Computational Chemistry Research Papers - Academia.edu (original) (raw)

2025

We introduce the SFIT genus, a motivic topological quantum field theory encoding chiral coherence in molecules via derived tmf pushforwards and p-adic Laplacians. Key innovations in the SFIT genus, a motivic TQFT unifying: Derived... more

2025

2025, Journal of Climate Change

With a view to get a broader picture of paleoclimate/paleomonsoon variability we have selected 30 lakes with reliable chronologies from the climatically sensitive regions of India. An integrated review of different climate proxies i.e. grain size, C/N ratio, pollen, δ 13 C and δ 18 O and mineral magnetism on a radiocarbon dated sediment cores is carried out for present study. Here we present a climate-proxy record of monsoon variability over the past ~50,000 yr from monsoon and non-monsoon dominated regions. Our results based on multiproxy sediment records of lakes reveal that India experienced different climate and monsoon variability throughout geological past. Paleorecords give an insight of two climatically significant periods in this study area. A high monsoon activity has been noticed during the time resolution of 13 ka to 8 ka while a short dry period has prevailed during 5 ka-4 ka that is concurrent to the offset of Harappa civilization. Importantly, majority of paleoclimate records demonstrate that a Younger Dryas (12.9 ka-11.5 ka) records are not well preserved in lacustrine archives.

2025, Zenodo

This research presents a comparative study of Hartree-Fock (HF) and Density Functional Theory (DFT) methods, evaluating their computational efficiency and accuracy across multiple atomic systems. The study benchmarks orbital energy predictions, SCF convergence iterations, and total energy assessments across advanced quantum chemistry frameworks. Furthermore, Coupled-Cluster (CCSD and CCSD(T)) methodologies are assessed against HF and DFT to highlight performance trade-offs. The integration of machine learning (ML) and AI-driven optimization techniques in quantum chemistry models is also explored, showcasing potential improvements in accuracy and computational speed. The findings contribute to an enhanced understanding of computational resource allocation and methodological efficiency in quantum chemical simulations.

2025, PLOS Computational Biology

Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called Nbody Information Theory (NbIT) analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i)-channels for long-distance information sharing between functional sites, and (ii)-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD) trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems.

2025, Nature Communications

Both lipid and ion translocation by Ca 2+ -regulated TMEM16 transmembrane proteins utilizes a membrane-exposed hydrophilic groove. Several conformations of the groove are observed in TMEM16 protein structures, but how these conformations form, and what functions they support, remains unknown. From analyses of atomistic molecular dynamics simulations of Ca 2+ -bound nhTMEM16 we find that the mechanism of a conformational transition of the groove from membrane-exposed to occluded from the membrane involves the repositioning of transmembrane helix 4 (TM4) following its disengagement from a TM3/TM4 interaction interface. Residue L302 is a key element in the hydrophobic TM3/TM4 interaction patch that braces the open-groove conformation, which should be changed by an L302A mutation. The structure of the L302A mutant determined by cryogenic electron microscopy (cryo-EM) reveals a partially closed groove that could translocate ions, but not lipids. This is corroborated with functional assays showing severely impaired lipid scrambling, but robust channel activity by L302A.

2025, Chromatographia

Separation of rare earth elements (REE) by ion chromatography on a Dionex Ion Pac CS3 column (sulfonic acid type) has been studied at different temperatures (10-70 °C) and with both isocratic and gradient elution with a-hydroxyisobutyric acid (a-HIBA). Changes of column efficiency as a function of distribution coefficient and temperature could not be explained on the basis of classical Van Deemter or Glueckauf-Hamilton equations and possible explanation indicating the contribution of longitudinal diffusion in the resin phase to total zone spreading was provided. It was shown that the plate height for yttrium was distinctly smaller that those for lanthanides of similar ionic radii. An improved combined isocratic-gradient elution procedure was devised for separation of Sc, Y, La, and the lanthanides in one run. Column liquid chromatography Ion chromatography Effect of temperature Mechanism of zone spreading Rare earths and lanthanides

2025, Structural Chemistry

The synthesis and structure elucidation of two new compounds, 2-(methylthio)-1, 3-diazaspiro[4.4]non-2ene-4-one (1) and 2-(methylthio)-1,3-diazaspiro[4.4]non-2ene-4-thione (2), are presented. Both compounds crystalized in monoclinic crystal system. Compound 1 formed plate-like colorless crystals, while compound 2 gave yellow needles. The structural and spectral characteristics of both compounds are studied by IR and NMR spectroscopy and quantum chemistry. The optimized geometry, harmonic vibrational frequencies, and NMR shielding are calculated by DFT employing B3LYP functional using 6-311??G(d,p) basis set. Our results support the hydrogen bonding pattern observed in reported crystalline structure. Evidences are given indicating that the tautomeric form in solution is different from that one in solid state. The substantial difference between positions of the characteristic C=N band in nonpolar solvent and crystalline phase for both compounds suggests that in solid state a ''conjugated tautomeric form'' exists, while in solution phase there is ''non-conjugated tautomeric form''. In polar solvents, both tautomeric forms exist. It is suggested to call this phenomenon desmokatatropy-from Greeks derlo ´1 (bond) jasa 9rsarg (state) and sqo ´po1 (change).

2025, Bulletin of the American Physical Society

2025, Journal of Molecular Structure

The tautomeric and conformational equilibrium of acenaphthenequinonemonooxime was studied by liquid and solid state NMR spectroscopy and ab initio calculations. The compound studied exists in the solid state as a oxime tautomer. However, in solution both the oxime and the nitroso tautomeric forms are present. Ab initio 6-31G(d,p) calculations in agreement with the experimental data predict the oxime tautomer to be more stable. The calculations in CCl 4 and DMSO solutions (SCRF model) showed a decrease in the tautomerization barrier with increasing solvent polarity. It is also found that the oxime tautomer exists as two isomers. The calculated energy difference between the isomers is small and decreases upon increasing the solvent polarity.

2025

Current study was designed to evaluate Coumalic Acid theoretically, which is a Bio-organic molecule. The structural, spectroscopic like the Infrared and UV-Visible properties were investigated using a quantum calculation approach under the density functional theory at B3LYP/6–31G(d) data set. The Infrared spectrogram lies between 400-3800 cm-1 with a few coercion and minute peaks. Thermochemistry calculations show that molecule is exothermic in nature, NMR H1 and C13 prediction results are tabulated. Today’s Challenges in Computational Chemistry is use of the appropriate tool and method to highlight the chemical property of mention molecule which is also highlight in the current research. The main advantage of virtual analysis provides an edge to easily view the electron shift, donation and withdrawing effect easily. The computational evaluation approach used here could also be useful for investigation of other bio-organic compounds.

2025, arXiv (Cornell University)

The nuclear waste problem is one of the main interests of the rare earth and actinide elements chemistry. Studies of Actinide-containing compounds are at the frontier of the applications of current theoretical methods due to the need to consider relativistic effects and approximations to the Dirac equation in them. Here, we employ four-component relativistic quantum calculations and scalar approximations to understand the contribution of f-orbitals in the chemical bonding of actinides (Ac) to organic ligands. We studied the relativistic quantum structure of an isostructural family made of Plutonium (Pu), Americium (Am), Californium (Cf), and Berkelium (Bk) atoms with the redox-active model ligand; DOPO (2,4,6,8-tetra-tert-butyl-1oxo-1H-phenoxazin-9-olate). Crystallographic structures were available to validate our calculations for all mentioned elements except for Cf. State-of-the-art relativistic calculations were performed at different levels of theory to investigate their electronic structure: 1) the scalar relativistic zeroth order regular approximation (ZORA) in the hybrid density functional theory (DFT) and 2) the four-component Dirac equation with the Dirac-Hartree-Fock (4c-DHF) and Lévy-Leblond (LL) Hamiltonians. We show that scalar DFT-ZORA could be an efficient first approximation to predict and investigate the geometry and electronic properties of actinides that are difficult to synthesize or characterize, and that the higher level of theory, the 4c-DHF, gives closer results to experiments than scalar DFT-ZORA. We performed spin-free calculations of geometric parameters for the Americium compound and found that they are the same as that of DFT-ZORA. To the best of our knowledge, this is the first time that such kind of large actinide compounds (the largest contains 67 atoms and 421 electrons) are studied with highly accurate fourcomponent methods (all-electron with 6131 basis functions for the largest compound). Finally, we show for the first time that relativistic effects play a key role in the nature of f-type atomic orbitals contributions to the frontier orbitals of Ac-DOPO compounds.

2025, Journal of Physical Chemistry A

The reference values for NMR magnetic shieldings, σ ref , are of highest importance when theoretical analysis of chemical shifts are envisaged. The fact that the non relativistically valid relationship among spin-rotation constants and magnetic shieldings is not any longer valid for heavy atoms makes that the search for σ ref for such atoms needs new strategies to follow. We present here results of σ ref that were obtained applying an own simple procedure which mix accurate experimental chemical shifts (δ) and theoretical magnetic shieldings (σ). We calculated σ(Sn) and σ(Pb) in a family of heavy-halogen containing molecules. We found out that σ ref (Sn; Sn(CH 3 ) 4 ) in gas phase should be close to 3864.11 ± 20.05 ppm (0.5 %). For Pb atom, σ ref (Pb; Pb(CH 3 ) 4 ) should be close to 14475.1 ppm ± 500.7. Such theoretical values correspond to calculations with the relativistic * To whom correspondence should be addressed polarization propagator method, RelPPA, at RPA level of approach. They are closer to experimental values as compared to those obtained applying few different functionals like PBE0, B3LYP, BLYP, BP86, KT2 and KT3 of the density functional theory. We studied tin and lead shieldings of the XY 4-n Z n (X = Sn, Pb; Y , Z = H, F, Cl, Br, I) and PbH 4-n I n (n = 0, 1, 2, 3, 4) family of compounds with four-component functionals as implemented in the DIRAC code. For these systems results of calculations with RelPPA-RPA are more reliable than the DFT ones. We argue on why those DFT functionals must be modified in order to obtain more accurate results of NMR magnetic shieldings within the relativistic regime: first, there is a dependence among both, electron correlation and relativistic effects that should be introduced in some way in the functionals; and second, the DIRAC code uses standard non-relativistic functionals and the functionals B3LYP and PBE0 were parameterized only with data taken from light elements. It can explain why they are not able to properly introduce relativistic effects on nuclear magnetic shieldings. We finally show that in the analysis of magnetic shieldings for the family of compounds mentioned above, one must consider the newest and so called heavy-atom effect on vicinal heavy atoms, HAVHA. Such effects are among the most important relativistic effects in these kind of compounds.

2025, arXiv (Cornell University)

The nuclear waste problem is one of the main interests of the rare earth and actinide elements chemistry. Studies of Actinide-containing compounds are at the frontier of the applications of current theoretical methods due to the need to consider relativistic effects and approximations to the Dirac equation in them. Here, we employ fourcomponent relativistic quantum calculations and scalar approximations to understand the contribution of f-type atomic orbitals in the chemical bonding of actinides (Ac) to organic ligands. We studied the relativistic quantum structure of an isostructural family made of Plutonium (Pu), Americium (Am), Californium (Cf), and Berkelium (Bk) atoms with the redox-active model ligand; DOPO (2,4,6,8-tetra-tert-butyl-1-oxo-1H-phenoxazin-9-olate). Crystallographic structures were available to validate our calculations for all mentioned elements except for Cf. In short, state-of-the-art relativistic calculations were performed at different levels of theory to investigate the relativistic effects and electron correlations on geometrical structures and bonding energies of Ac-DOPO 3 complexes (Ac=Pu, Am, Cf, Bk) : 1) the scalar relativistic zeroth order regular approximation (ZORA) within the hybrid density functional theory (DFT) and 2) the four-component Dirac equation with the Dirac-Hartree-Fock (4c-DHF) and Lévy-Leblond (LL) Hamiltonians. We show that scalar DFT-ZORA could be used as an efficient theoretical approximation to first approximate the geometry and electronic properties of actinides which are difficult to synthesize or characterize; but knowing that the higher levels of theory, like the 4c-DHF, gives closer results to experiments than the scalar DFT-ZORA. We also performed spin-free calculations of geometric parameters for the Americium and Berkelium compounds. To the best of our knowledge, this is the first time that such kind of large actinide compounds (the largest contains 67 atoms and 421 electrons) are studied with highly accurate four-component methods (all-electron calculations with 6131 basis functions for the largest compound). We show that relativistic effects play a key role in the contribution of f-type atomic orbitals to the frontier orbitals of Ac-DOPO 3 complexes. The analysis of results obtained applying different theoretical schemes to calculate bonding energies are also given.

2025, Journal of Molecular Structure: THEOCHEM

Vicinal J(SnCCSn) and J(SnCCC) spin-spin coupling constants are calculated within the RPA MNDO method for different dihedral angles, 8, determined by the intervening bonds. in model compounds. For both types of couplings. calculated values closely follow Karplus-like dependences. Results are discussed in terms of experimental values. and the effects of substituents attached to the coupled atoms are briefly analyzed for the 6' = 0" and 0 = 180" conformations. These last values were also calculated using the RPA AM 1 method. Results indicate that the RPA MNDO and RPA AM I approaches show interesting potential for studying the structural dependences of ?I(SnSn) and 3J(SnC) couplings in tin-containing compounds. ", Part of a Ph.D. thesis (N.M.P.) to be presented to the University of La Plats.

2025, Magnetic Resonance in Chemistry

Several theoretical methods have been used to compute 2JHH in neutral, anionic and cationic HXH hydrides, X being the 14 nuclei from Li to Cl (28 molecules). Since the calculations also provide 1JXH spin–spin coupling constants (SSCC), these have also been analyzed. The best results were obtained using Second‐order polarization propagator approximation (SOPPA)/sadJ. The geminal coupling constants appear to be dependent on the electronegativity of the X‐atom. Copyright © 2008 John Wiley & Sons, Ltd.

2025, Journal of Organometallic Chemistry

The inner projection of the polarization propagator, using contributions from localized orbitals, IPPP -CLOPPA, and using the intermediate neglect of the differential overlap model parameterized for spectroscopy, INDO/S, was implemented and used to calculate indirect nuclear spin coupling constants. The resulting model was tested on a group of small-and medium-size model compounds by comparing its performance with that of other semi-empirical methods and experiments where available. It is shown that in general the INDO/S approximation with the use of S N 2 (0) and r N -3 atomic parameters taken from the INDO and AM1 approaches is the most suitable scheme to describe coupling constants. The introduction of atomic parameters for S N 2 (0) and r N -3 in the case of heavy nuclei like Sn, is a critical step. The correction of the bonding beta parameter for this nucleus was also necessary within the INDO/S approximation to improve the accuracy and to better account for indirect relativistic effects. The application of this parameterization was accomplished in a series of tetrastannacyclohexanes and different pathways for coupling transmission were analyzed.

2025, Chemical Physics

The reference value of NMR magnetic shieldings, r ref (X), of a nucleus X is of highest importance when theoretical analysis of chemical shifts are envisaged. For light atoms the absolute scale can be obtained using an old relationship among spin-rotation constants and magnetic shieldings, though for heavy-atom-containing molecules such nonrelativistic relationship is not valid any longer. Then, for such molecules the search for r ref needs new strategies to be followed. We present here new values of r ref (Si) and r ref (Ge) for tetramethyl silane and tetramethyl germanium that were obtained applying a simple procedure which mix accurate experimental chemical shifts and theoretically obtained magnetic shieldings in a set of selected molecular systems. We considered that in experiments one usually measures chemical shifts, (d). We calculated r ref (Si) and r ref (Ge) from a set of seventeen and sixteen heavy-halogen-containing molecules, respectively. We found out that r ref [Si; Si(CH 3 ) 4 ] in gas phase should be close to 410.49 ± 6.77 ppm and r ref [Ge; Ge(CH 3 ) 4 ] should be close to 1705.29 ± 19.51 ppm. Such theoretical values were obtained by performing calculations within the relativistic polarization propagator method, RelPPA, at RPA level of approach. Based on those values of r ref , we recalculated the chemical shifts of the whole set of molecular systems obtaining a good reproduction of known experimental results. We also obtained a highly correlated relationship among the absolute values of the nuclear magnetic shieldings of Si and Ge atoms in halogen substituted tetrahedral compounds.

2025, Journal of the American Chemical Society

The abnormal Brfnsted slopes observed for nitroalkanes are interpreted as a variation in the work terms, which is caused by a variation in hydrogen bond strengths with the free energy for proton transfer, rather than as an anomaly in the... more

2025, Australian Journal of Chemistry

The central functionalized tryptophan core of the celogentin/moroidin family of cyclic peptides has been prepared. The strategy incorporates a novel preparation of 4-iodobenzaldehyde and employs a Larock annulation as the key step.

2025, Asian Journal of Chemistry

Three new chiral diimine Schiff bases, 5,5'-methylene-bis-salicylidene-α-methylbenzylamine (2), 5,5'-methylenebis( ) including symmetric imine type have been synthesized. The 5,5'-methylenebis-salicylaldehyde (1) used as the starting material for the obtained Schiff bases was confirmed by single crystal X-ray diffraction. Characterization of novel symmetric diimine Schiff bases have been done by means of elemental analysis, FT-IR, 1 H and 13 C NMR spectral studies. Theoretical electronic structure calculations of the B3LYP/6-311+g(d,p) level were performed to optimize the molecular geometry. The non-linear optical properties such as dipole moment, polarizability and first order hyperpolarizability of 1, 2, 3 and 4 were determined. The HOMO and LUMO energy gaps revealed that the energy gaps reflected the chemical activity of the molecules. To obtain chemical reactivity of the molecules, the molecular electrostatic potential surface maps were plotted over the optimized geometry of the molecules.

2025, Diagnostics

Shortly after its emergence, Omicron and its sub-variants have quickly replaced the Delta variant during the current COVID-19 outbreaks in Vietnam and around the world. To enable the rapid and timely detection of existing and future variants for epidemiological surveillance and diagnostic applications, a robust, economical real-time PCR method that can specifically and sensitively detect and identify multiple different circulating variants is needed. The principle of target- failure (TF) real-time PCR is simple. If a target contains a deletion mutation, then there is a mismatch with the primer or probe, and the real-time PCR will fail to amplify the target. In this study, we designed and evaluated a novel multiplex RT real-time PCR (MPL RT-rPCR) based on the principle of target failure to detect and identify different variants of SARS-CoV-2 directly from the nasopharyngeal swabs collected from COVID-19 suspected cases. The primers and probes were designed based on the specific delet...

2025, Journal of Molecular Structure: THEOCHEM

First principles density functional calculations are performed on a number of square planar hydroxamate chelates of several divalent metal ions in order to determine their respective affinities for some biologically important ligands. The structures of the complexes are discussed, and the calculated binding mode is in agreement with experimental results. Extensive calculations have shown that, although the interactions are dominated mainly by electrostatic forces, there is a covalent contribution as well that introduces subtle variations in binding affinities of various metal ions. Thus, although a reasonable correlation is found between the complexation energies and reciprocals of the ionic radii of the metal ions, deviations may be attributed to some covalent character of the metal-ligand bonds, which modify a ligand's affinity for a metal ion and introduce subtle variations that are ultimately responsible for their biological action. A linear relationship between the partial charge on the metal ion and the LUMO energy shows that metal ions with lower lying vacant orbitals are able to form covalent coordination with the ligand. The affinity of the formohydroxamate ion for Ni(II) is satisfactorily explained on this basis. The bonding characteristics of the investigated complexes are discussed, as is the optimum size of the metal binding site. Some other hydroxamic acids are also investigated in this work. The electronic structures of urease from two microorganisms, and their acetohydroxamate complexes are also investigated in order to understand the inhibition mechanism. This study should prove useful not only for the understanding of coordination bonding, but also in the investigation of metalloenzymes and their inhibition.

2025, Journal of Climate Change

2025

Despite extensive studies in the past, deterioration of mechanical properties due to hydrogen environment exposure remains a serious problem for structural materials. More effective improvement of a material's resilience requires advanced computational methods to elucidate the fundamental mechanisms of the hydrogen effects. To enable accurate molecular dynamics (MD) studies of the hydrogen effects on metals, we have developed a high-fidelity analytical bond-order potential (BOP) for the copper-hydrogen binary system as a representative case. This potential is available through the publically available MD code LAMMPS. The potential parameters are optimized using an iterative process. First, the potential is fitted to static and reactive properties of a variety of elemental and binary configurations including small clusters and bulk lattices (with coordination varying from 1 to 12). Then the potential is put through a series of rigorous MD simulation tests (e.g., vapor deposition and solidification) that involve chaotic initial configurations. It is demonstrated that this Cu-H BOP not only gives structural and property trends close to those seen in experiments and quantum mechanical calculations, but also predicts the correct phase transformations and chemical reactions in direct MD simulations. The correct structural evolution from chaotic initial states strongly verifies the transferability of the potential. A highly transferable potential is the reason that a well-parameterized analytical BOP can enable MD simulations of metal-hydrogen interactions to reach a fidelity level not achieved in the past.

2025

Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.

2025, Modelling and Simulation in Materials Science and Engineering

New EAM potentials for the ternary palladium-silver-hydrogen system are developed by extending a previously developed palladium-hydrogen potential. The ternary potentials accurately capture the heat of mixing and structural properties associated with solid solution alloys of palladium-silver. Stable hydrides are produced with properties that smoothly transition across the compositions. Additions of silver to palladium are predicted to alter the properties of the hydrides by decreasing the miscibility gap and increasing the likelihood of hydrogen atoms occupying tetrahedral interstitial sites over octahedral interstitial sites.

2025, ChemMedChem

Muscarinic acetylcholine receptors (mAChRs) are important therapeutic targets for several diseases of the central nervous system and periphery. However, the lack of subtype-selective ligands for these receptors is a major challenge. A novel approach involving the integration of a natural product framework with a bioactive molecule (iNPBM) by using gephyrotoxin and the isoindoline framework is demonstrated for the discovery of new and selective mAChR modulators. We established a scalable and versatile synthetic scheme to enable the synthesis of various analogues that provided the first structure-activity relationship study of this class of compounds. Pharmacological profiling of these compounds demonstrated several ligands with high affinity and selectivity for mAChRs. Specifically, RG-06 and RG-09 were found to be antagonists of M3-mAChR, whereas RG-02 was found to be an agonist at M2-mAChR. Furthermore, RG-02 exhibited salutary effects in an established pharmacological model of a c...

2025, The Journal of Chemical Physics

Ab initio molecular orbital calculations have been performed to investigate the structures and energies of the adduct isomeric radicals arising from the addition reaction of chlorine atom to isoprene. Geometry optimizations of the four isomers of the Cl–isoprene adduct were carried out with density function theory (DFT)-B3LYP and the energies were computed using the single-point calculation of several methods, including MP2, MP4, and CCSD(T). The most energetically favorable isomer was found to be that with Cl addition to the terminal C1-position (isomer I). At the CCSD(T)/6-311G** level of theory, the energies of the other three isomeric radicals relative to I were 1.4, 14.2, and 14.7 kcal mol−1 for Cl additions to C4- (isomer IV), C3- (isomer III), and C2-positions (isomer II), respectively. The activation energy for Cl migration from the more energetic isomers to the lower energy ones (i.e., from isomers II to I or III to IV) was found to be relatively low (2.8–4.7 kcal mol−1), i...

2025, The journal of physical chemistry. A

Time-dependent density functional theory (TD-DFT) and correlated ab initio methods have been applied to explore the electronically excited states of vitamin B(12) (cyanocobalamin or CNCbl). Different experimental techniques have been used to probe the excited states of CNCbl, revealing many issues that remain poorly understood from an electronic structure point of view. Due to its efficient scaling with size, TD-DFT emerges as one of the most practical tools that can be used to study the electronic properties of these fairly complex molecules. However, the description of excited states is strongly dependent on the type of functional used in the calculations. In the present contribution, the choice of a proper functional for vitamin B(12) was evaluated in terms of its agreement with both experimental results and correlated ab initio calculations. Three different functionals, i.e., B3LYP, BP86, and LC-BLYP, were tested. In addition, the effect of the relative contributions of DFT and ...

2025, RSC Advances

Synthesis of l,2-azaphospholidines and extension to azaphosphacane and azaphosphanane higher homologues.

2025, RSC Advances

Synthesis of l,2-azaphospholidines and extension to azaphosphacane and azaphosphanane higher homologues.

2025, Crystal Growth & Design

Crystal structures of seven salts of 2-hydroxyethylamine with benzoic acid (1) and different substituted benzoic acids, such as p-methylbenzoic acid (2), p-methoxybenzoic acid (3), p-hydroxybenzoic acid (4), p-chlorobenzoic acid (5), p-bromobenzoic (6), and p-iodobenzoic (7) have been studied. The salts units of 1-7 serve as building blocks (BB) of the supramolecular architecture. In a crystal they are held together via proton-transferred N-H•••O and normal O-H•••O hydrogen bonds. The substituents on anions influence dipole-dipole interactions between anions and cations in molecular aggregates. As a result, they are organized in building blocks either via one charge-assisted (1, 2) hydrogen bond or via two (3-7) hydrogen bonds. The dispersion interaction significantly contributes to intermolecular force fields driving the organization of hydrogen bonds in BB. In all studied compounds, building blocks are consolidated into 2-D layers through the N-H•••O and O-H•••O hydrogen bonds. For the crystal structures of 2-7, with non-centrosymmetric space groups and the BB self-assembled by two hydrogen bonds, the macroscopic polarizations of a unit cell is practically perpendicular to the layers.

2025, American Journal of Physical Chemistry

Substituents play a major role in influencing the reactivity and biological activity of aromatic compounds. Substituents affect the conductivity of molecular electronic and photoresponsive switches, light harvesting dye-sensitized solar cells and organic electroluminescent devices. A number of quantum mechanical methods corresponding to stabilization energy, charge of substituent active region, energy dispersive analysis, and molecular electrostatic potential help in the description of substituent effect in aromatic systems. In the present work we carried out computational studies for the estimation of chemical and structural properties of a chemical library of nine ortho substituted naphthoic acids. The chemical reactivity of the selected substituted naphthoic acids was assessed from a number of physicochemical properties such as total energy, HOMO-LUMO gap, chemical hardness, binding energy, ionization potential, electron affinity, electronegativity, electrochemical potential, global softness, electrophilicity and dipole moment. The effect of the electron-donor groups on conjugation of ortho substituted naphthoic acid was investigated by correlating the calculated rotational barriers of transition state of cis and trans ortho-substituted naphthoic acids to observe change in single bond length, double bond length, bond angle, dihedral angle, and rotational frequency of carboxylic group of substituted napthoic acids. The rotational barrier correlated with the geometric, atomic, molecular, and spectroscopic parameters. Moreover, quantitative structure-activity relationship (QSAR) analyses was performed and the obtained structural properties were linked with biological activities.

2025, Organic Letters

Ab initio calculations were carried out on several metalloporphyrins complexed to several ligands. The experimental spectra of metalloporphyrin-ligand complexes show large upfield shifts for the ligand proton signals compared to the free ligand. These shifts are caused by the proximity of the porphyrin p-system. The 1 H NMR chemical shifts of these complexes were computed via ab initio calculations using the GIAO method at several levels of theory and the obtained values agree satisfactorily with experimental results.

2025, International Journal of Innovation and Applied Studies

Real public health problem, cancer is one of the pathologies that mobilize the entire scientific community. The conception of effective drugs against this pathology has become a challenge for all actors in research. Some molecules such as makaluvamines have shown important anticancer properties. These molecules belong to the family of alkaloids generally active in charged forms. The purpose of our work is to determine the protonation or methylation sites, relative stability and reactivity potential of some makaluvamines by a quantum chemistry method. B3LYP/6-311++G(d,p) theory level is used for all the calculations done. Firstly, we have estimated the gas phase basicity (GB) and proton affinity (PA) for the different heteroatoms of the molecules. Secondly, electronic energies, enthalpies of formation and free enthalpies of formation calculation permitted us to deduce the relative stability of the different forms of studied makaluvamines. Thirdly, Fukui functions, chemical softness a...

2025, International Journal of Chemistry

Benzothiazoles are organic compounds with multiple biological activities. Due to their biological interests, these are synthesized on a large scale at the industrial level and used in various fields. Their release into waters causes environmental problems which leads to public health problems. Finding solution which can help for their degradation become necessary. That is the reason why a theoretical study of the reactivity of five benzothiazole derivatives has been initiated in order to understand some aspect of their biodegradation. The calculations were carried out in gaseous and aqueous phase with B3LYP functional associated with bases 6-311G(d) and 6-31+G(d). The results revealed that the thione tautomer of the MBT derivative is more stable than the thiol form. These results are in agreement with previous experimental work which showed that the thiones forms in MBT metal complexes are the most stable. Moreover, the study of the reactivity based on the computation of the global ...

2025, Computational Chemistry

A theoretical study of the reactivity of quinoline-4-one derivatives is undertaken in order to understand the involved mechanisms. The calculations were carried out in gas phase and in N, N-Dimethylformamide (DMF) solution. The Density Functional Theory (DFT) with B3LYP functional associated to 6-311G (d) and 6-311+G (d) bases is used to perform these calculations. The results of the thermodynamic parameters showed that there is an equilibrium relation between the different tautomers. This equilibrium can be used to explain the failure to obtain tetrahydroquinoline from 5,8-dimethoxy-quinolin-4-one. Reactivity analysis from Frontier Molecular Orbitals theory and Fukui function calculations revealed that ketone forms are less reactive than enol ones. The methoxyl substituent decreases the acidity of the nitrogen and oxygen atoms of quinolin-4-one while the bromine increases the acidity of the same sites. These results foresee that nitrogen deprotonation in the case of the brominated compound is easier than in the case of methoxylated ones.

2025, Acta Crystallographica Section B Structural Science

The hydrogen-bonding properties of galanthamine have been investigated experimentally from a thorough analysis of crystallographic data retrieved from the Protein Data Bank and Cambridge Structural Database databases and theoretically through ab initio [MP2/6-311++G(2d,p)] and density functional theory [MPWB1K/6-31++G(d,p)] calculations. The main hydrogen-bond acceptor (HBA) interaction sites of the molecule are the O atoms and their spatial proximity allows multi-centered hydrogen-bond (HB) motifs. The hydrogen-bond donor (HBD) sites of the molecule are the NH+ and OH groups as well as several CH donors. Among them, the preferred ones are those directly linked to the ammonium nitrogen, followed by aromatic CH and finally the methyl group of the methoxy substituent. All these observations are in fairly good agreement with the computed positions of the molecular electrostatic potential (MEP) minima and maxima of various galanthamine species. The galanthamine HBD and HBA properties, i...

2025, Global Journal of Science Frontier Research

Makaluvamines are used by intercalation in the DNA for the treatment of cancer cells such as colon cancer, prostate cancer, breast cancer.... This work studies energetic and geometrical parameters of stability of the 3-body complexes formed by six Makaluvamines, first protonated and then methylated by interactions with a water molecule and a glutamic acid molecule (Glu. Ac), a protein residue of topoisomerase II. This study was carried out by the quantum chemistry method of density functional theory (DFT). Firstly, we determined the energy of each super-molecule, the energies of all units of two fragments and one fragment in the geometries of the complexes. We have also determined the energies of 2-body and 3-body interaction, cooperativity, relaxation and total interaction. The results of these calculations helped to appreciate the rigidity of each fragment between the isolated and complex states. They also allowed knowing the stability of each complex and the contribution of each interaction term to this stability.

2025, Journal of Chemical Education

Gaussian-2-Blender is an open-source application programming interface (API) written in Python that allows for the conversion of Gaussian input files to 3D objects of different formats. This new tool was developed in response to the shortcomings of available programs to import Gaussian calculations into augmented reality (AR) or virtual reality (VR) applications, which are currently rising in numbers. Gaussian-2-Blender's distinguishing features include (1) molecule renderings with proportional, scaled, and accurate atomic and ionic sizes, (2) rendering transient, hydrogen, and delocalized bonds, (3) batch conversion of multiple files, and (4) retention of Gaussian input numerical labels. These features are either not supported or difficult to achieve in other programs. The following report describes the key features of the tool and provides a comparison between this new tool and available programs.

2025, IEEE Transactions on Magnetics

We developed a computational method for estimating magnetic dipole energy of slab materials using spin density obtained through a density functional approach. The new method can accurately estimate magnetic anisotropy energy (MAE) for slabs from magnetic dipole interaction called shape MAE (SMAE). We investigated ferromagnetic and antiferromagnetic slabs and found that a quadrupole component of atomic spin density suppresses SMAE in ferromagnetic slabs with Fe/MgO interface. In antiferromagnetic MnPt slabs, which have a perpendicular favor originating from the crystalline magnetic dipole interaction, a surface effect at the Mn edge appears as an enhancement of SMAE.

2025, Theoretical Chemistry Accounts

Similar free energy profiles for two enantiomers obtained using ABF calculations indicate that it is very hard to separate and identify the chiral conjugates within the framework of the natural β-cyclodextrin. Dedicated to Professor... more

2025, Frontiers in Plant Science

Phytochromes are the principle photoreceptors in light-regulated plant development, primarily acting via translocation of the light-activated photoreceptor into the nucleus and subsequent gene regulation. However, several independent lines of evidence indicate unambiguously that an additional cytoplasmic signaling mechanism must exist. Directional responses in filament tip cells of the moss Physcomitrella patens are steered by phy4 which has been shown to interact physically with the blue light receptor phototropin at the plasma membrane. This complex might perceive and transduce vectorial information leading to cytoskeleton reorganization and finally a directional growth response. We developed yeast two-hybrid procedures using photochemically functional, full-length phy4 as bait in Physcomitrella cDNA library screens and growth assays under different light conditions, revealing Pfr-dependent interactions possibly associated with phytochrome cytoplasmic signaling. Candidate proteins were then expressed in planta with fluorescent protein tags to determine their intracellular localization in darkness and red light. Of 14 candidates, 12 were confirmed to interact with phy4 in planta using bimolecular fluorescence complementation. We also used database information to study their expression patterns relative to those of phy4. We discuss the likely functional characteristics of these holophytochrome-interacting proteins (HIP's) and their possible roles in signaling.

2025, Frontiers in Plant Science

2025, The journal of physical chemistry. A

The hyperpolarizabilities of five prototypical and four recently synthesized long-range charge-transfer (CT) organic compounds are calculated using short- and middle-range (SR and MR) hybrid functionals. These results are compared with data from MP2 and other DFT methods including GGAs, global hybrids, long-range corrected functionals (LC-DFT), and optimally tuned LC-DFT. Although it is commonly believed that the overestimation of hyperpolarizabilities associated with CT excitations by GGA and global hybrid functionals is the result of their wrong asymptotic exchange potential, and that LC-DFT heals this issue, we show here that SR and MR functionals yield results similar to those from LC-DFT. Hence, the long-range correction per se does not appear to be the key element in the well-known improved description of hyperpolarizabilities by LC-DFT. Rather, we argue that the inclusion of substantial amounts of Hartree-Fock exchange, which reduces the many-electron self-interaction error, ...

2025, Theoretical Chemistry Accounts

The nonlinear optical (NLO) properties of Nethyl dicyanocarbazole (1), N-ethyl cyanoethylacetatecarbazole (2), and N-ethyl dimethylacetatecarbazole (3) are studied with traditional hybrid and long-range corrected (LC) density functional theory (DFT) methods. The carbazoles are predicted to have planar structures with a high degree of p-conjugation and charge transfer, resulting in measurable NLO responses. The DFT data here calculated allow us to refine and correct previously reported experimental hyperpolarizabilities for these compounds. Experimental UV-vis absorption bands (related to hyperpolarizabilities estimated via solvatochromism) are also accurately reproduced by LC-DFT when using gap fitting schemes. The effects of different functionals on the HOMO-LUMO energy gaps and eventually on the total hyperpolarizabilities are discussed.

2025, European Journal of Organic Chemistry

The matrix isolation and spectroscopic characterization of two C 6 F 4 isomers, the perfluorinated o-benzyne 4 and the m-benzyne 5, is reported. UV photolysis of tetrafluorophthalic anhydride 6 in solid argon at 10 K results in the formation of CO, CO 2 , and 1,2didehydro-3,4,5,6-tetrafluorobenzene (4) in a clean reaction. On subsequent 350 nm irradiation 4 is carbonylated to give the cyclopropenone 7. 1,3-Didehydro-2,4,5,6-tetrafluorobenzene (5) was synthesized by UV irradiation of 1,3diiodo-2,4,5,6-tetrafluorobenzene (8) via 2,3,4,6-tetrafluoro-5-iodophenylradical 9. Photolysis of 8 in solid neon at 3 K produces good yields of both radical 9 and benzyne 5, while in argon at 10 K no reaction is observed. Thus, the photo-chemistry in neon at extremely low temperature markedly differs from the photochemistry in argon. The formation of 5 from 8 via 9 is reversible, and annealing the neon matrix at 8 K leads back to the starting material 8. The benzynes 4 and 5 and the radical 9 were characterized by comparison of their matrix IR spectra with density functional theory (DFT) calculations.