Interaction of biologically relevant ions and organic molecules with titanium oxide (rutile) surfaces: A review on molecular dynamics studies

Characterization of aTiO2 surfaces functionalized with CAP-p15 peptide

Functionalization of Titanium implants using adequate organic molecules is a proposed method to accelerate the osteointegration process, which relates to topographical, chemical, mechanical, and physical features. This study aimed to assess the potential of a peptide derived from cementum attachment protein (CAP-p15) adsorbed onto aTiO2 surfaces to promote the deposition of calcium phosphate (CaP) minerals and its impact on the adhesion and viability of human periodontal ligament cells (hPDLCs). aTiO2 surfaces were synthesized by magnetron sputtering technique. The CAP-p15 peptide was physically attached to aTiO2 surfaces and characterized by atomic force microscopy, fluorescence microscopy, and water contact angle measurement. We performed in vitro calcium phosphate nucleation assays using an artificial saliva solution (pH 7.4) to simulate the oral environment. morphological and chemical characterization of the deposits were evaluated by scanning electronic microscopy (SEM) and spectroscopy molecular techniques (Raman Spectroscopy, ATR-FTIR). The aTiO2 surfaces biofunctionalized with CAP-p15 were also analyzed for hPDLCs attachment, proliferation, and in vitro scratch-healing assay. The results let us see that the homogeneous amorphous titanium oxide coating was 70 nanometers thick. The CAP-p15 (1 μg/mL) displayed the ability to adsorb onto the aTiO2 surface, increasing the roughness and maintaining the hydrophilicity of the aTiO2 surfaces. The physical adsorption of CAP-p15 onto the aTiO2 surfaces promoted the precipitation of a uniform layer of crystals with a flake-like morphology and a Ca/P ratio of 1.79. According to spectroscopy molecular analysis, these crystalline deposits correspond to carbonated hydroxyapatite. Regarding cell behavior, the biofunctionalized aTiO2 surfaces improved the adhesion of hPDLCs after 24 h of cell culture, achieving 3.4-fold when compared to pristine surfaces. Moreover, there was an increase in cell proliferation and cell migration processes. Physical adsorption of CAP-p15 onto aTiO2 surfaces enhanced the formation of carbonate hydroxyapatite crystals and promoted the proliferation and migration of human periodontal ligament-derived cells in in vitro studies. This experimental model using the novel bioactive peptide CAP-p15 could be used as an alternative to increasing the osseointegration process of implants.

Adsorption of Glycine on TiO2 in Water from On-the-fly Free-Energy Calculations and In Situ Electrochemical Impedance Spectroscopy

We report here an experimental-computational study of hydrated TiO2 anatase nanoparticles interacting with glycine, where we obtain quantitative agreement of the measured adsorption free energies. Ab initio simulations are performed within the tight binding and density functional theory in combination with enhanced free-energy sampling techniques, which exploit the thermodynamic integration of the unbiased mean forces collected on-the-fly along the molecular dynamics trajectories. The experiments adopt a new and efficient setup for electrochemical impedance spectroscopy measurements based on portable screen-printed gold electrodes, which allows fast and in situ signal assessment. The measured adsorption free energy is -30 kJ/mol (both from experiment and calculation), with preferential interaction of the charged NH3+ group which strongly adsorbs on the TiO2 bridging oxygens. This highlights the importance of the terminal amino groups in the adsorption mechanism of amino acids on hydrated metal oxides. The excellent agreement between computation and experiment for this amino acid opens the doors to the exploration of the interaction free energies for other moderately complex bionano systems.

Machine Learning Methods for Small Data Challenges in Molecular Science

Small data are often used in scientific and engineering research due to the presence of various constraints, such as time, cost, ethics, privacy, security, and technical limitations in data acquisition. However, big data have been the focus for the past decade, small data and their challenges have received little attention, even though they are technically more severe in machine learning (ML) and deep learning (DL) studies. Overall, the small data challenge is often compounded by issues, such as data diversity, imputation, noise, imbalance, and high-dimensionality. Fortunately, the current big data era is characterized by technological breakthroughs in ML, DL, and artificial intelligence (AI), which enable data-driven scientific discovery, and many advanced ML and DL technologies developed for big data have inadvertently provided solutions for small data problems. As a result, significant progress has been made in ML and DL for small data challenges in the past decade. In this review, we summarize and analyze several emerging potential solutions to small data challenges in molecular science, including chemical and biological sciences. We review both basic machine learning algorithms, such as linear regression, logistic regression (LR), k-nearest neighbor (KNN), support vector machine (SVM), kernel learning (KL), random forest (RF), and gradient boosting trees (GBT), and more advanced techniques, including artificial neural network (ANN), convolutional neural network (CNN), U-Net, graph neural network (GNN), Generative Adversarial Network (GAN), long short-term memory (LSTM), autoencoder, transformer, transfer learning, active learning, graph-based semi-supervised learning, combining deep learning with traditional machine learning, and physical model-based data augmentation. We also briefly discuss the latest advances in these methods. Finally, we conclude the survey with a discussion of promising trends in small data challenges in molecular science.

Applications of Material-Binding Peptides: A Review

Material-binding peptides (MBPs) are functionalized adhesive materials consisting of a few to several dozen amino acids. This affinity between MBPs and materials is regulated by multiple interactions, including hydrogen bonding, electrostatic, hydrophobic interactions, and π-π stacking. They show selective binding and high affinity to a diverse range of inorganic and organic materials, such as silicon-based materials, metals, metal compounds, carbon materials, and polymers. They are used to improve the biocompatibility of materials, increase the efficiency of material synthesis, and guide the controlled synthesis of nanomaterials. In addition, these can be used for precise targeting of proteins by conjugating to target biomolecules. In this review, we summarize the main designs and applications of MBPs in recent years. The discussions focus on more efficient and functional peptides, including evolution and overall design of MBPs. We have also highlighted the recent applications of MBPs, such as functionalization of material surfaces, synthesis of nanomaterials, drug delivery, cancer therapy, and plastic degradation. Besides, we also discussed the development trend of MBPs. This interpretation will accelerate future investigations to bottleneck the drawbacks of available MBPs, promoting their commercial applications.

Challenges of modeling nanostructured materials for photocatalytic water splitting

Understanding the water splitting mechanism in photocatalysis is a rewarding goal as it will allow producing clean fuel for a sustainable life in the future. However, identifying the photocatalytic mechanisms by modeling photoactive nanoparticles requires sophisticated computational techniques based on multiscale modeling. In this review, we will survey the strengths and drawbacks of currently available theoretical methods at different length and accuracy scales. Understanding the surface-active site through Density Functional Theory (DFT) using new, more accurate exchange-correlation functionals plays a key role for surface engineering. Larger scale dynamics of the catalyst/electrolyte interface can be treated with Molecular Dynamics albeit there is a need for more generalizations of force fields. Monte Carlo and Continuum Modeling techniques are so far not the prominent path for modeling water splitting but interest is growing due to the lower computational cost and the feasibility to compare the modeling outcome directly to experimental data. The future challenges in modeling complex nano-photocatalysts involve combining different methods in a hierarchical way so that resources are spent wisely at each length scale, as well as accounting for excited states chemistry that is important for photocatalysis, a path that will bring devices closer to the theoretical limit of photocatalytic efficiency.

The Impact of the Surface Modification on Tin-Doped Indium Oxide Nanocomposite Properties

This review provides an analysis of the theoretical methods to study the effects of surface modification on structural properties of nanostructured indium tin oxide (ITO), mainly by organic compounds. The computational data are compared with experimental data such as X-ray diffraction (XRD), atomic force microscopy (AFM) and energy-dispersive X-ray spectroscopy (EDS) data with the focus on optoelectronic and electrocatalytic properties of the surface to investigate potential relations of these properties and applications of ITO in fields such as biosensing and electronic device fabrication. Our analysis shows that the change in optoelectronic properties of the surface is mainly due to functionalizing the surface with organic molecules and that the electrocatalytic properties vary as a function of size.

Interaction of KRSR Peptide with Titanium Dioxide Anatase (100) Surface: A Molecular Dynamics Simulation Study

Due to its tensile strength and excellent biocompatibility, titanium (Ti) is commonly used as an implant material in medicine and dentistry. The success of dental implants depends on the formation of a contact between the oxidized surface of Ti implant and the surrounding bone tissue. The adsorption of proteins and peptides to the implant surface allows the bone-forming osteoblast cells to adhere to such modified surfaces. Recently, it has been observed that tetrapeptide KRSR (Lys-Arg-Ser-Arg) functionalization could promote osteoblast adhesion to implant surfaces. This may facilitate the establishment of an efficient bone-to implant contact and improve implant stability during the healing process. GROMACS, a molecular dynamics software package was used to perform a 200 ns simulation of adsorption of the KRSR peptide to the TiO₂ (anatase) surface in an aqueous environment. The molecule conformations were mapped with Replica Exchange Molecular Dynamics (REMD) simulations to assess the possible peptide conformations on the anatase surface, and the umbrella sampling method was used to calculate the binding energy of the most common conformation. The simulations have shown that the KRSR peptide migrates and attaches to the surface in a stable position. The dominant amino acid residue interacting with the TiO₂ surface was the N-terminal charged lysine (K) residue. REMD indicated that there is a distinct conformation that is taken by the KRSR peptide. In this conformation the surface interacts only with the lysine residue while the ser (S) and arg (R) residues interact with water molecules farther from the surface. The binding free energy of the most common conformation of KRSR peptide to the anatase (100) surface was ΔG = −8.817 kcal/mol. Our result suggests that the N-terminal lysine residue plays an important role in the adhesion of KRSR to the TiO₂ surface and may influence the osseointegration of dental implants.

Atomic Resolution Electron Microscopy: A Key Tool for Understanding the Activity of Nano-Oxides for Biomedical Applications

Transition metal oxides constitute one of the most fruitful sources of materials with continuously increasing potential applications prompted by the expectations derived from the reduction of the particle size. The recent advances in transmission electron microscopy, because of the development of lenses, have made it possible to reach atomic resolution, which can provide answers regarding the performance of the transition metal nano-oxides. This critical information is related not only to the ability to study their microstructural characteristics but also their local composition and the oxidation state of the transition metal. Exploring these features is a well-known task in nano-oxides for energy and electronic technologies, but they are not so commonly used for elucidating the activity of these oxides for biomedical applications. Nevertheless, the identification at the atomic level of a certain dopant or the unambiguous determination of the oxidation state of a transition metal in a nano-oxide can be important questions to be answered in a certain biomedical application. In this work, we provide several examples in transition metal nano-oxides to show how atomic-resolution electron microscopy can be a key tool for its understanding.

Adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO2 surfaces: A molecular dynamics study

In serval experimental researches, UV-induced hydrophilicity enabled better hemocompatibility in the TiO₂ surface, which was considered to be caused by the removal of the carboxylic acid contamination from the surface. In this paper, we altered the surface wetting property by applying the formate contamination on the rutile (110) surface, and systematically investigated the adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO₂ surface. Unique contacts were found between the charged residues and the hydrophilic surface, anchoring the protein on the surface. The small size and the heart shape of albumin make it easy to cross the stable water layers near the surface. Besides, albumin has a higher proportion of charged residues, so it can form more unique contacts on the hydrophilic surface. Therefore, the albumin tends to adsorb on the hydrophilic surface. For the hydrophobic surface, the water layers near the surface are weakened, which helps the fibrinogen diffusing to the surface and adjusting its orientation. Although the hydrophobic surface cannot form the unique contacts, the larger size of fibrinogen can provide more residues to form enough ordinary contacts after adjusting, and then achieves stable adsorption. Therefore, fibrinogen tends to adsorb on the hydrophobic surface.

A Review of Recent Developments in Molecular Dynamics Simulations of the Photoelectrochemical Water Splitting Process

In this review, we provide a short overview of the Molecular Dynamics (MD) method and how it can be used to model the water splitting process in photoelectrochemical hydrogen production. We cover classical non-reactive and reactive MD techniques as well as multiscale extensions combining classical MD with quantum chemical and continuum methods. Selected examples of MD investigations of various aqueous semiconductor interfaces with a special focus on TiO2 are discussed. Finally, we identify gaps in the current state-of-the-art where further developments will be needed for better utilization of MD techniques in the field of water splitting.

Surface Chemistry, Crystal Structure, Size and Topography Role in the Albumin Adsorption Process on TiO2 Anatase Crystallographic Faces and Its 3D-Nanocrystal: A Molecular Dynamics Study

TiO2 is widely used in biomaterial implants. The topography, chemical and structural properties of titania surfaces are an important aspect to study. The size of TiO2 nanoparticles synthetized by sol–gel method can influence the responses in the biological environment, and by using appropriate heat treatments different contents of different polymorphs can be formed. Protein adsorption is a crucial step for the biological responses, involving, in particular, albumin, the most abundant blood protein. In this theoretical work, using molecular mechanics and molecular dynamics methods, the adsorption process of an albumin subdomain is reported both onto specific different crystallographic faces of TiO2 anatase and also on its ideal three-dimensional nanosized crystal, using the simulation protocol proposed in my previous theoretical studies about the adsorption process on hydrophobic ordered graphene-like or hydrophilic amorphous polymeric surfaces. The different surface chemistry of anatase crystalline faces and the nanocrystal topography influence the adsorption process, in particular the interaction strength and protein fragment conformation, then its biological activity. This theoretical study can be a useful tool to better understand how the surface chemistry, crystal structure, size and topography play a key role in protein adsorption process onto anatase surface so widely used as biomaterial.

The Impacts of Crystalline Structure and Different Surface Functional Groups on Drug Release and the Osseointegration Process of Nanostructured TiO2

In implantable materials, surface topography and chemistry are the most important in the effective osseointegration and interaction with drug molecules. Therefore, structural and surface modifications of nanostructured titanium dioxide (TiO2) layers are reported in the present work. In particular, the modification of annealed TiO2 samples with -OH groups and silane derivatives, confirmed by X-ray photoelectron spectroscopy, is shown. Moreover, the ibuprofen release process was studied regarding the desorption-desorption-diffusion (DDD) kinetic model. The results proved that the most significant impact on the release profile is annealing, and further surface modifications did not change its kinetics. Additionally, the cell adhesion and proliferation were examined based on the MTS test and immunofluorescent staining. The obtained data showed that the proposed changes in the surface chemistry enhance the samples' hydrophilicity. Moreover, improvements in the adhesion and proliferation of the MG-63 cells were observed.

Surface Potential and Interfacial Water Order at the Amorphous TiO2 Nanoparticle/Aqueous Interface

Colloidal nanoparticles exhibit unique size-dependent properties differing from their bulk counterpart, which can be particularly relevant for catalytic applications. To optimize surface-mediated chemical reactions, the understanding of the microscopic structure of the nanoparticle-liquid interface is of paramount importance. Here we use polarimetric angle-resolved second harmonic scattering (AR-SHS) to determine surface potential values as well as interfacial water orientation of ∼100 nm diameter amorphous TiO₂ nanoparticles dispersed in aqueous solutions, without any initial assumption on the distribution of interfacial charges. We find three regions of different behavior with increasing NaCl concentration. At very low ionic strengths (0-10 μM), the Na⁺ ions are preferentially adsorbed at the TiO₂ surface as inner-sphere complexes. At low ionic strengths (10-100 μM), a distribution of counterions equivalent to a diffuse layer is observed, while at higher ionic strengths (>100 μM), an additional layer of hydrated condensed ions is formed. We find a similar behavior for TiO₂ nanoparticles in solutions of different basic pH. Compared to identically sized SiO₂ nanoparticles, the TiO₂ interface has a higher affinity for Na⁺ ions, which we further confirm with molecular dynamics simulations. With its ability to monitor ion adsorption at the surface with micromolar sensitivity and changes in the surface potential, AR-SHS is a powerful tool to investigate interfacial properties in a variety of catalytic and photocatalytic applications.

Tough synthetic spider-silk fibers obtained by titanium dioxide incorporation and formaldehyde cross-linking in a simple wet-spinning process

Due to its unique mechanical properties, spider silk shows great promise as a strong super-thin fiber in many fields. Although progress has been made in the field of synthesizing spider-silk fiber from recombinant spidroin (spider silk protein) in the last few decades, methods to obtain synthetic spider-silk fibers as tough as natural silk from small-sized recombinant protein with a simple spinning process have eluded scientists. In this paper, a recombinant spidroin (MW: 93.4 kDa) was used to spin tough synthetic spider-silk fibers with a simple wet-spinning process. Titanium oxide incorporation and formaldehyde cross-linking were used to improve the mechanical properties of synthetic spider-silk fibers. Fibers treated with incorporation or/and cross-linking varied in microstructure, strength and extensibility while all exhibited enhanced strength and toughness. In particular, one fiber possessed a toughness of 249 ± 22 MJ/m³. This paper presents a new method to successfully spin tough spider-silk fibers in a simple way.

Anisotropy in Stable Conformations of Hydroxylate Ions between the {001} and {110} Planes of TiO2 Rutile Crystals for Glycolate, Lactate, and 2-Hydroxybutyrate Ions Studied by Metadynamics Method

Control over TiO2 rutile crystal growth and morphology using additives is essential for the development of functional materials. Computer simulation studies on the thermodynamically stable conformations of additives at the surfaces of rutile crystals contribute to understanding the mechanisms underlying this control. In this study, a metadynamics method was combined with molecular dynamics simulations to investigate the thermodynamically stable conformations of glycolate, lactate, and 2-hydroxybutyrate ions at the {001} and {110} planes of rutile crystals. Two simple atom-atom distances were selected as collective variables for the metadynamics method. At the {001} plane, a conformation in which the COO- group was oriented toward the surface was found to be the most stable for the lactate and 2-hydroxybutyrate ions, whereas a conformation in which the COO- group was oriented toward water was the most stable for the glycolate ion. At the {110} plane, a conformation in which the COO- group was oriented toward the surface was the most stable for all three hydroxylate ions, and a second most stable conformation was also observed for the lactate ion at positions close to the {110} plane. For all three hydroxylate ions (α-hydroxycarboxylate ions), the stability of the most stable conformation was higher for the {110} plane than for the {001} plane. At both planes, the stability of the most stable conformation was highest for the 2-hydroxybutyrate ion and lowest for the glycolate ion. Supposing that all three hydroxylate ions serve to decrease the surface free energy at the rutile surface and that a more stable conformation at the rutile surface leads to a greater decrease in the surface free energy, the present results partially explain experimentally observed differences in the changes in growth rate and morphology of rutile crystals in the presence of glycolic, lactic, and 2-hydroxybutyric acids.

Regulatory effects of PRF and titanium surfaces on cellular adhesion, spread, and cytokine expressions of gingival keratinocytes

Dental implant material has an impact on adhesion and spreading of oral mucosal cells on its surface. Platelet-rich fibrin (PRF), a second-generation platelet concentrate, can enhance cell proliferation and adhesion. The aim was to examine the regulatory effects of PRF and titanium surfaces on cellular adhesion, spread, and cytokine expressions of gingival keratinocytes. Human gingival keratinocytes were cultured on titanium grade 4, titanium grade 5 (Ti5), and HA discs at 37 °C in a CO2 incubator for 6 h and 24 h, using either elutes of titanium-PRF (T-PRF) or leukocyte and platelet-rich fibrin (L-PRF), or mammalian cell culture medium as growth media. Cell numbers were determined using a Cell Titer 96 assay. Interleukin (IL)-1β, IL-1Ra, IL-8, monocyte chemoattractant protein (MCP)-1, and vascular endothelial growth factor (VEGF) expression levels were measured using the Luminex^® xMAP™ technique, and cell adhesion and spread by scanning electron microscopy. Epithelial cell adhesion and spread was most prominent to Ti5 surfaces. L-PRF stimulated cell adhesion to HA surface. Both T-PRF and L-PRF activated the expressions of IL-1 β, IL-8, IL-1Ra, MCP-1, and VEGF, T-PRF being the strongest activator. Titanium surface type has a regulatory role in epithelial cell adhesion and spread, while PRF type determines the cytokine response.

Effect of Ionic Compounds of Different Valences on the Stability of Titanium Oxide Colloids

Titanium oxide particles of various morphologies have been prepared for applications of scientific or industrial interest in recent decades. Besides development of novel synthetic routes and solid-state characterization of the obtained particles, colloidal stability of titanium oxide dispersions was the focus of numerous research groups due to the high importance of this topic in applications in heterogeneous systems. The influence of dissolved ionic compounds, including monovalent salts, multivalent ions and polyelectrolytes, on the charging and aggregation behaviour of titanium oxide materials of spherical and elongated structures will be discussed in the present review.

Modeling of solid–liquid interfaces using scaled charges: rutile (110) surfaces

The first application of the electronic continuum correction model with scaled charges to molecular dynamics simulations of solid–liquid interfaces.