Molecular dynamics study of the mechanical properties of drug loaded model systems: A comparison of a polymersome with a bilayer.

In this work we implement a new methodology to study structural and mechanical properties of systems having spherical and planar symmetries throughout Molecular Dynamics simulations. This methodology is applied here to a drug delivery system based in polymersomes, as an example. The chosen model drug was the local anesthetic prilocaine due to previous parameterization within the used coarse grain scheme. In our approach, mass density profiles (MDPs) are used to obtain key structural parameters of the systems, and pressure profiles are used to estimate the curvature elastic parameters. The calculation of pressure profiles and radial MPDs required the development of specific methods, which were implemented in an in-house built version of the GROMACS 2018 code. The methodology presented in this work is applied to characterize poly(ethylene oxide)-poly(butadiene) polymersomes and bilayers loaded with the model drug prilocaine. Our results show that structural properties of the polymersome membrane could be obtained from bilayer simulations, with significantly lower computational cost compared to whole polymersome simulations, but the bilayer simulations are insufficient to get insights on their mechanical aspects, since the elastic parameters are canceled out for the complete bilayer (as consequence of the symmetry). The simulations of entire polymersomes, although more complex, offer a complementary approach to get insights on the mechanical behavior of the systems.

Physical achirality in geometrically chiral rotamers of hydrazine and boranylborane molecules.

The diagonal components and the trace of tensors which account for chiroptical response of the hydrazine molecule N2 H4 , that is, static anapole magnetizability and frequency-dependent electric dipole-magnetic dipole polarisability, are a function of the ϕ ≡ ∠ H─N─N─H dihedral angle. They vanish for symmetry reasons at ϕ = 0° and ϕ = 180°, corresponding respectively to C2v and C2h point group symmetries, that is, cis and trans conformers characterized by the presence of molecular symmetry planes. Nonetheless, vanishing diagonal components have been observed also in the proximity of ∠ H─N─N─H = 90°, in which the point group symmetry is C2 and hydrazine is unquestionably chiral. In the boranylborane molecule B2 H4 , assuming the B─B bond in the y direction, the ayy component of the anapole magnetizability tensor approximately vanishes for dihedral angles ∠ H─B─B─H corresponding to chiral rotamers which belong to D2 symmetry. Such anomalous effects have been ascribed to physical achirality of these conformers, that is, to their inability to sustain electronic current densities inducing either anapole moments, or electric and magnetic dipole moments, about the chiral axis connecting heavier atoms, as well as perpendicular directions. In other terms, the structure of certain geometrically chiral rotamers may be such that neither toroidal nor helical flow, which determine chiroptical phenomenology, can take place in the presence of perturbing fields parallel or orthogonal to the chiral axis.

A Density Functional Theory Study of Optical Rotation in Some Aziridine and Oxirane Derivatives.

We present time-dependent density functional theory (TDDFT) calculations of the electronic optical rotation (ORP) for seven oxirane and two aziridine derivatives in the gas phase and in solution and compare the results with the available experimental values. For seven of the studied molecules it is the first time that their optical rotation was studied theoretically and we have therefore investigated the influence of several settings in the TDDFT calculations on the results. This includes the choice of the one-electron basis set, the exchange-correlation functional or the particular polarizable continuum model (PCM). We can confirm that polarized quadruple zeta basis sets augmented with diffuse functions are necessary for converged results and find that the aug-pc-3 basis set is a viable alternative to the frequently employed aug-cc-pVQZ basis set. Based on our study, we cannot recommend the generalized gradient functional KT3 for calculations of the ORP in these compounds, whereas the hybrid functional PBE0 gives results quite similar to the long-range correct CAM-B3LYP functional. Finally, we observe large differences in the solvent effects predicted by the integral equation formalism of PCM and the SMD variant of PCM. For the majority of solute/solvent combinations in this study, we find that the SMD model in combination with the PBE0 functional and the aug-pc-3 basis set gives the best agreement with the experimental values.

The Effects of Calcium on Lipid-Protein Interactions and Ion Flux in the Cx26 Connexon Embedded into a POPC Bilayer.

Gap junctions provide a communication pathway between adjacent cells. They are formed by paired connexons that reside in the plasma membrane of their respective cell and their activity can be modulated by the bilayer composition. In this work, we study the dynamic behavior of a Cx26 connexon embedded in a POPC lipid bilayer, studying: the membrane protein interactions and the ion flux though the connexon pore. We analyzed extensive atomistic molecular dynamics simulations for different conditions, with and without calcium ions. We found that lipid-protein interactions were mainly mediated by hydrogen bonds. Specific amino acids were identified forming hydrogen bonds with the POPC lipids (ARG98, ARG127, ARG165, ARG216, LYS22, LYS221, LYS223, LYS224, SER19, SER131, SER162, SER219, SER222, THR18 and TYR97, TYR155, TYR212, and TYR217). In the presence of calcium ions, we found subtle differences on the HB lifetimes. Finally, these MD simulations are able to identify and explain differential chlorine flux through the pore depending on the presence or absence of the calcium ions and its distribution within the pore.

Magnesium interactions with a CX26 connexon in lipid bilayers.

Following our previous work, where we described the interaction of calcium with the Cx26 hemichannel, we further explore the same system by atomistic molecular dynamics simulations considering a different di-cation, magnesium. Specifically, the interaction of magnesium di-cation with the previously reported calcium binding sites (ASP2, ASP117, ASP159, GLU114, GLU119, GLU120, and VAL226) was investigated to identify similarities and differences between them. In order to do so, four extensive simulations were carried out. Two of them considered a Cx26 hemichannel embedded on a POPC bilayer with one of the di-cations and a sodium-chlorine solution. For the remaining two, no di-cations were included and a sodium-chlorine or potassium-chlorine solution was considered. Potassium has a similar atomic mass to calcium, and sodium to magnesium, but they both differ in charge (1e and 2e respectively). Magnesium and calcium, even having the same charge, showed different affinity for the explored protein. From the calcium binding sites referred above, we found that the magnesium di-cations only binds strongly to the GLU114 site of one connexin. For the sodium and potassium simulations, no specific interactions with the protein were found. Altogether, these results suggest that mass and steric effects play an important role in determining cation binding to Cx26 hemichannels.

Calcium interactions with Cx26 hemmichannel: Spatial association between MD simulations biding sites and variant pathogenicity.

Connexinophaties are a collective of diseases related to connexin channels and hemichannels. In particular many Cx26 alterations are strongly associated to human deafness. Calcium plays an important role on this structures regulation. Here, using calcium as a probe, extensive atomistic Molecular Dynamics simulations were performed on the Cx26 hemichannel embedded in a lipid bilayer. Exploring different initial conditions and calcium concentration, simulation reached ∼4 µs. Several analysis were carried out in order to reveal the calcium distribution and localization, such as electron density profiles, density maps and distance time evolution, which is directly associated to the interaction energy. Specific amino acid interactions with calcium and their stability were capture within this context. Few of these sites such as, GLU42, GLU47, GLY45 and ASP50, were already suggested in the literature. Besides, we identified novel calcium biding sites: ASP2, ASP117, ASP159, GLU114, GLU119, GLU120 and VAL226. To the best of our knowledge, this is the first time that these sites are reported within this context. Furthermore, since various pathologies involving the Cx26 hemichannel are associated with pathogenic variants in the corresponding CJB2 gene, using ClinVar, we were able to spatially associate the 3D positions of the identified calcium binding sites within the framework of this work with reported pathogenic variants in the CJB2 gene. This study presents a first step on finding associations between molecular features and pathological variants of the Cx26 hemichannel.

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study.

In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have simulated loaded bilayers at different drug concentrations and at low (protonated PLC) and high (neutral PLC) pH levels. We have characterized key structural parameters of the loaded bilayers in order to understand the effects of encapsulation of PLC on the bilayer structure and mechanical properties. Neutral PLC was encapsulated in the hydrophobic region leading to a thickness increase, while the protonated species partitioned between the water phase and the poly(ethylene oxide)-poly(butadiene) (PBD) interface, relaxing the PBD region and leading to a decrease in the thickness. The tangential pressures of the studied systems were calculated, and their components were decomposed in order to gain insights on their compensation. In all cases, it is observed that the loading of the membrane does not significantly decrease the stability of the bilayer, indicating that the system could be used for drug delivery.

Diblock copolymer bilayers as model for polymersomes: A coarse grain approach.

This paper presents a new model for polymersomes developed using a poly(ethylene oxide)-poly(butadiene) diblock copolymer bilayer. The model is based on a coarse-grained approach using the MARTINI force field. Since no MARTINI parameters exist for poly(butadiene), we have refined these parameters using quantum mechanical calculations and molecular dynamics simulations. The model has been validated using extensive molecular dynamics simulations in systems with several hundred polymer units and reaching up to 6 µs. These simulations show that the copolymer coarse grain model self-assemble into bilayers and that NPT and NPNγT ensemble runs reproduce key structural and mechanical experimental properties for different copolymer length chains with a similar hydrophilic weight fraction.

Report on the sixth blind test of organic crystal structure prediction methods.

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

Computational study of basis set and electron correlation effects on anapole magnetizabilities of chiral molecules.

In the presence of a static, nonhomogeneous magnetic field, represented by the axial vector B at the origin of the coordinate system and by the polar vector C=∇×B, assumed to be spatially uniform, the chiral molecules investigated in this paper carry an orbital electronic anapole, described by the polar vector A. The electronic interaction energy of these molecules in nonordered media is a cross term, coupling B and C via a¯, one third of the trace of the anapole magnetizability aαß tensor, that is, WBC=-a¯B·C. Both A and W(BC) have opposite sign in the two enantiomeric forms, a fact quite remarkable from the conceptual point of view. The magnitude of a¯ predicted in the present computational investigation for five chiral molecules is very small and significantly biased by electron correlation contributions, estimated at the density functional level via three different functionals. © 2016 Wiley Periodicals, Inc.

Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine.

Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.

The structures of two aldazines: [1,1'-(1E,1'E)-hydrazine-1,2-diylidenebis(methan-1-yl-1-ylidene)dinaphthalen-2-ol] (Lumogen) and 2,2'-(1E,1'E)-hydrazine-1,2-diylidenebis(methan-1-yl-1-ylidene)diphenol (salicylaldazine) in the solid state and in solution.

A combination of NMR spectroscopy and theoretical methods Density functional theory including dispersion corrections (DFT-D) was used to study the structures of Lumogen and salicylaldazine. In the solid state, Lumogen exists as the dihydroxy tautomer 1a (an azine, C=N-N=C) as was already known from an X-ray determination. In a deuterated dimethyl sulfoxide solution, another tautomer is observed besides 1a; its structure corresponds to the hydroxy-oxo tautomer 1b (a hydrazone, C=N-NH-Csp(2)). In what concerns salicylaldazine, we have observed only the dihydroxy tautomer 2a.

Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide: a basis set and correlation study.

In this article, we present the so far most extended investigation of the calculation of the coupling constant polarizability of a molecule. The components of the coupling constant polarizability are derivatives of the nuclear magnetic resonance (NMR) indirect nuclear spin-spin coupling constant with respect to an external electric field and play an important role for both chiral discrimination and solvation effects on NMR coupling constants. In this study, we illustrate the effects of one-electron basis sets and electron correlation both at the level of density functional theory as well as second-order polarization propagator approximation for the small molecule hydrogen peroxide, which allowed us to perform calculations with the largest available basis sets optimized for the calculation of NMR coupling constants. We find a systematic but rather slow convergence with the one-electron basis set and that augmentation functions are required. We observe also large and nonsystematic correlation effects with significant differences between the density functional and wave function theory methods.

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.

Electric field effects on nuclear magnetic shielding of the 1:1 and 2:1 (homo and heterochiral) complexes of XOOX' (X, X' = H, CH3) with lithium cation and their chiral discrimination.

The set of 1:1 and 2:1 complexes of XOOX' (X, X' = H, CH(3)) with lithium cation has been studied to determine if they are suitable candidates for chiral discrimination in an isotropic medium via nuclear magnetic resonance spectroscopy. Conventional nuclear magnetic resonance is unable to distinguish between enantiomers in the absence of a chiral solvent. The criterion for experimental detection is valuated by the isotropic part of nuclear shielding polarisability tensors, related to a pseudoscalar of opposite sign for two enantiomers. The study includes calculations at coupled Hartree-Fock and density functional theory schemes for (17)O nucleus in each compound. Additional calculations for (1)H are also included for some compounds. A huge static homogeneous electric field, perpendicular to the magnetic field of the spectromer, as big as ≈1.7 × 10(8) V m(-1) should be applied to observe a shift of ≈1 ppm for (17)O magnetic shielding in the proposed set of complexes.

Transition from exo- to endo- Cu absorption in CuSi(n) clusters: A Genetic Algorithms Density Functional Theory (DFT) Study.

The characterization and prediction of the structures of metal silicon clusters is important for nanotechnology research because these clusters can be used as building blocks for nano devices, integrated circuits and solar cells. Several authors have postulated that there is a transition between exo to endo absorption of Cu in Si(n) clusters and showed that for n larger than 9 it is possible to find endohedral clusters. Unfortunately, no global searchers have confirmed this observation, which is based on local optimizations of plausible structures. Here we use parallel Genetic Algorithms (GA), as implemented in our MGAC software, directly coupled with DFT energy calculations to show that the global search of CuSi(n) cluster structures does not find endohedral clusters for n < 8 but finds them for n ≥ 10.

Theoretical study of the 1:1 and 2:1 (homo- and heterochiral) complexes of XOOX' (X, X' = H, CH3) with lithium cation.

A theoretical study of the 1:1 and 2:1 complexes of XOOX' (X, X' = H, CH(3)) with the lithium cation has been carried out by means of ab initio computational methods up to the MP2/aug-cc-pVTZ level. The optical rotatory power and NMR parameters (absolute chemical shielding and indirect coupling constants) have been calculated. In addition, the racemization barriers within the complexes formed have been evaluated. Special attention has been paid concerning the differences between the 2:1 homo- and heterochiral complexes.

Assembling Small Silicon Clusters Using Criteria of Maximum Matching of the Fukui Functions.

In this work, we present a methodology inspired by criteria of "maximum matching" between the Fukui functions to predict the best interaction between small silicon clusters to form larger ones. The model is based on the topological analysis of the Fukui functions. We tested the methodology in the formation of Si4-Si8 using a set of small Si2-Si6 clusters as building blocks in ground state structures in singlet and triplet multiplicities. In all of the cases, the Fukui function predicts the formation of the large cluster in its ground state structure, but the number of reaction channels increases with the cluster size.

Theoretical prediction of atomic and electronic structure of neutral Si6O(m) (m = 1-11) clusters.

In this paper we found the most stable structures of silicon-oxide clusters of Si(6)O(m) (m = 1-11) by using the genetic algorithm. In this work the genetic algorithm uses a semiempirical energy function, MSINDO, to find the best cluster structures of Si(6)O(m) (m = 1-11). The best structures found were further optimized using the density functional theory. We report the stable geometries, binding energies, lowest unoccupied molecular orbital-highest occupied molecular orbital gap, dissociation energies for the most favorable fragmentation channels and polarizabilities of Si(6)O(m) (m = 1-11). For most of the clusters studied here we report structures not previously found using limited search approaches on common structural motifs.

Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test.

We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.