Two-Dimensional MXene as a Promising Adsorbent for Trihalomethanes Removal: A Density-Functional Theory Study

This groundbreaking research delves into the intricate molecular interactions between MXene and trihalomethanes (THs) through a comprehensive theoretical study employing density-functional theory (DFT). Trihalomethanes are common carcinogenic chlorination byproducts found in water sanitation systems. This study focuses on a pristine MXene [Mn+1·Xn] monolayer and its various terminal [Tx] functional groups [Mn+1·XnTx], strategically placed on the surface for enhanced performance. Our investigation involves a detailed analysis of the adsorption energies of THs on different MXene types, with the MXene-Cl layer emerging as the most compatible variant. This specific MXene-Cl layer exhibits remarkable properties, including a total dipole moment (TDM) of 12.443 Debye and a bandgap of 0.570 eV, achieved through meticulous geometry optimization and computational techniques. Notably, THs such as trichloromethane (CHCl3), bromide-chloromethane (CHBrCl2), and dibromochloromethane (CHBr2Cl) demonstrate the highest TDM values, indicating substantial changes in electronic and optical parameters, with TDM values of 16.363, 15.998, and 16.017 Debye, respectively. These findings highlight the potential of the MXene-Cl layer as an effective adsorbent and detector for CHF3, CHClF2, CHCl3, CHBrCl2, and CHBr2Cl. Additionally, we observe a proportional increase in the TDM and bandgap energy, indicative of conductivity, for various termination atom combinations, such as Mxene-O-OH, Mxene-O-F, Mxene-O-Cl, Mxene-OH-F, Mxene-F-Cl, and Mxene-OH-Cl, with bandgap energies measured at 0.734, 0.940, 1.120, 0.835, and 0.927 eV, respectively. Utilizing DFT, we elucidate the adsorption energies of THs on different MXene surfaces. Our results conclusively demonstrate the significant influence of the termination atom nature and quantity on MXene's primitive TDM value. This research contributes to our understanding of MXene-THs interactions, offering promising avenues for the development of efficient adsorbents and detectors for THs. Ultimately, these advancements hold the potential to revolutionize water sanitation practices and enhance environmental safety.

Theoretical and Experimental In-vitro Studies of Novel Thiophene Based Organotellurium(IV) Complexes

Schiff bases are one of the important classes of organic compounds containing imine or azomethine functional groups with potential biological applications in medicinal chemistry. Nowadays, these compounds have attracted the scientific community's attention due to their ability to act as ligands in the formation of stable metal complexes with significant biological activity. In this connection, we have designed and synthesized six novel thiophene-based organoltellurium (IV) complexes using a novel N-((5-methylthiophen-2-yl) methylene)-2-nitroaniline (5MTCONA) schiff base. These complexes underwent analytical investigation (TGA, Powder XRD, SEM, EDAX) as well as spectral analysis (FT-IR, NMR, Mass spectrometry, UV-Vis). The in-vitro pharmacological evaluation of these compounds has been carried out as antimicrobial and antioxidant agents. To further corroborate our findings, we have implemented computational analyses (Semi empirical PM3 method, Molecular Docking, and ADMET) of all the compounds with Spartan-14, Hex-8.0., Swiss ADME software. Precisely, our study integrates experimental and theoretical aspects, offering innovative insights in the field of pharmaceutical sciences.

Exploring the antimalarial and antioxidant efficacy of transition metal(II) chelates of thiosemicarbazone ligands: spectral investigations, molecular docking, DFT, MESP and ADMET

Malaria, a relentless and ancient adversary, continues to cast its shadow over vast swathes of the globe, afflicting millions of people and have a heavy toll on human health and well-being. Despite substantial progress in the fight against this parasitic disease in recent decades, malaria still persists as a substantial global health concern, especially in some specific region which have limited resources and vulnerable populations. Thus, to ascertain an combating agent for malaria and its associated dysfunction, 4-(4-ethylphenyl)-3-thiosemicarbazide and benzaldehydes based two new thiosemicarbazone ligands (1-2) and their cobalt(II), nickel(II), copper(II), zinc(II) metal complexes (3-10) were synthesized in the present research work. The synthesized compounds were comprehensive characterized through spectral and physical investigations, demonstrating octahedral stereochemistry of the complexes. Further, the antimalarial and antioxidant potential of the compounds (1-10) were analyzed by micro assay and DPPH assay protocols, respectively, to examine the therapeutic aspect of the compounds. The performed biological evaluations revealed that the complexes are more efficient in controlling infectious ailment in comparison of ligands. The complexes (5), (6), (10) shows significant efficiency for malarial and oxidant dysfunctions whereas Zn(II) complex (6) exhibit highest potency with 1.02 ± 0.07 and 2.28 ± 0.05 µM IC50 value. Furthermore, to support the highest antimalarial potency of the (3-6) complexes and their associated ligand (1), the computational studies like molecular docking, DFT, MESP and ADMET analysis were executed which were supported the biological efficacy of the complex (6) by providing numerous parameters like binding interaction electronegativity, electrophilicity, HOMO value and electron density.

Quantum chemical studies on the binding domain of SARS-CoV-2 S-protein: human ACE2 interface complex

A two-layer ONIOM(B3LYP/6-31G*:PM7) method is used to model the binding of several drug/drug-like molecules (L) at the SARS-CoV-2 S-protein: human ACE2 protein interface cavity. The selected molecules include a set of thirty-five ligands from the study of Smith and Smith which showed a high docking score in the range of -7.0 to -7.7 kcal/mol and another set of seven repurposing drugs, viz. favipiravir, remdesivir, EIDD, galidesivir, triazavirin, ruxolitinib, and baricitinib. The ONIOM model of the cavity (M) showed a highly polarized electron distribution along its top-to-bottom direction while Ls with lengths in the range 1.0 - 1.5 nm fitted well inside the cavity in a head-to-tail fashion to yield ML complexes. The ligands showed a large variation in the ONIOM-level binding energy (Eb), in the range -2.7 to -85.4 kcal/mol. The Eb of ML complexes better than -40.0 kcal/mol is observed for myricetin, fidarestat, protirelin, m-digallic acid, glucogallin, benserazide hydrochlorideseradie, remdesivir, tazobactum, sapropterin, nitrofurantoin, quinonoid, pyruvic acid calcium isoniazid, and aspartame, and among them the highest Eb -85.4 kcal/mol is observed for myricetin. A hydroxy substitution is suggested for the phenyl ring of aspartame to improve its binding behavior at the cavity, and the resulting ligand 43 showed the best Eb -84.5 kcal/mol. The ONIOM-level study is found to be effective for the interpretation of the noncovalent interactions resulting from residues such as arginine, histidine, tyrosine, lysine, carboxylate, and amide moieties in the active site and suggests rational design strategies for COVID-19 drug development.Communicated by Ramaswamy H. Sarma.

Systematic Photophysical Interaction Studies Between Newly Synthesised Oxazole Derivatives and Silver Nanoparticles: Experimental and DFT Approach

In this study, the photophysical properties of oxazole derivatives such as 5-(furan-2-yl) -4-tosyloxazole (OX-1) and 5-(2-bromothiazol-4-yl)-4-tosyloxazoles (OX-2) were investigated using theoretical and experimental techniques. The ground and excited state dipole moments were empirically obtained utilising the solvatochromic shift technique and several solvatochromic correlations such as Lippert's, Bakhshiev's, KawskiChamma- Viallet's, and solvent polarity equations. The ground state dipole moments, HOMO-LUMO and molecule electrostatic potential map were also computed using ab initio calculations and evaluated using Gaussian 09 W software. Furthermore, spectroscopic interactions between newly synthesised dyes (OX-1 and OX-2) and freshly synthesised silver nanoparticles (size 40 nm) were studied. Increased absorbance and widening of absorption spectra for both dyes in the presence of varied quantities of silver nanoparticles show the potential of dye-nanoparticle interactions. Fluorescence quenching has been detected for both dyes in the presence of colloidal silver nanoparticles, indicating dynamic quenching, and a significant overlap between the absorption and emission spectra of the silver nanoparticle reveals that fluorescence quenching is also due to energy transfer.

Methylammonium Tetrel Halide Perovskite Ion Pairs and Their Dimers: The Interplay between the Hydrogen-, Pnictogen- and Tetrel-Bonding Interactions

The structural stability of the extensively studied organic-inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX₃ (MA = CH₃NH₃⁺; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH₃NH₃⁺) and an inorganic anion (TtX₃^-). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N-H···X and C-H···X hydrogen bonds but also the C-N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX₃ in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX₃^-) together. We have demonstrated that each Tt in each [CH₃NH₃⁺•TtX₃^-] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX₃^- units, thus causing the emergence of an infinite array of 3D TtX₆^4- octahedra in the crystalline phase. The TtX₄^4- octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions.

Experimental and theoretical analyses and investigation of intermolecular interactions and antibacterial activity of a novel proton transfer compound:8-hydroxyquinolinium oxalate monohydrate

A novel proton transfer compound, 8-hydroxyquinolinium oxalate monohydrate was synthesised by solid state grinding of 8-hydroxyquinoline and oxalic acid. The resulting compound is characterised by single crystal X-ray diffraction (SXRD), FT-IR, UV-Visible, TG/DTG, DTA and DSC analyses. The compound crystallizes in monoclinic crystal system with space group P21/n. The carboxylate oxygen O₂ which acts as a tetrafurcated acceptor of four hydrogen bonds is the main feature of the crystal structure. The molecules are linked together by O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds. Carbonyl-carbonyl interactions play a crucial role in stabilising the crystal packing. Hirshfeld surface analysis and the associated finger print plots facilitates the comparison of intermolecular interactions. The nature of charge density distribution and topological parameters of the proton transfer region N₁-H_1A⋯O₂ hydrogen bond reveals that the bond has considerable covalent character. Natural Bond Orbital (NBO) has been extended to analyse the nature and strength of intermolecular interactions. Topology analysis using ELF and LOL reveals electron localisation and depletion regions. ADMET analysis reveals that the compound satisfies Lipinski's rule of five and drug likeness. Antibacterial activity was screened against 3 g positive - Bacillus subtilis, Enterococcus faecalis, Staphylococcus aureus and 2 g negative strains- Klebsiella pneumonia and Salmonella typhi by employing disc diffusion method.

A pair of carbazate derivatives as novel Schiff base ligands: DFT and POM theory supported spectroscopic and biological evaluation

Schiff bases are mentioned as strongly important molecular scaffolds of industrial and medicinal purposes. Due to wide range applications of carbazate derivatives herein synthesis and characterization of a new Schiff base ligand, (E)-ethyl 2-(4-methoxybenzylidene)hydrazinecarboxylate and 4-(nitrobenzaldehyde)ethylcarbazate are reported. The compound was characterized on the basis of experimental and density functional theory calculations (using the B3LYP and 6-31 G(d,p)formalism combination). Among characterization techniques elemental analysis, FT-IR, UV-Vis and NMR spectroscopic evaluations were mainly employed to carry out the formulation of the compound. In addition to computational validation of characterization other significant molecular parameters were also evaluated including geometry optimization, frontier molecular orbital analysis (FMO) and Columbic interaction of different constituent atoms of the title compound. A good agreement has been found between DFT and experimental outcomes confined to prove the structure of the compound. Moreover, molecular docking and antimicrobial studies have proven the Schiff base as an effective bioactive compound.Communicated by Ramaswamy H. Sarma.

Formal proof of the requirement of MESP1 and MESP2 in mesoderm specification and their transcriptional control via specific enhancers in mice

MESP1 and MESP2 are transcriptional factors involved in mesoderm specification, somite boundary formation and somite polarity regulation. However, Mesp quadruple mutant zebrafish displayed only abnormal somite polarity without mesoderm specification defects. In order to re-evaluate Mesp1/Mesp2 mutants in mice, Mesp1 and Mesp2 single knockouts (KOs), and a Mesp1/Mesp2 double KO were established using genome-editing techniques without introducing selection markers commonly used before. The Mesp1/Mesp2 double KO embryos exhibited markedly severe mesoderm formation defects that were similar to the previously reported Mesp1/Mesp2 double KO embryos, indicating species differences in the function of MESP family proteins. However, the Mesp1 KO did not display any phenotype, including heart formation defects, which have been reported previously. We noted upregulation of Mesp2 in the Mesp1 KO embryos, suggesting that MESP2 rescues the loss of MESP1 in mesoderm specification. We also found that Mesp1 and Mesp2 expression in the early mesoderm is regulated by the cooperation of two independent enhancers containing T-box- and TCF/Lef-binding sites. Deletion of both enhancers caused the downregulation of both genes, resulting in heart formation defects. This study suggests dose-dependent roles of MESP1 and MESP2 in early mesoderm formation.

Structure-based virtual screening and computational study towards identification of novel inhibitors of hypoxanthine-guanine phosphoribosyltransferase of Trypanosoma cruzi

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is the key regulatory enzyme of the purine salvage pathway present in the members of trypanosomatids. The parasite solely depends on this pathway for the synthesis of nucleotides due to the absence of the de novo pathway. This study intends to identify putative inhibitors towards Trypanosoma cruzi HGPRT (TcHGPRT). Initial virtual screening was performed with substructures of phosphoribosyl pyrophosphate (PRPP), an original substrate of HGPRT. Twenty compounds that had greater binding energy than the substrate was treated as hits and was further screened and narrowed down through induced fit docking which resulted in top five compounds which was distinguished into two groups based on the ligand occupancy within the PRPP binding site of TcHGPRT. Group-I compounds (PubChem CID 130316561 and 134978234) are analogous to PRPP structure with greater occupancy, were preferred over Group-II compounds which had lesser occupancy than the substrate. However, one compound (22404820) among Group II was chosen for further analysis considering its significant electrostatic interactions. Molecular docking studies revealed the requirement of an electronegative moiety like phosphate group to be present in the ligand due to the presence of metal ions in the substrate binding site. The three chosen compounds along with PRPP were subjected to molecular dynamics analysis, which indicated a strong presence of electrostatic interaction. Considering the dynamic stability of interactions as well as pharmacological properties of ligands based on absorption, distribution, metabolism, excretion prediction, Group-I compounds were selected as lead compounds and were subjected to molecular electrostatic potential analysis to determine the charge distribution of the compound. The overall analysis thus suggests both 130316561 and 134978234 can be used as TcHGPRT inhibitors. Furthermore, these computational results emphasize the requirement of phosphorylated ligands which are essential in mediating electrostatic interactions and to compete with the binding affinity of the original substrate.

The conformational change of Plukenetia conophora oil derivatives and their acidic resistance, intra-fragment interactions, stability in different solvent media

The synthesis of derivatives of bio-based lubricants from vegetable oil as an alternative to petroleum oil is significant due to the oil crisis, global warming, higher demand and serious environmental threat. In this study, the molecular properties of three derivatives of oil derived from Plukenetia conophora seeds, namely Plukenetia conophora oil (PK), rpoxidised Plukenetia conophora oil (EP) and poly(hydroxybutanethiol-ether) derivative of Plukenetia conophora oil (BP), were examined in acidic media and crystal form. The derivative BP has the highest resistance to acidic attack as evident from their poor interaction with acidic H₃O⁺ from both HCl and HNO₃. BP also has the best tendency of forming a crystal as evident from the lowest atomic diffusion in crystal model (L12). However, the result of the molecular electrostatic potential (MESP) analysis shows that BP has more electron-deficient surface compare to EP derivatives. The derivative BP is also found to have the lowest potential energy and higher root means square deviation (RMSD) of its atoms. Density clustering analysis further confirms that BP did not retain its most stable conformation for a longer period of simulation compared to PK and EP. The most visited conformation from the hierarchical and density clustering also corresponds to the minimum potential energy on the potential energy surface.Graphical abstract.

Absorption and emission properties of 5-phenyl tris(8-hydroxyquinolinato) M(III) complexes (M = Al, Ga, In) and correlations with molecular electrostatic potential

Substituent effect for a series of 5-phenyl tris(8-hydroxyquinolinato) M(III) complexes (Mq3) of aluminum, gallium, and indium are investigated using density functional theory (DFT) for the ground state properties and the time-dependent version of DFT (TDDFT) for their absorption and emission properties. A comparison between the ground state energy of mer and fac isomers of all the complexes revealed that the mer configuration is always more stable than fac. The substituent effect is significantly reflected at the fluorescence maximum (λ_F ) values whereas the effect is moderate at the absorption maximum (λ_abs ) values. The molecular electrostatic potential (MESP) at the metal center (V_M ) and the most electron rich region indicated by MESP minimum (V_min ), located at the oxygen of phenoxide ring exhibit excellent correlations with the λ_F and Stokes shift (λ_F -λ_abs ) values. The study suggests the use of Stokes shift as an experimental quantity to measure the excited state substituent effect while the V_min or V_M emerge as theoretical quantities to measure the same.

Structural, vibrational and electronic spectroscopic study of 6-hydroxycoumarin using experimental and theoretical methods

Understanding the photochemical behavior of structural isomers of hydroxycoumarin (HC) having different properties of consequence in biological activities demand spectroscopic information of this class of compounds. Barring 6-hydroxycoumarin (6-HC), other isomers of HC's are well studied spectroscopically. To understand and compare the photochemical activity of 6-HC with other isomers, a detailed study of this molecule has been taken up. For this purpose, electronic, vibrational and structural properties of 6-HC have been studied using ultraviolet absorption and Infrared spectroscopy techniques. Quantum chemical calculations have been performed at DFT/B3LYP level of theory to get the optimized geometry and vibrational frequencies of normal modes to support and analyze experimental data. The detailed vibrational assignments were made on the basis of potential energy distributions. Chemical activity, molecular orbital energies, band gap and hyper-polarizability information have been computed from quantum chemical simulations. NBO analysis helped in understanding the stability of the molecule arising from hyper-conjugative interaction and charge delocalization. UV-Visible spectrum of the compound was recorded in the region 300-600 nm helped in obtaining band gap data of the compound. Molecular Electrostatic Potentials (MESP) were plotted and the respective centers of electrophilic and nucleophilic attacks were predicted with the help of Fukui functions calculations. Further, it was observed that the negative electrostatic potential regions are mainly localized over the oxygen atoms and the positive regions are localized over the benzene ring. Details of the results and analysis of experimental and theoretical spectroscopy studies are presented in this paper.

Crystal structure analysis of [5-(4-meth-oxy-phen-yl)-2-methyl-2H-1,2,3-triazol-4-yl](thio-phen-2-yl)methanone

The title compound, C15H13N3O2S, crystallizes in the monoclinic space group P21/n and its mol-ecular conformation is stabilized via intra-molecular C-H⋯O and C-H⋯N contacts. The supra-molecular structure is mainly governed by C-H⋯N hydrogen-bonded centrosymmetric dimers, C-H⋯O and C-H⋯S hydrogen bonds and S⋯π and π-π stacking inter-actions which, together, lead to the formation of a layered crystal packing. The inter-molecular inter-actions were further evaluated through the mol-ecular electrostatic potential map and Hirshfeld fingerprint analysis.

Assessment of density prediction methods based on molecular surface electrostatic potential

We compared the effectiveness of different molecular surface electrostatic potential (MESP)-based methods for calculating the density of CHNO explosives. Densities computed for 221 CHNO explosives of different chemical nature and functional groups and compared with the experimental values. The CHNO explosives in this work are divided into seven groups as group I nitrate-esters, group II nitramines, group III azides, group IV energetic materials containing benzene ring, group V energetic materials containing caged and strained rings, group VI energetic materials containing heterocyclic backbone, and group VII are the energetic materials containing fused ring. The computed densities using molecular volume method, Lee method, Kim method, Politzer method, and Rice method judged with experimental data indicates that Politzer and Rice method can be applied for the prediction of density. This study will be useful in selecting an MESP-based approach for the density estimation and directing research efforts towards the development of new CHNO explosives. Graphical Abstract The effectiveness of different molecular surface electrostatic potential (MESP)-based methods such as Lee method, Kim method, Politzer method, and Rice method for calculating the density of 221 CHNO explosives is assessed. The CHNO explosives are divided into seven groups as nitrate-esters, nitramines, azides, energetic materials containing- benzene ring, -caged and strained rings, -heterocyclic backbone, and -fused ring.

Computational study of molecular electrostatic potential, docking and dynamics simulations of gallic acid derivatives as ABL inhibitors

Chronic myeloid leukemia (CML), a hematological malignancy arises due to the spontaneous fusion of the BCR and ABL gene, resulting in a constitutively active tyrosine kinase (BCR-ABL). Pharmacological activity of Gallic acid and 1,3,4-Oxadiazole as potential inhibitors of ABL kinase has already been reported. Objective of this study is to evaluate the ABL kinase inhibitory activity of derivatives of Gallic acid fused with 1,3,4-Oxadiazole moieties. Attempts have been made to identify the key structural features responsible for drug likeness of the Gallic acid and the 1,3,4-Oxadiazole ring using molecular electrostatic potential maps (MESP). To investigate the inhibitory activity of Gallic acid derivatives towards the ABL receptor, we have applied molecular docking and molecular dynamics (MD) simulation approaches. A comparative study was performed using Bosutinib as the standard which is an approved CML drug acting on the same receptor. Furthermore, the novel compounds designed and reported here in were evaluated for ADME properties and the results indicate that they show acceptable pharmacokinetic properties. Accordingly these compounds are predicted to be drug like with low toxicity potential.

Long-term variability in sugarcane bagasse feedstock compositional methods: sources and magnitude of analytical variability

BACKGROUND

In an effort to find economical, carbon-neutral transportation fuels, biomass feedstock compositional analysis methods are used to monitor, compare, and improve biofuel conversion processes. These methods are empirical, and the analytical variability seen in the feedstock compositional data propagates into variability in the conversion yields, component balances, mass balances, and ultimately the minimum ethanol selling price (MESP). We report the average composition and standard deviations of 119 individually extracted National Institute of Standards and Technology (NIST) bagasse [Reference Material (RM) 8491] run by seven analysts over 7 years. Two additional datasets, using bulk-extracted bagasse (containing 58 and 291 replicates each), were examined to separate out the effects of batch, analyst, sugar recovery standard calculation method, and extractions from the total analytical variability seen in the individually extracted dataset. We believe this is the world's largest NIST bagasse compositional analysis dataset and it provides unique insight into the long-term analytical variability. Understanding the long-term variability of the feedstock analysis will help determine the minimum difference that can be detected in yield, mass balance, and efficiency calculations.

RESULTS

The long-term data show consistent bagasse component values through time and by different analysts. This suggests that the standard compositional analysis methods were performed consistently and that the bagasse RM itself remained unchanged during this time period. The long-term variability seen here is generally higher than short-term variabilities. It is worth noting that the effect of short-term or long-term feedstock compositional variability on MESP is small, about $0.03 per gallon.

CONCLUSIONS

The long-term analysis variabilities reported here are plausible minimum values for these methods, though not necessarily average or expected variabilities. We must emphasize the importance of training and good analytical procedures needed to generate this data. When combined with a robust QA/QC oversight protocol, these empirical methods can be relied upon to generate high-quality data over a long period of time.

Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations

11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) is a potential target for the treatment of numerous human disorders, such as diabetes, obesity, and metabolic syndrome. In this work, molecular modeling studies combining molecular docking, 3D-QSAR, MESP, MD simulations and free energy calculations were performed on pyridine amides and 1,2,4-triazolopyridines as 11β-HSD1 inhibitors to explore structure-activity relationships and structural requirement for the inhibitory activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by docking strategy. The derived pharmacophoric features were further supported by MESP and Mulliken charge analyses using density functional theory. In addition, MD simulations and free energy calculations were employed to determine the detailed binding process and to compare the binding modes of inhibitors with different bioactivities. The binding free energies calculated by MM/PBSA showed a good correlation with the experimental biological activities. Free energy analyses and per-residue energy decomposition indicated the van der Waals interaction would be the major driving force for the interactions between an inhibitor and 11β-HSD1. These unified results may provide that hydrogen bond interactions with Ser170 and Tyr183 are favorable for enhancing activity. Thr124, Ser170, Tyr177, Tyr183, Val227, and Val231 are the key amino acid residues in the binding pocket. The obtained results are expected to be valuable for the rational design of novel potent 11β-HSD1 inhibitors.

Vibrational spectra, NBO, HOMO-LUMO and conformational stability studies of 4-hydroxythiobenzamide

In this work, the experimental and theoretical study on molecular structure, vibrational spectral analysis of 4-hydroxythiobenzamide (HTB) have been reported. The solid phase FTIR (4000-400 cm(-1)) and FT-Raman spectra (3500-50 cm(-1)) were recorded. The molecular geometry, harmonic vibrational frequencies and bonding features of HTB in the ground-state have been calculated by the density functional method (B3LYP) with 6-311+G(d,p) and 6-311++G(d,p) as basis sets. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Stability of the molecule arising from hyperconjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that the value of electron density (ED) in the σ(∗) antibonding orbitals and E((2)) energies confirms the occurrence of ICT (intra-molecular charge transfer) within the molecule. The UV spectrum was measured in ethanol solution. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) correlates with the experimental findings. The calculated molecular electrostatic potential (MESP), HOMO and LUMO energies show that charge transfer occurs within the molecule. Besides, the simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra.

Vibrational spectra, NLO analysis, and HOMO-LUMO studies of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid by density functional method

The FTIR and FT-Raman spectra of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of fundamental modes of the compounds were carried out. The optimized molecular geometries, vibrational frequencies, thermodynamic properties and atomic charge of the compounds were calculated by using density functional theory (B3LYP) method with 6-311+G and 6-311++G basis sets. The difference between the observed and scaled wave number values of most of fundamentals is very small. Unambiguous vibration assignment of all the fundamentals is made up the total energy distribution (TED). The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules. Besides, molecular electro static potential (MESP), Mulliken's charge analysis, first order hyper polarizability and several thermodynamic properties were performed by the DFT method.

Experimental and theoretical studies of (FT-IR, FT-Raman, UV-Visible and DFT) 4-(6-methoxynaphthalen-2-yl) butan-2-one

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 4000-50 cm(-1) and 4000-450 cm(-1) respectively for 4-(6-methoxynaphthalen-2-yl) butan-2-one (abbreviated as 4MNBO) molecule. Theoretical calculations were performed by density functional theory (DFT/B3LYP) method using 6-311G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and calculated wavenumber value of most of the fundamentals were very small. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The UV-Vis spectrum was recorded in the methanol solution. The energy, wavelength and oscillator's strength were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Thermodynamic properties of 4MNBO at different temperature have been calculated. The molecular electrostatic potential surface (MESP) and Frontier molecular orbital's (FMO's) analysis were investigated using theoretical calculations.

Molecular structure, vibrational spectral assignments, HOMO-LUMO, MESP, Mulliken analysis and thermodynamic properties of 2,6-xylenol and 2,5-dimethyl cyclohexanol based on DFT calculation

The FT-IR and FT-Raman spectra of 2,6-xylenol and 2,5-dimethyl cyclohexanol are recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The spectral data obtained are assigned to different normal modes by using of comparison with the theoretical values obtained by applying density functional theory (DFT/B3LYP) method with 6-31+G and 6-31++G basis set. The total energy distribution contributions of vibrations modes are distinguished through scaling factors. The calculated HOMO and LUMO energies shows that the charge transfers occur within the molecules. The harmonic frequencies obtained from these two methods are compared. The Mulliken, molecular electrostatic potentials analysis are calculated theoretically.

Spectroscopic (FT-IR, FT-Raman and UV) investigation, NLO, NBO, molecular orbital and MESP analysis of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid

In this work, FT-IR and FT-Raman spectra of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid (abbreviated as 2DCPAPAA) have been reported in the regions 4000-450cm(-1) and 4000-50cm(-1), respectively. The molecular structure, geometry optimization, intensities, vibrational frequencies were obtained by the ab initio and DFT levels of theory B3LYP with 6-311++G(d,p) standard basis set and a different scaling of the calculated wave numbers. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using vibrational energy distribution analysis (VEDA 4) program. The harmonic frequencies were calculated and the scaled values were compared with experimental FT-IR and FT-Raman data. The observed and the calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The thermodynamic properties of the title compound at different temperature reveal the correlations between standard heat capacities (C) standard entropies (S) standard enthalpy changes (ΔH). The important non-linear optical properties such as electric dipole momentum, polarizability and first hyperpolarizability of 2DCPAPAA have been computed using B3LYP/6-311++G(d,p) quantum chemical calculations. The Natural charges, HOMO, LUMO, chemical hardness (η), chemical potential (μ), Electro negativity (χ) and electrophilicity values (ω) are calculated and reported. The oscillator's strength, wave length, and energy calculated by TD-DFT and 2DCPAPAA is approach complement with the experimental findings. The molecular electrostatic potential (MESP) surfaces of the molecule were constructed.

Molecular dynamics simulation studies for DNA sequence recognition by reactive metabolites of anticancer compounds

The discovery of novel anticancer molecules 5F-203 (NSC703786) and 5-aminoflavone (5-AMF, NSC686288) has addressed the issues of toxicity and reduced efficacy by targeting over expressed Cytochrome P450 1A1 (CYP1A1) in cancer cells. CYP1A1 metabolizes these compounds into their reactive metabolites, which are proven to mediate their anticancer effect through DNA adduct formation. However, the drug metabolite-DNA binding has not been explored so far. Hence, understanding the binding characteristics and molecular recognition for drug metabolites with DNA is of practical and fundamental interest. The present study is aimed to model binding preference shown by reactive metabolites of 5F-203 and 5-AMF with DNA in forming DNA adducts. To perform this, three different DNA crystal structures covering sequence diversity were selected, and 12 DNA-reactive metabolite complexes were generated. Molecular dynamics simulations for all complexes were performed using AMBER 11 software after development of protocol for DNA-reactive metabolite system. Furthermore, the MM-PBSA/GBSA energy calculation, per-nucleotide energy decomposition, and Molecular Electrostatic Surface Potential analysis were performed. The results obtained from present study clearly indicate that minor groove in DNA is preferable for binding of reactive metabolites of anticancer compounds. The binding preferences shown by reactive metabolites were also governed by specific nucleotide sequence and distribution of electrostatic charges in major and minor groove of DNA structure. Overall, our study provides useful insights into the initial step of mechanism of reactive metabolite binding to the DNA and the guidelines for designing of sequence specific DNA interacting anticancer agents.

Synthesis, characterization and quantum chemical investigation of molecular structure and vibrational spectra of 2,5-dichloro-3,6-bis-(methylamino)1,4-benzoquinone

2,5-Dichloro-3,6-bis-methylamino-[1,4]benzoquinone has been synthesized by condensing methyl amine hydrochloride with chloranil in presence of condensing agent sodium acetate. FT-IR (4000-400 cm(-1)) and FT-Raman (4000-400 cm(-1)) spectral measurements of dmdb have been done. Ab initio and DFT (B3LYP/6-311+G(**)) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, infrared intensities and Raman activities. The optimized molecular structure of the compound is found to possess C2h point group symmetry. A detailed interpretation of the observed IR and Raman spectra of dmdb is reported on the basis of the calculated potential energy distribution. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using NBO analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The thermodynamic functions of the title compound have also been computed.