H-bond Energy Research Articles

Evaluating interaction energy versus electron density relationships to estimate inter and intramolecular H-bonding

We investigate the computational effects on the relationships between interaction energy (ΔE) and electron density (ρ), at the critical point obtained from 19 intermolecular H-bonded dimers, to estimate inter and intramolecular interactions of larger H-bonded systems. Our analysis examines basis set superposition error (BSSE) effects, dispersion energy corrections, and the exchange-correlation energy model on the ΔE vs. ρ linear regressions. The calculations were carried out within density functional theory (DFT) combined with the 6-31+G(d,p) and def2-TZVPP basis sets. This procedure quantifies the average effects of BSSE for different levels of approximation, and underscore the sensitivity of the ΔE estimation together with dispersion corrections. This is valuable for the development of DFT-based estimators of multiple interaction energies of large H-bonded systems with low computational cost. We have applied this procedure by analyzing H-bonded biological molecules, such as DNA base pairs, an asparagine side chain, and an AZT molecule. Our estimated H-bond interaction energies are in agreement with previous studies, and emphasize the importance of methodological considerations for accurately predicting interaction energies using DFT combined with topological parameters.

Geometric descriptors for beta turns.

Beta turns, in which the protein backbone abruptly changes direction over four amino acid residues, are the most common type of protein secondary structure after alpha helices and beta sheets and play key structural and functional roles. Previous work has produced classification systems for turn geometry at multiple levels of precision, but these operate in backbone dihedral-angle (Ramachandran) space, and the absence of a local Euclidean-space coordinate system and structural alignment for turns, or of any systematic Euclidean-space characterization of turn backbone shape, presents challenges for the visualization, comparison and analysis of the wide range of turn conformations and the design of turns and the structures that incorporate them. This work derives a turn-local coordinate system that implicitly aligns turns, together with a set of geometric descriptors that characterize the bulk BB shapes of turns and describe modes of structural variation not explicitly captured by existing systems. These modes are shown to be meaningful by the demonstration of clear relationships between descriptor values and the electrostatic energy of the beta-turn H-bond, the overrepresentations of key side-chain motifs, and the structural contexts of turns. Geometric turn descriptors complement Ramachandran-space classifications, and they can be used to select turn structures for compatibility with particular side-chain interactions or contexts. Potential applications include protein design and other tasks in which an enhanced Euclidean-space characterization of turns may improve understanding or performance. The web-based tools ExploreTurns, MapTurns, and ProfileTurn, available at www.betaturn.com, incorporate turn-local coordinates and turn descriptors and demonstrate their utility.

Differential scanning calorimetry of proteins and Zimm–Bragg model in water

Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. Hydrogen bonds play a crucial role in stabilizing the three-dimensional structure of proteins. Naturally, information about the strength of hydrogen bonds is contained in the measured DSC profiles. Despite its obvious importance, there is no approach that would allow the extraction of such information from the heat capacity measurements. In order to connect the measured profile to microscopic properties of a polypeptide chain, a proper model is required to fit. Using recent advances in the Zimm–Bragg (ZB) theory of protein folding in water, we propose a new and efficient algorithm to process the DSC experimental data and to extract the H-bonding energy among other relevant constants. Thus, for the randomly picked set of 33 proteins, we have found a quite narrow distribution of hydrogen bonding energies from 1 to 8 kJ/mol with the average energy of intra-protein hydrogen bonds h¯=4.2±1.5 kJ/mol and the average energy of water–protein bonds as hps¯=3.8±1.5 kJ/mol. This is an important illustration of a tiny disbalance between the water–protein and intraprotein hydrogen bonds. Fitted values of the nucleation parameter σ belong to the range from 0.001 to 0.01, as expected. The reported method can be considered as complementary to the classical two-state approach and together with other parameters provides the protein–water and intraprotein H-bonding energies, not accessible within the two-state paradigm.

2D hydrogen bonded organic framework (2D-HOF) in benzodioxane-coupled-pyridine as a charge carrier: Synthesis, structural, quantum computational investigation

This research presents a comprehensive investigation into the synthesis, structural features, and charge carrier properties of a novel 2D Hydrogen-Bonded Organic Framework (2D-HOF) formed by Benzodioxane-Coupled-Pyridine. The synthesis involves the reaction of 2,3-dihydrobenzo[b][1,4]dioxin-6-carbaldehyde with pyridine-2-carbohydrazide in the presence of acetic acid and ethanol solvent, leading to the formation of (E)-2-(2-((2,3-dihydrobenzo[b][1,4]dioxin-6-yl)methylene)hydrazinyl)pyridine (DDMP). Single crystal X-ray diffraction analysis reveals the monoclinic crystal system with the P21/n space group, showcasing a non-planar structure due to a distinctive twisting motion in the dioxane ring. The crystal packing is governed by a complex network of intermolecular interactions, including hydrogen bonds, short contacts, and π-stacking, ultimately forming a stable 2D-HOF. Hirshfeld Surface (HS) analysis provides insights into key interactions, emphasizing the significance of hydrogen bonding, short contacts, and stacking interactions in molecular packing. The 2D fingerprint (FP) plots quantitatively highlight crucial interatomic contacts, with hydrogen bonding, CH…H, and O…H interactions dominating. Molecular Electrostatic Potential (MEP) analysis reveals potential sites for electrophilic and nucleophilic attacks, aiding in predicting reactive sites and charge carrier behavior. Energy framework analysis sheds light on the pairwise interaction energies within the crystal structure, emphasizing the role of dispersive forces in stabilizing the crystal lattice. Density functional theory calculations indicate the molecule's charge transfer capabilities, suggesting its suitability for applications such as batteries, supercapacitors, and solar cells. Additionally, global reactivity parameters suggest that the 2D HOF material has electron and proton conduction capabilities, making it versatile for various applications. Atoms-in-molecules (AIM) topology analysis, particularly non-covalent interaction (NCI) analysis, provides a detailed understanding of intra and intermolecular interactions, highlighting hydrogen bonding and π…π interactions. H-bond binding energy analysis confirms the non-covalent nature of identified interactions, emphasizing their strength and significance.

Prebiotic Chemistry and Sepiolite: A Density Functional Theory Approach

In this study, the molecular interactions of sepiolite, a biocompatibility clay mineral with known as biomaterial, and purine and pyrimidine molecules forming the bases of DNA and RNA molecules were modeled by Density Functional Theory. In addition to the geometry optimization, interaction energy, bond critical point, and electrostatic potential calculations revealed that essential molecules for our source of life interact with the basal surface of the clay. For example, the best interaction energies between bases / sepiolite were found to be -127.47, -121.35 kJ / mol for guanine and cytosine, respectively. Looking at the modeling results, one of the most important factors affecting the interaction energies is H-bond. In order to reveal this, bond critical points analyze were performed and it was computed that a large amount of intermolecular interaction energies came from H-bonds. For example, it has been calculated that close to 70% of the total energy in the guanine/TOT model is from H-bonds. Besides, this value of the cytosine/TOT model was found to be around 72%. The most effective indexes in these two models are 145 and 135, and the H-bond energies were recorded as -22.41 and 31.41 kJ/mol, respectively. Considering all the analyzes run, it can be concluded that the basal surfaces of the sepiolite are a suitable host for the nitrogenous bases, which are the main sources of life.

The effect of hydrogen bonds on the reactivity of coniferous and deciduous dioxan lignins

The slightly altered samples of dioxan lignin were extracted from coniferous (spruce and juniper) and deciduous wood (aspen) by the Pepper’s method. Lignins were characterized by data of elemental, functional composition, macromolecular and reactive (acid–base and redox) properties. IR spectra of lignins were recorded by the attenuated total refection method. The absorption band of lignins in the 3000–3700 cm−1 region corresponds to the valence vibrations of hydroxyl groups involved in hydrogen bonds. This band was divided into separate Gaussian contours by deconvolution method. The characteristic parameters (energy, length, and relative content) were calculated on the basis of correlation dependencies for each type of H-bonds. The relationship between reactivity (acid–base and redox properties) and the involvement of hydroxyl groups of a natural polymer in H-bonds was shown. The highest reactivity of aspen lignins is caused by the presence of syringyl structures and lower H-bond energies involving reaction centers of macromolecules.

Noncovalent and Covalent O-H···O Interactions in PPh3O Cocrystals: A Correlation Study Involving QTAIM, SAPT, NBO, and IBSI Methods.

PPh3O.hemihydrate polymorphs and 11 assorted PPh3O cocrystals collectively constitute a reliable stock to pursue a systematic analysis aiming to investigate the impacts of some vital issues on the TPPO.H-bond donor aggregates. The issues highlighted herein are (i) effect of varying acidity of H-bond donors on the degeneracy of lone pairs of the H-bond acceptor (PPh3O), (ii) effectiveness of the |V(r)|/G(r) and H(r)/ρ(r) parameters as a covalency metric, (iii) 3c-4e bonding in the covalent PPh3O.nitric acid cocrystal, (iv) salient features of H-bond interaction energy and an interplay of its components, (v) an intrinsic bond strength scale for the PPh3O cocrystals, and (vi) reliable empirical relations between several bond descriptors for a quick estimation of interaction energy. To be specific about point (vi), we have propounded two promising avenues for a fast semiquantitative calculation of interaction energy from an endearing nonenergetic parameter, viz., bond length: dO-H···O → ρBCP (MAPE = 2.36%) → ESAPT0 (MAPE = 9.26%), and dO-H···O → IBSI (MAPE = 1.87%) → ESAPT0 (MAPE = 9.66%). All the aforesaid issues have been explored in detail through the QTAIM, NBO, and IBSI analyses (M06-2X-D3/def2-TZVP level), as well as by the SAPT study at the SAPT0/aug-cc-pVDZ platform. The statistically valid correlation studies can be particularly conducive for practical purposes as a transformative extension of the established facts into postulates for the unknown cocrystals.

In silico docking of anti-Alzheimer’s molecules from plant derivatives

Alzheimer’s disease is a progressive neurodegenerative disease and most often associated with memory deficits and cognitive decline. This study pertains to the development of plant based molecules that can help treating the Alzheimer’s conditions. Plant based molecules usually render no side effects, compared to the Allopathic drugs. Also, this study is based on the novel approach of Computer aided drug design. The molecules selected for study are screened for drug likeness property using DruLiTo software. The molecules are also screened for presence of carcinogenicity and mutagenicity using T.E.S.T software. The molecule is then docked with the receptor using the Molegro software. The best pose is selected and results are tabulated and concluded. Any molecule can be considered as ‘well-bound’ or ‘well-docked’ if it expresses a fairly negative docking score. The H-bond energy is also a parameter to be considered. Negative H-bond energy is correlated with strong H-bond interaction between the amino acid residues and the molecule. Out of the 3 compounds, Compound 1 [Punicic acid] docked with Acetylcholine Esterase Receptor[1ACJ] displayed the highest negative moldock score [-156.709] and is very well bound to the receptor, followed by compound 2 [Ferrulic acid] and compound 3[Caeffic acd]. These plant based molecules can be further tested to evaluate the extent of their anti-Alzheimer’s activity through pre-clinical and clinical testing and may also be incorporated in Ayurvedic medicine for treating Alzheimer’s disease.

S288T mutation altering MmpL3 periplasmic domain channel and H-bond network: a novel dual drug resistance mechanism.

Mycobacterial membrane proteins Large 3 (MmpL3) is responsible for the transport of mycobacterial acids out of cell membrane to form cell wall, which is essential for the survival of Mycobacterium tuberculosis (Mtb) and has become a potent anti-tuberculosis target. SQ109 is an ethambutol (EMB) analogue, as a novel anti-tuberculosis drug, can effectively inhibit MmpL3, and has completed phase 2b-3 clinical trials. Drug resistance has always been the bottleneck problem in clinical treatment of tuberculosis. The S288T mutant of MmpL3 shows significant resistance to the inhibitor SQ109, while the specific action mechanism remains unclear. The results show that MmpL3 S288T mutation causes local conformational change with little effect on the global structure. With MmpL3 bound by SQ109 inhibitor, the distance between D710 and R715 increases resulting in H-bond destruction, but their interactions and proton transfer function are still restored. In addition, the rotation of Y44 in the S288T mutant leads to an obvious bend in the periplasmic domain channel and an increased number of contact residues, reducing substrate transport efficiency. This work not only provides a possible dual drug resistance mechanism of MmpL3 S288T mutant but also aids the development of novel anti-tuberculosis inhibitors. In this work, molecular dynamics (MD) and quantum mechanics (QM) simulations both were performed to compare inhibitor (i.e., SQ109) recognition, motion characteristics, and H-bond energy change of MmpL3 after S288T mutation. In addition, the WT_SQ109 complex structure was obtained by molecular docking program (Autodock 4.2); Molecular Mechanics/ Poisson Boltzmann Surface Area (MM-PBSA) and Solvated Interaction Energy (SIE) methods were used to calculate the binding free energies (∆Gbind); Geometric criteria were used to analyze the changes of hydrogen bond networks.

Dynamics of terminal fraying-peeling and hydrogen bonds dictates the sequential vs. cooperative melting pathways of nanoscale DNA and PNA triplexes.

Peptide nucleic acids (PNAs) are charge-neutral synthetic DNA/RNA analogues. In many aspects of biology and biotechnology, the details of DNA and PNA melting reaction coordinates are crucial, and their associative/dissociative details remain inadequately understood. In the current study, we have attempted to gain insights into comparative melting pathways and binding affinity of iso-sequences of an 18-mer PNA-DNA-PNA triplex and the analogous DNA-DNA-DNA triplex, and DNA-DNA and PNA-DNA duplexes. It is intriguing that while the DNA-DNA-DNA triplex melts in two sequential steps, the PNA-DNA-PNA triplex melts in a single step and the mechanistic aspects for this difference are still not clear. We report an all-atom molecular dynamics simulation of both complexes in the temperature range of 300 to 500 K with 20 K intervals. Based on the trajectory analysis, we provide evidence that the association and dissociation are dictated by the differences in fraying-peeling effects from either terminus to the center in a zipper pattern among the PNA-DNA-PNA triplex and DNA-DNA-DNA triplexes. These are shown to be governed by the different characteristics of H-bonding, RMSD, and Free Energy Landscape (FEL) as analyzed by PCA, leading to the DNA-DNA-DNA triplex exhibiting sequential melting, while the PNA-DNA-PNA triplex shows cooperative melting of the whole fragment in a single-step. The PNA-DNA-PNA triplex base pairs are thermodynamically more stable than the DNA-DNA-DNA triplex, with the binding affinity of PNA-TFO to the PNA : DNA duplex being higher than that of DNA-TFO to the DNA : DNA duplex. The investigation of the association/dissociation of PNA-TFO to the PNA-DNA duplex has relevance and importance in the emerging effective applications of oligonucleotide therapy.

Uracil-water interaction revisited - in search of single H-bonded secondary minima.

Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method). The results reveal that these new structures are very shallow secondary minima between two deep wells or next to a deep well of primary minima (double H-bonded structures) in the potential energy surface. The H-bond energy of these single H-bonded complexes is found to be less sensitive to a wide range (about 15-20 degrees) of O⋯HO and NH⋯O angles, and the linearity is preferred in the stable three single H-bonded structures. The technical method used to locate such a shallow minimum is described in detail and may be useful for identifying local minima in other cases where consecutive multiple H-bonded structures are global minima. Energy decomposition (using symmetry adapted perturbation theory (SAPT)) of interaction energy, electron redistribution, and relevant vibrational modes are discussed.

Mechanistic insights to sorptive removal of four sulfonamide antibiotics from water using magnetite-functionalized biochar

Magnetite-functionalized biochar (MBC) is a promising engineered material for remediation of antibiotic-contaminated fields. However, sorption mechanisms of ionizable organic compounds such as sulfonamide antibiotics (SAs) on MBC are still unclear. This study employed four representative SAs including sulfamethazine (SMT), sulfamerazine (SMR), sulfadiazine (SDZ), and sulfamethoxazole (SMX), to compare the difference in sorption on MBC. Results showed that the sorption capacities and affinities of the four SAs varied with their substituents, hydrophobic properties, and dissociation constants (pKa). Synergistic effect during co-pyrolysis with Fe3+ enhanced the sorption performance of MBC towards SAs compared to original BC. Spectral methods confirmed structural changes of MBC such as the variance in oxygen-containing groups and defective/graphitized phases. Results of modeling pH-dependent sorption revealed that H-bonding or π-bond assisted H-bonding determined the sorption affinities and capacities of SAs. In particular, the SAs with lower pKa were thermodynamically favorable to form H-bonding with MBC via proton exchange with water molecules. Quantum calculation results quantified the contributions of H-bonding strengths and found that the energies of H-bonding were correlated with affinities of SAs. Moreover, contributions of oxygen-containing groups instead of minerals dominated the H-bonding energies. Mechanistic insights from this study can be valuable in exploring engineered BC composites for practical application in field remediation.Graphical

Hydrogen bond interaction and mechanical property of polycarbonate polyurethane solid electrolyte

The previously unconsidered hydrogen bond (H-bond) networks in polyurethane solid polymer electrolytes (PUSPE) were studied by density functional theory. We further understood the H-bond interaction in PU, judged H-bond path, and quantified H-bond energy through atomic in molecular theory topological analysis. The frequency of the theoretical model is compared with the experimental value by Fourier transform infrared spectroscopy. The effect of H-bond on mechanical property of four kinds of polycarbonate (PCDL) PUSPE with different hard segments (diphenylmethane diisocyanate MDI/4,4′-dicycloethyl methane diisocyanate HMDI/toluene diisocyanate TDI/isoflurone diisocyanate IPDI) were discussed by double-chains models. The higher tensile strength and lower elongation at break of MDI-PUSPE result from the higher H-bond interaction strength between hard segments. The H-bond interaction between TFSI- and hard segment is studied, and it is determined by kinetic analysis that it reduces the migration energy barrier. These findings provide theoretical guidance for designing PU electrolytes in the future.

COMPARATIVE ANALYSIS OF SMALL MOLECULES AND NATURAL PLANT COMPOUNDS AS THERAPEUTIC INHIBITORS TARGETING RdRp AND NUCLEOCAPSID PROTEINS OF SARS COV 2: AN IN SILICO APPROACH

Objective: Coronavirus disease 2019 (COVID-19) is a virus-borne infection caused by the severe acute respiratory syndrome coronavirus disease-2 (SARS-CoV-2) virus. Nucleocapsid protein and RNA-dependent RNA polymerase (RdRp) activity in viral structural membrane, transcription, and replication have been identified as desirable targets for the development of novel antiviral strategies. The SARS-COV-2 N protein binds to the viral genome to promote the precise folding of the hammerhead ribozyme, preventing ineffective RNA confirmations, and directs them into a helical capsid shape or ribonucleoprotein complex, which is vital for viability. RNA synthesis requires RdRp to form phosphodiester bonds based on the RNA template. SARS-CoV-2 RNA synthesis, transcription, and replication depend on RdRp’s complex with nsp7 and nsp8. Methods: Our study targeted SARS-COV-2 RdRp and N proteins with natural plant compounds and small molecules. Hyperchem software optimized their structures geometrically and energetically. Based on MolDock, Rerank, and H-bonding energy, the best ligands were selected using the Molegro virtual docker. Results: In our analysis, we have identified nine compounds against N protein and seven compounds against RdRp protein that had more potent inhibitory effects with the lowest MolDock scores. The top 6 (Alpha solanine, Betanin, cairicoside I, Ginsenoside rb 1, Naringin, Polyphyllin I) compounds that have better inhibitory effects against both proteins. Conclusion: We conclude that the top six compounds have greater inhibitory efficacy against N and RdRp protein than other compounds. However, in vitro and in vivo experimental studies, as well as clinical trials, are required to achieve the desired result.

PH and H-bonding energy for pure water

This paper is devoted to the estimation of pH for pure water. We assume that the dissociation of water molecules is mainly caused by binary high energetic collisions. The dissociation energy in liquid water is identified with the energy of H-bonding. The density dependence of the dissociation energy TD is described. It is shown that this dependence allows to successfully reproduce the experimental values of pH up to the boiling temperature.

Structural, spectroscopic, electronic, Hirshfeld, QTAIM and biological predications of a hybrid 2,6-dichloropurine compound: A detailed density functional theoretical study

Extensive research into the optimized structure, spectroscopic and biological properties of 2,6-dichloropurine (6DCP) was conducted using IR/Raman and NMR techniques, as well as theoretically using the DFT approach with B3LYP, CAM-B3LYP, and PBEPBE function levels at 6-311++G(d, p) basis set. The computational results from DFT approaches such as geometrical, IR/Raman and NMR spectra were compared with the experimental results. All our theoretical calculations were in good agreement with observed data. The electronic HOMO-LUMO, H-bonding and strong conjugative interactions across different molecular entities are discussed to reveal the accompanying pharmaceutical intermediate. The molecular properties such as chemical reactivity descriptors, mapped ESP, dipole moment, mean polarizability, and first order hyperpolarizability of the title molecule were calculated by quantum mechanical calculations. The high value of the electronic dipole moment and polarizability estimate for the 6DCP molecule may improve its biological activity. The NBO study has enabled researchers to investigate hyper-conjugate interactions, intramolecular bonding, and strong H-bonding interactions. Strong H-bonding interaction energies of 120.47 kcal/mol have been performed at the DFT/PBEPBE level.

A combined in silico approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives

Inhibition of human mitochondrial peptide deformylase (HsPDF) plays a major role in reducing growth, proliferation, and cellular cancer survival. In this work, a series of 32 actinonin derivatives for HsPDF (PDB: 3G5K) inhibitor’s anticancer activity was computationally analyzed for the first time, using an in silico study considering 2D-QSAR modeling, and molecular docking studies, and validated by molecular dynamics and ADMET properties. The results of multilinear regression (MLR) and artificial neural networks (ANN) statistical analysis reveal a good correlation between pIC50 activity and the seven (7) descriptors. The developed models were highly significant with cross-validation, the Y-randomization test and their applicability range. In addition, all considered data sets show that the AC30 compound, exhibits the best binding affinity (docking score = −212.074 kcal/mol and H-bonding energy = −15.879 kcal/mol). Furthermore, molecular dynamics simulations were performed at 500 ns, confirming the stability of the studied complexes under physiological conditions and validating the molecular docking results. Five selected actinonin derivatives (AC1, AC8, AC15, AC18 and AC30), exhibiting best docking score, were rationalized as potential leads for HsPDF inhibition, in well agreement with experimental outcomes. Furthermore, based on the in silico study, new six molecules (AC32, AC33, AC34, AC35, AC36 and AC37) were suggested as HsPDF inhibition candidates, which would be combined with in-vitro and in-vivo studies to perspective validation of their anticancer activity. Indeed, the ADMET predictions indicate that these six new ligands have demonstrated a fairly good drug-likeness profile.

Polypyridyl Coordinated Re(I) complexes for human tenascin-C (TNC) as an Antibreast Cancer Agent: An Intuition from Molecular Modeling and Simulations

Breast cancer continues to be the biggest cause of mortality for women worldwide, taking the lives of millions each year. As a result, scientists are now exploring the possibility of metal-based complexes as anticancer therapies. Notwithstanding, polypyridyl coordinated Re(I) complexes have demonstrated tremendous promise as cancer-fighting medications. Therefore, the intent of this research is to investigate theoretically the spectral properties, compute density functional theory (DFT), and simulate molecular docking of polypyridyl coordinated Re(I) complexes containing functionalized 2,2′-bipyridine N,N′-donor bidentate ligands: 5,5′-DiMBpy coordinated in (1a), 4,4′-DiMBpy coordinated in (2a), and 4,4′-DiMoxBp coordinated in (3a) for cancer therapy application. Intriguingly, the complex Re(2a) achieved the greatest MolDock score and H-bond energy following interactions with the target receptors utilized, followed by Re(1a) and Re(3), respectively. Thus elucidating the studied compounds to be efficient in the mitigation of breast cancer.

Acetylacetone and imidazole coordinated Re(I) tricarbonyl complexes: Experimental, DFT studies, and molecular docking approach

The research work presents the synthesis, spectral characterization (UV, FT-IR, and NMR), and modelling of tricarbonyl rhenium complexes (R1, R2, R3, R4, and R5) bearing the β-diketone ligand and acetylacetone (Acac) for potential application as cancer drugs. The theoretical investigation was carried out within the framework of density functional theory (DFT) computation at the ωB97XD/Gen/6–311++G (d,p)/LanL2DZ level of theory. The studied rhenium complexes: fac-[Re(Acac)(CO)3(H2O)] (R1),fac-[Re(Acac)(CO)3(Py)] (R2), fac-[Re(Acac)(CO)3(Im)] (R3), fac-[Re(Acac)(CO)3(1-CH3Im)] (R4),fac-[Re(Acac)(CO)3(Pz)] (R5) follows an increasing pattern of stability: R5 < R4 < R2 < R3 < R1, with energy gap values of 6.4487, 6.6281, 7.6758, 7.7487 and 8.0608 eV respectively. The MolDock score ranges from -65.769 to -42.141 kcal/mol compared to the much smaller value of -13.191 kcal/mol for Cisplatin (Cispt) interaction with 2ES3, indicating that the rhenium complex ligands exhibit higher inhibitory activities against TNC to promote apoptosis and regulate cell cycle associated with breast cancer compared to Cispt. The highest score is R4 at -115.954 with HBond energy of -2.923 kcal/mol, then followed by R2 with a score of -103.773 and H-Bond energy bond of -0.392 kcal/mol due to only Steric interaction and R3 with a score of -102.885 and H-bond of -0.2259 kcal/mol due to steric interaction with Phe16(I), Val17(I), Cys53(B) amino acid similar to R2. Due to their stability and MolDock score, R2 and R3 complexes exhibit the potency to be used as potential anti-breast cancer drug participants.

Molecular dynamics simulation of CO2 hydrate growth in salt water

To achieve the “carbon peaking and carbon neutrality goals”, carbon capture, utilization, and storage (CCUS) is a research hotspot. In our work, molecular dynamics simulation method is used to simulate the CO2 hydrate growth in NaCl aqueous solution with pure structure I CO2 hydrate as seed, at a temperature of 275 K, a pressure of 10 MPa, and a total simulation time of 5000 ns. It was found that not all water molecules participated in the formation of hydrate. The F3 and F4 order parameters and cage numbers proved the formation of structure I CO2 hydrate. According to independent gradient model based on Hirshfeld partition (IGMH) analysis, one water molecule could form four H-bonds with adjacent water molecules in a perfect hydrate; single Cl− could form multiple H-bonds with adjacent water molecules; but the specific water molecule which was near the Cl− might not form four H-bond with its adjacent water molecules, resulting in the inability to form a perfect hydrate and thus water molecules remain liquid; Na+ does not participate in the formation of hydrates. In addition, Na+ and Cl− always come in pairs, so we do believe that NaCl always act as hydrate inhibitor, regardless of its concentration. This is the mechanism how hydrate inhibitor works and plays a significant guiding role in developing highly effective hydrate inhibitors. From the perspective of binding energies of H-bonds, we believe that HOH···Cl− is stronger than HOH···OH2. The density of CO2 hydrate is higher than that of seawater, which could help CO2 hydrate sink spontaneously on the seabed.