Density Functional Theory Study on Hydrogen Bonding Interaction of Catechin-(H2O)n

Density functional theory B3LYP method with 6‐31G* basis set has been used to optimize the geometries of the catechin, water and catechin‐(H₂O)_n complexes. The vibrational frequencies have been studied at the same level to analyze these complexes. Six and eleven stable structures for the catechin‐H₂O and catechin‐(H₂O)₂ have been found, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are from ?13.27 to ?83.56 kJ/mol. All calculations also indicate that there are strong hydrogen‐bonding interactions in catechin‐water complexes. The strong hydrogen‐bonding contributes to the interaction energies dominantly. The O–H stretching motions in all the complexes are red‐shifted relative to that of the monomer.     

聚合物{[CuII(Hpb) (mal)]H2O}n :单体的量子化学计算和磁性研究

{[Cu^Ⅱ（Hpb）（mal）]H=O}n （Hpb=2-2＇-pyridylbenzimidazole, mal=maleic acid） is a helical chain-like polymer complex. In order to investigate the electronic structure of the complex, the monomer Cu^Ⅱ（Hpb）（mal） was obturated with different functional groups respectively. For these selective segments, the geometry optimizations were conducted by using hybrid DFT （B3LYP）methods to find that the structure obturated with H2O was better consistent with the experiment, and then this model would be used to latter calculations, such as the frontier molecular orbital and the NBO charge population analysis. In addition the magnetic behaviors of this complex were analyzed by experiments and the weak antiferromagnetic couple between copper（Ⅱ） ions was observed. The exchange coupling constant was calculated by DFT based on the spin broken symmetry formalism. The calculated coupling constants were in good agreement with the experimental data.     

DFT study on the intermolecular interactions between Aun (n = 2–4) and thymine

Density functional B3LYP method with 6-31++G** basis set is applied to optimize the geometries of the luteolin, water and luteolin–(H₂O)_n complexes. The vibrational frequencies are also studied at the same level to analyze these complexes. We obtained four steady luteolin–H₂O, nine steady luteolin–(H₂O)₂ and ten steady luteolin–(H₂O)₃, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) are used to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are within −13.7 to −82.5 kJ/mol. The strong hydrogen bonding mainly contribute to the interaction energies, Natural bond orbital analysis is performed to reveal the origin of the interaction. All calculations also indicate that there are strong hydrogen bonding interactions in luteolin–(H₂O)_n complexes. The OH stretching modes of complexes are red-shifted relative to those of the monomer.     

Theoretical investigation of geometry and stability of small lithium‐iodide LinI (n = 2–6) clusters

We present theoretical investigation of the structural characteristics and stabilities of neutral and positively charged Li_nI (n = 2‐6) species. The structural isomers were found by using a randomized algorithm to search for minima structures, followed by B3LYP optimizations; the single‐point RCCSD(T)/cc‐pwCVTZ(‐PP) calculations were performed in order to compute relative energies, binding energies per atom, adiabatic and vertical ionization energies, and dissociation energies. Stability was compared to the pure lithium clusters; there is a typical odd‐even alternation; iodine doped clusters are more stable than pure lithium clusters. Lithium “cage” transfers its valence electron to the iodine atom to form neutral and cationic clusters. An electron departures the lithium cage upon ionization. An important reason for the larger stability of closed‐shell species is the existence of the HOMO 3c/2e natural bond orbitals. © 2013 Wiley Periodicals, Inc.     

Density functional theory study of geometry and stability of small Zrn (n = 2–10) clusters

Geometric structures, electronic properties, and stabilities of small Zr_n and Zr (n = 2–10) clusters have been investigated using density functional theory with effective core potential LanL2DZ basis set. For both neutral and charged systems, several isomers and different multiplicities were studied to determine the lowest energy structures. Many most stable states with high symmetry were found for small Zr_n clusters. The most stable structures and symmetries of Zr clusters are the same as the neutral ones except n = 4 and 7. We found that the clusters with n > 3 possess highly compact structures. The clusters are inclined to form the caged‐liked geometry containing pentagonal structures for n > 8, which is in favor of energy. From the formation energy and second‐order energy difference, we obtained that 2‐, 5‐, 7‐atoms of neutral and 4‐, 7‐atoms cationic clusters are the magic numbers. Furthermore, the highest occupied molecular orbital‐lowest unoccupied molecular orbital gaps display that the Zr₃, Zr₆, Zr, and Zr are more stable in chemical stability. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Relativistic effects on geometry and electronic structure of small Pdn species (n=1, 2, 4)

Relativistic effects on the properties of small neutral Pd_n species (n=1, 2, 4) and Pd₂⁻ have been examined for the first time at the all‐electron level by performing scalar‐relativistic and nonrelativistic density functional calculations using a gradient‐corrected density functional. Relativistic effects are found to be important: They lead to a contraction of bond lengths, increase of vibrational frequencies, and a significant enhancement of binding energies. While relativistic effects are quite uniform for several states of Pd₄, they vary for the states examined for Pd₂, leading to a change of ground state due to relativity. The calculated relativistic properties of Pd₂ and Pd₂⁻ are in good agreement with available experimental data from mass spectrometry and photoelectron spectroscopy. For Pd₄ three‐dimensional structures are found to be preferred to planar ones and many nearly isoenergetic isomers exist. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 405–416, 1999     

HCCO自由基与LiX(X=F,Cl,Br)锂键复合物的从头算研究

在MP2/6-311++G**水平上优化乙烯酮自由基与LiX(X=F,Cl,Br)形成锂键复合物.当卤素的电负性很强(如F元素),使得Li原子处于缺电子状态,此时,电子给体会把电子偏移向锂,形成共价性较强的锂键.而当卤素的电负性减弱时,锂键中主要成分逐渐变为离子键,并且此时锂键性质还要受电子给体影响.另外,由于HCCO为缺电子结构,电负性较弱且体积较大的卤素中的孤对电子会与HCCO之间通过静电相互作用,使得HCCO…Li—X键夹角变小,接近120°.锂键性质对HCCO…LiX(X=F,Cl,Br)复合物中Li—X的伸缩振动频率有直接影响.当锂键表现为共价性时,该频率红移,而当锂键表现为离子性时,该频率蓝移.但是,由于Cl的电负性与O的接近,C的电负性与Br接近所以,在O…Li…Cl和C…Li…Br中容易形成共振结构,导致远大于在其他复合物中的红移.     

Investigation of substituent effects in aerogen‐bonding interaction between ZO3 (Z=Kr,Xe) and nitrogen bases

The substituent effects in aerogen bond interactions between ZO₃ (Z = Kr, Xe) and different nitrogen bases are studied at the MP2/aug‐cc‐pVTZ level of theory. The nitrogen bases include the sp bases NCH, NCF, NCCl, NCBr, NCCN, NCOH, NCCH₃ and the sp³ bases NH₃, NH₂F, NH₂Cl, NH₂Br, NH₂CN, NH₂OH, and NH₂CH₃. The nature of aerogen bonds in these complexes is analyzed by means of molecular electrostatic potential, electron localization function, quantum theory atoms in molecules, noncovalent interaction index, and natural bond orbital analyses. The interaction energy (E_int) ranges from ?4.59 to ?9.65 kcal/mol in the O₃Z···NCX complexes and from ?5.30 to ?13.57 kcal/mol in the O₃Z···NH₂X ones. The dominant charge‐transfer interaction in these complexes occurs across the aerogen bond from the nitrogen lone‐pair (n_N) of the Lewis base to the σ*_Z‐O antibonding orbital of the ZO₃. Besides, the formation of aerogen bond tends to decrease the ⁸³Kr or ¹³¹Xe chemical shielding values in these complexes. © 2016 Wiley Periodicals, Inc.     

Theoretical investigation of the adsorption of oxygen on small bimetallic LimCun (m,n ≤ 4) clusters

A theoretical study of the adsorption of molecular oxygen on small bimetallic Li_mCu_n (m, n ≤ 4) clusters was carried out using density functional methods, and it was compared with the adsorption of O₂ on copper (Cu_n, n ≤ 8) clusters. The study of O₂‐Li_mCu_n system is important to understand the promotion effects of the alkali atoms on the copper surface participating in the catalytic processes. Adsorption energies ranging from 7.9 to 51 kcal/mol were found, which represented values over 30% to those calculated for the adsorption of O₂ on copper clusters in a previous study. Thus, the reactivity of molecular oxygen on bimetallic clusters is more favorable with high tendency being in favor of the dissociation of the O₂ molecule. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Comprehensive study of threonine adsorption on carbon nanotube: A dispersion complemented density functional theory‐based treatment

The interaction mechanism of threonine (Thr) on the sidewall of (8, 8) single‐walled carbon nanotubes (CNTs) was investigated by density functional tight‐binding method. All the functional groups of Thr were used to interact with the surface of CNT. The structural parameters were analyzed to identify the noncovalent interactions, and the binding energy and strain energy were used to indicate the binding properties. We found that the CH/π interactions play more important roles than NH/π and OH/π interactions in stabilizing the complex structures. Furtherly, the charge transfer properties, density of states (DOS) and partial density of states, and highest occupied molecular orbitals and lowest unoccupied molecular orbitals were also studied to illustrate the adsorbed interactions. The results show that the DOS structure of CNT could be modified by the adsorption of Thr, and, therefore, the conductivity of CNT will be improved by introducing proper amino acids. Our data should be helpful for the design of biocompatible molecules for CNT modification. © 2015 Wiley Periodicals, Inc.     

Comparative DFT study of N2 and no adsorption on vanadium clusters Vn (n = 2–13)

Using gradient‐corrected density functional theory, we have comparatively studied the adsorption properties of diatomic molecules N₂ and NO on vanadium clusters up to 13 atoms. Spontaneous dissociation is found for N₂ adsorbing on V_n with n = 4–6, 12, and for NO with n = 3–12, respectively, whereas for the rest of the clusters, N₂ (NO) molecularly adsorbs on the cluster for all the possible sites. The incoming N₂ retains the magnetism of V_n except for V₂ and V₆ whose moments are quenched from 2 μ_B to zero. Consequently, the moments of V_nN₂ (n = 2–13) show even/odd oscillation between 0 and 1 μ_B. On the adsorption of NO, the magnetic moments of V_n with closed electronic shell are raised to 1 μ_B at n = 4, 8, and 10, and 3 μ_B at n = 12, whereas for open shell clusters, their magnetic moments increase for n = 5 and 9 and decrease for n = 2, 3, 5–7, 11, and 13 by 1 μ_B. These findings are rationalized by combinatory analysis from several aspects, for example, the geometry and stability of bare clusters, charge transfer induced by the adsorption, feature of frontier orbitals, and spin density distribution. © 2012 Wiley Periodicals, Inc.     

MX2(AsH3)2(M=Pd,Pt;X=Cl,Br,I)的含时密度泛函理论研究

采用密度泛函方法(B3LYP)优化了MX2(AsH3)2[M=Pd；X=Cl(1)，Br(2)，I(3)和M=Pt；X=Cl(4)，Br(5)，I(6)]的基态结构，得到的几何参数与实验结果符合．以基态几何为基础，将TD-DFT方法用于计算标题配合物的电子吸收光谱．研究结果表明，金属的dx2-y2与配体所组成的反键轨道为LUMO轨道，从而该类配合物具有d-d跃迁属性的吸收带；在多数跃迁过程中，配体也有较大的贡献．     

New insight into the electronic structure of iron(IV)‐oxo porphyrin compound I. A quantum chemical topological analysis

The electronic structure of iron‐oxo porphyrin π‐cation radical complex Por^·+Fe^IV?O (S? H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology analysis: electron localization function (ELF) η(r) and electron density ρ(r). The formation of this complex leads to essential perturbation of the topological structure of the carbon–carbon bonds in porphyrin moiety. The double C?C bonds in the pyrrole anion subunits, represented by pair of bonding disynaptic basins V_i=1,2(C,C) in isolated porphyrin, are replaced by single attractor V(C,C)_i=1–20 after complexation with the Fe cation. The iron–nitrogen bonds are covalent dative bonds, N→Fe, described by the disynaptic bonding basins V(Fe,N)_i=1–4, where electron density is almost formed by the lone pairs of the N atoms. The nature of the iron–oxygen bond predicted by the ELF topological analysis, shows a main contribution of the electrostatic interaction, Fe^δ+···O^δ?, as long as no attractors between the C(Fe) and C(O) core basins were found, although there are common surfaces between the iron and oxygen basines and coupling between iron and oxygen lone pairs, that could be interpreted as a charge‐shift bond. The Fe? S bond, characterized by the disynaptic bonding basin V(Fe,S), is partially a dative bond with the lone pair donated from sulfur atom. The change of electronic state from the doublet (M = 2) to quartet (M = 4) leads to reorganization of spin polarization, which is observed only for the porphyrin skeleton (?0.43e to 0.50e) and S? H bond (?0.55e to 0.52e). © 2012 Wiley Periodicals, Inc.     

Electronic structure and stability of BP clusters: theoretical calculations for (BP)n (n = 2–4)

The geometry, electronic configurations, harmonic vibrational frequencies, and stability of the structural isomers of boron phosphide clusters have been investigated using density functional theory (DFT). CCSD(T) calculations show that the lowest‐energy structures are cyclic (IIt, IVs) with D_nh symmetry for dimers and trimers. The caged structure for B₄P₄ lie higher in energy than the monocyclic structure with D_2d symmetry (VIs). The B–P bond dominates the structures for many isomers, so that one preferred dissociation channel is loss of the BP monomer. The hybridization and chemical bonding in the different structures are also discussed. Comparisons with boron nitride clusters, the ground state structures of B_nP_n (n = 2, 3) clusters are analogous to those of their corresponding B_nN_n (n = 2, 3) counterparts. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Theoretical study on AlnO2 (n = 1–10) clusters and O2 adsorption on the Al(111) surface

The structural properties of neutral and ionic Al_nO₂ (n = 1–10) clusters have been systematically investigated using the density functional method B3LYP with a standard 6‐311+G(d) basis set. The calculated results show that in the Al_nO, Al_nO₂, and Al_nO (n ≥ 3) clusters, O atoms tend to penetrate into the aluminum clusters with some Al atoms moving outward. The binding energies and natural charges populations indicate that the oxygen‐etching is generally stronger in the order Al < Al_n < Al for n < 3, and Al > Al_n > Al for n ≥ 3. To further understand the mechanism of interaction between Al and O₂, the adsorption of O₂ on the Al(111) surface was studied using the density functional theory with plane wave pseudopotential method. The calculated results are consistent with the experimental observation that the O₂ molecule would dissociate on the Al(111) surface and be adsorbed in adjacent hollow sites, forming a local structure of Al₃O–Al₃O. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10 0)

We assess the consequences of the interface model—embedded‐cluster or periodic‐slab model—on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic‐slab calculations indicate a delocalized charge‐transfer state. Our example is Cu atom adsorption on ZnO(10 0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded‐cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom‐centered and plane‐waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10 0), as long as care is taken to account for the effects of CT. © 2015 Wiley Periodicals, Inc.     

A comprehensive computational study of N2H–XH, N2H–X2, and N2H–XY(YX) (X=Y=F, Cl, and Br) proton bound complexes

The results of theoretical studies on structures and energetics are presented for proton-bound complexes N₂H⁺–XH, N₂H⁺–X₂, and N₂H⁺–XY(YX) (X=Y=F, Cl, and Br). In all the monocations complexes, the halogen atom shares a proton with N₂. The calculated energetic results show that the stability decreases when descending in the corresponding periodic table column. The possible proton transfer dissociation processes of N₂H⁺+XH, N₂H⁺+X₂, and N₂H⁺+XY systems into XH₂⁺, X₂H⁺, XYH⁺, and YXH⁺ and molecular N₂ are calculated to be endothermic for share of the processes. The NBO results show that the largest intermolecular charge transfer is found in the Br bonded complexes.     

A first principle study of the structural,vibrational and electronic properties of tetrathiafulvalene adsorbed on Ag(110) and Au(110) surfaces

We have studied the adsorption properties of a charge donor organic molecule, tetrathiafulvalene (TTF), on the (110) surfaces of silver and gold by means of the generalized gradient approach of the density functional theory using periodic slab models. This molecule is the core building block of a host of molecular materials exhibiting extremely reach phase diagrams with a variety of ground states. The interfaces formed with metallic surfaces have received only limited attention, despite of their relevance. We have determined the stable adsorption sites for two unit cells representing high and low coverage, which are determinant for the adsorption properties of TTF on the surface. The preferential chemisorption is via the direct interaction of sulfur atoms with the Ag or Au atoms on top sites. All adsorbed TTF are more stable than gas phase TTF. The simulation of the vibrational spectra has permitted us to find the fingerprints of these structures to characterize them on this surface. The donor nature of TTF induces charge transfer to the metallic surfaces. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

H/D isotope effect on charge‐inverted hydrogen‐bonded systems: Systematic classification of three different types in H3XH…YH3 (X = C,Si, or Ge,and Y = B,Al, or Ga) with multicomponent calculation

Three different H/D isotope effect in nine H₃XH(D)^…YH₃ (X = C, Si, or Ge, and Y = B, Al, or Ga) hydrogen‐bonded (HB) systems are classified using MP2 level of multicomponent molecular orbital method, which can take account of the nuclear quantum nature of proton and deuteron. First, in the case of H₃CH(D)^…YH₃ (Y = B, Al, or Ge) HB systems, the deuterium (D) substitution induces the usual H/D geometrical isotope effect such as the contraction of covalent R(C? H(D)) bonds and the elongation of intermolecular R(H(D)^…Y) and R(C^…Y) distances. Second, in the case of H₃XH(D)^…YH₃ (X = Si or Ge, and Y = Al or Ge) HB systems, where H atom is negatively charged called as charge‐inverted hydrogen‐bonded (CIHB) systems, the D substitution leads to the contraction of intermolecular R(H(D)^…Y) and R(X^…Y) distances. Finally, in the case of H₃XH(D)^…BH₃ (X = Si or Ge) HB systems, these intermolecular R(H(D)^…Y) and R(X^…Y) distances also contract with the D substitution, in which the origin of the contraction is not the same as that in CIHB systems. The H/D isotope effect on interaction energies and spatial distribution of nuclear wavefunctions are also analyzed. © 2015 Wiley Periodicals, Inc.