A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets.

Structure-based generative chemistry is essential in computer-aided drug discovery by exploring a vast chemical space to design ligands with high binding affinity for targets. However, traditional in silico methods are limited by computational inefficiency, while machine learning approaches face bottlenecks due to auto-regressive sampling. To address these concerns, we have developed a conditional deep generative model, PMDM, for 3D molecule generation fitting specified targets. PMDM consists of a conditional equivariant diffusion model with both local and global molecular dynamics, enabling PMDM to consider the conditioned protein information to generate molecules efficiently. The comprehensive experiments indicate that PMDM outperforms baseline models across multiple evaluation metrics. To evaluate the applications of PMDM under real drug design scenarios, we conduct lead compound optimization for SARS-CoV-2 main protease (Mpro) and Cyclin-dependent Kinase 2 (CDK2), respectively. The selected lead optimization molecules are synthesized and evaluated for their in-vitro activities against CDK2, displaying improved CDK2 activity.

Liquid-liquid phase separation (LLPS) in DNA and chromatin systems from the perspective of colloid physical chemistry.

DNA is a highly charged polyelectrolyte and is prone to associative phase separation driven by the presence of multivalent cations, charged surfactants, proteins, polymers and colloids. The process of DNA phase separation induced by positively charged species is often called DNA condensation. Generally, it refers to either intramolecular DNA compaction (coil-globule transition) or intermolecular DNA aggregation with macroscopic phase separation, but the formation of a DNA liquid crystalline system is also displayed. This has traditionally been described by polyelectrolyte theory and qualitative (Flory-Huggins-based) polymer theory approaches. DNA in the cell nucleus is packed into chromatin wound around the histone octamer (a protein complex comprising two copies each of the four histone proteins H2A, H2B, H3 and H4) to form nucleosomes separated by linker DNA. During the last decade, the phenomenon of the formation of biomolecular condensates (dynamic droplets) by liquid-liquid phase separation (LLPS) has emerged as a generally important mechanism for the formation of membraneless organelles from proteins, nucleic acids and their complexes. DNA and chromatin droplet formation through LLPS has recently received much attention by in vitro as well as in vivo studies that established the importance of this for compartmentalisation in the cell nucleus. Here, we review DNA and chromatin LLPS from a general colloid physical chemistry perspective. We start with a general discussion of colloidal phase separation in aqueous solutions and review the original (pre-LLPS era) work on DNA (macroscopic) phase separation for simpler systems with DNA in the presence of multivalent cations and well-defined surfactants and colloids. Following that, we discuss and illustrate the similarities of such macroscopic phase separation with the general behaviour of LLPS droplet formation by associative phase separation for DNA-protein systems, including chromatin; we also note cases of segregative association. The review ends with a discussion of chromatin LLPS in vivo and its physiological significance.

Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail.

We provide a molecular-level description of the thermodynamics and mechanistic aspects of drug permeation through the cell membrane. As a case study, we considered the antimalaria FDA approved drug chloroquine. Molecular dynamics simulations of the molecule (in its neutral and protonated form) were performed in the presence of different lipid bilayers, with the aim of uncovering key aspects of the permeation process, a fundamental step for the drug's action. Free energy values obtained by well-tempered metadynamics simulations suggest that the neutral form is the only permeating protomer, consistent with experimental data. H-bond interactions of the drug with water molecules and membrane headgroups play a crucial role for permeation. The presence of the transmembrane potential, investigated here for the first time in a drug permeation study, does not qualitatively affect these conclusions.

C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids.

Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.

Organically Templated Uranyl Sulfates and Selenates: Structural Complexity and Crystal Chemical Restrictions for Isotypic Compounds Formation.

This paper reviews the state of the art in the structural chemistry of organically templated uranyl sulfates and selenates, which are considered as the most representative groups of U-bearing synthetic compounds. In total, there are 194 compounds known for both groups, the crystal structures of which include 84 various organic molecules. Structural studies and topological analysis clearly indicate complex crystal chemical limitations in terms of the isomorphic substitution implementation, since the existence of isotypic phases has to date been confirmed only for 24 compounds out of 194, which is slightly above 12%. The structural architecture of the entire compound depends on the combination of the organic and oxyanion parts, changes in which are sometimes realized even while maintaining the topology of the U-bearing complex. An increase in the size of the hydrocarbon part and number of charge functional groups of the organic cation leads to the formation of rare and more complex topologies. In addition, the crystal structures of two novel uranyl sulfates and one uranyl selenate, templated by isopropylammonium cations, are reported.

Recent Progress in Crystalline Borates with Edge-Sharing BO4 Tetrahedra.

Crystalline borates have received great attention due to their various structures and wide applications. For a long time, the corner-sharing B-O unit is considered a basic rule in borate structural chemistry. The Dy4B6O15 synthesized under high-pressure is the first oxoborate with edge-sharing [BO4] tetrahedra, while the KZnB3O6 is the first ambient pressure borate with the edge-sharing [BO4] tetrahedra. The edge-sharing connection modes greatly enrich the structural chemistry of borates and are expected to expand new applications in the future. In this review, we summarize the recent progress in crystalline borates with edge-sharing [BO4] tetrahedra. We discuss the synthesis, fundamental building blocks, structural features, and possible applications of these edge-sharing borates. Finally, we also discuss the future perspectives in this field.

Teaching and assessing undergraduate collaboration skills scaffolded through the biochemistry curriculum using collaboration rubrics and student learning contracts.

The Department of Chemistry and Biochemistry at St. Mary's College of Maryland has scaffolded collaboration skills throughout the Biochemistry curriculum and developed several assessment tools to evaluate these skills. Biochemistry I and II have used team contracts at the beginning of extensive team projects where students identify their strengths, review expectations, and plan for group communication. At the conclusion of each project, each student assesses their own contributions and team members for various parts of the project. A common collaboration rubric was also applied in Biochemistry I and II as well as in two other courses, General Chemistry II Lab and Physical Chemistry I Lab, for students to evaluate themself and team members using the following subcategories: quality of work, commitment, leadership, communication, and analysis. In Biochemistry I and II, we used this rubric for multiple assignments that are part of the projects in the lecture courses. In the General Chemistry II Lab, we provided elements of this rubric within an evaluation form that reflects these collaboration attributes after each lab experience, so students can assess and report privately on their experiences as part of their collaboration grade for the course. A similar collaboration rubric is completed by students for each team-based laboratory within Physical Chemistry I. We also demonstrate different ways that instructors can use the data from these assessment tools. In our department, we are using these tools to frame the importance of collaboration skills and collecting data to inform our teaching of these skills. Preliminary data suggest that our curriculum is successfully teaching students how to be good collaborators.

Molecular Fingerprint Detection Using Raman and Infrared Spectroscopy Technologies for Cancer Detection: A Progress Review.

Molecular vibrations play a crucial role in physical chemistry and biochemistry, and Raman and infrared spectroscopy are the two most used techniques for vibrational spectroscopy. These techniques provide unique fingerprints of the molecules in a sample, which can be used to identify the chemical bonds, functional groups, and structures of the molecules. In this review article, recent research and development activities for molecular fingerprint detection using Raman and infrared spectroscopy are discussed, with a focus on identifying specific biomolecules and studying the chemical composition of biological samples for cancer diagnosis applications. The working principle and instrumentation of each technique are also discussed for a better understanding of the analytical versatility of vibrational spectroscopy. Raman spectroscopy is an invaluable tool for studying molecules and their interactions, and its use is likely to continue to grow in the future. Research has demonstrated that Raman spectroscopy is capable of accurately diagnosing various types of cancer, making it a valuable alternative to traditional diagnostic methods such as endoscopy. Infrared spectroscopy can provide complementary information to Raman spectroscopy and detect a wide range of biomolecules at low concentrations, even in complex biological samples. The article concludes with a comparison of the techniques and insights into future directions.

Effects of Electrode Materials on Electron Transport for Single-Molecule Junctions.

The contact at the molecule-electrode interface is a key component for a range of molecule-based devices involving electron transport. An electrode-molecule-electrode configuration is a prototypical testbed for quantitatively studying the underlying physical chemistry. Rather than the molecular side of the interface, this review focuses on examples of electrode materials in the literature. The basic concepts and relevant experimental techniques are introduced.

Determining the Physico-Chemical Composition of Biomolecular Condensates from Spatially-Resolved NMR.

Liquid-Liquid phase separation has emerged as fundamental process underlying the formation of biomolecular condensates. Insights into the composition and structure of biomolecular condensates is, however, complicated by their molecular complexity and dynamics. Here, we introduce an improved spatially-resolved NMR experiment that enables quantitative analysis of the physico-chemical composition of multi-component biomolecular condensates in equilibrium and label-free. Application of spatially-resolved NMR to condensates formed by the Alzheimer's disease-associated protein Tau demonstrates decreased water content, exclusion of the molecular crowding agent dextran, presence of a specific chemical environment of the small molecule DSS, and ≈150-fold increased concentration of Tau inside the condensate. The results suggest that spatially-resolved NMR can have a major impact in understanding the composition and physical chemistry of biomolecular condensates.

Embarking on a New Journey.

Everyone on board! It's all about science and the great people behind it at ChemPhysChem. In this Editorial, we look back at 2022, which has brought many changes and achievements to the journal, and delve into what is in store for 2023. We also introduce ChemPhysChem's first Early Career Advisory Board and welcome new faces to the Editorial Advisory Board. We are happy and honored to have the support of so many outstanding scientists from around the world working in all areas of physical chemistry and chemical physics.

Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory.

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers.

E-Z Isomerization in Guanidine: Second-order Saddle Dynamics, Non-statisticality, and Time-frequency Analysis.

Our recent work on the E-Z isomerization reaction of guanidine using ab initio chemical dynamics simulations [Rashmi et al., Regul. Chaotic Dyn. 2021, 26, 119] emphasized the role of second-order saddle (SOS) in the isomerization reaction; however, we could not unequivocally establish the non-statistical nature of the dynamics followed in the reaction. In the present study, we performed thousands of on-the-fly trajectories using forces computed at the MNDO level to investigate the influence of second-order saddle in the E-Z isomerization reaction of guanidine and the role of intramolecular vibrational energy redistribution (IVR) on the reaction dynamics. The simulations reveal that while majority of the trajectories follow the traditional transition state pathways, 15 % of the trajectories follow the SOS path. The dynamics was found to be highly non-statistical with the survival probabilities of the reactants showing large deviations from those obtained within the RRKM assumptions. In addition, a detailed analysis of the dynamics using time-dependent frequencies and the frequency ratio spaces reveal the existence of multiple resonance junctions that indicate the existence of regular dynamics and long-lived quasi-periodic trajectories in the phase space associated with non-RRKM behavior.

Development, physicochemical evaluation, and in vivo permeation studies of topical formulations containing 0.1% tacrolimus

Abstract The objective of this paper was to develop and evaluate two semi-solid pharmaceutical forms containing 0.1% tacrolimus: cream (CRT01) and gel (GLT01). For the evaluation of physicochemical stability, at times 0, 30, 60 and 90 days, at 23°C and at 40°C, High Performance Liquid Chromatography coupled with a Diode Array Detector (HPLC-DAD) was employed. This method was developed and validated for tacrolimus quantification. The occlusivity test and skin permeation assay were also performed, using an animal model (Wistar rats), and the CRT01 and GLT01 were compared to the 0.1% tacrolimus ointment (PFU01) obtained from the University Pharmacy, Federal University of Rio de Janeiro, Brazil. CRT01 and GLT01 presented a homogeneous aspect and consistency adequate for topical products, along with sensory characteristics above PFU01. They also presented adequate physicochemical stability for 90 days and a lower occlusive effect than PFU01 (p<0.05). CRT01 showed greater affinity for the skin when compared to PFU01 and GLT01, with low systemic absorption. The CRT01 semi-solid formulation was considered the most adequate one to treat patients with atopic dermatitis or other dermatologic inflammatory diseases, promoting rational use of tacrolimus

Hydrated Collagen: Where Physical Chemistry, Medical Imaging, and Bioengineering Meet.

It is well-known that collagen is the most abundant protein in the human body; however, what is not often appreciated is its fascinating physical chemistry and molecular physics. In this Perspective, we aim to expose some of the physicochemical phenomena associated with the hydration of collagen and to examine the role collagen's hydration water plays in determining its biological function as well as applications ranging from radiology to bioengineering. The main focus is on the Magic-Angle Effect, a phenomenon observed in Nuclear Magnetic Resonance (NMR) spectroscopy and Magnetic Resonance Imaging (MRI) of anisotropic collagenous tissues such as articular cartilage and tendon. While the effect has been known in NMR and MRI for decades, its exact molecular mechanism remains a topic of debate and continuing research in scientific literature. We survey some of the latest research aiming to develop a comprehensive molecular-level model of the Magic-Angle Effect. We also touch on other fields where understanding of collagen hydration is important, particularly nanomechanics and mechanobiology, biomaterials, and piezoelectric sensors.

Energy Electronegativity and Chemical Bonding.

Historical development of the concept of electronegativity (EN) and its significance and prospects for physical and structural chemistry are discussed. The current cutting-edge results are reviewed: new methods of determining the ENs of atoms in solid metals and of bond polarities and effective atomic charges in molecules and crystals. The ENs of nanosized elements are calculated for the first time, enabling us to understand their unusual reactivity, particularly the fixation of N2 by nanodiamond. Bond polarities in fluorides are also determined for the first time, taking into account the peculiarities of the fluorine atom's electronic structure and its electron affinity.