Statistical and theoretical investigations on the directionality of nonbonded S...O interactions. Implications for molecular design and protein engineering

Weak nonbonded interactions between a divalent sulfur (S) atom and a main-chain carbonyl oxygen (O) atom have recently been characterized in proteins. However, they have shown distinctly different directional propensities around the O atom from the S...O interactions in small organic compounds, although the linearity of the C-S...O or S-S...O atomic alignment was commonly observed. To elucidate the observed discrepancy, a comprehensive search for nonbonded S.O interactions in the Cambridge Structural Database (CSD) and MP2 calculations on the model complexes between dimethyl disulfide (CH(3)SSCH(3)) and various carbonyl compounds were performed. It was found that the O atom showed a strong intrinsic tendency to approach the S atom from the backside of the S-C or S-S bond (in the sigma(S) direction). On the other hand, the S atom had both possibilities of approach to the carbonyl O atom within the same plane (in the n(O) direction) and out of the plane (in the pi(O) direction). In the case of S...O(amide) interactions, the pi(O) direction was significantly preferred as observed in proteins. Thus, structural features of S...O interactions depend on the type of carbonyl groups involved. The results suggested that S.O interactions may control protein structures to some extent and that the unique directional properties of S...O interactions could be applied to molecular design.     

Experimental and theoretical studies on the nature of weak nonbonded interactions between divalent selenium and halogen atoms

To investigate the nature of weak nonbonded selenium...halogen interactions (Se...X interactions; X = F, Cl, and Br), three types of model compounds [2-(CH(2)X)C(6)H(4)SeY (1-3), 3-(CH(2)X)-2-C(10)H(6)SeY (4-6), and 2-XC(6)H(4)CH(2)SeY (7-9); Y = CN, Cl, Br, SeAr, and Me] were synthesized, and their (77)Se NMR spectroscopic behaviors were analyzed in CDCl(3). The gradual upfield shifts of (77)Se NMR absorptions observed for series 1-3 and 4-6 suggested that the strength of Se...X interaction decreases in the order of Se...F > Se...Cl > Se...Br. The quantum chemical calculations at the B3LYP/631H level using the polarizable continuum model (PCM) revealed that the most stable conformer for 1-3 is the one with an intramolecular short Se...X atomic contact in CHCl(3) (epsilon = 4.9) and also that the n(X) --> sigma(Se-Y) orbital interaction (E(Se...X)) can reasonably explain the order of strength for the Se...X interactions. On the other hand, the (77)Se NMR absorptions observed for series 7-9 did not shift significantly from the reference compounds (C(6)H(5)CH(2)SeY), indicating the absence of the Se...X interaction for 7-9 presumably due to attenuation of basicity for the halogen atom that is substituted directly to the aromatic ring. These observations suggested that the n(X) --> sigma(Se-Y) orbital interaction is a dominant factor for formation of weak Se...X interactions. Electron correlation was also suggested to be important for the stability.     

Donor-acceptor nature of specific nonbonded interactions of sulfur and halogen atoms. Influence on the geometry and packing of molecules

Chemistry Faculty, Moscow State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 33, No. 3, pp. 105–118, May–June 1, 1992.     

Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation

In a previous aqueous protein dynamics study, we compared the rms deviation relative to the crystal structure for distance-dependent and constant dielectric models with and without a nonbonded cutoff. The structures obtained from a constant dielectric simulation with a cutoff were substantially different from the structures obtained from a distance-dependent dielectric simulation, with and without cutoff, and a constant dielectric model without a cutoff. In fact, structures from the distance-dependent dielectric simulations were insensitive to the nonbonded cutoff and in good agreement with the structures generated from the constant dielectric simulation without a cutoff. In addition, the solute-solvent temperature differential and solvent evaporation artifacts, characteristic of the constant dielectric simulation with a cutoff, were not present for the distance-dependent dielectric simulations. In this current work, we explore whether this dielectric-dependent cutoff-sensitive behavior for a constant dielectric model arises from the discontinuities in the forces at the nonbonded cutoff or from neglecting the structure-stabilizing interactions beyond the nonbonded cutoff. We also examine the origin of the dielectric-dependent artifacts, and its potential influence on the structural disparity. Several protocols for protein dynamics simulations are compared using both constant and distance-dependent dielectric models, including implementation of a switching function and a nonbonded cutoff and two different temperature coupling algorithms. We show that the distance-dependent dielectric model conserves energy in the SPASMS molecular mechanics and dynamics software for the time steps and nonbonded cutoffs commonly used in macromolecule simulations. Although the switching function simulation also conserved energy over a range of commonly used cutoffs, the constant dielectric model with a switching function yielded conformational results more similar to a constant dielectric simulation without a switching function than to a constant dielectric model without a nonbonded cutoff. Therefore, the conformational disparity between the dielectric models arises from neglecting important structure-stabilizing interactions beyond the cutoff, rather than differences in energy conservation. © 1993 John Wiley & Sons, Inc.     

Off-lattice Monte Carlo method with constraints: Long-time dynamics of a protein model without nonbonded interactions

A method is proposed to perform computer simulations of protein dynamics in the long-time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 10⁶ scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End-to-end distance autocorrelation functions decay to 1/e of its initial value in about 10³–10⁴ scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.     

Characterization of the interactions between the active site of a protein tyrosine kinase and a divalent metal activator

Background  

Protein tyrosine kinases are important enzymes for cell signalling and key targets for anticancer drug discovery. The catalytic mechanisms of protein tyrosine kinase-catalysed phosphorylation are not fully understood. Protein tyrosine kinase Csk requires two Mg²⁺ cations for activity: one (M1) binds to ATP, and the other (M2) acts as an essential activator.     

Halogen bonding to a divalent sulfur atom: an experimental study of the interactions of CF3X (X = Cl, Br, I) with dimethyl sulfide

Using FTIR and Raman spectroscopy, the formation of halogen bonded complexes of the trifluorohalomethanes CF(3)Cl, CF(3)Br and CF(3)I with dimethyl sulfide (DMS) dissolved in liquid krypton has been investigated. For CF(3)Br and CF(3)I, evidence was found for the formation of C-XS halogen bonded 1:1 complexes. At higher concentrations of CF(3)I weak absorptions due to a 2:1 complex were also observed. Using spectra recorded at temperatures between 118 and 163 K, the complexation enthalpies for the complexes were determined to be -9.5(5) kJ mol(-1) for CF(3)Br·DMS, -17.4(1) kJ mol(-1) for CF(3)I·DMS and -30.8(16) kJ mol(-1) for (CF(3)I·)(2)DMS. The results from the cryospectroscopic study are compared with ab initio calculations at the MP2/aug-cc-pVDZ(-PP) level. Apart from vibrational modes localized in the trifluorohalomethanes and the DMS moieties, for both CF(3)Br and CF(3)I, an additional band, which we assign as the intermolecular stretching mode in the complex, was identified in the infrared and Raman spectra.     

Influence of nonbonded intramolecular interactions on the vibrational frequencies of molecules

The nature of the displacement of the frequency of a characteristic vibration under the influence of the nonbonded interactions of atoms within a molecule (the field effect) has been studied. It has been shown in the example of the interaction of the bonds in the tetratomic Cl-C-C=O fragment that the (C=O) frequency increases under the influence of the dipole-dipole interaction of the C=O and C-Cl bonds; the same interaction causes a decrease in the freqency, if the Cl atom is replaced by an electropositive atom. The physical meaning which should be imparted to the Urey-Bradley potential, in particular, follows from the analysis presented.Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 24, No. 1, pp. 100–104, January–February, 1988.     

On the polarizability of the sulfur atom

Using both Thole's and Birge's semiclassical models, the atomic polarizability of the sulfur atom is calculated. It is concluded that the former model is adequate for calculating polarizabilities of atoms belonging to the second row of the periodic table.     

Conformational analysis of sulfur-containing 6-deoxy-l-hexose derivatives by molecular modeling and NMR spectroscopy. A theoretical study and experimental evidence of intramolecular nonbonded interactions between sulfur and oxygen

6-Deoxy-l-mannose diphenyldithioacetal (1) unexpectedly gave the rearranged products phenyl 3,4-di-O-acetyl-2-S-phenyl-1,2-dithio-6-deoxy-beta-l-glucopyranoside (9) and 3,4-di-O-acetyl-2,5-anhydro-6-deoxy-l-glucose diphenyldithioacetal (10) upon treatment with acetyl chloride, while 6-deoxy-l-mannose ethylenedithioacetal (3) yielded (4aR,6S,7S,8R,8aS)-7,8-diacetyloxy-6-methylhexahydro-4aH-[1,4]dithiino[2,3b]pyran (11), whose structure was further confirmed by X-ray diffraction, and 3,4-di-O-acetyl-2,5-anhydro-l-rhamnose ethylenedithioacetal (12). The geometry of the four rearranged products as well as that of 1-thio-6-deoxy-l-mannopyranosides 5 and 7 and their acetyl derivatives 6 and 8 was studied by density functional theory (B3LYP/6-31G) molecular models, in combination with a Karplus-type analysis of the NMR vicinal coupling constants, revealing that the six-membered ring of pyranosides 5-9 and 11 exists in a slightly distorted chair conformation (6-13% distortion) and that the conformational behavior of the 2,5-anhydro-6-deoxy-l-glucose dithioacetals 10 and 12 is strongly influenced by the presence of stabilizing intramolecular nonbonded sulfur-oxygen 1,4- and 1,5-interactions. Compounds 9-12 were formed by a molecular rearrangement via sulfonium ion intermediates followed by stereoselective intramolecular cyclizations as formulated by the quantum chemical calculations performed in the present study.     

On the role of nonbonded interactions in vibrational energy relaxation of cyanide in water

The vibrationally excited cyanide ion (CN(-)) in H2O or D2O relaxes back to the ground state within several tens of picoseconds. Pump-probe infrared spectroscopy has determined relaxation times of T1 = 28 ± 7 and 71 ± 3 ps in H2O and D2O, respectively. Atomistic simulations of this process using nonequilibrium molecular dynamics simulations allow determination of whether it is possible at all to describe such a process, what level of accuracy in the force fields is required, and whether the information can be used to understand the molecular mechanisms underlying vibrational relaxation. It is found that, by using the best electrostatic models investigated, absolute relaxation times can be described rather more qualitatively (T1(H2O) = 19 ps and T1(D2O) = 34 ps) whereas the relative change in going from water to deuterated water is more quantitatively captured (factor of 2 vs 2.5 from experiment). However, moderate adjustment of the van der Waals ranges by less than 20% (for NVT) and 7.5% (for NVE), respectively, leads to almost quantitative agreement with experiment. Analysis of the energy redistribution establishes that the major pathway for CN(-) relaxation in H2O or D2O proceeds through coupling to the water-bending plus libration mode.     

Contributions of resonance,hybridization, and nonbonded interactions to the structure of butadiene

The fully optimized geometries of four rotational conformers of butadiene have been calculated ab initio in order to investigate the relative importance of resonance, hydridization and nonbonded interactions. The results indicate that the short central CC bond is primarily due to hybridization, although resonance makes a minor contribution. The resonance stabilization of the planar conformers is responsible for the relatively large barrier to internal rotation, whereas the nonbonded interactions are only important in destabilizing the sterically crowded cis conformer.     

On the contributions of resonance,hybridization and nonbonded interactions to the structure of butadiene

A recent ab initio molecular orbital calculation on butadiene has been interpreted by Skaarup, Boggs and Skancke as indicating that the shortness of the central C-C bond is due primarily to hybridization. Resonance was considered to make a minor contribution and nonbonded interactions were judged to be unimportant. Unfortunately, this analysis failed to take into account the crucial role of geminal nonbonded interactions, and the calculations were, accordingly, not designed to discriminate between the hybridization and nonbonded models. A more direct investigation of intramolecular nonbonded interactions based on ab initio computations has been earned out on other systems, however, providing evidence that the effects of nonbonded contributions are substantial.     

Quantitative evaluation of weak nonbonded Se...F interactions and their remarkable nature as orbital interactions

To evaluate weak intramolecular nonbonded Se...F interactions recently characterized for a series of o-selenobenzyl fluoride derivatives (Iwaoka et al., Chem. Lett. 1998, 969-970), the temperature dependence of the nuclear spin coupling between Se and F (J(Se...F)) was investigated for 2-(fluoromethyl)phenylselenenyl cyanate (1a) and bis[2-(fluoromethyl)phenyl] diselenide (1e) in CD2Cl2 and CD3CN. A significant increase in the magnitude of J(Se...F) was observed for both 1a and 1e upon lowering temperature, whereas the values of J(Se...F) for the corresponding trifluoromethyl compounds slightly reduced or remained unchanged at low temperatures. Application of the rapid equilibrium model between two possible conformers revealed that conformer A with an intramolecular Se...F interaction is more stable in enthalpy (DeltaH) by 1.23 kcal/mol for 1a (in CD2Cl2) and by 0.85 and 0.83 kcal/mol for 1e (in CD2Cl2 and CD3CN, respectively) than conformer B, which does not have close Se...F contact. The negligible solvent effects for 1e suggested marginal electrostatic nature of the Se...F interactions. Instead, importance of the n(F) -->sigma*(Se-X) orbital interaction was suggested by quantum chemical (QC) calculations and the natural bond orbital (NBO) analysis.     

Intermolecular stretching vibration of hydrogen bonds involving a sulfur atom

The intermolecular stretching vibration of hydrogen bonded complexes between phenol derivatives and tetramethylthiourea or dimethylthioformamide is observed in the range 113 – 131 cm⁻¹. The corresponding force constants k_σ are computed using the Lippincott-Schroeder potential function and the matrix method of Wilson. The k_σ values are higher than these previously reported for the complexes of the same phenols with aliphatic amides. These results are in qualitative agreement with the theoretical predictions.     

Synthesis and antibacterial activity of new 1beta-methylcarbapenems having the potential for intramolecular nonbonded S...O interactions.

Mercaptoacetyliminothiadiazoline derivatives (19, 20) useful for the pendant moiety of 1beta-methylcarbapenem antibiotics were efficiently synthesized. Acetyl derivative (18) of 20 was submitted to X-ray analysis, and a significant nonbonded S...O close contact was recognized in the crystallographic structure. New 1beta-methylcarbapenems (5, 6) were synthesized by exploiting 19 and 20, and exhibited considerable antibacterial activities in vitro.