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Raman spectroscopy is widely used to examine the carbonate content within bone apatite, but Raman spectra are also sensitive to orientation effects between the polarisation of the incoming laser light and the sample orientation. This may lead to discrepancies when using Raman spectroscopy to evaluate the carbonate content as the extent of crystal organisation can change depending on the type of bone, age, and presence of mineralisation disorders in the organism. It is experimentally very challenging to evaluate the effect of orientation using individual bone crystals. Therefore, we have used density functional theory to examine the effect of orientation in apatitic materials. We examined hydroxyapatite and three different types of carbonated apatite: A-type where the carbonate ion substitutes the two OH groups in the unit cell, B-type where co-substitution occurs between carbonate in a phosphate position and Na+ for Ca2+ to maintain charge balance, and AB-type where carbonate sits in both A-site and B-site. Our simulations show that the OH group in hydroxyapatite has a strong orientation dependence, consistent with previous literature. In addition, the phosphate and carbonate bands of the apatitic structures are predicted to be orientation dependent, where the maximum scattering efficiency occurs in configurations in which the laser polarisation is parallel to the crystallographic axes of the material. The intensity changes of the phosphate and carbonate bands are not consistent upon changing orientations and thus may lead to an underestimation of carbonate contents if insufficient sampling points are used during bone analysis.

Excitation-energy transfer is a key step in processes such as photosynthesis that convert light into other forms of energy. Time-dependent density functional theory (DFT) in real time is ideal for the first-principles simulation of such processes due to its computational efficiency. We here demonstrate how real-time DFT can be used for analyzing excitation-energy transfer from first-principles. We discuss several measures of energy transfer that are based solely on the time-dependent density, are well founded in the DFT framework, allow for intuitive understanding and visualization, and reproduce important limiting cases of an analytical model. We demonstrate their usefulness in calculations for model systems, both with static nuclei and in the context of DFT-based Ehrenfest dynamics.

Mebendazole, (5-benzoil-1H-benzimidazol-2-il) -karbamik asit metil ester) (MBZ) 'nin çeşitli çoklu bileşenleri, WHO tarafından sentetik bir antelmintik ilaç olarak kabul edilmektedir. Bu çok bileşenli moleküller, özelliklerinde, özellikle çözünürlüklerinde ve solucan enfeksiyonlarını kontrol etmedeki etkinliklerinde farklılıklar gösterir. Bu farklılıklar, bu çoklu bileşenlerin farklı yapılarına atanabilir. Teorik araştırmalar kullanılarak yapı özelliği ilişkisinin anlaşılması, bize MBZ'nin yeni çoklu bileşenini sentezlemek ve özelliklerini tahmin etmek için bir yol sağlayabilir. Bu nedenle, burada, Yoğunluk fonksiyonel teorisi (DFT) yaklaşımını kullanarak yeni bir MBZ çok bileşenli Aktif Farmasötik Bileşen (API) Mebendazol nitrat tuzu (MBZ-N) üzerine elektronik ve spektroskopik araştırmaları rapor ediyoruz. Becke'nin üç parametreli hibrit işlevsel (B3LYP) yöntemi, doğruluk ve hesaplama maliyeti arasında en iyi uzlaşmayı sağlayan 6-311 ++ G (d, p) temel setine sahip tüm hesaplamalar için kullanılmıştır. doğal bağ analizi (NBO), HOMO-LUMO ve Moleküler Elektrostatik Potansiyel (MEP) gibi titreşim spektrumları ve moleküler reaktivite özellikleri analizi. Protein inhibe etme gibi bilojik aktivitesini anlamak için, MBZ-N molekülünün Tirozin-protein kinaz ABL ile moleküler kenetlenme çalışması da rapor edilmiştir., Various multicomponent of Mebendazole , (5-benzoyl-1H-benzimidazole- 2-yl)-carbamic acid methyl ester) (MBZ), are recognised by WHO as a synthetic anthelmintic drug. These multicomponent molecules show differences in their properties, mainly in their solubility and efficacy in controlling worm infections. These differences may be assigned to different structure of these multicomponents. Understanding of structure property relationship using theoretical investigations may provide us a way to synthesise new multicomponent of MBZ and estimating their properties. Therefore, here we report electronic and spectroscopic investigations on a new MBZ multicomponent Active Pharmaceutical Ingredient (API) Mebendazole nitrate salt (MBZ-N) using Density functional theory (DFT) approach. Becke’s three- parameter hybrid functional (B3LYP) method has been used for all computations with 6-311++G(d,p) basis set, which gives the best compromise between accuracy and computational cost.Optimized geometry was further used for the calculation of vibrational spectra and molecular reactivity properties analysis such as natural bond analysis (NBO), HOMO-LUMO, and Molecular Electrostatic Potential (MEP). To understand its bilogical activity such as protein inhibiting, the molecular docking study of the MBZ-N molecule with Tyrosine-protein kinase ABL is also reported.

As diseases caused by solar radiation have gained great prominence, several methods to prevent them have been developed. Among the most common, the use of sunscreens is customary and accessible. The application of theoretical methods has helped to design new compounds with therapeutic and protective functions. Natural compounds with described photoprotective potential properties (3-O-methylquercetin, gallic acid, aloin, catechin, quercetin, and resveratrol) were selected to perform theoretical studies. Computational methods were applied to predict their absorption spectra, using DFT and TD-DFT methods with functional B3LYP/6−311+g(d,p) basis sets and methanol (IEFPCM) as a solvent. The main electronic transitions of the compounds were evaluated by observing whether the differences in HOMO and LUMO energies that absorb in the UV range are UVA (320–400 nm), UVB (290–320 nm), or UVC (100–290 nm). Experimental validation was carried out for EMC, quercetin, and resveratrol, demonstrating the consistency of the computational method. Results obtained suggest that resveratrol is a candidate for use in sunscreens. The study provided relevant information about the in silico predictive power of natural molecules with the potential for use as photoprotective adjuvants, which may result in fewer time and resource expenditures in the search for photoprotective compounds.

The accurate description of the structures of water and hydrated ions is important in electrochemical desalination, ion separation, and supercapacitors. In this work, we present an ab initio atomistic simulation-based study to explore the structure of water and hydrated monovalent ions (Li

The computationally very demanding evaluation of the 4-center-2-electron (4c2e) integrals and their respective integral derivatives typically represents the major bottleneck within hybrid Kohn-Sham density functional theory molecular dynamics simulations. Building upon our previous works on seminumerical exact-exchange (sn-LinK) [Laqua, H., Thompsons, T. H., Kussmann, J., Ochsenfeld, C.

Liposomes are emerging therapeutic formulations for site-specific delivery of chemotherapeutic drugs. The efficiency and selectivity of drug delivery by these carriers largely rely on their surface properties, shape, and size. There is a growing demand for analytical approaches that can be used for structural and morphological characterization of liposomes at the single-vesicle level. AFM-IR is a modern optical nanoscopic technique that combines the advantages of scanning probe microscopy and infrared spectroscopy. Our findings show that AFM-IR can be used to probe conformational changes in phospholipids that take place upon their assembly into liposomes. Such conclusions can be made based on the corresponding changes in intensities of the lipid vibrational bands as the molecules transition from a solid state into large unilamellar vesicles (LUVs). This spectroscopic analysis of LUV formation together with density functional theory calculations also reveals the extent to which the molecular conformation and local environment of the functional groups alter the AFM-IR spectra of phospholipids. Using melittin as a test protein, we also examined the extent to which LUVs can be used for protein internalization. We found that melittin enters LUVs nearly instantaneously, which protects it from possible structural modifications that are caused by a changing environment. This foundational work empowers AFM-IR analysis of liposomes and opens new avenues for determination of the molecular mechanisms of liposome-drug interactions.

Whereas the proper choice of reaction solvent constitutes the cornerstone of the green solvent concept, solvent effects on chemical reactions are not mechanistically well understood due to the lack of feasible molecular models. Herein, by taking the case study of nucleophilic addition reaction in aqueous solution, we extend the proposed multiscale reaction density functional theory (RxDFT) method to investigate the intrinsic free energy profile and total free energy profile, and study the solvent effect on the activation and reaction free energy for the nucleophilic addition reactions of hydroxide anion with methanal and carbon dioxide in aqueous solution. The predictions of the free energy profile in aqueous solution for these two nucleophilic addition reactions from RxDFT have a satisfactory agreement with the results from the RISM and MD-FEP simulation. Meanwhile, the solvent effect is successfully addressed by examining the difference of the free energy profile between the gas phase and aqueous phase. In addition, we investigate the solvent effect on the reactions occurred near solid–liquid interfaces. It is shown that the activation free energy is significantly depressed when reaction takes place in the region within 10 A distance to the substrate surface owing to the decrease of hydration free energy at the solid–liquid interface.

Chagas disease is caused by Trypanosoma cruzi. Benznidazole and nifurtimox are drugs used for its therapy; nevertheless, they have collateral effects. NADH-fumarate (FUM) reductase is a potential pharmacological target since it is essential for survival of parasite and is not found in humans. The objectives are to design and characterize the electronic structure of imidazole and nitroimidazole derivatives at DFT-M06-2X level in aqueous solution; also, to model the NADH-FUM reductase and analyze its intermolecular interactions by molecular docking. Quantum-chemical descriptors allowed to select the molecules with the best physicochemical properties and lowest toxicity. A high-quality three-dimensional structure of NADH-FUM reductase was obtained by homology modeling. Water molecules do not have influence in the interaction between FUM and NADH-FUM reductase. The main hydrogen-binding interactions for FUM were identified in NADH, Lys172, and Arg89; while hydrophobic interactions in Phe479, Thr174, Met63. The molecules S3-8, S2-8, and S1-8 could be inhibitors of NADH-FUM reductase.

The uploaded data contains (i) "01_Data"optimized molecular structure in XYZ format and theprimary attributes and SMILES, (ii)"02_Datasets" datasets used in the publication, and (iv) "03_pynb_script" a Jupyter-Notebook. The01_Data directory contains more than 8000 subdirectories. Each is for a molecule that undergoes a two-proton two-electron transfer reaction. In each subdirectory, one finds the following files: (1) directories named corresponding to the ones in Figure 1 of the paper. Inside each, there are geometries and properties in XYZ and CSV format, respectively. (2) "freeEnergy.dat"contains the free energy of different states. (3) "schemesquare.dat" hasthe parameters of the electrochemical scheme of square representation. ├── A │├── info.csv │└── pos.xyz ├── A1- │├── info.csv │└── pos.xyz ├── A2- │├── info.csv │└── pos.xyz ├── AH │├── info.csv │└── pos.xyz ├── AH1+ │├── info.csv │└── pos.xyz ├── AH1- │├── info.csv │└── pos.xyz ├── AH2 │├── info.csv │└── pos.xyz ├── AH21+ │├── info.csv │└── pos.xyz ├── AH22+ │├── info.csv │└── pos.xyz ├── freeEnergy.dat └── schemesquare.dat &nbsp

Epidermal growth factor receptor (EGFR) is a prominent target for anticancer therapy due to its role in activating several cell signaling cascades. Clinically approved EGFR inhibitors are reported to show treatment resistance and toxicity, this study, therefore, investigates Moringa oleifera phytochemicals to find potent and safe anti-EGFR compounds. For that, phytochemicals were screened based on drug-likeness and molecular docking analysis followed by molecular dynamics simulation, density functional theory analysis and ADMET analysis to identify the effective inhibitors of EGFR tyrosine kinase (EGFR-TK) domain. Known EGFR-TK inhibitors (1-4 generations) were used as control. Among 146 phytochemicals, 136 compounds showed drug-likeness, of which Delta 7-Avenasterol was the most potential EGFR-TK inhibitor with a binding energy of −9.2 kcal/mol followed by 24-Methylenecholesterol (–9.1 kcal/mol), Campesterol (–9.0 kcal/mol) and Ellagic acid (–9.0 kcal/mol). In comparison, the highest binding affinity from control drugs was displayed by Rociletinib (–9.0 kcal/mol). The molecular dynamics simulation (100 ns) exhibited the structural stability of native EGFR-TK and protein-inhibitor complexes. Further, MM/PBSA computed the binding free energies of protein complex with Delta 7-Avenasterol, 24-Methylenecholesterol, Campesterol and Ellagic acid as −154.559 ± 18.591 kJ/mol, −139.176 ± 19.236 kJ/mol, −136.212 ± 17.598 kJ/mol and −139.513 ± 23.832 kJ/mol, respectively. Non-polar interactions were the major contributors to these energies. The density functional theory analysis also established the stability of these inhibitor compounds. ADMET analysis depicted acceptable outcomes for all top phytochemicals without displaying any toxicity. In conclusion, this report has identified promising EGFR-TK inhibitors to treat several cancers that can be further investigated through laboratory and clinical tests.

Considering as test case a family of organic rod like push-pull molecules, we derived and applied density based index enabling the description and diagnostic of the electronic density evolution in real time-time dependent density functional theory (RT-TDDFT) simulations. In particular, both the charge transfer (CT) distance and a diagnostic index, the D

Iron(II) porphyrins play critical roles in enzymes and synthetic catalysts. Computationally determining the spin-state ordering for even the unsubstituted iron(II) porphyrin (FeP) is challenging due to its large size. Multiconfiguration pair-density functional theory (MC-PDFT), a method capable of accurately capturing correlation with lower cost than comparably accurate methods, was previously used to predict a triplet ground state for FeP across a wide range of active spaces up to (34e, 35o). The purpose of this present MC-PDFT study is to determine the effects of including nonlocal exchange in the energy calculation and of using a larger active space size [DMRG(40e, 42o) and RAS(40, 2, 2; 16, 6, 20)] on the calculated FeP spin-state ordering. The recently developed hybrid MC-PDFT method, which uses a weighted average of the MC-PDFT energy and the energy expectation value of the reference wave function, is applied with a weight of the reference wave function energy of λ. We find that increasing λ stabilizes the quintet relative to the triplets. The hybrid tPBE0 functional (tPBE with λ set to 0.25) consistently predicts a triplet ground state with the quintet lying above by 0.10-0.16 eV, depending on the reference wave function. These values are particularly interesting in light of tPBE0's very strong performance for a diverse set of other systems.

An improved understanding of the P450 structure is relevant to the development of biomimetic catalysts and inhibitors for controlled CH-bond activation, an outstanding challenge of synthetic chemistry. Motivated by the experimental findings of an unusually short Fe-S bond of 2.18 Å for the wild-type (WT) OleT P450 decarboxylase relative to a cysteine pocket mutant form (A369P), a computational model that captures the effect of the thiolate axial ligand on the iron-sulfur distance is presented. With the computational efficiency and streamlined analysis in mind, this model combines a cluster representation of the enzyme─40-110 atoms, depending on the heme and ligand truncation level─with a density functional theory (DFT) description of the electronic structure (ES) and is calibrated against the experimental data. The optimized Fe-S distances show a difference of 0.25 Å between the low and high spin states, in agreement with the crystallographic structures of the OleT WT and mutant forms. We speculate that this difference is attributable to the packing of the ligand; the mutant is bulkier due to an alanine-to-proline replacement, meaning that it is excluded from the energetically favored low-spin minimum because of steric constraints. The presence of pure spin-state pairs and the intersection of the low/high spin states for the enzyme model is indicative of the limitations of single-reference ES methods in such systems and emphasizes the significance of using the proper state when modeling the hydrogen atom transfer (HAT) reaction catalyzed by OleT. At the same time, the correct characterization of both the short and long Fe-S bonds within a small DFT-based model of 42 atoms paves the way for quantum dynamics modeling of the HAT step, which initiates the OleT decarboxylation reaction.

The transformations of CO2 molecules into valuable products are of increasing interest due to the negative impact of anthropogenic CO2 emissions on global warming. The CO2-to-methanol hydrogenation is an economically profitable reaction of carbon fixation, but it still steps away from widespread industrialization because of the lack of efficient and selective catalysts. Recently, single-atom alloy (SAA) catalysts have been developed to work remarkably in CO2 hydrogenation reactions. Doping isolated single atoms into metallic catalyst can dramatically alter the catalytic performance of the host. We have performed a screening discovery on Ru and 6 RuX (X = Fe, Co, Ni, Cu, Ir and Pt) SAAs using density functional theory (DFT) computations. We considered 13 possible elementary reactions in 4 possible reaction pathways on Ru and all RuX surfaces. In the computed mechanisms, we found that the formation of *H2COOH and *HCOO intermediates plays a critical role in determining catalysts’ activities. Doping Co and Pt isolated single atoms into Ru surface can thermodynamically and kinetically facilitate these intermediates formation processes, eventually promoting the production of methanol. The combination of weak binding and enhanced charge redistribution on RuCo and RuPt surfaces give them improved catalytic activities over pure Ru. This work will ultimately facilitate the discovery and development of SAAs for CO2 to methanol, serving as guidance to experiments and theoreticians alike.

Hypothesis The interactions of organic molecules with mineral surfaces are influenced by several factors such as adsorbate speciation, surface atomic and electronic structure, and environmental conditions. When coupled with thermodynamic techniques, energetics from atomistic modeling can provide a molecular-level picture of which factors determine reactivity. This is paramount for evaluating the chemical processes which control the fate of these species in the environment. Experiments Inner-sphere adsorption of oxalate and pyrocatechol on (001), (110), and (012) α-Fe2O3 surfaces was modeled using Density Functional Theory (DFT). Unique bidentate binding modes were sampled along each facet to study how different adsorbate and surface factors govern site preference. Adsorption energetics were then calculated using a DFT + thermodynamics approach which combines DFT energies with tabulated data and Nernst-based corrective terms to incorporate different experimental parameters. Findings Instead of a universal trend, each facet displays a unique factor that dominates site preference based on either strain (001), functional groups (110), or topography (012). Adsorption energies predict favorable inner-sphere adsorption for both molecules but opposite energetic trends with varying pH. Additionally, vibrational analysis was conducted for each system and compared to experimental IR data. The work presented here provides an effective, computational methodology to study numerous adsorption processes occurring at the surface-aqueous interface.

This paper describes the spectroscopic (FT-IR and UV–Visible), electronic, structural, vibrational properties of celecoxib compound using density functional theory. The optimized geometry structure of the titled molecule is explained by the method of B3LYP with 6–31 + G (d, p) basis set. We found that the simulated optimized geometry of the titled molecule is simulated to the experimental ones. The infrared spectrum of celecoxib compound is represented in the present work. The computational information about the organic molecule can be explained by the charge transfer properties, which is a computational tool for the precise quantum chemical calculations of space charge density distribution and HOMO-LUMO states. The transition states of celecoxib compound have explained by the time-dependent density functional theory (TD-DFT) which is observed by the UV–visible spectrum. Docking research [1] is a modeling method, with the help of docking method we can find out new drug and chemical behavior of the drug which is useful in the application purpose of the drug, the interaction between protein and legends provides the information of the binding energy and physical parameter like partition function, free energy, internal energy, entropy.

Recently, G-quadruplexes (Gq) formed in B-DNA as secondary structures are found important therapeutic targets as well as material for developing nanodevices. Gq are guanine-rich and thus susceptible to oxidative damage by producing short-lived intermediate radicals via proton transfer reactions. Understanding the mechanisms of radical formation in Gq is of fundamental interest to understand the early stages of DNA damage. Herein, we used density functional theory including aqueous phase (ωB97XD-PCM/6–31++G**) and considered single layer of Gq (G-quartets (G4): association of four guanines in a cyclic Hoogsteen hydrogen-bonded arrangement (Scheme 1)) to unravel the mechanisms of formation of intermediates by calculating the relative Gibbs free energies and spin density distributions of one-electron oxidized G4 and its various proton transfer states: G(•+), G(N(1)-H)(•), G(N(2)-H′)(•), G(N(2)-H″)(•), G(N(1)-H)(•)-(H(+)O(6))G and G(N(2)-H)(•)-(H(+)N(7))G. The present calculation predicts the formation G(N(2)-H)(•)-(H(+)N(7))G which is only ca. 0.8 kcal/mol higher in energy than the initially formed G(•+). The formation of G(N(2)-H)(•)-(H(+)N(7))G plays a key role role in explaining the formation of 8-OG along with G(N(1)-H)(•) formation via tautomerization from G(N(2)-H)(•) as proposed recently.

Selective conversion of lignocellulosic biomass-derived chemicals is of critical significance for sustainable fine and commodity chemical industries. Cellulose-derived levoglucosenone (LGO) has a promising potential for producing 5-hydroxymethylfurfural (HMF) with a substantial yield under acid conditions, but the mechanism is unidentified. Herein, we disclose the mechanism of LGO conversion to HMF in the aqueous phase without and with H

Recent efforts towards developing novel lead electrodes involving carbon and lead composites have shown potential for increasing the cycle life of lead–acid (LA) batteries used to store energy in various applications. In this study, first-principles calculations are used to examine the structural stability, defect formation energy, and migration barrier of C in Pb for LA batteries. Density functional theory with the GGA-PBE functional performed the best out of various functionals used for structural stability calculations. Furthermore, with the complete incorporation of C in the Pb matrix, the results show that C is energetically preferred to be at the octahedral interstitial (CiOcta) site in the FCC structure of Pb. Additionally, climbing-image nudged elastic band calculations show a minimum energy pathway for C diffusing from a stable octahedral site to the adjacent octahedral site assisted by a tetrahedral intermediate site. Therefore, the minimum energy pathway for C migration is envisioned to be CiOcta→CiTetra→CiOcta, where the total energy barrier is observed to be ~90% and more than 100% lower than the CiTetra→CiTetra and CiOcta→CiOcta barriers, respectively.

Na0.5(Bi3/4RE1/4)0.5TiO3 (RENBT, RE = Nd, Gd, Dy, and Ho) compounds were investigated in the framework of first-principles calculations using the full potential linearized augmented plane wave (FP-LAPW) method based on the spin-polarized density functional theory implemented in the WIEN2k code. Combined charge density distribution and Ti K-edge X-ray absorption spectra revealed that the RENBT compositions with high polarization values were accompanied by a higher TiO6 distortion, DyNBT, and NdNBT compounds. The effect of the rare-earth elements on the polarization were confirmed experimentally with the collection of the hysteresis loops. The investigation of the electronic properties of the compounds highlighted the emergence of a magnetization owing to the 4f orbital effect of the rare-earth elements. Besides, the investigation of the chemical ordering showed a short-range chemical ordering for the pure composition and an increased A-site disorder for dysprosium doped NBT system. The increased disorder may speak for increased relaxor properties in the RE doped compositions.

In this paper, utilization of density functional theory (DFT) to obtain mechanical, electrical and thermal properties of crystalline materials are reviewed. DFT has resulted as an efficient tool for predicting ground states of many body systems thus aiding in resolving dispersion spectrums of complex atomic arrangements where solution by traditional Schr dinger (SH) equation is infeasible. Great success has been reported by previous researchers on utilizing DFT for functional property predictions of crystalline solids.

Single-atom catalysis is the new frontier of heterogeneous catalysis, and have attracted considerable attention for they exhibit great potential in hydrogen evolution to mitigate energy crisis and environmental issues. The support materials of single-atom catalysts (SACs) play a significant role in stabilizing the metal atoms, preventing their aggregation, and enhancing the catalytic activity. Two-dimensional sp2 hybridized PHE-graphene might be a real support for SACs due to the potential energy well induced by its enneagon, hexgon and pentagon carbon rings. In this study, eleven transitional metal (TM) atoms adsorbed on the PHE-graphene (TM@PHEs) are taken into account based on density functional theory (DFT) and the PHE-graphene is proved to be an ideal single-atom carrier for water splitting. In particular, the TM@PHEs (TM= Fe, Ni, Ru, and Pd) exhibit high catalytic activity toward hydrogen evolution reaction (HER). The reaction path of water splitting is also determined. Due to much lower energy barrier, both Fe@PHE and Ru@PHE are more promising SACs. In addition, the charge density difference, Bader charge analysis and spin projected density of states (PDOS) are investigated.

Benzimidazole derivatives, especially 2-phenylbenzimidazole with various substituents on the C-5, C-2 and C-6 positions, are so important in pharmaceutical chemistry. Multiple linear regression was applied to predict the activity of 27 novel 2-phenylbenzimidazole derivatives as anticancer agents. At first, we made an effort to create a QSAR model for a selected series of novel 2-phenylbenzimidazole with density functional theory and molecular docking descriptors. Then, we tried to investigate the nature of the interactions between 2-phenylbenzimidazole derivatives and the estrogen receptor using the molecular docking method. Six descriptors of MATS4e, GATS5e, R6v, R1v+, dipole moment, and torsional free energy were selected for modelling. Due to docking results, increase in the binding energy, and decrease in the dipole moment could increase inhibitor activity.

The sorption-enhanced water-gas shift (SE-WGS) reaction promoted by Ni-doped CaO (Ni-CaO) was sufficiently investigated by experiments that only displayed macroscopic results instead of microscopic reaction mechanisms. In this work, density functional theory (DFT) was employed to clarify the mechanisms of SE-WGS reaction which was catalyzed by Ni in the presence of CaO. The SE-WGS reaction only promoted by CaO was used as a comparison to clarify the catalysis of Ni. The analysis of electron differential densities, the partial density of states, and formation energy indicate that Ni causes the higher stability and reactivity of the Ni-CaO model than the CaO model. The Ni promotes the release of H2* by rising the adsorption energy of H2* (-0.05 eV) and retains the efficient CO2 capture with the adsorption energy of -1.56 eV. The transient state calculations indicate the SE-WGS reaction prefers to proceed along with the redox mechanism compared with the carboxyl and formate mechanisms on the Ni-CaO surface. The energy barriers for the CO2* generation, H2* generation and desorption are respectively 0.74, 1.77 and 0.10 eV on the Ni-CaO surface, which are lower than those on the CaO surface. Therefore, Ni helps to improve CO conversion and H2 productivity which is consistent with the previous experimental results.

Density Functional Theory calculations are used to study adsorption of carbon monoxide gas on transition metal doped armchair graphene nanoribbon. Sensing behaviour of pristine armchair graphene nanoribbon (Pr-AGNR) and different geometries of osmium doped AGNR such as one-edge doped AGNR, center doped AGNR and both-edge doped AGNR have been investigated. Most stable adsorption geometry, adsorption energy, binding distance, band structure and density of states of different geometries using in our work have been discussed. Electronic properties of different sensing materials can be interpreted in terms of band structure and density of states. It was studied that a weak type of physical adsorption process took place when CO molecule interacts with pristine AGNR with a very small amount of adsorption energy of amount −0.22 eV. This suggests that pristine graphene is not a good adsorber for CO adsorption. In contrast, doping of graphene with osmium atom enhances the adsorption energy of Pr-AGNR to greater extent. Computational results concluded that osmium doping in graphene nanoribbon at one-edge and both-edge position increases the adsorption energies with values −6.77 eV and −9.53 eV respectively which is 30 times and 43 times greater than in comparison to Pr-AGNR. Energy gap calculations proves that large band gap variations are observed for both-edge doped graphene nanoribbon. Sharp and intense peaks at various energy levels from density of states analysis of both-edge doped geometry confirms adsorption of CO. Our results predicts that both-edge osmium doped sensing material can be considered as promising sensing material for CO adsorption.

In this paper, the effects of the sulfur vacancy (VS) distribution in 2H–MoS2 monolayer on the H2 evolution mechanism and activity are researched by density functional theory (DFT) calculations. The calculation results reveal that the H2 generation on VS follows the Volmer-Heyrovsky mechanism with the Heyrovsky reaction as the rate determined step (RDS) with an energy barrier of 18.5 kcal/mol. When two VS are separated by one S atom, the H2 evolution on VS remains the Heyrovsky-step-determined Volmer-Heyrovsky mechanism and the RDS energy barrier increases to 20.0 kcal/mol. Removing adjacent S of VS causes that the Tafel-step-determined Volmer-Tafel mechanism works for HER and the barrier of RDS increases to 21.4 kcal/mol. Though the barriers of RDS ascend when the concentration of VS is enhanced by these two strategies, the Tafel step can take place at a lower potential and more VS are exposed. Therefore, two adjacent or next-near VS may obtain better H2 generation performance. Three adjacent or spaced out VS by one S may be less favorable for HER.

The impact of external fields on the molecular structure and reactivity properties has been of considerable interest in the recent literature. Benzoic acid as one of the most widely used compounds in medicinal and materials sciences is known for its dual propensity in aromaticity and acidity. In this work, we systematically investigate the impact of a uniform external electric field on these properties. We apply density functional theory, conceptual density functional theory, and an information-theoretic approach to appreciate the change pattern of aromaticity and acidity properties in external fields with different strengths. Our results show that they possess different change patterns under external fields, which can be satisfactorily rationalized by variations in reactivity descriptors and partial charges. The surprising yet novel results from this study should enrich the body of our knowledge about the impact of external fields for different kinds of electronic properties and provide guidance and foundation for future studies of this phenomenon in other molecular systems.

The valence electronic structures of two dinuclear alkyl compounds containing sigma(2)pi(4) triple bonds between group 6 metals, viz., M-2(CH2CMe3)(6) (M = Mo, W), have been investigated using a combination of molecular orbital theory and variable photon energy photoelectron spectroscopy (PES). Density functional theory (DFT) calculations using PBEO-dDsC functionals, which include dispersion forces, have been performed on the title compounds as well as several closely related M2X6 (M = Mo, W) compounds. The DFT calculations on the dinuclear neopentyl complexes are in excellent agreement with the solid-state structures, measured PES spectra, and ultraviolet-visible (UV-vis) spectra. The top nine filled orbitals in both cases are associated with M-M and M-C bonding. The orbital energy pattern conforms to that anticipated for a D-3d (staggered) M2C6 skeleton. For both Mo and W, the highest-energy pair of orbitals are of e(u) (pi) symmetry, followed by one of a(1g) (sigma) symmetry, and comprise the metal-metal triple bond. The orbital energies are higher for W than for Mo, and the separation between the pi and sigma orbitals is greater for W, reflecting a greater relativistic stabilization of the tungsten 6s orbital compared to that of the Mo 5s orbital. The spin-orbit splitting in the pi ionization of W-2(CH2CMe3)(6) has been resolved and successfully modeled. A graphical comparison of valence orbital energies for Mo2X6, where X = CH2CMe3, NMe2, and OCH2CMe3, shows how the Mo-Mo pi and sigma levels vary as a function of the ligand set.

The structural confirmation of the 1-(4-Bromophenyl)-3-(2-chloro-6-fluorophenyl) prop-2-en-1-one compound is done by experimental techniques. Experimental techniques FTIR, proton NMR, UV-Visible, performed for the compound. The experimentally obtained results are compared with density functional theory obtained results. The decomposition and melting point of the compound is obtained by TGA & DTA. Density functional theory is performed for the 1-(4-Bromophenyl)-3-(2- chloro-6-fluorophenyl) prop-2-en-1-one compound B3LYP/6-311G++(d,p) basis set. Time dependent density functional theory calculated for three different methods B3LYP, Hartree-Fock and CAMB3LYP also employed for the 2C6FBC at 6-311G++(d,p) basis set. Keywords: DFT Study, HOMO-LUMO, FTIR, 1H NMR, TGA/DTA, chalcone

The spectroscopic data for a range of cyclopenta-[d][1,2,3]-triazine derivative dyes have been evaluated using various standard computational approaches. Absorption data of these dyes were obtained using the ZINDO/S semi-empirical model for vertical excitation energies of structures optimised with the AM1, PM3, and PM6 methods. These studies were conducted under vacuum and solution states using the polarisation continuum model (PCM) for implicit solvation in the linear response model. The accuracy, along with the modest computational costs of using the ZINDO/S prediction, combined with the PM3 optimisation method for absorption data was reliable. While a higher computational cost is required for the time-dependent density functional theory (TDDFT), this method offers a reliable method for calculating both the absorption and emission data for the dyes studied (using vertical and adiabatic excitation energies, respectively) via state-specific solvation. This research demonstrates the potential of computational approaches utilising solvation in evaluating the spectroscopic properties of dyes in the rational design of fluorescent probes.

Icotinib is an epidermal growth factor receptor tyrosine kinase inhibitor used in the treatment of non-small cell lung cancer. The charge transfer effect between gold nanoparticles (AuNPs) and icotinib molecules can be used as a model to study the adsorption mechanism between molecules and metal. The adsorption of icotinib on the AuNP surface was confirmed by UV-vis and transmission electron microscopy (TEM) experiments. To explain the nature of chemisorption between icotinib and AuNPs from a theoretical perspective, the molecular correlation properties of the complex model of icotinib-Au6 were studied by the density functional theory method. By studying the molecular electrostatic potential of an icotinib molecule, four potential binding sites of the icotinib molecule were predicted. The calculation results of binding energy showed that the complex formed by chemisorption of icotinib through acetylene group and Au6 was the most stable one. The molecular frontier orbitals of icotinib and icotinib-Au6 confirmed that the charge transfer effect occurred on the acetylene group, benzene ring, and quinazoline ring of the icotinib molecule. The Herzberg-Teller surface selection rule was used to explain selective enhancement in the theoretically calculated Raman spectra. By comparing the spectra of theory and experiment, the cause of spectral peak shift and broadening that appeared in the surface-enhanced Raman scattering spectrum compared with the normal Raman spectrum was explained as well. This work would contribute to the development and application of the icotinib-Au drug carrier system.

The formation and migration of polarons have important influences on physical and chemical properties of transition metal oxides. Density functional theory plus the Hubbard U correction (DFT+U) and constrained density functional theory (cDFT) are often used to obtain the transfer properties for small polarons. In this work we have implemented the cDFT plus the Hubbard U correction method in the projector augmented wave (PAW) framework, and applied it to study polaron transfer in the bulk phases of TiO2. We have confirmed that the parameter U can have significant impact on theoretical prediction of polaronic properties. It was found that using the Hubbard U calculated by the cDFT method with the same orbital projection as used in DFT+U, one can obtain theoretical prediction of polaronic properties of rutile and anatase phases of TiO2 in good agreement with experiment. This work indicates that the cDFT+U method with consistently evaluated U is a promising first-principles approach to polaronic properties of transition metal oxides without empirical input.

Conventional active coolers including water heat pumps and air conditioning have moving components that can cause mechanical failure and fatigue over time. They cannot be down-scaled to micron sizes and cannot be integrated into on-chip small-scale designs. Thermomagnetic and thermoelectric cooling systems emerged as an alternative to conventional active cooling systems. Thermomagnetic cooling systems are based on the Nernst- Ettingshausen effect that was observed in Bismuth for the first time. In the presence of an electric current and a perpendicular magnetic field, electrons and holes are pushed to opposite sides due to the Lorentz force. The migration of charge carriers develops a temperature gradient across the material, perpendicular to both electric current and magnetic field. Hence, heat can be pumped across the sample, this is the basis of Ettingshausen coolers. Similarly, applying a magnetic field perpendicular to a temperature gradient generates a transverse voltage difference, the so-called Nernst Voltage. The primary objective of this dissertation is to develop a code to calculate the response of a system to the simultaneous presence of a magnetic field and a temperature gradient using first-principles density functional theory. First, I obtained the Nernst coefficient within constant relaxation time approximation to establish an insight into the Nernst effect and how it is related to the details of the band-structure. The aforementioned method is, however, unable to reconstruct the experimentally measured values as the Nernst coefficient is sensitive to the details of the relaxation times and in particular, it is proportional to the carrier mobility. Therefore, I implement the charge carrier relaxation time due to various scattering mechanisms including electron-phonon and electron-ionized impurity scattering in our theory. Experimental data of germanium, silicon, indium antimonide, and bismuth in a wide range of temperatures and doping concentrations were successfully reproduced. Furthermore, with the help of analytical models, I obtained a simplified model for the Nernst coefficient in order to find the material descriptors to predict the Nernst coefficient which turned out to be effective mass. Lastly, I propose an approach to evaluate anomalous Nernst transport within the density functional theory framework. The semi-classical Boltzmann transport was modified by adding the effect of Berry curvature. Once the formalism was completed, the approach was implemented on the basis set of maximally localized Wannier functions and applied to Fe3Sn to replicate the experimental data.

The covalent grafting of alkyl gallates onto pectin using a lipase-catalyzed reaction in a tetrahydrofuran/aqueous medium process acylated pectin molecules with excellent antioxidant and antibacterial properties. The alkyl gallates including methyl, ethyl, and propyl gallates were enzymatically grafted onto pectin molecule, in order to study the effect of alkyl gallates on the functional modification of pectin. The grafting mechanism was analyzed by ultraviolet-visible spectrum (UV-Vis), Fourier transform infrared spectrum (FTIR), proton nuclear magnetic resonance (

Theoretical and experimental investigations on the molecular structure of 2-amino-5-chloro-3-nitropyridine (2A5Cl3NP) are presented. The molecular equilibrium geometry of the title molecule is fully optimized. Quantum chemical calculations of the HOMO-LUMO energies, energy gap (ΔE), electron negativity (χ), and chemical potential (μ), global hardness (ƞ), and global softness (S) are calculated for the title molecule. The title compound has a low softness value (0.2770) and the calculated value of electrophilicity index (7.7250) describes the biological activity. The stability and charge delocalization of the title molecule are studied by Natural Bond Orbital Analysis (NBO), Non-Linear Optical (NLO) behaviour in terms of first order hyperpolarizability, dipole moment, anisotropy of polarizability are accounted. The computed values of dipole moment (μ) for 2A5Cl3NP molecule is 3.0173 Debye, polarizability (α) is 1.6017 × 10–23esu, hyperpolarizability (β) is 5.08173 × 10–30esu. The high β value and non-zero value of μ indicate that the title compound might be a good candidate for NLO material. The strength of the interaction between electron donors and electron acceptors is measured by the magnitude of energy of hyper conjugative interactions E (2). The second-order Fock matrix is calculated to study the donor–acceptor interactions in NBO analysis.

Structural variations of lead halide perovskites (LHPs) upon light illumination play an important role in their photovoltaic applications. However, density functional theory (DFT)-based simulations have often been performed to unveil the nature of defects in LHPs without light illumination. So far, the nature of traps in LHPs triggered by the light remains largely unexplored. In this work, hole traps induced by the halogen interstitial in LHPs are studied by combining DFT and time-dependent DFT approaches, the latter of which treats electron-hole and electron-nuclei interactions on the same footing. Both a semilocal exchange functional and hybrid functional are adopted to relax the ground-state and excited-state geometries followed by the calculations of energy levels of hole traps. The effect of the self-interaction corrections on the light-triggered geometric deformation and the electronic structure of hole traps is analyzed. Relaxation energies that correspond to the light-triggered geometric deformation are also calculated with different functionals. The relationship between the hole traps and light-triggered geometric variations are then explored.

Nanoporous carbons (NPCs) are ideal materials for the dry process of flue gas desulfurization (FGD) due to their rich pore structure and high specific surface area. To study the effect of edge-functionalized NPCs on the physisorption mechanism of sulfur dioxide, different functional groups were embedded at the edge of NPCs, and the physisorption behavior was simulated using the grand canonical Monte Carlo method (GCMC) combined with density functional theory (DFT). The results indicated that the insertion of acidic oxygenous groups or basic nitrogenous groups into NPCs could enhance the physisorption of SO2. The influence of edge functionalization on the pore structure of NPCs is also analyzed. To further explore the interaction in the adsorption process, the van der Waals (vdW) interaction and electrostatic interaction between the SO2 molecule and the basic structural unit (BSU) were investigated. Simulated results showed that edge functionalization had limited influence on vdW interaction and did not significantly change the distribution characteristics of vdW interaction. According to the study on electrostatic interaction, edge functionalization was found to promote inhomogeneity of the surface charge of the adsorbent, enhance the polarity of the adsorbent, and thus enhance the physisorption capacity of SO2. More importantly, we provide an idea for studying the difference in adsorption capacity caused by different functional groups connected to carbon adsorbents.

Perylene and its derivatives are some of the promising organic semiconductors. They have found vast applications in many areas such as photovoltaic systems, organic light-emitting diodes, and so on. The instability of organic molecules under ambient conditions is one factor deterring the commercialization of organic semiconductor devices. Currently, most of the investigation of Perylene and its derivatives concentrated on its diimide and bisimide derivatives. In this work, an investigation of the effects of doping Bromine and Fluorine on the electronic and non-linear optical properties was carried out based on Density Functional Theory (DFT) as implemented in the Gaussian 09 software package. We computed the Molecular geometries of the molecules, HOMO-LUMO energy gap, global chemical indices and non-linear optical properties using the same method. The bond lengths and angles of the mono-halogenated molecules at different charge states were found to be less than that of the isolated Perylene. 1-fluoroperylene was found to be the most stable amongst the studied molecule for having the least bond angles and bond lengths. In the calculation of the energy bandgap neutral 1-fluoroperylene was observed to have the highest energy gap 3.0414 eV and 3.0507 eV for 6-31++G(d,p) and 6-311++G(d,p) basis sets respectively. These results were found to agree with the existing literature. This reconfirmed 1-fluoroperylene as the most stable molecule. The computations of the ionic molecules reported small values of the energy gap. The molecule with the most chemical hardness was obtained to be the neutral 1-fluoroperylene with a chemical hardness of 1.5253eV. All the ionic molecules results were found to be more reactive than their neutral form for having lower values of chemical hardness. For NLO calculations, the results showed an increment in their values with the ionic hybrid molecules having the largest values. In the case of first-order hyper-polarizability, 1-bromoperylene (neutral), 1-fluoroperylene (neutral), 1-bromoperylene (anionic), 1-fluoroperylene (anionic), 1-bromoperylene (cationic) and 1-fluoroperylene (cationic) were found to be 73.93%, 1.71%, 83.9%, 39.2%,38.7% and 41.7% larger than that of Urea respectively. These calculated results make these hybrid molecules suitable for a wide range of optoelectronic applications.

The adsorption mechanism of xenon on three noble metal clusters (M = Ag, Au, and Cu) has been investigated in the framework of density functional theory (DFT) within generalized gradient approximation (GGA-PBE). The ab initio calculations were performed with the quantum molecular dynamics (QMD) package ABINIT using the projector augmented (PAW) formalism. The spin–orbit coupling (SOC) and dispersion effects (Van der Waals DFT-D3) have been taken into account. According to these calculations, the M–Xe bonds are partly covalent and electrostatic and their contribution depends on the cluster size and nature. This study underlines the importance of using the SOC and the Van der Waals (VdW) effects. Based on these results, copper nanoparticles have the highest affinity for interaction with xenon compared with silver and gold.

Thanks to its advantages, 19 F-NMR is an increasingly popular technique for the structural characterization of F-containing molecules, among which polymers, materials, fluorophores, pharmaceuticals, and so forth. However, the computational calculation of the 19 F-NMR chemical shifts, both for prediction and interpretation of experimental spectra, remains a challenge. In this work a density functional theory (DFT) based protocol for the calculation of the chemical shifts is established within the framework of the gauge-independent atomic orbital method, upon verifying the performance of Hartree-Fock and 60 DFT functionals coupled with seven different basis sets. The benchmark is conducted using two sets of molecules, namely one used for testing methods and another used for probing; the former set consists of 134 molecules, the latter 50, yet both of them with F in different chemical environments. Following Bally-Rablen-Tantillo strategy, the scaling parameters and other statistical quantities were computed for each method upon least squares linear regression between experimental and computed chemical shifts. The designed computational workflow is computationally inexpensive and represents a significant improvement with respect to the current state of the art.

A density functional theory method was employed to investigate the mechanism of C-O bond activation of butanoic acid substrates bearing the 8-aminoquinoline (AQ) group catalyzed by Pd(OAc)2. The whole reaction consists of five fundamental steps: the chelation of substrate A1, the C-H activation step, the C-N coupling step, the protodepalladation step, and the release of the final product. The calculated results indicated that the protodepalladation step is the rate-determining step with a free energy barrier of 24.3 kcal/mol. This theoretical study pointed out that the energy barriers of C-H activation in the presence and absence of AQ are 11.3 and 26.6 kcal/mol, respectively. This is to say that the installation of the AQ directing group is critical to the regioselectivity of C-H activation and the β-O elimination steps, and this reason enables selective activation of the γ C-O bond. Furthermore, this chelating functionality facilitated the protodepalladation step because the energy barrier of the protodepalladation step was decreased with the coordination of the AQ directing group with a Pd center, and that was 39.3 kcal/mol in the absence of AQ. This also explains why no product formation was observed in the experiment upon changing the directing AQ group to a phenylamino group. Finally, other substrates bearing the phenol leaving group at the β- and δ-positions of carbonyl were investigated in order to expand the applicability of the AQ directing strategy. This work could provide new theoretical insights into the activation of strong alkyl C(sp3) covalent bonds via the AQ directing strategy.

A density functional theory (DFT) computation on oxygen species adsorbed on platinum (Pt) catalyst surfaces has been carried out to elucidate oxygen isotope fractionation observed at the cathode of a polymer electrolyte membrane fuel cell (PEMFC). The Pt(111) catalyst surface was modelled by a Pt19 cluster, and O, OH, OHH, OO, OOH, OHOH and HOHOH were assumed to be the oxygen species adsorbed on the Pt(111) surface. The oxygen isotope reduced partition function ratios (RPFRs) of the adsorbed species were calculated using the vibrational frequencies obtained by normal mode analyses performed on the optimized structures. Various oxygen isotope exchange equilibria among the adsorbed oxygen species and oxygen and water molecules in the gas phase were examined using their RPFRs. Experimental observation that the lighter 16O is enriched in water molecules exhausted from the cathode is explainable in a satisfactory manner by assuming oxygen isotope exchange equilibria of O2 molecule with O, OH, OO and OOH adsorbed on the Pt(111) surface that appear in the first half of the conversion reaction from O2 to H2O and those of H2O molecule with the adsorbed oxygen species, OHH, OHOH and HOHOH, formed in the latter half of the conversion reaction.

Direct dynamics simulations of chemical reactions typically require the selection of a method for generating the potential energy surfaces and a method for the dynamical propagation of the nuclei on these surfaces. The nuclear-electronic orbital (NEO) framework avoids this Born-Oppenheimer separation by treating specified nuclei on the same level as the electrons with wave function methods or density functional theory (DFT). The NEO approach is particularly applicable to proton, hydride, and proton-coupled electron transfer reactions, where the transferring proton(s) and all electrons are treated quantum mechanically. In this manner, the zero-point energy, density delocalization, and anharmonicity of the transferring protons are inherently and efficiently included in the energies, optimized geometries, and dynamics.This Account describes how various NEO methods can be used for direct dynamics simulations on electron-proton vibronic surfaces. The strengths and limitations of these approaches are discussed, and illustrative examples are presented. The NEO-DFT method can be used to simulate chemical reactions on the ground state vibronic surface, as illustrated by the application to hydride transfer in C4H9+. The NEO multistate DFT (NEO-MSDFT) method is useful for simulating ground state reactions in which the proton density becomes bilobal during the dynamics, a characteristic of hydrogen tunneling, as illustrated by proton transfer in malonaldehyde. The NEO time-dependent DFT (NEO-TDDFT) method produces excited electronic, vibrational, and vibronic surfaces. The application of linear-response NEO-TDDFT to H2 and H3+, as well as the partially and fully deuterated counterparts, shows that this approach produces accurate fundamental vibrational excitation energies when all nuclei and all electrons are treated quantum mechanically. Moreover, when only specified nuclei are treated quantum mechanically, this approach can be used to optimize geometries on excited state vibronic surfaces, as illustrated by photoinduced single and double proton transfer systems, and to conduct adiabatic dynamics on these surfaces. The real-time NEO-TDDFT method provides an alternative approach for simulating nonequilibrium nuclear-electronic dynamics of such systems. These various NEO methods can be combined with nonadiabatic dynamics methods such as Ehrenfest and surface hopping dynamics to include the nonadiabatic effects between the quantum and classical subsystems. The real-time NEO-TDDFT Ehrenfest dynamics simulation of excited state intramolecular proton transfer in o-hydroxybenzaldehyde illustrates the power of this type of combined approach. The field of multicomponent quantum chemistry is in the early stages, and the methods discussed herein provide the foundation for a wide range of promising future directions to be explored. An appealing future direction is the expansion of the real-time NEO-TDDFT method to describe the dynamics of all nuclei and electrons on the same level. Direct dynamics simulations using NEO wave function methods such as equation-of-motion coupled cluster or multiconfigurational approaches are also attractive but computationally expensive options. The further development of NEO direct dynamics methods will enable the simulation of the nuclear-electronic dynamics for a vast array of chemical and biological processes that extend beyond the Born-Oppenheimer approximation.