Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers. Molecular computing is a branch of computing that uses DNA, biochemistry, and molecular biology hardware, instead of traditional s...
Advantages in CMOS MOSFET-based electronics served as a basis for modern ubiquitous computerization. At the same time, theoretical and practical developments in material science, analytical chemistry and molecular biology have presented the possibili...
The design and the synthesis of molecule-based crystalline salts made up of simple cationic and/or anionic building blocks with multiple, occasionally stimulus-responsive, chemical (host–guest, catalytic, acid–base, or redox) and physical...
Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment w...
17 December 2024
Spin-crossover (SCO) and single-ion magnets (SIMs), or their mixed SCO-SIM derivatives, are a convenient solution in the evolution from molecular magnetism toward molecular spintronics and quantum computing. Herein, we report on the current trends an...
Molecular magnetism has made a long journey, from the fundamental studies on through-ligand electron exchange magnetic interactions in dinuclear metal complexes with extended organic bridges to the more recent exploration of their electron spin trans...
Drug discovery is a complex and expensive process in which only a small proportion of candidate molecules reach clinical approval. Computational methods, particularly computer-aided drug design (CADD), have become fundamental to accelerate and optimi...
We introduce and study the computational power of Oritatami, a theoretical model that explores greedy molecular folding, whereby a molecular strand begins to fold before its production is complete. This model is inspired by our recent experimental wo...
In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry...
Distinct PAEs are implicated in breast cancer progression through multiple molecular pathways. This study aims to elucidate the potential mechanisms in common by which PAEs promote breast cancer progression. Dibutyl phthalate (DBP), benzyl butyl phth...
Molecular docking plays an increasingly necessary role in interdisciplinary research, particularly in modern drug design. Pharmaceutical companies compose a trillion dollar per year industry and the public is generally unaware of how beneficial pharm...
High-pressure chemistry of organic compounds is a hot topic of modern chemistry. In this work, basic computational concepts for high-pressure phase transition studies in molecular crystals are described, showing their advantages and disadvantages. Th...
Cancer remains one of the leading causes of morbidity and mortality worldwide, highlighting the need for safe and effective therapeutic strategies targeting multiple oncogenic pathways. Cinnamon (Cinnamomum spp.) contains several bioactive phytochemi...
Graph-based neural networks have proven to be useful in molecular property prediction, a critical component of computer-aided drug discovery. In this application, in response to the growing demand for improved computational efficiency and localized e...
Skin sensitization remains a critical toxicological endpoint in cosmetic ingredient development, particularly under accelerated innovation cycles and increasingly stringent safety requirements. Although NAMs have achieved substantial regulatory matur...
The demand for new novel flavour and fragrance (F&F) molecules has boosted the need for a systematic approach to designing fragrance molecules. However, the F&F-related industry still relies heavily on experimental approaches or on existing d...
Gutman and Trinajstić (1972) defined the connection-number based Zagreb indices, where connection number is degree of a vertex at distance two, in order to find the electron energy of alternant hydrocarbons. These indices remain symmetric for the iso...
Thiophene and sulfonamide derivatives serve as biologically active compounds, used for the manufacture of large numbers of new drugs. In this study, 11 selected derivatives of thiophene sulfonamide were computed for their geometric parameters, such a...
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a global COVID-19 pandemic, challenging healthcare systems worldwide. Effective therapeutic strategies against this novel coronavirus remain limited, unde...
Building polymers implemented into building panels and exterior façades have been determined as the major contributor to severe fire incidents, including the 2017 Grenfell Tower fire incident. To gain a deeper understanding of the pyrolysis pr...
Cytochrome P450 3A (CYP3A) enzymes catalyze the metabolism of a wide range of endogenous and exogenous compounds. Genetic variations in the 3 CYP3A isoforms (CYP3A28, CYP3A74, and CYP3A76) may influence their expression and activity, leading to inter...
As shown by Jarzynski, free energy differences between equilibrium states can be expressed in terms of the statistics of work carried out on a system during non-equilibrium transformations. This exact result, as well as the related Crooks fluctuation...
The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter...
Metals are beneficial to life, but the presence of these elements in excessive amounts can harm both organisms and the environment; therefore, detecting the presence of metals is essential. Currently, metal detection methods employ powerful instrumen...
Prediction of molecular parameters and material functions from the macroscopic viscoelastic properties of complex fluids are of great significance for molecular and formulation design in fundamental research as well as various industrial applications...
The growing importance of the membrane-based air separation processes results in an increasing demand for suitable polymeric membrane structures. This has spurred the interest in designing polymer structures for O2/N2 separation by employing a system...
The unbalanced assignment problem (UAP) is to optimally resolve the problem of assigning n jobs to m individuals (m < n), such that minimum cost or maximum profit obtained. It is a vitally important Non-deterministic Polynomial (NP) complete probl...
To minimize the fuel consumption of an automobile, one of the parameters that car manufacturers modify is car geometry. Through aerodynamics testing, it is determined whether the final car geometry will produce a lower coefficient of drag. If the coe...
Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we...
Here, we present a general framework for computing the infrared anharmonic vibrational spectra of polyatomic molecules using Born–Oppenheimer molecular dynamics (BOMD) with PyRAMD software. To account for nuclear quantum effects, we suggest usi...
Recent research in DNA nanotechnology has demonstrated that biological substrates can be used for computing at a molecular level. However, in vitro demonstrations of DNA computations use preprogrammed, rule-based methods which lack the adaptability t...
In this paper, we consider the inevitable large fluctuations of pressure in typical molecular dynamics (MD) simulations of ligand–protein binding problems. In simulations under the constant pressure of one bar, the pressure artifactually fluctu...
Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlyi...
Chiral liquid chromatography (cLC) using chiral stationary phases (CSPs) has become a crucial technique for separating enantiomers. Understanding enantiomeric discrimination is essential for improving chromatographic conditions and elucidating chiral...
The most popular modern programs for quantum chemical and molecular dynamics (classical, ab initio, and QM/MM) calculations, which are relevant for the investigation of nature and various properties of different molecules and periodic chemical system...
Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer’s is the most common neurodegenerative dis...
In response to recent advances in computer-aided drug discovery (CADD) enabled by high-performance computing, computational approaches were employed to support and rationalize the investigation of a VEGFR-2-targeted anticancer candidate, combining mo...
How can cellular interactions in solid tumors guide molecular interventions against immune suppression? This critical review examines how computer-aided drug design (CADD) connects immunosuppressive tumor microenvironment (TME) states to testable mol...
Neuropsychiatric diseases are characterized by complex molecular underpinnings that remain challenging to fully elucidate. Molecular dynamics (MD) simulations have emerged as a powerful computational tool, providing a crucial bridge between static ge...
Antimicrobial resistance (AMR) is one of the most significant public health threats today. The need for new antimicrobials against multidrug-resistant infections is growing. The development of computational models capable of predicting new drug&ndash...
The rational design of molecularly imprinted polymers has evolved along with state-of-the-art experimental imprinting strategies taking advantage of sophisticated computational tools. In silico methods enable the screening and simulation of innovativ...
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...
Background: Paclitaxel is a cornerstone chemotherapeutic agent widely used in breast cancer treatment, primarily through the stabilization of microtubule dynamics. Beyond its canonical tubulin-targeting activity, increasing evidence suggests that pac...
Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimul...
Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo...
Molecular-level investigations of the Central Nervous System have been revolutionized by the development of computational methods, computing power, and capacity advances. These techniques have enabled researchers to analyze large amounts of data from...
Glutamate is the major excitatory neurotransmitter in the human brain whose binding to receptors on neurons excites them while excess glutamate are removed from synapses via transporter proteins. Determination of the crystal structures of bacterial a...
Molecular docking is among the most widely used techniques in structure-based drug discovery and has become integral to natural-product research. Despite substantial advances in computational algorithms and artificial intelligence, the methodological...
The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Rec...
Four carbanion monosubstituted 4’-aryl-1,2,4-triazol-1-ium-4-R2-phenacylids, used as precursors in obtaining new heterocyclic compounds, and their corresponding derivatives belonging to the C2v point group of symmetry were studied by computatio...
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