Density functional study of platinum polyyne monomer,oligomer, and polymer: Ground state geometrical and electronic structures

Geometries of monomers and oligomers of a platinum polyyne and its free ligands were optimized using density functional theory with B3LYP hybrid functional. The LANL2DZ basis set was used for Pt and the 6‐31G* for other atoms in geometry optimizations. The electronic structures of these compounds were analyzed using Stuttgart/Dresden ECPs (SDD) basis set for metal atoms and 6‐311G* for others. The polymerization has very little effect on the bond lengths and by introducing the metal, the acetylide bond length increases slightly. The strong overlap between metal sp_x orbitals and σp_x orbitals of acetylides results in localized σ bonding. The hybridization between the ligand pπ orbitals and the platinum dπ orbital resulted in the π‐conjugation enhancement. This conjugation enhancement causes some effects such as the highest‐occupied molecular orbital–lowest‐unoccupied molecular orbital gap reduction and charge transfer characteristic of low‐energy vertical transitions. © 2013 Wiley Periodicals, Inc.     

Formation of Short Zn−Zn Bonds Stabilized by Simple Cyanide and Isocyanide Ligands

Cyanogen diluted in argon was reacted with laser ablated Zn atoms to produce the NCZnCN and NCZnZnCN cyanides and higher energy isocyanides ZnNC, CNZnNC, and CNZnZnNC, which were isolated in excess argon at 4 K. These reaction products, identified from the matrix infrared spectra of their ‐CN and ‐NC chromophore ligand stretching modes, were confirmed by ¹³C and ¹⁵N isotopic substitution and comparison with frequencies calculated by the B3LYP and CCSD(T) methods using the all electron aug‐cc‐pVTZ basis sets. The cyanide and isocyanide products were increased markedly by mercury arc UV photolysis, which covers the zinc atomic absorption. The above electronic structure calculations that produce appropriate ligand frequencies for these dizinc products also provide their Zn?Zn bond lengths: CCSD(T) calculations find a short 2.367 Å Zn?Zn bond in the NCZnZnCN cyanide, a shorter 2.347 Å Zn?Zn bond in the 37.4 kJ mol^?1 higher energy isocyanide CNZnZnNC, and a longer 4.024 Å bond in the dizinc van der Waals dimer. Thus, the diatomic cyanide (‐CN) and isocyanide (‐NC) ligands are as capable of stabilizing the Zn?Zn bond as many much larger ligands based on their measured and our calculated Zn?Zn bond lengths. This is the first example of dizinc complexes stabilized by different ligand isomers. Additional weaker bands in this region can be assigned to the analogous trizinc molecules NCZnZnZnCN and CNZnZnZnNC.     

Consistent gaussian basis sets of double‐ and triple‐zeta valence with polarization quality of the fifth period for solid‐state calculations

Consistent basis sets of double‐ and triple‐zeta valence with polarization quality for the fifth period have been derived for periodic quantum‐chemical solid‐state calculations with the crystalline‐orbital program CRYSTAL. They are an extension of the pob‐TZVP basis sets, and are based on the full‐relativistic effective core potentials (ECPs) of the Stuttgart/Cologne group and on the def2‐SVP and def2‐TZVP valence basis of the Ahlrichs group. We optimized orbital exponents and contraction coefficients to supply robust and stable self‐consistent field (SCF) convergence for a wide range of different compounds. The computed crystal structures are compared to those obtained with standard basis sets available from the CRYSTAL basis set database. For the applied hybrid density functional PW1PW, the average deviations of calculated lattice constants from experimental references are smaller with pob‐DZVP and pob‐TZVP than with standard basis sets. © 2018 Wiley Periodicals, Inc.     

Structural chemistry of a green fluorescent protein Zn biosensor

We designed a green fluorescent protein mutant (BFPms1) that preferentially binds Zn(II) (enhancing fluorescence intensity) and Cu(II) (quenching fluorescence) directly to a chromophore ligand that resembles a dipyrrole unit of a porphyrin. Crystallographic structure determination of apo, Zn(II)-bound, and Cu(II)-bound BFPms1 to better than 1.5 A resolution allowed us to refine metal centers without geometric restraints, to calculate experimental standard uncertainty errors for bond lengths and angles, and to model thermal displacement parameters anisotropically. The BFPms1 Zn(II) site (KD = 50 muM) displays distorted trigonal bipyrimidal geometry, with Zn(II) binding to Glu222, to a water molecule, and tridentate to the chromophore ligand. In contrast, the BFPms1 Cu(II) site (KD = 24 muM) exhibits square planar geometry similar to metalated porphyrins, with Cu(II) binding to the chromophore chelate and Glu222. The apo structure reveals a large electropositive region near the designed metal insertion channel, suggesting a basis for the measured metal cation binding kinetics. The preorganized tridentate ligand is accommodated in both coordination geometries by a 0.4 A difference between the Zn and Cu positions and by distinct rearrangements of Glu222. The highly accurate metal ligand bond lengths reveal different protonation states for the same oxygen bound to Zn vs Cu, with implications for the observed metal ion specificity. Crystallographic anisotropic thermal factor analysis validates metal ion rigidification of the chromophore in enhancement of fluorescence intensity upon Zn(II) binding. Thus, our high-resolution structures reveal how structure-based design has effectively linked selective metal binding to changes in fluorescent properties. Furthermore, this protein Zn(II) biosensor provides a prototype suitable for further optimization by directed evolution to generate metalloprotein variants with desirable physical or biochemical properties.     

Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

Formation of Short Zn−Zn Bonds Stabilized by Simple Cyanide and Isocyanide Ligands

Cyanogen diluted in argon was reacted with laser ablated Zn atoms to produce the NCZnCN and NCZnZnCN cyanides and higher energy isocyanides ZnNC, CNZnNC, and CNZnZnNC, which were isolated in excess argon at 4 K. These reaction products, identified from the matrix infrared spectra of their -CN and -NC chromophore ligand stretching modes, were confirmed by ¹³C and ¹⁵N isotopic substitution and comparison with frequencies calculated by the B3LYP and CCSD(T) methods using the all electron aug-cc-pVTZ basis sets. The cyanide and isocyanide products were increased markedly by mercury arc UV photolysis, which covers the zinc atomic absorption. The above electronic structure calculations that produce appropriate ligand frequencies for these dizinc products also provide their Zn−Zn bond lengths: CCSD(T) calculations find a short 2.367 Å Zn−Zn bond in the NCZnZnCN cyanide, a shorter 2.347 Å Zn−Zn bond in the 37.4 kJ mol⁻¹ higher energy isocyanide CNZnZnNC, and a longer 4.024 Å bond in the dizinc van der Waals dimer. Thus, the diatomic cyanide (-CN) and isocyanide (-NC) ligands are as capable of stabilizing the Zn−Zn bond as many much larger ligands based on their measured and our calculated Zn−Zn bond lengths. This is the first example of dizinc complexes stabilized by different ligand isomers. Additional weaker bands in this region can be assigned to the analogous trizinc molecules NCZnZnZnCN and CNZnZnZnNC.     

6‐31G* basis set for third‐row atoms

Medium basis sets based upon contractions of Gaussian primitives are developed for the third‐row elements Ga through Kr. The basis functions generalize the 6‐31G and 6‐31G* sets commonly used for atoms up to Ar. A reexamination of the 6‐31G* basis set for K and Ca developed earlier leads to the inclusion of 3d orbitals into the valence space for these atoms. Now the 6‐31G basis for the whole third‐row K through Kr has six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split‐valence pair of three and one primitives for valence orbitals, which are 4s, 4p, and 3d. The nature of the polarization functions for third‐row atoms is reexamined as well. The polarization functions for K, Ca, and Ga through Kr are single set of Cartesian d‐type primitives. The polarization functions for transition metals are defined to be a single 7f set of uncontracted primitives. Comparison with experimental data shows good agreement with bond lengths and angles for representative vapor‐phase metal complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 976–984, 2001     

A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Modeling metal cation-phosphate interactions in nucleic acids in the gas phase via alkali metal cation-triethyl phosphate complexes

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations, Na+, K+, Rb+, and Cs+, to triethyl phosphate (TEP). The primary and lowest energy dissociation pathway in all cases is the endothermic loss of the neutral TEP ligand. Theoretical electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory are used to determine the structures, molecular parameters, and theoretical estimates for the BDEs of these complexes. For the complexes to Rb+ and Cs+, theoretical calculations were performed using hybrid basis sets in which the effective core potentials and valence basis sets of Hay and Wadt were used to describe the alkali metal cation, while the standard basis sets were used for all other atoms. The agreement between theory and experiment is excellent for the complexes to Na+ and K+ and is somewhat less satisfactory for the complexes to the heavier alkali metal cations, Rb+ and Cs+, where effective core potentials were used to describe the cation. The trends in the binding energies are examined. The binding of alkali metal cations to triethyl phosphate is compared with that to trimethylphosphate.     

Theoretical study of third‐row transition metal monofluorides

The 5d‐metal (excluding La) monofluorides were studied using second order Moller‐Plesset (MP2) perturbation theory. The basis set used was Stuttgart/Dresden (SDD) effective core potentials (ECPs). The ground state multiplicity for these dimers was obtained. The cation and anion of these dimers were also studied at the same level of theory. Relative stability, atomic charges, electron affinity, ionization potential, binding energy (BE), vibrational frequencies, and electronic configuration for these dimers were also obtained. The properties of the neutral dimers were compared with those of their anion and cation. The electronic states of each neutral dimer as well as its ions at their ground state were also defined. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A remark on doublet stability of allyl radical restricted SCF solutions

The doublet stability of ab-initio SCF LCAO solutions for the allyl radical is re-examined for a wide range of CC bond lengths with the minimum, double zeta and double zeta plus polarization atomic orbital basis sets.     

水分子配位对叶绿素a氧化还原势与红外光谱的影响

以光系统I反应中心电子传递链上的辅助叶绿素a为目标,采用密度泛函理论中的B3LYP方法,结合三种基组,系统计算了该叶绿素及其两种配位分子模型在气相、模拟蛋白质环境和水中的氧化还原势和离解能;同时计算了这三种模型在气相中的几何结构、红外光谱及其13C、15N和2H的同位素标记谱.计算及分析结果表明:水分子配位引起镁离子偏离叶绿素a的卟啉环平面中央,导致以镁原子为中心的键角减小,Mg—N键长增长;而天冬酰胺对配位的水分子施加氢键影响后,使得Mg—N键进一步增长,镁离子与水分子中氧原子的配位键Mg—O键长减小,离解能增加,合成分子的氧化还原势减少;另外,分子的氧化还原势和配位键离解能随着相对介电常数的增加以及计算基组的增大而减小;三种分子模型的羰基(C襒O)和卟啉环上C襒C键的特征振动频率差值小于7cm-1,而同位素标记引起其峰位变化量的差值小于3cm-1.该计算为研究光合反应中心电子传递链上叶绿素a的作用与功能提供理论参考依据.     

(5656)Macrotetracyclic chelates of doubly charged 3d-element ions with 1,4,8,11-tetraazacyclotetradecane-2,3,9,10-tetrathione and their molecular structures according to density functional theory data

The OPBE/TZVP density functional theory (DFT) calculations were performed to study the molecular structures of (5656)macrotetracyclic M(II) complexes with a tetradentate ligand with (NNNN)-coordination of the donor sites formed upon template reactions in the M(II)-dithiooxamide-propane-1,3-diol ternary systems (M = Mn, Fe, Co, Ni, Cu, Zn). The bond lengths and bond angles for the resulting complexes are presented. The standard enthalpy, entropy, and Gibbs energy of formation of these compounds were calculated.     

Quantum-chemical simulation of structure of isomeric asymmetric (555)macrotricyclic chelates of 3d elements arising via self-assembly in quaternary systems metal(II)-ethanedithioamide-hydrazinomethanethioamide-ethanedial

We utilized the OPBE/TZVP (GAUSSIAN-09) hybrid density functional method to compute thermodynamic (full energy; standard enthalpy, entropy, and Gibbs energy of formation) and geometry (bond lengths, bond angles, and torsion angles) parameters of (555)macrotricyclic complexes of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) with (NSSN) coordination of the ligand donor centers. Such complexes can be formed upon interaction of hexacyanoferrate(II) of the listed metals, ethanedithioamide, hydrazinomethanethioamide, and ethanedial in gelatin-immobilized matrix implants. Complexes of Cu(II) and Zn(II) are slightly nonplanar, the other complexes are almost flat. In all cases the additionally formed five-membered cycle is practically flat.     

The effect of the functional,basis set,and solvent in the simulation of the geometry and spectroscopic properties of VIVO2+ complexes. chemical and biological applications

The geometry of 32 V^IVO²⁺ complexes with different donor set, electric charge, geometry, arrangement of the ligands with respect to the V?O bond and type of ligand was calculated by density functional theory methods. 32 V?O, 45 V? O, 16 V? OH, 40 V? N, 24 V? S, and 14 V? Cl bonds were examined. The performance of several functionals (B3LYP, B3P86, B3PW91, HCTH, TPSS, PBE0, and MPW1PW91), keeping constant the Pople triple‐zeta basis sets 6‐311g, was tested. The order of accuracy of the functional in the prediction of the bond distances, expressed in terms of mean of the deviation Δd (Δd = d^calcd ? d^exptl) and absolute deviation |Δd| (|Δd| = |d^calcd ? d^exptl|) from the experimental values and of the corresponding standard deviations (SD(Δd) and SD(|Δd|)), is: B3P86 ～ PBE0 ～ MPW1PW91 > B3PW91 ? TPSS > B3LYP ? HCTH. In the gas phase the prediction of V?O, V? O, V? N bond lengths is rather good, but that of V? OH, V? S and V? Cl distances is by far worse. An improvement in the optimization of V? S and V? Cl lengths is reached by adding polarization and diffuse functions on the sulfur and chlorine atoms. Finally, a general improvement in the prediction of all the calculated bond lengths and angles is obtained by simulating the structures in the solvent where they are isolated within the framework of the polarizable continuum model. The last choice allows also to improve the prediction of structural (the deviation of a penta‐coordinate geometry toward the trigonal bipyramid) and spectroscopic parameters (⁵¹V and ¹⁴N hyperfine coupling constants and ¹⁴N nuclear quadrupolar coupling constant). In most of the cases, the structures optimized in solution closely approach the experimental ones and this can be of great help in the simulations of naturally occurring vanadium compounds and metal site of V‐proteins, like amavadin and the reduced form of vanadium bromoperoxidase (VBrPO). © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structural aspects of metal–amide complexes

An exhaustive survey of crystal structure data on simple amides and metal complexes containing monodentate amide ligands has been performed. Statistical analysis of structural features are reported as a function of the degree of alkylation of the amide functional group, the type of metal ion in the amide complex, and the type of binding to the metal ion. Average values are reported for bond lengths, bond angles, and torsional angles. Orientational preferences of the coordinated amide ligand are discussed in terms of M–O–C bond angles and M–O–C–N torsion angles.     

<Emphasis Type="Italic">Ab Initio</Emphasis> quantum chemical calculation of the structures of coordination compounds arising at template synthesis in ion M(II)-hydrozinomethane thiohydrazide-acetone (M = Co,Ni, Cu) systems

Using a hybrid B3LYP density functional method with the 6-31G(d) basis set and the Gaussian-98 program, the geometrical parameters of macrocyclic complexes of Co(II), Ni(II) and Cu(II) with NNSS-coordination of donor centers of the chelate ligand, formed due to template processes in M(II)-hydrozinomethane thiohydrazide-acetone systems, are calculated. Coordinates of atoms, selected bond lengths and angles, and dihedral angles in complexes with MN₂S₂ metal-chelate site are given. It is noted that for all considered M(II) ions the additional six-membered metal cycle, formed because of template stitching, is turned at a considerable angle to two five-membered cycles, and this cycle itself is not planar either.