对ABEEM极化力场(ABEEM PFF)对核酸碱基、氨基酸侧链以及它们之间的相互作用进行研究.ABEEM PFF将体系的电荷密度分解到了原子区域、σ键区域、π键区域和孤对电子区域,各个区域的电荷可以随着体系结构的变化以及周围环境不同而浮动,很好体现了体系极化效应.在碱基和氨基酸之间的相互作用中氢键起到了很重要的关键作用.ABEEM PFF通过氢键拟合函数对氢键相互作用区域进行特殊的考虑和处理.研究结果表明,应用ABEEM电荷模型计算得到4个碱基模型、5个氨基酸侧链模型和20个相互作用模型的电荷分布以及偶极矩,计算结果与量子力学方法(QM)相媲美.应用ABEEM PFF对29个模型分子进行结构的优化得到稳定结构,与QM计算的结果以及实验的构象有很好的一致性.应用ABEEM PFF和QM方法计算20个碱基和氨基酸相互作用模型的相互作用能,计算结果表明带电的氨基酸侧链与碱基的相互作用能大于不带电氨基酸侧链.氨基酸侧链与碱基的相互作用能的顺序为:Lys>Asp/Glu>Arg>Asn/Gln>Ser/Thr.ABEEM PFF研究碱基和氨基酸侧链的相互作用,为研究和揭示蛋白质和核酸的相互识别机理奠定了良好的基础.

MFX (AlF30, AlF4- and MgF3-) as transition state analogues of phosphoryl transfer enzymes (enzyme-MFX-TSAs) is of great significance for study of the catalytic mechanism of phosphoryl transfer enzymes. Bonded model and non-bonded model based on the ABEEM polarizable force field (ABEEM PFF) are developed and applied to study the coordination of enzyme-MFX-TSAs. The bond stretching of the bond containing metal is simulated by Morse potential energy function, because the change of chemical bond is described more accurately in a large range. The charge distribution of the system is distributed to multiple-charge-sites, including atomic site, σ bond site, π bond site and lone pair electron site. Partial charge can fluctuate according to the surrounding environment and molecular conformation. The reasonable charge distribution of 68 model molecules can be obtained, and the energy minimizations are performed in vacuum. Then, with the same parameters the charge distribution and the charge transfer of four complexes are obtained, and the energy minimization and molecular dynamics simulation in NVT ensemble are carried out in vacuum and explicit water solution. The results verify the correctness, rationality and transferability of the new parameters of ABEEM PFF, and the bonded model simulates more reasonable charge distribution and geometry. The parameters determined in this paper make up the blank of the parameters of MFX and phosophoryl transfer enzymes containing Mg2+. The development of ABEEM PFF provides a refined tool for MFX-TSAs to study the catalytic mechanism of phosphoryl transfer enzymes.

首次开发ABEEM方法应用于含金属离子Ga3+蛋白体系的研究.ABEEM方法将分子电荷分解到了原子区域、σ键区域、π键区域和孤对电子区域.对金属离子Ga3+与蛋白之间的相互作用采用成键模型,Ga3+与配体原子之间有键电荷分布.通过蛋白晶体数据库的搜索,总结出Ga3+离子和蛋白相互作用的模型分子,确定了相关的新的电荷参数.应用ABEEM方法对模型分子的电荷分布、电荷转移和Ga3+离子的电荷进行了计算和分析.结果表明,ABEEM方法计算的电荷可以和从头算的HF/STO-3G方法的结果相比拟,可以快速给出所有的模型分子的电荷分布.并且通过金属离子Ga3+蛋白大分子体系的电荷计算验证了ABEEM方法以及电荷参数的正确性和可转移性.高价态的Ga3+离子和蛋白的相互作用的理论研究,为其动力学模拟研究奠定了基础.

Boronic acid, an inhibitor of β-lactamase, has begun to be applied to the treatment of biological infections and tumors. Scientists are working to develop new and more effective boronic acid. Molecular dynamics (MD) simulation provides a powerful auxiliary tool for drug design. However, the current force fields have no boron-related parameters. In this work, an atom-bond electronegativity equalization method at the σπ level (ABEEMσπ) polarizable force field (ABEEMσπ PFF) of boronic acid and β-lactamase has been developed to determine the potential functions and parameters. The interaction between boron and serine in β-lactamase is regarded as a bonded mode. The interaction between them is simulated by the Morse potential energy function, which is close to the experimental change of the stretching potential energy in a large range. The potential energy surfaces of the bond length, bond angle, and dihedral angle of boronic acid-β-lactamase have the same stability point and change trend as M06-2X/6-311G**. For 47 boronic acid-β-lactamase training molecules, the linear correlation coefficient (R) of the charge distribution between the ABEEMσπ PFF and HF/STO-3G is greater than 0.96. Attributed to the fact that the charge distribution of the ABEEMσπ PFF can fluctuate with the change of geometry and environment, the polarization effect and charge-transfer effect are well reflected. The binding ability of different boronic acids with the same β-lactamase is different. A total of 10 boronic acid-β-lactamase model molecules and 10 boronic acid-β-lactamase and water complexes are simulated. The order of binding energy of five large model molecules calculated by the ABEEMσπ PFF is consistent with that of the MP2 method. The binding energies of boronic acid-β-lactamase and water complexes are close to those of the MP2 method. The results of MD simulation of five aqueous boronic acid-β-lactamase complexes in the NVT ensemble verify the rationality of boron-related parameters of the ABEEMσπ PFF, which have a good application prospect. This study lays a solid theoretical foundation for further study of the inhibition of boronic acid on β-lactamase.

Based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), two fluctuating charge models of OH--water system were proposed. The difference between these two models is whether there is charge transfer between OH- and its first-shell water molecules. The structures, charge distributions, charge transfer, and binding energies of the OH-(H2O)n (n = 1-8, 10, 15, 23) clusters were studied by these two ABEEM/MM models, the OPLS/AA force field, the OPLS-SMOOTH/AA force field, and the QM methods. The results demonstrate that two ABEEM/MM models can search out all stable structures just as the QM methods, and the structures and charge distributions agree well with those from the QM calculations. The structures, the charge transfer, and the strength of hydrogen bonds in the first hydration shell are closely related to the coordination number of OH-. Molecular dynamics simulations on the aqueous OH- solution are performed at 298 and 278 K using ABEEM/MM-I model. The MD results show that the populations of three-, four-, and five-coordinated OH- are 29.6%, 67.1%, and 3.4% at 298 K, respectively, and those of two-, three-, four-, and five-coordinated OH- are 10.8%, 44.9%, 39.2%, and 4.9% at 278 K, respectively; the average hydrogen bond lengths and the hydrogen bond angle in the first shell increase with the temperature decreasing.

As the two-dimensional square ice in graphene nanocapillaries 10 was observed by transmission electron microscopy (TEM), a variety of theoretical methods have been applied to explore this phenomenon. However, a satisfactory model has not yet been described. Here, we investigate the structural properties and phase behavior of the confined water in graphene nanocapillaries by using the ABEEM sigma pi polarizable force field (PFF) with the ABEEM-7P water model and ABEEM sigma pi graphene model. The ordered AB-stacked bilayer and ABA-stacked trilayer square ice samples are acquired in 8.0 and 10.2 angstrom graphene nanocapillaries, respectively, at 298 K at a constant volume. Furthermore, the bilayer and trilayer ices demonstrate rhombus-square-triangular ice as the graphene nanocapillary changes from 7.8 to 8.6 and 10.0 to 11.0 angstrom, respectively. The results yielded by using a fixed charge force field with the SPC/E water model are different from those obtained by ABEEM sigma pi PFF. By changing the constant pressure from 0.5 to 1.5 GPa, the monolayer (bilayer) triangular ice is transformed to bilayer (trilayer) square ice in a 6.5 (9.0) angstrom graphene nanocapillary system. Additionally, the van der Waals interactions, density of the confined water, confinement width, polarization effects, and pressure all play decisive roles in the distribution of the confined water. Our study provides some clues for clarifying the experimental consequences of TEM.

Nitrosylation reaction mechanisms of the hydrolysates of NAMI‐A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI‐A occur in both the triplet and the singlet states. The Ru‐N‐O angle of the triplet ruthenium nitrosyl complexes is in the range of 132.0°–138.2°. However, all the ruthenium nitrosyl complexes at the singlet state show an almost linear Ru‐N‐O angle. The nitrosylation reaction happens prior to the hydrolysis reaction for the first‐step hydrolysates. The activation free energies of the nitrosylation reactions show that the H 2 O‐NO exchange reaction of [RuCl 4 (Im)(H 2 O)] in the singlet spin sate is the most likely one. Comparing with the activation free energies of the hydrolysis reactions of the ruthenium nitrosyl complexes, the results indicate that the rate of the DMSO–H 2 O exchange reaction of [RuCl 3 (NO)(Im)(DMSO)] is faster than that of [RuCl 3 (H 2 O)(Im)(DMSO)] in both the triplet spin state and the singlet spin state. © 2018 Wiley Periodicals, Inc.

It has been acknowledged that molecular oxygen produced in photosynthesis originates from water, rather than carbon dioxide. Dioxygen releases in the S-4-S-0 transition immediately prior to a new water binding to the oxygen-evolving complex, but hardly any investigation has been carried out on the binding mechanism up to date. Based on the open-cubane oxo-oxyl coupling mechanism in the S-4 state of photosynthetic oxygen evolution, in this study we propose three possible pathways of water binding to the oxygen-evolving complex Mn4CaO4 during the S-4-S-0 transition, i.e. water binding to Ca trans to O-5, water binding to Ca cis to O-5, and water binding to Mn4 trans to O-5. Broken-symmetry density functional theory (BS-DFT) calculations have demonstrated the thermodynamic feasibility for all these possible modes, without an overwhelming inclination for a certain manner. Besides, all these styles do not bring about any difference embodied in the experimental kinetic data on substrate water exchange in the S-1, S-2 and S-3 states, for the basically same structures of the S-0 state derived from these different routes. Therefore, it is considered that the alternative mechanisms could coexist coordinately in the connecting stage between S-state cycles. Importantly, diverse forms of substrate selectivity are deduced according to different water binding ways, which exert obvious influences on the present and later S-cycles. In the long run, however, it can be seen that the two waters binding in the S-4-S-0 and S-2-S-3 periods together constitute the components of the released O-2. What matters is variation of the time to become substrates for different water binding modes during the S-4-S-0 transition, either in the current cycle or in the following cycles. Meanwhile, it is indicated that the dangler Mn4(III)/(IV) which possesses a five-coordinated pyramidal ligand field in both S-0'/S-3' states, along with Ca(II) on which the carrousel rearrangement of water ligands can also occur, are essential structural elements of the S-state advancement and oxygen evolution. Thus, Mn4 and Ca may be in charge of water delivery to the active sites of Mn4CaO5 from the nearby external water channels formed by crystal waters in hydrogen-bond interactions. On the whole, the geometric flexibility of the Mn cluster plays an important role in photosynthetic water oxidation. In the respects of water binding modes in the S-4-S-0 transition and corresponding substrate identifications for a specific S-cycle, we are looking forward to further confirmations or supplements from the experimental evidences of the targeted isotope labeling combined with mass spectrometry, infrared spectroscopy and site directed mutagenesis, etc. Our investigation may provide useful information and references for the mechanistic elucidations on photosynthetic water oxidation, especially in substrate water identifications.

DNA damage caused by oxidized bases can lead to aging and cancer in living beings. Luckily, a repair enzyme is able to repair the oxidized bases. The key step is to accurately recognize the oxidized bases, which mainly rely on complex hydrogen bond interactions. We have calibrated the charge parameters and torsional parameters of the ABEEMσπ polarization force field (ABEEMσπ PFF) to accurately describe the intermolecular and intramolecular interactions. Taking the experiment and quantum chemical method as the benchmark, a series of properties of base pair-amino acid residue systems, DNA and DNA-protein interaction systems were calculated and compared with those of other force fields. We have done a tremendous amount of tasks in testing, calibrations, and analyses. The ABEEMσπ PFF not only explicitly gives the position and the partial charge of lone-pair electrons but also introduces a function kHB to fit special electrostatic interactions in hydrogen bond interaction regions. Therefore, it can accurately simulate the polarization effect and charge transfer of hydrogen bond interactions, especially for charged systems and sulfur-containing systems, such as the binding energy between amino acid and base pairs (24-28 kcal/mol), which is induced by charge transfer. The RMSD of ABEEMσπ PFF is 1.18 kcal/mol, whereas the RMSD of Amber OL15 is 8.21 kcal/mol. The relative positions of the amino acid residue have significantly changed, and the hydrogen bonds were broken when simulated by fixed charge force fields. In addition, owing to refitting the reasonable torsional parameters, the geometric structures optimized by ABEEMσπ PFF were well consistent with those of the M06-2X/6-311++G** method, but the simulations by fixed force fields have a large rotation of methyl and distortion of the plane of the base pair. After extensive MD simulation with four test DNAs and a DNA-protein system, we conclude that ABEEMσπ PFF shows better agreement when compared to experimental structures, which illustrates the reliability of our model and the transferability of the parameters.

Nuclease S1 can catalyze the nonspecific endo- and exonucleolytic cleavage of single-stranded DNA and RNA to yield nucleoside 5′-phosphates and 5′-phosphooligonucleotides. However, it cannot hydrolyze double-stranded DNA, double-stranded RNA, or DNA-RNA hybrid. Inspired by this specific property, a simple electrochemical method was developed for microRNA detection based on hybridization protection against nuclease S1 digestion. In the absence of hybridization process, the assembled probe DNA on the electrode surface can be easily digested by nuclease S1 and a strong electrochemical signal can be generated due to the decreased repulsive force towards the redox probe. However, after hybridization with target microRNA, the digestion activity of nuclease S1 is inhibited, which can lead to a weak electrochemical signal. Based on the change of the electrochemical signal, the detection of target microRNA-319a can be achieved. Under optimal experiment conditions, the electrochemical signal was proportional to microRNA-319a concentration from 1000 to 5 pM and the detection limit was 1.8 pM (S/N = 3). The developed method also showed high detection selectivity and reproducibility. Furthermore, the proposed method was successfully applied to assay the expression level of microRNA-319a in the leaves of rice seedlings after being incubated with different concentrations of 6-benzylaminopurine.

One of the primary oxidative DNA damage is 2,6-diamino-4-hydroxy-5-formamido pyrimidine, named Fapy-guanine(Fapy-G), which is the product of guanine oxidized at C8. The properties of 20 oxidative base pairs which contains Fapy-G were investigated via quantum chemistry methods. All model molecular structures were optimized with B3 LYP/6-31+G* method and the frequency calculations were carried out to confirm that all the structures obtains were geometrically stable. The energies were determined at the MP2/aug-cc-pVDZ level with BSSE corrections. The calculation results show that N7, N9 became hydrogen bond donor from accepter. Natural atomic charge of N7, N9 and O6 get more negative. The ability of O6 as H-bond donor enhanced. The bond lengths of C5—N7 and N7—C8 were increased by 0. 0045 and 0. 0063 nm, C4—N9 was decreased by 0. 0015 nm. Compared with bases monomers, natural atomic charge of proton acceptors in hydrogen bond complexes increased by 0. 05 e averagely, which is 8% of the original charge;natural atomic charges for proton donors have a decrease of 0. 02 e, which is 4% of the original charge. Com-pared with Fapy-G, when the N atom in Fapy-G six-membered ring was formed H-bond, the ring breathing and N-para-C vibrational frequencies were blue shifts. The vibrational frequencies were related to H-bond red shifts in all the base pairs. NH…N is stronger than NH…O in all the base pairs and in NH…N the hydrogen bond energy of donor N atom in six-membered ring are bigger than donor N atom in NH2 or open-ring. When Fapy-G pairs with base A, the binding energy region order is 1>2>4>3. When Fapy-G pairs with base T(R), the binding energy region order is 3=4>1>2. In water solvent, the binding energies of Fapy-G pairs with base C reduced to 41. 84—58. 58 kJ/mol, and the order of the binding energy was changed.

A fluctuating charge interaction potential function for alanine-water was constructed in the spirit of newly developed ABEEMσπ/MM(atom-bond electronegativity equalization method at the σπ level fused into molecular mechanics). The properties of gaseous neutral alanine-(H2O) n (n=1–7) clusters were systematically investigated by quantum mechanics(QM) and the constructed ABEEMσπ/MM potential, such as conformations, hydrogen bonds (H-bonds), interaction energies, charge distributions, and so on. The results of ABEEMσπ/MM model are in fair agreement with those of QM and available experimental data. For isolated alanine, compared with those of experimental structure, the average absolute deviations(AAD) of bond length and bond angle are 0.002 nm and 1.4°, respectively. For alanine-water clusters, the AAD of interaction energies and H-bond lengths are only 3.77 kJ/mol and 0.012 nm, respectively, compared to the results of MP2/aug-cc-pVDZ//MP2/6-311+G** method. The ABEEMσπ charges fluctuate with the changing conformation of the system, and can accurately and reasonably reflect the interpolarization between water and alanine. The presented alanine-water potential function may provide a basis for further simulations on related aqueous solutions of biomolecules.

Cu2O nanoparticles (nano-Cu2O) modified glassy carbon electrode (GCE) was fabricated and used to investigate the electrochemical behaviour of 4-nitrophenol (4-NP) by cyclic voltammetry (CV), chronoamperometry (CA), chronocoulometry (CC) and differential pulse voltammetry (DPV). Compared with GCE, a remarkable increase in oxidation peak current was observed. It indicates that nano-Cu2O exhibits remarkable enhancement effect on the electrochemical oxidation of 4-NP. Under the optimised experimental conditions, the oxidation peak currents were propotional to 4-NP concentration in the range from 1.0 x 10(-6) to 4.0 x 10(-4) mol L-1 with a detection limit of 5.0 x 10(-7) mol L-1 (S/N = 3). The fabricated electrode presented good repeatability, stability and anti-interference. Finally, the proposed method was applied to determine 4-NP in water samples. The recoveries for these samples were from 94.60% to 105.5%.

A simply and sensitively electroanalytical method for determination of bisphenol A (BPA) using poly(amidoamine) (PAMAM) and Fe3O4 magnetic nanoparticles modified glassy carbon electrode (GCE) was presented. Compared with bare electrode, PAMAM–Fe3O4 modified electrode not only significantly enhanced the oxidation peak current of BPA, but also lowered the oxidation overpotential, suggesting that the modified electrode can remarkably improve the determining sensitivity of BPA. Factors influencing the detection processes were optimised and kinetic parameters were calculated. Under the optimal conditions, the oxidation current increased linearly with increasing the concentration of BPA in the range of 1×10−8–3.07×10−6M with the correlation coefficient of 0.9996 and the detection limit of 5×10−9M. The current reached 95% of the steady-state current within about 6s. The proposed method was successfully applied to determine BPA in milk samples and satisfactory results were obtained.

A glassy carbon electrode was modified with hydroxyapatite nanopowder (HA-NP) and characterized in terms of electrochemical oxidation of 4-nitrophenol (4-NP) via cyclic voltammetry, differential pulse voltammetry, chronoamperometry, and chronocoulumetry. The oxidation peak current of 4-NP at the modified electrode was increased (compared to the bare GCE), thus indicating that the HA-NP exhibits a remarkable enhancement effect on the electrochemical oxidation of 4-NP. The effects of loading with HA-NP, pH value, scan rate and accumulation time were examined. The oxidation peak current of 4-NP is proportional to its concentration in the range from 1.0 μM to 300 μM, with a correlation coefficient of 0.9996. The detection limit is 0.6 μM (at an S/N = 3). The method is simple, selective and sensitive. It was successfully applied to the determination of 4-NP in water samples, with recoveries ranging from 96% to 104%.

The electrochemical behavior of guanine and adenine on the graphene and Nafion composite film modified glassy carbon electrode was investigated by differential pulse voltammetry (DPV). The results indicated that the modified electrode exhibited an excellent electrocatalytic activity towards the oxidation of guanine and adenine, testified by the increased oxidation peak current and decreased oxidation potential. The experimental conditions were optimized. The separation of the two oxidation peaks was 0.364V in 0.1M pH 4.4 acetate buffer solution (ABS). Based on this, a novel electrochemical method was proposed to simultaneously determine guanine and adenine with the detection limit of 0.58 (guanine) and 0.75 (adenine)μM (S/N=3). The proposed method was applied to determine guanine and adenine in milk powder, urine and herring sperm DNA samples with satisfactory results. The value of (G+C)/(A+T) in herring sperm DNA was calculated to be 0.8065. The fabricated electrode showed excellent reproducibility, stability and anti-interference.

Various properties of water clusters in the n = 2–34 size regime with the change of cluster size have been systemically explored based on the newly developed flexible-body and charge-fluctuating ABEEM/MM water potential model. The ABEEM/MM water model is to take ABEEM charges of all atoms, bonds, and lone-pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The computed correlating properties characterizing water clusters (H2O) n (n = 2–34) include optimal structures, structural parameters, ABEEM charge distributions, binding energies, hydrogen bonds, dipole moments, and so on. The study of optimal structures shows that the ABEEM/MM model can correctly predict the following important structural features, such as the transition from two-dimensional (from dimer to pentamer) to three-dimensional (for clusters larger than the hexamer) structures at hexamer region, the transition from cubes to cages at dodecamer (H2O)12, the transition from all-surface (all water molecules on the surface of the cluster) to one water-centered (one water molecule at the center of the cluster, fully solvated) structures at (H2O)17, the transition from one to two internal molecules in the cage at (H2O)33, and so on. The first three structural transitions are in good agreement with those obtained from previous work, while the fourth transition is different from that identified by Hartke. Subsequently, a systematic investigation of structural parameters, ABEEM charges, energetic properties, and dipole moments of water clusters with increasing cluster size can provide important reference for describing the objective trait of hydrogen bonds in water cluster system, and also provide a strong impetus toward understanding how the water clusters approach the bulk limit.

The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H 2 O) n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k lpO=,H and k lpO–,HN– , respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.

Various properties of typical structures of water clusters in the n = 2-34 size regime with the change of cluster size have been systematically explored. Full optimizations are carried out for the structures presented in this article at the Hartree-Fock (HF) level using the 6-31G(d) basis set by taking into account the positions of all atoms within the cluster. The influence of the HF level on the results has been reflected by the comparison between the binding energies of (H2O)(n) (n = 2-6, 8, 11, 13, 20) calculated at the HF level and those obtained from high-level ab initio calculations at the second-order Moller-Plesset (MP2) perturbation theory and the coupled cluster method including singles and doubles with perturbative triples (CCSD(T)) levels. HF is inaccurate when compared with MP2 and CCSD(T), but it is more practical and allows us to study larger systems. The computed properties characterizing water clusters (H2O)(n) (n = 2-34) include optimal structures, structural parameters, binding energies, hydrogen bonds, charge distributions, dipole moments, and so on. When the cluster size increases, trends of the above various properties have been presented to provide important reference for understanding and describing the nature of the hydrogen bond. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 110: 1923-1937, 2010

The ABEEM/MM force field for protein model is the fluctuating charge model for protein combined atom-bond electronegativity equalization method (ABEEM) and molecular methanics(MM). It can be explicitly responsive to the ambient environment and calculate polypeptide structures and properties in gas and solution. In this paper, the ABEEM/MM force field for protein model is first applied to study conformational properties of cysteine dipeptide, such as, energies of conformation, hydrogen bonds, etc. In addition, quantum chemistry calculations are carried out for calculating conformational properties of cysteine dipeptide at the HF/6-31G~ ** level. The ABEEM/MM force field for protein model can depict the polypeptide structures very well and obtain the different stable conformational properties fast and accurately. The results may compare in fair agreement with those of ab initio method. The above study will help us to further understand the cysteine dipeptide conformational properties, and provide the reliable evidence for testing the correctness of our model and the reasonableness of the parameters.