Confined Water Molecules Research Articles

Confined Water Dynamics in Topological Networks Hydrogel for Aqueous Electrochemical Devices.

The unique properties of confined water molecules within polymer networks have garnered extensive research interest in energy storage, catalysis, and sensing. Confined water molecules exhibit higher thermodynamic stability compared to free water, which reduces decomposition and evaporation of water in hydrogel electrolyte system. Herein, a facile strategy is developed to limit active water molecules in a hydrogel network via hydrogen bonding within a topological network. The design of this gel enhances hydrogen bonding between the gel network and water molecules, thereby improving stability by constructing interpenetrating networks. Using this design, the topological network gel is selected as the electrolyte for batteries, demonstrating an extended electrochemical window from 2.37V with polyvinyl alcohol gel to 2.96V, indicating superior confinement of water molecules by hydrogen bonds in the topological network. Additionally, batteries and capacitors assembled with the topological gel exhibit high-capacity retention rates of 94.25% after 20000 cycles at a current density of 1.0 A g-1 and 87.63% after 10000 cycles at a current density of 0.5 A g-1, respectively. This study demonstrates the feasibility of using a topological gel design to enhance gel electrolyte stability, offering a promising avenue for future research in regulating topological networks within gels for various applications.

Probing the Electric Field Response of a Water Molecule Confined in Small Carbon Nanocages: A Density Functional Theory Investigation.

We consider a water molecule under tight confinement in the small-sized fullerenes (C , C , C ) within the density functional theory (DFT) calculations with suitable exchange-correlation functionals. Such nanoscopic molecular cages provide an ideal setup to study their characteristic properties not present in the condensed phase. The water molecule entirely loses its feature of typical water when it is confined in small fullerenes of size equal to C or smaller, in which the asymmetric O-H stretching vibration occurs at a lower wavenumber than the symmetric stretching. We study the response of the confined water molecule to the applied electric fields in terms of change in geometrical parameters, NMR spin-spin coupling constants, dipole moment, HOMO-LUMO (HL) gap, and vibrational frequency shift. The electric field shielding property of small-sized fullerene cages is explored and found to be strongly correlated with the HL gap. Since the electric field modulates the gap to decrease generally, shielding efficiency varies with field strength, thereby making large fields better shielded than small fields for the small penetration factor at large fields. The results that hold significance for technological applications are discussed.

Hydration level dependent dynamics of supercooled water confined in water harvester metal organic framework-303

Crystallization of bulk water cannot be avoided in the temperature range 150–235 K, which is known as no man’s land in the literature focused on the dynamics of the supercooled water. Dynamics of the supercooled water in this temperature range can be accessed by confining water in the nanopores. In the present study, we have investigated dynamics of the supercooled water confined in the pore network of a water harvester metal organic framework (MOF-303) at two different hydration levels (63.4 and 37.0 %). The framework was chosen as a confining host, because the hydrogen bonded–structure of the confined water molecules during adsorption–desorption (i.e. at different hydration levels) is explicitly known. All the relaxation processes observed in the supercooled region are comparatively slower than the bulk–like water dynamics due to the modified hydrogen-bonded structure and the interactions with the pore walls. The confined water, not directly interacting with the pore walls, undergoes a liquid-to-liquid transition (Ts) at ∼186 K followed by its glassy freezing with glass transition temperature Tg ∼ 108 K which is consistent with high density liquid phase of amorphous ice. Both Ts as well as Tg are observed to increase with the decrease in hydration level. It confirmed that the evolved hydrogen-bonded network and the interactions with the pore walls play deterministic roles in the glassy freezing of the confined water. No crystallization as well as the glassy freezing of the water molecules directly interacting with the pore walls through the hydrogen bonding is observed at both the hydration level. The observed relaxation processes corresponding to these molecules in the supercooled region can be attributed to rearrangement of their hydrogen-bonded structure.

Water in the micropores of CPO-27 metal-organic frameworks: A comprehensive study

The metal-organic framework CPO-27 exhibits free coordination sites (open metal sites) and can be prepared with a wide range of metals that influence its properties. It is therefore an intriguing structure to study sorption phenomena. We analyze the water resistance and sorption behavior of these frameworks, with particular attention to the sorption mechanism in detail and the structure of the confined water molecules. For this purpose, we use manometric water vapor sorption analysis and FTIR spectroscopy. The respective metal center orchestrates both the adsorption behavior and the arrangement of the water molecules in the micropores of the framework. The extent to which water molecules form hydrogen bonds (with each other and with framework oxygen atoms) plays a crucial role in the stability of the framework towards water. Water adsorption is governed by the coordination of water molecules to the open metal sites (except for CPO-27-Cu) and subsequent H-bonding. A stepwise adsorption of water is observed, with significant differences depending on the choice of metal.

Thermal transport of confined water molecules in quasi-one-dimensional nanotubes

Dimensions and molecular structures play pivotal roles in the principle of heat conduction. The dimensional characteristics of a solution within nanoscale systems depend on the degrees of confinement. However, the influence of such variations on heat transfer remains inadequately understood. Here, we perform quasi-one-dimensional non-equilibrium molecular dynamics simulations to calculate the thermal conductivity of water molecules confined in carbon nanotubes. The structure of water molecules is determined depending on the nanotube radius, forming a single-file, a single-layer, and a double-layer structure, corresponding to an increasing radius order. We reveal that the thermal conductivity of liquid water has a sublinear dependency on nanotube length exclusively when water molecules form a single file. A stronger confinement leads to behavioral and structural characteristics closely resembling a one-dimensional nature. Moreover, single-layer-structured water molecules exhibit enhanced thermal conductivity. We elucidate that this is due to the increase in the local water density and the absence of transitions to another layer, which typically occurs in systems with double-layer water structures within relatively large radius nanotubes.

Principles determining the aggregation of graphene oxide in aqueous solutions: The effect of heterogeneous distribution of oxygen-containing groups

Molecular dynamics (MD) simulations were conducted to investigate the effects of heterogeneous distribution of oxygen-containing groups on the aggregation modes of graphene oxide (GO) flakes in aqueous solution. The results show that the aggregation of GO flakes can be divided into Brownian motion, adsorption, and adjustment steps, where the adsorption step further can be classified as point-falling-line-squeezing-plane (PFLSP) mode and bridge adsorption of confined water molecules mode. When the aggregation happens at the non-oxidized region, the successful aggregation is always accompanied by the PFLSP mode. In contrast, at the oxidized region, the bridge adsorption of CWMs mode is preferred.

Water Molecules Confined in Cryptophane Nanocages: Structures and Dynamics Driven by Hydrogen Bonding and Water Chains.

Cryptophanes (Crs) are roughly spherical organic nanocages used as vehicles for hosting xenon atoms in 129Xe NMR biosensor (XBS) structures. Crs also bind other guests, importantly water, which is abundant in biological systems. In other host cages, it has been found that the release of "high-energy" water from confinement constitutes an important contribution to the binding affinity of nonwater guests. Despite that, the role of water has received little attention in the XBS field. Based on molecular dynamics simulations in explicit water solvent, we here study the properties of confined water in three different CrA cages that have an identical interior but are functionalized with 0, 3, or 6 water solubility-enhancing, hydrophilic CH2COOH moieties. The number of the solubility groups is found to be a decisive factor for the structures and dynamics of the confined water. Formation of stable water-molecule chains is predicted within the cage with six hydrophilic groups, starting with the anchoring of one water molecule at the portal between the cage and the bulk solution. We find that the experimentally measured differences in the Xe-binding affinities of the cages can be related to the average number of hydrogen bonds per confined water molecule. The rotational dynamics of the confined water is significantly slower than that in the bulk, suggesting NMR relaxation measurements to study the intracavity water. The present findings reveal new details about the microscopic cryptophane-H2O host-guest chemistry, which will become important in the design of improved XBS devices.

Density functional theory and molecular dynamics simulation of water molecules confined between parallel graphene oxide surfaces using new interaction potentials

In this study, the interaction potential of water molecule with a graphene oxide (GO) plate containing OH and O groups has been calculated using the M06-2X/6-31g(d,p) level of theory at different orientations and intermolecular distances and fitted to the Born-Huggins-Meyer (BHM) model. There are good agreements between the calculated and the OPLS-AA and Dreiding models, especially for the GO(O)-H2O interactions. To examine the new computed models, we have used the closer potentials to the OPLS-AA and Dreiding models in the molecular dynamics (MD) simulations. We have calculated several properties using the different obtained interaction potentials including average number of hydrogen bonds per water molecule (〈HB〉) between confined water molecules and between water and GO-surfaces, radial distribution function (RDF), self-diffusion coefficient, and angle distribution function of the confined water molecules between the GO plates. Our results showed good agreements between the OPLS-AA and Dreiding models and some calculated potentials. However, some calculated models showed completely different behavior which discussed in details. According to the results, we concluded that the OH-2 and O1-OH2 models show totally better agreement with the famous force fields than the other calculated potentials. This work provides a simple method for the development of new force fields specifically for these types of systems which are in good agreement with the well-known force fields.

Hydrogen bonding regulation on phase change in stimuli responsive copolymer aqueous solution

Hydrogen bonding (HB) is vital for the phase transition and physical properties of stimuli responsive copolymers. However, the governing mechanism remains unclear. Herein, we investigated the HB dynamics in a representative thermo-responsive copolymer (PNIPAM-AM) aqueous solution. Three types of HB were identified: polymer-polymer chain (CO:H–N), polymer chain-water molecule (CO:H–O) and water-water molecules (H–O:H–O) by vibrational spectroscopy. Increasing polymer concentration, the H–O:H–O softened and CO:H–O stiffened, leading to the destruction of HB network in water-water clusters. Upon increasing solution temperature, CO:H–O softened while CO:H–N stiffened, resolving the dehydration and cross-linking of polymer chains. Confinement of water molecules in the “cages” (∼ tens to hundreds of micrometers) after sol-gel phase transition was visualized, disclosing the mechanism of water holding capacity of PNIPAM-AM. The correlation of molecule vibration and copolymer microscopic structure was established, contributing to the fundamental understanding of phase behavior and physical properties regulations in stimuli responsive copolymer aqueous solution.

Possible formation of H2 hydrates in different nanotubes and surfaces using molecular dynamics simulation.

In this work, we simulated water molecules confined in carbon, boron nitride (BN), and silicon carbide (SiC) nanotubes with similar sizes. We also simulated water molecules confined between parallel graphene, BN, and SiC surfaces in two cases: (a) a similar geometric surface density of water of 0.177/Å2, in which the number of gas molecules was 18% of the total water molecules, and (b) a similar density profile of water of 0.04-0.05 dalton per Å3. To examine H2 hydrate formation, we added guest H2 molecules to the confined water molecules in the nanotube and surface systems. We analyzed the formed shapes, adsorption energies, radial distribution functions (RDFs), and self-diffusion coefficients of the confined molecules in gas hydrate formation. Our results showed that a more ordered heptagonal ice nanotube was formed in the BN nanotube than that in the other systems. After the addition of H2 molecules in the different nanotubes, some of the H2 molecules occupied the wall of the ice nanotube and some of them positioned in the hollow space. Although gas hydrates were created in all surface systems, ordered gas hydrate shapes were formed only in the graphene system. The adsorption energy for guest H2 molecules between the different surfaces was negative, which means that the formation of H2 hydrates between these surfaces is a spontaneous process (unlike that in the nanotube systems). According to RDF results, the BN nanotube and graphene surfaces are proper systems to form more ordered H2 hydrate structures. The confined water molecules have much higher diffusion coefficients in the BN nanotube and graphene surfaces than in the other systems. The F 4 parameter also substantiated hydrate formation in the different nanostructures. In a new configuration of BN and SiC systems with density profiles similar to that of the graphene system, the H2 hydrate was not formed completely as in the case of the graphene system. H2 hydrates formed in the new BN and SiC surfaces were less than those formed in the primary structures (with a geometrical density similar to that of the graphene system) and the graphene system.

Uniqueness of Nanoscale Confinement for Fast Water Transport: Effect of Nanotube Diameter and Hydrophobicity.

Inspired by the enhanced water permeability of carbon nanotubes (CNTs), molecular dynamics simulations were performed to investigate the transport behavior through nanotubes made of boron nitride (BNNT), silicon carbide (SiC), and silicon nitride (SiN) alongside carbon nanotubes (which have different hydrophobic attributes) considering their implication for reverse osmosis (RO) membranes under different practical environments. According to our findings, not only do CNTs but also other kinds of nanotubes exhibit transition anomalies with increasing diameter. Utilizing the robust two-phase thermodynamic (2PT) methods, the current examinations shed light on thermodynamic origin of favorable water filling of these nanotubes. The results show that regardless of the nanotube material, the filling of water inside small nanopores (d < 10 Å) as well as within pores of diameter larger than 15 Å will always be favored by the entropy of filling. However, the entropic preference for filling nanotubes with a diameter of 10-15 Å depends on the constituent material. In particular, the enhancement in total entropy of confined water was mainly due to the increased rotational freedom of confined water molecules. The thermodynamic origin of water transport was correlated with the structural and fluidic behavior of water inside these nanotubes. The observed data for density, flow, structure correlation functions, water-water coordination, tetrahedral order parameter, hydrogen bonds, and density of states functions quantitatively support the observed entropy behavior. Of critical importance is that the present study demonstrates the effectiveness of RO filtration using nanotubes of boron nitride rather than carbon. Furthermore, it was found that one should avoid the use of silicon nanotubes unless filtration needs to be performed under harsh environments where nanotube of other materials cannot survive. Specifically, the results show that both the structural and dynamic properties of water confined in BNNTs are similar to those of CNT's, and for SiNT it is similar as SiC. Our results show that besides the nanotube material, the chirality index of the nanotube also plays a significant role in determining the structure, dynamics and thermodynamics of confined water molecules.

Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes.

Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with confined water molecules playing pivotal roles in their structure and function. This study investigates the structure and dynamics of diphenylalanine peptide nanotubes (FFPNTs) using all-atom molecular dynamics (MD) and grand canonical Monte Carlo combined with MD (GCMC/MD) simulations with both the CHARMM additive and Drude polarizable force fields. The occupancy and dynamics of confined water molecules were also examined. It was found that less than 2 confined water molecules per FF help stabilize the FFPNTs on the x-y plane. Analyses of the kinetics of confined water molecules revealed distinctive transport behaviors for bound and free water, and their respective diffusion coefficients were compared. Our results validate the importance of polarizable force field models in studying peptide nanotubes and provide insights into our understanding of nanoconfined water.

Enhanced Hydrogen Bonds of the (H2O)n (n = 4-8) Clusters Confined in Uranyl Peroxide Cluster Na20(UO2)20(O2)30.

Water is a basic resource and an essential component of living organisms. It often exhibits some novel properties under confinement. The water clusters (H2O)n (n = 4-8) confined in the cavity of uranyl peroxide cluster Na20(UO2)20(O2)30 (U20) have been computationally investigated by using ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) calculations in this study. The results show that the confined water clusters can form hydrogen bonds with the internal oxygen atoms (Ouranyl) of U20, and their conformations changed significantly. The average lengths (2.553-2.645 Å) of hydrogen bonds in confined (H2O)n are shorter than those (2.731-2.841 Å) in the corresponding free water clusters. Moreover, these confined hydrogen bonds show better hydrogen bond patterns according to the quantified indices. The natural bond orbital (NBO) calculations determine that there is electron transferring from the U20 to its interior (H2O)n. It is the main reason for enhancing hydrogen bond interactions among the confined water molecules because their oxygen atoms are more negatively charged and their hydrogen atoms are more positively charged. The quantum theory of atoms in molecules (QTAIM) and interacting quantum atoms (IQA) analyses indicate that the confined hydrogen bonds are more covalent, based on the significant electron density ρ(r) and local energy density H(r) at the bond critical points (BCPs), and the stronger energies of interatomic exchange interactions (Vxc). These findings may help to promote the communication of confined water clusters and enrich the understating of confined hydrogen bonds.

Spectroscopic studies on the supramolecular interactions of methyl benzoate derivatives with p-sulfocalix[6]arene macrocycles

This paper is a continuation of our previous research and aims to further investigate and elucidate the nature and mechanisms of noncovalent supramolecular interactions between four methyl benzoate derivatives (I-IV), which are capable of exhibiting Twisted Intramolecular Charge Transfer (TICT) and/or Excited State Intramolecular Proton Transfer (ESIPT)‐type behavior, and chemical and biological nanocavities. Photophysical and photochemical properties of molecules I-IV in aqueous solution in the presence of well-recognized macrocyclic host p-sulfocalix[6]arenes (SCA[6]) have been studied using steady-state, time-resolved and 1H NMR spectroscopic techniques. The changes in the ground- and excited-state spectroscopic characteristics (absorption and fluorescence spectra, time-resolved fluorescence spectra, fluorescence decay times and 1H NMR spectra) undergo significant modifications upon encapsulation of the investigated methyl benzoate derivative in the macromolecular cavity. For the two compounds (I and II), the interactions with the macrocycles with a hydrophobic SCA[6] cavity lead to the formation of stable inclusion complexes with 1:1 stoichiometry, both in the ground and excited state, while the stoichiometry of the III-SCA[6] and IV-SCA[6] complexes in the ground and excited states is 1:2. The values of the equilibrium constants have been determined from the spectroscopic data using Benesi-Hildebrand and nonlinear regression procedures. The location of the organic molecule inside the SCA[6] has been investigated by 1H NMR experiments. The changes in macrocyclic compound-induced NMR chemical shifts clearly indicate that the chemical structure of inclusion complexes is very different for methyl benzoate derivative-SCA[6] and methyl benzoate derivative-CB[7] systems. Finally, we have shown, using time-dependent fluorescence Stokes shift, that very fast solvation dynamics of pure water is markedly different from that of the confined water molecule in SCA[6] system.

Molecular dynamics simulation of desalination process using polyoxometalate ionic liquid confined in carbon nanotubes

In this work, the effect of positioning of [Keggin][emim]3 ionic liquid (IL) into carbon nanotubes (CNTs) with different concentrations has been examined in the desalination process at different external pressures using molecular dynamics (MD) simulations. Another membrane was also modelled composed of four similar CNTs with almost equal space from each other. Using of only Keggin anions into the charged CNT was also studied in the desalination process. To study the mechanism of the water and ions fluxes, the potential of mean force, average number of hydrogen bonds, and self-diffusion coefficient have been also computed and discussed. The results showed that the placing of [Keggin][emim]3 IL into a CNT decreases the water flux (Nwaterns=74at150MPa) relative to the empty CNT (Nwaterns=834). However, the four CNTs configuration shows increase in the water flux (Nwaterns=183at150MPa) than the one CNT system. The placing of one polyoxometallate IL into the CNT increases the salt rejection 10 to 20 times than the empty-CNT system at low and high pressures, respectively. Moreover, positioning of the two ILs results in the complete salt rejection at all pressures. These results indicate that the use of polyoxometalate ILs into the CNT efficiently increases the salt rejection. The self-diffusion of confined water molecules in the single IL-CNT composite (D = 0.73 × 10-9 m2/s) is also smaller than the empty CNT at 150 MPa (D = 1.89 × 10-9 m2/s). The results also indicated that using of the Keggin anions into the charged CNT leads to the more water flux (Nwaterns=250at150MPa) and complete salt rejection relative to the fixing of [Keggin][emim]3 IL into the uncharged CNT. The effects of CNT charge distributions, temperature, and CNT chirality have been also examined on the desalination process.

Hydrogen-bonded structures and low temperature transitions of the confined water in subnano channels

The interfacial and confined water have long been attractive objects due to their crucial roles in biological, geological processes, etc. In this paper, we investigate the hydrogen-bonded structures of water and their low temperature transitions in the subnano channels of AlPO4-11 for the first time on the basis of infrared spectroscopy. The number of the adsorbed water molecules is estimated to be 8.45 per channel in one unit cell by thermogravimetric analysis. It is found that the confined water molecules are involved in saturated and unsaturated coordination with different hydrogen bond strengths at ambient temperature. The former refers to ice-like four-coordinated water and the latter includes liquid-like structures, Al-coordinated and relatively free water molecules. Unique coordination between water molecules and framework Al sites is responsible for the ice-like structures in the channels above the ice melting point. The appearance of liquid-like structures is closely related to the strong channel confinement, which does not allow the formation of extensive tetrahedral hydrogen-bonded configuration. As temperature decreases, a structural transformation of confined water happens in the channels of AlPO4-11. Isolated small water oligomers and two new components with stronger hydrogen bonds, such as low-density amorphous ice-like structures and a kind of low-density liquid-like structures are preferred. Our results provide important insights into the structural organizations and thermal-dynamic behaviors of confined water in extreme narrow channels.

Molecular Dynamics of Jelly Candies by Means of Nuclear Magnetic Resonance Relaxometry

1H spin-lattice Nuclear Magnetic Resonance relaxation studies have been performed for different kinds of Haribo jelly and Vidal jelly in a very broad frequency range from about 10 kHz to 10 MHz to obtain insight into the dynamic and structural properties of jelly candies on the molecular level. This extensive data set has been thoroughly analyzed revealing three dynamic processes, referred to as slow, intermediate and fast dynamics occurring on the timescale of 10-6 s, 10-7 s and 10-8 s, respectively. The parameters have been compared for different kinds of jelly for the purpose of revealing their characteristic dynamic and structural properties as well as to enquire into how increasing temperature affects these properties. It has been shown that dynamic processes in different kinds of Haribo jelly are similar (this can be treated as a sign of their quality and authenticity) and that the fraction of confined water molecules is reduced with increasing temperature. Two groups of Vidal jelly have been identified. For the first one, the parameters (dipolar relaxation constants and correlation times) match those for Haribo jelly. For the second group including cherry jelly, considerable differences in the parameters characterizing their dynamic properties have been revealed.

Does twist angle affect the properties of water confined inside twisted bilayer graphene?

Graphene nanoslit pores are used for nanofluidic devices, such as, in water desalination, ion-selective channels, ionic transistors, sensing, molecular sieving, blue energy harvesting, and protein sequencing. It is a strenuous task to prepare nanofluidic devices, because a small misalignment leads to a significant alteration in various properties of the devices. Here, we focus on the rotational misalignment between two parallel graphene sheets. Using molecular dynamics simulation, we probe the structure and dynamics of monolayer water confined inside graphene nanochannels for a range of commensurate twist angles. With SPC/E and TIP4P/2005 water models, our simulations reveal the independence of the equilibrium number density- n ∼ 13nm-2 for SPC/E and n ∼ 11.5nm-2 for TIP4P/2005- across twists. Based on the respective densities of the water models, the structure and dielectric constant are invariant of twist angles. The confined water structure at this density shows square ice ordering for SPC/E water only. TIP4P/2005 shows ordering at the vicinity of a critical density (n ∼ 12.5nm-2). The average perpendicular dielectric constant of the confined water remains anomalously low (∼2 for SPC/E and ∼6 for TIP4P/2005) for the studied twist angles. We find that the friction coefficient of confined water molecules varies for small twist angles, while becoming independent for twists greater than 5.1°. Our results indicate that a small, angular misalignment will not impair the dielectric properties of monolayer water within a graphene slit-pore, but can significantly influence its dynamics.

Investigation of small inhibitor effects on methane hydrate formation in a carbon nanotube using molecular dynamics simulation.

In this work, we simulated water molecules in fixed and rigid (15,0) CNTs and the confined water molecules formed a hexagonal ice nanotube in the CNT. After the addition of methane molecules in the nanotube, the hexagonal structure of confined water molecules disappeared and were replaced by almost all the guest methane molecules. The replaced molecules formed a row of water molecules in the middle of the hollow space of the CNT. We also added five small inhibitors with different concentrations (0.8 mol% and 3.8 mol%) to methane clathrates in CNT: benzene, 1-ethyl-3-methylimidazolium chloride ionic liquid ([emim+][Cl-] IL), methanol, NaCl, and tetrahydrofuran (THF). We investigated the thermodynamic and kinetic inhibition behaviors of the different inhibitors on the methane clathrate formation in the CNT using the radial distribution function (RDF), hydrogen bonding (HB), and angle distribution function (ADF). Our results showed that the [emim+][Cl-] IL is the best inhibitor from both aspects. It was also shown that the effect of THF and benzene is better than that of NaCl and methanol. Furthermore, our results showed that the THF inhibitors tended to aggregate in the CNT, but the benzene and IL molecules were distributed along the CNT and can affect the inhibitor behavior of THF in the CNT. We have also examined the effect of CNT chirality using the armchair (9,9) CNT, the effect of CNT size using the (17,0) CNT, and the effect of CNT flexibility using the (15,0) CNT by the DREIDING force field. Our results showed that the IL has stronger thermodynamic and kinetic inhibition effects in the armchair (9,9) and the flexible (15,0) CNT than the other systems, respectively.

Vibrational spectra of human tissues: Experimental data and density functional theory calculations comparison

Biophotonics techniques enabling molecular sensing of tissues and biological samples of had been widely applied to biomedical problems. Vibrational spectroscopy technologies like Fourier-Transform Infrared (FTIR) spectroscopy is a well-reported example. However, the correct interpretation of measured vibrational spectra of macromolecules and tissues emerging from the complexity of structures is a challenge. Computer simulations can be used as a strategic method to understand interactions between specific parts of a macromolecule. Here we present two implementations of vibrational calculations based on diagonalization of Hessian matrix obtained via Density Functional Theory calculations using Car-Parrinello Molecular Dynamics (CPMD package), Born-Oppenheimer Molecular Dynamics quickstep GPW (CP2K package), and a molecular dynamics calculations based on tight binding (CP2K-TB) was also employed to obtain FTIR spectra via electric dipole correlation function. These calculations were proposed to capture vibrational pieces of information related to FTIR of the human oral mucosa. Eleven models of peptide which represents collagen type I macromolecule including confined water molecules (ranging from 0 to 8 waters), were tested. CPMD and CP2K methods presented an excellent agreement of vibrational bands positions and maximum intensity to experimental data (goodness-of-fit R2 ∼ 0.90). On the other hand, this agreement was very poor for the CP2K-TB case in spite of the correct overall relative spectral intensity with respect to experimental data. We found that the peptide model enclosing eight waters (labeled C8) in CPMD calculations presented the highest value of R2 = 0.99. The CPMD method, despite some limitations, outperformed the CP2K calculation in our case. Here we only used a collagen cutout and confined water, but it is possible to add other molecules such as proteoglycans to investigate and characterize a tissue. The short collagen mimetic peptide has implications for the conformational behavior of native collagen. The method itself can be used for other macromolecules. Furthermore, we assignment of vibrational modes in the high-wavenumber region ( > 2, 000▒cm−1) is also presented.