Theoretical Studies On Metalloproteins Containing Transition Metal Elements By ABEEMσπ Fluctuating Charge Polarizable Force Field

Develop the atom-bond electronegativity equalization method(ABEEMσπ)fluctuating charge polarizable force field,for the first time in the expression of total potential energy function,introduce a reference charge and new parameters.Extend the application of ABEEMσπ fluctuating charge polarizable force field,so that it covers all the transition metal elements in the periodic table of elements.We select over a thousand of metalloprotein model molecules,most of metalloprotein model molecules come from the Protein Data Bank(PDB).We set different reference charges for different apparent valence states transition metals and calibrate the parameters of reference charges,valence state electronegativities and valence state hardnesses in ABEEMσπ method through linear regression and least square method.We calculate the charge distributions of model molecules,and compare it with the results obtained by ab initio method.Quite good linear correlations of the two kinds of charge distributions are shown.ABEEMσπ fluctuating charge polarizable force field can calculate the charge distributions with high accuracy and good reliability.The reason why the STO-3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail.Meanwhile,ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules,which consistent with dipole moments of high level ab initio method or the experimental value very well.Molecular dynamics optimizations of metalloproteins show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6-311G method,which means the rationality of parameters of the ABEEMσπ fluctuating charge polarizable force field,laid the foundation for further molecular dynamics simulations of actual systems that contain metalloproteins.Also apply ABEEMσπ model to study related properties of alkali and alkaline earth metal halides and non metal borides,such as charge distributions,dipole moments,etc,charge distributions of ABEEMσπ model and ab initio calculations are in good agreement,dipole moments of ABEEMσπ model and experimental data are also in good agreement,which lay a solid foundation for the later model extended greater range.Specific contents of this article are as follows:1.Develop the ABEEMσπ model contains all the transition metal elements in the periodic table of elementsBecause literatures of transition metals are simple and not comprehensive,most literatures study only one transition metal or a period transition metal,and this paper studies the ABEEMσπ model contains all transition metals elements.Develop theABEEMσπ method,first introduce the reference charge,describe the derivation of formulas and basic principles,we use a six-digit number label system to denote all the regions of atoms,σ and π bonds,and lone-pair electrons in ABEEMσπ fluctuating charge polarizable force field.As well as determine the reference charge,valence state electronegativity and hardness parameters of 57 elements in ABEEMσπ fluctuating charge polarizable force field.These parameters have good transferability,and can be well applied to the study of all the transition metal elements in the periodic table of elements in ABEEMσπ model.2.Charge distributions of metalloprotein model moleculesCalculate over a thousand metalloprotein model molecules of 57 elements for the first time.This section describes how to select model molecules from PDB interceptions and Gauss optimizations,the reason why we choose the STO-3G basis set in Mulliken population analysis for the parameter calibration,and the comparison of charge distributions of the ABEEMσπ method and ab initio(HF/STO-3G)method.Correlations coefficients are most over 0.93,which shows ABEEMσπ fluctuating charge polarizable force field can calculate the charge distributions with high accuracy and reliability.Charge distributions of ABEEMσπ model are based on different configurations and environments,can well reflect the polarization effect.ABEEMσπ model for the study of metallproteins actual system shows great advantage.3.Dipole moments of metalloprotein model moleculesAs a measure of whether the partial atomic charges calculated by a model is reasonable or not,one often calculates dipole moment of a system and then compares it with that obtained from experimental measurement or calculated by a high-level ab initio method.Here we calculate molecular dipole moments of total 25 models of 8 elements,apply various calculation methods to calculate dipole moments and compare calculation results with different methods.The linear correlation of dipole moments obtained from ABEEMσπ model and high level ab initio calculations(HF/6-311G(d,p))method is better than the dipole moments obtained from ABEEMσπmodel and HF/STO-3G method.The correlations coefficients are over 0.96,which shows that the ABEEMσπ method can quickly and accurately calculate molecular dipole moments.4.Preliminary study on dynamic properties of metalloprotein model molecules by ABEEMσπ fluctuating charge polarizable force fieldIn order to prove the reasonability,reliability and transferability of ABEEMσπparameters,we study dynamic properties of the metalloproteins containing Mo ion.First establish potential energy of metalloproteins containing molybdenum by ABEEMσπ fluctuating charge force field,and determine relevant force field parameters.Give a comparison of MP2 optimization and ABEEMσπ program optimization results of the 3bdja,lti4j,lvlfj,lg8ja and lg8ka five model molecules containing Moo+,the root mean square deviation values of bond length and bond angle of each model molecule are presented.The RMSDs of bond lengths of 3bdja,lti4j,lvlfj,lg8ja,and lg8ka model molecules are in order 0.0396,0.2158,0.2008,0.1309 and 0.0238A,respectively.The RMSDs of bond angles are 7.93°,8.91°,9.25°,6.96° and 6.06°,respectively.Results show that the ABEEMσπ fluctuating charge force field can be used to optimize the geometry of the metalloproteins containing Mo ion.5.Apply ABEEMσπ model to study the properties of alkali and alkaline earth metal halides and non metal boridesThis part gives model molecules of alkali and alkaline earth metal halides and non metal borides,charge distributions are calculated by HF/STO-3G method,the variation of the charge,at the same time charge distributions and their dipole moments are calculated in ABEEMσπ model,charge distributions of ABEEMσπ model and the results of the HF/STO-3G method are in good agreement.Dipole moments and experimental values are in good linear correlation,the correlations coefficients are most over 0.99.ABEEMσπ model can be applied to study properties of alkali and alkaline earth metal halides and non metal borides.