An empirical correlation between structure and optical activity in a series of labdane diterpenoids

On the basis of the results of an analysis of the optical rotatory dispersion curves and a consideration of possible conformations of labdane diterpenoids, the conclusion has been drawn that labd-8(17)-ene derivatives with a 13E double bond or a voluminous substituent in the side chain do not obey Garman's additive scheme, and when there are no asymmetric centers in the side chain they have more negative values of the molecular optical rotation than is preducted by this scheme.Novosibirsk Institute of Organic Chemistry, Siberian Branch, Academy of Sciences of the USSR. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 169–174, March–April, 1981.     

A combined SAMO-ZDO method for the evaluation of ionization potentials

A scheme for the ab initio calculation of vertical ionization potentials without the necessity to compute two-electron repulsion integrals is discussed. The method employs the simulated ab initio molecular orbital (SAMO) method to generate Koopman's theorem eigenvalues. These are then corrected for the change in relaxation and correlation effects due to ionization by a Green's function perturbation scheme, in which all necessary integrals are evaluated using the zero differential overlap (ZDO) approximations, in this case the complete neglect of differential overlap (CNDO) method.     

Molecular Mechanisms of Amylin Turnover,Misfolding and Toxicity in the Pancreas

Amyloidosis is a common pathological event in which proteins self-assemble into misfolded soluble and insoluble molecular forms, oligomers and fibrils that are often toxic to cells. Notably, aggregation-prone human islet amyloid polypeptide (hIAPP), or amylin, is a pancreatic hormone linked to islet β-cells demise in diabetics. The unifying mechanism by which amyloid proteins, including hIAPP, aggregate and kill cells is still matter of debate. The pathology of type-2 diabetes mellitus (T2DM) is characterized by extracellular and intracellular accumulation of toxic hIAPP species, soluble oligomers and insoluble fibrils in pancreatic human islets, eventually leading to loss of β-cell mass. This review focuses on molecular, biochemical and cell-biology studies exploring molecular mechanisms of hIAPP synthesis, trafficking and degradation in the pancreas. In addition to hIAPP turnover, the dynamics and the mechanisms of IAPP–membrane interactions; hIAPP aggregation and toxicity in vitro and in situ; and the regulatory role of diabetic factors, such as lipids and cholesterol, in these processes are also discussed.     

Theoretical study of molecular conduction: I. Effective Green's function based on perturbation theory

There have been many experimental and theoretical studies on molecular conduction, as it is a fundamental parameter in the study of molecular‐scale electronics. We have investigated the features of molecular conduction using a Green's function method, which has often been used to solve problems in quantum transport and is also effective in elucidating electron transport in molecules. We have obtained the novel effective Green's functions, including the first‐order energy corrections, by accommodating the self‐energy of the electrodes as perturbation terms. Although these approximate Green's functions only provide information on the first‐order energy corrections, they can involve the elementary properties of molecular conduction. We propose a scheme for the analysis of the relations between molecular orbitals and their roles in molecular conduction and present analytical calculations for normal and cyclic polyenes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields

Summary A methodology aimed at improving the accuracy of current docking–scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.     

Laser-induced low-temperature fluorescence spectroscopy

The absorption and fluorescence spectra of molecules are often very sharp under cryogenic sampling conditions. When a tunable laser is used to excite fluorescence, selective determinations of individual constituents of very complex samples are possible, and the highly resolved fluorescence spectra can serve as 'molecular fingerprints'     

An energy decomposition scheme applicable to strongly interacting systems

An energy decomposition scheme useful for the analysis of the coupled types of interactions in strongly interacting systems is developed within the Hartree-Fock approximation. A dominant characteristic of the scheme is that it involves the interactions between vacant orbitals of component molecules, as can be justified from the third-order perturbation theory. On the basis ofab initio molecular orbital calculations, the utility of the scheme is illustrated for the BH₃-NH₃ complexation and the S_N2 reaction of CH₄ with H^–. It is found that the charge transfer from electron donor (i.e. NH₃ or H^–) to acceptor (i.e. BH₃ or CH₄) is strongly coupled with the polarization of the acceptor, to contribute appreciably to the stabilization of the entire system. A specific role of this coupling mode in the progress of reactions is discussed.     

Markov State Models and Molecular Dynamics Simulations Provide Understanding of the Nucleotide-Dependent Dimerization-Based Activation of LRRK2 ROC Domain

Mutations in leucine-rich repeat kinase 2 (LRRK2) are recognized as the most frequent cause of Parkinson’s disease (PD). As a multidomain ROCO protein, LRRK2 is characterized by the presence of both a Ras-of-complex (ROC) GTPase domain and a kinase domain connected through the C-terminal of an ROC domain (COR). The bienzymatic ROC–COR–kinase catalytic triad indicated the potential role of GTPase domain in regulating kinase activity. However, as a functional GTPase, the detailed intrinsic regulation of the ROC activation cycle remains poorly understood. Here, combining extensive molecular dynamics simulations and Markov state models, we disclosed the dynamic structural rearrangement of ROC’s homodimer during nucleotide turnover. Our study revealed the coupling between dimerization extent and nucleotide-binding state, indicating a nucleotide-dependent dimerization-based activation scheme adopted by ROC GTPase. Furthermore, inspired by the well-known R1441C/G/H PD-relevant mutations within the ROC domain, we illuminated the potential allosteric molecular mechanism for its pathogenetic effects through enabling faster interconversion between inactive and active states, thus trapping ROC in a prolonged activated state, while the implicated allostery could provide further guidance for identification of regulatory allosteric pockets on the ROC complex. Our investigations illuminated the thermodynamics and kinetics of ROC homodimer during nucleotide-dependent activation for the first time and provided guidance for further exploiting ROC as therapeutic targets for controlling LRRK2 functionality in PD treatment.     

Self-assembly of “patchy” nanoparticles: a versatile approach to functional hierarchical materials

The solution-phase self-assembly or “polymerization” of discrete colloidal building blocks, such as “patchy” nanoparticles and multicompartment micelles, is attracting growing attention with respect to the creation of complex hierarchical materials. This approach represents a versatile method with which to transfer functionality at the molecular level to the nano- and microscale, and is often accompanied by the emergence of new material properties. In this perspective we highlight selected recent examples of the self-assembly of anisotropic nanoparticles which exploit directional interactions introduced through their shape or surface chemistry to afford a variety of hierarchical materials. We focus in particular on the solution self-assembly of block copolymers as a means to prepare multicompartment or “patchy” micelles. Due to their potential for synthetic modification, these constructs represent highly tuneable building blocks for the fabrication of a wide variety of functional assemblies.     

Graphical approach for defining natural internal coordinates

A simple, customizable connectivity scheme is rigorously defined in which pairs of atoms are classified into three categories. The tools of graph theory are used to analyze the molecular graph and to efficiently find rings and ring assemblies through a combination of pruning and homeomorphic reduction. The definition of natural internal coordinates is extended in a nonredundant fashion for the various cases of weakly interacting components and for fused ring systems. The ring system coordinates were tested and found to be superior to Z-matrix coordinates. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 504–511, 1998     

Isolation and study of an inhibitor of the intrinsic proteolytic enzyme of cotton seeds

A scheme has been developed for the isolation of an inhibitor of cottonseed protease A using affinity chromatography on protease-A—Sepharose 4B followed by gel filtration on Sephadex G-150. The molecular mass of the inhibitor is 20 kDa. The protein molecule consists of two subunits with different molecular masses.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Fax (3712) 62 73 48. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 274–277, March–April, 1994.     

Dynamic viscosity estimation of hydrogen sulfide using a predictive scheme based on molecular dynamics

An approach based on molecular dynamics results on Lennard–Jones spheres is proposed to model the viscosity of hydrogen sulfide, H₂S. The molecular parameters, that have a strong physical meaning, are the depth of the potential, and the length at which the potential is null (the “molecular diameter”), which take into account the dipolar moment of the hydrogen sulfide through an isotropic dipolar approximation. The interest of the method is that the adjustment does not involve any viscosity data because only density values have been used in order to estimate the molecular parameters. Consequently, the model is entirely predictive. A comparison between the data generated by our model, REFPROP7 and REFPROP8 database and the few available experimental viscosity data (dilute gas and saturated liquid) is performed and it clearly demonstrates the performance of this predictive model. It is even shown that this model is, without fitting, slightly better than REFPROP7 and REFPROP8 which uses viscosity experimental database to adjust their parameters. In addition, in typical petroleum reservoirs conditions, it is shown that non-negligible deviations appear when comparing results predicted by REFPROP7, REFPROP8 and the model proposed. Due to its predictive nature, we believe that the values evaluated by the proposed model make sense in such reservoir conditions, at least for industrial purposes. Moreover, the scheme proposed is shown to be very easily extended to deal with mixtures involving H₂S with the limit that the Lennard–Jones fluid model is appropriate for the other species of the mixtures.     

Antibiotics and the Nervous System—Which Face of Antibiotic Therapy Is Real,Dr. Jekyll (Neurotoxicity) or Mr. Hyde (Neuroprotection)?

Antibiotics as antibacterial drugs have saved many lives, but have also become a victim of their own success. Their widespread abuse reduces their anti-infective effectiveness and causes the development of bacterial resistance. Moreover, irrational antibiotic therapy contributes to gastrointestinal dysbiosis, that increases the risk of the development of many diseases, including neurological and psychiatric. One of the potential options for restoring homeostasis is the use of oral antibiotics that are poorly absorbed from the gastrointestinal tract (e.g., rifaximin alfa). Thus, antibiotic therapy may exert neurological or psychiatric adverse drug reactions which are often considered to be overlooked and undervalued issues. Drug-induced neurotoxicity is mostly observed after beta-lactams and quinolones. Penicillin may produce a wide range of neurological dysfunctions, including encephalopathy, behavioral changes, myoclonus or seizures. Their pathomechanism results from the disturbances of gamma-aminobutyric acid-GABA transmission (due to the molecular similarities between the structure of the β-lactam ring and GABA molecule) and impairment of the functioning of benzodiazepine receptors (BZD). However, on the other hand, antibiotics have also been studied for their neuroprotective properties in the treatment of neurodegenerative and neuroinflammatory processes (e.g., Alzheimer’s or Parkinson’s diseases). Antibiotics may, therefore, become promising elements of multi-targeted therapy for these entities.     

Comparing two K-category assignments by a K-category correlation coefficient

Predicted assignments of biological sequences are often evaluated by Matthews correlation coefficient. However, Matthews correlation coefficient applies only to cases where the assignments belong to two categories, and cases with more than two categories are often artificially forced into two categories by considering what belongs and what does not belong to one of the categories, leading to the loss of information. Here, an extended correlation coefficient that applies to K-categories is proposed, and this measure is shown to be highly applicable for evaluating prediction of RNA secondary structure in cases where some predicted pairs go into the category “unknown” due to lack of reliability in predicted pairs or unpaired residues. Hence, predicting base pairs of RNA secondary structure can be a three-category problem. The measure is further shown to be well in agreement with existing performance measures used for ranking protein secondary structure predictions. Server and software is available at http://rk.kvl.dk/     

Different phosphorylation and farnesylation patterns tune Rnd3–14-3-3 interaction in distinct mechanisms

Protein posttranslational modifications (PTMs) are often involved in the mediation or inhibition of protein–protein interactions (PPIs) within many cellular signaling pathways. Uncovering the molecular mechanism of PTM-induced multivalent PPIs is vital to understand the regulatory factors to promote inhibitor development. Herein, Rnd3 peptides with different PTM patterns as the binding epitopes and 14-3-3ζ protein were used as models to elucidate the influences of phosphorylation and farnesylation on binding thermodynamics and kinetics and their molecular mechanism. The quantitative thermodynamic results indicate that phosphorylated residues S210 and S218 (pS210 and pS218) and farnesylated C241 (fC241) enhance Rnd3–14-3-3ζ interactions in the presence of the essential pS240. However, distinct PTM patterns greatly affect the binding process. Initial association of pS240 with the phosphate-binding pocket of one monomer of the 14-3-3ζ dimer triggers the binding of pS210 or pS218 to another monomer, whereas the binding of fC241 to the hydrophobic groove on one 14-3-3ζ monomer induces the subsequent binding of pS240 to the adjacent pocket on the same monomer. Based on the experimental and molecular simulation results, we estimate that pS210/pS218 and pS240 mediate the multivalent interaction through an additive mechanism, whereas fC241 and pS240 follow an induced fit mechanism, in which the cooperativity of these two adjacent PTMs is reflected by the index ε described in our established thermodynamic binding model. Besides, these proposed binding models have been further used for describing the interaction between 14-3-3ζ and other substrates containing adjacent phosphorylation and lipidation groups, indicating their potential in general applications. These mechanistic insights are significant for understanding the regulatory factors and the design of PPI modulators.

Different protein posttranslational modifications (PTMs) patterns affect the binding thermodynamics and kinetics and their molecular mechanism of multivalent protein–protein interaction (PPIs).     

Calculation of absolute molecular entropies and heat capacities made simple

We propose a fully-automated composite scheme for the accurate and numerically stable calculation of molecular entropies by efficiently combining density-functional theory (DFT), semi-empirical methods (SQM), and force-field (FF) approximations. The scheme is systematically expandable and can be integrated seamlessly with continuum-solvation models. Anharmonic effects are included through the modified rigid-rotor-harmonic-oscillator (msRRHO) approximation and the Gibbs–Shannon formula for extensive conformer ensembles (CEs), which are generated by a metadynamics search algorithm and are extrapolated to completeness. For the first time, variations of the ro-vibrational entropy over the CE are consistently accounted-for through a Boltzmann-population average. Extensive tests of the protocol with the two standard DFT approaches B97-3c and B3LYP-D3 reveal an unprecedented accuracy with mean deviations <1 cal mol⁻¹ K⁻¹ (about <1–2%) for the total gas phase molecular entropy of medium-sized molecules. Even for the hardship case of extremely flexible linear alkanes (C₁₄H₃₀–C₁₆H₃₄), errors are only about 3 cal mol⁻¹ K⁻¹. Comprehensive tests indicate a relatively strong variation of the conformational entropy on the underlying level of theory for typical drug molecules, inferring the complex potential energy surfaces as the main source of error. Furthermore, we show some application examples for the calculation of free energy differences in typical chemical reactions.

A novel scheme for the automated calculation of the conformational entropy together with a modified thermostatistical treatment provides entropies with unprecedented accuracy even for large, complicated molecules.     

Cyclodimerization of vinylpyridines

When isomeric 2- and 4-vinylpyridines, as well as 2-methyl-5-vinylpyridine, are heated in polyphosphoric or acetic acid, they undergo dimerization, which proceeds via a 1,4-cycloaddition scheme to give pyridyl-substituted 5,6,7,8-tetrahydroquinclines or isoquinolines. Quantum-chemical calculations with the use of the concepts of molecular orbital perturbation theory make it possible to predict the regiospecificity of the reaction. The regiospecific cross cycloaddition of 4-vinylpyridine to 2-methyl-5-vinylpyridine was proposed theoretically and proven experimentally.Deceased.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1248–1254, September, 1980.     

Optical imaging with dynamic contrast agents

Biological imaging applications often employ molecular probes or nanoparticles for enhanced contrast. However, resolution and detection are still often limited by the intrinsic heterogeneity of the sample, which can produce high levels of background that obscure the signals of interest. Herein, we describe approaches to overcome this obstacle based on the concept of dynamic contrast: a strategy for elucidating signals by the suppression or removal of background noise. Dynamic contrast mechanisms can greatly reduce the loading requirement of contrast agents, and may be especially useful for single-probe imaging. Dynamic contrast modalities are also platform-independent, and can enhance the performance of sophisticated biomedical imaging systems or simple optical microscopes alike. Dynamic contrast is performed in two stages: 1) a signal modulation scheme to introduce time-dependent changes in amplitude or phase, and 2) a demodulation step for signal recovery. Optical signals can be coupled with magnetic nanoparticles, photoswitchable probes, or plasmon-resonant nanostructures for modulation by magnetomotive, photonic, or photothermal mechanisms, respectively. With respect to image demodulation, many of the strategies developed for signal processing in electronics and communication technologies can also be applied toward the editing of digital images. The image-processing step can be as simple as differential imaging, or may involve multiple reference points for deconvolution by using cross-correlation algorithms. Periodic signals are particularly amenable to image demodulation strategies based on Fourier transform; the contrast of the demodulated signal increases with acquisition time, and modulation frequencies in the kHz range are possible. Dynamic contrast is an emerging topic with considerable room for development, both with respect to molecular or nanoscale probes for signal modulation, and also to methods for more efficient image processing and editing.