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The structural geometry, electronic and reactivity characteristics, vibrational assignments and the fundamental modes of 6-methylcoumarin have been carried out. The effect of methyl group on the pyrone skeletal vibrations was also discussed. The experimental vibrational frequencies were compared with the wavenumbers obtained theoretically from the B3LYP method employing the high level 6-311++G** and cc-pVTZ basis sets. Frontier molecular orbital (FMO) energy and the LUMO-HOMO energy gap was measured. The atomic charges and the bond properties were examined by natural bond orbital analysis. The hydrogen and carbon environment were examined by NMR spectra. The nuclophilic, electrophilic and free radical attacking sites of 6-methylcoumarin were also analyzed.

The present era finds the implementation of small-scale solar thermal applications to overcome emissions caused by fossil fuels. In this connection, a forced convection co-axial pipe evacuated tube solar air heater is fabricated and examined under various operating parameters and in Bilaspur Chhattisgarh climatic conditions in the months from October 2021 to March 2022. The performance parameters under consideration were outlet air temperature, collector efficiency, exergy efficiency, and overall system efficiency. The experiments have been performed for different mass flow rates 9.36, 15.84, 18.36, 22.32, and 26.28 kg/h of air. The ambient air temperature varied in the range of 20.8 °C to 41.6 °C. The air temperature at the inlet of the heater varies from 28.4 °C to 66.7 °C. The maximum outlet air temperature and temperature rise recorded were 82.9 °C and 37.2 °C in the month of March and February, respectively, for the low mass flow rate of 9.36 kg/h. It was observed that the maximum collector efficiency, exergy efficiency, and overall system efficiency were achieved as 82.95%, 6.4%, and 81.92%, respectively, for a moderate mass flow rate of 15.84 kg/h. All the performance parameters seem to be strongly dependent on the solar intensity and were found to be highest when the intensity was at its peak value. It is found that the increase in mass flow rates beyond 15.84 kg/h tends to decrease the temperature rise as well as the efficiency of the solar heater. No significant temperature rise is observed for a mass flow rate beyond 26.28 kg/h. The study finds that the fabricated setup can effectively produce a low to moderate temperature range (40 °C–80 °C) and can be used for domestic as well as small-scale industrial applications.

This study focuses on fabricating aluminium hybrid metal matrix with eco-friendly agro waste, cow dung ash and boron carbide by two stage stir casting. Weight percentage of cow dung ash and boron carbide were reinforced in ratios of 2.5:7.5, 5:5, and 7.5:2.5. The fabricated samples were subjected to optical microscope, scanning electron microscopy (SEM) with energy dispersive X-ray analysis (EDX) to identify micro structural analysis and phase identification of the reinforcements respectively. The effects on mechanical properties like density, hardness, tensile strength, impact strength and flexural strength properties were studied, and the results are compared to the base alloy (Al 7075). Fracture mechanisms for tensile and impact specimens were analysed through SEM and EDX. Micro structural and SEM images reveal uniform distribution of particles in the matrix. Increasing CDA particles has reduced the density of the hybrid composite up to 8%. A maximum increase in hardness and tensile strength was up to 30% and 56% respectively, and then a slight decrease was found in increasing the CDA particles. The flexural strength has increased to a maximum of 12% at 7.5% CDA and decrement in impact strength was inferred in all the hybrid composites when compared with base alloy. Dimples, transgranular cleavage facets and cracks are revealed from the fractured specimens of tensile and impact specimens.

The geometry of 3-trifluoromethylphenylchloroformate (FMPCF) was optimized with B3LYP method using 6–311++G** and cc–pVTZ basis sets. The molecular structural parameters and thermodynamic properties of the compound have been determined. The vibrational frequencies of the fundamental modes of the compound have been precisely assigned, analyzed and the theoretical results were compared with the experimental data. The energies of important molecular orbitals of the compound are also evaluated from DFT method. The Frontier orbital energy gap (ELUMO–EHOMO) is found to be 6.2143 eV. The extreme limits of the electrostatic potential is +8.301e × 10–3 to –8.301e × 10–3 while the total electron density spreads between +3.835e × 10–2 to –3.835e × 10–2. 1H NMR and 13C NMR chemical shifts are measured and compared with their gauge independent atomic orbital (GIAO) calculated values. The n(O7) →π*(C13–O14) and π(C1–C6) →π*(C2–C3) transitions are best stablized with 48.40 and 21.03 kcal mol–1, respectively. In 3-trifluoromethylphenylchloroformate, the atoms C13 is favourable for electrophilic attack. The atoms C2 and C8 are more favourable for nucleophilic attack. The dual descriptors (Δfk, Δsk and Δωk) revealed that the order of nucleophilic attack is C1 > C4 > C2 > C8 > C5. Thus, the present investigation provides complete structure, vibrations and reactivity characteristics of the compound.

Certain copy number alterations (CNAs) are strongly associated with particular cancer types. However, the mechanisms that underlie selection of specific CNAs remain unknown. Here, we identified functional relationships between recurrent CNAs in colorectal cancers (CRCs) and adenomatous polyposis coli (APC) mutations. Quantitative phenotyping of mitotic spindles highlighted APC functions at centrosomes where APC positively regulated Aurora A kinase (AURKA). Upon APC inactivation, elevated β-catenin levels blocked AURKA activation, which caused chromosome instability and suppressed proliferation, resulting in the generation and selection of AURKA-activating CNAs. Arm-level amplification of chromosomes that contained AURKA and AURKA activator genes was observed in APC-mutant CRCs, early stage mouse tumours, and cells in culture, which was concomitant with an increase in growth potential. Our findings demonstrate a mechanism that restores tumour cell fitness through compensatory chromosome alterations to overcome adverse effects of prior mutations, which may affect the course of cancer type-specific CNA formation.

Eukaryotic cells transmit extracellular signal information to cellular interiors through the formation of a ternary complex made up of a ligand (or agonist), G-protein, and G-protein coupled receptor (GPCR). Previously formalized theories of ternary complex formation have mainly assumed that observable states of receptors can only take the form of monomers. Here, we propose a multiary complex model of GPCR signaling activations via the vector representation of various unobserved aggregated receptor states. Our results from model simulations imply that receptor aggregation processes can govern cooperative effects in a regime inaccessible by previous theories. In particular, we show how the affinity of ligand-receptor binding can be largely varied by various oligomer formations in the low concentration range of G-protein stimulus., 6 pages, 4 figures

The stable conformer of 4–hydroxy–6–(trifluoromethyl)pyrimidine (HFMP) has been determined. The conformer (a) has 5.30 kcal mol–1 less energy than the conformer (b). The pyrimidine ring is characterised by alternating of bond angle distortions: the bond angles at N1, N3 and C5 atoms (115.6˚, 116.4˚, 115.1˚) are all less than 120˚, whereas the remaining angles in the ring at C2, C4 and C6 atoms (126.6˚, 122.6˚, 123.7˚) are more than 120˚. The chemical shifts are determined by GIAO method. Due to the electron withdrawing environment, the H7 and H8 chemical shifts are observed in the deshielded region at 8.30 and 7.29 ppm appear as singlet peak. The local reactivity descriptors (fk, sk and ωk) shows the more reactive sites for the nucleophilic and free radical attacks are N1 and N3. The favourable electrophilic attacking sites are C6 and N3. Amoung all the atoms N1 is the most attacking site by nucleophilic and free radical while C6 is for the electrophilic substitution.

The interaction of electromagnetic interaction by comprehensive theoretical and experimental FT‒IR, FT‒Raman and FT‒NMR spectroscopic studies of (1,3‒benzodioxol‒5‒yl)acetic acid (BDA) have been carried out. DFT/B3LYP method with 6‒311++G** and cc‒pVTZ basis sets have been used to determine the molecular properties of BDA. Five different conformers I, II, III, IV and V of BDA has been determined by potential energy profile. The most stable BDA molecule adopts a non‒planar (puckered) conformation I. The total energy, heat capacity, entropy, vibrational energy and zero point energy calculated by B3LYP/cc‒pVTZ basis sets are 106.34 kcal mol‒1, 40.22 kcal mol‒1 K‒1, 103.44 kcal mol‒1, 104.56 kcal mol‒1 and 99.72 kcal mol‒1, respectively. The total electron density of the BDA molecule spread between + 5.53e ×10‒2 and ‒5.531e ×10‒2. The electrostatic potential are lie in the range ± 1.123e ×10‒2. In BDA molecule n(O12) → π* C11‒O13 interaction is strongly stablised by 42.5 kcal mol‒1. The carbon atoms C3 and C4 are highly deshielded due to –I effect of highly electronegative oxygen. The symmetrical O‒C‒O vibration is blue shifted by 20 and 24 cm‒1 in FT‒IR and FT‒Raman spectra, respectively, when compared to methylenedioxy benzene. The reactivity order for the electrophilic attack is C9 > C10 > C11 while the reactivity order for the nucleophilic attack is C10 > C9 > C3.

The experimental and theoretical studies on the structure and vibrations of 1–acetyl–3–indolecarboxaldehyde (AIC) have been carried out by utilising FT–IR, FT–Raman, FT–NMR and quantum chemical density functional theory (DFT) method. The FT–IR and FT–Raman spectra are recorded in the region 4000–400 cm−1 and 4000–100 cm−1, respectively. The geometry of AIC is optimised by B3LYP method with 6–31G**, 6–311++G** and cc–pVTZ basis sets. The more stable minimum energy conformer has been found by analyzing the potential energy profile. The fundamental vibrational frequencies, infrared intensities, Raman intensities and bonding features of this compound are determined. The HOMO and LUMO energy difference show that, the charge transfer occurs within the molecule. The electrostatic potential and thermodynamic properties of the compound at the different temperatures have been calculated. 1H and 13C NMR chemical shifts of the compound are determined by Gauge Invariant Atomic Orbital (GIAO) by using B3LYP/6–311++G** method. The electrostatic potential of AIC lie in the range +1.22e × 10−2 to −1.22e × 10−2. The limits of total electron density of the complex is +4.906e × 10−2 to −4.906e × 10−2.

The FT–IR and FT–Raman spectra of 4–trifluoromethylbenzylamine (TFMBA) have been recorded in the range 4000–450 and 4000–100 cm−1 respectively. The conformational analysis of the compound has been carried out to attain stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT–Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers obtained theoretically from the B3LYP gradient calculations employing the standard high level 6–311++G** and cc–pVTZ basis sets for the optimised geometry of the compound. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. The electronic properties, highest occupied molecular orbital and lowest unoccupied molecular orbital energies are measured by DFT approach. The charges of the atoms by natural bond orbital (NBO) analysis are determined by B3LYP/cc–pVTZ method. The structure–chemical reactivity relations of the compound are determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods.

The stable conformer of 4−bromoisophthalic acid (BIPA) has been identified by potential energy profile analysis. All the structural parameters of 4−bromoisophthalic acid are determined by B3LYP method with 6–311++G**, 6−31G** and cc−pVTZ basis sets. The fundamental vibrations are analysed with the use of FT−IR (4000–400 cm−1) and FT−Raman (4000−100 cm−1) spectra. The harmonic vibrational frequencies are theoretically calculated and compared with experimental FTIR and FT−Raman frequencies. The 1H and 13C NMR spectra have been analysed and compared with theoretical 1H and 13C NMR chemical shifts calculated by gauge independent atomic orbital (GIAO) method. The electronic properties, such as HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energies are determined by B3LYP/cc−pVTZ method. The electron density distribution and site of chemical reactivity of BIPA molecule have been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP). Stability of the molecules arising from hyperconjugative interactions, charge delocalizations have been analysed by using natural bond orbital (NBO) analysis. The thermodynamic properties and atomic natural charges of the compound are analysed and the reactive sites of the molecule are identified. The global and local reactivity descriptors are evaluated to analyse the chemical reactivity and site selectivity of molecule through Fukui functions.

The structure of 4−nitroindole (4NI) and 7−nitroindole (7NI) is optimised by B3LYP level using 6 − 31++G** and cc−pVTZ basis sets. The FT−IR and FT−Raman and NMR spectra of 4NI and 7NI are analysed in detail and compared. The observed 1H and 13C NMR chemical shifts are found good correlation with theoretical chemical shifts calculated by GIAO method. The vibrational frequencies of 4NI and 7NI have been precisely assigned and analysed. The electron density and electrostatic potential of 4NI is more than that 7NI molecule. The bond orbital analysis (NBO) is carried out. The dual Fukui descriptors (Δfk), the dual local softness (Δsk) and the multiphilicity descriptors (Δωk) have clearly reveals that the atoms N1, C2, C3, C4, C8 are more favourable for nucleophilic attack in both 4NI. In the case of 7NI molecule N1, C2, C3, C5, C7 are more prone to nucleophilic attack. The local reactivity descriptors favours electrophilic attack at the carbon atom C9 of 4NI and 7NI molecules.

Complete structural, electronic and vibrational properties of 1,2–epoxy–3–phenoxy propane (EPOP) and 1,2–epoxy–3–(p–tolyloxy)propane (ETOP) molecules have been investigated with the help of FT–IR, FT–Raman and FT–NMR spectra of the compounds with the support of the theoretical calculations carried out by DFT/B3LYP method of calculations with 6–311 + + G** and cc–pVTZ basis sets. Various possible conformers of the compounds are determined by analyzing the potential energy profile. In EPOP, the stable conformer I is more stable than the second II by 0.1776 kcal mol–1. Similarly, the conformer I of ETOP is more stable than the conformer II 0.8435 kcal mol–1. The various modes of vibrational frequencies are assigned and analysed with the help of FT–IR and FT–Raman spectra. The electronic properties, such as HOMO and LUMO energies are determined. In both the cases of EPOP and ETOP, the HOMO space distribution reveals that all the carbon atoms of the phenyl ring, the methyl carbon atom and the methylene hydrogen atoms H8 and H9 are more favourable for electrophilic attack. The lone pair donor orbital, n(O10) → π*C11–C16 interaction in EPOP is strongly stabilised by 29.34 kcal mol–1. In the case of ETOP compound, πC12–C13 → π*C11–C16 interaction has more stabilisation energy, 21.34 kcal mol–1. The stabilisation energy of lone pair donor orbital, n(O10) → σ*C11–C16 is 28.80 kcal mol–1. 1H and 13C chemical shifts of the molecules are calculated by GIAO method and discussed. For EPOP, the hydrogen atoms H4, H5 and H6 present in the epoxy ring shows peaks at 2.72, 2.85 and 3.32 ppm, respectively. In the case of ETOP the epoxy hydrogen shows up field peak at 2.70, 2.84 and 2.30 ppm, because of the presence of hyperconjugative effect of the methyl group. The chemical reactivity and site selectivity of the molecule has been determined with the help of global and local reactivity descriptors. The Δfk, Δsk and Δωk values of ETOP suggests that C14 and C11 carbon atoms are more prone to nucleophilic attack while in EPOP the Δfk and Δωk values shows that C14 and C11 is the active sites for the nucleophilic attack but Δsk is only favourable for C11 and not for C14 atom.

The new hydrogen bonded molecular complex 1,2,4–triazolium hydrogenselenate (THS) is prepared by the reaction of 1H–1,2,4–triazole and selenic acid. This complex is stabilised by N–H⋯O and C–H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4–triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H–1,2,4–triazole molecule, results in the formation of 1,2,4–triazolium hydrogenselenate which contains 1,2,4–triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc–pVTZ and B3LYP/6–311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO–1, LUMO+1 and LUMO–HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT–IR and FT–Raman spectra.

The conformational analysis of 1–(diaminomethylene)thiourea (MTU) has been done to find out the more stable conformer. The more stable geometry of MTU and 2–imino–4–thiobiuret (ITB) are optimised with B3LYP method using 6–311++G** and cc–pVTZ basis sets. The molecules are not planar. The complete molecular structural parameters and thermodynamic properties of the optimised geometry have been determined. The molecule of MTU is not a planar but twisted. The MEP of MTU lies in the region from +1.175e × 10 −2 to −1.175e × 10 −2 while the total electron density spread between +6.371e × 10 −2 and −6.371e × 10 −2 . The MEP of ITB distributed between +1.179e × 10 −2 and −1.179e × 10 −2 while the total electron density of ITB lies in the region +7.729e × 10 −2 and −7.729e × 10 −2 . The energies of important MOs of the compound were also evaluated from DFT method. The LUMO shows that the nitrogen and sulphur atoms are the most nucleophilic attacking sites whereas the HOMO reveals that nitrogen, sulphur and carbon atoms are for the electrophilic substitutions. The vibrational frequencies of the fundamental modes of the compounds have been precisely assigned, analysed and the theoretical results were compared with the experimental wavenumbers. 1 H and 13 C NMR isotropic chemical shifts were determined and the assignments are compared with the experimental values. In MTU molecule, the n → π* transitions such as n(N5) → π* C4–S6 and n(N1) → π* C2–N3 interactions are strongly stabilised by 66.60 and 41.24 kcal mol −1 , respectively. In the case of ITB compound, the stabilisation energy of lone pair donor orbital, n(N5) → σ* C4–S6 is 46.03 kcal mol −1 . The dual descriptors Δf k , Δs k and Δω k values clearly indicate that the order of nucleophilic attack in MTU is S6 > N11 > N1 > N5 > N3 while in ITB the order follows as N1 > N11 > N5>S6 > N3.

The hydrogen bonded molecular complex bis(1–hydroxy–2–methylpropan–2–aminium)selenate (C 8 H 24 N 2 O 6 Se) has been prepared by the reaction of 2–amino–2–methyl propanol and selenic acid. The X–ray diffraction analysis revealed that the intermolecular proton transfer from selenic acid (SeO 4 H 2 ) to 2–amino–2–methylpropanol results in the formation of bis(1–hydroxy–2–methylpropan–2–aminium)selenate (HMPAS) salt and the fragments are connected through H–bonding and ion pairing. The N–H⋯O and O–H⋯O interactions between 2–amino–2–methylpropanol and selenic acid determine the supramolecular arrangement in three–dimensional space. The salt crystallises in the space group P121/n1 of monoclinic system. The complete vibrational assignments of HMPAS have been performed by FTIR and FT–Raman spectroscopy. The experimental data are correlated with the structural properties namely the energy, thermodynamic parameters, atomic charges, hybridization concepts and vibrational frequencies determined by quantum chemical studies performed with B3LYP method using 6–311++G*, 6–31+G* and 6–31G** basis sets.

Background Studies using quantitative experimental methods have shown that intracellular spatial distribution of molecules plays a central role in many cellular systems. Spatially resolved computer simulations can integrate quantitative data from these experiments to construct physically accurate models of the systems. Although computationally expensive, microscopic resolution reaction-diffusion simulators, such as Spatiocyte can directly capture intracellular effects comprising diffusion-limited reactions and volume exclusion from crowded molecules by explicitly representing individual diffusing molecules in space. To alleviate the steep computational cost typically associated with the simulation of large or crowded intracellular compartments, we present a parallelized Spatiocyte method called pSpatiocyte. Results The new high-performance method employs unique parallelization schemes on hexagonal close-packed (HCP) lattice to efficiently exploit the resources of common workstations and large distributed memory parallel computers. We introduce a coordinate system for fast accesses to HCP lattice voxels, a parallelized event scheduler, a parallelized Gillespie’s direct-method for unimolecular reactions, and a parallelized event for diffusion and bimolecular reaction processes. We verified the correctness of pSpatiocyte reaction and diffusion processes by comparison to theory. To evaluate the performance of pSpatiocyte, we performed a series of parallelized diffusion runs on the RIKEN K computer. In the case of fine lattice discretization with low voxel occupancy, pSpatiocyte exhibited 74% parallel efficiency and achieved a speedup of 7686 times with 663552 cores compared to the runtime with 64 cores. In the weak scaling performance, pSpatiocyte obtained efficiencies of at least 60% with up to 663552 cores. When executing the Michaelis-Menten benchmark model on an eight-core workstation, pSpatiocyte required 45- and 55-fold shorter runtimes than Smoldyn and the parallel version of ReaDDy, respectively. As a high-performance application example, we study the dual phosphorylation-dephosphorylation cycle of the MAPK system, a typical reaction network motif in cell signaling pathways. Conclusions pSpatiocyte demonstrates good accuracies, fast runtimes and a significant performance advantage over well-known microscopic particle methods in large-scale simulations of intracellular reaction-diffusion systems. The source code of pSpatiocyte is available at https://spatiocyte.org.

While cooperativity in ligand-induced receptor dimerization has been linked with receptor-receptor couplings via minimal representations of physical observables, effects arising from higher-order oligomer (e.g., trimer and tetramer) formations of unobserved receptors have received less attention. Here, we propose a dimerization model of ligand-induced receptors in multivalent form representing physical observables under basis vectors of various aggregated receptor-states. Our simulations of multivalent models not only reject Wofsy-Goldstein parameter conditions for cooperativity, but show higher-order oligomer formations can shift cooperativity from positive to negative., Comment: 6 pages, 3 figures

The molecular structural parameters and thermodynamic properties of trans–3,4–(methylenedioxy)cinnamic acid have been determined by B3LYP method by using 6–311++G** and cc–pVTZ basis sets. The vibrational frequencies of the compound have been precisely assigned, analysed and the theoretical results are compared with FT-IR and FT-Raman data. The energies of important MOs of the compound are also evaluated from DFT method. The frontier orbital energy gap (ELUMO–EHOMO) is found to be 4.1032 eV. The hydrogen and carbon chemical shifts are elaborately discussed. The dual descriptors Δfk, Δsk and Δωk reveals that the order of reactivity towards nucleophilic attack is C1 > O13 > O12 > C3 > C8 > C6. The minimum and maximum limits of the electrostatic potential observed in MDCA is –1.448e × 10–2(red) and +1.448e × 10–2 (blue). Thus, the present investigation provides complete structural, vibrational and reactivity characteristics of the compound .

The stable conformers of trans –2–methoxycinnamic acid ( trans –2MCA) are determined by potential energy profile analysis. The energies of the s–cis and s–trans conformers of trans –2MCA determined by B3LYP/cc–pVTZ method are −612.9788331 Hartrees and −612.9780953 Hartrees, respectively. The vibrational and electronic investigations of the stable s–cis and s–trans conformers of trans –2–methoxycinnamic acid have been carried out extensively with FTIR and FT–Raman spectral techniques. The s–cis conformer (I) with a (C16–C17–C18–O19) dihedral angle equal to 0° is found to be more favoured relative to the one s–trans (II) with (C16–C17–C18–O19) = 180°, possibly due to delocalization, hydrogen bonding and steric repulsion effects between the methoxy and acrylic acid groups. The DFT studies are performed with B3LYP method by utilizing 6–311++G** and cc–pVTZ basis sets to determine the structure, thermodynamic properties, vibrational characteristics and chemical shifts of the compound. The total dipole moments of the conformers determined by B3LYP/cc–pVTZ method are 3.35 D and 4.87 D for s–cis and s–trans , respectively. It reveals the higher polarity of s–trans conformer of trans –2MCA molecule. The electronic and steric influence of the methoxy group on the skeletal frequencies has been analysed. The energies of the frontier molecular orbitals and the LUMO-HOMO energy gap have been determined. The MEP of s–cis conformer lie in the range +1.374e × 10 −2 to −1.374e × 10 −2 while for s–trans it is +1.591e × 10 −2 to −1.591e × 10 −2 . The total electron density of s–cis conformer lie in the range +5.273e × 10 −2 to −5.273e × 10 −2 while for s–trans it is +5.403e × 10 −2 to −5.403e × 10 −2 . The MEP and total electron density shows that the s–cis conformer is less polar, less reactive and more stable than the s–trans conformer. All the reactivity descriptors of the molecule have been discussed. Intramolecular electronic interactions and their stabilisation energies have analysed by NBO method.

The crystals of 1,3-diammonium propylselenate monohydrate (DAPS) were prepared and characterised X ray diffraction (XRD), FT-IR, FT-Raman spectroscopy, and DFT/B3LYP methods. It comprises protonated propyl ammonium moieties (diammonium propyl cations), selenate anions and water molecule which are held together by a number of hydrogen bonds and form infinite chains. The XRD data confirm the transfer of two protons from selenic acid to 1,3-diaminopropane molecule. The DAPS complex is stabilised by the presence of O-H center dot center dot center dot O and N-H center dot center dot center dot O hydrogen bonds and the electrostatic interactions as well. The N center dot center dot center dot O and O center dot center dot center dot O bond distances are 2.82-2.91 and 2.77 A, respectively. The FT-IR and FT Raman spectra of 1,3-diammonium propyl selenate monohydrate are recorded and the complete vibrational assignments have been discussed. The geometry is optimised by B3LYP method using 6-311G, 6-311+G and 6-311+G* basis sets and the energy, structural parameters, vibrational frequencies, IR and Raman intensities are determined. Differential scanning colorimetry (DSC) data were also presented to analyse the possibility of the phase transition. Complete natural bonding orbital (NBO) analysis is carried out to analyse the intramolecular electronic interactions and their stabilisation energies. The electrostatic potential of the complex lies in the range +1.902e x 10(-2) to -1.902e x 10(-2). The limits of total electron density of the complex is +8.43e x 10(-2) to 8.43e x 10(-2). (C) 2015 Elsevier B.V. All rights reserved.

The structure, electronic properties, vibrational fundamental modes and thermodynamic properties of 3–acetylindole (3AI) and indole–3–acetamide (3IAM) compounds are investigated. The most stable geometry, structural parameters and vibrational wavenumbers are determined by using B3LYP method with 6–311++G∗∗ and cc–pVTZ basis sets. FT–IR and FT–Raman spectrum of the compounds are recorded in the range of 4000–400 and 4000–100 cm−1, respectively. The molecular electrostatic potential and total electron density of the compounds have been analysed. The chemical reactivity and site selectivity of the molecules have been investigated by utilising global and local reactivity descriptors.

The most stable conformer of isoquinoline–1–carboxylic acid (IQ1CA) and isoquinoline–3–carboxylic acid (IQ3CA) are determined and the geometry has been optimised with B3LYP method using high level 6–311++G** and cc–pVTZ basis sets. The structure, electronic properties, vibrational fundamental modes, thermodynamic properties and chemical shifts of the compounds are investigated. The vibrational fundamental modes are assigned and analysed by utilising FT–IR and FT–Raman spectrum of the compounds recorded in the range of 4000–400 and 4000–100 cm−1, respectively. The LUMO–HOMO energy difference is determined to explain the charge transfer within the molecule. The molecular electrostatic potential and total electron density of the molecules are determined to explain the size, shape and the reactive sites (polar) of the molecules. The 1H and 13C NMR chemical shifts of the compounds are determined by Gauge Invariant Atomic Orbital (GIAO) method using DMSO–d6 solvent by B3LYP/cc–pVTZ method. The local and global chemical reactivity properties of the compounds have been investigated with the help of global and local reactivity descriptors.

Microscopic models of reaction-diffusion processes on the cell membrane can link local spatiotemporal effects to macroscopic self-organized patterns often observed on the membrane. Simulation schemes based on the microscopic lattice method (MLM) can model these processes at the microscopic scale by tracking individual molecules, represented as hard-spheres, on fine lattice voxels. Although MLM is simple to implement and is generally less computationally demanding than off-lattice approaches, its accuracy and consistency in modeling surface reactions have not been fully verifed. Using the Spatiocyte scheme, we study the accuracy of MLM in diffusion-influenced surface reactions. We derive the lattice-based bimolecular association rates for two-dimensional surface-surface reaction and one-dimensional volume-surface adsorption according to the Smoluchowski-Collins-Kimball model and random walk theory. We match the time-dependent rates on lattice with off-lattice counterparts to obtain the correct expressions for MLM parameters in terms of physical constants. The expressions indicate that the voxel size needs to be at least 0.6% larger than the molecule to accurately simulate surface reactions on triangular lattice. On square lattice, the minimum voxel size should be even larger, at 5%. We also demonstrate the ability of MLM-based schemes such as Spatiocyte to simulate a reaction-diffusion model that involves all dimensions: three-dimensional diffusion in the cytoplasm, two-dimensional diffusion on the cell membrane and one-dimensional cytoplasm-membrane adsorption. With the model, we examine the contribution of the 2D reaction pathway to the overall reaction rate at different reactant diffusivity, reactivity and concentrations.

Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal scales but cannot directly account for the microscopic effects in the cell such as volume exclusion and diffusion-influenced reactions. Nonetheless, schemes based on the high-resolution microscopic lattice method (MLM) can directly simulate these effects by representing each finite-sized molecule explicitly as a random walker on fine lattice voxels. The theory and consistency of MLM in simulating diffusion-influenced reactions have not been clarified in detail. Here, we examine MLM in solving diffusion-influenced reactions in 3D space by employing the Spatiocyte simulation scheme. Applying the random walk theory, we construct the general theoretical framework underlying the method and obtain analytical expressions for the total rebinding probability and the effective reaction rate. By matching Collins-Kimball and lattice-based rate constants, we obtained the exact expressions to determine the reaction acceptance probability and voxel size. We found that the size of voxel should be about 2% larger than the molecule. MLM is validated by numerical simulations, showing good agreement with the off-lattice particle-based method, eGFRD. MLM run time is more than an order of magnitude faster than eGFRD when diffusing macromolecules with typical concentrations in the cell. MLM also showed good agreements with eGFRD and mean-field models in case studies of two basic motifs of intracellular signaling, the protein production-degradation process and the dual phosphorylation cycle. Moreover, when a reaction compartment is populated with volume-excluding obstacles, MLM captures the non-classical reaction kinetics caused by anomalous diffusion of reacting molecules.

Tapentadol is a novel opioid pain reliever drug with a dual mechanism of action, having potency between morphine and tramadol. Quantum chemical calculations have been carried out for tapentadol hydrochloride (TAP.Cl) to determine the properties. The geometry is optimised and the structural properties of the compound were determined from the optimised geometry by B3LYP method using 6–311++G(d,p), 6–31G(d,p) and cc–pVDZ basis sets. FT-IR and FT–Raman spectra are recorded in the solid phase in the region of 4000–400 and 4000–100 cm −1 , respectively. Frontier molecular orbital energies, LUMO–HOMO energy gap, ionisation potential, electron affinity, electronegativity, hardness and chemical potential are also calculated. The stability of the molecule arising from hyperconjugative interactions and charge delocalisation has been analysed using NBO analysis. The 1 H and 13 C nuclear magnetic resonance chemical shifts of the molecule are analysed.

We propose a computational method to quantitatively evaluate the systematic uncertainties that arise from undetectable sources in biological measurements using live-cell imaging techniques. We then demonstrate this method in measuring biological cooperativity of molecular binding networks: in particular, ligand molecules binding to cell surface receptor proteins. Our results show how the non-statistical uncertainties lead to invalid identification of the measured cooperativity. Through this computational scheme, the biological interpretation can be more objectively evaluated and understood under a specific experimental configuration of interest., Comment: 110 pages, 96 figures

Aromatic epoxides are causative factors for mutagenic and carcinogenic activity of polycyclic arenes. The 1,2- or 2,3-epoxy compounds are widely used to a considerable extent in the textile, plastics, pharmaceutical, cosmetics, detergent and photochemical industries. The FTIR and FT-Raman spectra of (1,2-epoxyethyl)benzene and (1,2-epoxy-2-phenyl)propane are recorded in the regions 4000–400 cm −1 and 4000–100 cm −1 , respectively. The observed fundamentals are assigned to different normal modes of vibration. The structure of the compound has been optimised with B3LYP method using 6-311++G ** and cc-pVTZ basis sets. The IR and Raman intensities are determined. The total electron density and molecular electrostatic potential surfaces of the molecule are constructed by using B3LYP/6-311++G(d,p) method to display electrostatic potential (electron + nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. Natural bond orbital analysis of the compounds has been performed to indicate the presence of intramolecular charge transfer. The 1 H and 13 C NMR chemical shifts of the molecules have been analysed.

Melaminium glutarate monohydrate has been synthesised and FTIR and FT-Raman spectral investigations are carried out. The molecular geometry and vibrational frequencies of melaminium glutarate monohydrate in the ground state have been determined by using B3LYP method with 6-31++G**, 6-31++G and cc-pVDZ basis sets. The stability of the system, inter molecular hydrogen bonding and the electron donor–acceptor interactions of the complex have been investigated by using natural bonding orbital analysis. It reveals that the N H⋯O and O H⋯O intermolecular interactions significantly influence crystal packing of this molecular complex. The glutarate anion forms hydrogen bonds to the melaminium cation as the proton donor of the type N H⋯O with a distance (N⋯O) = 2.51 A. It is also linked by other hydrogen bonds to the water molecule of the type O H⋯O with (O⋯O) = 2.82 A and to the amino ( NH2) group of melaminium cation of the type N H⋯O with (N⋯O) = 2.82 A as the proton acceptor. The electrostatic potential of the complex is in the range +1.892e × 10−2 to −1.892e × 10−2. The limits of total electron density of the complex is +6.679e × 10−2 to −6.679e × 10−2.

The Fourier transform infrared (FTIR) and FT-Raman spectra of cis -2-methoxycinnamic acid have been measured in the range 4000–400 and 4000–100 cm −1 , respectively. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The geometry was optimised without any symmetry constrains using the DFT/B3LYP method utilising 6-311++G ∗∗ and cc-pVTZ basis sets. The thermodynamic stability and chemical reactivity descriptors of the molecule have been determined. The exact environment of C and H of the molecule has been analysed by NMR spectroscopies through 1 H and 13 C NMR chemical shifts of the molecule. The energies of the frontier molecular orbitals have also been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. The vibrational frequencies which were determined experimentally are compared with those obtained theoretically from density functional theory (DFT) gradient calculations employing the B3LYP/6-311++G ∗∗ and cc-pVTZ methods.

As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle simulator for biochemical reaction and diffusion processes. Simulations can be performed at single molecule and compartment spatial scales simultaneously. Molecules can diffuse and react in 1D (filament), 2D (membrane), and 3D (cytosol) compartments. The implications of crowded regions in the cell can be investigated because each diffusing molecule has spatial dimensions. Spatiocyte adopts multi-algorithm and multi-timescale frameworks to simulate models that simultaneously employ deterministic, stochastic, and particle reaction-diffusion algorithms. Comparison of light microscopy images to simulation snapshots is supported by Spatiocyte microscopy visualization and molecule tagging features. Spatiocyte is open-source software and is freely available at http://spatiocyte.org .

The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000–450 and 4000–100 cm −1 respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G ** , high level 6-311++G ** and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1 H (400 MHz; CDCl 3 ) and 13 C (100 MHz; CDCl 3 ) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure–chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors.

The FTIR and FT-Raman vibrational spectra of N-(4-bromophenyl)-2,2-dichloroacetamide molecule has been recorded and analysed the complete vibrational fundamental modes of the most stable geometry of the compound using the experimental FTIR and FT-Raman data on the basis of peak positions, relative intensities and quantum chemical studies. The observed vibrational frequencies were compared with the theoretical wavenumbers of the optimised geometry of the compound obtained from the DFT-B3LYP gradient calculations employing the high level 6-311++G** and cc-pVTZ basis sets. The effect of substituent Br in the amide moiety have been analysed and compared. The kinetic and thermodynamic stability and chemical reactivity descriptors of the molecule have been determined. The reactive centres are found from the molecular electrostatic potential and the atomic charges. The limits of electrostatic potential are −9.617e × 10−3 and +9.617e × 10−3. The molecule has great electronegativity difference, charge is very polarized, and there are significant differences in electron density in different regions of the molecule. The lone pair donor orbital, nN → π*CO interaction possess a strong stabilisation of 64.21 kcal mol−1.

Optimised geometrical structural parameters, harmonic vibrational frequencies, natural bonding orbital analysis and frontier molecular orbitals are determined by B3LYP and B3PW91 methods. The exact geometry of 5-chloro-1-methyl-4-nitroimidazole is determined through conformational analysis. The experimentally observed infrared and Raman bands have been assigned and analysed. The (13)C and (1)H NMR chemical shifts of the compound are investigated. The total electron density and molecular electrostatic potentials are determined. The electrostatic potential (electron+nuclei) distribution, molecular shape, size and dipole moments of the molecule have been displayed. The energies of the frontier molecular orbitals and LUMO-HOMO energy gap are measured. The possible electronic transitions of the molecule are studied by TD-DFT method along with the UV-Visible spectrum. The structure-activity relationship of the compound is also investigated by conceptual DFT methods.

O-desmethyltramadol is one of the main metabolites of tramadol widely used clinically and has analgesic activity. The FTIR and FT-Raman spectra of O-desmethyl tramadol hydrochloride are recorded in the solid phase in the regions 4000-400 cm(-1) and 4000-100 cm(-1), respectively. The observed fundamentals are assigned to different normal modes of vibration. Theoretical studies have been performed as its hydrochloride salt. The structure of the compound has been optimised with B3LYP method using 6-31G(**) and cc-pVDZ basis sets. The optimised bond length and bond angles are correlated with the X-ray data. The experimental wavenumbers were compared with the scaled vibrational frequencies determined by DFT methods. The IR and Raman intensities are determined with B3LYP method using cc-pVDZ and 6-31G(d,p) basic sets. The total electron density and molecular electrostatic potential surfaces of the molecule are constructed by using B3LYP/cc-pVDZ method to display electrostatic potential (electron+nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. Natural bond orbital analysis of O-desmethyltramadol hydrochloride has been performed to indicate the presence of intramolecular charge transfer. The (1)H and (13)C NMR chemical shifts of the molecule have been anlysed.

The FTIR and FT-Raman spectra of 4-bromomethyl-5-methyl-1,3-dioxol-2-one and 4,5-bis(bromomethyl)-1,3-dioxol-2-one have been recorded in the regions 4000–400 and 4000–100 cm −1 , respectively. The geometry of the compounds are optimised with B3LYP method using 6-311++G ∗∗ and cc-pVTZ basis sets to characterise all the structural parameters. The optimised structural parameters of the most stable geometry are used in the vibrational frequency calculations. The total electron density and molecular electrostatic potential surfaces of the molecules are constructed by NBO analysis using B3LYP/6-311++G ∗∗ method to display the electrostatic potential (electron + nuclei) distribution, molecular shape, size, dipole moments and the reactive centres of the molecules. The energy gap between HOMO and LUMO is measured. The influences of methyl and bromomethyl groups on the skeletal vibrations have been investigated. The global and local reactivity descriptors are also determined to provide the informations on the electrophilic, nucleophilic and free radical prone reactive sites of the molecules.

The crystal structure investigations of melamine with phosphorous acid, namely melaminium dihydrogenphosphite monohydrate (C 3 N 6 H 7 ·H 2 PO 3 ·H 2 O) have been investigated by means of single crystal X-ray diffraction method. The title compound crystallizes in monoclinic crystal system, and the space group is P 2 1 / c with a = 10.069 A, b = 21.592 A, c = 12.409 A and Z = 12. The vibrational assignments and analysis of melaminium dihydrogen phosphite monohydrate have also been performed by FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical simulations were performed with DFT (B3LYP) method using 6-31G ** , cc-pVTZ, and 6-311++G ** basis sets to determine the energy, structural, thermodynamic parameters and vibrational frequencies of melaminium dihydrogen phosphite monohydrate. The hydrogen atom from phosphorous acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak O H···O and N H···O hydrogen bonds shows notable vibrational effects.

The FTIR and FT-Raman spectra of 1,2,4-benzenetricarboxylic-1,2-anhydride (BTCA) have been recorded in the range 4000-400 and 4000-100 cm(-1), respectively. The complete vibrational assignments and analysis of BTCA have been performed. More support on the experimental findings was added from the quantum chemical studies performed with DFT (B3LYP, MP2, B3PW91) method using 6-311++G(**), 6-31G(**) and cc-pVTZ basis sets. The structural parameters, energies, thermodynamic parameters, vibrational frequencies and the NBO charges of BTCA were determined by the DFT method. The (1)H and (13)C isotropic chemical shifts (δ ppm) of BTCA with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. The delocalization energies of different types of interactions were determined.

The solid phase FTIR and FT-Raman spectra of primidone were recorded in the regions 4000–400 cm−1 and 4000–100 cm−1, respectively. The vibrational spectra were analysed and the observed fundamentals were assigned and analysed. The experimental wavenumbers were compared with the theoretical scaled vibrational wavenumbers determined by DFT methods. The Raman intensities were also determined with B3LYP/6-31G(d,p) method. The total electron density and molecular electrostatic potential surface of the molecule were constructed by using B3LYP/6-311++G(d,p) method to display electrostatic potential (electron + nuclei) distribution. The HOMO and LUMO energies were measured. Natural bond orbital analysis of primidone has been performed to indicate the presence of intramolecular charge transfer. The 1H and 13C NMR spectra were recorded and the chemical shifts of the molecule were calculated.