Accuracy of Different Electronic Basis Set Families for Anharmonic Molecular Vibrations: A Comprehensive Benchmark Study

In this work, the accuracy and convergence of different electronic basis set families for the computation of anharmonic molecular vibrational spectroscopic calculations are benchmarked. A series of 39 different basis sets from different families following their hierarchy are assessed on VSCF and VSCF-PT2 algorithms with commonly used MP2 and DFT based B3LYP-D potentials for a set of molecular systems. Such an effort has been validated in a previous work ( J. Phys. Chem. A 2020, 124, 9203-9221) with split-valence basis sets for fundamentals and intensities. Here, fundamental transitions, vibrationally excited states, and intensities are compared with the experimental data to estimate the accuracy for a series of Jensen, Dunning, Calendar, Karlsruhe, and Sapporo basis set families. The convergence of basis sets are also compared with the large ANO basis set. Comprehensive statistical error analysis in terms of accuracy and precision was carried out to assess the performance of each basis set. It is observed that the improvement for the calculated harmonic and anharmonic values from the smaller basis sets to the medium (i.e., triple-ξ) is considerable. Beyond this, from medium to large basis sets, the convergence is slow and mostly posits nearly converged values. Basis sets with and without diffuse functions offer characteristically different accuracies and convergence patterns. Finally, recommendations are given on the choice of basis set chosen as black-box which can balance between accuracy and computational time, estimation of the errors, and their selections especially for large molecules.

Performance of Vibrational Self-Consistent Field Theory for Accurate Potential Energy Surfaces: Fundamentals, Excited States, and Intensities

The performance of vibrational structure calculations beyond harmonic approximation in the framework of the vibrational self-consistent field method with second-order perturbation corrections (VSCF-PT2) is investigated in conjunction with very accurate potential energy surfaces (PESs) given by various coupled-cluster electronic structure theories. The quality of anharmonic calculations depends on the accuracy of the underlying multidimensional PES obtained from its functional form, which is given by the level of electronic structure theory. Two such highest levels of typical coupled-cluster electronic structure methods, CCSD and the ″gold standard″ CCSD(T), along with their variants such as CCD, CR-CCL (completely renormalized CR-CC(2,3) approach), and CCSD(TQ) are tested for the construction of accurate anharmonic potentials without any fitting or ad hoc scaling and using cc-pVTZ basis sets. The accuracy of VSCF-PT2 theory in comparison to experimental values is tested for a series of 16 molecules with 135 fundamental bands, 64 overtones, and combination bands and also for 39 intensities. It is found that CCD and CCSD bind the potential tighter than CCSD(T) and the computed VSCF-PT2 transitions are more blue-shifted showing higher deviation from the experiment. In general, VSCF-PT2 results computed at the CCSD(T) potential offer a good cost/accuracy ratio, with the mean absolute deviation and the mean absolute percentage error with the experiment being ∼16 cm^-1 and 1.38, respectively, for fundamentals. Additionally, while the CR-CCL and CCSD(TQ) methods offer similar levels of accuracies as compared to CCSD(T), the former offers a better accuracy/cost ratio than the latter and is a suitable alternative to CCSD(T).

Halloysite Nanotubes Functionalized Sulfonic Acid: Synthesis, Spectroscopic Characterization, Computational Studies and Application for the Synthesis of 1,4-Dihydropyridines

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In this study, naturally occurring clay halloysite has been used to synthesize novel halloysite functionalized sulfonic acid in two steps, i.e. functionalization followed by oxidation, and its catalytic activity has been estimated for one-pot synthesis of Hantzsch 1,4-dihydropyridines under green solventfree conditions. Spectroscopic studies such as FTIR, TGA, elemental analysis and first-principles-based quantum chemical studies have been employed to characterize the catalyst. Recyclability without significant loss of catalytic activity has been observed for several runs.

Biochemical and nutritional characterization of dragon fruit (Hylocereus species)

Nutritional and biochemical composition of dragon fruit (Hylocereus) species H. undatus (fruits with white pulp and pink skin), and H. polyrhizus (fruits with red pulp and pink skin) were investigated to develop the nutritional composition data for dragon fruit and compare the difference between H. undatus and H. polyrhizus. The pH, TSS, total sugar, moisture, ash, protein, and dietary fibre content varied between 4.8 and 5.4, 8-12%, 5.13-7.06%, 82-85%, 0.7-0.85%, 0.90-1.1% and 0.8-1.0%, respectively. Total phenolics and flavonoids content varied between 25 and 55 mg GAE and 15-35 mg CE per 100 g, respectively. H. polyrhizus have a significantly high quantum of phenolics and antioxidant potential than H. undatus. 100 g fruit contained about 120-200 mg K, 30-45 mg Mg, 20-45 mg Ca, 20-35 mg P, 0.70-1.5 mg Fe, and 0.20-0.40 mg Zn. Vitamin C was found maximum (6 mg/100 g), followed by vitamin E (150 µg), pantothenic acid (50 µg), and vitamin K1 (25 µg). It is an ideal fruit for maintaining good health as it has low calories.

Porphyrin bearing phenothiazine pincers as hosts for fullerene binding via concave–convex complementarity: synthesis and complexation study

Free base porphyrin hosts, m-(PTZ)4-H2P and p-(PTZ)4-H2P, tethered with four phenothiazine moieties at the meso-position via a flexible ethoxy phenyl linker were synthesized and used for the selective complexation of fullerenes, C60 and C70.

Dual Basis Approach for Ab Initio Anharmonic Calculations of Vibrational Spectroscopy: Application to Microsolvated Biomolecules

A dual electronic basis set approach is introduced for more efficient but accurate calculations of the anharmonic vibrational spectra in the framework of the vibrational self-consistent field (VSCF) theory. In this approach, an accurate basis set is used to compute the vibrational spectra at the harmonic level. The results are used to scale the potential surface from a more modest but much more efficient basis set. The scaling is such that at the harmonic level the new, scaled potential agrees with one of the accurate basis sets. The approach is tested in the application of the microsolvated, protected amino acid Ac-Phe-OMe, using the scaled anharmonic hybrid potential in the VSCF and VSCF-PT2 algorithms. The hybrid potential method yields results that are in good accord with the experiment and very close to those obtained in calculations with the high-level, very costly potential from the large basis set. At the same time, the hybrid potential calculations are considerably less expensive. The results of the hybrid calculations are much more accurate than those computed from the potential surface corresponding to the modest basis set. The results are very encouraging for using the hybrid potential method for inexpensive yet sufficiently accurate anharmonic calculations for the spectra of large biomolecules.

Design, synthesis, characterization and evaluation of the anticancer activity of water-soluble half-sandwich ruthenium(ii) arene halido complexes

Synthesis, crystal structure determination, DFT studies, experimental and theoretical evaluation of DNA/BSA interactions and cytotoxicity studies of three piano-stool Ru(ii)(p-cymene)chloride complexes (1–3) are presented herein.

Conjugated small organic molecules: synthesis and characterization of 4-arylpyrazole-decorated dibenzothiophenes

4-Arylpyrazole-decorated dibenzothiophenes have been synthesized.

Diagnostic Performance of RBC Indices in Beta Thalassaemia Trait

Beta thalassaemia trait is one of the most common forms of thalassaemia in Bangladesh. This clinical entity usually remains undiagnosed because they present with mild anaemia or sometimes no anaemia. Determination of trait is the mainstay of prevention of thalassaemia. RBC indices can provide valuable diagnostic tool for beta thalassaemia trait. This was a hospital based cross-sectional, analytical study, done at Department of Paediatrics, Rangpur Medical College Hospital, Rangpur, Bangladesh from July 2014 to June 2016. A total of 150 anaemic children, aged 1-15 years from inpatient and outpatient department were included by purposive sampling. Blood samples were collected and sent to the Department of Biochemistry, Rangpur Medical College to determine the value of RBC indices. Out of 150 anaemic children 37(24.66%) children were diagnosed as E-trait, 9(9%) E-disease 6(4%) as E-Beta thalassaemia, 1(0.66%) had error in the report, a total of 53 children were excluded from the study. Finally, 32(21.3%) children, diagnosed as beta thalassaemia trait and 65(43.33%) children, diagnosed as normal Hb variant, so a total of 97 children were enrolled in this study. Age of the children was 1-15 years. Their mean age was 6.4 years. Male female ratio was 1.15:1. There was significant difference of HbA₂ between BTT and non BTT group of participants (p value <0.001). Value of MCV and MCH were significantly greater in BTT than non BTT group (p value <0.05). Sensitivity, Specificity, Positive predictive value, Negative predictive value and Youden index of MCV were 81.25%, 90.76%, 81%, 90% and 71 respectively. Sensitivity, Specificity, Positive predictive value, Negative predictive value and Youden index of MCH were 84.37%, 92.30%, 84%, 92% and 76 respectively.

Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy

The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed the presence of only one highly abundant conformer of the singly protonated ALE, isolated and cryogenically cooled in the gas phase. High-level quantum mechanical calculations of electronic structures in conjunction with a systematic conformational search allowed for finding a few low-energy candidate structures. In order to identify the observed structure, we computed vibrational spectra of the candidate structures and employed the theory at the semi-empirically scaled harmonic level and at the first-principles based anharmonic VSCF levels. The best match between the calculated "anharmonic" and the measured spectra appeared, indeed, for the most stable candidate. An average of two spectra calculated with different quantum mechanical potentials is proposed for the best match with experiment. The match thus validates the calculated intrinsic structure of ALE and demonstrates the predictive power of first-principles theory for solving structures of such large molecules.

Azo-dyes based small bifunctional molecules for metal chelation and controlling amyloid formation

Chemical tools are needed to discover new effective drugs for tackling multifaceted complex neurodegenerative diseases like Alzheimer's disease (AD). Multifunctional nature of two compounds, 5-((4-nitro-phenyl)diazenyl)quinolin-8-ol (HL1) and 4-((4-nitrophenyl)diazenyl)benzene-1,3-diol (HL2) is reported w.r.t. their ability to bind Cu2+ ions and amyloid aggregates related to AD. HL1 and HL2 have half congo-red type azo-stilbene structural framework incorporated with metal chelating groups, designed to chelate metal ions from metal-amyloid species. Metal binding studies of HL1 and HL2 are established by the methods of Job's Plot, UV-vis spectra with metal ions and stability constant determination. In addition, their metal complexes are isolated, purity checked by elemental analysis, spectroscopically characterized and their structural analyses were obtained from DFT based calculations including binding energy determination. Chicken egg white Lysozyme (CEWL) was used as a model peptide for fibrillation studies. HL1 is found as an excellent colorimetric sensor for amyloid fibrils. Inhibitory effect of HL1 and HL2 and their isolated metal complexes L1-Cu and L2-Cu on CEWL fibrillation was studied using ThT and ANS fluorescence assay along with TEM imaging. In addition, the cell toxicity studies on these compounds suggest that although azo dyes may be non-toxic but having a nitro-substitution lead to significant cell toxicity. Overall, these results suggest that this new class of multifunctional small molecules can interact with amyloids as well as metal ions and could be potential anti-aggregation metal chelating agents.

A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy

The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2). Guided and validated by the available cold ion spectroscopy data, the computational analysis identifies structures of the three experimentally observed conformers of the complex. They, mainly, differ by the hydration sites, of which the one at the Orn side chain is the most important for reshaping the peptide toward its native structure. The study demonstrates the ability of a quantum chemistry approach that intelligently combines the semiempirical and ab initio computations to disentangle a complex interplay of intra- and intermolecular hydrogen bonds in large molecular systems.

Acinar Cell Carcinoma of the Pancreas: A Case Report

Acinar cell carcinoma (ACC) of the pancreas is a very rare neoplasm. We report a case of pancreatic acinar cell carcinoma involving the uncinate process of the pancreas. A 45 year old man presented with a painful upper abdominal mass without any jaundice or weight loss. Computed Tomography (CT) and Magnetic Resonance Cholangio-Pancreatography (MRCP) indicated a mass lesion in the uncinate process of the pancreas. He underwent Whipple's procedure (Pancreaticoduodenectomy). Histological slides revealed features of Acinar cell carcinoma (ACC) in the uncinate process of the pancreas and a lymph node.

Hypochlorite-promoted inhibition of photo-induced electron transfer in phenothiazine–borondipyrromethene donor–acceptor dyad: a cost-effective and metal-free “turn-on” fluorescent chemosensor for hypochlorite

APTZ-BODIPY based fluorescent chemosensor was designed and used for hypochlorite detection.

Ruthenium Catalyzed Intramolecular C-S Coupling Reactions: Synthetic Scope and Mechanistic Insight

A ruthenium catalyzed intramolecular C-S coupling reaction of N-arylthioureas for the synthesis of 2-aminobenzothiazoles has been developed. Kinetic, isotope labeling, and computational studies reveal the involvement of an electrophilic ruthenation pathway instead of a direct C-H activation. Stereoelectronic effect of meta-substituents on the N-arylthiourea dictates the final regioselective outcome of the reaction.

First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments

First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data.

A catalyst-free, one-pot multicomponent synthesis of spiro-benzimidazoquinazolinones via a Knoevenagel–Michael-imine pathway: a microwave assisted approach

A multi-component route for the synthesis of spiro-benzimidazoquinazolinones was developed and its mechanism was studied.

Mechanistic studies of malonic acid-mediated in situ acylation

We have previously introduced an easy to perform, cost-effective and highly efficient acetylation technique for solid phase synthesis (SPPS). Malonic acid is used as a precursor and the reaction proceeds via a reactive ketene that acetylates the target amine. Here we present a detailed mechanistic study of the malonic acid-mediated acylation. The influence of reaction conditions, peptide sequence and reagents was systematically studied. Our results show that the methodology can be successfully applied to different types of peptides and nonpeptidic molecules irrespective of their structure, sequence, or conformation. Using alkyl, phenyl, and benzyl malonic acid, we synthesized various acyl peptides with almost quantitative yields. The ketenes obtained from the different malonic acid derived precursors were characterized by in situ (1) H-NMR. The reaction proceeded in short reaction times and resulted in excellent yields when using uronium-based coupling agents, DIPEA as a base, DMF/DMSO/NMP as solvents, Rink amide/Wang/Merrifield resins, temperature of 20°C, pH 8-12 and 5 min preactivation at inert atmosphere. The reaction was unaffected by Lewis acids, transition metal ions, surfactants, or salt. DFT studies support the kinetically favorable concerted mechanism for CO2 and ketene formation that leads to the thermodynamically stable acylated products. We conclude that the malonic acid-mediated acylation is a general method applicable to various target molecules.

Rectovaginal Fistula of Different Etiologies: Clinical Case Reports

We report three cases of recto vaginal fistula (RVF) due to different etiologies. First case was due to sexual trauma (vaginal intercourse) which is not very common. The second case was due to obstetric trauma (the most common etiology of RVF) and the third case was caused by chronic lower genito-urinary infection in a HIV positive lady. We have included the successful surgical procedures of first two cases. But the repairing of the third case was failed hence planned to operate after six months. DOI: http://www.dx.doi.org/10.3126/njog.v7i2.11143   Nepal Journal of Obstetrics and Gynaecology / Vol 7 / No. 2 / Issue 14 / July-Dec, 2012 / 43-46

Approximate first-principles anharmonic calculations of polyatomic spectra using MP2 and B3LYP potentials: comparisons with experiment

Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations have been performed for the molecules HNO3, C2H4, C2H4O, H2SO4, CH3COOH, glycine, and alanine. Both MP2 and B3LYP give results in good accord with experimental frequencies, though, on the whole, MP2 gives very slightly better agreement. A statistical analysis of deviations in frequencies from experiment is carried out that gives interesting insights. The most probable percentage deviation from experimental frequencies is about -2% (to the red of the experiment) for B3LYP and +2% (to the blue of the experiment) for MP2. There is a higher probability for relatively large percentage deviations when B3LYP is used. The calculated intensities are also found to be in good accord with experiment, but the percentage deviations are much larger than those for frequencies. The results show that both MP2 and B3LYP potentials, used in VSCF-PT2 calculations, account well for anharmonic effects in the spectroscopy of molecules of the types considered.

A tandem in situ peptide cyclization through trifluoroacetic acid cleavage

We present a new approach for peptide cyclization during solid phase synthesis under highly acidic conditions. Our approach involves simultaneous in situ deprotection, cyclization and trifluoroacetic acid (TFA) cleavage of the peptide, which is achieved by forming an amide bond between a lysine side chain and a succinic acid linker at the peptide N-terminus. The reaction proceeds via a highly active succinimide intermediate, which was isolated and characterized. The structure of a model cyclic peptide was solved by NMR spectroscopy. Theoretical calculations support the proposed mechanism of cyclization. Our new methodology is applicable for the formation of macrocycles in solid-phase synthesis of peptides and organic molecules.

A highly efficient in situ N-acetylation approach for solid phase synthesis

In situ peptide acetylation.

Assessment of noise environment during construction of a major bridge and associated approach road

In this paper a methodology to quantify the noise environment, during a major bridge construction and upgrading approach road connectivity, has been provided. Noise levels were monitored at eleven sites. These eleven sites have been classified into three categories - commercial, residential and silence zones. The study was carried out to measure the ambient noise levels in all the eleven sites falling in the above three categories during both day and night times considering both "working" and "non-working" days. It was found that the mean noise level during night time was more, compared to that during day time for commercial, residential as well as silence zones. The likely causes of more noise during night time have been explored. Appropriate remedial measures have been suggested to reduce the noise levels. In addition, the noise levels in the above three zones have been compared, wherever feasible statistically, with the respective zonal standards. Significance has been found in all the cases. The underlying causes and remedies have been provided.

Role of oxidative stress and the activity of ethylene biosynthetic enzymes on the formation of spongy tissue in 'Alphonso' mango

Spongy tissue formation in 'Alphonso' mangoes (Mangifera indica L) is a major national problem leading to loss for farmers and traders. Spongy tissue is whitish sponge like tissue formed near the seed with insipid taste and off odour. Lipid peroxidation of membranes as studied by malondialdehyde formation was significantly higher in spongy tissue. Activities of antioxidative enzymes like superoxide dismutase, catalase, peroxidase and polyphenol oxidase were lower in spongy tissue. Among the antioxidative enzymes, activities of catalase and peroxidases were severely reduced leading to membrane damage in spongy tissue. A significant reduction in 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase and accumulation of ACC was also observed in spongy tissue. However, ACC synthase activity in spongy tissue was more compared to healthy tissue. Results indicate that the membrane peroxidation leading to lower activity of ACC oxidase might lead to the formation of spongy tissue in 'Alphonso' mango.

Can women's childbearing and contraceptive intentions predict contraceptive demand? Findings from a longitudinal study in Central India

CONTEXT

To predict the need for contraceptive services, family planning program managers often rely on levels of unmet need derived from measures of childbearing intentions. However, women's intention to use a method has not received as much attention as a measure of contraceptive demand.

METHODS

A survey was conducted in 1999 in rural Madhya Pradesh, India, among a subsample of women who had participated in the 1992-1993 National Family Health Survey (NFHS). The women's childbearing and contraceptive behaviors were compared with the intentions they had stated in the NFHS, and logistic regression was performed to analyze the association between socioeconomic and demographic variables and inconsistent behavior.

RESULTS

Among women who were fecund and married in 1992-1993, 29% of those who intended to have children and 61% of those who intended not to have children failed to adhere to their intentions by 1999. Furthermore, 51% of women who were not practicing contraception at the time of the NFHS but planned to do so acted against their intention by 1999, as did 29% of those who planned not to use a method. NFHS respondents who intended both not to have children and to use a method were more likely than others to have used a method by 1999 (63% vs. 25-41%). Age and history of child death were key factors associated with inconsistency between women's intentions and behavior.

CONCLUSIONS

In India, use of both contraceptive and childbearing intentions predicts contraceptive demand better than use of either indicator alone, and may thus help program planners estimate future demand for contraceptive services.

Microbiological and electron microscopic studies of urea treated Rhizobium sp. cells

Microbiological investigation of urea treated Rhizobium sp. cells showed a gradual decrease of colony forming unit from initial 100% to 2.13% value. Maximum effect was reached at 90 min onwards. The liquid holding recovery in phosphate buffer saline at pH 7.0 also was studied. Electron microscopic studies revealed important structural changes in treated cells.