QM/MM study of the active site of free papain and of the NMA-papain complex.

Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations using restricted and unrestricted Hartree-Fock and B3LYP ab initio (QM) and Amber force field (MM), respectively, have been applied to study the catalytic site of papain in both free and substrate bonded forms. Ab initio geometry optimizations have been performed for the active site of papain and the N-methyl-acetamide (NMA)-papain complex within the molecular mechanical treatment of the protein environment. A covalent tetrahedral intermediate structure could be obtained only when the amide N atom of the substrate molecule was protonated through a proton transfer from the His-159 in the catalytic site. Our results support the previous assumption that a proton transfer from His-159 to the amide N atom of the substrate occurs prior to or concerted with the nucleophilic attack of the Cys-25 sulfur atom to the carbonyl group of the substrate. The electron correlation effect will reduce the proton transfer barrier. Therefore, this proton transfer can be easily observed in the B3LYP/6-31G* calculations. The HF/6-31G* method overestimates the reaction barrier against this proton transfer. The sulfur atom of Cys-25 and the imidazole ring of His-159 are found to be coplanar in the free form of the enzyme. However, the rotation of the imidazole ring of His-159 was observed during the formation of the tetrahedral intermediate. Without the papain environment, the coplanar thiolate-imidazolium ion pair RS-...ImH+ is much less stable than the neutral form of RSH....Im. Within the protein environment, however, the thiolate-imidazolium ion pair becomes more stable than its neutral form by 4.1 and 0.4 kcal/mol in HF/6-31G* and B3LYP/6-31G* calculations, respectively. The barrier of proton transfer from S-H group of Cys-25 to the imidazole ring of His-159 was reduced from 22.0 kcal/mol to 15.2 kcal/mol by the protein environment in HF/6-31G* calculations. This barrier is found to be much smaller (2.5 kcal/mol) in B3LYP/6-31G* calculations.     

Theoretical investigations of the hydrolysis pathway of verdoheme to biliverdin

Conversion of iron(II) verdoheme to iron biliverdin in the presence of OH(-) was investigated using B3LYP method. Both 3-21G and 6-31G* basis sets were employed for geometry optimization calculation as well as energy stabilization estimation. Calculation at 6-31G* level was found necessary for a correct spin state estimation of the iron complexes. Two possible pathways for the conversion of iron verdoheme to iron biliverdin were considered. In one path the iron was six-coordinate while in the other it was considered to be five-coordinate. In the six-coordinated pathway, the ground state of bis imidazole iron verdoheme is singlet while that for open chain iron biliverdin it is triplet state with 4.86 kcal/mol more stable than the singlet state. The potential energy surface suggests that a spin inversion take place during the course of reaction after TS. The ring opening process in the six-coordinated pathway is in overall -2.26 kcal/mol exothermic with a kinetic barrier of 9.76 kcal/mol. In the five-coordinated pathway the reactant and product are in the ground triplet state. In this path, hydroxyl ion attacks the iron center to produce a complex, which is only 1.59 kcal/mol more stable than when OH(-) directly attacks the macrocycle. The activation barrier for the conversion of iron hydroxy species to the iron biliverdin complex by a rebound mechanism is estimated to be 32.68 kcal/mol. Large barrier for rebound mechanism, small barrier of 4.18 kcal/mol for ring opening process of the hydroxylated macrocycle, and relatively same stabilities for complexes resulted by the attack of nucleophile to the iron and macrocycle indicate that five-coordinated pathway with direct attack of nucleophile to the 5-oxo position of macrocycle might be the path for the conversion of verdoheme to biliverdin.     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

DFT studies of the conversion of four mesylate esters during reaction with ammonia

The energetics of the Menshutkin-like reaction between four mesylate derivatives and ammonia have been computed using B3LYP functional with the 6-31+G** basis set. Additionally, MPW1K/6-31+G** level calculations were carried out to estimate activation barrier heights in the gas phase. Solvent effect corrections were computed using PCM/B3LYP/6-31+G** level. The conversion of the reactant complexes into ion pairs is accompanied by a strong energy decrease in the gas phase and in all solvents. The ion pairs are stabilized with two strong hydrogen bonds in the gas phase. The bifurcation at C2 causes a significant activation barrier increase. Also, bifurcation at C5 leads to noticeable barrier height differentiation. Both B3LYP/6-31+G** and MPW1K/6-31+G** activation barriers suggest the reaction 2 (2a?+?NH₃) to be the fastest in the gas phase. The reaction 4 is the slowest one in all environments.

Density functional models of the mechanism for decarboxylation in orotidine decarboxylase

The mechanism of orotidine 5-monophosphate decarboxylase (ODCase) has been modeled using hybrid Density Functional Theory (B3LYP functional). The main goal of the present study was to investigate if much larger quantum chemical models of the active site than previously used could shed new light on the mechanism. The models used include the five conserved amino acids expected to be the most important ones for catalysis. One result of this model is that a mechanism involving a direct cleavage of the C–C bond followed by a protonation of C6 by Lys93 appears unlikely, with a barrier for decarboxylation 20 kcal mol^–1 too high. Additional effects like electrostatic stress and ground-state destabilization have been estimated to have only a minor influence on the reaction barrier. The conclusion from the calculations is that the negative charge developing on the substrate during decarboxylation must be stabilized by a protonation of the carbonyl O2 of the substrate. For this mechanism, the addition of the catalytic amino acids decreases the reaction barrier by 25 kcal mol^–1, but full agreement with experimental results has still not been reached. Further modifications of this mechanism are discussed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located a http://dx.doi.org/10.1007/s00894-002-0080-2.Electronic Supplementary Material available.     

Density functional theory investigation of electrophilic addition reaction of bromine to tricyclo[4.2.2.22,5]dodeca-1,5-diene1

The geometry and the electronic structure of tricyclo[4.2.2.2^2,5]dodeca-1,5-diene (TCDD) molecule were investigated by DFT/B3LYP and /B3PW91 methods using the 6-311G(d,p) and 6-311++G(d,p) basis sets. The double bonds of TCDD molecule are syn-pyramidalized. The structure of π-orbitals and their mutual interactions for TCDD molecule were investigated. Potential energy surface (PES) of the TCDD-Br₂ system was studied by B3LYP/6-311++G(d,p) method and the configurations [molecular charge-transfer (CT) complex, transition states (TS1 and TS2), intermediate (INT) and product (P)] corresponding to the stationary points (minima or saddle points) were determined. Initially, a molecular CT-complex forms between Br₂ and TCDD. With a barrier of 22.336 kcal mol^-1 the CT-complex can be activated to an intermediate (INT) with energy 15.154 kcal mol^-1 higher than that of the CT-complex. The intermediate (INT) then transforms easily (barrier 5.442 kcal mol^-1) into the final, N-type product. The total bromination is slightly exothermic. Accompanying the breaking of Br-Br bond, C1-Br, C5-Br and C2-C6 bonds are formed, and C1 = C2 and C5 = C6 double bonds transform into single bonds. The direction of the reaction is determined by the direction of intramolecular skeletal rearrangement that is realized by the formation of C2-C6 bond.

Effects of FADS and ELOVL polymorphisms on indexes of desaturase and elongase activities: results from a pre-post fish oil supplementation

Polymorphisms (SNPs) within the FADS gene cluster and the ELOVL gene family are believed to influence enzyme activities after an omega-3 (n-3) fatty acid (FA) supplementation. The objectives of the study are to test whether an n-3 supplementation is associated with indexes of desaturase and elongase activities in addition to verify whether SNPs in the FADS gene cluster and the ELOVL gene family modulate enzyme activities of desaturases and elongases. A total 208 subjects completed a 6-week supplementation period with 5 g/day of fish oil (1.9–2.2 g/day of EPA + 1.1 g/day of DHA). FA profiles of plasma phospholipids were obtained by gas chromatography (n = 210). Desaturase and elongase indexes were estimated using product-to-precursor ratios. Twenty-eight SNPs from FADS1, FADS2, FADS3, ELOVL2 and ELOVL5 were genotyped using TaqMan technology. Desaturase indexes were significantly different after the 6-week n-3 supplementation. The index of δ-5 desaturase activity increased by 25.7 ± 28.8 % (p < 0.0001), whereas the index of δ-6 desaturase activity decreased by 17.7 ± 18.2 % (p < 0.0001) post-supplementation. Index of elongase activity decreased by 39.5 ± 27.9 % (p < 0.0001). Some gene–diet interactions potentially modulating the enzyme activities of desaturases and elongases involved in the FA metabolism post-supplementation were found. SNPs within the FADS gene cluster and the ELOVL gene family may play an important role in the enzyme activity of desaturases and elongases, suggesting that an n-3 FAs supplementation may affect PUFA metabolism.     

Theoretical study on the ground state intramolecular proton transfer (IPT) and solvation effect in two Schiff bases formed by 2-aminopyridine with 2-hydroxy-1- naphthaldehyde and 2-hydroxy salicylaldehyde

The tautomerization mechanism the isolated and monohydrated forms of two Schiff bases 1 and 2, and the effect of solvation on the proton transfer from enol-imine form to the keto-enamine form have been investigated using the B3LYP hybrid density functional method at the 6-31G** basis set level. The barrier heights for H₂O-assisted reactions are significantly lower than that of unassisted tautomerization reaction in the gas phase. Nonspecific solvent effects have also been taken into account by using the continuum model (IPCM) of four different solvent. The tautomerization energies and the potential energy barriers are decreased by increasing solvent polarity. Figure The tautomerization mechanism the isolated and monohydrated forms of two Schiff bases 1 and 2, and the effect of solvation on the proton transfer from enol-imine form to the keto-enamine form have been investigated using the B3LYP hybrid density functional method at the 6-31G** basis set level     

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be kcal mol⁻¹ for MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.     

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol⁻¹. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol⁻¹. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol⁻¹. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries. Figure Calculated structure of the complex ion [Ta₆Cl₁₂]²⁺ (footnote): Reference value in parenthesis Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparison between predicted and measured resting energy expenditures in Korean male collegiate soccer players

[Purpose] This study aimed to evaluate the differences between predicted resting energy expenditure (REE), using fat-free mass (FFM)-based prediction equations, and measured REE in Korean male collegiate soccer players.[Methods] Fifteen male collegiate soccer players (18-21 years) participated in this study. The REE measurements were conducted using the Douglas bag method. Body composition was measured by dual-energy X-ray absorptiometry (DXA). The differences between the measured REE and predicted REE, using the five FFM-based REE equations, were analyzed using the t-test, calculation of errors, regression analysis, and the Bland-Altman method.[Results] The Cunningham (1980) and ten Haaf and Weijs (2014) equations showed significantly overestimated REE (1,808 ± 99 kcal/d, p <0.01; 1,838 ± 103 kcal/d, p <0.01; respectively), but the Owen (1988), Taguchi (2011), and Kim (2015) equations’ estimations were not significantly different from the measured REE (1,589 ± 106 kcal/d, 1,640 ± 124 kcal/d, and 1,622 ± 68 kcal/d, respectively). The Taguchi equation gave the best prediction of REE with the lowest constant error (-6 ± 125) and effect size (-0.05), and a non-significant proportional bias (p = 0.95).[Conclusion] The Taguchi equation is recommended for predicting REE in Korean collegiate soccer players. The selection process of a REE-prediction equation must take into consideration the target population’s characteristics. Future studies are recommended to evaluate the validity of the different FFM-based REE-prediction equations in various Korean athletes.     

Conformational stabilities, infrared, and vibrational dichroism spectroscopy studies of tris(ethylenediamine) zinc(II) chloride

The conformational stabilities of the transition metal complex of Zn (en)₃Cl₂ were studied using density functional theory (DFT). Deformational potential energy profiles (PEPs), and pathways between the different isomeric conformational energies were calculated using DFT/B3LYP/6–31G. The relative conformational energies of Δ(λλλ), Δ(λλδ), Δ(λδδ) and Δ(δδδ) are 10.48, 7.08, 3.56, and 0.0 kcal/mol, respectively, which are small compared to the barrier heights for reversible phase transitions (49.56, 49.55, 49.52 kcal/mol, respectively). Frequency assignment was carried out by decomposing Fourier transform infrared (FTIR) spectra using Gaussian and Gaussview. The theoretical IR and vibrational dichroism spectroscopy (VCD) absorption spectra are presented for all conformations within the range of 400–3,500 cm^-1.     

Mechanism for intein C-terminal cleavage: a proposal from quantum mechanical calculations

Inteins are autocatalytic protein cleavage and splicing elements. A cysteine to alanine mutation at the N-terminal of inteins inhibits splicing and isolates the C-terminal cleavage reaction. Experiments indicate an enhanced C-terminal cleavage reaction rate upon decreasing the solution pH for the cleavage mutant, which cannot be explained by the existing mechanistic framework. We use intein crystal structure data and the information about conserved amino acids to perform semiempirical PM3 calculations followed by high-level density functional theory calculations in both gas phase and implicit solvent environments. Based on these calculations, we propose a detailed “low pH” mechanism for intein C-terminal cleavage. Water plays an important role in the proposed reaction mechanism, acting as an acid as well as a base. The protonation of the scissile peptide bond nitrogen by a hydronium ion is an important first step in the reaction. That step is followed by the attack of the C-terminal asparagine side chain on its carbonyl carbon, causing succinimide formation and simultaneous peptide bond cleavage. The computed reaction energy barrier in the gas phase is ~33 kcal/mol and reduces to ~25 kcal/mol in solution, close to the 21 kcal/mol experimentally observed at pH 6.0. This mechanism is consistent with the observed increase in C-terminal cleavage activity at low pH for the cleavage mutant of the Mycobacterium tuberculosis RecA mini-intein.     

Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure

The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.     

A definitive mechanism for chorismate mutase

In previous research presentations, we have described the important features of the chorismate --> prephenate reaction using molecular dynamics (MD) and thermodynamic integration studies. This investigation of the reaction in Escherichia coli and water involves QM/MM procedures (SCCDFTB/MM two-dimensional reaction coordinates to identify transition state structures in the water, enzyme, and gas phase followed by B3LYP/6-31+G* single-point computations which allow the determination of activation energies in water and in the E. coli enzyme). Computed activation energies of 11.3 kcal/mol in enzyme and 20.3 kcal/mol in water may be compared to the experimental values of 12.7 and 20.7 kcal/mol, respectively. The transition state structures in the gas phase, water, and enzyme are much the same. The transition states are characteristic of a concerted pericyclic rearrangement. The very small differences in the partial charges of O13 in NAC and TS support only a small preferential (10%) electrostatic stabilization of TS. The free energy of NAC formation in water exceeds that in enzyme by 8.5 kcal/mol, and it is this favored formation of NAC that provides the major kinetic advantage to the enzymatic reaction. These findings compare most favorably with those previous observations of this laboratory employing molecular dynamics and thermodynamic integrations. A definitive mechanism for the chorismate mutase enzymes is provided.     

Deposition Velocity of PM2.5 in the Winter and Spring above Deciduous and Coniferous Forests in Beijing,China

To estimate the deposition effect of PM2.5 (particle matter with aerodynamic diameter <2.5 µm) in forests in northern China, we used the gradient method to measure the deposition velocity of PM2.5 during the winter and spring above a deciduous forest in Olympic Forest Park and above a coniferous forest in Jiufeng National Forest Park. Six aerosol samplers were placed on two towers at each site at heights of 9, 12 and 15 m above the ground surface. The sample filters were exchanged every four hours at 6∶00 AM, 10∶00 AM, 2∶00 PM, 6∶00 PM, 10∶00 PM, and 2∶00 AM. The daytime and nighttime deposition velocities in Jiufeng Park and Olympic Park were compared in this study. The February deposition velocities in Jiufeng Park were 1.2±1.3 and 0.7±0.7 cm s⁻¹ during the day and night, respectively. The May deposition velocities in Olympic Park were 0.9±0.8 and 0.4±0.5 cm s⁻¹ during the day and night, respectively. The May deposition velocities in Jiufeng Park were 1.1±1.2 and 0.6±0.5 cm s⁻¹ during the day and night, respectively. The deposition velocities above Jiufeng National Forest Park were higher than those above Olympic Forest Park. The measured values were smaller than the simulated values obtained by the Ruijgrok et al. (1997) and Wesely et al. (1985) models. However, the reproducibility of the Ruijgrok et al. (1997) model was better than that of the Wesely et al. (1985) model. The Hicks et al. (1977) model was used to analyze additional forest parameters to calculate the PM2.5 deposition, which could better reflect the role of the forest in PM2.5 deposition.     

Molecular docking analysis of selected pyrimidine derivatives with human cyclin-dependent kinase 2

A series of pyrimidine were synthesized, characterized and evaluated for their antioxidant properties using the human cyclin-dependent kinase-2 protein model. Data shows that the pyrimidine derivatives (compound ID 4G) with para fluoro groups substitution at phenyl ring attached to the 4th position (IC50: 98.5µg/ml), compound 4B bearing hydroxy group at para position of phenyl ring (IC50: 117.8 µg/ml) have significant antioxidant activity. Docking data infer that compounds 4c, 4a, 4h and 4b possess binding energy (-7.9, -7.7, -7.5 and -7.4 kcal.mol-1) with 1HCK (PDB ID) receptor.