Additional Base‐Pair Formation in DNA Duplexes by a Double‐Headed Nucleotide

We have designed and synthesised a double‐headed nucleotide that presents two nucleobases in the interior of a dsDNA duplex. This nucleotide recognises and forms Watson–Crick base pairs with two complementary adenosines in a Watson–Crick framework. Furthermore, with judicious positioning in complementary strands, the nucleotide recognises itself through the formation of a T:T base pair. Thus, two novel nucleic acid motifs can be defined by using our double‐headed nucleotide. Both motifs were characterised by UV melting experiments, CD and NMR spectroscopy and molecular dynamics simulations. Both motifs leave the thermostability of the native dsDNA duplex largely unaltered. Molecular dynamics calculations showed that the double‐headed nucleotides are accommodated in the dsDNA by entirely local perturbations and that the modified duplexes retain an overall B‐type geometry with the dsDNA unwound by around 25 or 60°, respectively, in each of the modified motifs. Both motifs can be accommodated twice in a dsDNA duplex without incurring any loss of stability and extrapolating from this observation and the results of modelling, it is conceivable that both can be multiplied several times within a dsDNA duplex. These new motifs extend the DNA recognition repertoire and may form the basis for a complete series of double‐headed nucleotides based on all 16 base combinations of the four natural nucleobases. In addition, both motifs can be used in the design of nanoscale DNA structures in which a specific duplex twist is required.     

The Stability of α‐Hydroperoxyalkyl Radicals

High‐level ab initio and Born–Oppenheimer molecular dynamic calculations have been carried out on a series of hydroperoxyalkyl (α‐QOOH) radicals with the aim of investigating the stability and unimolecular decomposition mechanism into QO+OH of these species. Dissociation was shown to take place through rotation of the C?O(OH) bond rather than through elongation of the CO?OH bond. Through the C?O(OH) rotation, the unpaired electron of the radical overlaps with the electron density on the O?OH bond, and from this overlap the C=O π bond forms and the O?OH bond breaks spontaneously. The CH₂OOH, CH(CH₃)OOH, CH(OH)OOH, and α‐hydroperoxycycloheptadienyl radical were found to decompose spontaneously, but the CH(CHO)OOH has a decomposition energy barrier of 5.95 kcal mol^?1 owing to its steric and electronic features. The systems studied in this work provide the first insights into how structural and electronic effects govern the stabilizing influence on elusive α‐QOOH radicals.     

Theoretical study of p‐methacryloyl‐aminophenylarsonic acid

Conformations of p‐methacryloylaminophenylarsonic acid (p‐MAPHA) are determined through molecular mechanics and DFT/B3LYP calculations. Solvation effects are studied within the self‐consistent isodensity continuum model (SCI‐PCM). The stationary points were found to correspond to minima as verified by the analysis of vibrational frequencies in the molecule. The molecular optical absorption was obtained by using different solvent environments. The present results are in good agreement with the available experimental data. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Understanding the Role of Water in Aqueous Ruthenium‐Catalyzed Transfer Hydrogenation of Ketones.

We report an accurate computational study of the role of water in transfer hydrogenation of formaldehyde with a ruthenium‐based catalyst using a water‐specific model. Our results suggest that the reaction mechanism in aqueous solution is significantly different from that in the gas phase or in methanol solution. Previous theoretical studies have shown a concerted hydride and proton transfer in the gas phase (M. Yamakawa, H. Ito, R. Noyori, J. Am. Chem. Soc. 2000 , 122, 1466–1478;J.‐W. Handgraaf, J. N. H. Reek, E. J. Meijer, Organometallics 2003 , 22, 3150–3157; D. A. Alonso, P. Brandt, S. J. M. Nordin, P. G. Andersson, J. Am. Chem. Soc. 1999 , 121, 9580–9588; D. G. I. Petra, J. N. H. Reek, J.‐W. Handgraaf, E. J. Meijer, P. Dierkes, P. C. J. Kamer, J. Brussee, H. E. Schoemaker, P. W. N. M. van Leeuwen, Chem. Eur. J. 2000 , 6, 2818–2829), whereas a delayed, solvent‐mediated proton transfer has been observed in methanol solution (J.‐W. Handgraaf, E. J. Meijer, J. Am. Chem. Soc. 2007 , 129, 3099–3103). In aqueous solution, a concerted transition state is observed, as in the previous studies. However, only the hydride is transferred at that point, whereas the proton is transferred later by a water molecule instead of the catalyst.     

Theoretical Study on the Dual Behavior of XeO3 and XeF4 toward Aromatic Rings: Lone Pair–π versus Aerogen–π Interactions

In this study, several lone pair–π and aerogen–π complexes between XeO₃ and XeF₄ and aromatic rings with different electronic natures (benzene, trifluorobenzene, and hexafluorobenzene) are optimized at the RI‐MP2/aug‐cc‐pVTZ level of theory. All complexes are characterized as true minima by frequency analysis calculations. The donor/acceptor role of the ring in the complexes is analyzed using the natural bond orbital computational tool, showing a remarkable contribution of orbital interactions to the global stabilization of the aerogen–π complexes. Finally, Bader's AIM analysis of several complexes is performed to further characterize the lone pair–π and aerogen–π interactions.     

Theoretical Study on Cooperativity Effects between Anion–π and Halogen‐Bonding Interactions

This article analyzes the interplay between lone pair–π (lp–π) or anion–π interactions and halogen‐bonding interactions. Interesting cooperativity effects are observed when lp/anion–π and halogen‐bonding interactions coexist in the same complex, and they are found even in systems in which the distance between the anion and halogen‐bond donor molecule is longer than 9 Å. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods. Bader′s theory of “atoms in molecules” is used to characterize the interactions and to analyze their strengthening or weakening depending upon the variation of charge density at critical points. The physical nature of the interactions and cooperativity effects are studied by means of molecular interaction potential with polarization partition scheme. By taking advantage of all aforementioned computational methods, the present study examines how these interactions mutually influence each other. Additionally, experimental evidence for such interactions is obtained from the Cambridge Structural Database (CSD).     

Ultrafast Structural Dynamics of Biomolecules Examined by Multiple‐Mode 2D IR Spectroscopy: Anharmonically Coupled Motions are in Harmony

Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L ‐α‐glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal‐mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two‐dimensional infrared (2D IR) spectra, which are simulated using time‐domain third‐order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.     

The Molecular Structure of gauche‐1,3‐Butadiene: Experimental Establishment of Non‐planarity

The planarity of the second stable conformer of 1,3‐butadiene, the archetypal diene for the Diels–Alder reaction in which a planar conjugated diene and a dienophile combine to form a ring, is not established. The most recent high level calculations predicted the species to adopt a twisted, gauche structure owing to steric interactions between the inner terminal hydrogens rather than a planar, cis structure favored by the conjugation of the double bonds. The structure cis‐1,3‐butadiene is unambiguously confirmed experimentally to indeed be gauche with a substantial dihedral angle of 34°, in excellent agreement with theory. Observation of two tunneling components indicates that the molecule undergoes facile interconversion between two equivalent enantiomeric forms. Comparison of experimentally determined structures for gauche‐ and trans‐butadiene provides an opportunity to examine the effects of conjugation and steric interactions.     

Parallel Water/Aromatic Interactions of Non‐Coordinated and Coordinated Water

The parallel interactions of non‐coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel‐down orientation in which one O?H bond is parallel to the aromatic ring, whereas the other O?H bond points to the plane of the ring. The interactions of aqua complexes with parallel‐down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is ?14.89 kcal mol^?1. The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.     

Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Difluoroamine Complex

Introduction　　ApplicationsofabinitiocalculationstointermolecularinteractionsincludingeitherweakvanderWaalsorstrongerhydrogenbondinghavedrawnmuchattentioninthepastdecadesbecausetheyareimportantinawiderangeofphysical,chemicalandbiologicalfields .1 5Inre centyears ,wehaveappliedtheintermolecularinteractionstoenergeticsystemsandobtainedsomemeaningfulinfor mationthatisvaluableforthestudyofenergeticmateri als .6 14 Thebehaviorofmolecularcomplexesisusuallybe tweentwoextremes :thegasphaseandthecrys…     

Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Dimethylnitroamine Clusters

Ab initio SCF and Mφller-Plesset correlation correction methods in combination with counterpose procedure for BSSE correction have been applied to the theroetical studying of dimethylnitroamine and its dimers and trimers.Three optimized stable dimers and two trimers have been obtained.The corrected binding energies of the most stable dimer and trimer were predicted to be -24.68kJ/mol and -47.27kJ/mol,respectively at the MP2/6-31G^*//HF/6-31G^* level.The proportion of correlated interation energies to their total interaction energies for all clusters was at least 29.3 percent,and the BSSE of ΔE(MP2) was at least 10.0kJ/mol.Dispersion and/or electrostatic force were dominant in all clusters.There exist cooperative effects in both the chain and the cyclic trimers.The vibrational frequencies associated with N-O stretches or wags exhibit slight red shifts,but the modes associated with the motion of hydrogen atoms of the methyl group show somewhat blue shifts with respect to those of monomer.Thermodynamic properties of dimethylnitroamine and its clusters at different temperatures have been calculated on the basis of vibrational analyses.The changes of the Gibbs free energies for the aggregation from monomer to the most stable dimer and trimer were predicted to be 14.37kJ/mol and 30.40kJ/mol,respectively,at 1 atm and 298.15K.     

Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Nitroamine Dimers

Ab initio self-consistent field(SCF) and Mφller-Plesset correlation correction methods employing 6-31G^** basis set have been applied to the optimizations of nitroamine dimers.The binding energies have been corrected for the basis set superposition error (BSSE) and the zero-point energy.Theree optimized dimers have been obtained.The BSSE corrected binding energy of the most stable dimer is predicted to be -31.85kJ/mol at the MP4/6-31G^**//MP2/6-31G^** level.The energy barriers of the Walden conversion for -NH2 group are 19.7kJ/mol and 18.3kJ/mol for monomer and the most stable dimer,respectively.The molecular interaction makes the internal rotation around N1-N2 even more difficult.The thermodynamic properties of nitroamine and its dimers at different temperatures have been calculated on the basis of vibrational analyses.The change of the Gibbs free energy for the aggregation from monomer to the most stable dimer at standard pressure and 298.2 K is predicted to be 14.05kJ/mol.     

Intermolecular Interactions in Weak Donor–Acceptor Complexes from Symmetry‐Adapted Perturbation and Coupled‐Cluster Theory: Tetracyanoethylene–Benzene and Tetracyanoethylene–p‐Xylene

The interactions in the complexes of tetracyanothylene (TCNE) with benzene and p‐xylene, often classified as weak electron donor–acceptor (EDA) complexes, are investigated by a range of quantum chemical methods including intermolecular perturbation theory at the DFT‐SAPT (symmetry‐adapted perturbation theory combined with density functional theory) level and explicitly correlated coupled‐cluster theory at the CCSD(T)‐F12 level. The DFT‐SAPT interaction energies for TCNE–benzene and TCNE–p‐xylene are estimated to be ?35.7 and ?44.9 kJ mol^?1, respectively, at the complete basis set limit. The best estimates for the CCSD(T) interaction energy are ?37.5 and ?46.0 kJ mol^?1, respectively. It is shown that the second‐order dispersion term provides the most important attractive contribution to the interaction energy, followed by the first‐order electrostatic term. The sum of second‐ and higher‐order induction and exchange–induction energies is found to provide nearly 40 % of the total interaction energy. After addition of vibrational, rigid‐rotor, and translational contributions, the computed internal energy changes on complex formation approach results from gas‐phase spectrophotometry at elevated temperatures within experimental uncertainties, while the corresponding entropy changes differ substantially.     

Angular‐Resolved Magnetometry Beyond Triclinic Crystals: Out‐of‐Equilibrium Studies of Cp*ErCOT Single‐Molecule Magnet

Angular‐resolved single‐crystal magnetometry is a key tool to characterise lanthanide‐based materials with low symmetry, for which conjectures based on idealised geometries can be totally misleading. Unfortunately the technique is strictly successful only for triclinic structures, thus reducing significantly its application. By collecting out‐of‐equilibrium magnetisation data the technique was extended to the orthorhombic organometallic Cp*ErCOT single‐molecule magnet (SMM), thus allowing for the first time the reconstruction of the molecular anisotropy tensor notwithstanding the two molecular orientations in the crystal lattice. The results, flanked by state‐of‐the‐art ab initio calculations, confirmed the expected orientation of the molecular easy axis of magnetisation and thus validated the synthetic strategy based on organometallic complexes of a single lanthanide ion.     

Transport Processes at α‐Quartz–Water Interfaces: Insights from First‐Principles Molecular Dynamics Simulations

Car–Parrinello molecular dynamics (CP–MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the α‐quartz–water interface. The model system initially consists of a periodically repeated quartz slab with O‐terminated and Si‐terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H₂O molecules into H⁺ and OH^? is observed at the Si‐terminated surface. The OH^? fragments immediately bind chemically to the Si‐terminated surface while Grotthus‐type proton diffusion through the water film leads to protonation of the O‐terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO₂ present as Si(OH)₄ in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)₄ molecule as would have been indicated by a substantial lowering of the Si(OH)₄ diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP–MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two Si? O bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new Si? O bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz Si? O bond. The final solute species is Si(OH)₄.     

Pressure‐Tuneable Visible‐Range Band Gap in the Ionic Spinel Tin Nitride

The application of pressure allows systematic tuning of the charge density of a material cleanly, that is, without changes to the chemical composition via dopants, and exploratory high‐pressure experiments can inform the design of bulk syntheses of materials that benefit from their properties under compression. The electronic and structural response of semiconducting tin nitride Sn₃N₄ under compression is now reported. A continuous opening of the optical band gap was observed from 1.3 eV to 3.0 eV over a range of 100 GPa, a 540 nm blue‐shift spanning the entire visible spectrum. The pressure‐mediated band gap opening is general to this material across numerous high‐density polymorphs, implicating the predominant ionic bonding in the material as the cause. The rate of decompression to ambient conditions permits access to recoverable metastable states with varying band gaps energies, opening the possibility of pressure‐tuneable electronic properties for future applications.     

Excited‐State Deactivation of Branched Phthalocyanine Compounds

The excited‐state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis‐ and trisphthalocyanines) are studied by using steady‐state and femtosecond transient absorption spectral measurements, where the excited‐state energy‐transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis‐Pc). In trisphthalocyanine (tris‐Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre‐associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady‐state spectra also show a face‐to‐face conformation in bis‐Pc, whereas in tris‐Pc, two of the three phthalocyanine branches form a pre‐associated face‐to‐face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure–property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems.