NLO response of derivatives of benzene,stilbene and diphenylacetylene:MP2 and DFT calculations

MP2 method and different functionals such as M06-HF, M06-2X, CAM-B3 LYP, PBE0, B3 LYP and M06 L incorporating different XC amounts were used to calculate the static first hyperpolarizabilies β(0) of eight molecules which are derivatives of benzene, stilbene and diphenylacetylene. The values were then compared to the experimental ones. The M06-2X functional was then selected for further calculations. NBO calculations were also performed to define the intramolecular charge transfer in each molecule. TD-DFT calculations were performed taking into account the solvent effect using the IEF-PCM formalism. Some parameters characterizing the vertical transitions such as the wavelength of the maximum absorption λ_(max) were compared to the experimental ones. Finally,solvation Gibbs free enthalpy ΔG_(solv) values have also been examined in order to determine which the specific solvent for a given molecule is.     

A density dependent dispersion correction

Density functional approximations fail to provide an accurate treatment of weak interactions. More recent, but not readily available functionals can lead to significant improvements. A simple alternative to correct for the missing weak interactions is to add, a posteriori, an atom pair-wise dispersion correction. We here present a density dependent dispersion correction, dDXDM, which dramatically improves the performance of popular functionals (e.g., PBE-dDXDM or B3LYP-dDXDM) for a set of 145 systems featuring both inter- and intramolecular interactions. Whereas the highly parameterized M06-2X functional, the long-range corrected LC-BLYP and the fully non-local van der Waals density functional rPW86-W09 also lead to improved results as compared to standard DFT methods, the enhanced performance of dDXDM remains the most impressive.     

Conformational Analysis of Thioether Musks Using Density Functional Theory

A conformational analysis of nine macrocyclic thioether musks has been carried out using molecular mechanics (MMFF), density functional theory (DFT) using both B3LYP and M06 functionals, as well as Hartree-Fock and post-Hartree-Fock (MP2) ab initio methods. 6-Thia-, 10-thia- and 4-methyl-5-thia-14-tetradecananolide, 4-thia-, 7-thia-, 11-thia- and 12-thia-15-pentadecanolide and 6-thia- and 12-thia-16-hexadecanolide were modeled. Unfortunately, there was little agreement between the computational methods at the levels of theory used in this study.     

The Se–S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study

The inhibition mechanism of the main protease (M^pro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of M^pro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se–S covalent bond mediated by EBS and EBS-OH on M^pro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of M^pro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.     

A Computational Study of Density of Some High Energy Molecules

The detonation pressure depends quadratically on the loading density of the explosives. A precise estimate of the density is thus crucial to decide if a novel energetic material is worth pursuing. In this work we investigate theoretically the crystal densities of the energetic compounds RDX, TNT, NTO, DNAM, CL‐20, DADNE, and HMX. We calculate the crystal densities by using Materials Studio 7.0 Polymorph Predictor, employing force fields and exploring molecular packing arrangements with minima in total energy. Geometry optimized molecular structures computed by density functional theory (DFT) are used as input to the density predictions. In an additional DFT study we apply two functionals, B3LYP and M06 with the 6‐31G(d) and the 6‐31G(d,p) basis sets, and the program package GAUSSIAN09. In this part of the work crystal densities are calculated by using the molecular isosurface volume (defined by the volume within a surface with an electron density of 0.001 electrons per Bohr³) alone or combined with the variance of the electrostatic potential (ESP). The Polymorph Predictor seems to overestimate the densities, but the values are very dependent on the force field strength determined by charges assigned to atoms. In the GAUSSIAN09 DFT study the densities derived by using the M06 functional are in similar agreement with experimental data as what we experienced for the B3LYP results, although both functionals appear to give slightly lower densities than reported experimentally for the majority of the molecules. On average, the densities derived by the ESP method correlate equally well with measured values as the results obtained by the isosurface method.     

Theoretical thermodynamics for large molecules: walking the thin line between accuracy and computational cost

The thermodynamic properties of molecules are of fundamental interest in physics, chemistry, and biology. This Account deals with the developments that we have made in the about last five years to find quantum chemical electronic structure methods that have the prospect of being applicable to larger molecules. The typical target accuracy is about 0.5-1 kcal mol(-1) for chemical reaction and 0.1 kcal mol(-1) for conformational energies. These goals can be achieved when a few physically motivated corrections to first-principles methods are introduced to standard quantum chemical techniques. These do not lead to a significantly increased computational expense, and thus our methods have the computer hardware requirements of the corresponding standard treatments. Together with the use of density-fitting (RI) integral approximations, routine computations on systems with about 100 non-hydrogen atoms (2000-4000 basis functions) can be performed on modern PCs. Our improvements regarding accuracy are basically due to the use of modified second-order perturbation theory to account for many-particle (electron correlation) effects. Such nonlocal correlations are responsible for important parts of the interaction in and between atoms and molecules. A common example is the long-range dispersion interaction that lead to van der Waals complexes, but as shown here also the conventional thermodynamics of large molecules is significantly influenced by intramolecular dispersion effects. We first present the basic theoretical ideas behind our approaches, which are the spin-component-scaled M?ller-Plesset perturbation theory (SCS-MP2) and double-hybrid density functionals (DHDF). Furthermore, the effect of the independently developed empirical dispersion correction (DFT-D) is discussed. Together with the use of large atomic orbital basis sets (of at least triple- or quadruple-zeta quality), the accuracy of the new methods is even competitive with computationally very expensive coupled-cluster methods, but they still remain routinely applicable for day-to-day chemical problems. This is demonstrated for the G3/99 benchmark set of heats of formation, 34 organic isomerization energies, and barriers for a number of pericyclic reactions. As an electronically complicated example, the relative energies of three isomeric Au(8) clusters are considered. In general, we recommend the very robust B2PLYP-D density functional approach for heat of formation calculations and for electronically complicated situations like transition metal complexes or open-shell species. With B2PLYP-D, an unprecedented low mean absolute deviation for the G3/99 test set with a DFT approach of 1.7 kcal mol(-1) has been achieved. For closed-shell main-group molecules and many relative energies, SCS-MP2 is the method of choice, because it completely avoids the self-interaction error problem that still plagues current DFT. In critical cases, it is recommended to apply SCS-MP2 and B2PLYP-D simultaneously, where also the comparison with standard MP2 and density functionals like B3LYP may lead to additional insight.     

Performance of hybrid density functional theory methods toward oxygen electroreduction over platinum

The performance of a large number of hybrid density functional theory methods is evaluated toward calculating potential-dependent activation energies for uncatalyzed and Pt-catalyzed oxygen reduction and hydroperoxyl oxidation. This reaction is the first step and the rate-determining step in the electrochemical oxygen reduction, which is the cathodic process in electrolyte-based fuel cells. Special focus is put on determining methods that allow results comparable to those previously calculated using MP2 method with the 6-31G(d,p) basis set for O and H and the LANL2DZ basis set for Pt. This level of theory was shown to reproduce well, within the model used here, key features of experimental data. It is found that hybrid density functional theory methods with small (less than 30%) Hartree-Fock exchange contributions give less accurate results mainly due to underestimated calculated activation energies while methods with higher (around 50%) Hartree-Fock exchange contributions give results closer to the target ones. New hybrid density functional theory methods with specific reaction parameters that give superior results are proposed. The best overall performance is found for the method denoted as B1B95-50 in which the Hartree-Fock exchange contribution is half. This method is computationally affordable and offers promise as a reliable method in applications to larger systems.     

A Theoretical Study on SERS Intensity of Pyridine Adsorbed on Transition Metal Electrodes

Since the mid-1990s good quality surface-enhanced Raman spectra have been obtained from many transition metal (TM) electrodes. It has been observed quite often that SERS band intensities, i.e., the relative intensities of different vibrational modes, of the adsorbate are very sensitive to the nature of the metal. Since transition metals interact with adsorbed molecules much more strongly than the typical SERS substrates, i.e., Au, Ag, and Cu, it is desirable to give a detailed and quantitative explanation of the spectroscopic behavior on TM electrodes. In the present study, a hybrid density functional approach with 6–311+G**/LanL2DZ basis sets and the B3LYP nonlocal exchange-correlation functionals has been used for the Raman intensity analysis on totally symmetric modes of pyridine adsorbed at transition metal electrodes, e.g., iron, cobalt, nickel, palladium, and platinum. Among all studied metal electrodes, iron and cobalt are predicted to be the most effective SERS substrates involving chemical enhancement, a result in good agreement with the experiments. The chemical bonding enhancement plays a role in pyridine interaction with the transition metal electrodes. The charge transfer enhancement as the most common chemical mechanism is also discussed for comparison.     

对苯二甲酸丁二醇酯二聚体水/醇/氨解机理的理论研究

采用密度泛函理论M06-2X/6-311G（d）方法,对对苯二甲酸丁二醇酯二聚体的水/醇/氨解反应机理进行了量子化学理论研究。提出了各种可能的水/醇/氨解反应路径,对各反应的中间体、过渡态及产物进行了几何结构优化和频率计算以获得热力学与动力学参数值,分析了对苯二甲酸丁二醇酯二聚体主链酯键中的酰氧键位置水/醇/氨降解的反应机理。计算结果表明：水/醇/氨解条件下能够降低对苯二甲酸丁二醇酯二聚体主链酯键中的酰氧键裂解的反应活化能,使反应更易于进行,水/醇/氨解中主要基元反应步的反应能垒分别约为170.0、155.0和165.0 kJ/mol。对苯二甲酸丁二醇酯二聚体水解产物主要为对苯二甲酸和1,4-丁二醇,醇解产物主要为对苯二甲酸二甲酯和1,4-丁二醇,氨解产物主要为芳香腈和1,4-丁二醇等,其中1,4-丁二醇会进一步降解形成四氢呋喃。在对苯二甲酸丁二醇酯二聚体水/醇/氨解反应过程中,甲醇介质中的裂解反应优于氨气气氛中的反应、氨气气氛中的反应优于水分子环境中的反应,且反应温度的升高可以增加其自发性。     

己基乙二胺-TFS型质子化离子液体与水分子间氢键相互作用的研究

通过前期实验研究,己基乙二胺-三氟甲磺酸([HHex][TFS])型质子化离子液体(protic ionic liquid,PIL)的极性部位具有两个氨基,亲水性较强,能够与水混溶90%(质量)(H₂O/ PIL)以上。因此利用密度泛函理论(density functional theory,DFT),在M06-2X/6-311G(d,p)的水平下,对 [HHex][TFS]与H₂O分子间形成的氢键作用进行了研究。设计了[HHex][TFS]分别与nH₂O (n = 1, 2, 6) 相结合的构型,并得到了较稳定构型共8种(S1~S8),计算了其分子间的相互作用能(ΔE ₀ ^BSSE)、分子振动频率(Δν)、二阶微扰能、电子密度(ρ _c)以及Laplace值(?² ρ _c)。分析结果显示,[HHex][TFS]与水分子间形成了较强的氢键,[HHex][TFS]与H₂O结合数量增加,构型中氢键相互作用增强,即S4(n=1)＜S6(n=2)＜S8(n=6)。     

Experimental and theoretical insight into the electronic properties of 4-aryl-5-arylazo-3-cyano-6-hydroxy-2-pyridone dyes

In this paper, spectroscopic and quantum mechanical investigation of nine 4-aryl-5-arylazo-3-cyano-6-hydroxy-2-pyridone dyes was performed, and obtained density functional theory (DFT) results were compared with experimental data. The structural and spectroscopic properties of azo-2-pyridone dyes were studied by DFT using B3LYP, CAM-B3LYP, and M06-2X methods with a 6-311++G(d,p) basis set. Comparison of results reveals that the scaled theoretical vibrational frequencies of azo dyes are in good agreement with experimental data. The time-dependent DFT calculated and experimental ultraviolet-visible (UV-vis) absorption spectra are also in good agreement. The effect of electron-donating –OCH₃ and electron-withdrawing –NO₂ groups on the structural parameters, vibrational frequencies, UV-vis absorption, and natural bond orbital (NBO) atomic charges were thoroughly analysed. Vibrational, UV-vis, and NBO analyses confirm that investigated dyes exist in the hydrazo tautomeric form in the solid state and ethanol solution. These analyses signify the occurrence of intramolecular charge transfer in these azo-pyridone dyes.     

Density functional theory (DFT) study of triphenylamine-based dyes for their use as sensitizers in molecular photovoltaics

In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6-31+G(d,p) basis set. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the absorption and emission spectra, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. Also, the pK(a) values were calculated with the semi-empirical PM6 method.     

Hydrogen on and in Selected Overlayer Near-Surface Alloys and the Effect of Subsurface Hydrogen on the Reactivity of Alloy Surfaces

The interaction of hydrogen with the close-packed facets of seventeen transition metals overlaid with 1 ML of five transition metals (Au, Ag, Cu, Pt, and Pd) has been studied using periodic self-consistent (GGA-PW91) density functional theory (DFT) calculations. For noble metal overlayers (Au, Ag, and Cu), hydrogen at the host-metal/overlayer interface (subsurface hydrogen) is more stable than subsurface hydrogen in the pure host. For certain Au and Ag overlayers, subsurface hydrogen is more stable than surface hydrogen in the same system. The presence of subsurface hydrogen was found to have a significant effect on the electronic structure of the overlayer, resulting in its modified surface reactivity.     

Coordination structures of organically bound paramagnetic metals in coal and their transformation upon solvent extraction

In this paper the organically bound paramagnetic (transition) metals (Fe, Cr, Mn, Co, Ni, V, Zn and Cu) were studied by a combination of sequential acid leaching and electron spin resonance spectroscopy. Additional investigation was also conducted on the occurrence of these metals in coal extracts generated by solvent extraction at 360 °C. The results indicate that, a sequential leaching by acetic acid (1 M), HCl (3 M), HNO₃ (2 M) and HF (48%) can remove most the inorganic species in a coal. The remaining elements are mainly transition metals. Of those, Fe is the most prevalent, which is mainly present as octahedral Fe³⁺ complex associated with phenolic hydroxyl or nitrogen-bearing functional groups. Nanometric ferric oxide/hydroxide and highly ordered Fe-rich crystals were also observed in coal extract. They are finely dispersed in the closed voids in the carbonaceous matrix, which may have been of biological origin, such as ferritin iron in proteins and iron porphyrin complexes that have undergone complex transformation during coalification. The water-derived colloidal iron phase can be one possible source as well. Regarding the other transition metals, they mostly have the hyperfine configurations that co-exist with Fe. The amounts of these organically bound species may depend on coal rank, but their relationship has not been clarified yet. Comparison between acid-washed coal and the respective coal extract also indicates the non-uniform distribution of organically bound transition metals within coal matrix.     

Understanding Trends in Catalytic Activity: The Effect of Adsorbate–Adsorbate Interactions for CO Oxidation Over Transition Metals

Using high temperature CO oxidation as the example, trends in the reactivity of transition metals are discussed on the basis of density functional theory (DFT) calculations. Volcano type relations between the catalytic rate and adsorption energies of important intermediates are introduced and the effect of adsorbate–adsorbate interaction on the trends is discussed. We find that adsorbate–adsorbate interactions significantly increase the activity of strong binding metals (left side of the volcano) but the interactions do not change the relative activity of different metals and have a very small influence on the position of the top of the volcano, that is, on which metal is the best catalyst.     

DFT法研究钯原子催化活化甲烷碳氢键的反应机理

首先采用M06L泛函研究了钯原子催化活化甲烷C-H的反应势能面(PES),并与已有的实验结果和理论基准进行了比较。随后,对反应复合物(RC)、过渡态(TS)和产物(P)分子进行了电子密度拓扑分析。势能面结合拓扑分析结果更清晰明确地表述了反应机理。     

苄胺在超临界水中脱氮机理的量子化学计算

针对苄胺在超临界水中的脱氮机理,通过实验和量子化学计算相结合的方法进行了研究.使用Gaussian09计算软件在M06/6-311G(d,p)和M06-2X/6-311+G(d,p)计算水平上进行量子化学计算.结果表明,苄胺在超临界水中的脱氮过程遵循协同反应机理而不是自由基机理.两步脱氢反应是苄胺的主要脱氢反应,其能垒...     

Electrochemical and quantum chemical studies of the reactions of transition metals M (M = Co, Fe and Ni) with LiF and Li2O

It has been a puzzle that transition metals can unexpectedly react with lithium-based matrixes of LiF and Li₂O in the potential versus Li/Li⁺ range from 0.01 to 3.5 V at room temperature. The electrochemical and theoretical investigations on the reactions of transition metals M (M = Co, Fe and Ni) with LiF and Li₂O were carried out. The electrochemical reactivity of metal cobalt with LiF and Li₂O has been examined by the discharge and charge, X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) measurements. Density functional theoretical calculation results suggested that the stable compounds MLiF and MLi₂O could be formed by the insertion of transition metal (M) in lithium-based matrixes with exothermic as an intermediate. The theoretical calculations provide an understanding in chemical reaction of M with LiF and Li₂O. The small molecular or clusters reaction may play an important role in the electrochemical reaction of metal with transition Li₂O or LiF, which could be used to explain for the unexpectedly reaction of transition metal with LiF and Li₂O.     

Current status of ab initio quantum chemistry study for oxygen electroreduction on fuel cell catalysts

Recent progress in the ab initio quantum chemistry study of cathode oxygen reduction on fuel cell catalysts is reviewed with emphasis on density functional theory and ab initio molecular dynamics methods. The capabilities of these methods are illustrated using examples of oxygen adsorption on transition metals and alloys, and the reduction mechanism. Ab initio studies can calculate adsorption geometry, energy, the dissociation energy barrier, reversible potential, activation energy, and potential dependant properties for elementary electron transfer steps. Even though ab initio study in this field is still at an early stage, it has already demonstrated its predictive ability in the trend of adsorption energy on transition metals and alloys, and illustrated its potential in identifying better electrocatalysts.