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The solid-state synthesis and fast crystallization under kinetic control of poly-[n]-catenanes self-assembled of mechanically interlocked metal organic cages (MOCs) is virtually unexplored. This is in part, due to the lack of suitable crystals for single crystal X-ray diffraction (SC-XRD) analysis which limits their progress as advanced functional materials. Here we report the unprecedented inclusion of paracetamol in the cavities of amorphous materials constituted of M12L8, interlocked MOCs synthesized by mechanochemistry under kinetic control. Full structure determination of a low-crystallinity and low-resolution powders of the M12L8 poly-[n]-catenane including paracetamol has been carried out combining XRD data and Density Functional Theory (DFT) calculations using a multi-step approach. Each M12L8 cage contains six paracetamol guests which is confirmed by thermal analysis and NMR spectroscopy. The paracetamol loading has been also carried out by the instant synthesis method using a saturated paracetamol solution in which TPB and ZnI2 self-assemble immediately (i. e., 1-5â seconds) encapsulating ~7â paracetamol molecules in the M12L8 nanocages under kinetic control also giving a good selectivity. Benzaldehyde has been included in the M12L8 cages using amorphous M12L8 polycatenanes showing that the icosahedral cages can serve as potential nanoreactors for instance to study Henry reactions in the solid-state.
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Poly-[n]-catenanes (PCs) self-assembled of three-dimensional (3D) metal organic cages (MOCs) (hereafter referred to as PCs-MOCs) are a relatively new class of mechanically interlocked molecules (MIMs) that combine the properties of MOCs and polymers. The synthesis of PCs-MOCs is challenging because of the difficulties associated with interlocking MOCs, the occurrence of multiple weak supramolecular electrostatic interactions between cages, and the importance of solvent templating effects. The high density of mechanical bonds interlocking the MOCs endows the MOCs with mechanical and physical properties such as enhanced stability, responsive dynamic behavior and low solubility, which can unlock new functional properties. In this Minireview, we highlight the benefit of interlocking MOCs in the formation of PCs-MOCs structures as well as the synthetic approaches exploited in their preparation, from thermodynamic to kinetic methods, both in the solution and solid-states. Examples of PCs-MOCs self-assembled from various types of nanosized cages (i.e., tetrahedral, trigonal prismatic, octahedral and icosahedral) are described in this article, providing an overview of the research carried out in this area. The focus is on the structure-property relationship with examples of functional applications such as electron conductivity, X-ray attenuation, gas adsorption and molecular sensing. We believe that the structural and functional aspects of the reviewed PCs-MOCs will attract chemists in this research field with great potential as new functional materials in nanotechnological disciplines such as gas adsorption, sensing and photophysical properties such as X-ray attenuation or electron conductivity.
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The proliferation of polymer science and technology in recent decades has been remarkable, with synthetic polymers derived predominantly from petroleum-based sources dominating the market. However, concerns about their environmental impacts and the finite nature of fossil resources have sparked interest in sustainable alternatives. Bio-based polymers, derived from renewable sources such as plants and microbes, offer promise in addressing these challenges. This review provides an overview of bio-based polymers, discussing their production methods, properties, and potential applications. Specifically, it explores prominent examples including polylactic acid (PLA), polyhydroxyalkanoates (PHAs), and polyhydroxy polyamides (PHPAs). Despite their current limited market share, the growing awareness of environmental issues and advancements in technology are driving increased demand for bio-based polymers, positioning them as essential components in the transition towards a more sustainable future.
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The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.
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Compostos Férricos , Heme , Heme/química , Espectroscopia de Ressonância de Spin Eletrônica/métodos , Compostos Férricos/química , Prótons , Ferro/química , Imidazóis/química , Sistema Enzimático do Citocromo P-450RESUMO
In general, due to the lack of efficient specific molecular interactions, achieving host-guest molecular recognition inside large and neutral metal-organic cages (MOCs) is challenging. Preferential molecular recognition of aromatics using the internal binding sites of interlocked icosahedral (i. e., spherical) M12 L8 MOCs within poly-[n]-catenane (1) is reported. The guest absorption was monitored directly in the solid-state by consecutive single-crystal-to-single-crystal (SCSC) reactions in a gas-solid environment, in single-crystal X-ray diffraction (SC-XRD) experiments. The preferential guest uptake was corroborated by density functional theory (DFT) calculations by determining the host-guest interaction energy (Ehost-guest ) with a nitrobenzene (NB)â«p-xylene (p-xy)â«o-dichlorobenzene (o-DCB) trend (i. e., from 44 to 25â kcal mol-1 ), assessing the XRD outcomes. Combining SC-XRD, DFT and solid-state 13 C NMR, the exceptional stability of the M12 L8 cages, together with the guest exchange/release properties were rationalized by considering the presence of mechanical bonds (efficient π-π interactions) and by the pyridine's rotor-like behaviour (with 3â kcal mol-1 rotational energy barrier). The structure-function properties of M12 L8 makes 1 a potential candidate in the field of molecular sensors.
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Designing metal sites into de novo proteins has significantly improved, recently. However, identifying the minimal coordination spheres, able to encompass the necessary information for metal binding and activity, still represents a great challenge, today. Here, we test our understanding with a benchmark, nevertheless difficult, case. We assemble into a miniature 28-residue protein, the quintessential elements required to fold properly around a FeCys4 redox center, and to function efficiently in electron-transfer. This study addresses a challenge in de novo protein design, as it reports the crystal structure of a designed tetra-thiolate metal-binding protein in sub-Å agreement with the intended design. This allows us to well correlate structure to spectroscopic and electrochemical properties. Given its high reduction potential compared to natural and designed FeCys4-containing proteins, we exploit it as terminal electron acceptor of a fully artificial chain triggered by visible light.
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Here, we show that in a supramolecular system with more than 20 building blocks forming large icosahedral M12L8 metal-organic cages (MOCs), using the instant synthesis method, it is possible to kinetically trap and control the formation of interlocking M12L8 nanocages, giving rare M12L8 TPB-ZnI2 poly-[n]-catenane. The catenanes are obtained in a one-pot reaction, selectively as amorphous (a1) or crystalline states, as demonstrated by powder X-ray diffraction (powder XRD), thermogravimetric (TG) analysis and 1H NMR. The 300 K M12L8 poly-[n]-catenane single crystal X-ray diffraction (SC-XRD) structure including nitrobenzene (1) indicates strong guest binding with the large M12L8 cage (i.e., internal volume ca. 2600 Å3), allowing its structural resolution. Conversely, slow self-assembly (5 days) leads to a mixture of the M12L8 poly-[n]-catenane and a new TPB-ZnI2 (2) coordination polymer (i.e., thermodynamic product), as revealed by SC-XRD. The neat grinding solid-state synthesis also yields amorphous M12L8 poly-[n]-catenane (a1'), but not coordination polymers, selectively in 15 min. The dynamic behavior of the M12L8 poly-[n]-catenanes demonstrated by the amorphous-to-crystalline transformation upon the uptake of ortho-, meta- and para-xylenes shows the potential of M12L8 poly-[n]-catenanes as functional materials in molecular separation. Finally, combining SC-XRD of 1 and DFT calculations specific for the solid-state, the role of the guests in the stability of the 1D chains of M12L8 nanocages is reported. Energy interactions such as interaction energies (E), lattice energies (E*), host-guest energies (Ehost-guest) and guest-guest energies (Eguest-guest) were analysed considering the X-ray structure with and without the nitrobenzene guest. Not only the synthetic control achieved in the synthesis of the M12L8 MOCs but also their dynamic behavior either in the crystalline or amorphous phase are sufficient to raise scientific interest in areas ranging from fundamental to applied sides of chemistry and material sciences.
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De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rameâ 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Typeâ 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.
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Cobre , Metaloproteínas , Cobre/química , Catecóis/química , Metaloproteínas/química , OxirreduçãoRESUMO
Despite their potential applications in host-guest chemistry, there are only five reported structures of poly-[n]-catenanes self-assembled by elusive M12L8 icosahedral nanocages. This small number of structures of M12L8 poly-[n]-catenanes is because self-assembly of large metal-organic cages (MOCs) with large windows allowing catenation by means of mechanical bonds is very challenging. Structural reports of M12L8 poly-[n]-catenanes are needed to increase our knowledge about the self-assembly and genesis of such materials. Poly-[n]-catenane (1·p-CT) self-assembly of interlocked M12L8 icosahedral cages (M = Zn(II) and L = 2,4,6-tris-(4-pyridyl)benzene (TPB)) including a new aromatic guest (p-chlorotoluene (p-CT)) is reported by single-crystal XRD. Despite the huge internal M12L8 voids (> 2500 Å3), p-CT is ordered, allowing a clear visualization of the relative host-guest positions. DFT calculations have been used to compute the electrostatic potential of the TPB ligand, and various aromatic guests (i.e., o-dichlorobenzene (o-DCB), p-chloroanisole (p-CA), and nitrobenzene (NBz)) included (ordered) within the M12L8 cages were determined by single-crystal XRD. The computed maps of electrostatic potential (MEPs) allow for the rationalization of the guest's inclusion seen in the 3D X-ray structures. Although more crystallographic X-ray structures and DFT analysis are needed to gain insights of guest inclusion in the large voids of M12L8 poly-[n]-catenanes, the reported combined experimental/DFT structural analyses approach can be exploited to use isostructural M12L8 poly-[n]-catenanes as hosts for molecular separation and could find applications in the crystalline sponge method developed by Fujita and co-workers. We also demonstrate, exploiting the instant synthesis method, in solution (i.e., o-DCB), and in the solid-state by neat grinding (i.e., without solvent), that the isostructural M12L8 poly-[n]-catenane self-assembled with 2,4,6-tris-(4-pyridyl)pyridine (TPP) ligand and ZnX2 (where X = Cl, Br, and I) can be kinetically synthesized as crystalline (yields ≈ 60%) and amorphous phases (yields ≈ 70%) in short time and large quantities. Despite the change in the aromatic nature at the center of the rigid exo-tridentate pyridine-based ligand (TPP vs TPB), the kinetic control gives the poly-[n]-catenanes selectively. The dynamic behavior of the TPP amorphous phases upon the uptake of aromatic guest molecules can be used in molecular separation applications like benzene derivatives.
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This paper documents the dataset obtained from the Electron Paramagnetic Resonance (EPR) study of the electronic properties of a self-sufficient cytochrome P450, CYP116B5hd, which possesses an interesting catalytic activity for synthetic purposes. In fact, when isolated, its heme domain can act as a peroxygenase on different substrates of biotechnological interest. Raw data shown in Famulari et al. (2022) and supplementary data in raw and processed forms (figures) are documented and available in this paper. Additionally, simulations of the experimental data together with simulation scripts based for EasySpin, a widespread MATLAB toolbox for EPR spectral simulations, are provided. The procedure for g-value analysis based on a crystal-field theory is also detailed here, offering an interesting tool for comparison of FeIII-heme P450 systems. Due to the catalytic interest of the protein, which has been recently discovered, and the correlation that has been reported between g-values and peroxidase function, both, CW-EPR and HYSCORE spectra and data set of the model CYPBM3hd are also provided. Finally, the materials and methods for enzyme production and purification, sample preparation and experimental and spectroscopic procedures a together with instrumental details are described in detail. The data files and simulation scripts can be found in: https://doi.org/10.5281/zenodo.6418626.
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CYP116B5 is a self-sufficient cytochrome P450 (CYP450) with interesting catalytic properties for synthetic purposes. When isolated, its heme domain can act as a peroxygenase on different substrates of biotechnological interest. Here, by means of continuous wave and advanced EPR techniques, the coordination environment of iron in the isolated CYP116B5 heme domain (CYP116b5hd) is characterized. The ligand-free protein shows the characteristic EPR spectrum of a low-spin (S = 1/2) FeIII-heme with [gz = 2.440 ± 0.005, gy = 2.25 ± 0.01, gx = 1.92 ± 0.01]. These g-values reflect an electronic ground state very similar to classical P450 monooxygenases rather than P450 peroxygenases. Binding of imidazole results in g-values very close to the ones reported for CYP152 peroxygenases. The detection of hyperfine interactions through HYperfine Sub-level CORrElation (HYSCORE) Spectroscopy experiments, shows that this is due to a nitrogen-mediated axial coordination. This work adds a piece of experimental evidence to the research, aimed at elucidating the features that distinguish the classical P450 enzymes from peroxygenases. It shows that the electronic environment of heme iron of CYP116B5 in the resting state is similar to the classical P450 monooxygenases. Therefore, it is not the critical factor that confers to CYP116B5hd its peroxygenase-like activity, suggesting a crucial role of the protein matrix.
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Compostos Férricos , Heme , Sistema Enzimático do Citocromo P-450/metabolismo , Espectroscopia de Ressonância de Spin Eletrônica/métodos , Compostos Férricos/química , Heme/química , Ferro/químicaRESUMO
The controlled oxidation reaction of L-selenocystine under neutral pH conditions affords selenocysteine seleninic acid (3-selenino-L-alanine) which is characterized also by means of single-crystal X-ray diffraction. This technique shows that selenium forms three chalcogen bonds (ChBs), one of them being outstandingly short. A survey of seleninic acid derivatives in the Cambridge Structural Database (CSD) confirms that the C-Se(=O)O- functionality tends to act as a ChB donor robust enough to systematically influence the interactional landscape in the solid. Quantum Theory of Atom in Molecules (QTAIM) analysis proves the attractive nature of the short contacts observed in crystals containing the seleninic functionality and calculation of surface molecular electrostatic potential (MEP) reveals that remarkably positive σ-holes can frequently be found opposite to the covalent bonds at selenium. Both CSD searches and QTAIM and MEP approaches show that also the sulfinic acid moiety can function as a ChB donor, albeit less frequently than the seleninic acid one. These findings may contribute to a better understanding, at the atomic level, of the mechanism of action of the enzymes that control oxidative stress and ROS deactivation and that contain selenocysteine seleninic acid and cysteine sulfinic acid in the active site.
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Pyridine-based bispidine ligands L1-L7, which differ in the substituent at the N7 position of the bispidine scaffold, have been studied by single crystal X-ray diffraction and density functional theory (DFT) calculations, also including solid-state algorithms. Qualitative description of the packing interactions and quantitative data on the stability of each ligand in the solid-state have been employed to draw reasonable predictions on the ligand potential for the formation of linear 1D coordination polymers (CPs) with Mn(ii)Cl2 and on their resulting dynamic properties, in terms of adsorption and solvent exchange capabilities. The basic assumption lies in the fact that volume and polarizability of the ligands would similarly affect packing energies in both molecular solids and CP materials. The results here obtained confirm the data previously reported on CPs (those made from L4 are less dynamic than the ones with L1), but they also allow the prediction that CPs made with L2 and L5 should be more dynamic than expected, while CPs with L6 and L7 should not form altogether. This latter prediction was derived from the analysis of the steric and electronic factors of the ligand substituents on the N7 position and it is further substantiated by the obtainment of a 2 : 1 molecular complex, and not a CP, by crystallization of L6 with MnCl2.
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Kinetic control in the presence of six aromatic solvents has been successfully applied in the synthesis of a poly-[n]-catenane composed of interlocked M12L8 icosahedral nanometric cages (i.e., internal voids of 2500 Å3). When the exotridentate tris-pyridyl benzene ligand and ZnCl2 with appropriate templating molecules because of good ligand aromatic interactions are used, the metal-organic cages can be synthesized very fast, homogeneously, and in large quantities as microcrystalline materials. Synchrotron single-crystal X-ray data (100 K) allowed the resolution of nitrobenzene guest molecules at the internal walls of the M12L8 nanocages, whereas in the central part of the cages the solvent is highly disordered. The guest release occurs in two steps with the disordered nitrobenzene guests released in the first step (lower temperatures) because of the absence of strong cage-guest interactions. Density functional theory calculations provided a rationalization of these outcomes and, in particular, solid-state approaches, showed theoretical evidence of the kinetic nature in the formation of the poly-[n]-catenane by the analysis of the packing energy in terms of monomeric and dimeric cages.
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The conformational isomerism of the chelating agent 2,6-bis(1-(3-hydroxypropyl)-1,2,3-triazol-4-yl)pyridine (PTD), exploited in fuel reprocessing in spent nuclear waste, has been studied by single crystal X-ray diffraction analysis in combination with an extensive DFT conformational investigation. In the solid-state, the elucidated crystal structure (i.e., not yet published) shows that by thermal treatment (DSC) no other phases are observed upon crystallization from the melt, indicating that the conformation observed by X-ray data is rather stable. Mapping of intermolecular and intramolecular noncovalent interactions has been used to elucidate the unusual arrangement of the asymmetric unit. Considerations relating to the stability of different conformational isomers in aqueous and non-aqueous solutions are also presented. The accurate structural description reported here might open various research topics such as the potential of PTD to act as an outer sphere ligand in the formation of second sphere coordination complexes and their interconversion by mechanochemical means.
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Polymorphism and related solid-state phase transitions affect the structure and morphology and hence the properties of materials, but they are not-so-well understood. Atomistic computational methods can provide molecular-level insights, but they have rarely proven successful for transitions between polymorphic forms of crystalline polymers. In this work, we report atomistic molecular dynamics (MD) simulations of poly(3-alkylthiophenes) (P3ATs), widely used organic semiconductors to explore the experimentally observed, entropy-driven transition from form II to more common form I type polymorphs, or, more precisely, to form I mesophases. The transition is followed continuously, also considering X-ray diffraction evidence, for poly(3-hexylthiophene) (P3HT) and poly(3-butylthiophene) (P3BT), evidencing three main steps: (i) loss of side chain interdigitation, (ii) partial disruption of the original stacking order and (iii) reorganization of polymer chains into new, tighter, main-chain stacks and new layers with characteristic form I periodicities, substantially larger than those in the original form II. The described approach, likely applicable to other important transitions in polymers, provides previously inaccessible insight into the structural organization and disorder features of form I structures of P3ATs, not only in their development from form II structures but also from melts or solutions.
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An anthracene derivative, 9,10-dicyanoanthracene, crystallizes as fluorescent needle-like single crystals that can be readily plastically bent in two directions. Spatially resolved photoluminescence analysis revealed that this material has robust optoelectronic properties that are preserved upon extreme crystal deformation. The highly flexible crystals were successfully tested as efficient switchable optical waveguiding elements for both active and passive light transduction, and the mode of operation depends on the wavelength of the incident light. This prototypical dual-mode organic optical crystalline fiber brings mechanically compliant molecular organic crystals closer to applications as novel light-transducing media for wireless transfer of information in all-organic micro-optoelectronic devices.
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The occurrence of stable van der Waals complexes of small saturated hydrocarbons with molecular iodine is assessed in order to investigate the ability of sp3-hybridized carbon atoms to act as either electron donors or electron acceptors depending on the ligand orientation. Systematic ab initio potential energy surface exploration of methane-I2 and ethane-I2 model dimers was followed by thorough characterization. Despite modest evidence of whole-adduct polarization, the resulting interactions feature a dominant dispersive character. The noncovalent interaction descriptors employed comprise NBO, AIM, NCI, and source function analyses. The relevance of bonding C-H orbitals in donor-acceptor interactions involving saturated hydrocarbons is highlighted. The results here presented corroborate existing literature regarding the electrophilicity of the aliphatic C-H group, and also indicate that the nucleophilic character of C(sp3) shares a dependence on electron withdrawing/donating substituents similar to that extensively documented for σ-holes. Indeed, the sole difference between the two, aside from the nucleophilicity/electrophilicity switch, seems to lie in their directionality. Nucleophilic sites on C(sp3) are not limited to the outermost region of C along a covalent bond axis, but can also engage electrophiles via the bifurcation plane of a CH2 unit. Since valence electrons on these carbon atoms are engaged in covalent bonds, they can only interact with polarizing ligands via the electron density accumulation/depletion in the four corresponding σ orbitals. These, however, do not seem to interact individually with the accompanying electrophile. Source function and NCI results suggest instead that nucleophilic carbon centres participate in the noncovalent bond themselves by drawing electron density from their shared electron pairs.
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The effect of the withdrawing ability of -CF3 groups in a large and flexible bidentate ligand has been evaluated by monitoring the course of solid-state dehydrochlorination reactions. We demonstrate that the coordination bond formation does not occur by mechanochemical means from a second coordination sphere adduct. Quantum mechanical calculations have shown that frontier molecular orbital energy and net charges at N centers can justify the less reactive nature of the partially fluorinated ligand, corroborating the experimental results.
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Gas-solid chemisorption of HCl and adsorption of MeOH/EtOH by nonporous chiral copper(II) coordination complexes 1·MeOH and 1â³·MeOH occur in a cooperative and dynamic manner to give solvated second sphere adducts 1'·MeOH/EtOH. The chemisorption process involves dramatic atomic rearrangements in the crystalline state upon cleavage and formation of H-Cl, N-H, Cu-N, and Cu-Cl coordination and covalent bonds from the gas and solid state, respectively. Using mechanochemistry, the chloride-bridged coordination complex 1â³·MeOH is selectively produced by means of a dehydrochlorination reaction, but not in solution in which a mixture of 1·MeOH and 1â³·MeOH is obtained. 1â³·MeOH also via chemisorption and adsorption can trap HCl and MeOH to give the second sphere adduct 1'·MeOH. The adsorption process is confirmed by forming the second sphere adduct 1'·EtOH by exposing both 1·MeOH and 1â³·MeOH to HCl and ethanol. Quantum-mechanical (QM) calculations specific for solid phases give insights into the relative stabilities of the hybrid metal organic materials involved in the mechanochemical reaction producing selectively 1â³·MeOH, giving a good agreement with the experimental results.