Hydrogen-bonding Patterns Research Articles

Structural and theoretical analysis of 2-chloro-4-nitroaniline and 2-methyl-6-nitroaniline salts.

The crystal structures of five new salts of 2-chloro-4-nitroaniline (2Cl4na) and 2-methyl-6-nitroaniline (2m6na) with inorganic acids, namely, 2-chloro-4-nitroanilinium bromide, C6H6ClN2O2+·Br- (1), 2-chloro-4-nitroanilinium hydrogen sulfate, C6H6ClN2O2+·HSO4- (2), 2-methyl-6-nitroanilinium bromide, C7H9N2O2+·Br- (3), 2-methyl-6-nitroanilinium triiodide, C7H9N2O2+·I3- (4), and 2-methyl-6-nitroanilinium hydrogen sulfate, C7H9N2O2+·HSO4- (5), were determined by single-crystal X-ray diffraction. Theoretical calculations of the relaxed potential energy surface (rPES) revealed that the energy barriers for the rotation of the nitro group for isolated H2Cl4na+ and H2m6na+ cations are 4.6 and 11.6 kcal mol-1, respectively. The ammonium group and respective anions form hydrogen bonds which are the most important interactions and are arranged in zero- (in 3), one- (in 1 and 4) or two-dimensional (in 2 and 5) networks. Hydrogen-bonding patterns were analyzed by means of mathematical relationships between graph-set descriptors and compared with previously reported nitroaniline salts. Hirshfeld surface analysis indicates that the nitro group plays a dominant role among the weak interactions, i.e. C-H...O(NO2), NO2...π(Ar) and O(NO2)...π(NO2). The frequency of the νsNO2 vibration is correlated with the type of interaction in which the NO2 group is involved. Analysis of the νsNO2 band observed in the IR and Raman spectra allowed an assessment of its shift in the sequence (H2m6na)I3 (4) < (H2m6na)HSO4 (5) < (H2m6na)Br (3) < (H2Cl4na)Br (1) < (H2Cl4na)HSO4 (2).

Watson-Crick versus Hoogsteen Base Pairs: Chemical Strategy to Encode and Express Genetic Information in Life.

Nucleic acids typically form a double helix structure through Watson-Crick base-pairing. In contrast, non-Watson-Crick base pairs can form other three-dimensional structures. Although it is well-known that Watson-Crick base pairs may be more unstable than non-Watson-Crick base pairs under some conditions, the importance of non-Watson-Crick base pairs has not been widely examined. Hoogsteen base pairs, the non-Watson-Crick base pairs, contain important hydrogen-bond patterns that form the helices of nucleic acids, such as in Watson-Crick base pairs, and can form non-double helix structures such as triplexes and quadruplexes. In recent years, non-double helix structures have been discovered in cells and were reported to considerably influence gene expression. The complex behavior of these nucleic acids in cells is gradually being revealed, but the underlying mechanisms remain almost unknown.Quantitatively analyzing the structural stability of nucleic acids is important for understanding their behavior. A nucleic acid is an anionic biopolymer composed of a sugar, base, and phosphoric acid. The physicochemical factors that determine the stability of nucleic acid structures include those derived from the interactions of nucleic acid structures and those derived from the environments surrounding nucleic acids. The Gibbs free energy change (ΔG) of structure formation is the most commonly used physicochemical parameter for analyzing quantitative stability. Quantitatively understanding the intracellular behavior of nucleic acids involves describing the formation of nucleic acid structures and related reactions as ΔG. Based on this concept, we quantitatively analyzed the stability of double helix and non-double helix structures and found that decreased water activity, an important factor in crowded cellular conditions, significantly destabilize the formation of Watson-Crick base pairs but stabilizes Hoogsteen base pairs.Here, we describe a physicochemical approach to understand the regulation of gene expressions based on the stability of nucleic acid structures. We developed new methods for predicting the stability of double and non-double helices in various molecular environments by mimicking intracellular environments. Furthermore, the physicochemical approach used for analyzing gene expression regulated by non-double helix structures is useful for not only determining how gene expression is controlled by cellular environments but also for developing new technologies to chemically regulate gene expression by targeting non-double helix structures. We discuss the roles of Watson-Crick and Hoogsteen base pairs in cells based on our results and why both types of base pairing are required for life. Finally, a new concept in nucleic acid science beyond that of Watson and Crick base pairing is introduced.

Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA

The interaction of positively charged N-terminal histone tails with nucleosomal DNA plays an important role in chromatin assembly and regulation, modulating their susceptibility to post-translational modifications and recognition by chromatin-binding proteins. Here, we report residue-specific 15 N NMR relaxation rates for histone H4 tails in reconstituted nucleosomes. These data indicate that H4 tails are strongly dynamically disordered, albeit with reduced conformational flexibility compared to a free peptide with the same sequence. Remarkably, the NMR observables were successfully reproduced in a 2-μs MD trajectory of the nucleosome. This is an important step toward resolving an apparent inconsistency where prior simulations were generally at odds with experimental evidence on conformational dynamics of histone tails. Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).

Extension of the CL&Pol Polarizable Force Field to Electrolytes, Protic Ionic Liquids, and Deep Eutectic Solvents.

The polarizable CL&Pol force field presented in our previous study, Transferable, Polarizable Force Field for Ionic Liquids (J. Chem. Theory Comput. 2019, 15, 5858, DOI: http://doi.org/10.1021/acs.jctc.9b0068910.1021/acs.jctc.9b00689), is extended to electrolytes, protic ionic liquids (PIL), deep eutectic solvents (DES), and glycols. These systems are problematic in polarizable simulations because they contain either small, highly charged ions or strong hydrogen bonds, which cause trajectory instabilities due to the pull exerted on the induced dipoles. We use a Tang-Toennies (TT) function to dampen, or smear, the interactions between charges and induced dipole at a short range involving small, highly charged atoms (such as hydrogen or lithium), thus preventing the "polarization catastrophe". The new force field gives stable trajectories and is validated through comparison with experimental data on density, viscosity, and ion diffusion coefficients of liquid systems of the above-mentioned classes. The results also shed light on the hydrogen-bonding pattern in ethylammonium nitrate, a PIL, for which the literature contains conflicting views. We describe the implementation of the TT damping function, of the temperature-grouped Nosé-Hoover thermostat for polarizable molecular dynamics (MD) and of the periodic perturbation method for viscosity evaluation from non-equilibrium trajectories in the LAMMPS MD code. The main result of this work is the wider applicability of the CL&Pol polarizable force field to new, important classes of fluids, achieving robust trajectories and a good description of equilibrium and transport properties in challenging systems. The fragment-based approach of CL&Pol will allow ready extension to a wide variety of PILs, DES, and electrolytes.

Infrared spectra of hydrogen bond network in lamellar perfluorocarboxylic acid monohydrates

The infrared spectra of the long-chain perfluorocarboxylic acid monohydrates differ markedly from those of the anhydrous dimers. Consequently, the structure of the solid perfluorocarboxylic acid monohydrates must differ from any known dimer-containing carboxylic acid crystals. Consideration of the significant features of the infrared spectra of the long-chain perfluorocarboxylic acid monohydrates, supplemented by their Raman spectra, and comparison with the spectra of auxiliary substances have led us to conclude that the rather strong neutral carboxyl-hydroxyl to water bonding can best explain the observations. The infrared spectra indicate the presence of fairly short hydrogen bonds connecting the water molecules to the carbonyl groups. In the construction of the hydrogen bonding pattern of the perfluorocarboxylic acid monohydrates, the oxalic acid dihydrate plays the key role. The striking similarity between the infrared spectra of the oxalic acid dihydrates and the perfluorocarboxylic acid monohydrates in the regions characteristic of water and OH⋯O vibration suggests that the structure of the hydrated carboxyl groups is the same in both crystals. These regions are characterized by the sharp doublet at 3539 cm−1 and 3464 cm−1, which is due to the H2O ν1 and ν3 stretching vibrations, respectively, and the broad absorption between 3000 cm−1 and 1500 cm−1 with the intense band at 1970 cm−1, both associated with the vibration of the OH⋯O group. The later peak consists of two band components at near 1980 cm−1 and 2020 cm−1. These band components show different behaviour when the temperature, polarization or deuteration is changed. In general, the infrared spectra of long-chain perfluorocarboxylic acids represent the system with very short hydrogen bonds connecting the water molecules to the carboxylates. This hydrogen bond pattern should be very similar to that found in the crystals of α-oxalic acid dihydrate.

Functional Porous Organic Polymers with Conjugated Triaryl Triazine as the Core for Superfast Adsorption Removal of Organic Dyes.

Developing efficient adsorbents for the removal of water pollutants is of great significance for environmental protection. In this study, conjugated triaryl triazines (CTT), containing intramolecular hydrogen-bonding patterns, were recognized to be intriguing building blocks for the construction of porous organic polymer (POP) adsorbents. These planar monomers with multiple phenolic hydroxyl groups facilitated the formation of aza-linked polymers with hierarchical porous structures, sheet-like morphology, good surface wettability, and high degree of functionality. Such structural characteristics of the CTT-POP adsorbents provided superfast adsorption of various cationic dyes from water. For the adsorption of methylene blue dye, the pseudo-second-order rate constant of CTT-POP-1 is 12.9 g mg-1 min-1, superior to those reported in the existing literature. In addition, CTT-POP-1 can be regenerated at least seven times with no loss in performance, indicating its potential application in water treatment.

Quasi self-inclusion of a 1-D coordination polymer within a 2-D hydrogen-bonded grid: a chaperone effect

The one-dimensional (1-D) coordination polymer [Ni(bdc)(pico)2(H2O)2] (where bdc = terephthalate, pico = 4-picoline) is hosted within a two-dimensional (2-D) hydrogen-bonded grid [Ni(bdc)(pico)2(H2O)2]·(pyz) (where pyz = pyrazine). Both coordination polymers are comprised of the same components and differ only by their hydrogen-bonding patterns. The polymers of the 2-D grids engage in O–H···N hydrogen bonds to the included pyz. The grid contains rhombohedral cavities that lie along the crystallographic ac-plane. The grids self-assemble by C–H···π interactions involving the methyl group of pico and the aromatic ring of the bdc anion. The included polymer interacts with the 2-D grids via O–H···O hydrogen bonds involving coordinated water and the bdc anion.

Influence of molecular geometry on the formation, architecture and dynamics of H-bonded supramolecular associates in 1-phenyl alcohols

Combination of calorimetric, dielectric, infrared, diffraction studies and quantum DFT computations was used to analyze the impact of the molecular architecture of a set of four 1-phenyl alcohols (1-phenylethanol, 1-phenyl-1-propanol, 1-phenyl-1-butanol and 2-methyl-1-phenyl-1-propanol) on their glass transition temperature, molecular dynamics, relaxation processes, hydrogen-bonding pattern and intermolecular association. We showed that all these alcohols form H-bonded supramolecular nanoassociates even at room temperature, despite containing a steric hindrance in the form of the phenyl ring in the most disfavored position. However, the concentration and the size of the H-bonded structures as well as the mutual arrangement of molecules in these clusters are tremendously affected by the molecular architecture. In linear-shaped 1-phenyl alcohols, i.e., 1-phenylethanol, 1-phenyl-1-propanol, 1-phenyl-1-butanol, the intermolecular O-H···O bonds organize themselves into chain-like patterns. Moreover, these alcohols are characterized by similar strength of intermolecular H bonds at each temperature and similar glass transition temperature. In turn, the globular molecular shape of 2-methyl-1-phenyl-1-propanol leads to a weakening of H bonds in this system, an increase in the glass transition temperature and the formation of supramolecular clusters in which O-H···O connections imply ring-like organization of molecules. Finally, these studies clearly show that unlike the glass transition temperature, the molecular dynamics of the 1-phenyl alcohols in the liquid state is not only affected by the molecular architecture and hydrogen bond strength but also by the morphology of the associates composed of H-linked molecules.

Conformational analysis of two new organotin(IV) structures completed with a CSD survey.

The conformational flexibilities are studied in two new organotin(IV) complexes, namely, trans-dichloridodimethylbis[N,N',N''-tris(2-chlorobenzyl)phosphoric triamide]tin(IV), [Sn(CH3)2(C21H21Cl3N3OP)2Cl2] or Sn(CH3)2Cl2{OP[NHCH2C6H4(2-Cl)]3}2, (I), and bis(dipropylammonium) tetrachloridodimethylstannate(IV), [(CH3CH2CH2)2NH2]2[Sn(CH3)2Cl4], (II), and their analogous structures from the Cambridge Structural Database (CSD). The conformations are considered based on the N-P=O-Sn torsion angles for (I) and the C-C-C-N, C-C-N-C, C-N-C-C and N-C-C-C torsion angles for the two symmetry-independent [CH3CH2CH2NH2CH2CH2CH3]+ cations in (II), and the ±ac±sp±ac (ac = anticlinal and sp = synperiplanar) and ±ap±ap±ap±ap (ap = antiperiplanar) conformations are observed, respectively. In both structures, the four atoms in the corners of the square-planar segment of the octahedral shape around the Sn atom participate in normal hydrogen-bonding interactions as acceptors, which include two O and two Cl atoms for (I), and four Cl atoms for (II). However, the phosphoric triamide ligands block the environment around the Sn atom and limit the hydrogen-bond pattern to form a supramolecular ribbon assembly, while in the presence of small organic cations in (II), a two-dimensional hydrogen-bonded architecture is achieved. The weak interactions π-π, C-H...π and C-Cl...π in (I), and C-H...Cl in (II) do not change the dimensionality of the hydrogen-bond pattern. The 62 CSD structures analogous to (I), i.e. with an SnOPN3 segment (including 83 entries) fall into four categories of conformations based on the N-P=O-Sn torsion angles. The 132 [(CH3CH2CH2)2NH2]+ cations from 85 CSD structures are classified into seven groups based on the torsion angles noted for (II). Most of the CSD structures adopt the same associated conformations noted for (I) and (II). 15 [Sn(CH3)2Cl4]2- anions extracted from the CSD are compared with the structure of (II).

On the role of water in the hydrogen bond network in DESs: an ab initio molecular dynamics and quantum mechanical study on the urea-betaine system.

We herein report an ab initio molecular dynamics study on a natural DES composed of urea and betaine in a 3 : 2 ratio, as a test case for evaluating the water effect. The article deals with a theoretical study using both ab initio molecular dynamics and quantum chemistry computations in order to unravel the role of water in the nanostructure of a urea-betaine mixture. Preliminary molecular dynamics outcomes (both radial and spatial distribution functions) suggest that water promotes the association between urea and betaine by increasing the hydrogen bond network and precluding the aggregation of urea molecules. In other words, the presence of water allows a less restrictive hydrogen bond network, presenting a regimen where the strong hydrogen bond interactions are replaced by a wide variety of weaker hydrogen bond interactions. On the other hand, in a water free DES there is a regimen where strong urea-betaine interactions are dominant. It is shown that second order perturbation theory energy analysis provides cogent insights into charge spreading and hydrogen bond patterns. A vibrational analysis (both IR and power spectrum) over the ab initio molecular dynamics trajectories in the water free DES as well as in the urea-betaine-water systems reveals that our results are consistent with the second order perturbation theory analysis and with the hydrogen bond network pattern.

Crystal structure of correianevesite from the Emmons pegmatite, Uncle Tom Mountain, Greenwood, Oxford County, Maine

Correianevesite, Fe2+Mn2+2(PO4)2·3H2O, is an uncommon secondary phosphate in granitic pegmatites. Described for the first time from the Cigana pegmatite (Conselheiro Pena, Brazil), it was subsequently reported only at the Berry-Havey pegmatite (Androscoggin County, Maine, U.S.A.). A single crystal from a new occurrence at the Emmons pegmatite, Oxford Co., Maine, gave the following unit cell unit cell parameters: a = 9.4872(19), b = 10.121(2), c = 8.7023(17) (Å), V 835.6(3) (Å3). The structure was anisotropically refined in the orthorhombic system, space group Pbna down to a R = 1.6% and the hydrogen-bond pattern could be determined. Microprobe chemical analysis, and bond valence calculation show the expected values for all the atomic sites and confirmed the valence of all ions in the structure.

Adaptive Chirality of an Achiral Cage: Chirality Transfer, Induction, and Circularly Polarized Luminescence through Aqueous Host–Guest Complexation

Chirality transfer, induction, and circularly polarized luminescence (CPL) using supramolecular hosts, such as macrocycles and cages, have been explored for wide-ranging applications in chiral reco...

Effect and regulation of the secondary structure of synthetic poly(&amp;alpha;-amino acid) based on ring-opening polymerization

Protein is one of the most important components that constitute the organism. A unique property of protein is the adoption of highly ordered secondary structure formed by hydrogen bond. Poly(α-amino acid)s are protein mimics that also present hydrogen bonds in the backbone and similarly adopt secondary structure (e.g., α-helix and β-sheet). In addition, poly(α-amino acid)s usually possess desired biocompatibility and biodegradability. Therefore, they have demonstrated extensive utilities in the biological fields. In this review, we firstly introduced the formation mechanism of ordered secondary structure of poly(α-amino acid)s. In general, α-helix exhibits rigid rod-like structure due to the intramolecular hydrogen bonds, while β-sheet structure is mainly formed based on the intermolecular hydrogen bonds. The polymerization degree of poly(α-amino acid)s that form β-sheet is often lower than that of poly(α-amino acid)s with α-helix structure. Besides, the formation of the random coil structure is often due to the distortion of the backbone. Then, we discussed the impact of side-chain functionalization on the secondary structure and introduced the existing approaches in modulating the secondary structure, such as controlling the electrostatic interaction, polarity, and hydrogen bonds. By maintaining a separation distance of more than 11 σ-bond between the backbone and side charged groups, the poly(α-amino acid) could adopt α-helical structure due to the diminished interference with the backbone hydrogen bonds. The electrostatic interaction among the side chains disturbs the hydrogen bonding, thereby destabilizing the α-helical structure. For instance, the conformation of light-responsive helical poly(α-amino acid)s can transform into random coil due to side-chain electrostatic attraction after irradiation, while random coil-to-helix transition of zwitterionic poly(α-amino acid)s was achieved via elimination of the side-chain electrostatic interaction in response to phosphatase or acidic pH. In addition, the increased polarity of the side chains of polycysteine and poly(homocysteine) derivatives upon oxidation can also realize the order-order and order-disorder transition of the secondary structure. Moreover, the conformation of poly(α-amino acid)s with triazole groups in the side chains can be transformed from random coil to α-helix when the pH value is decreased, mainly due to the change in the side-chain hydrogen bond pattern. We further summarized the impact of secondary structure on the bio-applications of poly(α-amino acid)s, including cell penetration, gene delivery, anti-microbial therapy, self-assembly, and protein modification. Normally, α-helical conformation features strong membrane penetration and thus α-helical poly(α-amino acid)s can mediate effective gene transfection. pH-responsive, coil-helix transitional poly(α-amino acid)s can allow helix formation in the acidic endolysosomes to specifically penetrate endolysosomal membranes, while light-triggered distortion of the helix at the post-transfection state can diminish the long-term materials toxicity. α-Helical poly(α-amino acid)s with well-tailored structure can also enable potent anti-microbial efficiency by disruption bacterial membranes, and conformation transitionable poly(α-amino acid)s can mediate potent yet selective killing of bacteria upon coil-to-helix transition in response to over-produced phosphatases in infected sites or acidic pH in the stomach. In addition, the secondary structure also has a huge impact on the self-assembly behavior of poly(α-amino acid)s or the pharmacological properties of protein drugs modified with poly(α-amino acid)s. Therefore, the research on the secondary structure and function of poly(α-amino acid)s renders great inspiration for its further application.

Why Does the Novel Coronavirus Spike Protein Interact so Strongly with the Human ACE2? A Thermodynamic Answer.

The SARS-CoV-2 pandemic is the biggest health concern today, but until now there is no treatment. One possible drug target is the receptor binding domain (RBD) of the coronavirus' spike protein, which recognizes the human angiotensin-converting enzyme 2 (hACE2). Our in silico study discusses crucial structural and thermodynamic aspects of the interactions involving RBDs from the SARS-CoV and SARS-CoV-2 with the hACE2. Molecular docking and molecular dynamics simulations explain why the chemical affinity of the new SARS-CoV-2 for hACE2 is much higher than in the case of SARS-CoV, revealing an intricate pattern of hydrogen bonds and hydrophobic interactions and estimating a free energy of binding, which is consistently much more negative in the case of SARS-CoV-2. This work presents a chemical reason for the difficulty in treating the SARS-CoV-2 virus with drugs targeting its spike protein and helps to explain its infectiousness.

Structural Insight into Integrin Recognition and Anticancer Activity of Echistatin.

Echistatin (Ech) is a short disintegrin with a long 42NPHKGPAT C-terminal tail. We determined the 3-D structure of Ech by X-ray crystallography. Superimposition of the structures of chains A and B showed conformational differences in their RGD loops and C-termini. The chain A structure is consistent with our NMR analysis that the GPAT residues of the C-terminus cannot be observed due to high flexibility. The hydrogen bond patterns of the RGD loop and between the RGD loop and C-terminus in Ech were the same as those of the corresponding residues in medium disintegrins. The mutant with C-terminal HKGPAT truncation caused 6.4-, 7.0-, 11.7-, and 18.6-fold decreases in inhibiting integrins αvβ3, αIIbβ3, αvβ5, and α5β1. Mutagenesis of the C-terminus showed that the H44A mutant caused 2.5- and 4.4-fold increases in inhibiting αIIbβ3 and α5β1, and the K45A mutant caused a 2.6-fold decrease in inhibiting αIIbβ3. We found that Ech inhibited VEGF-induced HUVEC proliferation with an IC50 value of 103.2 nM and inhibited the migration of A375, U373MG, and Panc-1 tumor cells with IC50 values of 1.5, 5.7, and 154.5 nM. These findings suggest that Ech is a potential anticancer agent, and its C-terminal region can be optimized to improve its anticancer activity.

Control of self-assembly pathways toward conglomerate and racemic supramolecular polymers

Homo- and heterochiral aggregation during crystallization of organic molecules has significance both for fundamental questions related to the origin of life as well as for the separation of homochiral compounds from their racemates in industrial processes. Herein, we analyse these phenomena at the lowest level of hierarchy – that is the self-assembly of a racemic mixture of (R,R)- and (S,S)-PBI into 1D supramolecular polymers. By a combination of UV/vis and NMR spectroscopy as well as atomic force microscopy, we demonstrate that homochiral aggregation of the racemic mixture leads to the formation of two types of supramolecular conglomerates under kinetic control, while under thermodynamic control heterochiral aggregation is preferred, affording a racemic supramolecular polymer. FT-IR spectroscopy and quantum-chemical calculations reveal unique packing arrangements and hydrogen-bonding patterns within these supramolecular polymers. Time-, concentration- and temperature-dependent UV/vis experiments provide further insights into the kinetic and thermodynamic control of the conglomerate and racemic supramolecular polymer formation.

Synthesis, antiproliferative activity, and molecular docking of some N‐heterocycles bearing a pyrazole scaffold against liver and breast tumors

AbstractA new series of some 1,3‐diphenylpyrazole‐based heterocycles were constructed from 2‐cyano‐3‐(1,3‐diphenyl‐1H‐pyrazol‐4‐yl)propenoyl chloride (1). The titled acid chloride was submitted to react with mono‐nucleophilic reagents, including oxygen, sulfur, or nitrogen, to afford new acrylate, thioacrylate, and acrylamide derivatives, respectively. Meanwhile, condensation of 1 with some 1,2‐ and 1,3‐binucleophiles led to the construction of oxadiazepine, pyridopyrimidine, and thiadiazolopyrimidine derivatives (16, 18, 20, 23). In turn, two benzoxazinone derivatives (27, 28) were synthesized upon treating 1 with substituted anthranilic acids followed by heating with acetic anhydride. The antiproliferative activity of the compounds developed against two tumors (HePG2 and MCF7) was evaluated. Compounds 4, 6, 11, 25, and 26 exhibited strong activity and compounds 3, 5, 16, 18, 27, and 28 exhibited moderate activity. A molecular modeling study was conducted by utilizing molecular modeling environment to test the binding free energies of the studied compounds toward human cyclin‐dependent kinase 2. The compounds, 4, 25, and 26, displayed the best docking score. The orientation and hydrogen bond pattern of these compounds in the active site correspond to that of PNU‐292137, which had been approved as a selective CDK2 inhibitor.

Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates.

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car–Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.

All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site.

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 are required for the normal larval-to-pupal transition in Drosophila. Second, our molecular dynamic analyses have revealed that hCDK8 has higher hydrogen bond occupation of His149-Asp151 and Asp151-Asn156 than dCDK8. Third, the substructure of Asp282, Phe283, Arg285, Thr287 and Cys291 can distinguish human and Drosophila CDK8 structures. In addition, there are two hydrogen bonds in the LXXLL motif: a lower occupation between L312 and L315, and a relatively higher occupation between L312 and L316. Human CDK8 has higher hydrogen bond occupation between L312 and L316 than dCDK8. Moreover, L312, L315 and L316 in the LXXLL motif of CDK8 have the specific pattern of hydrogen bonds and geometries, which could be crucial for the binding to nuclear receptors. Furthermore, the P154L mutation dramatically decreases the hydrogen bond between L312 and L315 in hCDK8, but not in dCDK8. The mutations of P154L and AQKAA modestly alter the local structures around residues 154. Finally, we identified the inhibitor-induced conformational changes of hCDK8, and our results suggest a structural difference in the drug-binding site between hCDK8 and dCDK8. Taken together, these results provide the structural insights into the roles of the LXXLL motif and the kinase activity of CDK8 in vivo.

4-(Di-methyl-amino)-benzohydrazide.

The title compound, C9H13N3O, crystallizes in the monoclinic space group C2/c and all non-hydrogen atoms are within 0.1 Å of the mol-ecular mean plane. In the crystal, the hydrogen-bonding pattern results in [001] chains built up from fused R 2 2(6) and R 2 2(10) rings; the former consists of N-H⋯N bonds and the latter N-H⋯O bonds. Electrostatic and dispersion forces are major contributors to the lattice energy, which was estimated by DFT calculations to be -215.7 kJ mol-1.