The electronic structure and conformation of dimethylaminobenzonitrile

Ab initio molecular orbital (MO) computations on the closed shell singlet ground state ofN, N-dimethylaminobenzonitrile (DMABN) are reported. Fully optimized structures of several conformers of DMABN were calculated at the HF/6-31G level of theory. Our results indicate that for each of these conformations the minimum energy structure has a trigonal (sp² hybridized] amino nitrogen. The most stable DMABN conformer was found to be planar with its methyl groups eclipsed. The Koopmans ionization potentials and dipole moments of the various ground state conformers are compared. The implications for dynamical models of twisted-intramolecular charge transfer (TICT) are discussed. Moreover, the use of qualitative MO theory arguments provides an interpretation of the computational results in a simple orbital interaction framework.A. Mellon Foundation Fellow (1989–1992).Operated for the U.S. Department of Energy by Battelle Memorial Institute under Contract DE-AC06-76RLO 1830.     

Stepwise evolution of the structure and electronic properties of DNA

The optical properties of a family of duplex DNA conjugates possessing from 1 to 11 A:T base pairs and covalently attached stilbene chromophores at both ends have been investigated. As few as from two to four base bairs are needed to establish base-pair absorption and circular dichroism spectra similar to those of longer oligomers. The stilbene chromophores exhibit exciton-coupled circular dichroism, which can be observed even with 11 intervening base pairs, a distance of ca. 40 A. The dependence of the sign and amplitude of these spectra reveals the ability of B-DNA to serve as a helical ruler.     

The evolution of electronic structure in AlnCom

The ionization potentials of Al_nCo_m clusters (n>m) have been bracketed using laser photoionization mass spectrometry. We find the electronic shell structure manifested in the ionization potentials of Al_n for n≥7 is observed also for Al_nCo and Al_nCo₂, and is consistent with cobalt contributing one electron to the conduction band of the cluster. However, with increasing number of cobalt atoms, this simple picture breaks down; all vestiges of aluminum cluster electronic shell structure are absent for m≥4.     

The electronic structure of transition metal dihelide dications

Multi-reference configuration interaction (MRCI) calculations have been employed to characterize the low-lying states of first-row transition metal dihelide dications, He(2)TM(2+) (TM = Sc-Cu). The most important state-ordering principles were determined to be the occupation of the 4s orbital and orientation of the occupied 3d orbital. The ground states of all species are predicted to be of D(infinityh) symmetry arising from a 3d(n+1) electronic configuration. For excited states with singly occupied 4s or doubly occupied 3d(sigma) orbitals, bending to C(2v) symmetry typically lowers the energy and shortens the He-TM bond length. Coupled cluster singles and doubles with a perturbative treatment of triple excitations (CCSD(T)) results for ground state spectroscopic properties are in agreement with the MRCI predicted trends.     

Molecular vibrations,electronic structure and conformation of diprotonated thiocarbohydrazide

The infrared spectra of diprotonated species of thiocarbohydrazide and its perdeuterated derivative have been examined in the crystalline state. A complete vibrational assignment with a full normal coordinate treatment based on a Urey—Bradley type intramolecular potential Function supplemented with a valence force function for the out of plane and torsional modes is proposed and the origin of the amide II band splittings is explained. A CNDO/2 study of diprotonated thiocarbohydrazide and its neutral molecule is undertaken and the changes in the molecular electronic structures and conformations consequent to protonation are determined and briefly discussed. The magnitude of the N—N⁺H₃ torsional barrier is estimated to be 21 kJ mol^? (5.0 kcal mol^?1) whereas the barrier for the C—N group is found to be 92 kJ mol^?1 (22.0 kcal mol^?1).     

The influence of structure and conformation on electronic interactions of 4′-nitro-10-phenylphenothiazine

The crystal structure of 4′-nitro-10-phenylphenothiazine, 1 , has been determined by the single crystal x-ray diffraction studies and consists of two independent molecules in the asymmetric cell unit with a pseudo-center of symmetry. The crystal belongs to the monoclinic System with the space group P2₁/c. The central ring of the phenothiazine ring system is in a boat conformation and the 4′-nitro substituent is in a boat-axial conformation with respect to the central ring of phenothiazine. Compound 1 is the first reported 10-aryl phenothiazine in which the 10-phenyl ring is perpendicular to the plane bisecting the dihedral angle of the phenothiazine nucleus. This geometry allows for resonance interaction between the lone pair of electrons on N₁₀ and the 4′-nitro-10-phenyl ring which influences both the spectral properties and structure of the phenothiazine tricyclic ring. The correlation between the x-ray structure and ¹³C nmr spectral properties of 1 is discussed. The uv/vis and esr studies of the radical cation of 1 indicate that the 10-aryl ring is twisted with respect to the phenothiazine ring.     

Adsorption-induced intramolecular dipole: correlating molecular conformation and interface electronic structure

The interfaces formed between pentacene (PEN) and perfluoropentacene (PFP) molecules and Cu(111) were studied using photoelectron spectroscopy, X-ray standing wave (XSW), and scanning tunneling microscopy measurements, in conjunction with theoretical modeling. The average carbon bonding distances for PEN and PFP differ strongly, that is, 2.34 A for PEN versus 2.98 A for PFP. An adsorption-induced nonplanar conformation of PFP is suggested by XSW (F atoms 0.1 A above the carbon plane), which causes an intramolecular dipole of approximately 0.5 D. These observations explain why the hole injection barriers at both molecule/metal interfaces are comparable (1.10 eV for PEN and 1.35 eV for PFP) whereas the molecular ionization energies differ significantly (5.00 eV for PEN and 5.85 eV for PFP). Our results show that the hypothesis of charge injection barrier tuning at organic/metal interfaces by adjusting the ionization energy of molecules is not always readily applicable.     

The electronic structure of the flavin cofactor in DNA photolyase.

Density functional theory is used to calculate the electronic structure of the neutral flavin radical, FADH(*), formed in the light-induced electron-transfer reaction of DNA repair in cis,syn-cyclobutane pyrimidine dimer photolyases. Using the hybrid B3LYP functional together with the double-zeta basis set EPR-II, (1)H, (13)C, (15)N, and (17)O isotropic and anisotropic hyperfine couplings are calculated and explained by reference to the electron densities of the highest occupied molecular orbital and of the unpaired spin distribution on the radical. Comparison of calculated and experimental hyperfine couplings obtained from EPR and ENDOR/TRIPLE resonance leads to a refined structure for the FAD cofactor in Escherichia coli DNA photolyase. Hydrogen bonding at N3H, O4, and N5H results in significant changes in the unpaired spin density distribution and hyperfine coupling constants. The calculated electronic structure of FADH(*) provides evidence for a superexchange-mediated electron transfer between the cyclobutane pyrimidine dimer lesion and the 7,8-dimethyl isoalloxazine moiety of the flavin cofactor via the adenine moiety.     

Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.     

显脉香茶菜素的晶体结构及其抗癌活性区的电子结构研究

显脉香茶菜素是从抗癌中草药,显脉叶香茶菜中,提取出来的一种具有抗癌活性的化合物.由X射线衍射测定结果可知,其晶体属正交晶系,空间群为P2~12~12~1,a=0.7629(2),b=0.9557(4),c=2.6473(9)nm,z=4 .晶体结构表明,分子中含有部分共轭的α-亚甲基环戊酮的五元环,该五元环具有较大的内应力,是一个抗癌活性区.由量子化学计算结果可知.抗癌活性区的LUMO是πMO,能级较高,容易接受电子参与反应,因此,该分子是亲电型的.     

The electronic structure of N-methyl-3pyridone and its representation

Quasi-localized MO's have been constructed for the electron system of the three pyridone isomers.     

Molecular conformation and electronic structure of 1,1'-bipyrrole. an ab initio approach

Internal rotation about the N-N ' interannular bond of 1,1'-bipyrrole has been investigated by means of STO-3G and 4-31G ab initio calculations. A perpendicular disposition of the pyrrole rings is predicted as the most stable conformation. The highest occupied π MOs of 1,1'-bipyrrole are correlated with those of pyrrole and their evolution with the twisting angle is analyzed. Electronic structure predictions are in good agreement with experimental photoelectron spectral data.     

硫化聚乙炔结构对其电子性能的影响

本文用硫原子和共轭多烯的复合物模拟硫化聚乙炔结构, 并采用一维紧束缚的LCAO-SCF-MO法, 探讨了硫化聚乙炔结构对其电子性能的影响, 揭示出影响的原因, 确定了最佳结构, 为实验合成提供了理论依据。     

Computational convergence of electronic structure calculations of transition metal ligand complexes

Calculations of binding energies and optimum geometries of compounds of the series M(H₂O)⁺ with M = Sc to Zn have been carried out and compared with gas-phase experimental data and with the Rosi and Bauschlicher MCPF calculations. Hartree–Fock calculations and correlated calculations at MP2, MP4, and QCISD(T) levels were used to test the dependence of the results upon the level of correlation. A test of basis set dependence was also carried out, using parallel calculations on four basis sets ranging in size from a small DZ set to a TZ contraction. Correlation levels above MP2 and elaboration of the metal d-function basis set to (4d/3d) size or greater were both necessary for convergence with the most uniformly reliable results obtained from QCISD(T) calculations on a basis set with a (6d/4d) contraction for the d-function space. However, MP2 or higher-level calculations with a contracted four or five d function set [(5d/3d) or (4d/3d)] are capable of yielding results on binding energies and geometries close to the current gas-phase experimental uncertainty on electrostatically bound transition metal complexes. © 1993 John Wiley & Sons, Inc.     

Extension of the PS-GVB electronic structure code to transition metal complexes

We have developed a parameterization enabling ab initio electronic structure calculation via the PS-GVB program on transition-metal-containing systems using two standard effective core potential basis sets. Results are compared with Gaussian-92 for a wide range of complexes, and superior performance is demonstrated with regard to computational efficiency for single-point energies and geometry optimization. Additionally, the initial guess strategy in PS-GVB is shown to provide considerably more reliable convergence to the ground state. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1863–1874, 1997     

Influence of solvent structure on the conformation of the native DNA molecule

The investigation of the factors determining the formation and stability of the higher biopolymers structures is one of the most important trends of the development of molecular biophysics. A feature common to most macromolecular systems under physiological conditions is that they function in an aqueous environment. Thus, it is natural to assume that the peculiarities of biological macromolecules structures and their functional activity as well are closely related to the specific properties of such a unique solvent as water. The investigations of the conformational changes of biopolymer, induced by dehydration of the macromolecule, give information about the nature of the forces stabilizing its structure. The dehydration of the macromolecule in solution can be attained by addition of a nonaqueous cosolvent. Generally low-molecular-weight aliphatic alcohols, amides, and amines are used as a nonaqueous component. At present a vast number of experimental and theoretical data concerning the properties of water and aqueous systems are available. The specificity of water as a solvent arises primarily from the spatial hydrogen-bonded structure. The addition of a nonaqueous component exerts changes in this structure, which evolve to the singularities of the physical characteristics of water-nonelectrolyte mixtures. It is generally assumed that nonelectrolytes may be divided, according to their effect on the spatial water structure, largely into two basic classes: (1) the structure makers, i.e., the compounds of aliphatic alcohols type; (2) the structure breakers, i.e., the compounds of urea type. The agents belonging to the first class show a stabilizing effect in the range of low nonelectrolyte content. At a certain critical concentration, C_crit, characteristic of each substance, the nonaqueous solute molecules leave the cavities of the spatial water structure which leads to a disruption of the latter. The agents belonging to the second class exert a structure-breaking effect even in the range of extremely low concentrations, which arises from their high competitive ability for hydrogen bonding.