The effect of cation-π interactions on the stability and electronic properties of anticancer drug Altretamine: a theoretical study

The present work utilizes density functional theory (DFT) calculations to study the influence of cation-π interactions on the electronic properties of the complexes formed by Altretamine [2,4,6-tris(dimethylamino)-1,3,5-triazine], an anticancer drug, with mono- and divalent (Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺ and Ca²⁺) metal cations. The structures were optimized with the M06-2X method and the 6-311++G(d,p) basis set in the gas phase and in solution. The theory of `Atoms in Molecules' (AIM) was applied to study the nature of the interactions by calculating the electron density ρ(r) and its Laplacian at the bond critical points. The charge-transfer process during complexation was evaluated using natural bond orbital (NBO) analysis. The results of DFT calculations demonstrate that the strongest/weakest interactions belong to Be²⁺/K⁺ complexes. There are good correlations between the achieved densities and the amounts of charge transfer with the interaction energies. Finally, the stability and reactivity of the cation-π interactions can be determined by quantum chemical computation based on the molecular orbital (MO) theory.

The effect of metal alkali cations on the properties of hydrogen bonds in tautomeric forms of adenine - Guanine mismatch

The effect of interactions of Li⁺, Na⁺ and K⁺ cations with two preferred configuration of the A-G mispairs, A_antiG_anti and A_synG_anti, on the geometries and hydrogen bond energies have been studied at the MP2/6-311++G(d,p) level of theory. For each ion type, the most stable complex in A_antiG_anti and A_synG_anti configurations are related to binding cation to N3 atom of guanine and N1 atom of adenine, respectively. The A_antiG_anti configuration is higher in the absolute values of binding energy than the A_synG_anti configuration, indicating that A_antiG_anti configuration is more stable than A_synG_anti ones. The results indicate that the strength of hydrogen bonds depends on the type and position of cations in considered systems. The values of hydrogen bonding energies estimated by the EML formula in A_antiG_anti mismatch are higher than A_synG_anti case. The influences of cations binding in hydrogen bond strength are confirmed by the results of natural bond orbital (NBO) and atoms in molecules (AIM) analyses.

Influence of alkali substituents on the strength, properties, and nature of tetrel bond between TH3F and pyridine

Ab initio calculations have been performed for the complexes of TH₃F (T=C, Si, and Ge) with pyridine and its alkali derivatives to study the influence of an alkali substituent on the strength, properties, and nature of tetrel bond. The introduction of an alkali atom into the electron donor has a prominent enhancing effect on the strength of tetrel bond, which depends on the T atom as well as the alkali atom and its substitution position. The enhancing effect becomes larger in the C < Ge < Si, Li < Na < K, and para- < meta- < ortho- patterns. The interaction energy varies in a wide range from 2 to 40 kcal/mol. Both electrostatic and polarization including charge transfer are responsible for the enhancing effect of an alkali atom. The formation of a tetrel bond results in an elongation of F-T bond and a red shift of F-T stretch vibration, which is big enough to be detected with infrared spectroscopy. Electrostatic interaction is dominant in all complexes, while polarization is smaller or larger than dispersion in the complexes of CH₃F or TH₃F(T=Si and Ge).

Gonadal Hormones E2 and P Mitigate Cerebral Ischemia-Induced Upregulation of the AIM2 and NLRC4 Inflammasomes in Rats

Acute ischemic stroke (AIS) is a devastating neurological condition with a lack of neuroprotective therapeutic options, despite the reperfusion modalities thrombolysis and thrombectomy. Post-ischemic brain damage is aggravated by an excessive inflammatory cascade involving the activation and regulation of the pro-inflammatory cytokines IL-1β and IL-18 by inflammasomes. However, the role of AIM2 and NLRC4 inflammasomes and the influence of the neuroprotective steroids 17β-estradiol (E2) and progesterone (P) on their regulation after ischemic stroke have not yet been conclusively elucidated. To address the latter, we subjected a total of 65 rats to 1 h of transient Middle Cerebral Artery occlusion (tMCAO) followed by a reperfusion period of 72 h. Moreover, we evaluated the expression and regulation of AIM2 and NLRC4 in glial single-cell cultures (astroglia and microglia) after oxygen–glucose deprivation (OGD). The administration of E2 and P decreased both infarct sizes and neurological impairments after cerebral ischemia in rats. We detected a time-dependent elevation of gene and protein levels (Western Blot/immunohistochemistry) of the AIM2 and NLRC4 inflammasomes in the post-ischemic brains. E2 or P selectively mitigated the stroke-induced increase of AIM2 and NLRC4. While both inflammasomes seemed to be exclusively abundant in neurons under physiological and ischemic conditions in vivo, single-cell cultures of cortical astrocytes and microglia equally expressed both inflammasomes. In line with the in vivo data, E and P selectively reduced AIM2 and NLRC4 in primary cortical astrocytes and microglial cells after OGD. In conclusion, the post-ischemic elevation of AIM2 and NLRC4 and their down-regulation by E2 and P may shed more light on the anti-inflammatory effects of both gonadal hormones after stroke.

Neuromuscular diseases and Covid-19: Advices from scientific societies and early observations in Italy

The risk of a severe course of COVID-19 is increased in patients suffering with Neuromuscular disorders (NMD) due to the following comorbidities: muscular weakness of the chest and diaphragm, use of ventilator supports and/or presence of tracheostoma, weak airway clearance, cardiac involvement, rhabdomyolysis, comoribities, steroid and immunosuppressant treatments. NMD display varying levels of disability in people with the same diagnosis, thus it is difficult to give COVID-19 related general recommendations. Present advicess were designed for patients, caregivers, general neurologists and non-specialist medical providers. They address frequently asked questions and basic service requirements and are supported by a series of in-depth references. In this truly unprecedented situation, the clinical management of neuromuscular patients during the COVID-19 epidemics - taking into account the related difficulties (patients who have suspended ERT, difficulty in contacting the doctors, etc.) - we propose to use a telemedicine device, i.e. the AIGkit application (AIGkit app), promoted and developed in 2018 by Fabrizio Seidita on behalf of the Italian Glycogenosis Association (AIG). The app was born to allow patients with Pompe disease to receive as far as possible continuous monitoring of their health. The support of all colleagues of the Italian Association for Myology (AIM) should extend its use to all NMD patients and beyond.

Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities

Structural optimization, molecular docking analysis, electronic and vibrational properties have been investigated for the 1-benzofuran-2-carboxylic acid (2BF) and 1-benzofuran-3-carboxylic acid (3BF) using DFT/B3LYP/6-311++G(d,p) level of theory. The theoretical parameters have a very good consistency with the experimental ones. The weak intermolecular interactions were analyzed by different tool such as: Hirshfeld surfaces, topological analysis and natural bond orbital studies. The nonlinear optical properties have been investigated. Molecular electrostatic potential and frontier molecular orbitals (FMOs) analysis have been carried out to understand the reactivity of the molecule. In addition, TD-DFT calculation is initiated to simulate the UV-vis absorption spectrum and to determine several important electronic properties like HOMO-LUMO gap energy and electronic transitions. The complete vibrational assignments and the force constants were reported for monomer and dimers of both acids. The biological activities of the tow acids have been studied via molecular docking analysis. The later calculations prove that the studied acids have an inhibitor effect against cancer and microbial diseases.

Multiple Functions of ATG8 Family Proteins in Plant Autophagy

Autophagy is a major degradation process of cytoplasmic components in eukaryotes, and executes both bulk and selective degradation of targeted cargos. A set of autophagy-related (ATG) proteins participate in various stages of the autophagic process. Among ATGs, ubiquitin-like protein ATG8 plays a central role in autophagy. The ATG8 protein is conjugated to the membrane lipid phosphatidylethanolamine in a ubiquitin-like conjugation reaction that is essential for autophagosome formation. In addition, ATG8 interacts with various adaptor/receptor proteins to recruit specific cargos for degradation by selective autophagy. The ATG8-interacting proteins usually contain the ATG8-interacting motif (AIM) or the ubiquitin-interacting motif (UIM) for ATG8 binding. Unlike a single ATG8 gene in yeast, multiple ATG8 orthologs have been identified in the plant kingdom. The large diversity within the ATG8 family may explain the various functions of selective autophagy in plants. Here, we discuss and summarize the current view of the structure and function of ATG8 proteins in plants.

Intermolecular hydrogen bond interactions in the thiourea/water complexes (Thio-(H2O)n) (n = 1, …, 5): X-ray, DFT, NBO, AIM, and RDG analyses

This study aims to experimentally and theoretically examine the nature and energy of intermolecular bond interactions between thiourea and water molecules using natural bond orbital (NBO), non-linear optical (NLO), atoms in molecules (AIM), and reduced density gradient (RDG) analyses based on the quantum chemical approach and spectroscopic analysis on X-ray and FTIR. Geometry optimizations of Thio-(H₂O)_1-5 complexes were carried out in the gas phase by B3LYP/6-311++G(d,p) level of density functional theory. The nature of the molecular interactions between the water and thiourea through hydrogen bonding has been investigated using RDG and AIM methods. NBO analysis shows that the Thio-(H₂O)₅ complex has higher stabilization energy values than the other complexes. The non-linear optical properties, such as dipole moment (μ), the polarizability (α₀), and the first hyperpolarizability (β_tot), and thermodynamic functions, such as entropy (S), specific heat capacity (C_v), and thermal energy (E), were calculated using the same method. It was observed that thermodynamic parameters, polarizability, and the first hyperpolarizability increased with the number of water molecules. X-ray diffraction analysis confirmed that thiourea is single crystal, and the thiourea/water complexes are crystalline in nature. Besides, the infrared spectrum shows the existence of water molecules and it is used to get details of the structure of the complex.

A reconnaissance DFT study of the full conformational analysis of N-formyl-L-serine-L-alanine-NH2 dipeptide

Theoretical conformational analysis of N-formyl-L-serine-L-alanine-NH₂ dipeptide model was investigated using B3LYP/6-311+G(d,p) and M06-2X/6-311+G(d,p) calculations. In this research, 243 total possible conformations of the dipeptide model were optimized including 87 stable conformers and the other disappeared ones migrated to more stable geometries. Migration pattern suggests more stability of the dipeptide model with the serine (ser) in β_L, γ_L, and γ_D and the alanine (ala) in γ_D and γ_L configurations, along with 26 of the found conformers having β-turn structures. Our calculations reveal that the most stable conformer, γ_L⁺γ_D, is in β-turn region of Ramachandran map; therefore, serine-alanine (ser-ala) dipeptide model should be adopted with a β-turn conformation. The atoms in molecules (AIM) topological analysis was carried out to characterize the nature of the intramolecular hydrogen bonding in β-turn structures. The γ_L⁺γ_D, including three hydrogen bonds, has the highest stability, while α_L^aγ_L as the most unstable β-turn conformer bears two and one hydrogen bonds at the B3LYP/6-311+G(d,p) and M06-2X/6-311+G(d,p) levels of theory, respectively. Graphical abstract.

Prediction of explosive properties of newly synthesized amino nitroguanidine-based energetic complexes via density functional theory

Density functional theory calculations were performed to explore four octahedral energetic complexes including [CoCl₂ (ANQ)₂], [Co (ANQ)₂(H2O)₂]²⁺, [CuCl₂ (ANQ)₂], and [Cu(NO3)₂ (ANQ)₂], (ANQ = amino nitroguanidine). In this work, an attempt has been made to present useful structural data in order to investigate and predict the explosive properties of these complexes. In this regard, interaction energy (IE), natural bond orbital (NBO), atoms in a molecule (AIM) as well as the three-dimensional Hirshfeld surface analysis and the two-dimensional fingerprint plots, charge transfers, HUMO-LUMO gap, oxygen balance (%OB) amounts, and molecular electrostatic potential (MEP) maps were utilized to assign intermolecular interactions, bond lengths, the nature of metal-ligand bonds, and energies in subject compounds. The results reveal that among the five applied levels of theory, interaction energies obtaining from M06-2X/Def2TZVP were in excellent compliance with the experiments. Additionally, the N⋯O interaction, oxygen balance, density, and HOMO-LUMO gap were the most contributing factors in assigning sensitivity and detonation properties. In general, the sensitivity and detonation properties are increased in the following order: ANQ < complex1 < complex3 < complex2 < complex4. Graphical abstract.

Comparison of acidity and metal ion affinity of D-Glucosamine and N-acetyl-D-glucosamine, a DFT study

The derivatives of glucose such as glucosamine (β-D-GlcN) and N-acetyl-D-β-glucosamine (GlcNAc) are significant in several biological systems. D-GlcN has been used widely to treat osteoarthritis in humans and animal models as well as GlcNAc has been proposed as a treatment for autoimmune diseases. The DFT/B3LYP/6-311++G (d,p) method as well as QTAIM and NBO analyses were used to the acidity values of D-GlcN and GlcNAc sugars and their complexes with alkali ions in the gas phase. The Li⁺, Na⁺ and K⁺ prefer bi-dentate chelate in these complexes. The computed results indicate that metal ion affinity (MIA) in GlcNAc is higher than that in D-GlcN. There are direct correlations between the MIA values of D-GlcN and GlcNAc sugars and the atomic numbers of Li, Na, and K. The calculated acidity values for GlcNAc at C₂-NH and C₆-HO₆ sites are 331 and 333 kcal mol^-1, respectively. Whereas the calculated acidity values for D-GlcN at C₂-NH and C₆-HO₆ sites are 365 and 372 kcal mol^-1, respectively. The AIM and NBO analyses indicate the presence of intramolecular H-bonds in GlcNAc sugar in both its neutral form and conjugate base; whereas D-GlcN indicates intramolecular H-bonds in only its conjugate base.

A SNP panel for early detection of artificial chimerism in HSCT patients using TaqMan technology

The monitoring of chimerism status in a hematopoietic stem cell transplantation patient is a crucial process and is performed periodically in a short time interval. A short tandem repeat marker is widely used for chimerism analysis due to its high discrimination power. However, the sensitivity of this approach was limited to 5% of a minor contributor and the interpretation is usually interrupted with PCR stochastic phenomena. Here, we developed an SNP panel for chimerism analysis using TaqMan technology. A set of SNPs was selected from Thai ancestry informative markers and open-access databases with proper criteria. We examined the 30 recipient-donor pairs that underwent HSCT and showed that the panel can provide an informative marker from 90% of all pairs. An early detection of artificial chimerism in post-HSCT samples was observed when compared with STR analysis. In addition, the detail of cases was discussed.

Apoptosis Inhibitor of Macrophage, Monocyte Chemotactic Protein-1, and C-Reactive Protein Levels Are Increased in Patients with Metabolic Syndrome: A Pilot Study

Background: Apoptosis inhibitor of macrophage (AIM) and monocyte chemotactic protein-1 (MCP-1) are molecules that cause migration of M1 macrophages to visceral adipocytes, which is the first step in development of metabolic syndrome. The aim of this study is to evaluate the status of AIM and MCP-1 in metabolic syndrome and to investigate their use as biomarkers. Methods: Forty metabolic syndrome patients and 40 healthy individuals were enrolled in the study. Serum AIM, MCP-1, and C-reactive protein (CRP) levels were measured by enzyme-linked immunosorbent assay. Results: AIM, MCP-1, and CRP levels were significantly higher in the metabolic syndrome group (P < 0.01, P < 0.01, and P < 0.05, respectively). There was a positive correlation of serum AIM, MCP-1, and CRP levels with waist circumference (r = 0.480, r = 0.663, and r = 0.418, respectively; P < 0.01). Receiver operating characteristic (ROC) curve analyses revealed AIM, MCP-1, and CRP cutoff points as 2383.7 ng/mL, 172.8 pg/mL, and 0.366 mg/dL, which could be used in the diagnosis of metabolic syndrome with highest sensitivity and specificity. In the logistic regression model, including age, AIM, CRP, and MCP-1 as covariates, having serum AIM and CRP levels above cutoffs were significant independent predictors for metabolic syndrome (odds ratios 13.8 and 21.3), whereas the serum MCP-1 level was not a significant independent predictor, although the odds ratio was 2.6 (P = 0.193). Conclusions: These results suggest that AIM and MCP-1 may play a role in the pathogenesis of metabolic syndrome. AIM and CRP levels may be used as biomarkers in the diagnosis of metabolic syndrome. Although MCP-1 is not an independent predictor, its elevation in metabolic syndrome is noteworthy, which warrants further analyses in larger groups.

Molecular structure, NLO properties and vibrational analysis of l-Histidine tetra fluro borate by experimental and computational spectroscopic techniques

l-histidine tetra fluroborate (L-HTFB) is a semi-organic NLO material. Ab-initio computations were performed at CAM-B3LYP/ 6-311++g(d,p) level of theory to arrive at the structures, energies, and vibrational wave numbers. The experimental FT-IR and FT-Raman spectra of L-HTFB have been recorded and analyzed. It is compared with the simulated spectra. The scaled wave numbers obtained are in good agreement with the experimental values. Hirshfeld surface analysis represented in the 2D fingerprint plot reveals the interaction within the compound. Optimized geometry reveals that the complexes l -histidine (L-H) and tetrafluoroborate (TFB) are linked by H-F bond which provides inter and intra molecular hydrogen bonded interactions such as N₁₀-H₁₆⋯F₂₅, N₁₁-H₁₇⋯F₂₂, N₁₁-H₁₄⋯F₂₄, N₁₁-H₁₄⋯N₁₀ and N₁₁-H₁₅⋯O₁₂. The inter-molecular distances H₁₇⋯F₂₂, H₁₄⋯F₂₄ and H₁₆⋯F₂₅ are in between 1.82 Å and 2.53 Å. The intra molecular distances H₁₄⋯N₁₀ and H₁₅⋯O₁₂ are found to be at 2.17 Å and 1.71 Å which stabilizes lone pair electron of N₁₀ and O₁₂ with energies 11.89 and 59.91 KJ/mol respectively. The intra and inter molecular hyperconjugations responsible for the stability of the molecule are well identified theoretically using the NBO analysis. Third order optical nonlinearity is measured by means of the open aperture Z-scan technique which reveals that the crystal has optical limiting property. Photoluminescence results clearly indicate the use of L-HTFB as a new violet-light emitting material.

Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop to promote autophagy

Macroautophagy (autophagy) is driven by the coordinated actions of core autophagy-related (Atg) proteins. Atg8, the core Atg protein generally considered acting most downstream, has recently been shown to interact with other core Atg proteins via their Atg8-family-interacting motifs (AIMs). However, the extent, functional consequence, and evolutionary conservation of such interactions remain inadequately understood. Here, we show that, in the fission yeast Schizosaccharomyces pombe, Atg38, a subunit of the phosphatidylinositol 3-kinase (PtdIns3K) complex I, interacts with Atg8 via an AIM, which is highly conserved in Atg38 proteins of fission yeast species, but not conserved in Atg38 proteins of other species. This interaction recruits Atg38 to Atg8 on the phagophore assembly site (PAS) and consequently enhances PAS accumulation of the PtdIns3K complex I and Atg proteins acting downstream of the PtdIns3K complex I, including Atg8. The disruption of the Atg38-Atg8 interaction leads to the reduction of autophagosome size and autophagic flux. Remarkably, the loss of this interaction can be compensated by an artificial Atg14-Atg8 interaction. Our findings demonstrate that the Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop between Atg8 and the PtdIns3K complex I to promote efficient autophagosome formation, underscore the prevalence and diversity of AIM-mediated connections within the autophagic machinery, and reveal unforeseen flexibility of such connections. Abbreviations: AIM: Atg8-family-interacting motif; AP-MS: affinity purification coupled with mass spectrometry; Atg: autophagy-related; FLIP: fluorescence loss in photobleaching; PAS: phagophore assembly site; PB: piggyBac; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol 3-phosphate.

A theoretical investigation on the complexes of B3O3H3 with acetylene and its substituted derivatives

The complexes of B₃O₃H₃ with acetylene and its substituted derivatives C₂HX (X=H, F, Cl, Br, CH₃, NH₂) are explored by theoretical calculations using MP2 and M06-2X methods with aug-cc-pVDZ as the basis set. The different molecular electrostatic potential features of B₃O₃H₃ with benzene (C₆H₆) and borazine (B₃N₃H₆) result in different stable structures of the complexes with C₂HX. The geometric analysis indicates that the global minimum is the parallel stacked (PS) structure with the linear C-C triple bond lies on the top of B₃O₃H₃, and this is much different from that of the B₃N₃H₆...C₂HX complex, in which the C-H bond directs towards the B₃N₃H₆ ring (T-shaped). The H-bonded structure where the C-H interacts with the O atom of B₃O₃H₃ is found to be a local minimum. Besides, there is an additional X…O halogen-bonded structures for the B₃O₃H₃…C₂HX (X=Cl, Br) complexes. As for the PS geometry, when one H atom in C₂H₂ is replaced by different X groups, the binding energies of the complexes increases in the order of F<H<Cl<Br<CH₃<NH₂, which is mainly determined by the strength of the π-hole bond. The nature of interaction in these complexes is further studied by the atoms-in-molecules (AIM) and noncovalent interaction (NCI) analysis. The natural bond orbital (NBO) analysis indicates that the main orbital interaction arises from LP_X→BD*_B‑O for B₃O₃H₃…C₂HX (X=Cl, Br, NH₂), and BD_C‑C→BD*_B‑O for B₃O₃H₃…C₂HX (X=H, CH₃) complexes. Complexes of B₃O₃H₃ with acetylene and its substituted derivatives.

PIMA: A population informative multiplex for the Americas

We describe an ancestry-informative autosomal SNP multiplex designed to be a small-scale, flexible panel that can complement uniparental markers in assessing the American variability (i.e. pre-Colombian) found in contemporary indigenous American populations. This study centered on choosing SNPs with the specific characteristics of: 1) extreme allele frequency differences between indigenous Americans and the African, European and East Asian population groups that contribute to present-day population variation in the Americas; 2) high informativeness-for-assignment I_n values; and 3) well-spaced genomic distribution and chromosomal separation from existing small-scale forensic ancestry marker sets. The resulting capillary electrophoresis SNaPshot single base extension test was named: PIMA (Population Informative Multiplex for the Americas), comprising 26 autosomal SNPs, a single X-chromosome SNP plus the amelogenin sex marker adapted for SNaPshot. PIMA complements the established 34plex forensic ancestry panel to provide a powerful and simple tool for the analysis of American populations, including those with admixed histories, commonly encountered in America. Comparing the results obtained with the combined marker panels of PIMA and 34plex to SNP data from a much larger ancestry panel allowed us to gauge their relative efficiency. PIMA+34plex gives equivalent power to the 314-SNP 'LACE' genomic ancestry control panel, while requiring a much smaller genotyping effort. The ancestry profiles and genetic structure of 22 populations spread across the American continent were estimated using PIMA+34plex data, and those estimates were contrasted with information provided by uniparental markers (mtDNA and Y-chromosome loci) for a small set of admixed individuals from Venezuela. Our results indicate that an American genetic component is efficiently detected in contemporary American populations using a small set of ancestry informative SNPs, and these co-ancestry estimates are consistent with the known history and demography of the Americas. The small scale and high population differentiation power of PIMA, particularly when combined with 34plex, provides a practical and powerful tool for genetic studies of American populations as well as forensic DNA analyses.

Secreted IgM: New tricks for an old molecule

Secreted IgM (sIgM) is a multifunctional evolutionary conserved antibody that is critical for the maintenance of tissue homeostasis as well as the development of fully protective humoral responses to pathogens. Constitutive secretion of self- and polyreactive natural IgM, produced mainly by B-1 cells, provides a circulating antibody that engages with autoantigens as well as invading pathogens, removing apoptotic and other cell debris and initiating strong immune responses. Pathogen-induced IgM production by B-1 and conventional B-2 cells strengthens this early, passive layer of IgM-mediated immune defense and regulates subsequent IgG production. The varied effects of secreted IgM on immune homeostasis and immune defense are facilitated through its binding to numerous different cell types via different receptors. Recent studies identified a novel function for pentameric IgM, namely as a transporter for the effector protein ″apoptosis-inhibitor of macrophages″ (AIM/CD5L). This review aims to provide a summary of the known functions and effects of sIgM on immune homeostasis and immune defense, and its interaction with its various receptors, and to highlight the many critical immune regulatory functions of this ancient and fascinating immunoglobulin.

Nitrofurantoin-melamine monohydrate (cocrystal hydrate): Probing the role of H-bonding on the structure and properties using quantum chemical calculations and vibrational spectroscopy

Cocrystal monohydrate of nitrofurantoin (NF) with melamine (MELA) has been studied as NF is an antibacterial drug used for the treatment of urinary tract infections. The structure of nitrofurantoin-melamine-monohydrate (NF-MELA-H₂O) is characterized by FT-IR and FT-Raman spectroscopy. The energies and vibrational frequencies of the optimized structures calculated using quantum chemical calculations. Supported by normal coordinate analyses and potential energy distributions (PEDs), the complete vibrational assignments recommended for the observed fundamentals of cocrystal hydrate. With the aim of inclusion of all the H-bond interactions, dimer of NF-MELA-H₂O has been studied as only two molecules of cocrystal hydrate are present in the unit cell. By the study of dimeric model consistent assignment of the FT-IR and FT-Raman spectrum obtained. H-bonds are of essential importance in an extensive range of molecular sciences. The vibrational analyses depict existence of H-bonding (O-H⋯N) between water O-H and pyridyl N atom of MELA in both monomer and dimer. To probe the strength and nature of H-bonding in monomer and dimer, topological parameters such as electron density (ρ_BCP), Laplacian of electron density (∇²ρ_BCP), total electron energy density (H_BCP) and H-bond energy (E_HB) at bond critical points (BCP) are evaluated by quantum theory of atoms in molecules (QTAIM). Natural bond orbitals (NBOs) analyses are carried out to study especially the intra and intermolecular H-bonding and their second order stabilization energy (E⁽²⁾). The value of HOMO-LUMO energy band gap for NF-MELA-H₂O (monomer and dimer both) is less than NF, showing more chemical reactivity for NF-MELA-H₂O. Chemical reactivity has been described with the assistance of electronic descriptors. Global electrophilicity index (ω = 7.3992 eV) shows that NF-MELA-H₂O behaves as a strong electrophile than NF. The local reactivity descriptors analyses such as Fukui functions, local softnesses and electrophilicity indices performed to determine the reactive sites within NF-MELA-H₂O. In MEP map of NF-MELA (monomer and dimer) electronegative regions are about NO₂ and C=O group of NF, although the electropositive regions are around NH₂, N-H group and H₂O molecule. Molar refractivity (MR) value of NF-MELA-H₂O (monomer and dimer) lies within the range set by Lipinski's modified rules. This study could set as an example to study the H-bond interactions in pharmaceutical cocrystals.

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro-3'-(1,2,4,5,7-tetraoxazocane): single-crystal X-ray and theoretical study

Single crystals of (2S,5R)-2-isopropyl-5-methyl-7-(5-methylisoxazol-3-yl)cyclohexanespiro-3'-(1,2,4,5,7-tetraoxazocane), C₁₆H₂₆N₂O₅, have been studied via X-ray diffraction. The tetraoxazocane ring adopts a boat-chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6-31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,-1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O-C-O and N-C-O fragments. There is a two-cross hyperconjugation in the N-C-O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C-O bond (σ*_C-O) and vice versa between lpO and σ*_C-N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,-1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C-H...N and C-H...O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,-1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C-H...N interactions being electrostatic in origin. The molecules are further stacked due to C-H...O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.

Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study

Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg²⁺ (-49.6 kcal/mol), Zn²⁺ (-45.3 kcal/mol) and Cu²⁺ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg²⁺ and Cu²⁺ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn²⁺ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu²⁺ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg²⁺ and Zn²⁺ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu²⁺ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg²⁺, Zn²⁺, and Cu²⁺ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg²⁺ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn²⁺, Cu²⁺) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu²⁺ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.

Theoretical insights into the hydrogen bonding interaction in the complexation of epinephrine with uracil

The present study is aimed at probing the hydrogen bonding interaction between epinephrine and uracil by means of density functional theory calculations concerning their complexation's geometries, interaction energies, and vibrational frequencies. Geometry optimization was carried out giving 19 stable geometries of epinephrine-uracil complex with interaction energies in a range of - 21.51 to - 62.37 kJ mol^-1 using the basis set superposition error (BSSE) correction. The analysis of structure and vibration shows that the hydrogen bonding elongates the length of corresponding bond O(N)-H and decreases the symmetric stretching vibrational frequency, which indicates red-shifted H-bonding interactions in all the geometries. Additionally, the analysis with theories of natural bond orbital (NBO), atoms in molecules (AIM), and the reduced density gradient (RDG) of hydrogen bonding properties and characteristics of the 19 geometries suggests that the hydrogen bonding in all the optimized structures of epinephrine-uracil complex is kind of a closed-shell interaction and mainly electrostatic dominant.

Coinage-Metal Bond between [1.1.1]Propellane and M2/MCl/MCH3 (M = Cu, Ag, and Au): Cooperativity and Substituents

A coinage-metal bond has been predicted and characterized in the complexes of [1.1.1]propellane (P) and M₂/MCl/MCH₃ (M = Cu, Ag, and Au). The interaction energy varies between −16 and −47 kcal/mol, indicating that the bridgehead carbon atom of P has a good affinity for the coinage atom. The coinage-metal bond becomes stronger in the Ag < Cu < Au sequence. Relative to M₂, both MCl and MCH₃ engage in a stronger coinage-metal bond, both -Cl and -CH₃ groups showing an electron-withdrawing property. The formation of coinage-metal bonding is mainly attributed to the donation orbital interactions from the occupied C-C orbital into the empty metal orbitals and a back-donation from the occupied d orbital of metal into the empty C-C anti-bonding orbital. In most complexes, the coinage-metal bond is dominated by electrostatic interaction, with moderate contribution of polarization. When P binds simultaneously with two coinage donors, negative cooperativity is found. Moreover, this cooperativity is prominent for the stronger coinage-metal bond.

DL-3-Aminoisobutyric acid: vibrational, NBO and AIM analysis of N-H⋯O bonded-zwitterionic dimer model

A zwitterionic dimer model constructed of inter-molecular -N-H⋯O bonding has been proposed for the solid sample of DL-3-Aminoisobutyric acid consistent with IR absorption and Raman spectral features measured in the 3500-400/50 cm^-1. This zwitterionic dimer model in water as solvent has been computed at B3LYP/6-311++G(d,p) and B3LYP-D3/6-311++G(d,p) levels including Grimme's dispersion correction associated with the -N-H⋯O interaction and SCRF-SMD method. Of the several possible monomer and dimer conformational structures, the most stable dimer constructed of two zwitterion monomer units has produced vibrational modes due to the -NH₃ ⁺ cation and -CO₂‾ anion involved in the -N-H⋯O bonding in fair agreement with the observed broad but composite IR modal features near the 3500-2000 cm^-1. Except for the frequency of asymmetric stretching mode of the -NH₃ ⁺ cation, its symmetric and bending modes agree with the observed values. As for the -CO₂‾ anion, the frequencies of all of its modes are in good agreement with the experiment. Natural bond orbital (NBO), molecular electrostatic potential (MEP), atoms-in-molecules (AIM) and non-covalent interaction (NCI) analyses have been used to understand electronic characterization of the -N-H⋯O bonding.

A Large-Scale Advanced Illness Intervention Informs Medicare's New Serious Illness Payment Model

Patients with advanced illness receive fragmented, hospital-based care that is unaligned with their preferences near the end of life. We describe a team-based intervention that provides home-based, coordinated care to more than 2,000 seriously ill patients daily in nineteen urban, suburban, or rural counties in California. In the last month of life, compared to matched Medicare beneficiaries in similar counties, this program reduced hospital days by 1,361 per 1,000 beneficiaries, hospital deaths by 8.2 percent, inpatient payments by $6,127, and the total cost of care by $5,657 per beneficiary. The Centers for Medicare and Medicaid Services (CMS) has announced a new Medicare payment model for serious illness care, based in part on this program. To inform model development and implementation, we describe lessons learned about changing the focus of care for advanced illness from hospital to home, broadening care coordination to achieve system integration, and developing methods for payment and quality accountability that transform care delivery.