Search Results (17)

Heterobimetallic iron–group 9 carbonyl cations, FeM(CO)_n⁺ (M = Rh, Ir; n = 9–11), were generated in the gas phase via pulsed laser vaporization within a supersonic expansion and characterized by infrared photodissociation spectroscopy in the carbonyl stretching region. By combining experimental spectra with density functional theory simulations, the geometric and electronic structures of these clusters were unambiguously assigned. Mass spectrometry and photodissociation results identified FeM(CO)₉⁺ as the saturated species for M = Rh and Ir, in contrast to the lighter cobalt analog FeCo(CO)₈⁺. The FeM(CO)₉⁺ cations adopt a C_4v-symmetric singlet ground-state structure with all carbonyl ligands terminally bound, corresponding to a (OC)₅Fe–M(CO)₄ configuration. These complexes can be formally described as combination products of the stable neutral Fe(CO)₅ and cationic M(CO)₄⁺ fragments. Analyses based on canonical molecular orbitals, Mayer bond orders, and fragment-based correlation diagrams reveal the presence of a dative Fe→M interaction in FeM(CO)₉⁺, which formally enables the heavier Rh/Ir metal center to attain an 18-electron configuration. However, this bond is weaker than a typical covalent single bond, as the key molecular orbitals involved possess antibonding character. This study provides important insights into the structure and bonding of heteronuclear transition metal carbonyl clusters, highlighting distinctive coordination behavior between late 3d and heavier 4d/5d congeners. Full article

Quantum mechanics (QM) revolutionizes drug discovery by providing precise molecular insights unattainable with classical methods. This review explores QM’s role in computational drug design, detailing key methods like density functional theory (DFT), Hartree–Fock (HF), quantum mechanics/molecular mechanics (QM/MM), and fragment molecular orbital (FMO). These methods model electronic structures, binding affinities, and reaction mechanisms, enhancing structure-based and fragment-based drug design. This article highlights the applicability of QM to various drug classes, including small-molecule kinase inhibitors, metalloenzyme inhibitors, covalent inhibitors, and fragment-based leads. Quantum computing’s potential to accelerate quantum mechanical (QM) calculations is discussed alongside novel applications in biological drugs (e.g., gene therapies, monoclonal antibodies, biosimilars), protein–receptor dynamics, and new therapeutic indications. A molecular dynamics (MD) simulation exercise is included to teach QM/MM applications. Future projections for 2030–2035 emphasize QM’s transformative impact on personalized medicine and undruggable targets. The qualifications and tools required for researchers, including advanced degrees, programming skills, and software such as Gaussian and Qiskit, are outlined, along with sources for training and resources. Specific publications on quantum mechanics (QM) in drug discovery relevant to QM and molecular dynamics (MD) studies are incorporated. Challenges, such as computational cost and expertise requirements, are addressed, offering a roadmap for educators and researchers to leverage quantum mechanics (QM) and molecular dynamics (MD) in drug discovery. Full article

The [2 + 2] cycloaddition reactions of the heterocumulene (N=C=N) with the heavy imine-like molecule Ge=G15-Rea (G15 = Group 15 element) were examined using density functional theory (M06-2X-D3/def2-TZVP). The theoretical findings indicate that the doubly bonded Ge=G15 moiety in Ge=G15-Rea (L₁L₂Ge=G15L₃) is characterized by electron-sharing bonding between the triplet L₁L₂Ge and triplet G15–L₃ fragments. All five Ge=G15-based heavy imine analogues readily undergo [2 + 2] cycloaddition reactions with N=C=N. Energy decomposition analysis (EDA–NOCV) suggests that the [2 + 2] cycloaddition reaction between Ge=G15-Rea and N=C=N involves a donor–acceptor (singlet–singlet) interaction instead of an electron-sharing (triplet–triplet) interaction. Frontier molecular orbital (FMO) theory and the energy decomposition analysis–natural orbitals for chemical valence (EDA–NOCV) findings emphasize that the key bonding interaction involves the occupied p-π orbital of Ge=G15-Rea and the vacant p-π* orbital of C=N=C. Based on the activation strain model results, the activation barrier of the [2 + 2] cycloaddition reaction is predominantly controlled by the deformation energies of Ge=G15-Rea and N=C=N. Full article

Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides’ structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster. Full article

The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe₂ and 2-Y with Y = H, CN, NO₂, OMe, NMe₂) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level of theory using the energy partitioning method of Interacting Quantum Atoms/Fragments (IQA/IQF). The partitioned energies are analysed by the Relative Energy Gradient (REG) method, which calculates the correlation between these energies and the total energy of a system, thereby explaining the role atoms have in the energetic behaviour of the total system. The traditional “back-of-the-envelope” open and closed conformations of molecular balances do not correspond to those of the lowest energy. Hence, more care needs to be taken when considering which geometries to use for comparison with the experiment. The REG-IQA method shows that the 1-H and 1-OMe balances behave differently to the 1-Me and 1-NMe₂ balances because the latter show more prominent electrostatics between carbonyl groups and undergoes a larger dihedral rotation due to the bulkiness of the functional groups. For the 2-Y balance, REG-IQA shows the same behaviour across the series as the 1-H and 1-OMe balances. From an atomistic point of view, the formation of the closed conformer is favoured by polarisation and charge-transfer effects on the amide bond across all balances and is counterbalanced by a de-pyramidalisation of the amide nitrogen. Moreover, focusing on the oxygen of the amide carbonyl and the α-carbon of the remaining carbonyl group, electrostatics have a major role in the formation of the closed conformer, which goes against the well-known n-π* interaction orbital overlap concept. However, REG-IQF shows that exchange–correlation energies overtake electrostatics for all the 2-Y balances when working with fragments around the carbonyl groups, while they act on par with electrostatics for the 1-OMe and 1-NMe₂. REG-IQF also shows that exchange–correlation energies in the 2-Y balance are correlated to the inductive electron-donating and -withdrawing trends on aromatic groups. We demonstrate that methods such as REG-IQA/IQF can help with the fine-tuning of molecular balances prior to the experiment and that the energies that govern the probed interactions are highly dependent on the atoms and functional groups involved. Full article

Steroid [60]fullerene hybrids have been synthesized by the Bingel−Hirsch reaction as a contribution to the chemistry of carbon nanoforms. The hybrids were characterized by different spectroscopic experiments and analytical techniques. Theoretical calculations using the Density functional theory and the PBE functional were performed to predict the most stable conformations for the synthesized compounds and the frontier molecular orbitals energy. Some properties, such as polarizability, dipole moment, lipophilicity, solvent-accessible surface area, and topological polar surface area, were calculated. Fullerenes and their derivatives have potential antiviral activity due to their specific binding interactions with biological molecules. The ability of fullerene derivatives to interact with the active site of HIV and SARS-Cov-2 proteases was studied by the Autodock Vina program. The C₆₀ cage exhibited an interaction with the phenyl group of phenylalanine residues through π–π and T-shape interactions. Furthermore, it was observed that the steroid moieties formed H-bonds with the amino acid residues in the active sites of proteins. In addition, van der Waals contacts with the nonpolar protease surface, thereby improving the binding relative to the tested compound. Protein-ligand docking revealed several important molecular fragments that are responsible for the interaction, thus paving the way to study the possible application of these hybrids in medicinal chemistry. Full article

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the pathogenic cause of coronavirus disease 2019 (COVID-19). The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is a potential target for the treatment of COVID-19. An RdRp complex:dsRNA structure suitable for docking simulations was prepared using a cryo-electron microscopy (cryo-EM) structure (PDB ID: 7AAP; resolution, 2.60 Å) that was reported recently. Structural refinement was performed using energy calculations. Structure-based virtual screening was performed using the ChEMBL database. Through 1,838,257 screenings, 249 drugs (37 approved, 93 clinical, and 119 preclinical drugs) were predicted to exhibit a high binding affinity for the RdRp complex:dsRNA. Nine nucleoside triphosphate analogs with anti-viral activity were included among these hit drugs, and among them, remdesivir-ribonucleoside triphosphate and favipiravir-ribonucleoside triphosphate adopted a similar docking mode as that observed in the cryo-EM structure. Additional docking simulations for the predicted compounds with high binding affinity for the RdRp complex:dsRNA suggested that 184 bioactive compounds could be anti-SARS-CoV-2 drug candidates. The hit bioactive compounds mainly consisted of a typical noncovalent major groove binder for dsRNA. Three-layer ONIOM (MP2/6-31G:AM1:AMBER) geometry optimization calculations and frequency analyses (MP2/6-31G:AMBER) were performed to estimate the binding free energy of a representative bioactive compound obtained from the docking simulation, and the fragment molecular orbital calculation at the MP2/6-31G level of theory was subsequently performed for analyzing the detailed interactions. The procedure used in this study represents a possible strategy for discovering anti-SARS-CoV-2 drugs from drug libraries that could significantly shorten the clinical development period for drug repositioning. Full article

This work explores the electronic structure as well as the reactivity of singlet diradicals, making use of multistate density functional theory (MSDFT). In particular, we show that a minimal active space of two electrons in two orbitals is adequate to treat the relative energies of the singlet and triplet adiabatic ground state as well as the first singlet excited state in many cases. This is plausible because dynamic correlation is included in the first place in the optimization of orbitals in each determinant state via block-localized Kohn–Sham density functional theory. In addition, molecular fragment, i.e., block-localized Kohn–Sham orbitals, are optimized separately for each determinant, providing a variational diabatic representation of valence bond-like states, which are subsequently used in nonorthogonal state interactions (NOSIs). The computational procedure and its performance are illustrated on some prototypical diradical species. It is shown that NOSI calculations in MSDFT can be used to model bond dissociation and hydrogen-atom transfer reactions, employing a minimal number of configuration state functions as the basis states. For p- and s-types of diradicals, the closed-shell diradicals are found to be more reactive than the open-shell ones due to a larger diabatic coupling with the final product state. Such a diabatic representation may be useful to define reaction coordinates for electron transfer, proton transfer and coupled electron and proton transfer reactions in condensed-phase simulations. Full article

This work aimed to synthesize safe antihyperglycemic derivatives bearing thiazolidinedione fragment based on spectral data. The DFT theory discussed the frontier molecular orbitals (FMOs), chemical reactivity of compounds, and molecular electrostatic potential (MEP) to explain interaction between thiazolidinediones and the biological receptor. α-amylase is known as the initiator-hydrolysis of the of polysaccharides; therefore, developing α-amylase inhibitors can open the way for a potential diabetes mellitus drug. The molecular docking simulation was performed into the active site of PPAR-γ and α-amylase. We evaluated in vitro α-amylase’s potency and radical scavenging ability. The compound 6 has the highest potency against α-amylase and radical scavenging compared to the reference drug and other members. They have been applied against anti-diabetic and anti-hyperlipidemic activity (in vivo) based on an alloxan-induced diabetic rat model during a 30-day treatment protocol. The most potent anti hyperglycemic members are 6 and 11 with reduction percentage of blood glucose level by 69.55% and 66.95%, respectively; compared with the normal control. Other members exhibited moderate to low anti-diabetic potency. All compounds showed a normal value against the tested biochemical parameters (CH, LDL, and HDL). The ADMET profile showed good oral bioavailability without any observed carcinogenesis effect. Full article

This work presents a method to move beyond the recently introduced atomic fragment approximation. Like the bare atomic fragment approach, the new method is an ab initio, parameter-free, orbital-free implementation of density functional theory based on the bifunctional formalism that treats the potential and the electron density as two separate variables, and provides access to the Kohn–Sham Pauli kinetic energy for an appropriately chosen Pauli potential. In the present ansatz, the molecular Pauli potential is approximated by the sum of the bare atomic fragment approach, and a so-called deformation potential that takes the interaction between the atoms into account. It is shown that this model can reproduce the bond-length contraction due to multiple bonding within the list of second-row homonuclear dimers. The present model only relies on the electron densities of the participating atoms, which themselves are represented by a simple monopole expansion. Thus, the bond-length contraction can be rationalized without referring to the angular quantum numbers of the participating atoms. Full article

This article presents N²⁺ fragment yields following nitrogen K-shell photo-absorption in the NH⁺ molecular ion measured at the SOLEIL synchrotron radiation facility in the photon energy region 390–450 eV. The combination of the high sensitivity of the merged-beam, multi-analysis ion apparatus (MAIA) with the high spectral resolution of the PLEIADES beamline helped to resolve experimentally vibrational structures of highly excited [N1s⁻¹H]*⁺ electronic states with closed or open-shell configurations. The assignment of the observed spectral features was achieved with the help of density functional theory (DFT) and post-Hartree Fock Multiconfiguration Self-Consistent-Field/Configuration Interaction (MCSCF/CI) ab-initio theoretical calculations of the N1s core-to-valence and core-to-Rydberg excitations, including vibrational dynamics. New resonances were identified compared to previous work, owing to detailed molecular modeling of the vibrational, spin-orbit coupling and metastable state effects on the spectra. The latter are evidenced by spectral contributions from the ⁴Σ⁻ electronic state which lies 0.07 eV above the NH⁺²Π ground state. Full article

The selective PPARα modulator (SPPARMα) is expected to medicate dyslipidemia with minimizing adverse effects. Recently, pemafibrate was screened from the ligand library as an SPPARMα bearing strong potency. Several clinical pieces of evidence have proved the usefulness of pemafibrate as a medication; however, how pemafibrate works as a SPPARMα at the molecular level is not fully known. In this study, we investigate the molecular mechanism behind its novel SPPARMα character through a combination of approaches of X-ray crystallography, isothermal titration calorimetry (ITC), and fragment molecular orbital (FMO) analysis. ITC measurements have indicated that pemafibrate binds more strongly to PPARα than to PPARγ. The crystal structure of PPARα-ligand binding domain (LBD)/pemafibrate/steroid receptor coactivator-1 peptide (SRC1) determined at 3.2 Å resolution indicates that pemafibrate binds to the ligand binding pocket (LBP) of PPARα in a Y-shaped form. The structure also reveals that the conformation of the phenoxyalkyl group in pemafibrate is flexible in the absence of SRC1 coactivator peptide bound to PPARα; this gives a freedom for the phenoxyalkyl group to adopt structural changes induced by the binding of coactivators. FMO calculations have indicated that the accumulation of hydrophobic interactions provided by the residues at the LBP improve the interaction between pemafibrate and PPARα compared with the interaction between fenofibrate and PPARα. Full article

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR²⁺ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs. Full article

Ten novel fullerene-derivatives (FDs) of C₆₀ and C₇₀ had been designed as acceptor for polymer solar cell (PSC) by employing the quantitative structure-property relationship (QSPR) model, which was developed strategically with a reasonably big pool of experimental power conversion efficiency (PCE) data. The QSPR model was checked and validated with stringent parameter and reliability of predicted PCE values of all designed FDs. They were assessed by the applicability domain (AD) and process randomization test. The predicted PCE of FDs range from 7.96 to 23.01. The obtained encouraging results led us to the additional theoretical analysis of the energetics and UV-Vis spectra of isolated dyes employing Density functional theory (DFT) and Time-dependent-DFT (TD-DFT) calculations using PBE/6-31G(d,p) and CAM-B3LYP/6-311G(d,p) level calculations, respectively. The FD4 is the best C₆₀-derivatives candidates for PSCs as it has the lowest exciton binding energy, up-shifted lowest unoccupied molecular orbital (LUMO) energy level to increase open-circuit voltage (V_OC) and strong absorption in the UV region. In case of C₇₀-derivatives, FD7 is potential candidate for future PSCs due to its strong absorption in UV-Vis region and lower exciton binding energy with higher V_OC. Our optoelectronic results strongly support the developed QSPR model equation. Analyzing QSPR model and optoelectronic parameters, we concluded that the FD1, FD2, FD4, and FD10 are the most potential candidates for acceptor fragment of fullerene-based PSC. The outcomes of tactical molecular design followed by the investigation of optoelectronic features are suggested to be employed as a significant resource for the synthesis of FDs as an acceptor of PSCs. Full article

In this work, we present a simple decomposition scheme of the Kohn-Sham optimized orbitals which is able to provide a reduced basis set, made of localized polycentric orbitals, specifically designed for Quantum Monte Carlo. The decomposition follows a standard Density functional theory (DFT) calculation and is based on atomic connectivity and shell structure. The new orbitals are used to construct a compact correlated wave function of the Slater–Jastrow form which is optimized at the Variational Monte Carlo level and then used as the trial wave function for a final Diffusion Monte Carlo accurate energy calculation. We are able, in this way, to capture the basic information on the real system brought by the Kohn-Sham orbitals and use it for the calculation of the ground state energy within a strictly variational method. Here, we show test calculations performed on some small selected systems to assess the validity of the proposed approach in a molecular fragmentation, in the calculation of a barrier height of a chemical reaction and in the determination of intermolecular potentials. The final Diffusion Monte Carlo energies are in very good agreement with the best literature data within chemical accuracy. Full article