based on transition state theory is searched computing method and has been obtained ripe and perfect development, and is able to widespread use in chemistry research by the Quantum chemical calculation based on from the beginning calculating.Yet chemical reaction is quite complicated under the particular surroundingss such as enzymatic system, solid surface, solvent medium and medium, this complexity is from diversity and the molecular structure complicacy of reaction intermediate.Although classic method is orienting response transition state structures fast and effeciently, it is very difficult and poor efficiency realizing the search location of all key structures on many response paths (comprising reaction intermediate, reaction transition state).Moreover, the structural complexity existing for reactant self, the reaction coordinate of low dimension has been not suitable for the reaction potential energy surface of a complete response path of approximate description.Therefore, current chemistry means are also difficult to the angle from chemical reaction, accurately and in the total space, search orienting response transition state.Meanwhile, laboratory facilities are difficult to catch the reaction intermediate that relative energy is higher, and in the aspect of molecular modification, molecular screening, depend on the result of calculation of theoretical research.
Summary of the invention
The present invention is directed to prior art above shortcomings, a kind of complex system reaction path computing system and its implementation are proposed, in mode system, the feature potential energy surface of low dimension is set out, set up reaction network path, and record the reaction coordinate of potential energy surface local minizing point and saddle point in network, and based on reaction coordinate information guiding, realize the molecule grafting that is reduced to complex (complexity) by mode system (simply).Under the condition fettering at characteristic coordinates by molecular conformation search technique, the conformation set of searching target system reactant, and the concentrated molecule of conformation is carried out to structure optimization, and the response characteristic on response path is collected effective reactant ground state and transition state molecular structure according to characteristic coordinates.
The present invention is achieved by the following technical solutions:
The present invention relates to a kind of complex system reaction path computing system, comprise: molecular simulation and quantum chemistry calculation module, molecular conformation search module and accurate Calculation and application module, wherein: molecular simulation and quantum chemistry calculation module, according to the initial molecular structure of reactant mode system, adopt molecular dynamics simulation to obtain with the method for quantum chemistry calculation the key reaction coordinate that reacts ground state and transition state structures; Molecular conformation search module be take key reaction coordinate as oriented information guiding, and for reactant real system, complex is carried out molecular conformation search, expands the conformational space that obtains reactant; Accurate Calculation and application module be according to conformational space, accurate optimization reactant ground state and transition state structures under the quantum chemistry calculation level of high-order, and calculate energy and thermodynamic data.
The implementation method that the present invention relates to said system, comprises the following steps:
Step 1) builds the pattern reaction system and parsing characteristic reaction path that molecular structure is simplified, and specifically comprises the following steps:
1.1) simplify reactant molecule structure, set up the pattern reaction materil structure system that retains the relevant feature structure of reaction;
1.2) molecular dynamics simulation builds mode system reaction potential energy surface;
1.3) abstraction reaction path and ground state, the transition state structures characteristic reaction coordinate in potential energy surface.
Step 2) the relevant key structure of the reaction of searching target reaction system, containing ground state, transition state, specifically comprises the following steps:
2.1) in the situation that retain the characteristic reaction coordinate of response feature structure, the approximation steady state structure of reduction establishing target reactant;
2.2), under the fixing pattern of characteristic reaction coordinate, carry out the molecular conformation search of reactant;
2.3) collect the conformation collection of reactant, and respectively reactant is carried out the structure optimization of structure optimization completely and transition state direction according to the response feature under reaction materil structure;
2.4) collect reactant ground state, the set of transition state molecular structure.
Technique effect
Compared with prior art, the present invention can solve prior art means and be difficult to the fast resolving complex molecule system that the realizes key structure in chemical reaction, calculates reaction activity, and provides strong theoretical foundation for the response characteristic research of biological enzyme system.
By complex system of the present invention, react path computing system orienting response transition state fast, and calculate reaction activity.The reaction activity of reaction molecular system is often subject to the molecular composition of system and the impact of peripheral chemical environment and changes.Therefore, in the fields such as molecule industrial design and chemical preparation, the present invention can predict what molecular composition (as changed substituting group) or be equipped with which kind of chemical reagent by being conducive to the generation of reaction, effectively reduces reaction activity, improves chemical production efficiency.Meanwhile, the Accurate Prediction chemical test that effectively alternative cost is high and process is numerous and diverse calculating based on theory, thus reduce production costs.
In addition, in biosynthesizing industry, the present invention can be effectively for biology enzyme provides rational substrate structure (ground state, transition state), and predict that by follow-up molecular simulation different biology enzymes are for the impact of enzyme-catalyzed reaction and reaction activity.On this basis, for enzyme molecular modification in biosynthesizing provides direction accurately, to optimize course of reaction, improve reaction efficiency, and be finally applied to enzyme and prepare relative enzyme reaction chemical technology.
Accompanying drawing explanation
Fig. 1 is quick orienting response architectural feature molecular structure techniqueflow chart.
Fig. 2 is the reaction pattern figure of phenol free radical-propylene compound hydrogen transfer process, and wherein phenol free radical-propylene compound is mode system schematic diagram of the present invention.
Fig. 3 is the two-dimentional scatter diagram of the characteristic reaction coordinate of Eugenol free radical-Eugenol system hydrogen transfer process reaction transition state;
Wherein: Eugenol free radical-Eugenol system is complex system of the present invention.
Fig. 4 is some feature structure schematic diagram of Eugenol free radical-Eugenol system hydrogen transfer process reaction transition state.
Embodiment
Below embodiments of the invention are elaborated, the present embodiment is implemented take technical solution of the present invention under prerequisite, provided detailed embodiment and concrete operating process, but protection scope of the present invention is not limited to following embodiment.
Embodiment 1
The present embodiment reacts path computing system by complex system and is achieved, this system comprises: molecular simulation and quantum chemistry calculation module, molecular conformation search module and accurate Calculation and application module, wherein: molecular simulation and quantum chemistry calculation module, according to the initial molecular structure of reactant mode system, adopt molecular dynamics simulation to obtain with the method for quantum chemistry calculation the key reaction coordinate that reacts ground state and transition state structures; Molecular conformation search module be take key reaction coordinate as oriented information guiding, and for reactant real system, complex is carried out molecular conformation search, expands the conformational space that obtains reactant; Accurate Calculation and application module be according to conformational space, accurate optimization reactant ground state and transition state structures under the quantum chemistry calculation level of high-order, and calculate energy and thermodynamic data.
Described molecular simulation and quantum chemistry calculation module comprise: preparation unit, molecular simulation unit and reaction coordinate and data analysis unit, wherein: preparation unit is determined the simplified model that meets reaction establishment condition according to goal response system; Molecular simulation unit is by three kinds of technological means structure of realization response paths and reaction coordinate respectively: 1) Metadynamics method for the little reaction system of molecular scale can rapid build one dimension to the potential energy surface of reacting of multidimensional, 2) the umbellate form method of sampling is applicable to one dimension response path, 3) by Quantum chemical calculation, directly calculate the reaction transition state that reaction mechanism is clear and definite; Reaction coordinate receives and reacts potential energy surface by the multidimensional of Metadynamics technique construction with data analysis unit, collects the reaction coordinate of reactant ground state and transition state.
Described molecular conformation search module comprises: molecule grafting unit, molecular conformation search unit and structure optimization unit, wherein: it is foundation that the reaction coordinate being obtained in molecular simulation and quantum chemistry calculation module be take in molecule Graft Method unit, realization response system is reduced to the process of complex by mode system, build reactant ground state and transition state analog structure; Molecular conformation search unit is usingd reactant ground state and transition state analog structure as initial configuration, realizes molecular conformation search, and produce molecular conformation collection under the constant condition of molecular reaction coordinate; Structure optimization unit receives molecular conformation collection, optimizes molecular structure in the level of quantum chemistry calculation completely, collects reactant effectively ground state and transition state structures set of duplicate removal on response path.
Described accurate Calculation and application module comprise: accurate optimization unit, reaction activity computing unit and interpretation of result and output unit, wherein: accurate optimization unit is taked Higher Order Quantum chemical calculation method to carry out structure to the reactant ground state of having optimized and transition state structures to optimize again; Reaction activity computing unit receives accurate optimization unit for the energy result of calculation of reactant ground state and transition state, and the true path of reduction reaction system and routing are calculated the true energy of activation of reaction; Interpretation of result and output unit record computation process, the accuracy of the result and rationality, output result of calculation.
The intermolecular hydrogen transfer process of Eugenol free radical-Eugenol transition state is searched.
The concrete implementation step of the present embodiment is as follows:
Step 1) determines that the mode system of formation hydrogen transfer process is phenol free radical-propylene compound intermediate, and according to the initial composite thing structure of document definition structure mode system, determines the reaction coordinate CV of its independent transition state structures
0(d1, d2);
Step 2) at coordinate CV
0(d
1, d
2) under fixing pattern, by the molecular conformation space of polymolecular conformation search engine traversal seek mode system compound;
Step 3) adopts the structure optimization collection mode system compound of transition state direction about the conformation set of hydrogen transfer process transition state structures;
The reaction coordinate of step 4) cluster analysis mode system transition state conformation set, concludes and draws crucial characteristic reaction coordinate set { CV
0(d
1, d
2) |
i=1,2 ... };
Step 5) builds labyrinth system Eugenol free radical-Eugenol compound intermediate based on characteristic coordinates set, and repeating step 2 and step 3, collects the transition state structures of complex;
The conformational analysis of step 6) based on result.
Eugenol is a kind of propenylbenzene compounds being extensively present in plant.As a kind of natural, Eugenol can suppress to depend on the oxidation of low-density lipoprotein and the generation of active oxygen of copper.Its oxidizing process forms quinone methyl intermediate by secondary oxidation, by building Phenoxy radical and Eugenol reaction model, finds key reaction path and transition state structures, thereby illustrates secondary oxidation process, as shown in Figure 2.
Two kinds of different structures of the transition state apokoinou construction A of mode system phenol free radical-propylene compound intermediate and structure B and mirror-image structure separately thereof.These two kinds of different structures have the closely similar architectural feature in many places: 1) the key component O-H-C of hydrogen transfer is approximately a straight line; 2) heavy atom at hydrogen two ends forms to be similar to electronic structure and the hydrogen of ground state the effect that is weaker than less chemical bond; 3) phenol part is partly similar to and is in parallel each other plane with propylene.These two kinds of structures have identical reaction coordinate simultaneously, so the characteristic coordinates set of Phenoxy radical hydrogen transfer system is a unit set:
Eugenol free radical-Eugenol is the structure extension of phenol free radical-propylene intermediate, at least comprises 7 main dimensions, and its intermediate structure surpasses 100 kinds, belongs to complex system described in the invention.Therefore to understand reaction path and the reaction transition state of this system, need to have automatable technological means, from the reaction intermediate of global search system.Reaction mechanism and phenol free radical-propylene system of Eugenol free radical-Eugenol system are similar, and phenol free radical-propylene system is a simplified model of the type hydrogen transfer process, and it is relatively fixing and limited to have the mode configuration of intermediate.Therefore,, as described in implementation step, phenol free radical-propylene system can be used as the mode system of Eugenol free radical-Eugenol system.
Under step of the present invention, obtain altogether 178 effective transition state structures (the relative energy threshold value 0 ~ 20.0KJ/mol of take is standard).As phenol free radical-propylene system of mode system, and expansion obtains Eugenol free radical-Eugenol system on its basis, and the reaction coordinate of these two kinds of different systems is close, but has deviation.In the sample of Eugenol free radical-Eugenol system, actual reaction coordinate point group has three kinds of features: 1) with characteristic reaction coordinate
compare to exist and depart from, illustrate in the Eugenol free radical-Eugenol system stronger repulsive interaction of existence cause reaction intermediate in the operating distance of hydrogen and two ends hydrogen acceptor longer; 2) than phenol free radical-propylene reaction intermediate with fixed sturcture, Eugenol free radical-Eugenol system has presented the diversity of transition state structures, has specifically also shown that the discreteness of coordinate point group distributes, as shown in Figure 3; 3) distribution of point group is approximate meets negative linear correlation (r=-0.967), that is to say that hydrogen can be partial to a wherein side to some extent.
Fig. 4 has enumerated the representational reaction intermediate structure of part, relatively can represent with Δ H:
Δ H=H
eugenol free radical-Eugenol-H
eugenol free radical-H
eugenol.
Some low energy conformations in transition state structures have the feature that phenyl ring is parallel to each other and superposes, and this may can help stablize the structure of transition state because the π between bimolecular-π interacts.
Claims (7)
1. a complex system reacts path computing system, it is characterized in that, comprise: molecular simulation and quantum chemistry calculation module, molecular conformation search module and accurate Calculation and application module, wherein: molecular simulation and quantum chemistry calculation module, according to the initial molecular structure of reactant mode system, adopt molecular dynamics simulation to obtain with the method for quantum chemistry calculation the key reaction coordinate that reacts ground state and transition state structures; Molecular conformation search module be take key reaction coordinate as oriented information guiding, and for reactant real system, complex is carried out molecular conformation search, expands the conformational space that obtains reactant; Accurate Calculation and application module be according to conformational space, accurate optimization reactant ground state and transition state structures under the quantum chemistry calculation level of high-order, and calculate energy and thermodynamic data.
2. system according to claim 1, is characterized in that, described molecular simulation and quantum chemistry calculation module comprise: preparation unit, molecular simulation unit and reaction coordinate and data analysis unit, wherein:
Preparation unit is determined the simplified model that meets reaction establishment condition according to goal response system;
Molecular simulation unit is by three kinds of technological means structure of realization response paths and reaction coordinate respectively: 1) Metadynamics method for the little reaction system of molecular scale can rapid build one dimension to the potential energy surface of reacting of multidimensional, 2) the umbellate form method of sampling is applicable to one dimension response path, 3) by Quantum chemical calculation, directly calculate the reaction transition state that reaction mechanism is clear and definite;
Reaction coordinate receives and reacts potential energy surface by the multidimensional of Metadynamics technique construction with data analysis unit, collects the reaction coordinate of reactant ground state and transition state.
3. system according to claim 1, it is characterized in that, described molecular conformation search module comprises: molecule grafting unit, molecular conformation search unit and structure optimization unit, wherein: it is foundation that the reaction coordinate being obtained in molecular simulation and quantum chemistry calculation module be take in molecule Graft Method unit, realization response system is reduced to the process of complex by mode system, build reactant ground state and transition state analog structure; Molecular conformation search unit is usingd reactant ground state and transition state analog structure as initial configuration, realizes molecular conformation search, and produce molecular conformation collection under the constant condition of molecular reaction coordinate; Structure optimization unit receives molecular conformation collection, optimizes molecular structure in the level of quantum chemistry calculation completely, collects reactant effectively ground state and transition state structures set of duplicate removal on response path.
4. system according to claim 1, it is characterized in that, described accurate Calculation and application module comprise: accurate optimization unit, reaction activity computing unit and interpretation of result and output unit, wherein: accurate optimization unit is taked Higher Order Quantum chemical calculation method to carry out structure to the reactant ground state of having optimized and transition state structures to optimize again; Reaction activity computing unit receives accurate optimization unit for the energy result of calculation of reactant ground state and transition state, and the true path of reduction reaction system and routing are calculated the true energy of activation of reaction; Interpretation of result and output unit record computation process, the accuracy of the result and rationality, output result of calculation.
5. according to an implementation method for system described in above-mentioned arbitrary claim, it is characterized in that, comprise the following steps:
Step 1) builds the pattern reaction system and parsing characteristic reaction path that molecular structure is simplified;
Step 2) the relevant key structure of the reaction of searching target reaction system, containing ground state, transition state.
6. method according to claim 5, is characterized in that, described step 1) specifically comprises following operation:
1.1) simplify reactant molecule structure, set up the pattern reaction materil structure system that retains the relevant feature structure of reaction;
1.2) molecular dynamics simulation builds mode system reaction potential energy surface;
1.3) abstraction reaction path and ground state, the transition state structures characteristic reaction coordinate in potential energy surface.
7. method according to claim 5, is characterized in that, described step 2) specifically comprise following operation:
2.1) in the situation that retain the characteristic reaction coordinate of response feature structure, the approximation steady state structure of reduction establishing target reactant;
2.2), under the fixing pattern of characteristic reaction coordinate, carry out the molecular conformation search of reactant;
2.3) collect the conformation collection of reactant, and respectively reactant is carried out the structure optimization of structure optimization completely and transition state direction according to the response feature under reaction materil structure;
2.4) collect reactant ground state, the set of transition state molecular structure.
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