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Piezoelectric semiconductors can be polarized and used in mechanoredox systems and photoredox catalysis. Conventional non-piezoelectric semiconductors have limitations when it comes to charge carrier recombination and slow transport rates in catalytic reactions, which can be overcome by piezoelectric polarization processes in piezoelectric semiconductors. Heterostructures based on semiconducting piezoelectrics often offer enhanced catalytic reactivities that are related to their mechanical, piezoelectric, optical, and electronic characteristics. We review how to use such heterostructures to convert mechanical energy into chemical energy, and how the related piezoelectric polarization tunes the band structures and provides advantages in piezophotocatalysis over regular photocatalysis. We discuss fundamental concepts of piezoelectricity, piezoelectric potential, and examine different piezoelectric heterostructures for piezo- and piezophotocatalysis. A review of dynamic investigations of piezo- and piezophotocatalytic processes is presented. The complementary developments in the understanding of the piezotronic and piezophototronic effects are described, which include the induced charge-transfer mechanisms for piezo- and piezophotocatalytic reactions that can occur with piezoelectric heterostructures. Finally, we derive design principles and suggest future research directions in the emerging field of piezo- and piezophotocatalysis employing semiconductive heterostructures. Because piezoelectric semiconductors have mechanical, piezoelectric, optical, and electronic properties, the formation of piezoelectric polarization leads to piezotronic and piezophototronic effects, which can be used to tune their surface and bulk charge-transfer processes. With piezoelectric heterostructures the charge transport is enhanced and results in high efficiency piezo- and piezophotocatalytic performances, as compared with single components. [Display omitted] • Review advances in using heterostructures to convert mechanical energy into chemical energy. • Dynamic investigations of piezo- and piezophotocatalytic processes are reviewed. • Complementary developments in the understanding of the piezotronic and piezophototronic effects are described. • Suggest possible future research directions for piezo- and piezophotocatalysis with semiconductive heterostructures. [ABSTRACT FROM AUTHOR]

Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG) approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD) simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1-100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties. [ABSTRACT FROM AUTHOR]

Anapproach to a straightforward reparametrization of the generalAMBER force field (GAFF) for small organic solutes and druglike compoundsis presented. The parametrization is based on specific pair interactionsbetween the solvent and the solute, namely, the interactions betweenthe constituting atoms of the solute and the oxygen of water weretuned in order to reproduce experimental hydration free energies forsmall model compounds. The key of the parametrization was to abandonthe Lorentz–Berthelot combination rules for the van der Waalsinteractions. These parameters were then used for larger solutes inorder to validate the newly derived pair interactions. In total closeto 600 hydration free energies are computed, ranging from simple alkanesto multifunctional drug compounds, and compared to experimental data.The results show that the proposed parameters work well in describingthe interactions between the solute and the solvent and that the agreementin absolute numbers is good. This modified version of GAFF is a goodcandidate for computing and predicting hydration free energies ona large scale, which has been a long-sought goal of computationalchemists and can be used in rational drug design. [ABSTRACT FROM AUTHOR]

The Monte Carlo approach with the approximation of a dielectric continuum and radii of the small ions obtained from modeling of simple electrolyte solutions can give a reason for the selectivity of DNA for Li+, Na+ and K+ in oriented DNA fibers.

The high pressure structural behavior of H2 and Ne clathrate hydrates with approximate composition H2/Ne·~4H2O and featuring cubic structure II (CS-II) was investigated by neutron powder diffraction using the deuterated analogues at ~95 K. CS-II hydrogen hydrate transforms gradually to isocompositional C1 phase (filled ice II) at around 1.1 GPa but may be metastably retained up to 2.2 GPa. Above 3 GPa a gradual decomposition into C2 phase (H2·H2O, filled ice Ic) and ice VIII' takes place. Upon heating to 200 K the CS-II to C1 transition completes instantly whereas C1 decomposition appears sluggish also at 200 K. C1 was observed metastably up to 8 GPa. At 95 K C1 and C2 hydrogen hydrate can be retained below 1 GPa and yield ice II and ice Ic, respectively, upon complete release of pressure. In contrast, CS-II neon hydrate undergoes pressure-induced amorphization at 1.9 GPa, thus following the general trend for noble gas clathrate hydrates. Upon heating to 200 K amorphous Ne hydrate crystallizes as a mixture of previously unreported C2 hydrate and ice VIII'. [ABSTRACT FROM AUTHOR]

Free energies of solvation (Δ G) in water and n-octanol have been computed for common drug molecules by molecular dynamics simulations with an additive fixed-charge force field. The impact of the electrostatic interactions was investigated by computing the partial atomic charges with four methods that all fit the charges from the quantum mechanically determined electrostatic potential (ESP). Due to the redistribution of electron density that occurs when molecules are transferred from gas phase to condensed phase, the polarization impact was also investigated. By computing the partial atomic charges with the solutes placed in a conductor-like continuum, the charges were effectively polarized to take the polarization effects into account. No polarization correction term or similar was considered, only the partial atomic charges. Results show that free energies are very sensitive to the choice of atomic charges and that Δ G can differ by several kB T depending on the charge computing method. Inclusion of polarization effects makes the solutes too hydrophilic with most methods and in vacuo charges make the solutes too hydrophobic. The restrained-ESP methods together with effectively polarized charges perform well in our test set and also when applied to a larger set of molecules. The effect of water models is also highlighted and shows that the conclusions drawn are valid for different three-point models. Partitioning between an aqueous and a hydrophobic phase is also described better if the two environment's polarization is taken into account, but again the results are sensitive to the charge calculation method. Overall, the results presented here show that effectively polarized charges can improve the description of solvating a drug-like molecule in a solvent and that the choice of partial atomic charges is crucial to ensure that molecular simulations produce reliable results. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

An all-atomistic force field (FF) has been developedfor fullysaturated phospholipids. The parametrization has been largely basedon high-level ab initio calculations in order to keep the empiricalinput to a minimum. Parameters for the lipid chains have been developedbased on knowledge about bulk alkane liquids, for which thermodynamicand dynamic data are excellently reproduced. The FFs ability to simulatelipid bilayers in the liquid crystalline phase in a tensionless ensemblewas tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid,and three different kinds of bilayer thicknesses, have been investigated.Most importantly NMR order parameters and scattering form factorsagree in an excellent manner with experimental data under a rangeof temperatures. Further, the compatibility with the AMBER FF forbiomolecules as well as the ability to simulate bilayers in gel phasewas demonstrated. Overall, the FF presented here provides the importantbalance between the hydrophilic and hydrophobic forces present inlipid bilayers and therefore can be used for more complicated studiesof realistic biological membranes with protein insertions. [ABSTRACT FROM AUTHOR]

The effective solvent-mediated potentials for Na+and Cl−ions in aqueous solution were calculated in a wide range of temperatures from 0 to 100 °C. The potentials have been determined using the inverse Monte Carlo approach, from the ion–ion radial distribution functions computed in 50 ns molecular dynamics simulations of ions and explicit water molecules. We further separated the effective potentials into a short-range part and an electrostatic long-range part represented by a coulombic potential with some dielectric permittivity. We adjusted the value of the dielectric permittivity to provide the fastest possible decay of the short-range potentials at larger distances. The obtained temperature dependence of the dielectric permittivity follows well the experimental data. We show also that the largest part of the temperature dependence of the effective potentials can be attributed to the temperature-dependent dielectric permittivity. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of a Ni2+ ion in water have been carried out to investigate the structure and dynamics of water molecules around the nickel, extending the analysis to the second hydration shell. The structural parameters as well as the motions of water molecules in various sub-structures of the solution have been evaluated giving a detailed picture of the motional modes of water molecules [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation of the decamer d(ATGCAGTCAG)[SUB2] in aqueous solution, electroneutralized by Li[SUP+] ions has been carried out. Emphasis is on the verification of the equilibrium conditions and the related structural and dynamical properties. Applicability of the kinetic part of Boltzmann's H function as a measure of thermodynamic equilibrium is tested. Overall structural stability has been confirmed by different RMSDs. Conformational and helicoidal parameters have been analyzed statistically and dynamically. Dynamical ana- lysis reveals the existence of dynamical sub-states, which typically appear as abrupt changes from a mean level to another in the value of parameter. In statistical analysis these sub-states cannot often be detected. Correlation analysis shows concerted motions among many nearby structural parameters. [ABSTRACT FROM AUTHOR]

Aggregation of amyloid- β (Aβ) peptides, cleaved from the amyloid precursor protein, is known as a precursor of the Alzheimer's disease (AD). It is also known that Alzheimer's disease is characterized by a substantial decrease of the amount of polyunsaturated lipids in the neuronal membranes of the frontal gray matter. To get insight into possible interconnection of these phenomena, we have carried out molecular dynamics simulations of two fragments of A β peptide, A β 1 - 28 and A β 26 - 40 , in four different lipid bilayers: two monocomponent ones (14:0-14:0 PC, 18:0-22:6 PC), and two bilayers containing mixtures of 18:0-18:0 PE, 22:6-22:6 PE, 16:0-16:0 PC and 18:1-18:1 PC lipids of composition mimicking neuronal membranes in a "healthy" and "AD" brain. The simulations showed that the presence of lipids with highly unsaturated 22:6cis fatty acids chains strongly affects the interaction of amyloid- β peptides with lipid membranes. The polyunsaturated lipids cause stronger adsorption of A β -peptides by the membrane and lead to weaker binding between peptides when the latter form aggregates. This difference in the behaviour observed in monocomponent bilayers is propagated in a similar fashion to the mixed membranes mimicking composition of neuronal membranes in "healthy" and "AD" brains, with "healthy" membrane having higher fraction of polyunsaturated lipids. Our simulations give strong indication that it can be physical–chemical background of the interconnection between amyloid fibrillization causing Alzheimer's disease, and content of polyunsaturated lipids in the neuronal membranes. [ABSTRACT FROM AUTHOR]

Ionized water clusters, OH[sup -](H[sub 2]O)[sub N] and H[sub 3]O[sup +](H[sub 2]O)[sub N], of different sizes (N=19 and 26) have been studied at temperatures ranging from 10 to 200 K using molecular dynamics simulations. The solid–liquid phase transitions are investigated to estimate the effects of the presence of an ion on the melting temperature of the clusters. It was found that the behavior of the aggregates during the melting is determined mainly by water–water interactions. Compared to corresponding pure water clusters, the observed changes in the melting temperature, T[sub m], are small and within the statistical uncertainty of the simulations. A weak trend can be observed with the hydroxyl ion reducing the T[sub m], while there is a slight tendency for an increase of T[sub m] for clusters containing the hydronium ion. In general, the ions disrupt the hydrogen bond network and at the same time, the formation of a strong hydration shell contributes to a decrease of the mobility of the molecules. These two phenomena affect the solid–liquid phase transition temperature to opposite directions and seem to largely compensate each other in the simulated clusters. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA–protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP–NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed. [ABSTRACT FROM AUTHOR]

The packaging of genomic DNA into chromatin in the eukaryotic cell nucleus demands extensive compaction. This requires attractive nucleosome–nucleosome interactions to overcome repulsion between the negatively charged DNA segments as well as other constraints. At the same time, DNA must be dynamically accessible to the cellular machinery that operates on it. Recent progress in the experimental characterisation of the higher order structure and dynamics of well-defined chromatin fibres has stimulated the attempts at theoretical description of chromatin and the nucleosome. Here we review the present status of chromatin modelling, with particular emphasis on coarse-grained computer simulation models, the role of electrostatic interactions, and discuss future perspectives in the field. [Copyright &y& Elsevier]

Abstract: Molecular dynamics computer simulations have been performed to investigate dynamical and structural properties of a lidocaine local anesthetic. Both charged and uncharged forms of the lidocaine molecule were investigated. Properties such as membrane area per lipid, diffusion, mass density, bilayer penetration and order parameters have been examined. An analysis of the lidocaine interaction with the lipid surrounding according to a simple mean field theory has also been performed. Almost all examined properties were found to depend on which of the two forms of lidocaine, charged or uncharged, is studied. The overall picture is a rather static behavior determined by the lipids for the charged molecules and more mobile situation of the uncharged form with higher diffusion and lower orientational and positional order. [Copyright &y& Elsevier]

Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions between them are computationally prohibitive, hence development of coarse-grained models is an important part of the methodological development in this area. Here we apply systematic bottom-up coarse-graining to model different phase structures formed by 1,2-dioleoylphosphatidylethanolamine (DOPE) lipid molecules. We started from atomistic simulations of DOPE lipids in water carried out at two different water/lipid molar ratio corresponding to the lamellar Lα and inverted hexagonal HII structures at low and high lipid concentrations respectively. The atomistic trajectories were mapped to coarse-grained trajectories, in which each lipid was represented by 14 coarse-grained sites. Then the inverse Monte Carlo method was used to compute the effective coarse-grained potentials which for the coarse-grain model reproduce the same structural properties as the atomistic simulations. The potentials derived from the low concentration atomistic simulation were only able to form a bilayer structure, while both Lα and HII lipid phases were formed in simulations with potentials obtained at high concentration. The typical atomistic configurations of lipids at high concentration combine fragments of both lamellar and non-lamellar structures, that is reflected in the extracted coarse-grained potentials which become transferable and can form a wide range of structures including the inverted hexagonal, bilayer, tubule, vesicle and micellar structures. [ABSTRACT FROM AUTHOR]

It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex3+) at submillimolar concentrations leads to bundling (condensation) of double-stranded DNA molecules, which is caused by DNA-DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex3+ has previously not been demonstrated. In order to obtain a rigorous description of CoHex3+-nucleic acid interactions and CoHex3+-induced DNA condensation to be used in MD simulations, we have derived optimized force field parameters of the CoHex3+ ion. They were obtained from Car-Parrinello molecular dynamics simulation of a single CoHex3+ ion in the presence of 125 water molecules. The new set of force field parameters reproduces the experimentally known transition of DNA from B- to A-form, and qualitatively describes changes of DNA and RNA persistence lengths. We then carried out a 2 μs long atomistic simulation of four DNA oligomers each consisting of 36 base pairs in the presence of CoHex3+. We demonstrate that, in this system, DNA molecules display attractive interactions and aggregate into bundle-like structures. This behavior depends critically on the details of the CoHex3+ interaction with DNA. A control simulation with a similar setup but in the presence of Mg2+ does not induce DNA-DNA attraction, which is also in agreement with experiment. [ABSTRACT FROM AUTHOR]

Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan-Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the Ȧqvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted. [ABSTRACT FROM AUTHOR]

In this work, the polymorphism of the active pharmaceutical ingredient carbamazepine (CBZ) was investigated by using molecular dynamics simulations with an enhanced sampling scheme. A single molecule of CBZ attaching to flat surfaces of different polymorphs was used as a model for secondary nucleation in water. A novel approach was developed to compute the free energy profile characterizing the adsorption of molecules with orientation aligned with the crystal structure of the surface. The distribution of states that showed alignment was used to rescale the adsorption free energy to include only the contribution that is consistent with crystal growth. The resulting free energy surfaces showed favorable thermodynamics for the most stable form, Form III and the second most stable form, Form I. The primary crystallization product, a dihydrate, was found to be less favorable, implying a nonclassical crystallization pathway. We suggest that a major contribution determining the energetics is the hydrophobicity of the surface. This thermodynamic ranking provides valuable information about the molecular pathways of polymorph growth and will further contribute to the understanding of the crystallization process of CBZ, which is imperative since polymorph formation can alter the physical properties of a drug significantly., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom-up coarse-graining approach for modeling titanium dioxide (TiO   2 ) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small-scale all-atom simulations of TiO   2 surfaces with lipids in aqueous solution. The resulting coarse-grained models are able to accurately reproduce the structural details of lipid adsorption on different titania surfaces without the use of an explicit solvent, enabling significant computational resource savings and favorable scaling. Our coarse-grained simulations show that small spherical TiO   2 nanoparticles ( r = 2 nm) can only be partially wrapped by a lipid bilayer with phosphoethanolamine headgroups, however, the lipid adsorption increases with the radius of the nanoparticle. The current approach can be used to study the effect of the size and shape of TiO   2 nanoparticles on their interactions with cell membrane lipids, which can be a determining factor in membrane wrapping as well as the recently discovered phenomenon of nanoquarantining, which involves the formation of layered nanomaterial-lipid structures., (© 2024 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.)

Due to the vast length scale inside the cell nucleus, multiscale models are required to understand chromatin folding, structure, and dynamics and how they regulate genomic activities such as DNA transcription, replication, and repair. We study the interactions and structure of condensed phases formed by the universal building block of chromatin, the nucleosome core particle (NCP), using bottom-up multiscale coarse-grained (CG) simulations with a model extracted from all-atom MD simulations. In the presence of the multivalent cations Mg(H 2 O) 6 2+ or CoHex 3+ , we analyze the internal structures of the NCP aggregates and the contributions of histone tails and ions to the aggregation patterns. We then derive a "super" coarse-grained (SCG) NCP model to study the macroscopic scale phase separation of NCPs. The SCG simulations show the formation of NCP aggregates with Mg(H 2 O) 6 2+ concentration-dependent densities and sizes. Variation of the CoHex 3+ concentrations results in highly ordered lamellocolumnar and hexagonal columnar phases in agreement with experimental data. The results give detailed insights into nucleosome interactions and for understanding chromatin folding in the cell nucleus., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.