Fractal phenomena in molecular mechanics calculation

It is proposed that in molecular mechanics calculation points belonging to various stable or meta-sta-ble conformtrs are mixed up and form fractal structures in conformation space.The calculation results show the following two phenomena:(i)Two levels of structure with fractal feature were observed.Around the conformer without mirror symmetry points belonging to the conformer and its enantiomer are mixed up and form the first level of fractal structure; on the boundary of the attractive basin o{ each atlractor,points belonging to different attractors form the second level of fractal structure.(ii) The variation of molecular mechanics parameters will influence the structure and area of each attractive basin significantly The above phenomena may become the basis of a new method for solving the troublesome multi-minimum-point problem in molecular mechanics calculation.     

Molecular mechanics study on conformation of perylene-quinonoid photosensitizers

Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) Th     

Molecular mechanics on bonding and non-bonding interactions in (atom@C_(60))

The interactions between the embedded atom X (X=Li,Na,K,Rb,Cs; F,Cl,Br,I) and C60cage in the endohedral-form complexes (X@C60) are calculated and discussed according to molecular mechanics from the point of view of the bonding and non-bonding.It is found from the computational results that for atoms with radii larger than Li's,their locations with the minimum interaction in (X@C60) are at the cage center,while atom Li has an off-center location with the minimum interaction deviation of-0.05 nm,and the cage-environment in C60 can be regarded as sphero-symmetry in the region with radius r of ~0.2 nm.It is shown that the interaction between X and C60 cage is of non-bonding characteristic,and this non-bonding interaction is not purely electrostatic.The repulsion and dispersion in non-bonding interactions should not be neglected,which make important contribution to the location with minimum interaction of X,at center or off center.Some rules about the variations of interactions with atomic radii have been ob     

Molecular mechanics calculations on the differentiation of diastereomeric complexes ofcis-decalin withβ-cyclodextrin

Molecular mechanics calculations with the latest available version of Allinger's MM2 force field (MM2(91)) on the diastereomeric complexes of both enantiomeric conformations ofcis-decalin with -cyclodextrin show a small preference (1.67 kJ mol^–1) for one of them, in agreement with the available¹³C-NMR results. Calculations were found to be sensitive to the procedure used.     

Extending ligand field molecular mechanics to modelling organometallic π-bonded systems: applications to ruthenium-arenes

The ligand field molecular mechanics method has been extended to treat η(6)-arene ligands coordinated to a ruthenium(II) centre by employing a dummy atom located at the centroid of the arene ring and distributing the forces on the dummy to the arene carbon atoms. Angular overlap model parameters based on orbital energies derived from Kohn-Sham density functional theory (KS-DFT) calculations show that, relative to the Ru-dummy vector, the arene behaves as a very strong π donor and weak σ donor. Based on KS-DFT geometries, partial atomic charges and potential energy scans for a series of homoleptic and half sandwich complexes spanning arene, am(m)ine, imine, pyridyl, hydride and chloride ligands, a new LFMM force field has been developed which accurately reproduces the KS-DFT data. This FF was validated against 47 half-sandwich complexes obtained from the Cambridge Structural Database which, after minor corrections to account for the systematic errors between our chosen functional (BP86) and the experimental structures, yields a 'structurally tuned' FF where 93% of the Ru-L contacts are reproduced to 0.05 ? or better and all bar two bond lengths are within 0.1 ? of experiment. Over half the systems have non-hydrogen-atom rmsds of less than 0.5 ?. Larger differences are usually due to rotation of the arene moiety which is shown by ligand field molecular dynamics (LFMD) simulations to be an inherently low-energy process. Comparisons between LFMD and Car-Parrinello MD for [Ru(p-cymene)(ethylenediamine)Cl](+)show that LFMD is equally accurate but much faster enabling modelling of dynamic properties which occur on a timescale beyond the scope of CPMD.     

Excited states of conjugated hydrocarbon radicals using the molecular mechanics – valence bond (MMVB) method

By using a parameterised Heisenberg Hamiltonian coupled to a molecular mechanics force field, excited-state geometries were optimised for three conjugated hydrocarbon radicals: cyclopentadienyl, phenalenyl (perinaphthenyl), and triphenylmethyl. The results are compared with ab initio calculations, and with recent spectroscopic measurements. Electronic Supplementary Material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0461-3     

Hybrid density functional∕molecular mechanics studies on activated adsorption of oxygen on zeolite supported gold monomer

Density functional theory calculations on oxygen adsorption over gas phase and faujasite supported Au monomer has been studied using hybrid quantum mechanics∕molecular mechanics method, surface integrated molecular orbital molecular mechanics implemented in GAMESS package. Three different oxidation states of Au (0, +1, +3) and three different adsorption modes viz., top, bridge, and dissociative adsorption of oxygen have been considered in our calculations. Redshift in the ν(O-O) value from that in gas phase O(2) indicates activation of O(2) upon adsorption over faujasite supported gold monomer. The activation of O(2) is an important step in the catalytic oxidation of CO. The presence of adsorbed O(2) increases the interaction of the Au monomer with the faujasite support. In faujasite supported cationic Au monomer, O(2) preferably remains bridge bonded to Au rather than being dissociated.     

A simple molecular mechanics potential for μm scale graphene simulations from the adaptive force matching method

A simple molecular mechanics force field for graphene (PPBE-G) was created by force matching the density functional theory Perdew-Burke-Ernzerhof forces using the adaptive force matching method recently developed in our group. The PPBE-G potential was found to provide significantly more accurate forces than other existing force fields. Several properties of graphene, such as Young's modulus, bending rigidity, and thermal conductivity, have been studied with our potential. The calculated properties are in good agreement with corresponding density functional theory and experimental values. The thermal conductivity calculated with reverse non-equilibrium molecular dynamics depends sensitively on graphene size thus requiring the simulation of large sheets for convergence. Since the PPBE-G potential only contains simple additive energy expressions, it is very computationally efficient and is capable of modeling large graphene sheets in the μm length scale.     

Consequence of hydrogen atom abstraction from 5’-hydroxyl group of 2’-deoxyadenosine. Theoretical quantum mechanics study

Reactive oxygen species (ROS) may generate different nucleoside/nucleotide radicals in a cell environment. In this study, the possibility of cyclic-2’-deoxyadenosines formation by a rearrangement of their free radicals was investigated. It seems that for cyclic-nucleosides formation, adoption of an O4’-exo conformation by the sugar moiety is necessary. However, this is the energetically unfavoured form of the 2-deoxyribose ring. Moreover, the creation of a O5’, C8 bond in purine deoxy-nucleosides/nucleotides leads to the termination of the DNA elongation process.      

DNA—metal(ii) ion—phosphatidylcholine complexes: structure calculations and stability estimates by molecular mechanics

The structures and formation energies of nucleic acid—phospholipid complexes both in the absence and in the presence of Mg²⁺ ions were calculated taking double-stranded trinucleoside diphosphates NpNpN or heptanucleotides ApAp(NpNpN)pApA, composed of 64 possible combinations of genetic code, and phosphatidylcholine as model compounds. The dependence of intramolecular interactions on the primary structure of nucleic acid molecules and on the presence of a cationic bridge was revealed. The formation energies and structure of oligonucleotides were found by molecular mechanics calculations with the AMBER force field. The structures of phospholipid and MgCl₂ molecules were calculated by the semiempirical PM3 method, while the energies of phospholipid—oligonucleotide complexes were calculated by the molecular mechanics method. Calculations of complexes were carried our with consideration of solvation effects. Considerable gain in the formation energy of triple complexes (13–14 kcal mol⁻¹) is achieved due to the presence of the electroneural metal bridge. A tendency toward increasing the stability of triple complexes containing guanosine-and cytidine-enriched triplets was revealed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2068–2071, November, 1999.     

Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?

Halogenated compounds are gaining an increasing importance in medicinal chemistry and materials science. Ab initio quantum chemistry (QC) has unraveled the existence of a “sigma hole” along the C? X (X = F, Cl, Br, I) bond, namely, a depletion of electronic density prolonging the bond, concomitant with a build‐up on its sides, both of which are enhanced along the F < Cl < Br < I series. We have evaluated whether these features were intrinsically built‐in in an anisotropic, polarizable molecular mechanics (APMM) procedure such as SIBFA (sum of interactions between fragments ab initio computed). For that purpose, we have computed the interaction energies of fluoro‐, chloro‐, and bromobenzene with two probes: a divalent cation, Mg(II), and water approaching X through either one H or its O atom. This was done by parallel QC energy‐decomposition analyses (EDA) and SIBFA computations. With both probes, the leading QC contribution responsible for the existence of the sigma hole is the Coulomb contribution E_c. For all three halogenated compounds, and with both probes, the in‐ and out‐of‐plane angular features of E_c were closely mirrored by the SIBFA electrostatic multipolar contribution (E_MTP). Resorting to such a contribution thus dispenses with empirically‐fitted “extra”, off‐centered partial atomic charges as in classical molecular mechanics/dynamics. © 2013 Wiley Periodicals, Inc.     

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.     

Influence of solvent polarity on the separation of leucine enantiomers by β-cyclodextrin: a molecular mechanics and dynamics simulation

The interaction between leucine and β-cyclodextrin with different solvents was studied by molecular mechanics and dynamics simulations. In order to analyse the influence of the solvent polarity on the inclusion complex formation and separation process of leucine enantiomers by β-cyclodextrin, the organic modifiers were characterised by the same value of dielectric constant in the electrostatic contribution to the interaction energy, and a different molecular configuration of amino acids (neutral or zwitterion). The complexes formed in polar solvents were more stable than those in non-polar solvents with the same dielectric constant, because the electrostatic contribution is negative for the former and positive for the latter. The optimized structures obtained for leucine enantiomers and β-cyclodextrin in vacuo are non-inclusion complexes. The solvent polarity contributes to increasing the probability of the presence in an inner position for the guest, whereas the results for non-polar configurations were smaller and distributed in larger areas. The regions where the enantiomers spend more time in the simulation correspond to locations with greater chiral discrimination. d-Leu was the first eluted enantiomer in every case, except for a polar solvent with $\epsilon =26$.     

What is an element? What is the periodic table? And what does quantum mechanics contribute to the question?

This article considers two important traditions concerning the chemical elements. The first is the meaning of the term “element” including the distinctions between element as basic substance, as simple substance and as combined simple substance. In addition to briefly tracing the historical development of these distinctions, I make comments on the recent attempts to clarify the fundamental notion of element as basic substance for which I believe the term “element” is best reserved. This discussion has focused on the writings of Fritz Paneth which are here analyzed from a new perspective. The other tradition concerns the reduction of chemistry to quantum mechanics and an understanding of chemical elements through their microscopic components such as protons, neutrons and electrons. I claim that the use of electronic configurations has still not yet settled the question of the placement of several elements and discuss an alternative criterion based on maximizing triads of elements. I also point out another possible limitation to the reductive approach, namely the failure, up to now, to obtain a derivation of the Madelung rule. Mention is made of some recent similarity studies which could be used to clarify the nature of ‘elements’. Although it has been suggested that the notion of element as basic substance should be considered in terms of fundamental particles like protons and electrons, I resist this move and conclude that the quantum mechanical tradition has not had much impact on the question of what is an element which remains an essentially philosophical issue.     

Spectrofluorometric, thermal, and molecular mechanics studies of the inclusion complexation of selected imidazoline-derived drugs with β-cyclodextrin in aqueous media

The inclusion complexes of selected imidazoline-derived drugs, namely Antazoline (AN), Naphazoline (NP) and Xylometazoline (XM) with β-cyclodextrin (β-CD) were investigated using steady-state fluorescence spectroscopy, differential scanning calorimetry (DSC), and molecular mechanics (MM) calculations and modeling. The modified form of the Benesi-Hildebrand relation was employed for estimating the formation constant (K_f) of the 1:1 inclusion complexes, which was applied based on measuring the variation in the fluorescence intensity of the guest molecule as a function of growing β-CD concentration. On the other hand, the formation of the inclusion complexes was verified by analyzing solid samples of the complexes using DSC. The thermodynamics of the inclusion complexation, standard enthalpy (ΔH°) and entropy changes −(ΔS°) were obtained from the temperature-dependence of K_f. Obtained values of ΔH° and ΔS° indicated that the inclusion process favorably proceeds through enthalpy changes that was sufficiently predominant to compensate for the unfavorable entropy changes. MM calculations revealed that the proposed drugs molecules can form 1:1 inclusion complexes with β-CD that are stabilized predominantly through van der Waals forces. In addition, MM calculation provided the energetically favored configuration of the inclusion complexes, where NP and XM can be included inside the β-CD cavity through its wide rim, whereas AN can penetrate through the narrow rim of the β-CD cavity.     

Young’s modulus calculations for cellulose I<Subscript>β</Subscript> by MM3 and quantum mechanics

Quantum mechanics (QM) and molecular mechanics (MM) calculations were performed to elucidate Young’s moduli for a series of cellulose I_β models. Computations using the second generation empirical force field MM3 with a disaccharide cellulose model, 1,4′-O-dimethyl-β-cellobioside (DMCB), and an analogue, 2,3,6,2′,3′,6′-hexadeoxy-1,4′-O-dimethyl-β-cellobioside (DODMCB), that cannot make hydrogen bonds reveal a considerable contribution of intramolecular hydrogen bonding to the molecular stiffness of cellulose I_β; the moduli for DMCB and DODMCB being 85.2 and 37.6 GPa, respectively. QM calculations confirm this contribution with modulus values of 99.7 GPa for DMCB and 33.0 GPa for DODMCB. However, modulus values for DMCB were considerably lower than values previously reported for cellulose I_β. MM calculations with extended cellulose chains (10–40 glucose units) resulted in modulus values, 126.0–147.5 GPa, more akin to the values reported for cellulose I_β. Comparison of the cellodecaose model, 1,4′-O-dimethyl-β-cellodecaoside (DMCD), modulus with that of its hydrogen bonding-deficient analogue, 2,3,6,2′,3′,6′-hexadeoxy-1,4′-O-dimethyl-β-cellodecaoside (DODMCD), corroborates the observed stiffness conferred by intramolecular hydrogen bonds; the moduli for DMCD and DODMCD being 126.0 and 63.3 GPa, respectively. Additional MM3 determinations revealed that modulus values were not strongly affected by intermolecular hydrogen bonding, with multiple strand models providing values similar to the single strand models; 87.5 GPa for a 7-strand DMCB model and 129.5 GPa for a 7 strand DMCD model.     

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson–Boltzmann surface area calculations

The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson–Boltzmann surface area (MM–PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein–ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.     

Conformational investigation of α-methylthio and α-phenylthio derivatives of acetone and cyclohexanone by molecular mechanics. An x-ray study of α-phenylthioacetone

A conformational investigation of -methylthioacetone, -methylthiocyclohexanone, -phenylthioacetone, and -phenylthiocyclohexanone was undertaken in the MM2(87) force field. In all cases theac-G rotamers with unidirectional orientation of the C=O and S-R bonds are preferred in accordance with the experimental investigations. In all cases the energy of dipole-dipole interaction makes a contribution to the stabilization of these forms. For the eclipsedsp conformers the relatively high calculated values of the energies contradict the data of the experimental investigations, which take account of their participation in the equilibrium. X-ray crystallographic analysis of -phenylthioacetone (3) showed that thesp-T structure with a planar orientation of the thioanisole fragment is realized in the solid phase.A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan' Scientific Center, Russian Academy of Sciences, 420083 Kazan'. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1364–1371, June, 1992.