All-atom molecular dynamics studies of the full-length β-amyloid peptides

β-Amyloid peptides are believed to play an essential role in Alzheimer’s disease (AD), due to their sedimentation in the form of β-amyloid aggregates in the brain of AD-patients, and the in vitro neurotoxicity of oligomeric aggregates. The monomeric peptides come in different lengths of 39–43 residues, of which the 42 alloform seems to be most strongly associated with AD-symptoms. Structural information on these peptides to date comes from NMR studies in acidic solutions, organic solvents, or on shorter fragments of the peptide. In addition X-ray and solid-state NMR investigations of amyloid fibrils yield insight into the structure of the final aggregate and therefore define the endpoint of any conformational change of an Aβ-monomer along the aggregation process. The conformational changes necessary to connect the experimentally known conformations are not yet understood and this process is an active field of research.     

Molecular modeling study of tubulosine and other related ipecac alkaloids

A molecular modeling study of two alkaloids, tubulosine and psychotrine, isolated from the sap of Pogonopus speciosus, and other related ipecac alkaloids, showed that these flexible alkaloids favor a nonplanar structure. The biologically active compounds had conformations with a similar angle between aromatic ring A, the nitrogen in ring B, and ring D. This angle was related to the biological activity reported for these compounds. Our results support the hypothesis of two different types of receptor interactions, one for the nonplanar compounds and another for the planar compounds.     

Solvent effect on the synthesis of clarithromycin: A molecular dynamics study

Clarithromycin (6-O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4"-[O-bis(TMS)]erythromycin A 9-[O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the 'O-' of the anions. At distances shorter than 5 A, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.     

Efficient computation of root mean square deviations under rigid transformations

The computation of root mean square deviations (RMSD) is an important step in many bioinformatics applications. If approached naively, each RMSD computation takes time linear in the number of atoms. In addition, a careful implementation is required to achieve numerical stability, which further increases runtimes. In practice, the structural variations under consideration are often induced by rigid transformations of the protein, or are at least dominated by a rigid component. In this work, we show how RMSD values resulting from rigid transformations can be computed in constant time from the protein's covariance matrix, which can be precomputed in linear time. As a typical application scenario is protein clustering, we will also show how the Ward‐distance which is popular in this field can be reduced to RMSD evaluations, yielding a constant time approach for their computation. © 2014 Wiley Periodicals, Inc.     

Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".     

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     

Conformational analysis of 3,4-dihydropyridine and its alkyl derivatives

The geometry of dihydropyridine and its alkyl derivatives was studied by the molecular mechanics method. The dihydrocycle was found to be mobile; however, substituents exert little effect on its distorted sofa conformation. The alkyl groups attached to the saturated carbon atoms occupy pseudo-equatorial position in monosubstituted and pseudo-axial positions in disubstituted 3,4-dihydropyridines. Unusually high barriers to inversion of the dihydrocycle were observed incis-3,4-dialkyl-3,4-dihydropyridines caused by the eclipse of the substituents in the transition state.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1009–1012, June, 1994.     

Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain

Gelsolin is an actin-severing protein whose action is promoted by Ca²⁺ ions and inhibited by binding to lipid phosphoinositides incorporated in the inner leaflet of the plasma membrane inner lipid bilayer. In this study, we carried out molecular dynamics (MD) simulations to investigate the influence of calcium cations on the conformation of gelsolin S2 domain. First, gelsolin S2 domain taken from the crystal structure of apo-gelsolin (PDB code: 1D0N) was subjected to three 1100 ps MD simulations in a periodic water box with the 5.0 force field at T=298 K. In the first simulation (S2_Ca²⁺) excess concentration of Ca²⁺ was applied, in the second one (S2_phys) the concentration of Ca²⁺ ions was physiological and in the third one (S2_w) no Ca²⁺ ions were added. The results of MD simulations showed high conformational flexibility of the N-terminal part of the S2 domain. S2_w deviated from the starting structure considerably more that S2_phys and S2_Ca²⁺ suggesting that Ca²⁺ ions stabilize the conformation of the S2 domain of gelsolin.     

Essential dynamics for the study of microstructures in liquids

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic‐molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen‐bonded clusters. © 2014 Wiley Periodicals, Inc.     

Molecular structure and conformation flexibility of 2-oxo- and 2-thioxo-1,2,3,4-tetrahydropyrimidines and their derivatives

The conformational flexibility and effects of the substituents in 2-oxo- and 2-thioxo-1,2,3,4-tetrahydropyrimidines were studied by the semiempirical quantum-chemical AM1 method. The substituents at the double bond have no appreciable effect on the conformational characteristics of the heterocycle. The introduction of substituents to the saturated carbon atom results in the conversion of the tetrahydrocycle to a half-chair conformation and in a substantial decrease in the ring flexibility. The results of calculations are confirmed by the X-ray study of both compounds. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya No. 11, pp. 1941–1946, November, 1997.     

Tetrathiophene on Graphite: Molecular Dynamics Simulations

Summary: We describe molecular dynamics simulations of α‐tetrathiophene molecules deposited on a flat graphite substrate, at two different temperatures (300 K and 400 K) and several degrees of coverage (from approximately one to three molecular layers). The simulations employ a modified version of the CFF91 force field, with the torsion parameters tailored on high‐level ab initio calculations on 2,2′‐bithiophene. We found that the molecules in the first layer were relatively planar and packed against the underlying surface, while those outside it were not arranged in well‐defined layers and were more conformationally disordered. On the time scale of the simulation, the molecules did not crystallize but rather achieved a liquid crystalline‐like state with their average director parallel to the surface.

Side view of the final configuration in the simulation of 24 tetrathiophenes at 300 K. Molecules are depicted with different shades of gray according to their z coordinate (first, second or third layer).     

Molecular dynamics simulation study on zwitterionic structure to maintain the natural behavior of polyalanine13 in aqueous environment

Molecular dynamics simulations are applied to the initial stage of polyalanine13 conformational transi- tion from α-helix to random coil in aqueous environment and the interaction of polyalanine13 with zwitterionic and hydrophobic surfaces respectively in the same condition. The analysis of secondary structure, hydrogen bonds, RMSD, dihedral distribution, and the degree of adsorption are performed. The results show that zwitterionic structure maintains the natural behavior of polyalanine13 in water to a better extent, which should be an indirect proof of the hypothesis of "maintain of normal structure."     

KCl effect on the solubility of five different amino acids in water

Using the analytical gravimetric method the solubility of glycine and dl-alanine in aqueous systems of KCl at 323.15 K, and of l-isoleucine, l-threonine and l-serine in the same system, at 298.15 and 323.15 K, were measured for salt concentrations ranging up to 2.0 molal.     

Molecular architecture and conformation of macromolecules of novel polysilanes

Molecular-weight parameters of new silane homo- and copolymers were analyzed. For all polymers, theM _w values are close ((6.0–8.6)·10⁴), the curves of molecular weight distribution are unimodal, andM _w/M _n=2−2.5. Cyclic fragments or those containing the −C=C− groups make the major contribution to the polysilane chain rigidity. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2430–2433, December, 1998.     

Molecular dynamics simulation on influence of temperature effect on electro-coalescence behavior of nano-droplets

In electric dehydration of crude oil, the dewatering efficiency can be improved by raising emulsion temperature properly which reduces the viscosity of crude oil. However, it should be noticed that the emulsion temperature does not only affect the emulsion viscosity but also nano-droplets dynamics behavior which impacts the coalescence efficiency either. Therefore the influence of temperature effect on the electro-coalescence of nano-droplets is studied by a molecular dynamics method. The results show that the temperature presents an active or negative effect, depending on the competitive relation between electrostatic interaction and thermal motion. Two stages are distinguished according to the dominant mechanism. During stage I, governed by the electrostatic interaction, lower temperature promotes the polarization and leads to an acceleration of the droplets coalescence, but higher temperature restrains the coalescence process due to molecules thermal motion breaking the polarization process. During stage II, governed by the thermal motion, lower temperature improves the coalescence because of a diffusion effect, but higher temperature deteriorates electro-coalescence because of a violent molecular thermal motion. Additionally, hydrogen bond and radial distribution functions are obtained by statistics to describe droplets micromorphology, which explains the reason why the droplet forms longer chain structure at the critical electric field.     

Molecular dynamics simulation of copper nano-cluster melting on the graphite substrate

The melting processes of different-sized copper nano-clusters supported on graphite (0001) plane are investigated by the molecular dynamics method. In this work, the melting point is predicted through the caloric curve. The simulation results show that the melting point of the supported copper nano-cluster is higher than that of the isolated one with the same Cu atoms. In the heating process, the copper nano-particle will adhere to the (0001) face of graphite with its (111) face. Pair analysis results show that the copper atoms close to the graphite can keep with order arrangement even when the temperature is higher than the melt point of the isolated nano-cluster.     

熔融ZnCl2结构的分子动力学模拟研究

熔融ZnCl2作为一种离子性共价性参半的典型熔盐, 其近邻结构在实验测量和分子动力学模拟方面均作过一些研究。本文依据新近EXAFS实验结果, 比较了不同的有效势下模拟得到的径向分布函数,表明KDR势可作为一种实用势。并进一步在KDR势模拟产生的瞬态构型基础上, 使用键序参数方法研究了晶态和熔融态ZnCl2中的近邻结构。结果表明, 和晶态ZnCl2一样, 在熔融ZnCl2中存在稳定的Zn/Cl正四面体结构, 但熔态和晶态Zn/Cl近邻结构热波方差σ不同。计算表明300K晶态σ=5.0℃, 613K熔融态σ=12.2℃。也对熔融ZnCl2的网络状结构和宏观输运性质进行了讨论。     

Molecular dynamics simulation study of the structural features and inclusion capacities of cucurbit[6]uril derivatives in aqueous solutions

Molecular dynamics (MD) simulations were performed for cucurbit[6]uril (CB6) methyl and cyclohexyl derivatives in aqueous solutions. Furthermore, MD simulations have been conducted to study the inclusion complexes between each CB6 derivative with α,ω-pentane diammonium ion (NH₃⁺(CH₂)₅NH₃⁺) to estimate the binding free energies, the complex geometries and the intermolecular forces responsible for complex formation. Results show a complete inclusion of the guest molecule in the cavity of the host for all complexes. Results also indicate that the guest dynamics inside the cavity of the substituted host is similar to that for the unsubstituted host. This demonstrates that the molecular recognition of the host is not affected by the alkyl substitution at the equator. Also, there is an insignificant conformational change of the macrocyclic structure upon inclusion of the guest. Molecular mechanics/Poisson Boltzmann surface area method was used to estimate the binding free energy of each complex. Results indicate that host–guest electrostatic interactions make the largest contribution to the complex binding free energy. Moreover, van der Waals interactions add significantly to the complex stability. The guest molecules show more or less similar binding free energies with the substituted CB6 that exhibits slightly more negative values than unsubstituted CB6 which is proved also by umbrella sampling.     

Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis

Summary: The results of classical molecular simulations of cellulose oligomers are presented here. The conformations of the chains in the high temperature melt, room temperature quenched melt and gas phase are compared with respect to various geometrical parameters including square end‐to‐end distances, glycosidic link torsion correlations, ring puckering and hydrogen bonding. The cellulose oligomer melts were relaxed at 800 K with molecular dynamics, and then cooled down in three different ways to obtain dense amorphous systems at 500 K and at room temperature. The sample resulting from the quench (step) shows too much similarity with the melt at 800 K. The two other cooling schemes (ramp, 2ramps) give very similar results for all quantities investigated. The relevance of previous single molecule calculations with respect to the dense amorphous systems is called into question. Comparisons between the chains in the dense systems and those in the gas phase reveal that, even for these relatively short stiff chains, differences exist in the preferred conformations. At high temperatures, where both systems are in equilibrium, the distribution of square end‐to‐end distances are both fairly smooth, but the gas phase clearly prefers more compact conformations. At 300 K, the differences are exacerbated as the equilibrium distribution for the gas phase shows a high proportion of folded conformers, whereas the nonequilibrium quenched systems necessarily retain the extended envelope of the higher temperature. Differences are also evident in the puckering, the rotation of the hydroxymethyl groups and the pattern of hydrogen bonds.

The probability density distribution for the square end‐to‐end distance for octaose in the gas phase (light line) and in the dense phase (dark line) at 300 K.     

Molecular dynamics study of the water/n-alkane interface

Molecular dynamics simulations on the interface between liquid water and liquid n-alkane (including octane, nonane, decane, undecane and dodecane) have been performed with the purpose to study the interfacial properties: (Ⅰ) density profile; (Ⅱ) molecular orientation; (Ⅲ) interfacial tension and the temperature effect on the interfacial tension. Simulation results show that at the interface the structures of both water and n-alkane are different from those in the bulk. Water has an orientational preference ...