Intermolecular Conformation Research Articles

Unraveling Cordia myxa’s anti-malarial potential: integrative insights from network pharmacology, molecular modeling, and machine learning

Malaria is a potentially fatal infective illness caused due to parasites that belong to the Plasmodium genus, which are transferred to humans with the help of the stings of affected female Anopheles mosquitoes, and it persists as a serious public wellness problem worldwide. Cordia myxa is a medicinal plant that possesses various medicinal characteristics like antimicrobial, anti-inflammation, antioxidant, and antidiabetic activities, which makes it an important natural resource for the therapy of different maladies in traditional medicine. In this investigation, a certain network pharmacology method has been utilized to identify the potent active components, possible targets as well as signaling pathways present in C. myxa in relation to malaria therapy. The active compounds were submitted to molecular docking approaches to validate their successful activity against the potential targets. The study concluded that three constituents named cosmosiin, stigmastanol, robinetin, and quercetin were highly active and could regulate the expression of Interleukin 6 (IL6) and Cysteine-aspartic acid protease 3 (CASP3), which may act as a potential therapeutic target for malaria treatment. These analyses are validated by molecular dynamics simulation which reflects on the overall structural stability of the intermolecular conformation and interactions. These results can also be witnessed in simulation-based trajectories binding free energies, which concluded the significant role of electrostatic and van der Waals energies in total intermolecular interactions. Finally, we utilized machine learning to predict the anti-malarial activity of C. myxa compounds, comparing them with approved drugs. Using the Chemprop model and MAIP predictions, we assessed ten compounds, revealing their potential as lead anti-malarial agents. This study establishes a groundwork for comprehending the function of the anti-malaria action of C. myxa.

Cellulose Fiber with Enhanced Mechanical Properties: The Role of Co-Solvents in Gel-like NMMO System.

Cellulose has garnered attention in the textile industry, but it exhibits limitations in applications that require high strength and modulus. In this study, regenerated cellulose fiber with enhanced mechanical properties was fabricated from a gel-like N-methylmorpholine N-oxide (NMMO)-cellulose solution by modulating the intermolecular interaction and conformation of the cellulose chains. To control the interaction, two types of co-solvents (dimethyl acetamide (DMAc) and dimethyl formamide (DMF)) were added to the cellulose solutions at varying concentrations (10, 20, and 30 wt%). Rheological analysis showed that the co-solvents reduced the solution viscosity by weakening intermolecular interactions. The calculated distance parameter (Ra) in Hansen space confirmed that the co-solvent disrupted intermolecular hydrogen bonding within cellulose chains. The solutions were spun into fiber via a simple wet spinning process and were characterized by X-ray diffraction (XRD) and universal testing machine (UTM). The addition of co-solvent led to an increased crystallinity index (C.I.) owing to the extended cellulose chains. The modulus of the resulting fiber was increased when the co-solvent concentration was 10 wt%, regardless of the co-solvent type. This study demonstrates the potential for enhancing the mechanical properties of cellulose-based products by modulating the conformation and interaction of cellulose chains through the addition of co-solvent.

A Multi-Target mechanism of Withania somnifera bioactive compounds in autism spectrum disorder (ASD) Treatment: Network pharmacology, molecular docking, and molecular dynamics simulations studies

Autism spectrum disorder (ASD) is a developmental disorder resulting from variations in brain structure and function. Individuals with ASD often experience challenges in communication and social interaction, along with engaging in repetitive or restricted patterns of behavior and interests. The lack of documented data and the wide range of pathophysiological processes associated with ASDmake it challenging to work which causes a major financial burden on health care management. Withania somnifera, often referred to as ashwagandha is the tropical winter cherry in the Solanaceae family that can be used to treat several ailments such as asthma, stress, hypertension,diabetes, cancer, arthritic, and neural disorders including ASD. In this investigation, we examined the active compound-target-pathway network and discovered that Withanolide J, Withanone, and Withaferin A have a great role in the onset of ASD by influencing the IL6 gene. Later, the molecular docking method was applied for confirmation of the active compound's effective action against the prospective target. The molecular dynamics simulation exhibited that the complexes of Withanolide J and Withanone had stable intermolecular binding conformation and unveiled very stable dynamics during the simulation time. A combined network pharmacology and molecular docking approach demonstrated that W. somnifera exhibits a promising preventive impact on ASD by targeting relevant signaling pathways associated with the disorder. This establishes a foundation for comprehending the underlying mechanism of the anti-ASD activity of W. somnifera.

A hierarchical approach towards identification of novel inhibitors against L, D-transpeptidase YcbB as an anti-bacterial therapeutic target

The bacterial cell wall, being a vital component for cell viability, is regarded as a promising drug target. The L, D-Transpeptidase YcbB enzyme has been implicated for a significant role in cell wall polymers cross linking during typhoid toxin release, β-lactam resistance and outer membrane defect rescue. These observations have been recorded in different bacterial pathogens such as Salmonella Typhimurium, Citrobacter rodentium, and Salmonella typhi. In this work, we have shown structure based virtual screening of diverse natural and synthetic drug libraries against the enzyme and revealed three compounds as LAS_32135590, LAS_34036730 and LAS-51380924. These compounds showed highly stable energies and the findings are very competitive with the control molecule ((1RG or (4 R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid or ertapenem)) used. Compared to control (which has binding energy score of −11.63 kcal/mol), the compounds showed better binding energy. The binding energy score of LAS_32135590, LAS_34036730 and LAS-51380924 is −12.63 kcal/mol, −12.22 kcal/mol and −12.10 kcal/mol, respectively. Further, the docked snapshot of the lead compounds and control were investigated for stability under time dependent dynamics environment. All the three leads complex and control system showed significant equilibrium (mean RMSD < 3 Å) both in term of intermolecular docked conformation and binding interactions network. Further validation on the complex’s stability was acquired from the end-state MMPB/GBSA analysis that observed greater contribution from van der Waals forces and electrostatic energy while less contribution was noticed from solvation part. The compounds were also showed good drug-likeness and are non-toxic and non-mutagenic. In short, the compounds can be used in experimental testing’s and might be subjected to structure modification to get better results. Communicated by Ramaswamy H. Sarma

Design of a novel multi-epitopes vaccine against Escherichia fergusonii: a pan-proteome based in- silico approach.

Escherichia fergusonii a gram-negative rod-shaped bacterium in the Enterobacteriaceae family, infect humans, causing serious illnesses such as urinary tract infection, cystitis, biliary tract infection, pneumonia, meningitis, hemolytic uremic syndrome, and death. Initially treatable with penicillin, antibiotic misuse led to evolving resistance, including resistance to colistin, a last-resort drug. With no licensed vaccine, the study aimed to design a multi-epitope vaccine against E. fergusonii. The study started with the retrieval of the complete proteome of all known strains and proceeded to filter the surface exposed virulent proteins. Seventeen virulent proteins (4 extracellular, 4 outer membranes, 9 periplasmic) with desirable physicochemical properties were identified from the complete proteome of known strains. Further, these proteins were processed for B-cell and T-cell epitope mapping. Obtained epitopes were evaluated for antigenicity, allergenicity, solubility, MHC-binding, and toxicity and the filtered epitopes were fused by specific linkers and an adjuvant into a vaccine construct. Structure of the vaccine candidate was predicted and refined resulting in 78.1% amino acids in allowed regions and VERIFY3D score of 81%. Vaccine construct was docked with TLR-4, MHC-I, and MHC-II, showing binding energies of -1040.8 kcal/mol, -871.4 kcal/mol, and -1154.6 kcal/mol and maximum interactions. Further, molecular dynamic simulation of the docked complexes was carried out resulting in a significant stable nature of the docked complexes (high B-factor and deformability values, lower Eigen and high variance values) in terms of intermolecular binding conformation and interactions. The vaccine was also reported to stimulate a variety of immunological pathways after administration. In short, the designed vaccine revealed promising predictions about its immune protective potential against E. fergusonii infections however experimental validation is needed to validate the results.

Data-driven insights into the fluorescence of asphaltene aggregates using extended Frenkel exciton model

The origin of the fluorescence redshift during asphaltene aggregation remains debated due to the great diversity of asphaltene molecules, while the extended Frenkel exciton model provided a theoretical framework for studying multi-chromophore systems, such as asphaltene aggregates. We investigated the fluorescence energy of hundreds of asphaltene dimers based on 133 experimental revealed asphaltene monomer structures. Our result shows that the dimer's fluorescence energy is always lower than both of its monomers regardless of its intermolecular conformation, with its redshift dominated by superexchange. The dimer oscillator strength predominantly depends on the monomer with the lower fluorescence energy, and the involvement of charge-transfer states and the cancellation between monomer transition dipole moments suppressed the fluorescence especially when two monomers have similar fluorescence energy. The above-mentioned findings hold for all asphaltene dimers despite their diversity, which offers a theoretical interpretation for comprehending the relationship between asphaltene aggregation and its fluorescence variation. Furthermore, this work provides theoretical guidance to other research areas related to organic planar conjugated systems with multiple chromophores.

Identification and dynamics of novel scaffolds against Enterococcus faecium serine hydroxymethyltransferase enzyme: a potential target for antibiotics development

Serine hydroxymethyltransferase enzyme is a significant player in purine, thymidylate, and L-serine biosynthesis and has been tagged as a potential target for cancer, viruses, and parasites. However, this enzyme as an anti-bacterial druggable target has not been explored much. Herein, in this work, different computational chemistry and biophysics techniques were applied to identify potential computational predicted inhibitory molecules against Enterococcus faecium serine hydroxymethyltransferase enzyme. By structure based virtual screening process of ASINEX antibacterial library against the enzyme two main compounds: Top-1_BDC_21204033 and Top-2_BDC_20700155 were reported as best binding molecules. The Top-1_BDC_21204033 and Top-2_BDC_20700155 binding energy value is −9.3 and −8.9 kcal/mol, respectively. The control molecule binding energy score is −6.55 kcal/mol. The mean RMSD of Top-1-BDC_21204033, Top-2-BDC_20700155 and control is 3.7 Å (maximum 5.03 Å), 1.7 Å (maximum 3.05 Å), and 3.84 Å (maximum of 6.7 Å), respectively. During the simulation time, the intermolecular docked conformation and interactions were seen stable despite of few small jumps by the compounds/control, responsible for high RMSD in some frames. The MM/GBSA and MM/PBSA binding free energy of lead Top-2-BDC_20700155 complex is −79.52 and −82.63 kcal/mol, respectively. This complex was seen as the most stable compared to the control. Furthermore, the lead molecules and control showed good druglikeness and pharmacokinetics profile. The lead molecules were non-toxic and non-mutagenic. In short, the compounds are promising in terms of binding to the serine hydroxymethyltransferase enzyme and need to be subjected to experimental studies. Communicated by Ramaswamy H. Sarma

Role of concentration and hydrophobic nature of weak polyelectrolytes on adsorption structure and thermodynamics at oil-water interface: Study of several carboxylate polymers

Intermolecular structure, conformations, solvation and adsorption characteristics of four partially ionized polycarboxylic acids syndiotactic-poly(acrylic acid) (s-PAA), syndiotactic-poly(methacrylic acid) (s-PMA), isotactic-poly(methacrylic acid) (i-PMA) and atactic-poly(ethacrylic acid) (a-PEA) at oil (CCl4) - water interface is studied by molecular dynamics simulations over the range from dilute to monolayer coverage. Linearity and slope of Θ-Γ curves are correlated to conformational invariance and extent of adsorption (partial vs complete) respectively, within the range of concentration of study. Adsorption of i-PMA and a-PEA chains occurs deeper into the oil-side of interface region as driven by the greater hydrophobicity of these polymers. Higher tendency of highly extended s-PMA to desorb from the interface as compared to strong adsorption of compact coiled i-PMA is driven by their solvation behavior dictated by aspects of structural partitioning of chemical groups with respect to the solvents of the two phases. Hydrophobic side-group in the polyelectrolyte chain is responsible for the slower dynamics of the backbone. The observed variation in thickness of adsorbed layer and fractional interface coverage with concentration suggest partial adsorption of chain segments beyond saturation of interface rather than coiling of chains to accommodate additional chains. While a-PEA exhibits greater variation in interfacial tension, the change in electric potential difference across the interface indicates weak adsorption by s-PMA. The influence of the tacticity of PMA on dynamics and distribution of counter-ions is in agreement with experimental results. Results provide a significant advancement in our understanding of polyelectrolyte and polymer adsorption at oil-water liquid interface.

Design of a novel multi-epitopes based vaccine against brucellosis

Brucella melitensis is a gram-negative coccobacillus that causes brucellosis in humans. The lack of effective treatment and increasing antibiotic-resistant patterns shown by B. melitensis, warrant the search for novel therapeutics. In this study, comprehensive bioinformatics, reverse vaccinology, and biophysics techniques were employed to design a novel multi-epitopes based vaccine (MEBV) against B. melitensis. Core proteomics, subtractive proteomics and immunoinformatic studies revealed three core proteins: Flagellar hook protein (FlgE), TonB-dependent receptor, and Porin family protein as promising vaccine targets. The proteins have exposed topology, and are antigenic, and adhesive. Furthermore, B and T cell epitopes were predicted from these proteins. Highly antigenic, immunogenic, non-toxic and non-allergenic epitopes were shortlisted and used in the MEBV design. The designed MEBV also showed stable docked conformation with different immune receptors such as MHC-I, MHC-II, and TLR-4. The global energy of selected docked complexes was as; solution 4 of MEBV-TLR-4 (−45.73 kJ/mol), solution 5 of MEBV-MHC-I (−20.94 kJ/mol), and solution 1 of MEBV-MHC-II (−3.45 kJ/mol). Molecular dynamics simulation studies unveiled a steady root mean square deviation (RMSD) pattern for the systems. However, all of them were stable in terms of intermolecular binding conformation and chemical interactions. Further, the systems showed robust binding energies with net binding energy < −300 kcal/mol. The van der Waals and electrostatic energies were the dominating energies and were found as intermolecular stabilizing factors. The vaccine was also predicted to generate promising immunological responses and thus could be an attractive candidate to be evaluated in experimental studies.

X-ray Structures and Computational Studies of Two Bioactive 2-(Adamantane-1-carbonyl)-N-substituted Hydrazine-1-carbothioamides

Two biologically active adamantane-linked hydrazine-1-carbothioamide derivatives, namely 2-(adamantane-1-carbonyl)-N-(tert-butyl)hydrazine-1-carbothioamide) 1 and 2-(adamantane-1-carbonyl)-N-cyclohexylhydrazine-1-carbothioamide 2, have been synthesized. X-ray analysis was conducted to study the effect of the t-butyl and cyclohexyl moieties on the intermolecular interactions and conformation of the molecules in the solid state. X-ray analysis reveals that compound 1 exhibits folded conformation, whereas compound 2 adopts extended conformation. The Hirshfeld surface analysis indicates that the contributions of the major intercontacts involved in the stabilization of the crystal structures do not change much as a result of the t-butyl and cyclohexyl moieties. However, the presence and absence of these contacts is revealed by the 2D-fingerprint plots. The CLP-Pixel method was used to identify the energetically significant molecular dimers. These dimers are stabilized by different types of intermolecular interactions such as N-H···S, N-H···O, C-H···S, C-H···O, H-H bonding and C-H···π interactions. The strength of these interactions was quantified by using the QTAIM approach. The results suggest that N-H···O interaction is found to be stronger among other interactions. The in vitro assay suggests that both compounds 1 and 2 exhibit urease inhibition potential, and these compounds also display moderate antiproliferative activities. Molecular docking analysis shows the key interaction between urease enzyme and title compounds.

Identification of the Principle of Taste Sensors to Detect Non-Charged Bitter Substances by 1H-NMR Measurement.

A taste sensor with lipid/polymer membranes is attracting attention as a method to evaluate taste objectively. However, due to the characteristic of detecting taste by changes in membrane potential, taste sensors cannot measure non-charged bitter substances. Many foods and medicines contain non-charged bitter substances, and it is necessary to quantify these tastes with sensors. Therefore, we have been developing taste sensors to detect bitter tastes caused by non-charged substances such as caffeine. In previous studies, a sensor for detecting bitterness caused by caffeine and theobromine, theophylline, was developed, using a membrane modified with hydroxybenzoic acid (HBA) as the sensing part. The sensor was designed to form intramolecular hydrogen bonds (H-bonds) between the hydroxy group and carboxy group of HBA and to successively cause the intermolecular H-bonds between HBA and caffeine molecules to be measured. However, whether this sensing principle is correct or not cannot be confirmed from the results of taste sensor measurements. Therefore, in this study, we explored the interaction between HBA and caffeine by 1H-nuclear magnetic resonance spectroscopy (NMR). By the 1H NMR detection, we confirmed that both the substances interact with each other. Furthermore, the nuclear Overhauser effect (NOE) of intermolecular spatial conformation in solution was measured, by which 2,6-dihydroxybenzoic acid (2,6-DHBA) preferably interacted with caffeine via the H-bonding and stacking configuration between aromatic rings. Identifying the binding form of 2,6-DHBA to caffeine was estimated to predict how the two substances interact.

Conformations, inter-molecular structure and hydrogen bond dynamics of neutral and cationic poly(vinyl amine) in aqueous solution

ABSTRACT Intermolecular structure, hydration and conformations of Poly(vinylamine) (PVAm) in neutral as well as protonated (cationic) condition as polyelectrolyte in dilute aqueous solution, were studied via single-chain atomistic molecular dynamics simulations in explicit solvent. A parametric study of atomic partial charges was carried out at different values of degree-of-ionisation (f) of the amine group. A modification of generic GROMOS force-field is developed. The unusual non-monotonic behaviour of radius-of-gyration with an increase in f is captured, in agreement with experimental results of intrinsic viscosity. Cooperative solvation of PVAm chain occurs with an increase in f as assisted by counter-ion condensation. Three different regimes of the variation of radius-of-gyration of PVAm with change in f are identified. Changes in polymer-water hydrogen bonding is not the dominant effect for the behaviour of chain-size variation. The non-monotonous expansion of PVAm is attributed to the complex interplay between hydrogen bonding and intermolecular structure of polymer chain, water and counter-ions, all of which provide a cooperative solvation of the chain. With an increase in f at the higher range, the formation of ion pairs produces salt-bridges and bends in the chain, as well as ion-pair–ion-pair repulsion extending the chain at complete ionisation.

Machine Learning of Quasiparticle Energies in Molecules and Clusters.

We present a Δ-machine learning approach for the prediction of GW quasiparticle energies (ΔMLQP) and photoelectron spectra of molecules and clusters, using orbital-sensitive representations (OSRs) based on molecular Cartesian coordinates in kernel ridge regression-based supervised learning. Coulomb matrix, bag-of-bond, and bond-angle-torsion representations are made orbital-sensitive by augmenting them with atom-centered orbital charges and Kohn–Sham orbital energies, both of which are readily available from baseline calculations at the level of density functional theory (DFT). We first illustrate the effects of different constructions of the OSRs on the prediction of frontier orbital energies of 22k molecules of the QM8 data set and show that it is possible to predict the full photoelectron spectrum of molecules within the data set using a single model with a mean absolute error below 0.1 eV. We further demonstrate that the OSR-based ΔMLQP captures the effects of intra- and intermolecular conformations in application to water monomers and dimers. Finally, we show that the approach can be embedded in multiscale simulation workflows, by studying the solvatochromic shifts of quasiparticle and electron–hole excitation energies of solvated acetone in a setup combining molecular dynamics, DFT, the GW approximation, and the Bethe–Salpeter equation. Our findings suggest that the ΔMLQP model allows us to predict quasiparticle energies and photoelectron spectra of molecules and clusters with GW accuracy at DFT cost.

Alignment of linear polymeric grains for highly stable N-type thin-film transistors

Summary Temperature-insensitive properties are attractive for most electronics, including polymeric semiconducting devices. Especially, polymeric field-effect transistors (FETs) with high mobility have been important research targets due to their broad applications. However, polymeric FETs with stable charge transport operating at extremely cold or hot zones are faced with enormous challenges. In this study, the polyacrylonitrile was found to significantly tune the sizes of pre-aggregates of polymers in solutions and the crystallinity of the polymeric films. The orientation of 5–25 μm linear grains in the films were prepared through the bar-coating process with polyacrylonitrile as an additive, which stabilized the electron mobility over a wide range of temperatures. The linear-grain morphology of the film contributed to reducing the holes and grain boundaries in the transport paths of carriers. Typically, the top-gate FETs based on P(NDI2OD-T2) displayed a stable electron transporting behavior from 200 to 460 K, with mobility greater than 3.5 cm2V−1s−1.

An intermolecular hydrogen bond plays a determining role in product selection of a surface confined Schiff-base reaction.

Herein, we illustrate how the cooperation of intermolecular hydrogen bonds and conformation flexibility leads to the formation of diverse complex covalent nanostructures on the surface, while the relative abundance of the final products can be further tuned by adjusting the molar ratio and concentration of monomers.

Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1.

Mycobacterium smegmatis MutT1 (MsMutT1) is a sanitation enzyme made up ofan N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of MsMutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes MsMutT1 a versatile enzyme.

Structure and Dynamics of HIV-1 Env Trimers on Native Virions Engaged in Living T Cells

The HIV-1 envelope glycoprotein (Env) mediates viral entry into the host cell. Although the highly dynamic nature of Env intramolecular conformations has been shown with single molecule spectroscopy in vitro, the bona fide Env intra and intermolecular mechanics when engaged in live T cells remains unknown. We used two photon fast fluorescence lifetime imaging detection of single-molecule Forster Resonance Energy Transfer occurring between fluorescent labels on HIV-1 Env. Our observations of Env dynamics reveal transitions between four intramolecular conformations of Env trimer and two additional intermolecular conformations that mediate Env clustering. Furthermore, we show that three broadly neutralizing anti-Env antibodies directed to different epitopes destabilise Env intermolecular dynamics and their clusters engaged to living T cells. Thus, this study illuminates how different conformations and clusters of Env mediate HIV-1 Env–T cell interactions in real time and therefore might control immune evasion.

Oleogels and Their Contribution in the Production of Healthier Food Products: The Fats of the Future

Consumption of animal fats, calorie-dense and simple carbohydrate-rich diets along with a more sedentary life style have triggered the outcome of cardiovascular and obesity disorders. A worthy alternative is to replace these of saturated fats with healthier ingredients in a texturized oleogel. Oleogelation promises to decrease the incorporation of harmful fats granting good mechanical properties to food products by creating crystalline colloidal networks upon contact with a gelator. Thus, unsaturated fatty acids from oils are thus trapped and retained forming gels having microscopic self-assembled crystalline particles of different shapes. Currently, most oleogels have been developed with vegetable oils by applying gelators such as polymers, partial glycerides, waxes and fatty acids improving the mechanical and thermal properties of food products. This review is focused on the progress regarding oleogelation and the physical interactions responsible for the intermolecular conformation, physical properties, additives and microstructure required for the substitution of harmful saturated and trans fats. Likewise, the most recent advances, regarding their potential functionality and applications as the fats of the future are also discussed.

Intermolecular Complexes and Molecular Conformations Directed by Hydrogen Bonds: Matrix Isolation and Ab Initio Studies

Studies on hydrogen bonding interaction in various systems, involving phenylacetylene (PhAc), propargyl alcohol (PA), borazine (BNH), propargyl amine (PAm) were performed using matrix isolation infrared spectroscopy and supported by ab initio computations. Weak intermolecular interactions of the above mentioned precursors with water, methanol, ether, acetylene and benzene were studied. These systems manifested O–H···$$ \uppi $$ and n–$$ {{\upsigma}^{*}} $$ interactions, such as C–H···O, N–H···O, O–H···O and O–H···N. In several cases the complexes were multiply tethered involving two or more of the above mentioned contacts. Many of the weak complexes exhibited a number of isomers, and the relative importance of the multiple non-covalent contacts resulted in a competition between the various isomers for the global minimum. It was found that subtle changes in the structures of the precursors tilted the balance towards one isomer or the other. Our studies also threw up a systematic method of building possible structures for complex systems starting from the known structures of related simple systems. We also studied the homodimers of PA and BNH. The BNH dimer was particularly interesting as one of its isomers was characterized by a bis-dihydrogen bond. We also studied the influence of hydrogen bonding interactions in determining the conformational landscape and preference in amino acids. Here again we were able to draw some generalizations regarding the conformational stability of amino acids. The combination of matrix isolation and ab initio computation is a powerful tool for studies on weak intermolecular interactions and conformations.

Synthesis of Chiral Spin-Labeled Amino Acids.

Spin-labeled amino acids (SLAAs) are often used to determine intermolecular distances and conformations in proteins via double electron-electron resonance. Currently available SLAAs can be difficult to incorporate selectively and have little resemblance to natural side chains in proteins. Enantioselective synthesis of three spin-labeled l-amino acids is described, starting from readily available 2,2,6,6-tetramethyl-4-piperidinone. These SLAAs better replicate canonical residues in proteins and aim for biological incorporation via genetic incorporation or solid-phase peptide synthesis.