Hydrogen-bonded Network Of Water Molecules Research Articles

Substitution of the D1-Asn87 site in photosystem II of cyanobacteria mimics the chloride-binding characteristics of spinach photosystem II

Photoinduced water oxidation at the O2-evolving complex (OEC) of photosystem II (PSII) is a complex process involving a tetramanganese-calcium cluster that is surrounded by a hydrogen-bonded network of water molecules, chloride ions, and amino acid residues. Although the structure of the OEC has remained conserved over eons of evolution, significant differences in the chloride-binding characteristics exist between cyanobacteria and higher plants. An analysis of amino acid residues in and around the OEC has identified residue 87 in the D1 subunit as the only significant difference between PSII in cyanobacteria and higher plants. We substituted the D1-Asn87 residue in the cyanobacterium Synechocystis sp. PCC 6803 (wildtype) with alanine, present in higher plants, or with aspartic acid. We studied PSII core complexes purified from D1-N87A and D1-N87D variant strains to probe the function of the D1-Asn87 residue in the water-oxidation mechanism. EPR spectra of the S2 state and flash-induced FTIR spectra of both D1-N87A and D1-N87D PSII core complexes exhibited characteristics similar to those of wildtype Synechocystis PSII core complexes. However, flash-induced O2-evolution studies revealed a decreased cycling efficiency of the D1-N87D variant, whereas the cycling efficiency of the D1-N87A PSII variant was similar to that of wildtype PSII. Steady-state O2-evolution activity assays revealed that substitution of the D1 residue at position 87 with alanine perturbs the chloride-binding site in the proton-exit channel. These findings provide new insight into the role of the D1-Asn87 site in the water-oxidation mechanism and explain the difference in the chloride-binding properties of cyanobacterial and higher-plant PSII.

Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.

Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-time-scale molecular dynamics (MD) simulations, postanalysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of kon, koff, ΔH, ΔS, and ΔG using GAFF-CD and q4MD-CD force fields for β-CD could be compared with experimental data directly and agreed reasonably with experiment findings. In addition, our study further interprets experiments. Both force fields resulted in similar computed ΔG from independently computed kinetics rates, ΔG = -RT ln(kon·C0/koff), and thermodynamics properties, ΔG = ΔH - TΔS. The water entropy calculations show that the entropy gain of desolvating water molecules are a major driving force, and both force fields have the same strength of nonpolar attractions between solutes and β-CD as well. Water molecules play a crucial role in guest binding to β-CD. However, collective water/β-CD motions could contribute to different computed kon and ΔH values by different force fields, mainly because the parameters of β-CD provide different motions of β-CD, hydrogen-bond networks of water molecules in the cavity of free β-CD, and strength of desolvation penalty. As a result, q4MD-CD suggests that guest binding is mostly driven by enthalpy, while GAFF-CD shows that gaining entropy is the major driving force of binding. The study deepens our understanding of ligand-receptor recognition and suggests strategies for force field parametrization for accurately modeling molecular systems.

Taurine as a water structure breaker and protein stabilizer

The enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between osmolytes and two proteins: lysozyme and ubiquitin. Despite high structural similarity, both osmolytes exert different influence on protein stability: taurine is a stabilizer, TMT is a denaturant. We show also that taurine amino group interacts directly with the side chains of proteins, whereas TMT does not interact with proteins at all. Although two solutes weaken on average the structure of the surrounding water, their hydration spheres are different. Taurine is surrounded by two populations of water molecules: bonded with weak H-bonds around sulfonate group, and strongly bonded around amino group. The strong hydrogen-bonded network of water molecules around the amino group of taurine further improves properties of enhanced protein hydration sphere and stabilizes the native protein form. Direct interactions of this group with surface side chains provide a proper orientation of taurine and prevents the {text{SO}}_{3}^{ - } group from negative influence. The weakened {text{SO}}_{3}^{ - } hydration sphere of TMT breaks up the hydrogen-bonded network of water around the protein and destabilizes it. However, TMT at low concentration stabilize both proteins to a small extent. This effect can be attributed to an actual osmophobic effect which is overcome if the concentration increases.

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 Å using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inwardopen state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inwardopen state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.

Proton conduction in alkali metal ion-exchanged porous ionic crystals.

Proton conduction in alkali metal ion-exchanged porous ionic crystals A2[Cr3O(OOCH)6(etpy)3]2[α-SiW12O40]·nH2O [I-A+] (A = Li, Na, K, Cs, etpy = 4-ethylpyridine) is investigated. Single crystal and powder X-ray diffraction measurements show that I-A+ possesses analogous one-dimensional channels where alkali metal ions (A+) and water of crystallization exist. Impedance spectroscopy and water diffusion measurements of I-A+ show that proton conductivities are low (10-7-10-6 S cm-1) under low relative humidity (RH), and protons mostly migrate as H3O+ with H2O as vehicles (vehicle mechanism). The proton conductivity of I-A+ increases with the increase in RH and is largely dependent on the types of alkali metal ions. I-Li+ shows a high proton conductivity of 1.9 × 10-3 S cm-1 (323 K) and a low activation energy of 0.23 eV under RH 95%. Under high RH, alkali metal ions with high ionic potentials (e.g., Li+) form a dense and extensive hydrogen-bonding network of water molecules with mobile protons at the periphery, which leads to high proton conductivities and low activation energies via rearrangement of the hydrogen-bonding network (Grotthuss mechanism).

Development of Glassy Bicontinuous Cubic Liquid Crystals for Solid Proton-Conductive Materials.

Glassy bicontinuous cubic liquid crystals are developed to be a matrix having a hydrophilic infinite periodic minimal surface (IPMS). They function as a scaffold for water, leading to the formation of a 3D continuous hydrogen-bonding network of water molecules along the IPMS. This material design is advantageous for developing novel electrolytes with rigidity and high proton conductivity.

Molecular Dynamics Simulations of SFG Librational Modes Spectra of Water at the Water–Air Interface

At the water–air interface, the hydrogen-bond network of water molecules is interrupted, and accordingly, the structure and dynamics of the interfacial water molecules are altered considerably compared with the bulk. Such interfacial water molecules have been studied by surface-specific vibrational sum-frequency generation (SFG) spectroscopy probing high-frequency O–H stretch and H–O–H bending modes. In contrast, the low-frequency librational mode has been much less studied with SFG. Because this mode is sensitive to the hydrogen-bond connectivity, understanding the librational mode of the interfacial water is crucial for unveiling a microscopic view of the interfacial water. Here, we compute the SFG librational mode spectra at the water–air interface by using molecular dynamics simulation. We show that the modeling of the polarizability has a drastic effect on the simulated librational mode spectra, whereas the spectra are less sensitive to the force field models and the modeling of the dipole moment. Th...

Changes in hydration structure are necessary for collective motions of a multi-domain protein.

Conformational motions of proteins are necessary for their functions. To date, experimental studies measuring conformational fluctuations of a whole protein structure have revealed that water molecules hydrating proteins are necessary to induce protein functional motions. However, the underlying microscopic mechanism behind such regulation remains unsolved. To clarify the mechanism, multi-domain proteins are good targets because it is obvious that water molecules between domains play an important role in domain motions. Here, we show how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, through molecular dynamics simulation supported by structural analyses and biochemical experiments. We first identified collective domain motions of the protein, which open/close an active-site cleft between domains. The analyses on changes in hydration structure revealed that changes in local hydration in the depth of the cleft are necessary for the domain motion and vice versa. In particular, ‘wetting’/‘drying’ at a hydrophobic pocket and ‘adsorption’/‘dissociation’ of a few water molecules at a hydrophilic crevice in the cleft were induced by dynamic rearrangements of hydrogen-bond networks, and worked as a switch for the domain motions. Our results microscopically demonstrated the importance of hydrogen-bond networks of water molecules in understanding energy landscapes of protein motions.

(Invited) Interaction of Molecules with Single-Walled Carbon Nanotube Probed By Photoluminescence and Raman Spectroscopy

The interaction of molecules and material surfaces is one of the fundamental topics in surface science. Also, understanding the behavior of molecules in nano-space is increasingly important in nano- and biotechnologies. A single-walled carbon nanotube (SWNT) is a monolayered material composed of all surface atoms, which provide a simple van der Waals potential originated from a single layer both for the outer surface (quasi 2D) and inner nano-space (quasi 1D). Furthermore, the quasi 1D electronic structure of SWNT allows resonant optical transitions, which are sensitively affected by the surrounding environment of SWNT. SWNTs are thus an ideal material for examining the behaviors of molecules on the surface or in the nano-space by means of optical spectroscopy. We use a singly suspended SWNT between mesa structures to minimize the interactions with the substrate and other nanotubes, and expose it directly to the ambient gas. Semiconducting SWNTs suspended in space exhibit resonant photoluminescence (PL) and Raman scattering, and their optical responses depend on the state of molecules adsorbed on the SWNT surface or encapsulated in the tube [1-3]. Therefore, gas molecule adsorption/desorption on the SWNT surface or inside of the tube can be probed by PL and Raman spectroscopy. We have found that water molecules form an adsorption layer of two-monolayer thickness on the hydrophobic SWNT surface as a result of hydrogen-bonding network of water molecules [2]. The water adsorption layer has a sizable effect on the radial breathing mode frequency in Raman scattering [4]. The phase of water molecules can also affect those properties of SWNTs. The phase diagrams of the water both outside and inside of SWNT will be constructed based on the results of spectroscopy. Furthermore, PL peak energies from hybrids of single-stranded DNA and SWNT were found to depend on the DNA base type, namely thymine, adenine, cytosine, and guanine [5]. The base type dependence was attributed to the adsorption energy of the DNA bases on the SWNT surface. [1] S. Chiashi, et al. Nano Lett. 8, 3097 (2008). [2] Y. Homma, et al. Phys. Rev. Lett. 110, 157402 (2013). [3] S. Chiashi, et al. J. Phys. Chem. Lett. 5, 408 (2014). [4] S. Chiashi, et al. Phys. Rev. B 91, 155415 (2015). [5] M. Ito, et al. J. Phys. Chem. C 119, 21141 (2015).

Proton Transport in a Highly Conductive Porous Zirconium-Based Metal-Organic Framework: Molecular Insight.

The water stable UiO-66(Zr)-(CO2H)2 MOF exhibits a superprotonic conductivity of 2.3×10(-3) S cm(-1) at 90 °C and 95 % relative humidity. Quasi-elastic neutron scattering measurements combined with aMS-EVB3 molecular dynamics simulations were able to probe individually the dynamics of both confined protons and water molecules and to further reveal that the proton transport is assisted by the formation of a hydrogen-bonded water network that spans from the tetrahedral to the octahedral cages of this MOF. This is the first joint experimental/modeling study that unambiguously elucidates the proton-conduction mechanism at the molecular level in a highly conductive MOF.

Contrasting mechanisms for CO2 absorption and regeneration processes in aqueous amine solutions: Insights from density-functional tight-binding molecular dynamics simulations

CO2 chemical absorption and regeneration processes in aqueous amine solutions were investigated using density-functional tight-binding molecular dynamics simulations. Extensive analyses of the structural, electronic, and dynamical properties of 100 independent trajectories supported the contrasting mechanisms in the absorption and regeneration processes. In the CO2 absorption process, bicarbonate formed where the hydroxyl anion migrated through the hydrogen-bond network of water molecules, namely, by a Grotthuss-type mechanism. On the other hand, direct proton transfer from the protonated amine to the hydroxyl group of bicarbonate, which is called the ion-pair mechanism, was the key step to the release of CO2.

Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets.

MicroRNAs (miRNAs) direct post-transcriptional regulation of human genes by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. An enigmatic feature of many conserved mammalian miRNA target sites is that an adenosine (A) nucleotide opposite miRNA nucleotide-1 confers enhanced target repression independently of base pairing potential to the miRNA. In this study, we show that human Argonaute2 (Ago2) possesses a solvated surface pocket that specifically binds adenine nucleobases in the 1 position (t1) of target RNAs. t1A nucleotides are recognized indirectly through a hydrogen-bonding network of water molecules that preferentially interacts with the N6 amine on adenine. t1A nucleotides are not utilized during the initial binding of Ago2 to its target, but instead function by increasing the dwell time on target RNA. We also show that N6 adenosine methylation blocks t1A recognition, revealing a possible mechanism for modulation of miRNA target site potency.

Effects of mutations on the molecular dynamics of oxygen escape from the dimeric hemoglobin of Scapharca inaequivalvis

Like many hemoglobins, the structure of the dimeric hemoglobin from the clam Scapharca inaequivalvis is a “closed bottle” since there is no direct tunnel from the oxygen binding site on the heme to the solvent. The proximal histidine faces the dimer interface, which consists of the E and F helicies. This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules. Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the structure would seem to make that pathway less likely. Locally enhanced sampling molecular dynamics are used here to suggest alternative pathways in the wild-type and six mutant proteins. In most cases the point mutations change the selection of exit routes observed in the simulations. Exit via the histidine gate is rarely seem although oxygen molecules do occasionally cross over the interface from one subunit to the other. The results suggest that changes in flexibility and, in some cases, creation of new cavities can explain the effects of the mutations on ligand exit paths.

Effects of mutations on the molecular dynamics of oxygen escape from the dimeric hemoglobin of Scapharca inaequivalvis.

Like many hemoglobins, the structure of the dimeric hemoglobin from the clam Scapharca inaequivalvis is a "closed bottle" since there is no direct tunnel from the oxygen binding site on the heme to the solvent. The proximal histidine faces the dimer interface, which consists of the E and F helicies. This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules. Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the structure would seem to make that pathway less likely. Locally enhanced sampling molecular dynamics are used here to suggest alternative pathways in the wild-type and six mutant proteins. In most cases the point mutations change the selection of exit routes observed in the simulations. Exit via the histidine gate is rarely seem although oxygen molecules do occasionally cross over the interface from one subunit to the other. The results suggest that changes in flexibility and, in some cases, creation of new cavities can explain the effects of the mutations on ligand exit paths.

Role of water in stabilizing ferricyanide trianion and ion-induced effects to the hydrogen-bonding water network at long distance.

Structures and reactivities of gaseous Fe(CN)(6)(3-)(H(2)O)n were investigated using infrared photodissociation (IRPD) kinetics, spectroscopy, and computational chemistry in order to gain insights into how water stabilizes highly charged anions. Fe(CN)(6)(3-)(H(2)O)(8) is the smallest hydrated cluster produced by electrospray ionization, and blackbody infrared dissociation of this ion results in loss of an electron and formation of smaller dianion clusters. Fe(CN)(6)(3-)(H(2)O)(7) is produced by the higher activation conditions of IRPD, and this ion dissociates both by loss of an electron and by loss of a water molecule. Comparisons of IRPD spectra to those of computed low-energy structures for Fe(CN)(6)(3-)(H(2)O)(8) indicate that water molecules either form two hydrogen bonds to the trianion or form one hydrogen bond to the ion and one to another water molecule. Magic numbers are observed for Fe(CN)(6)(3-)(H(2)O)n for n between 58 and 60, and the IRPD spectrum of the n = 60 cluster shows stronger water molecule hydrogen-bonding than that of the n = 61 cluster, consistent with the significantly higher stability of the former. Remarkably, neither cluster has a band corresponding to a free O-H stretch, and this band is not observed for clusters until n ≥ 70, indicating that this trianion significantly affects the hydrogen-bonding network of water molecules well beyond the second and even third solvation shells. These results provide new insights into the role of water in stabilizing high-valency anions and how these ions can pattern the structure of water even at long distances.

Locating Protonated Amines in Clathrates

The structures and inherent stabilities of hydrated, protonated ammonia, select protonated primary, secondary, and tertiary amines as well as tetramethylammonium with 19-21 water molecules were investigated using infrared photodissociation (IRPD) spectroscopy and blackbody infrared radiative dissociation (BIRD) at 133 K. Magic number clusters (MNCs) with 20 water molecules were observed for all ions except tetramethylammonium, and the BIRD results indicate that these clusters have stable structures, which are relatively unaffected by addition of one water molecule but are disrupted in clusters with one less water molecule. IRPD spectra in the water free O-H stretch region are consistent with clathrate structures for the MNCs with 20 water molecules, whereas nonclathrate structures are indicated for tetramethylammonium as well as ions at the other cluster sizes. The locations of protonated ammonia and the protonated primary amines either in the interior or at the surface of a clathrate were determined by comparing IRPD spectra of these ions to those of reference ions; Rb(+) and protonated tert-butylammonia with 20 water molecules were used as references for an ion in the interior and at the surface of a clathrate, respectively. These results indicate that protonated ammonia is in the interior of the clathrate, whereas protonated methyl- and n-heptylamine are at the surface. Calculations suggest that the number of hydrogen bonds in these clusters does not directly correlate with structural stability, indicating that both the number and orientation of the hydrogen bonds are important. These experimental results should serve as benchmarks for computational studies aimed at elucidating ion effects on the hydrogen-bonding network of water molecules and the surface activity of ions.

Hydronium dynamics in the perchloric acid clathrate hydrate

Clathrate hydrates are nanoporous crystalline materials made of a network of hydrogen-bonded water molecules (forming host cages) stabilized by the presence of foreign (generally hydrophobic) guest molecules. The encapsulation of strong acids such as perchloric acid (with an acid to water ratio of 5.5) leads to an ionic clathrate structure formed with perchlorate anions within cationic cages. The excess protons, at the origin of the large protonic conductivity of the compound, are delocalized over the cage sub-structure through a Grotthus mechanism. Such ionic crystal constitutes a good model system for investigating the spatial and time characteristics of the elementary steps of the proton conduction. In this paper, the dynamics of hydronium ions are investigated by means of incoherent quasi-elastic neutron scattering (QENS) experiments performed by tuning the observation time to the timescale of the probed dynamical process met in the perchloric acid clathrate hydrate at 220 K. Thanks to the specific versatility of time-of-flight spectrometer, two elementary processes have been identified for modeling the hydronium ion dynamics: hydronium reorientations coupled to intermolecular proton transfer. The hydronium ions undergo reorientations with a characteristic time of 42 ± 8 ps while the proton transfer within the hydrogen bond between hydronium ion and neighboring water molecule occurs with a characteristic time of 1.4 ± 0.3 ps. A previous high-resolution QENS investigation has shown that water molecules surrounding the hydronium ions undergo reorientations with a characteristic time of 0.7 ± 0.1 ns at 220 K. Such experimental results outline the key role played by the relaxation of the water molecules surrounding the hydronium ions prior to any proton transfer.

Red and Orange Polymorphs of [Pt(terpy)Cl]Cl·2H2O

The crystal structures of new red (1) and orange (2) polymorphs of chloro(2,2′:6′2″-terpyridine)-platinum(II) chloride dihydrate, [Pt(terpy)Cl]Cl·2H2O, have been determined by single crystal X-ray diffraction. Compound 1 packs in a one-dimensional stacking structure with two unique intermolecular Pt···Pt distances (3.3278(5) A, 3.4444(5) A). The principal difference between this red polymorph and a previously reported yellow polymorph is in the cation stacking motif. This red polymorph has two alternating short intermolecular Pt···Pt distances while the yellow polymorph has one long and one short Pt···Pt distance. Channels between the cation stacks are occupied by a hydrogen-bonding network of water molecules and chloride anions. This red polymorph has a cation stacking motif similar to those found in a diverse collection of structures with different counterions and solvates of the chloro(2,2′:6′2″-terpyridine)-platinum(II) cation. The orange polymorph 2 possesses a stacking motif with two alternating long intermolecular Pt···Pt distances (4.2169(4) A, 5.1582(4) A). The hydrogen-bonding network involving the chloride counterions and water molecules differs significantly from either the red or yellow polymorphs as well. Structure 1: monoclinic, P 21/c, a = 12.2630(14) A, b = 6.7459(8) A, c = 20.121(2) A, β = 105.018(2)°, V = 1,607.7(3) A3, Z = 4, R 1 = 0.0338, wR 2 = 0.0665. Structure 2: monoclinic, P 21/c, a = 8.0236(7) A, b = 12.9393(1) A, c = 15.847(2) A, β = 101.068(7)°, V = 1,614.6(3) A3, Z = 4, R 1 = 0.0181, wR 2 = 0.0377. The crystal structures of new red (1) and orange (2) polymorphs of chloro(2,2′:6′2″-terpyridine)-platinum(II) chloride dihydrate, [Pt(terpy)Cl]Cl·2H2O show that the red polymorph stacks with two unique intermolecular Pt···Pt distances (3.3278(5) A, 3.4444(5) A) while the orange polymorph has no intermolecular Pt···Pt contacts less than 4.2 A.

Investigation of organelle-specific intracellular water structures with Raman microspectroscopy

The study of intracellular water in living cells is a challenge of fundamental importance. While the critical roles of water in maintaining and propagating life have been widely recognized and accepted, our understanding of water/biomolecule interactions is surprisingly limited. Using Raman microspectroscopic imaging of a living yeast cell followed by a multivariate analysis in form of the nonnegative matrix factorization method, we successfully resolve organelle-specific water structures. The intensities and the band profiles of the segregated water OH stretch spectra yield important and otherwise unobtainable information on the extensive effect of the water/biomolecule interactions in a given organelle on the hydrogen-bonding network of water molecules. Copyright © 2012 John Wiley & Sons, Ltd.

Energy landscape of clathrate hydrates

Clathrate hydrates are nanoporous crystalline materials made of a network of hydrogen-bonded water molecules (forming host cages) that is stabilized by the presence of foreign (generally hydrophobic) guest molecules. The natural existence of large quantities of hydrocarbon hydrates in deep oceans and permafrost is certainly at the origin of numerous applications in the broad areas of energy and environmental sciences and technologies (e.g. gas storage). At a fundamental level, their nanostructuration confers on these materials specific properties (e.g. their “glass-like” thermal conductivity) for which the host-guest interactions play a key role. These interactions occur on broad timescale and thus require the use of multi-technique approach in which neutron scattering brings unvaluable information. This work reviews the dynamical properties of clathrate hydrates, ranging from intramolecular vibrations to Brownian relaxations; it illustrates the contribution of neutron scattering in the understanding of the underlying factors governing chemical-physics properties specific to these nanoporous systems.