We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.
Molecular crystals are difficult to model with accurate first-principles methods due to large unit cells. On the other hand, accurate modeling is required as polymorphs often differ by only 1 kJ/mol. Machine learning interatomic potentials promise to provide accuracy of the baseline first-principles methods with a cost lower by orders of magnitude. Using the existing databases of the density functional theory calculations for molecular crystals and molecules, we train global machine learning interatomic potentials, usable for any molecular crystal. We test the performance of the potentials on experimental benchmarks and show that they perform better than classical force fields and, in some cases, are comparable to the density functional theory calculations.
For the first time, we directly measured the onset and completion temperatures of polymorphic transitions under thermo-mechanochemical conditions by simultaneous in situ synchrotron powder X-ray diffraction and temperature monitoring. We determined the thermo-mechanochemical polymorphic transition temperature in 1-adamantyl-1-diamantyl ether to be 31 °C lower than the transition temperature determined by DSC. Our findings highlight the uniqueness of thermo-mechanochemical conditions, with potential applications in polymorph screening.
A one-dimensional (1D) ladder-like coordination polymer {NH4[{Cu(bpy)}2(C2O4)Fe(C2O4)3]·H2O}n (1; bpy = 2,2'-bipyridine) containing [Cu(bpy)(µ-C2O4)Cu(bpy)]2+ cationic units linked by oxalate groups of [Fe(C2O4)3]3- building blocks was investigated as a new type of photoactive solid-state system. It exhibits a photocoloration effect when exposed to direct sunlight or UV/vis irradiation. The photochromic properties and mechanism were studied by powder and single-crystal X-ray diffraction, UV/vis diffuse reflectance, IR and electron paramagnetic resonance spectroscopy, magnetization and impedance measurements, and density functional theory calculations. The process of photochromism involves simultaneous intramolecular electron transfers from the oxalate ligand to Fe(III) and to [CuII(bpy)(µ-C2O4)CuII(bpy)]2+, leading to the reduction of the metal centers to the electronic states Fe(II) and Cu(I), accompanied by the release of gaseous CO2.
Tetrachlorocuprate(II) hybrids of the three anisidine isomers (ortho-, meta-, and para-, or 2-, 3-, and 4-methoxyaniline, respectively) were prepared and studied in the solid state via X-ray diffraction and magnetization measurements. Depending on the position of the methoxy group of the organic cation, and subsequently, the overall cation geometry, a layered, defective layered, and the structure comprising discrete tetrachlorocuprate(II) units were obtained for the para-, meta-, and ortho-anisidinium hybrids, respectively. In the case of layered and defective layered structures, this affords quasi-2D-layered magnets, demonstrating a complex interplay of strong and weak magnetic interactions that lead to the long-range ferromagnetic (FM) order. In the case of the structure with discrete CuCl42- ions, a peculiar antiferromagnetic (AFM) behavior was revealed. The structural and electronic origins of magnetism are discussed in detail. To supplement it, the method for calculation of dimensionality of the inorganic framework as a function of interaction length was developed. The same was used to discriminate between n-dimensional and "almost" n-dimensional frameworks, to estimate the organic cation geometry limits for layered halometallates, and to provide additional reasoning behind the observed relation between cation geometry and framework dimensionality, as well as their relation to differences in magnetic behavior.
Modeling the ultrafast photoinduced dynamics and reactivity of adsorbates on metals requires including the effect of the laser-excited electrons and, in many cases, also the effect of the highly excited surface lattice. Although the recent ab initio molecular dynamics with electronic friction and thermostats, (Te,Tl)-AIMDEF [Alducin, M.; Phys. Rev. Lett. 2019, 123, 246802], enables such complex modeling, its computational cost may limit its applicability. Here, we use the new embedded atom neural network (EANN) method [Zhang, Y.; J. Phys. Chem. Lett. 2019, 10, 4962] to develop an accurate and extremely complex potential energy surface (PES) that allows us a detailed and reliable description of the photoinduced desorption of CO from the Pd(111) surface with a coverage of 0.75 monolayer. Molecular dynamics simulations performed on this EANN-PES reproduce the (Te,Tl)-AIMDEF results with a remarkable level of accuracy. This demonstrates the outstanding performance of the obtained EANN-PES that is able to reproduce available density functional theory (DFT) data for an extensive range of surface temperatures (90-1000 K); a large number of degrees of freedom, those corresponding to six CO adsorbates and 24 moving surface atoms; and the varying CO coverage caused by the abundant desorption events.
Hybrid metal-organic compounds as relatively new and prosperous magnetoelectric multiferroics provide opportunities to improve the polarization, magnetization and magneto-electric coupling at the same time, which usually have some limitations in the common type-I and type-II multiferroics. In this work we investigate the crystal of guanidinium copper (II) formate [C(NH2)3]Cu(HCOO)3 and give novel insights concerning the structure, magnetic, electric and magneto-electric behaviour of this interesting material. Detailed analysis of crystal structure at 100 K is given. Magnetization points to the copper (II) formate spin-chain phase that becomes ordered below 4.6 K into the canted antiferromagnetic (AFM) state, as a result of super-exchange interaction over different formate bridges. The performed ab-initio colinear density functional theory (DFT) calculations confirm the AFM-like ground state as a first approximation and explain the coupling of spin-chains into the AFM ordered lattice. In versatile measurements of magnetization of a crystal, including transverse component besides the longitudinal one, very large anisotropy is found that might originate from canting of the coordination octahedra around copper (II) in cooperation with the canted AFM order. With cooling down in zero fields the generation of spontaneous polarization is observed step-wise below 270 K and 210 K and the effect of magnetic field on its value is observed also in the paramagnetic phase. Measured polarization is somewhat smaller than the DFT value in the c-direction, possibly due to twin domains present in the crystal. The considerable magneto-electric coupling below the magnetic transition temperature is measured with different orientations of the crystal in magnetic field, giving altogether the new light onto the magneto-electric effect in this material.
The heterodimetallic [CuFe] compounds [CuII4(terpy)4Cl5][FeIII(C2O4)3]·10H2O (1;terpy = 2,2':6',2''-terpyridine), [CuII2(H2O)2(terpy)2(C2O4)][CuIIFeIII(CH3OH)(terpy)(C2O4)3]2 (2), and {[Cu2IIFeIII(H2O)(terpy)2(C2O4)7/2]·6H2O}n (3) were obtained using building block approach, from reaction of aqueous solution of [Fe(C2O4)3]3- and a methanol solution containing Cu2+ ions and terpy by the layering technique. Interestingly, by changing only the anion of the starting salt of copper(II), Cu(NO3)2·3H2O instead of CuCl2·2H2O, an unexpected change in the type of bridge, oxalate (2 and 3) versus chloride (1), was achieved, thus affecting the overall structural architecture. Two polymorphs of 3D coordination polymer [CuIIFeII2(H2O)(terpy)(C2O4)3]n (4), crystallizing in the triclinic (a) and monoclinic (b) space groups, were formed hydrothermally, depending on whether CuCl2·2H2O or Cu(NO3)2·3H2O was added to the water, besides K3[Fe(C2O4)3]·3H2O and terpy, respectively. Under hydrothermal conditions iron(III) from initial building block is reduced to the divalent state, creating 2D honeycomb [FeII2(C2O4)3]n2n- layers, which are bridged by [Cu(H2O)(terpy)]2+ cations. Compounds were investigated by single-crystal X-ray diffraction, IR, and impedance spectroscopies, magnetization measurements, and density functional theory (DFT) calculations. In compounds 1 and 2, 0D magnetism is observed, with 1 having a ground-state spin of 1 due to different interactions through chloride bridges of Cu2+ ions in tetramer [CuII4(terpy)4Cl5]3+ and 2 showing strong antiferromagnetic coupling of Cu2+ ions mediated by oxalate ligand in [CuII2(H2O)2(terpy)2(C2O4)]2+ and weak ones between Cu2+ and Fe3+ ions through oxalate bridge in [CuIIFeIII(CH3OH)(terpy)(C2O4)3]-. Polymer 4 exhibits antiferromagnetic phase transition at 25 K: The [FeII2(C2O4)3]n2n- layers are antiferromagnetically ordered, and a small amount of interlayer interaction is transferred through [Cu(H2O)(terpy)]2+ cations via Oox-Cu-Oox bridges. Additionally, compounds 1 and 2 are electrical insulators, while 4a and 4b show proton conductivity.
Here we describe real-time, in situ monitoring of mechanochemical solid-state metathesis between silver nitrate and the entire series of sodium halides, on the basis of tandem powder X-ray diffraction and Raman spectroscopy monitoring. The mechanistic monitoring reveals that reactions of AgNO3 with NaX (X = Cl, Br, I) differ in reaction paths, with only the reaction with NaBr providing the NaNO3 and AgX products directly. The reaction with NaI revealed the presence of a novel, short-lived intermediate phase, while the reaction with NaCl progressed the slowest through the well-defined Ag2ClNO3 intermediate double salt. While the corresponding iodide and bromide double salts were not observed as intermediates, all three are readily prepared as pure compounds by milling equimolar mixtures of AgX and AgNO3. The in situ observation of reactive intermediates in these simple metathesis reactions reveals a surprising resemblance of reactions involving purely ionic components to those of molecular organic solids and cocrystals. This study demonstrates the potential of in situ reaction monitoring for mechanochemical reactions of ionic compounds as well as completes the application of these techniques to all major compound classes.
Engineering interfaces is an effective method to create efficient photocatalysts by reducing the recombination of photogenerated carriers. Still, there is a lack of proficient strategies to construct suitable interfaces. In this work, we design and synthesize an atom-precise heterometallic CuII4TiIV5 cluster, [Ti5Cu4O6(ba)16]·2CH3CN (1, Hba = benzoic acid), which is used as a precursor for fabricating efficient photocatalytic interfaces. The cluster has a precise composition and structure with hierarchical bimetal atom distribution and favorable binding properties. The resulting Cu/TiO2@N-doped C interfaces are obtained via the thermal treatment. Combined Cu/TiO2 with N-doped C interfaces provide multiple channels for the transmission of photogenerated carriers and effectively reduce the recombination probability of photogenerated charge carriers. Consequently, the novel interface structure exhibits an excellent hydrogen evolution rate via the photocatalytic water splliting. Density functional theory calculations also support high activity of the interfaces toward hydrogen evolution. As a proof-of-concept application, we show that choosing well-defined metal clusters as precursors can offer a valuable method for engineering photocatalytically efficient interfaces.
Tetratopic porphyrin-based metal-organic frameworks (MOFs) represent a particularly interesting subclass of zirconium MOFs due to the occurrence of several divergent topologies. Control over the target topology is a demanding task, and reports often show products containing phase contamination. We demonstrate how mechanochemistry can be exploited for controlling the polymorphism in 12-coordinated porphyrinic zirconium MOFs, obtaining pure hexagonal PCN-223 and cubic MOF-525 phases in 20-60 min of milling. The reactions are mainly governed by the milling additives and the zirconium precursor. In situ monitoring by synchrotron powder X-ray diffraction revealed that specific reaction conditions resulted in the formation of MOF-525 as an intermediate, which rapidly converted to PCN-223 upon milling. Electron spin resonance measurements revealed significant differences between the spectra of paramagnetic centers in two polymorphs, showing a potential of polymorphic Zr-MOFs as tunable supports in spintronics applications.
Peptides are very common recognition entities that are usually attached to surfaces using multistep processes. These processes require modification of the native peptides and of the substrates. Using functional groups in native peptides for their assembly on surfaces without affecting their biological activity can facilitate the preparation of biosensors. Herein, we present a simple single-step formation of native oxytocin monolayer on gold surface. These surfaces were characterized by atomic force spectroscopy, spectroscopic ellipsometry, and X-ray photoelectron spectroscopy. We took advantage of the native disulfide bridge of the oxytocin for anchoring the peptide to the Au surface, while preserving the metal-ion binding properties. Self-assembled oxytocin monolayer was used by electrochemical impedance spectroscopy for metal-ion sensing leading to subnanomolar sensitivities for zinc or copper ions.
Three heterometallic one-dimensional (1D) coordination polymers {A[CrCu2(bpy)2(C2O4)4]·H2O}n [A = K+ (1) and NH4+ (2); bpy = 2,2'-bipyridine] and [(Cr2O7)Cu2(C2O4)(phen)2]n (3; phen = 1,10-phenanthroline) with uncommon topology have been synthesized using a building block approach and characterized by single-crystal X-ray diffraction, IR and impedance spectroscopies, magnetization measurements, and DFT calculations. Due to the partial decomposition of the building block [Cr(C2O4)3]3-, all three compounds contain oxalate-bridged [Cu2(L)2(µ-C2O4)]2+ units [L = bpy (1 and 2) and phen (3)]. In compounds 1 and 2 these cations are mutually connected through oxalate groups from [Cr(C2O4)3]3-, thus forming ladder-like topologies. Unusually, three different bridging modes of the oxalate ligand are observed in these chains. In compound 3 copper(ii) ions from cationic units are bridged through the oxygen atoms of Cr2O72- anions in a novel ladder-like mode. Very strong antiferromagnetic coupling observed in all three compounds, determined from the magnetization measurements and confirmed by DFT calculations (J = -343, -371 and -340 cm-1 for 1, 2 and 3, respectively), appears between two copper(ii) ions interacting through the oxalate bridge.
Measured lifetimes of the CO internal stretch mode on various metal surfaces routinely lie in the picosecond regime. These short vibrational lifetimes, which are actually reproduced by current first-principles nonadiabatic calculations, are attributed to the rapid vibrational energy loss that is caused by the facile excitation of electron-hole pairs in metals. However, this explanation was recently questioned by the huge discrepancy that exists for CO on Au(111) between the experimental vibrational lifetime that is larger than 100 ps and the previous theoretical predictions of 4.8 and 1.6 ps. Here, we show that the state-of-the-art nonadiabatic theory does reproduce the long CO lifetime measured in Au(111) provided the molecule-surface interaction is properly described. Importantly, our new results confirm that the current understanding of the adsorbates' vibrational relaxation at metal surfaces is indeed valid.
We report the first cocrystal as an intermediate in a solid-state organic reaction wherein molecules of barbituric acid and vanillin assume a favorable orientation for the subsequent Knoevenagel condensation.
Three heterometallic oxo-bridged compounds, [Cr2(phen)4(µ-O)4Nb2(C2O4)4]·2H2O (1; phen = 1,10-phenanthroline), [Cr2(terpy)2(H2O)2(µ-O)4Nb2(C2O4)4]·4H2O (2; terpy = 2,2';6',2''-terpyridine) and [Cr(terpy)(C2O4)(H2O)][Cr2(terpy)2(C2O4)2(µ-O)2Nb(C2O4)2]·3H2O (3), have been synthesized using a building block approach and characterized by IR spectroscopy, single-crystal and powder X-ray diffraction, magnetization measurements, and DFT calculations. The molecular structures of 1 and 2, crystallizing in P42212 and P21/n space groups, respectively, contain a square-shaped {Cr(µ-O)4Nb} unit, while that of complex salt 3 (P1[combining macron] space group) consists of a mononuclear cation containing CrIII and trinuclear anions in which two CrIII ions are bridged by a -O-NbV-O- fragment. Besides hydrogen-bonding patterns resulting in a 1D- or 3D-supramolecular arrangement in 1-3, an unusual intermolecular contact has been noticed between parallel oxalate moieties occurring due to the electrostatic attraction of electron-rich carbonyl oxygen and severely electron-depleted carbon atoms in the crystal packing of 2. The antiferromagnetic coupling observed in all three compounds, determined from magnetization measurements (J = -13.51(2), -8.41(1) and -7.44(4) cm-1 for 1, 2 and 3, respectively) and confirmed by DFT calculations, originates from two CrIII ions with spin 3/2 interacting through diamagnetic -O-NbV-O- bridge(s).
Point defects significantly influence the optical and electrical properties of solid-state materials due to their interactions with charge carriers, which reduce the band-to-band optical transition energy. There has been a demand for developing direct optical imaging methods that would allow in situ characterization of individual defects with nanometer resolution. Here, we demonstrate the localization and quantitative counting of individual optically active defects in monolayer hexagonal boron nitride using single molecule localization microscopy. By exploiting the blinking behavior of defect emitters to temporally isolate multiple emitters within one diffraction limited region, we could resolve two defect emitters with a point-to-point distance down to ten nanometers. The results and conclusion presented in this work add unprecedented dimensions toward future applications of defects in quantum information processing and biological imaging.
Complete sticking at low incidence energies and broad angular scattering distributions at higher energies are often observed in molecular beam experiments on gas-surface systems which feature a deep chemisorption well and lack early reaction barriers. Although CO binds strongly on Ru(0001), scattering is characterized by rather narrow angular distributions and sticking is incomplete even at low incidence energies. We perform molecular dynamics simulations, accounting for phononic (and electronic) energy loss channels, on a potential energy surface based on first-principles electronic structure calculations that reproduce the molecular beam experiments. We demonstrate that the mentioned unusual behavior is a consequence of a very strong rotational anisotropy in the molecule-surface interaction potential. Beyond the interpretation of scattering phenomena, we also discuss implications of our results for the recently proposed role of a precursor state for the desorption and scattering of CO from ruthenium.
We perform a detailed study of the static and dynamical properties of molecular oxygen adsorption on Ag(110) based on semi-local density functional theory (DFT) calculations and compare the results to experimental studies. For the classical dynamics calculations we use two complementary approaches, ab initio molecular dynamics and dynamics on a precalculated potential energy surface. In contrast to the molecular beam experiments, at low beam incidence energies we obtain high molecular adsorption probabilities that are related to the physisorption-like adsorption wells at the bridge sites of Ag(110). Semi-local DFT seems to overbind O2 in these wells. Based on our dynamics calculations we propose a model for adsorption in the chemisorption wells via initial adsorption in the bridge wells. In this model the measured low adsorption probabilities at low incidence energies are explained by the existence of energy barriers between the physisorption-like and chemisorption wells.
We study the dissociative dynamics of O2 on Ag(110) by performing classical and quasiclassical trajectory calculations on an adiabatic six-dimensional potential energy surface (PES). The PES is constructed from the interpolation of a large set of energies that are calculated using spin-polarized density functional theory. The minimum energy barrier to dissociation amounts to 0.36 eV. This value, which is considerably lower than the barriers of about 1.1 eV found in the Ag(100) and Ag(111) surfaces, is in line with the measured much higher reactivity of the (110) surface. Our classical dynamics calculations show that under normal incidence conditions no significant dissociation occurs below an initial energy of 0.9 eV (0.6 eV in the quasiclassical calculations). This result is an indication of a very much reduced configurational space leading to dissociation and also explains why direct dissociation has not been observed experimentally at low incidence energies. Our calculations also show that for off-normal incidence, most of the dissociation takes place close to the long-bridge site, a region of the configurational space where the energy barriers to dissociation are higher than 0.7 eV, resulting in still lower dissociation probabilities.
