The effect of proton disorder on the structure of ice-Ih: a theoretical study

A precise and accurate measurement of the crystal structure of ice-Ih is hindered by its disordered H-bond network. In this work, we carried out first-principle calculations to study the effects of H-bond topology on the structure of ice-Ih with emphasis on the molecular geometry of water and the distortion in oxygen lattice. An analytic algorithm based on group and graph theory is employed to enumerate all possible configurations in a given unit cell and to select a set of structures for detailed examinations. In total we have studied more than 60 ice-Ih structures in a hexagonal unit cell of 48 water molecules by quantum-chemical methods and found a significant amount of static distortion in the oxygen positions from their crystallographic positions which is in good agreements with highly significant higher-order terms obtained from both x-ray and neutron-diffraction data. Much debated structural information such as H-O-H angle and O-H bond length is found to be 106.34+/-0.36 degrees and 0.9997+/-0.0008 A, compared to experimental value of 106.6+/-1.5 degrees and 0.986+/-0.005 A. Detailed benchmarking calculations were carried out to gauge the influence of using different exchange and correlation functionals, pseudopotentials, and unit-cell sizes. Our results have proven that first-principle methods are useful complementary tools to experiments, especially for cases in which experimental accuracy is limited by intrinsic orientational disorder.     

X-ray quality geometries of geodesic polyarenes from theoretical calculations: what levels of theory are reliable?

[structure: see text] Computational methods for calculating molecular geometries have not been well calibrated heretofore against X-ray data for bowl-shaped polycyclic aromatic hydrocarbons (PAHs). The analysis presented here capitalizes on a rare opportunity provided by corannulene to account explicitly for molecular distortions from crystal packing forces. Within the error limits of an extensive X-ray data set, B3LYP/6-31G* calculations were found to correctly reproduce all of the experimental bond distances and bond angles. The reliability and shortcomings of geometry calculations at other levels of theory are enumerated.     

Correlation of hydrogen bond lengths and angles in liquid water based on Compton scattering

The temperature-dependent hydrogen-bond geometry in liquid water is studied by x-ray Compton scattering using synchrotron radiation combined with density functional theory analysis. Systematic changes, related to the weakening of hydrogen bonding, are observed in the shape of the Compton profile upon increasing the temperature. Using model calculations and published distribution functions of hydrogen-bond geometries obtained from a NMR study we find a significant correlation between the hydrogen-bond length and angle. This imposes a new constraint on the possible local structure distributions in liquid water. In particular, the angular distortions of the short hydrogen bonds are significantly restricted.     

Calculations on the structure and spectral properties of cytochrome c551 using DFT and ONIOM methods

The active site geometry of cytochrome (Cyt) c(551) and its mutated form containing Fe(II) and Fe(III) ions have been calculated using density functional theory (DFT)-based Becke's three-parameter hybrid exchange and Lee-Yang-Parr correlation (B3LYP) method. In addition, calculations have also been carried out using hybrid meta DFT-based M06 functional. The effect of the protein milieu on the active site geometry has also been probed using two-layer via our own N-layered integrated molecular orbital + molecular mechanics (ONIOM) method. Evidence from the calculations reveal that the active site geometry is not significantly affected by the oxidation state of metal ion. The difference in the geometry of the active site and that of the same with the entire protein environment is only minimal, which shows that the protein milieu does not influence the structure of the active site. The calculated electronic transition energies from the time-dependent DFT (TDDFT) calculations are in close agreement with the experimental values. Although there are no significant variations in the active site geometry upon oxidation, the changes in the electronic transition energies have been attributed to the reduction in the overlap of metal ion with the ligand orbitals. In addition, it is found that mutation does not influence the active site geometry and the electronic transition energies. Nevertheless, mutation leads to the formation of more compact structure than the native Cyt c(551).     

Axial ligation of Fe(II)-bleomycin probed by XANES spectroscopy

Full multiple scattering calculations of the Fe K-edge X-ray absorption near edge structure of bleomycin have been performed. Structural insight is based on the comparison between experimental and theoretical data calculated for different active site models coming from NMR-informed molecular dynamic simulations. In all models considered, the equatorial ligands (secondary amine in beta-aminoalanine, pyrimidine and imidazole rings and the beta-hydroxyhistidine) were left unchanged. Seven models with two axial ligands (the primary amine in beta-aminoalanine and the carbomoyl group of the mannose or a solvent molecule) were tested. The best agreement between theoretical and experimental spectra is achieved for the model of bleomycin with the primary amine and the oxygen of the mannose sugar occupying the axial positions. The coordination environment is characterized by serious distortions of the Fe octahedron, including the presence of one ligand with a very short bond length and significant angular distortions.     

Highly congested nondistorted diheteroarylnaphthalenes: model compounds for the investigation of intramolecular pi-stacking interactions

[structure: see text] The rigid, highly congested structure of 1,8-diacridylnaphthalenes has been studied in solution and in the solid state. The unique geometry of these compounds forces the acridyl rings to undergo face-to-face interactions while rendering T-shaped orientations and face-to-edge interactions impossible. Crystallographic analysis shows that splaying between the heteroaryl rings decreases while twisting between the cofacial rings increases as the acridyl nitrogens of the 1,8-diacridylnaphthalene framework are subsequently oxidized. The peri-acridyl rings are slightly splayed but remain perfectly planar in all cases. The significant decrease in splaying indicates enhanced pi-pi-attraction between the electron-rich acridyl N-oxide moieties, which is in agreement with recently reported symmetry-adapted perturbation theory calculations. The pi-stacking and the molecular geometry between the acridyl rings observed in the solid state have been confirmed through in-solution studies showing characteristic proton NMR upfield shifts and optical properties indicative of static intramolecular arene-arene interactions. Acridyl protons located directly above the adjacent aryl moiety as a consequence of twisting between the heteroaryl rings were identified by COSY NMR measurements and found to intrude into the pi-cloud and diamagnetic ring current of the neighboring acridine. Different shapes and strong red shifts of the fluorescence emission maxima of the diacridylnaphthalenes in comparison to parental acridyl monomers have been attributed to static excimer emission.     

A combined experimental and theoretical evaluation of the structure of hydrated microporous aluminophosphate AlPO4-18

Water adsorption in the microporous aluminophosphate AlPO4-18 is studied by a combination of solid-state NMR, X-ray diffraction, and density functional theory calculations. The change of the framework structure upon hydration is moderate, and NMR gives local information on the environment of Al and P atoms. The structural distribution of water molecules in the channels has been explored by a combination of first-principle molecular dynamics simulations and of static geometry optimizations. Two starting points have been considered for the calculations. If the structure of the dehydrated aluminophosphate is used, the simulation result is not satisfactory with an incomplete hydration and no agreement with NMR results. Starting from a partial refinement of the aluminophosphate framework for the hydrated system, a structure with six tetrahedral and six octahedral Al atoms in the unit cell is obtained, involving twelve water molecules coordinated to Al atoms and twelve others in the channels, and in good agreement with experimental data.     

Experimental and theoretical study on cation radicals of cyclopropane,cyclobutane and cyclopentane

Cation radicals of cycloalkanes have been produced for the first time in γ-irradiated rigid solutions using fluoromethane as a matrix. Observed ESR spectra are analyzed by ab initio MO calculations; molecular geometries of the cations are optimized for several low-lying doublet states by the energy gradient method. Based on the optimized geometry thus determined the hyperfine splitting constants are calculated by the pseudo-orbital theory. Large Jahn-Teller distortions are calculated for the carbon rings and the H-C-H frames of the cation radicals. The distortions are consistent with the nodal picture of singly occupied orbitals. The calculated hfs constants are sensitive to the change in geometry due to a large contribution of spin-delocalization. The average of the calculated proton hfs constants is compatible with the observed ESR spectra which indicates that all the protons of the individual cations have become equivalent owing to the dynamic Jahn-Teller distortion.     

Activation entropy of electron transfer reactions

We report microscopic calculations of free energies and entropies for intramolecular electron transfer reactions. The calculation algorithm combines the atomistic geometry and charge distribution of a molecular solute obtained from quantum calculations with the microscopic polarization response of a polar solvent expressed in terms of its polarization structure factors. The procedure is tested on a donor–acceptor complex in which ruthenium donor and cobalt acceptor sites are linked by a four-proline polypeptide. The reorganization energies and reaction energy gaps are calculated as a function of temperature by using structure factors obtained from our analytical procedure and from computer simulations. Good agreement between two procedures and with direct computer simulations of the reorganization energy is achieved. The microscopic algorithm is compared to the dielectric continuum calculations. We found that the strong dependence of the reorganization energy on the solvent refractive index predicted by continuum models is not supported by the microscopic theory. Also, the reorganization and overall solvation entropies are substantially larger in the microscopic theory compared to continuum models.     

Molecular binding at gold transport interfaces. III. Field dependence of electronic properties

The behavior of the electronic structure in a metal/molecular/metal junction as a function of the applied electric field is studied using density functional methods. Although the calculations reported here do not include the electrode bulk, or intermolecular interactions, and do not permit actual transport to occur, nevertheless they illuminate the charging, energy shift, polarization and orbital occupation changes in the molecular junction upon the application of a static electric field. Specifically, external electric fields generally induce polarization localization on the two cluster ends. The HOMO/LUMO gap usually decreases and, for large enough fields, energy levels can cross, which presages a change of electronic state and, if found in molecular electronic circuits, a change in transmission. The calculations also show changes in the geometry both of the molecule and the molecule/cluster interface upon application of the electric field. These effects should be anticipated in whole circuit studies.     

A theoretical study of cohesion, structural deformation, inclusion, and dynamics in porous hydrogen-bonded molecular networks

Molecules with multiple sites of hydrogen bonding attached to suitable cores tend to crystallize as open networks. The resulting crystals can have the following unusual properties: They can include significant amounts of guest molecules; the guests are typically located in channels and can be exchanged without loss of crystallinity; and the geometry of the networks can change in response to new guests. We have found that DFT calculations can provide accurate simulations of the unusual structure and properties of such materials, represented by crystals of prototypic tetrapyridinone 1. These calculations have yielded three key insights that cannot be obtained directly from experiments. (1) The hypothetical porous network obtained by removing guests from crystals of compound 1 is highly flexible, and its deformations are inherently anisotropic, leading to lengthening or shortening of the channels along the c axis and no significant changes along the a and b axes. (2) Quantitative analysis of the total cohesive energy has revealed that hydrogen bonding within the network makes a dominant contribution, along with interactions of guests with the network. (3) Differences in the overall stability of crystals of compound 1 as the guests are varied do not arise primarily from significant changes in the cohesive energy of the network itself; instead, differences in guest-guest interactions play a key role, resulting from the nature of the guests and constraints imposed by the surrounding network. These insights, together with the results of ab initio molecular dynamics, help explain how hydrogen-bonded networks can be robust yet permit molecular movement that underlies the exchange of guests and adaptive porosity. These insights promise to be of general value to scientists studying ordered molecular materials in which strong directional interactions are prominent.     

Quantum mechanics/fluctuating charge calculations for absorption spectra of aqueous green fluorescent protein chromophore

We applied the quantum mechanics/fluctuating charges (QM/FQ) method to simulate the absorption spectra of three protonated forms of p-hydroxybenzylidene imidazolone (p-HBDI) in water. Configurations of solute-solvent were generated from molecular dynamics (MD) simulation within the context of a hybrid scheme in which solute and solvents were treated at QM and molecular mechanics, respectively. Nonperiodic spherical boundary condition was used. To examine the influence on simulated spectra coming from the geometrical relaxation of solute, the MD simulations were carried out for two cases: frozen and flexible molecular geometry of solute. As a result of our calculations, the simulations using the flexible solute's structure delivered vertical excitation energies closer to experimental data than those of a frozen solute, especially for the neutral case. For spectral broadening, changing from fixed geometry of solute to a flexible one led to a significant increase for both neutral and anionic forms of p-HBDI, but no effect happened for the cationic one.     

Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR and molecular mechanics on a model peptide prepared as silk I and II

The influence of the bulky and H-bonding Tyr side-chain on its Ala- and Gly-rich environment in Bombyx mori silk fibroin was examined by (13)C cross-polarization magic angle spinning (CP/MAS), static (2)H and (19)F NMR and molecular mechanics calculations. Model peptides of the type (AG)(15) were synthesized with Tyr in a number of different positions, precipitated under conditions favoring either of the two characteristic protein conformations, and the resulting structures were assigned from their (13)C chemical shifts. Dialysis of native fibroin or the simple (AG)(15) peptide from a 9 M LiBr solution against water produces silk I (the structure of silk before spinning), whereas drying from formic acid yields silk II (fibrous structure after spinning). We found that the introduction one or more Tyr into (AG)(15) can have a dramatic effect not only on the local backbone conformation but also on the long-range intermolecular chain packing in the samples. The antiparallel beta-sheet conformation of silk II is able readily to accommodate a single Tyr residue. Interestingly, the beta-turn conformation of silk I only remains stable when Tyr is positioned near the chain terminus in (AG)(12)YG(AG)(2), but the conformation is driven towards silk II when Tyr is located in the central region of (AG)(7)YG(AG)(7). The role of H-bonding was tested by replacing Tyr with Phe or 4F-Phe, which are no longer compatible with silk I and fully induced a silk II conformation. In the presence of several Tyr residues a mixture of distorted beta-sheet and beta-turn conformations was obtained, regardless of the precipitation conditions. Static (2)H NMR of ring-deuterated [3',5'-(2)H(2)]Tyr located in the central region of (AG)(7)YG(AG)(7) showed that the side-chain is immobilized in both silk I and II, which was also observed by static (19)F NMR of the 4F-Phe analogue. To visualize the local packing around the Tyr side-chain, molecular mechanics calculations were performed on a mixture of (AG)(4) and AGAGYGAG, starting from either the beta-turn type II or the antiparallel beta-sheet structure. The resulting structures show that the intermolecular chain arrangement is significantly affected by Tyr, thus explaining the long-range packing effects in the semi-crystalline regions of silk fibers compared with the crystalline regions that are devoid of Tyr.     

Prediction of the 1H and 13C NMR spectra of alpha-D-glucose in water by DFT methods and MD simulations

We have applied computational protocols based on DFT and molecular dynamics simulations to the prediction of the alkyl 1H and 13C chemical shifts of alpha-d-glucose in water. Computed data have been compared with accurate experimental chemical shifts obtained in our laboratory. 13C chemical shifts do not show a marked solvent effect. In contrast, the results for 1H chemical shifts provided by structures optimized in the gas phase are only fair and point out that it is necessary to take into account both the flexibility of the glucose structure and the strong effect exerted by solvent water thereupon. Thus, molecular dynamics simulations were carried out to model both the internal geometry as well as the influence of solvent molecules on the conformational distribution of the solute. Snapshots from the simulation were used as input to DFT NMR calculations with varying degrees of sophistication. The most important factor that affects the accuracy of computed 1H chemical shifts is the solute geometry; the effect of the solvent on the shielding constants can be reasonably accounted for by self-consistent reaction field models without the need of explicitly including solvent molecules in the NMR property calculation.     

Density-functional study of two Fe4-based single-molecule magnets

We present the results of our all-electron density-functional calculations on the electronic structure and magnetic anisotropy energy of the [Fe4(OMe)6(dpm)6] and [Fe4(thme)2(dpm)6] molecular clusters, which are experimentally found to behave as single-molecule magnets. The calculated magnetic anisotropy energy barriers are 2.65 and 15.8 K, respectively, which agree with the experimental data. We also present a density-functional study on the effect of the structure distortions on the magnetic anisotropy of the [Fe(H2O)6]3+ complex. This study, together with an analysis of the projected anisotropies of each iron ion in both molecular clusters, allows us to qualitatively understand why the magnetic anisotropy energy (MAE) barrier of the second single-molecule magnet (SMM) is larger than the MAE of the first SMM.     

Synthesis, Crystal Structure, and EPR Studies of the Five-Coordinate [CuCl(3)(H(2)O)(2)](-) Complex in (dabcoH(2))(2)Cl(3)[CuCl(3)(H(2)O)(2)].H(2)O

The compound (dabcoH(2))(2)Cl(3)[CuCl(3)(H(2)O)(2)].H(2)O, where dabco = 1,4-diazabicyclo[2.2.2]octane, has been synthesized, its structure has been determined by single-crystal structural analysis, and its properties have been investigated by powder and single-crystal EPR spectroscopy. The compound crystallizes in space group Pnma at room temperature with unit cell dimensions of a = 15.227(1) ?, b = 7.467(1) ?, and c = 20.166(2) ? with Z = 4. The structure was solved by the Patterson method and refined by full-matrix least-squares to R = 4.3% for 1681 observed reflections (I > 2sigma(I)). The [CuCl(3)(H(2)O)(2)](-) anion exists with a slightly distorted trigonal bipyramidal geometry in which the three Cl atoms lie in equatorial positions and the two water molecules are in axial positions. The distortion appears to be driven by the presence of N-H.Cl hydrogen bonds. The EPR spectra are also consistent with the presence of only a small distortion from trigonal bipyramidal geometry since g(1) approximately g(2) > g(3) approximately 2.0. Analysis of the geometry indicates the distortion consists primarily of a "negative" C(2)(v)() type. Analysis of the thermal parameters supports the supposition that the observed geometry corresponds to disorder over two "positive" C(2)(v)() distortions.     

Self-assembled metallacycles with pyrazine edges: a new example in which the unexpected molecular triangle prevails over the expected molecular square

The combination of cis-protected metal fragments with linear linkers is expected to yield molecular squares. We found instead that treatment of the 90 degrees angular precursor trans-[RuCl2(dmso-S)4] (1) with an equivalent amount of the linear and rigid pyrazine (pyz) linker unexpectedly yields, in a number of different experimental conditions, the molecular triangle [{trans,cis-RuCl2(dmso-S)2(mu-pyz)}3] (3), together with polymeric material. Very similar results were also obtained from the reaction between 1 and the preformed corner fragment trans,cis,cis-[RuCl2(dmso-S)2(pyz)2] (6). In both cases, the expected molecular square [{trans,cis-RuCl2(dmso-S)2(mu-pyz)}4] (4) was observed only as a transient species. These results suggest that 3, which is the first example of a neutral molecular triangle with octahedral metal corners and pyrazine edges, is both the thermodynamic and the kinetic product of the reactions described above. The X-ray structure of 3 shows that the main distortions from ideal coordination geometry concern the N-Ru-N angles, which are narrower than 90 degrees , and the coordination bonds of pyz. The pyrazine molecules, which are basically planar, are significantly tilted from linearity. Calculations performed on 6 indicated that the N-Ru-N angle is ca. six times more rigid than the tilt angle of pyrazine. The structural and theoretical findings on 3 and 6, together with the previous examples of molecular triangles and squares with cis-protected metal corners and linear pyz edges, suggest that the entropically favored molecular triangles might be preferred over the expected molecular squares with metal corner fragments that spontaneously favor Npyz-M-Npyz angles narrower than 90 degrees because of the presence of ancillary ligands with significant steric demand on the coordination plane. The rather-flexible coordination geometry of pyrazine can accommodate the moderate distortions from linearity required to close the small metallacycle with modest additional strain.     

The low-temperature proton-ordered phases of ice predicted by ab initio methods

The low-temperature proton-ordered counterparts for ice-Ih, ice-III, ice-VI and ice-VII are investigated by first principle methods in conjunction with a graph enumeration technique. Two experimentally well calibrated disorder/order transitions, ice-Ih/ice-XI and ice-VII/ice-VIII, are used to validate the methodology we used herein and in both cases our approach is able to reproduce major experimental features. For ice-III and ice-VI, direct structural determination on the fully proton-ordered counterparts by neutron diffraction is not available and in the literature different ordering schemes have been proposed. Our calculation results serve as an independent reference, and we shall discuss our findings and their relevance to previous experimental works.     

Structure elucidation with lanthanide induced shifts. 7—development of a reliable method for structure evaluation and the application to organic nitriles

A useful and reliable procedure has been developed for the evaluation of the structures of organic nitriles using lanthanide shift reagents. The procedure is based on a statistical comparison of the experimental lanthanide induced shifts (LIS) with values which are predicted with the pseudocontact equation for a proposed structure. The experimental LIS are obtained by nonlinear regression analysis of the chemical shifts observed in the presence of varying amounts of the shift reagent, Eu(fod)₃. The precise geometry for a proposed structure is obtained from molecular mechanics calculations. The LIS are then predicted with the pseudocontact equation using k=976.6 and a europium-nitrogen bond length of 2.50 Å. (Detailed arguments are presented in support of these values.) The carbon-nitrogen-europium array is approximately linear, although small distortions from linearity are both expected and observed.     

Redox and photoisomerization switching of the second-order optical nonlinearity of a tetrathiafulvalene derivative of spiropyran across five states: a DFT study

Second-order nonlinear optical properties of a tetrathiafulvalene (TTF) derivative of spiropyran have been studied based on density functional theory (DFT) combined with the finite field (FF) calculations. Our DFT-FF calculations confirm a switching behavior of the static first hyperpolarizability caused by the redox and photochromic reaction. The photochromic reaction generates spiropyran-merocyanine conversion by reversible cleavage of the C-O bond, which is relative to the close- and open-ring forms 1-c and 1-o. The open-ring form 1-o displays the large static first hyperpolarizability relative to its close-ring form 1-c according to our DFT-FF calculations with three functionals. The electronic structure analysis and spin unrestricted calculations show that the redox processes significantly affect the geometrical structure of the TTF unit, and thus enhance the static first hyperpolarizabilities. The one-electron-oxidized species having good planar structure of the TTF unit are ~30 and ~200 times as large as that of the neutral compounds 1-c and 1-o, respectively. But the difference in the static first hyperpolarizability between one- and two-electron-oxidized states of spiropyran species is not substantial according to our DFT-FF calculations, and the spiropyran-merocyanine conversion of two-electron-oxidized species does not largely affect their static first hyperpolarizability. On the basis of the large change in the static first hyperpolarizability, our DFT-FF calculations support a five-state switching of the static first hyperpolarizability based on the redox and photoisomerization.