Bond characterization on a Cr-Cr quintuple bond: a combined experimental and theoretical study

A combined experimental and theoretical charge density study on a quintuply bonded dichromium complex, Cr(2)(dipp)(2) (dipp = (Ar)NC(H)N(Ar) and Ar = 2,6-i-Pr(2)-C(6)H(3)), is performed. Two dipp ligands are bridged between two Cr ions; each Cr atom is coordinated to two N atoms of the ligands in a linear fashion. The Cr atom is in a low oxidation state, Cr(I), and in low coordination number condition, which stabilizes a metal-metal multiple bond, in this case, a quintuple bond. Indeed, it gives an ultrashort Cr-Cr bond distance of 1.7492(1) ? in the complex. The bond characterization of such a quintuple bond is undertaken both experimentally by high-resolution single-crystal X-ray diffraction and theoretically by density functional calculation (DFT). Electron densities are depicted via deformation density and Laplacian distributions. Bond characterizations of the complex are presented in terms of topological properties, Fermi hole function, source function (SF), and natural bonding orbital (NBO) analysis. The electron density at the Cr-Cr bond critical point (BCP) is 1.70 e/?(3), quite a high value for metal-metal bonding and mainly contributed from the metal ion itself. The quintuple bond is confirmed with one σ, two π, and two δ interactions by NBO analysis and Fermi hole function. The molecular orbitals (MOs) illustrate that five bonding orbitals are predominantly contributed from the 3d orbitals of the Cr(I) ion. The effective bond order from NBO analysis is 4.60. The detail comparison between experiment and theory will be given. Additionally, three closely related complexes are calculated for systematic comparison.     

1,4,7,10-四氮杂环十二烷:有前途的储氢媒介

运用密度泛函理论(DFT)的B3LYP方法对常见的大环胺类化合物1,4,7,10-四氮杂环十二烷(cyclen)进行结构优化;进而分析了其前线分子轨道和自然键轨道布居(NBO),并确定了吸附的活性点.通过在cyclen的活性点周围放置H2,研究了其储氢性能.结果表明,1,4,7,10-四氮杂环十二烷是一种很有前途的储氢...     

AMT异构体互变机理的理论研究

用密度泛函理论(DFT)的B3LYP/6-311G(d, p)和Müller-Plesset微扰理论的MP2/6-31G(d)方法，优化了AMT(2-氨基-5-巯基-1,3,4-噻二唑)各种异构体和过渡态结构的几何构型，并对它们的电子结构、振动光谱和化学键性质进行了研究.还研究了AMT异构体的互变机理，提出了AMT异构体abcda的循环式互变途径.进一步完成了对AMT异构体成键方式的自然键轨道(NBO)分析.     

Synthesis,Crystal Structure and Theoretical Calculations of N-Benzyl-1-(5-(3-chlorophenyl)-1,3,4-oxadiazol-2-yl)cyclopentanamine

N-benzyl-1-(5-(3-chlorophenyl)-1,3,4-oxadiazol-2-yl)cyclopentanamine was synthesized via one-pot reaction of appropriate benzylamine, cyclopentanone,(N-isocyanimino)triphenylphosphorane and m-chlorobenzoic acid. The quantum theoretical calculations for crystal structure were performed by density functional theory(DFT/B3LYP/6-311+G*). From the optimized structure, geometric parameters were obtained and experimental measurements were compared with the calculated data. Frontier molecular orbitals(FMOs), total density of states(DOS), molecular electrostatic potential(MEP), molecular properties, natural charges, NMR parameters and NBO analysis for the product were investigated by theoretical calculations.     

Analysis of vibrational spectra of L-alanylglycine based on density functional theory calculations

FT Raman and IR spectra of the crystallized biologically active molecule, L-alanylglycine (L-Ala-Gly) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of L-Ala-Gly have been investigated with the help of B3LYP density functional theory (DFT) method. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The optimized geometry shows the non-planarity of the peptide group of the molecule. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G** basis set. The red shifting of NH3+ stretching wavenumber indicates the formation of N-H...O hydrogen bonding. The change in electron density (ED) in the sigma* antibonding orbitals and E2 energies have been calculated by natural bond orbital analysis (NBO) using DFT method. The NBO analysis confirms the occurrence of strong intermolecular hydrogen bonding in the molecule.     

Au12M (M=Na,Mg, Al,Si, P,S, Cl)团簇的结构、稳定性和电子性质

采用基于密度泛函理论的第一性原理方法系统地研究了Au12M(M=Na,Mg,Al,Si,P,S,Cl)团簇的结构、稳定性和电子性质.对团簇的平均结合能、镶嵌能、垂直离化势、最高占据分子轨道(HOMO)和最低未占据分子轨道(LUMO)的能级差、电荷布居分析、自然键轨道(NBO)进行了计算和讨论.对于Au12M(M=Na,Mg,Al)团簇,它们形成了内含M原子的最稳定的笼状结构.然而对于Au12M(M=Si,P,S,Cl)团簇,它们却形成了以M元素为顶点的稳定锥形结构.在这些团簇中发现Au12S团簇相对是最稳定的,这是由于Au12S团簇形成了稳定的满壳层的电子结构.自然电荷布居分析表明:对于所有的Au12M(M=Na,Mg,Al,Si,P,S,Cl)团簇电荷总是从Au原子转向M原子.自然键轨道和HOMO分析表明Au12M团簇中发生了Au原子的s-d轨道和M原子的p轨道间的杂化现象.     

Theoretical studies on the structural properties of 2,3-bis(furan-2-yl)pyrazino-[2,3-f][1,10]phenanthroline

This paper reports the optimized geometrical parameters of the stationary point for 2,3-bis(furan- 2-yl)pyrazino[2,3-f][1,10]phenanthroline. The calculations are performed using the density functional theory (DFT) method at the B3LYP/ LanL2DZ level. Bond lengths and bond angles are determined for the compound and the amount of bond hybridization is calculated according to the natural bond orbital theory (NBO). The energy of frontier orbitals (HOMO and LUMO) are computed. In addition, the calculated data are accurately compared with the experimental results. This comparison shows that our theoretical data are in reasonable agreement with the experimental values.     

Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post‐processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis‐type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large‐scale calculations with the ONETEP linear‐scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long‐range electronic effects from the entire system. We show that by transforming the Non‐orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins—namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug‐receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.     

2-[(1H-benzimidazol-2-ylmethyl)-amino]-benzoic acid methyl ester: crystal structure, DFT calculations and biological activity evaluation

In the present study, structural properties of 2-[(1H-benzimidazol-2-ylmethyl)-amino]-benzoic acid methyl ester have been studied extensively by spectral methods and X-ray crystallography. Quantum mechanical calculations of energies, geometries, vibrational wavenumbers, NMR and electronic transitions were carried out by DFT using B3LYP functional combined with 6-31G(d) basis set. Natural bond orbitals (NBO) analysis and frontier molecular orbitals were performed at the same level of theory. DFT calculations showed good agreement between the theoretical and experimental values of optimized and X-ray structure as well as between the vibrational and NMR spectroscopy. The title compound was screened for its antibacterial activity referring to Tetracycline as standard antibacterial agent.     

Quantum chemical approaches to the explanation of differences in NO-donor activity of iron-sulfur nitrosyl complexes

The geometries and electronic structures of iron-sulfur nitrosyl complexes with azaheterocyclic thiols with μ-SCN bridging ligands, [Fe₂(SCN₄Ph)₂(NO)₄] (1) and [Fe₂(SCN₄Me)₂(NO)₄] (2), were calculated within the framework of the density functional theory (DFT) with the BP86, TPSS, B3LYP, and OPBE functionals in order to explain differences in their NO-donor activities. Chemical bonding in the complexes was analyzed using the NBO approach, according to Mulliken, and using the Voronoi scheme. NBO analysis of complex 1 revealed a strong interaction between orbitals of the lone electron pairs of the Fe atom and the antibonding orbitals of the Fe-N bond which leads to strengthening of the Fe-NO bond. In complex 2, the Fe-NO bond is more polar than in complex 1.     

Density Functional Theory Study of Hydrogen Bonds of Bipyridine with 1,3,5-Benzenetricarboxylic Acid

The hydrogen‐bonded dimer and trimer formed between 1,3,5‐benzenetricarboxylic acid and bipyridine have been investigated using a density functional theory (DFT) method and 6‐31++G** basis set. The interaction energies are ?45.783 and ?89.998 kJ·mol^?1 for the most stable dimer and trimer, respectively, after the basis set superposition error and zero‐point corrections. The formation of O–H...N hydrogen bonds makes O–H symmetric stretching modes in the dimer and trimer red‐shifted relative to those of the 1,3,5‐benzenetricarboxylic acid monomer. The natural bond orbit analysis shows that the inter‐molecular charge transfers are 0.60475e and 1.20225e for the dimer and trimer, respectively. Thermodynamic analysis indicates that the formation of trimer is an exothermic and spontaneous process at low and room temperature. A supramolecule can be constructed through the strong N···H–O intermolecular hydrogen bonds between bipyridine and 1,3,5‐benzenetricarboxylic acid, which is in good agreement with the experimental results.     

Experimental and DFT studies of ethyl N′-3-(1H-imidazol-1-yl) propylcarbamoyl benzohydrazonate monohydrate

The Imidazole compound, Ethyl N′-3-(1H-imidazol-1-yl) propylcarbamoyl benzohydrazonate monohydrate, has been synthesized and characterized by IR, NMR, electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state has been compared using the density functional method (B3LYP) with 6-31G+(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by DFT calculations with respect to two selected degrees of torsional freedom, which were varied from −180° to +180° in steps of 10°. Besides, molecular electrostatic potential (MEP), natural bond orbitals (NBO), frontier molecular orbitals (FMO), and thermodynamic properties were performed at B3LYP/6-31G+(d) level of theory.     

Structural,electronic properties and intramolecular hydrogen bonding of substituted 2-[(E)-imino methyl] benzenethiol in ground and first excited state by quantum chemical methods

Quantum chemical calculations of geometric structure, the intramolecular hydrogen bond, harmonic vibrational frequencies, NMR spin–spin coupling constants, and physical properties such as chemical potential and chemical hardness of the 2-(E)-imino methyl benzenethiol and its nineteen derivatives were carried out using density functional theory (DFT/B3LYP/6-311++G**) method in the gas phase and the water solution. Furthermore, the topological properties of the electron density distributions for S–H···N intramolecular hydrogen bond have been analyzed in terms of the Bader’s theory of atoms in molecules (AIM). Natural bond orbital (NBO) analysis also performed for better understanding the nature of intramolecular interactions, the results of analysis by quantum theory of AIM and NBO method fairly supported the DFT results. Besides, MEP was performed by the DFT method. On the other hand, the aromaticity of the formed ring has been measured using several well-established indices of aromaticity such as nucleus-independent chemical shift, harmonic oscillator models of the aromaticity, para-delocalization index, average two-center indices, and aromatic fluctuation index. Also, the excited-state properties of intramolecular hydrogen bonding in these systems have been investigated theoretically using the time-dependent DFT method.     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Actinium coordination chemistry: A density functional theory study with monodentate and bidentate ligands

In the current study, the coordination chemistry of nine-coordinate Ac(III) complexes with 35 monodentate and bidentate ligands was investigated using density functional theory (DFT) in terms of their geometries, charges, reaction energies, and bonding interactions. The energy decomposition analysis with naturals orbitals for chemical valence (EDA-NOCV) and the quantum theory of atoms in molecules (QTAIM) were employed as analysis methods. Trivalent Ac exhibits the highest affinities toward hard acids (such as charged oxophilic donors, fluoride), so its classification as a hard acid is justified. Natural population analysis quantified the involvement of 5f orbitals on Ac to be about 30% of total valence electron natural configuration indicating that Ac is a member of the actinide series. Pearson correlation coefficients were used to study the pairwise correlations among the bond lengths, ΔG reaction energies, charges on Ac and donor atoms, and data from EDA-NOCV and QTAIM. Strong correlations and anticorrelations were found between Voronoi charges on donor atoms with ΔG, EDA-NOCV interaction energies and QTAIM bond critical point densities.     

Cis Watson-Crick/Watson-Crick Base Pairs in DNA: A Density Functional Theory(DFT) Study

The four nucleic acid DNA bases(adenine, thymine, guanine, cytosine) and ten cis Watson-Crick/Watson-Crick(cis WC/WC) DNA base pairs were investigated by density functional theory(DFT) quantum chemical calculations. Geometry optimizations were carried out on the four bases and ten base pairs at the B3LYP level with 6-31G~(**) basis set. All the optimizations were performed within Cs symmetry. The optimum structures for the four bases and seven cis WC/WC base pairs were obtained, and Natural Bond Orbital analysis(NBO) was based on these structures. The possibilities of matches between any two of the four bases through their Watson-Crick(WC) edges were discussed. The structures of seven cis WC/WC base pairs change to a certain extent relative to these of the four bases due to the formation of hydrogen bonds. These base pairs existing in DNA have an important influence on the structural stability of the double helix. The analysis of the electronic structures and molecular orbitals for seven cis WC/WC base pairs can provide significant information about the relationship between charge transfer along the hydrogen bond and the Frontier orbitals of these base pairs.     

Mechanism of TBD-catalyzed hydrolysis of acetonitrile

1,5,7-Triazabicyclo[4.4.0]dec-5-ene (TBD) has recently been shown to be an effective organocatalyst for the hydrolysis reaction of acetonitrile. This reaction involves the acetamide-forming reaction of acetonitrile hydrolysis and the further hydrolysis of acetamide to form acetic acid and NH₃. Density functional theory (DFT) and Hartree–Fock (HF) methods were employed to comprehensively investigate these two hydrolysis steps to elucidate the TBD-catalyzation mechanism. Structures and energies of the reactants, intermediates, transition states and products along the reaction path were presented. Charge population and bond orders were given by natural bond orbital (NBO) analysis to clarify the computed atomic and molecular behaviors. The results showed that compared with the noncatalyzed reaction, the TBD-catalyzed process had significantly lower energy barriers in both the hydration steps and the isomerization steps. As a result, the whole reaction process could be accelerated and the TBD-catalyzation mechanism was clarified.     

Analyzing NMR shielding tensors calculated with two-component relativistic methods using spin-free localized molecular orbitals

A recently developed analysis method [J. Chem. Phys. 127, 124106 (2007)] for NMR spin-spin coupling constants employing two-component (spin-orbit) relativistic density functional theory along with scalar relativistic natural localized molecular orbitals (NLMOs) and natural bond orbitals (NBOs) has been extended for analyzing NMR shielding tensors. Contributions from a field-dependent basis set (gauge-including atomic orbitals) have been included in the formalism. The spin-orbit NLMO/NBO nuclear magnetic shielding analysis has been applied to methane, plumbane, hydrogen iodide, tetracholoplatinate(II), and hexachloroplatinate(IV).