Quantum chemical package Jaguar: A survey of recent developments and unique features

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.

Investigation of the interaction of thymine drugs with Be12O12 and Ca12O12 nanocages: A quantum chemical study

Based on the DFT in a Wb97xd/6-311+G* level of theory, the interaction of thymine derivatives with Be12O12 and Ca12O12 nanocages was investigated. It was found that adsorption energies of thymine molecules on the Be12/Ca12-O12 surface was around -43.16, -60.06 and -29.62, -50.71, -45.95, -30.27 kcal/mol, for thymine (TH1), 1-amino thymine (TH2) and thymine glycol (TH3), respectively and this result supported the drug's adsorption. Additionally, according to the FMOs and MEP studies, a charge transfer from TH's to nanocages. Additionally, both molecular orbitals demonstrate that the LUMO and HOMO are primarily found on the BeO's surface.

Investigation of Pharmaceutical Importance of 2H-Pyran-2-One Analogues via Computational Approaches

Highly functionalized spirocyclic ketals were synthesized through asymmetric oxidative spirocyclization via carbanion-induced ring transformation of 2H-pyran-2-ones with 1,4-cyclohexandione monoethyleneketal under alkaline conditions. Further acidic-hydrolysis of obtained spirocyclic ketals yields highly substituted 2-tetralone in good yield. Computational analysis based on the DFT calculations and MD simulations has been performed in order to predict and understand global and local reactivity properties of newly synthesized derivatives. DFT calculations covered fundamental reactivity descriptors such as molecular electrostatic potential and average local ionization energies. Nitrogen atom and benzene rings have been recognized as the most important molecular sites from these aspects. Additionally, to predict whether studied compounds are stable towards the autoxidation mechanism, we have also studied the bond dissociation energies for hydrogen abstraction and identified the derivative which might form potentially genotoxic impurities. Interactions with water, including both global and local aspects, have been covered thanks to the MD simulations and calculations of interaction energies with water, counting of formed hydrogen interactions, and radial distribution functions. MD simulations were also used to identify which excipient could be used together with these compounds, and it has been established that the polyvinylpyrrolidone polymer could be highly compatible with these compounds, from the aspect of calculated solubility parameters.

Investigation of the reactivity properties of a thiourea derivative with anticancer activity by DFT and MD simulations

Spectroscopic analysis of 1-(2-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (FPTT) is reported. Experimental and theoretical analyses of FPTT, with molecular dynamics (MD) simulations, are reported for finding different parameters like identification of suitable excipients, interactions with water, and sensitivity towards autoxidation. Molecular dynamics and docking show that FPTT can act as a potential inhibitor for new drug. Additionally, local reactivity, interactivity with water, and compatibility of FPTT molecule with frequently used excipients have been studied by combined application of density functional theory (DFT) and MD simulations. Analysis of local reactivity has been performed based on selected fundamental quantum-molecular descriptors, while interactivity with water was studied by calculations of radial distribution functions (RDFs). Compatibility with excipients has been assessed through calculations of solubility parameters, applying MD simulations. Graphical abstract Reactive sites identified.

Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a benzoic acid derivative

Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering of 4-((3-bromo-5-chloro-2-hydroxybenzylidene)amino)benzoic acid (BCHB) have been studied on different silver colloids concentrations in order to know the particular chemical species responsible for the spectra. For Raman and surface enhanced Raman scattering (SERS) wavenumbers, changes are observed. Observed variations in the modes of ring may be due to interaction of the π-electrons and presence of this indicated that RingII is more inclined than RingI and the BCHB assumes inclined orientation for concentration 10^-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to determine the electron-rich and poor sites of BCHB, the molecular electrostatic potential was also constructed. The molecular docking studies show that the bindings and interactions with the receptors may be supporting evidence for further studies in design further BCHB pharmaceutical applications.

Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative

Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of (E)-N'-(5-chloro-2-hydroxybenzylidene)-4-trifluoromethyl) benzohydrazide (CHTB) have been studied on different silver colloids in order to know the particular chemical species responsible for the spectra. Very significant shifts are observed for Raman and SERS wavenumbers. Observed changes in the υ-ring modes may be due to surface interaction of the π-electrons and the presence of this suggested that RingII is more tilted in both cases than RingI and the molecule assumes a tilted orientation for the concentration 10^-3 M. Orientation changes are seen in concentration dependent SERS spectra. The molecular electrostatic potential has also been constructed to determine the electron rich and poor site of CHTB. The molecular docking studies indicate that the binding affinity and hydrogen bond interactions with the receptors may be supporting evidence for further studies in designing other pharmaceutical applications of CHTB.Communicated by Ramaswamy H. Sarma.

Spectroscopic and computational study of chromone derivatives with antitumor activity: detailed DFT, QTAIM and docking investigations

Theoretical investigations of three pharmaceutically active chromone derivatives, (E)-3-((2,3,5,6-tetrafluorophenyl)hydrazono)methyl)-4H-chromen-4-one (TPC), (E)-3-((2-(2,4,6-trifluorophenyl)hydrazono)methyl)-4H-chromen-4-one (FHM) and(E)-3-((2-(perfluorophenyl)hydrazono)methyl)-4H-chromen-4-one (PFH) are reported. Molecular geometries, vibrational spectra, electronic properties and molecular electrostatic potential were investigated using density functional theory. Quantum theory of atoms in molecules (QTAIM) study shows that the maximum of ellipticity parameters in the existing bonds in TPC, FHM and PFH, attributes to the bonds involving in aromatic region points toward the π-bond interactions in the molecules. Based on energy gap (1.870, 1.649 and 1.590 eV) and electrophilicity index (20.233, 22.581 and 23.203 eV) values of TPC, FHM and PFH, we can conclude that all molecules have more biological activity. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of the molecule and also to describe the intermolecular interactions. All these studies including docking studies, help a lot in determining the biological activities of chromone derivatives. Activities of chromone derivatives are compared with 5-fluorouracil and azathioprine (antitumor, antiproliferative standards) and were found to be higher than reference ones.

Investigation of the chemical and optical properties of halogen-substituted N-methyl-4-piperidone curcumin analogs by density functional theory calculations

Halogen-substituted N-methyl-4-piperidone curcumin analog compounds were studied for their molecular structure, molecular vibration analysis, natural bond orbital, ultraviolet spectra, molecular reactivity analysis, and nonlinear optical properties. The molecules in interest were the (3E,5E)-3,5-dibenzylidene-1-methylpiperidin-4-one along with its substituted halogen (X = F- or Cl- or Br-) at the ortho, meta and para position in the phenyl ring. The calculated geometrical parameters at B3LYP/6-311++G(d,p) were in good agreement with the available experimental XRD data. Using the frequency calculations, the molecular vibrational modes have been analyzed. Meanwhile, the hyperconjugative stabilization energies have been calculated using NBO analysis to address the donor and acceptor in the hyperconjugation. The calculated UV spectra at TD-CAM-B3LYP/6-311++G(d,p) show strong absorption around 300 to 320 nm which corresponds to the absorption in the UV-A and UV-B region. From molecular electrostatic potential surface, CO moiety is one of the electronegative regions in the compounds where the CX moiety is the other electronegative region of the compounds. Fluoro-substituted compounds are the compounds with the most electronegativity while bromo-substituted compounds are the compounds with the least electronegativity. Calculations of average local ionization energy surfaces have been performed to obtain information related to the local reactivity of the molecules where the phenyl becomes less reactive after the substitution. The calculated first hyperpolarizability is 6 to 17 times larger than urea, the standard nonlinear optic material. These findings imply that all of the molecules considered have potential to be applied as active sunscreen material or nonlinear optic material.

Conformational profile, vibrational assignments, NLO properties and molecular docking of biologically active herbicide1,1-dimethyl-3-phenylurea

1,1-Dimethyl-3-phenylurea (known as fenuron) which is a phenyl urea-based widely used herbicide exhibits interesting structural and conformational properties and a notable biological activity. A detailed analysis on the vibrational, molecular and electronic characteristics of fenuron has been carried out. Potential energy scans (PESs) performed at the B3LYP/6-311++G(d,p) level of theory predicted two possible minima corresponding to the optimized anti and synforms resulting from the internal rotation about the N-C bond. The presence of an auxochrome together with the interaction with DMSO solvent exhibited a blue shift corresponding to the C=O orbitals. Delocalization of HOMO and LUMO orbital facilitated the charge transfer effect in the molecule. The calculated HOMO-LUMO energies, chemical potential, energy gap and global hardness suggested a low softness value for the compound while its biological activity was described by the value of electrophilicity. Chlorine substitution in the phenyl ring influenced the orbital delocalization for ortho and para substitutions but that of meta remained unaffected. NLO properties were noticed to increase due to chlorine substitution in the parent molecule. The docking results suggested that the compound exhibits an inhibitory activity against mitochondrial ubiquinol-cytochrome-c reductase and can be developed as a potential anticancer agent.

Synthesis of 5-(5-methyl-benzofuran-3-ylmethyl)-3H- [1, 3, 4] oxadiazole-2-thione and investigation of its spectroscopic, reactivity, optoelectronic and drug likeness properties by combined computational and experimental approach

This paper reports the synthesis of 5-(5-methyl-benzofuran-3-ylmethyl)-3H- [1, 3, 4] oxadiazole-2-thione (5MBOT) and characterization by FT-IR, FT-Raman, ¹H NMR, ¹³C NMR and UV spectral studies. The density functional theory (DFT) calculations have been executed for the 5MBOT using B3LYP/6-31++G (d, p) basis set. The fundamental modes of the vibrations were designated by the potential energy distribution (PED), and the computed and experimental values support each other. The ¹H NMR and ¹³C NMR chemical shifts of 5MBOT were estimated by gauge-including atomic orbitals (GIAO) method and compared with the experimental chemical shifts. The UV-Vis method used to study the visible absorption maxima (λ_max) by using Time-Dependent DFT. Further, the Mulliken population analysis (MPA), natural population analysis (NPA) charges, thermodynamic properties at different temperatures were presented. The calculated HOMO and LUMO energies show that charge transfer within the molecule. The natural bonds orbital (NBO) also computed. Optoelectronic properties have been carried out by combination of DFT calculations and molecular dynamics (MD) simulations, in order to assess the potential of this structure for applications in organic electronics. Further, the study encompassed calculations of reorganization energies for holes and electrons and charge transfer rates. DFT calculations have been also used in order to identify locations possibly sensitive towards the autoxidation mechanism, which correlates between bond dissociation energy for hydrogen abstraction and the mechanism. The MD simulations have been used to understand interaction of 5MBOT with water molecules. Molecular docking studies reveals the antifungal activity of 5MBOT may be due to hydrogen bonding and hydrophobic interactions with different antifungal proteins.

Remarkable colorimetric sensing behavior of pyrazole-based chemosensor towards Cu(ii) ion detection: synthesis, characterization and theoretical investigations

We report the synthesis of a new imine based ligand, 3-((3-methoxybenzylidene)amino)-1H-pyrazol-5-ol (HL) and its Cu(ii) complexes in 2 : 1 (HL : metal) and 1 : 1 : 1 (HL : metal : HQ) stoichiometric ratio using 8-hydroxyquinoline (HQ) as an additional bidentate ligand. The synthesized ligand (HL) and its Cu(ii) complexes (1 and 2) are structurally characterized using FT-IR, electronic absorption and emission, NMR and MS techniques. Furthermore, the complexation of Cu2+ with HL leads to the immediate formation of brown colour solution which indicates that HL can act as simple colorimetric sensor for Cu2+ ions. We further investigated that the sensor could selectively bind to the Cu2+ ions even in the presence of competitive ions such as Mn2+, Fe2+, Co2+, Ni2+, Zn2+, Ag+ and Na+ ions in aqueous solutions which was studied by electronic absorption spectroscopy. The HL ligand has been investigated for its reactive properties by density functional theory (DFT) calculations. Quantum molecular descriptors describing local reactive properties have been calculated in order to identify the most reactive molecule sites of title compounds. DFT calculations encompassed molecular electrostatic potential (MEP), local average ionization energies (ALIE), Fukui functions and bond dissociation energies for hydrogen abstraction (H-BDE).

Structural, electronic and optical properties of 2,5-dichloro-p-xylene: experimental and theoretical calculations using DFT method

The vibrational spectra including FT-IR and FT-Raman for 2,5-dichloro-p-xylene (DCPX) have been recorded.