Vibrational Spectra and Density Functional Theory Calculations of Metallotriphenylcorroles

The infrared absorption and Raman scattering spectra were measured for the metallotriph-enylcorroles (MTPCs, M=Cu, Co, Ni, Mn). The ground-state structures and vibrational spectra of MTPCs have been calculated with the density functional theory. The observedRaman and IR bands have been assigned based on the calculation results. Due to the symmetry lowering, the vibrational spectra of MTPCs are much more complex than metal-loporphyrins, and several skeletal modes are found strongly coupled to the phenyl vibrations.The relationship between the Raman/IR frequencies and the structures of TPC ring is in-vestigated. It is found that the vibrations involving the C^I_αC^I_α stretch and C_αC_mstretch are sensitive to the size of corrole core. In particular, the frequency of υ₅, which is assigned to C^I_αC^I_α stretch in coupling with the C_αC_m symmetric stretch, increases linearly with the decrease of the corrole core-sizes and may be used as a mark band to evaluate the structural change of the metallocorroles.     

Molecular Structures from Density Functional Calculations with Simulated Annealing

The geometrical structure of any aggregate of atoms is one of its basic properties and, in principle, straightforward to predict. One chooses a structure, determines the total energy E of the system of electrons and ions, and repeats the calculation for all possible geometries. The ground state structure is that with the lowest energy. A quantum mechanical calculation of the exact wave function Ψ would lead to the total energy, but this is practicable only in very small molecules. Furthermore, the number of local minima in the energy surface increases dramatically with increasing molecular size. While traditional ab initio methods have had many impressive successes, these difficulties have meant that they have focused on systems with relatively few local minima, or have used experiment or experience to limit the range of geometries studied. On the other hand, calculations for much larger molecules and extended systems are often forced to use simplifying assumptions about the interatomic forces that limit their predictive capability. The approach described here avoids both of these extremes: Total energies of predictive value are calculated without using semi-empirical force laws, and the problem of multiple minima in the energy surface is addressed. The density functional formalism, with a local density approximation for the exchange-correlation energy, allows one to calculate the total energy for a given geometry in an efficient, if approximate, manner. Calculations for heavier elements are not significantly more difficult than for those in the first row and provide an ideal way to study bonding trends. When coupled with finite-temperature molecular dynamics, this formalism can avoid many of the energetically unfavorable minima in the energy surface. We show here that the method leads to surprising and exciting results.     

Vibrational Spectra and Density Functional Theory Calculations of Metallo-tetra-(tert-butyl)-tetra-azaporphyrines

The infrared absorption and 514.5 nm excited Raman spectra were measured for the metallo-tetra-(tert-butyl)-tetraazaporphyrin (MT(tBu)TAP, M=Cu, Co, Ni, Zn). The ground-state structures and vibrational spectra of MT(tBu)TAPs have been calculated at the B3LYP level of theory. The observed Raman and IR bands have been assigned based on the calculation results and by comparing with the normal metalloporphyrins. The relationship between the Raman/IR frequencies and the structures of TAP ring was investigated. The results show that the frequencies of C_βC_β′ stretch (A_g), asymmetric C_αN_m stretch (A_g), and symmetric C_αN_m stretch (B_g) modes increase linearly with the decrease of the core-sizes of TAP ring.Among the three modes, the later two are more sensitive to the core-size change.     

Density Functional Theory Study of Infrared and Ultraviolet Spectra of Urea L-Malic Acid

During the measurement of atmospheric nitrate radical by long-path differential optical absorption spectroscopy, water vapor strong absorption could affect the measurement of nitrate radical and detection limits of system. Under the tropospheric condition, the optical density of water vapor absorption is non-linearly dependent on column density. An effective method was developed to eliminate the effect of water vapor absorption. Reference spectra of water vapor based on the daytime atmospheric absorption spectra, when fitted together with change of cross section with water vapor column densities, gave a more accurate fitting of water vapor absorptions, thus its effect on the measurements of nitrate radical could be restricted to a minimum and detection limits of system reached 3.6 ppt. The modified method was applied during an intensive field campaign in the Pearl River Delta, China. The NO3 concentration in polluted air masses varied from 3.6 ppt to 82.5 ppt with an average level of 23.6±1.8 ppt.     

石墨烯分子振动模式因子群分析与密度泛函计算

运用因子群分析法对石墨烯的分子振动模式进行了理论分析,得到石墨烯的分子振动模式,计算出各振动模式的光谱特性.对所建立的石墨烯晶体的布拉维单胞模型采用基于密度泛函理论的第一性原理进行分子振动频率与模式的计算,所得的振动模式数目以及各振动频率的光谱特性同因子群分析方法所得结论一致.结合上述计算结果,通过系统比较石墨与石墨烯之间的红外光谱和拉曼光谱的差别,从理论上解释了具有D6h对称的石墨烯的A2u、E1u红外活性特征振动模式没有在红外光谱中出现的原因.     

FT-IR, Raman and NMR Spectra, Molecular Geometry, Vibrational Assignments, ab initio and Density Functional Theory Calculations for Diethyl Phthalate

Phthalate acid esters (PAEs) possess endocrine disruptive effects and can produce reproductive and developmental toxicities. In this paper, both experimental and theoretical studies on FT-IR, Raman and 1H NMR spectra of diethyl phthalate (DEP) have been carried out. The geometrical structure of DEP was optimized at the HF/6-31G*, HF/6-311G**, B3LYP/6-31G*, and B3LYP/6-311G** levels, respectively. The harmonic vibrational frequencies, IR intensity, Raman activity and 1H NMR chemical shifts have been computed at the B3LYP/6-31G* and B3LYP/6-311G** levels. Anharmonic corrections to frequencies were obtained by means of second-order perturbation theory (PT2) at the B3LYP/6-31G* level. Based on potential energy distribution (PED), the vibrational assignments have also been performed. The theoretical calculation values were compared with the experimental observations and the results indicate they are in excellent agreement.     

Insight into Reaction Mechanism of Sirtuins via Molecular Simulation and Density Functional Theory Study

With density functional theory(DFT) and molecular mechanics method, the catalytic mechanism of silent information regulator(sirtuins) has been investigated. The calculations support the S N 2-like reaction of the initial step of the catalysis, and are consistent with experiment results. We further explored the second step of the catalysis and proposed that this step took place in a concerted reaction. In addition, the side chain of Phenylalanine33 may help to shield the glycosidic bond from water and be in a position to protect the developing oxacabenium transition state from hydrolysis. Our results of the calculations support this hypothesis that the phenylalanine33 plays a critical role in the sirtuins biology function.     

Density Functional Calculation of the Photoelectron Emission Spectra of BiSCl Crystal and Molecular Clusters

The photoelectron emission spectra of BiSCl crystal and molecular clusters have been calculated by the Density Functional Theory (DFT) method. Molecular clusters consists from 2 to 20 molecules in one double chain along z(c) axis. Total and partial density of states of BiSCl crystal and clusters have been weighted with atomic photoemission emission cross-section. The molecular clusters have been investigated including all normal modes of vibration. Theoretical results of BiSCl crystal and molecular clusters have been compared with experimental X-ray photoelectron emission spectra (XPS) of BiSI crystal.     

The Pentabromine(1+) Cation,Br5+. Local Density Functional Calculations and Vibrational Spectra

The geometry, vibrational spectra and charge distribution of Br₅⁺ were calculated by the use of the local density functional (LDF) method. The results show that for free Br₅⁺ the lowest energy configuration is a skew structure with the three central Br atoms forming an angle of 168.6° und the two terminal Br atoms exhibiting a dihedral angle of 82°. This skew configuration is in contrast to the planar trans configuration of C_2h symmetry found for Br₅⁺ in solid Br₅⁺MF₆^? (M = As, Sb). The small energy difference of 1.2 kcal mol^?1 between the skew and the trans configurations, combined with crystal packing effects, can account for the planar trans configuration of Br₅⁺ in solid Br₅⁺MF₆^?. The computed vibrational spectra were used to select the most likely set from three sets of previously published and widely diverging spectra. Contrary to previous STO-3G calculations for Cl₅⁺, the present LDF calculations for Br₅⁺ and Cl₅⁺ result in charge distributions which agree with a previously proposed simple valence bond model for pentahalogen(1+) cations.     

(Noble Gas)n-NC+ Molecular Ions in Noble Gas Matrices: Matrix Infrared Spectra and Electronic Structure Calculations

An investigation of pulsed-laser-ablated Zn, Cd and Hg metal atom reactions with HCN under excess argon during co-deposition with laser-ablated Hg atoms from a dental amalgam target also provided Hg emissions capable of photoionization of the CN photo-dissociation product. A new band at 1933.4 cm⁻¹ in the region of the CN and CN⁺ gas-phase fundamental absorptions that appeared upon annealing the matrix to 20 K after sample deposition, and disappeared upon UV photolysis is assigned to (Ar)_nCN⁺, our key finding. It is not possible to determine the n coefficient exactly, but structure calculations suggest that one, two, three or four argon atoms can solvate the CN⁺ cation in an argon matrix with C−N absorptions calculated (B3LYP) to be between 2317.2 and 2319.8 cm⁻¹. Similar bands were observed in solid krypton at 1920.5, in solid xenon at 1935.4 and in solid neon at 1947.8 cm⁻¹. H¹³CN reagent gave an 1892.3 absorption with shift instead, and a 12/13 isotopic frequency ratio–nearly the same as found for ¹³CN⁺ itself in the gas phase and in the argon matrix. The CN⁺ molecular ion serves as a useful infrared probe to examine Ng clusters. The following ion reactions are believed to occur here: the first step upon sample deposition is assisted by a focused pulsed YAG laser, and the second step occurs on sample annealing: (Ar)₂⁺+CN→Ar+CN⁺→(Ar)_nCN⁺.     

Experimental and Density Functional Theory Calculation Studies on Raman and Infrared Spectra of 1,1'-Binaphthyl-2,2'-diamine

The IR absorption, visible excited normal Raman, and UV-excited near-resonant Raman (UVRR) spectra of 1,1'-binaphthyl-2,2'-diamine (BINAM) were measured and analyzed. Density functional theory calculations were carried out to investigate its vibrational frequencies, infrared absorption, normal Raman, and near-resonance Raman intensities. The observed Raman and IR bands of BINAM were assigned with respect to the local vibrations of substituted 2-naphthylamine. Several Raman bands of BINAM were found selectively enhanced in the UVRR in comparison with the normal Raman spectrum. Possible excited state geometry distortion was discussed based on the resonance Raman intensity analysis.     

6-硫代黄嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G**水平下,对14种气相和水相中可能存在的6-硫代黄嘌呤异构体进行了几何构型的全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能。Onsager反应场溶剂模型用于水相的计算.计算结果表明,6-硫代黄嘌呤在气相中和水相中主要以硫酮的形式存在.在气相和水相中,硫酮-N7(H)均比硫酮-N9(H)更稳定.计算结果同已有实验结果一致.6-硫代黄嘌呤异构化的熵效应小,对互变异构平衡几乎没有显著的影响,而焓变对互变异构产生了主要的影响.较详细地讨论了水溶剂化作用对异构体的能量、几何结构、电荷分布和偶极矩的影响.     

基于GPU的Hartree-Fock与密度泛函算法及程序

基于图形处理单元(GPU)的算法和程序为解决量子化学中的计算瓶颈开辟了道路.作者设计了基于GPU的量子化学算法和程序,实现了Hartree-Fock方法和密度泛函理论中双电子排斥积分计算、Fock矩阵构造以及交换相关泛函的计算.由于计算内核使用OpenCL编程框架,程序可以在多种架构的计算设备上执行.对于不同计算模块和分子自洽场计算的测试表明,基于OpenCL的GPU程序相比CPU上的串行程序实现了最快148倍的加速.     

5-氟胞嘧啶互变异构的密度泛函理论计算

采用BH-HLYP/6-311＋G**方法对10种气相和水相中可能存在的5-氟胞嘧啶互变异构体进行了几何全优化, 并计算出它们的总能量和吉布斯自由能. Onsager反应场溶剂模型用于水相的计算. 计算结果表明, 5-氟胞嘧啶在气相中主要以烯醇式-氨基式形式存在, 在水相中主要以酮式-氨基式形式存在. 溶剂化自由能与异构体的气相偶极矩存在相关性．进一步求得互变异构化以及构象异构化和顺反异构化的过渡态, 探讨异构化过程中的几何结构和能量的变化.     

ChemInform Abstract: The Pentabromine(1+) Cation,Br+ 5. Local Density Functional Calculations and Vibrational Spectra.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

并五苯分子电荷注入导致自旋极化的密度泛函理论研究

用密度泛函理论研究了不带自旋的空穴注入并五苯后体系的自旋相关特性. 电荷注入后并五苯分子中存在自发自旋极化行为. 当注入电荷量达一定程度,分子磁矩随注入电荷量的增加呈线性增长,最大磁矩可达1μB. 注入电荷和并五苯分子的相互作用导致分子体系结构发生变化,同时电荷密度分布及自旋密度分布也发生了变化. 注入电荷先填充自旋劈裂的碳原子pz轨道.     

The Structure of (SCN)x: A Study Using Molecular and Solid‐State Density Functional Theory Calculations

A riddle solved! Despite its simple formula, the structure of the (SCN)_x polymer has remained elusive since its first synthesis in 1929. From energetics as well as NMR chemical shifts, based on DFT calculations, we have strong evidence that it is indeed a tangle of linear chains, made up from N‐linked S₂C₂N five‐membered rings.