The electronic structure evolution of DNA during its conformation transition process

We combined classical molecular dynamics (MD) simulation with ab initio calculations to study the electronic structure evolution of DNA during its conformation transition process. By using MD simulation, we obtained the conformation transition trajectory of an oligonucleotide poly(dC)-poly(dG), from which we selected a series of representative conformations and then performed ab initio calculations for these conformations to reveal their electronic structures. Counterintuitively, the results indicate that during the conformation transition process of DNA, thermal fluctuation plays a more important role than global conformation parameters in affecting the electronic structure of DNA.     

DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo

A complete scan of the potential‐energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller–Plesset second‐order perturbation theory (RI‐MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T‐shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol^?1. The different behaviors of nonmethylated and methylated trimers is also discussed. The high‐level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple‐zeta basis set predicts 11 uracil trimer interaction energies with a root‐mean‐square error of 2.3 kcal mol^?1 relative to highly correlated ab initio theoretical calculations.     

Structure of the HOOO radical in liquid water: a theoretical study.

The HOOO radical is supposed to play a role in ozone chemistry, both in the gas phase and aqueous media. We discuss the influence of the solvent on the electronic and geometrical structure of this radical using density functional and high-level ab initio calculations together with continuum, discrete, and discrete-continuum solvent models. Solute-solvent electrostatic interactions are shown to be fundamental, and lead to a noticeable stabilization of the radical, which should adopt a trans conformation in aqueous media. In fact, no energy minimum for the cis conformation is predicted in these conditions.     

Theoretical study on the phenyl torsional potentials of trans-diphenyldiphosphene

The phenyl torsional potentials of trans-diphenyldiphosphene ( trans-phosphobenzene; t-DPP), which is an analogue of trans-azobenzene ( t-AZB), have been examined by means of ab initio complete active space self-consistent field (CASSCF) calculations. Though the electronic structures of t-DPP are similar to those of t-AZB, the phenyl torsional potentials are different from each other. In S 0, the potential energy curve of t-DPP has double minima at nonplanar conformations with C 2 and C i symmetries, while that of t-AZB has only minimum at a planar conformation with C 2 h . In S 1, the phenyl torsion of t-AZB is impeded from a planar geometry more than that in S 0. On the other hand, the phenyl torsion of t-DPP is promoted so that the phenyl groups are perpendicularly twisted against the PP double bond around the Franck-Condon region. Comments on the experimental findings of realistic diphosphenes protected by bulky substituents are also made.     

Seven Conformations of the Macrocycle Cyclododecanone Unveiled by Microwave Spectroscopy

The physicochemical properties and reactivity of macrocycles are critically shaped by their conformations. In this work, we have identified seven conformations of the macrocyclic ketone cyclododecanone using chirped-pulse Fourier transform microwave spectroscopy in combination with ab initio and density functional theory calculations. Cyclododecanone is strongly biased towards adopting a square configuration of the heavy atom framework featuring three C–C bonds per side. The substitution and effective structures of this conformation have been determined through the observation of its ¹³C isotopologues. The minimisation of transannular interactions and, to a lesser extent, HCCH eclipsed configurations drive conformational preferences. Our results contribute to a better understanding of the intrinsic forces mediating structural choices in macrocycles.     

Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules: molecular mechanics and correlated ab initio study

Potential energy surfaces of monohydrated and dihydrated adenine-thymine and 9-methyladenine-1-methylthymine base pairs were examined by the molecular dynamics/quenching technique using the Cornell et al. force field (J. Am. Chem. Soc. 1995, 117, 5179). Long runs of molecular dynamics/quenching calculations allowed us to evaluate the free energy surface. The most stable and populated structures found were fully reoptimized at the correlated ab initio level employing the resolution of identity M?ller-Plesset method. A systematic study of the base pairs' microhydration using both the empirical and the high-level correlated ab initio approaches is presented for the first time. We show that the occurrence of water molecules and their gradually increasing number as well as the methylation of the bases favor stacked structures over the planar hydrogen-bonded ones. These results based on the correlated ab initio calculations are in the excellent agreement with data obtained from our previous empirical potential molecular dynamics study (Kabelác et al. Chem.-Eur. J. 2001, 7, 2067).     

Low energy structures of gold nanoclusters in the size range 3–38 atoms

Using a combination of first principles calculations and empirical potentials we have undertaken a systematic study of the low energy structures of gold nanoclusters containing from 3 to 38 atoms. A Lennard-Jones and many-body potential have been used in the empirical calculations, while the first principles calculations employ an atomic orbital, density functional technique. For the smaller clusters (n=3–5) the potential energy surface has been mapped at the ab initio level and for larger clusters an empirical potential was first used to identify low energy candidates which were then optimised with full ab initio calculations. At the DFT-LDA level, planar structures persist up to six atoms and are considerably more stable than the cage structures by more than 0.1 eV/atom. The difference in ab initio energy between the most stable planar and cage structures for seven atoms is only 0.04 eV/atom. For larger clusters there are generally a number of minima in the potential energy surface lying very close in energy. Furthermore our calculations do not predict ordered structures for the magic numbers n=13 and 38. They do predict the ordered tetrahedral structure for n=20. The results of the calculations show that gold nanoclusters in this size range are mainly disordered and will likely exist in a range of structures at room temperature.     

Structures of 1,2,3-trihydroxybenzene in the S0 and S1 states

In this paper we report on the structure and vibrations of gaseous pyrogallol (1,2,3-trihydroxybenzene) in the electronic ground state (S₀) and its first electronically excited state (S₁). Both ab initio CASSCF/CASMP2 calculations as well as R2PI spectroscopy have been performed. From the ab initio calculations three minimum energy structures are obtained and the vibrations of two structures are observed in the R2PI spectra. The minimum energy structures differ by their OH torsional angles. The full three-dimensional potential energy surface of the coupled torsional motions is investigated and the three-dimensional eigenvalues are calculated. The most stable structure of pyrogallol contains two intramolecular hydrogen bonds and turns out to be planar in the S₀ state. In the S₁ state the free OH group is rotated out of the plane of the aromatic ring by about 40°. The strong change in geometry of this structure is predicted by the CASSCF calculations and confirmed by the R2PI spectra of pyrogallol and its deuterated species. The low frequency region of the R2PI spectra can be explained by a torsional motion and the out of plane vibration 17b.     

Ab initio and density functional theory calculations of molecular structure and vibrational spectrum of ethyl azidoacetate

Here we report ab initio and density functional results for molecular properties of ethyl azidoacetate (N₃CH₂COOC₂H₅) and for the corresponding singly ionized structure (N₃CH₂COOC₂H₅⁺). Ab initio ionization energies based on Koopmans’ theorem are in excellent agreement with the experimental data from ultraviolet photoelectron spectroscopy. DFT adiabatic energy differences between neutral and ionized structures are very sensitive to electronic correlation effects and are not in very good agreement with experiment. The results for the structure and vibrational frequencies are compared with the experimental data of related molecular structures.     

镓原子链的结构稳定性和电子结构

The structural stabilities and electronic structures of Ga atomic chains are studied by the first-principles plane wave pseudopotential method based on the density functional theory. The present calculations show that gallium can form planar chains in linear-, zigzag- and ladder-form one-dimensional structures. The most stable one among the studied structures is the zigzag chain with a unit cell rather close to equilateral triangles with four nearest neighbors, and all the other structures are metastable. The relative structural stability, the energy bands and the charge densities are discussed based on the ab initio calculations and the Jahn-Teller effect.     

Conformational studies on 1,2-di- and 1,2,3-trisubstituted heterocycles. A spectroscopic and theoretical study of 3-acylaminopicolinic Acid derivatives and their N-oxides.

Theoretical studies involving minimization of model 3-propanoylaminopicolinic acids (10d-trans, 10d-cis), methyl ester (10a), and corresponding -N-oxide derivatives (10b, 10c-trans, 10c-cis) using AM1 gave conformations contrary to both sound chemical intuition and experimental data. RHF ab initio calculations using the 6-31G and 6-31G basis sets on the other hand corroborated spectroscopic data. 3-Amidopicolinic acid derivatives (7a-9a, 7b-9b, 7c-9c, 9d) were prepared and studied by NMR and IR spectroscopy. The results show that a strong intramolecular hydrogen bond between amide-H and the 2-carboxyl substituent results in a planar molecular conformation. This is particularly profound in the 3-acylaminopicolinic acid N-oxides (c-series). When the 2-substituent is a methyl ester on the other hand, repulsion between N-oxide and ester functions induces twisting of the carbomethoxy group out of the plane of the aromatic ring. The type of method used in molecular modeling can have profound impact on the final theoretical result in the case of the above-mentioned class of compounds. Our results indicate, that it is advisable to employ ab initio methods for modeling these types of compounds, and further, that the choice of basis set used for such calculations should depend on the type of information required. Thus, for most purposes pertaining to molecular conformation the 6-31G basis set provides sufficiently sound data in relatively short CPU time. For data related to electronic properties such as involvement of the N-oxide function or spectroscopic information such as IR frequencies or (1)H or (15)N NMR chemical shifts, the use of polarization functions as contained in the 6-31G basis set seems to be a must.     

Theoretical study on photophysical properties of bis-dipolar diphenylamino-endcapped oligoarylfluorenes as light-emitting materials

Bis-dipolar emissive oligoarylfluorenes, OF(2)Ar-NPhs(2), bearing an electron affinitive core, 9,9-dibutylfluorene, as conjugated bridges and diphenylamino as endcaps, show great potential for application in organic light-emitting diodes. The various electron affinitive central aryl cores that include thiophene S,S'-dioxide, dibenzothiophene S,S'-dioxide, 2,1,3-benzothiadiazole, 4,7-dithien-2-yl-2,1,3-benzothiazole, dibenzothiophene, and dibenzofuran produce a remarkable influence on their optical and electronic properties. In this contribution, we apply quantum-chemical techniques to investigate a series of bis-dipolar diphenylamino-endcapped oligoaryfluorenes, OF(2)Ar-NPhs(2). The geometric and electronic structures in the ground state are studied using density functional theory (DFT) and the ab initio HF, whereas the lowest singlet excited states are optimized with ab initio CIS. The maximal absorption and emission wavelengths are investigated by employing time-dependent density functional theory (TDDFT). As a result, HOMOs, LUMOs, energy gaps, ionization potentials, electron affinities, and reorganization energies are affected by varying the electron affinitive cores in OF(2)Ar-NPhs(2). The absorption and emission spectra of this series of bis-dipolar oligoarylfluorenes also exhibit red shifts to some extent due to the electron-withdrawing property and the conjugated length of the electron affinitive cores. Remarkably, their calculated emission spectra can cover the full UV-vis spectrum (from 412 to 732 nm). Also, the Stokes shifes are unexpectedly large, ranging from 34 to 234 nm, resulting from a more planar conformation of the excited state between the two adjacent units in the oligoarylfluorenes. All the calculated results show that the oligoarylfluorenes can be used as hole and electron transport/injection materials in organic light-emitting diodes.     

The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases

Using ab initio metadynamics we have computed the conformational free energy landscape of beta-D-glucopyranose as a function of the puckering coordinates. We show that the correspondence between the free energy and the Stoddard's pseudorotational itinerary for the system is rather poor. The number of free energy minima (9) is smaller than the number of ideal structures (13). Moreover, only six minima correspond to a canonical conformation. The structural features, the electronic properties, and the relative stability of the predicted conformers permit the rationalization of the occurrence of distorted sugar conformations in all the available X-ray structures of beta-glucoside hydrolase Michaelis complexes. We show that these enzymes recognize the most stable distorted conformers of the isolated substrate and at the same time the ones better prepared for catalysis in terms of bond elongation/shrinking and charge distribution. This suggests that the factors governing the distortions present in these complexes are largely dictated by the intrinsic properties of a single glucose unit.     

Pauling’s resonating valence bond theory of metals: some studies on lithium clusters

We report for the first time fully ab initio valence bond (VB) calculations with explicit use of the unsynchronized resonance structures introduced by Pauling [1]. We show that resonance involving these structures largely determines the stability and conformation of the Li ₄ cluster and plays a central role in a VB explanation of the 3-center bonds in planar alkali clusters. The theory can make qualitative predictions on the behaviour of general metallic clusters, and can relate stability and conformation to electronic structure, thus indicating the origin of magic numbers. This first ab initio test of Pauling’s resonating VB theory confirms the importance of the metallic orbital and the covalent character of the metal-metal bond.     

Electron Energy Loss Spectra of Carbodiimides

Compounds with carbodiimide bonds are of special interest to organic syntheses, materials science and biochemistry. The chemical reactivity of carbodiimides and their utilization ensue from their electronic structure, which can be studied via electron spectroscopic methods. Electron energy loss spectra of dicyclohexylcarbodiimide, polysilyl‐ and polytitanylcarbodiimides have been recorded. The energy loss near edge structures (ELNES) of the C–K, N–K, Si–L_2,3 and Ti–L_2,3‐ionization edges and their onsets as well as the features of the low‐loss region have been interpreted by ab‐initio quantumchemical calculations using density functional theory (DFT).     

Synthesis, structure, and computational studies of soluble conjugated multidentate macrocycles

[Chemical reaction: See text] Conjugated, shape-persistent macrocycles based on [3 + 3] Schiff-base condensation are of interest for supramolecular materials. In an effort to develop new discotic liquid crystals based on these compounds, a series of macrocycles with peripheral alkoxy groups of varying length have been prepared. The synthesis and mechanism of formation have been probed by isolation of oligomeric intermediates. A single-crystal X-ray diffraction study of one macrocycle revealed a nonplanar, strongly hydrogen-bonded structure. To our surprise, even with very long substituents, the macrocycles were not liquid crystalline. This has been rationalized by ab initio calculations that indicate the macrocycles are undergoing rotation of the dihydroxydiiminobenzene rings that may not allow a stable discotic liquid crystalline phase. These results provide new insight into the formation and properties of these large macrocycles and may provide guidance to developing stable liquid crystalline materials in the future.     

1,2-二硒方酸的从头计算

在ＲＨＦ／ＳＴＯ－３Ｇ和ＳＴＯ－３Ｇ＊水平上用ａｂｉｎｉｔｉｏＳＣＦ方法优化得到１，２－二硒方酸（３，４－二羟基－３－环丁烯－１，２－二硒酮）三种平面异构体的平衡几何构型，发现三种平面异构体中ＺＺ型是能量最低构象。用ａｂｉｎｉｔｉｏ数值方法在ＲＨＦ／ＳＴＯ－３Ｇ＊水平上计算了三种平面异构体的谐振动频率。     

Square planar vs tetrahedral coordination in diamagnetic complexes of nickel(II) containing two bidentate pi-radical monoanions

The reaction of three different 1-phenyl and 1,4-diphenyl substituted S-methylisothiosemicarbazides, H(2)[L(1-6)], with Ni(OAc)(2).4H(2)O in ethanol in the presence of air yields six four-coordinate species [Ni(L(1-6)(*))(2)] (1-6) where (L(1-6)(*))(1-) represent the monoanionic pi-radical forms. The crystal structures of the nickel complexes with 1-phenyl derivatives as in 1 reveal a square planar structure trans-[Ni(L(1)(-3)(*))(2)], whereas the corresponding 1,4-diphenyl derivatives are distorted tetrahedral as is demonstrated by X-ray crystallography of [Ni(L(5)(*))(2)] (5) and [Ni(L(6)(*))(2)] (6). Both series of mononuclear complexes possess a diamagnetic ground state. The electronic structures of both series have been elucidated experimentally (electronic spectra magnetization data). The square planar complexes 1-3 consist of a diamagnetic central Ni(II) ion and two strongly antiferromagnetically coupled ligand pi-radicals as has been deduced from correlated ab initio calculations; they are singlet diradicals. The tetrahedral complexes 4-6 consist of a paramagnetic high-spin Ni(II) ion (S(Ni) = 1), which is strongly antiferromagnetically coupled to two ligand pi-radicals. This is clearly revealed by DFT and correlated ab initio calculations. Electrochemically, complexes 1-6 can be reduced to form stable, paramagnetic monoanions [1-6](-) (S = (1)/(2)). The anions [1-3](-) are square planar Ni(II) (d,(8) S(Ni) = 0) species where the excess electron is delocalized over both ligands (class III, ligand mixed valency). In contrast, one-electron reduction of 4, 5, and 6 yields paramagnetic tetrahedral monoanions (S = (1)/(2)). X-band EPR spectroscopy shows that there are two different isomers A and B of each monoanion present in solution. In these anions, the excess electron is localized on one ligand [Ni(II)(L(4-6)(*))(L(4-6))](-) where (L(4-6))(2-) is the closed shell dianion of the ligands H(2)[L(4-6)] as was deduced from their electronic spectra and broken symmetry DFT calculations. Oxidation of 1 and 5 with excess iodine yields octahedral complexes [Ni(II)(L(1,ox))(2)I(2)] (7), [Ni(II)(L(1,ox))(3)](I(3))(2) (8), and trans-[Ni(II)(L(5,ox))(2)(I(3))(2)] (9), which have been characterized by X-ray crystallography; (L(1-)(6,ox)) represent the neutral, two-electron oxidized forms of the corresponding dianions (L(1-6))(2-). The room-temperature structures of complexes 1, 5, and 7 have been described previously in refs 1-5.     

Theoretical study on structural, electronic, and optical properties of ambipolar diphenylamino end-capped oligofluorenylthiophenes and fluoroarene-thiophene as light-emitting materials

Ambipolar diphenylamino end-capped oligofluorenylthiophenes and fluoroarene-thiophene show great potential for application in organic light-emitting diodes (OLEDs). Here, we provide an in-depth investigation on the optical and electronic properties of OF(2)TP-NPh ( 1a), OF(2)DTP-NPh ( 2a), OF(2)TTP-NPh ( 3a), OF(2)QTP-NPh ( 4a), and 2,5-bis-(2,3,5,6-tetrafluoro-4-trifluoromethyl-phenyl)-2,2':5',2':5',2'-quaterthiophene ( 5a). The geometric and electronic structures of the oligomers in the ground-state are studied with density functional theory (DFT) and ab initio Hartree-Fock, whereas the lowest singlet excited states are optimized by ab initio CIS. The energies of the lowest singlet excited states are calculated by employing time-dependent density functional theory (TDDFT). The results show that the highest occupied molecular orbitals, lowest unoccupied molecular orbitals, energy gaps, ionization potentials, and electron affinities for the oligomers are affected by the thiophene chain length and the different end-caps. The absorption and emission spectra exhibit red shifts to some extent due to the increasing thiophene chain length and the enhancing electron-donating property of the end-caps. Furthermore, the large Stokes shifts ranging from 58 to 80 nm are examined, resulting from a more planar conformation of the excited-state between the two adjacent units in the oligomers. All the calculated data show that the fluoroarene-thiophene has improved electron transport rate and charge transfer balance performance, and all the studied molecules can be used as ambipolar-transporting materials in OLEDs.     

The trans-isomer of formanilide studied by microwave Fourier transform spectroscopy

The rotational spectra of the trans-isomer of formanilide was recorded by microwave Fourier transform spectroscopy. The rotational and centrifugal distorsion constants as well as the quadrupole coupling constants have been accurately determined. It is shown that the stable conformation corresponds to a planar structure. The energy barrier between this conformation and the less stable one (the amino group lies in a plane perpendicular to the phenyl ring) has been evaluated by ab initio calculations.