QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift

The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry that has obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.     

Computational characterization of the chemical step in the GTP hydrolysis by Ras‐GAP for the wild‐type and G13V mutated Ras

The free energy profiles for the chemical reaction of the guanosine triphosphate hydrolysis GTP + H₂O → GDP + Pi by Ras‐GAP for the wild‐type and G13V mutated Ras were computed by using molecular dynamics protocols with the QM(ab initio)/MM potentials. The results are consistent with the recent measurements of reaction kinetics in Ras‐GAP showing about two‐order reduction of the rate constant upon G13V mutation in Ras: the computed activation barrier on the free energy profile is increased by 3 kcal/mol upon the G13V replacement. The major reason for a higher energy barrier is a shift of the “arginine finger” (R789 from GAP) from the favorable position in the active site. The results of simulations provide support for the mechanism of the reference reaction according to which the Q61 side chain directly participates in chemical transformations at the proton transfer stage. Proteins 2015; 83:1046–1053. © 2015 Wiley Periodicals, Inc.     

<Emphasis Type="Italic">Ab initio</Emphasis> Hartree-Fock calculations on linear and second-order nonlinear optical properties of new acridine-benzothiazolylamine chromophores

The calculation of optimized molecular structure and molecular hyperpolarizability of four new acridine-benzothiazolylamine chromophores (1–4) [2-nitro-6-(piperid-1-yl) acridine (1), 6-(benzothiazol-2-yl-amino)-2-nitro-acridine (2), 6-(6-ethylcarboxylate-benzothiazol-2-yl-amino)-2-nitroacridine (3), 6-(6-(β-hydroxyethyl-benzothiazol-2-yl-amino)-2-nitroacridine (4)] have been investigated using ab initio methods. Ab initio optimization were performed at the Hartree–Fock level using STO-3G basis set. The first hyperpolarizabilities have been calculated at the Hartree–Fock method with 6–31G and 6–311G basis sets using Gaussian 98W. In general, the first hyperpolarizability is dependent on the choice of method and basis set. To understand this phenomenon in the context of molecular orbital picture, we examined the frontier molecular orbital energies of all the molecules by using HF/6–31G, 6–311G levels. The polarizability, anisotropy of polarizability and ground state dipole moment of all the molecules have also been calculated. These acridine-benzothiazolylamine chromophores display significant second–order molecular nonlinearity, β (60.2–137.0 × 10⁻³⁰ esu) and provide the basis for future design of efficient nonlinear optical materials having the acridine-benzothiazolylamine core.     

AUGUSTUS at EGASP: using EST,protein and genomic alignments for improved gene prediction in the human genome

Background

A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were systematically evaluated and compared on test data from the human genome. AUGUSTUS was among the tools that were tested in this project.

Results

AUGUSTUS can be used as an ab initio program, that is, as a program that uses only one single genomic sequence as input information. In addition, it is able to combine information from the genomic sequence under study with external hints from various sources of information. For EGASP, we used genomic sequence alignments as well as alignments to expressed sequence tags (ESTs) and protein sequences as additional sources of information. Within the category of ab initio programs AUGUSTUS predicted significantly more genes correctly than any other ab initio program. At the same time it predicted the smallest number of false positive genes and the smallest number of false positive exons among all ab initio programs. The accuracy of AUGUSTUS could be further improved when additional extrinsic data, such as alignments to EST, protein and/or genomic sequences, was taken into account.

Conclusion

AUGUSTUS turned out to be the most accurate ab initio gene finder among the tested tools. Moreover it is very flexible because it can take information from several sources simultaneously into consideration.

     

Theoretical investigation of the triphosphate forms of azidothymidine and thymidine

In this paper we investigate (using AM1 semi-empirical as well as HF methods at the STO-3G, 3-21G, 6-31G, 6-31G* and 6-31+G** level) the conformations, geometrical parameters, Mulliken charges, and solvation effects of the triphosphate form of AZT (AZTTP), as well as the thymidine nucleotide (dTTP) structure. Our calculated geometrical parameters and Mulliken charges, with and without solvation effects, are correlated with recent experimental results.     

A computational study of a host-guest complex

The geometry and energetics of a complex involving pyrazine and an acridine diacid cleft-like host designed by Rebek were investigated at several levels of theory. Molecular mechanics (using the Tripos and CHARMm force fields), semiempirical quantum chemical approaches (with the AM1 and PM3 methods), and an ab initio quantum chemical method (RHF/STO-3G) were used in the complete relaxation of the complex. The geometry of the complex optimized by the RHF/STO-3G method is in excellent agreement with a published X-ray structure; upon superposition, the rms deviation between the corresponding cleft heavy atoms is only 0.17 Å and the pyrazine molecules are superimposable. In addition, ab initio quantum chemical techniques were used to study the complex when the cleft is modeled by a pair of acetic acid molecules. All the calculations presented herein support a two-point interaction mechanism. The similarities found in the results for the full complex and the truncated model are consistent with a purely structural role for the acridine linker of the host. © 1997 John Wiley & Sons, Ltd.     

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.     

Ab Initio and Molecular Mechanics Calculations of Various Substituted Ureas - Rotational Barriers and a New Parametrization for Ureas

High-level ab initio calculations have been performed on urea, methylurea, tetramethylurea and three isomers of dimethylurea to obtain accurate rotational barriers. Results of MP2(fc)/6-31 G(d) calculations are compared to those with lower basis sets and semiempirical calculations. The MM2(87) force field has been parameterized.     

A QM/MM analysis of the conformations of crystalline sucrose moieties

Both ab initio quantum mechanics (QM) and molecular mechanics (MM) were used to produce a hybrid energy surface for sucrose that simultaneously provides low energies for conformations that are observed in crystal structures and high energies for most unobserved structures. HF/6-31G* QM energies were calculated for an analogue based on tetrahydropyran (THP) and tetrahydrofuran (THF). Remaining contributions to the potential energy of sucrose were calculated with MM. To do this, the MM surface for the analogue was subtracted from the MM surface for the disaccharide, and the QM surface for the analogue was added. Prediction of the distribution of observable geometries was enhanced by reducing the strength of the hydrogen bonding. Reduced hydrogen-bonding strength is probably useful because many crystalline sucrose moieties do not have intramolecular hydrogen bonds between the fructose and glucose residues. Therefore, hydrogen bonding does not play a large role in determining the molecular conformation. On the hybrid energy surface that was constructed with a dielectric constant of 3.5, the average potential energy of 23 sucrose moieties from crystal structures is 1.16 kcal/mol, and the population of observed structures drops off exponentially as the energy increases.     

Computational study of Au_4 cluster on a carbon nanotube with and without defects using QM/MM methodology

We use ONIOM (QM/MM) methodology to carry out geometry calculations in a 4-atom nanocluster supported by an (8, 8) armchair carbon nanotube with and without defects employing LSDA/SDD for the QM system and UFF for MM. In two particular cases, defects were added in the carbon nanotube wall. These defects are a double oxygenated vacancy (Vac(2)O(2)) and a double vacancy but without oxygen which creates two pentagons and an octagon. Our results show how geometries using QM/MM and energies calculations carried out with QM, change on both the gold nanocluster and the carbon nanotube. In addition, an application of ONIOM methodology in a comparative study to predict behavior of structures as hybrid materials based in carbon nanotubes combined with gold nanoclusters is shown. In this work we examine geometry changes on both the gold nanocluster and the carbon nanotube. A comparison is made with the binding energy resulting values as well as with the orbital energies such as the frontier orbitals HOMO and LUMO.     

Theoretical Study of Antagonists and Inhibitors of Mammalian Adenosine Deaminase: I. Adenosine and Its Aza- and Deazaanalogues

Aza- and deazaanalogues of adenosine, including their 1-protonated forms (except for that of 1-deazaadenosine), were studied by computer computation to find a relationship between their molecular structures and substrate properties for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated for these compounds using the ab initio STO-3G method. The conformational studies are carried out by the MM⁺ method of molecular mechanics. The mechanism that determines the substrate selectivity of mammalian adenosine deaminase is discussed.     

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling

Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.     

Modelling flavin and substrate substituent effects on the activation barrier and rate of oxygen transfer by p-hydroxybenzoate hydroxylase

The simulation of enzymatic reactions, using computer models, is becoming a powerful tool in the most fundamental challenge in biochemistry: to relate the catalytic activity of enzymes to their structure. In the present study, various computed parameters were correlated with the natural logarithm of experimental rate constants for the hydroxylation of various substrate derivatives catalysed by wild-type para-hydroxybenzoate hydroxylase (PHBH) as well as for the hydroxylation of the native substrate (p-hydroxybenzoate) by PHBH reconstituted with a series of 8-substituted flavins. The following relative parameters have been calculated and tested: (a) energy barriers from combined quantum mechanical/molecular mechanical (QM/MM) (AM1/CHARMM) reaction pathway calculations, (b) gas-phase reaction enthalpies (AM1) and (c) differences between the HOMO and LUMO energies of the isolated substrate and cofactor molecules (AM1 and B3LYP/6-31+G(d)). The gas-phase approaches yielded good correlations, as long as similarly charged species are involved. The QM/MM approach resulted in a good correlation, even including differently charged species. This indicates that the QM/MM model accounts quite well for the solvation effects of the active site surroundings, which vary for differently charged species. The correlations obtained demonstrate quantitative structure activity relationships for an enzyme-catalysed reaction including, for the first time, substitutions on both substrate and cofactor.     

How many hydrogen-bonded α-turns are possible?

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311?+?G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i?+?4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i?+?4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an “ideal” α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the \( {{\hbox{C}}_\alpha } \)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i?+?4) hydrogen bond.     

A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation

Hydrogen bonding and polar interactions play a key role in identification of protein-inhibitor binding specificity. Quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations combined with DFT and semi-empirical Hamiltonian (AM1d, RM1, PM3, and PM6) methods were performed to study the hydrogen bonding and polar interactions of two inhibitors BEN and BEN1 with trypsin. The results show that the accuracy of treating the hydrogen bonding and polar interactions using QM/MM MD simulation of PM6 can reach the one obtained by the DFT QM/MM MD simulation. Quantum mechanics/molecular mechanics generalized Born surface area (QM/MM-GBSA) method was applied to calculate binding affinities of inhibitors to trypsin and the results suggest that the accuracy of binding affinity prediction can be significantly affected by the accurate treatment of the hydrogen bonding and polar interactions. In addition, the calculated results also reveal the binding specificity of trypsin: (1) the amidinium groups of two inhibitors generate favorable salt bridge interaction with Asp189 and form hydrogen bonding interactions with Ser190 and Gly214, (2) the phenyl of inhibitors can produce favorable van der Waals interactions with the residues His58, Cys191, Gln192, Trp211, Gly212, and Cys215. This systematic and comparative study can provide guidance for the choice of QM/MM MD methods and the designs of new potent inhibitors targeting trypsin.     

Modeling of Supramolecular Properties of Molecular Tweezers, Clips, and Bowls

The electrostatic potential surface (EPS) is calculated for molecular tweezers, clips, and bowls at different levels of theory (semiempirical AM1, ab initio HF/6-31G*, and density functional theory pBP/DN**). According to these calculations, the molecular electrostatic potential (MEP) on the concave side of the molecular tweezers and clips is suprisingly negative for hydrocarbons. This finding seems to be a general phenomenon in nonconjugated ?-electron systems with concave-convex topology and it explains the receptor properties of the molecular tweezers and clips. Analogous calculations performed for the conjugated aromatic molecular bowls show different results. The DFT calculations predict that in these systems the more negative MEP lies on the concave side similar to the findings for the nonconjugated molecular tweezer- and clip-systems, whereas the AM1 calculation leads to the opposite result that the MEP is more negative on convex side of the bowl-systems.     

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.     

Theoretical Study of Antagonists and Inhibitors of Mammalian Adenosine Deaminase: II. Isomeric Aza-deazaanalogues of Adenosine

Isomeric aza-deazaanalogues of adenosine and their N1-protonated forms (except for that of 8-aza-1-deazaadenosine) were studied by computer modeling to find a relationship between their molecular structures and the properties as substrates for the mammalian adenosine deaminase. The atomic charge distribution and maps of electrostatic potential around their van der Waals molecular surface were calculated using the ab initioSTO-3G method. The conformational studies were carried out by the MM⁺ method of molecular mechanics. The previously proposed mechanism of the substrate acceptance in the active site of mammalian adenosine deaminase was refined, and the potential substrate properties were predicted for two previously unstudied adenosine analogues, 5-aza-9-deazaadenosine and 8-aza-3-deazaadenosine.