Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N–H?···?N, N–H?···?O, O–H?···?O, O–H?···?N, C–H?···?O and C–H?···?N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N–H?···?O and N–H?···?N hydrogen-bond interactions with the contraction of the N–H bond varying from 0.001 to 0.0260?Å and the corresponding blue shift of the stretching frequency by 4–291?cm^?1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N–H?···?N and N–H?···?O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X–H bond in the complexes was studied using natural bond orbital (NBO) analysis.     

Theoretical studies on structure and performance of [1,2,5]‐oxadiazolo‐[3,4‐d]‐pyridazine‐based derivatives

Based on energetic compound [1,2,5]‐oxadiazolo‐[3,4‐d]‐pyridazine, a series of functionalized derivatives were designed and first reported. Afterwards, the relationship between their structure and performance was systematically explored by density functional theory at B3LYP/6‐311 g (d, p) level. Results show that the bond dissociation energies of the weakest bond (N–O bond) vary from 157.530 to 189.411 kJ · mol^?1. The bond dissociation energies of these compounds are superior to that of HMX (N–NO_2, 154.905 kJ · mol^?1). In addition, H1, H2, H4, I2, I3, C1, C2, and D1 possess high density (1.818–1.997 g · cm^?3) and good detonation performance (detonation velocities, 8.29–9.46 km · s^?1; detonation pressures, 30.87–42.12 GPa), which may be potential explosives compared with RDX (8.81 km · s^?1, 34.47 GPa ) and HMX (9.19 km · s^?1, 38.45 GPa). Finally, allowing for the explosive performance and molecular stability, three compounds may be suggested as good potential candidates for high‐energy density materials. Copyright © 2016 John Wiley & Sons, Ltd.     

Characterization of aromatic-thiol π-type hydrogen bonding and phenylalanine-cysteine side chain interactions through ab initio calculations and protein database analyses

In this study, the aromatic-thiol π hydrogen bonding and phenylalanine-cysteine side chain interactions are characterized through both molecular orbital calculations on a C₆H₆-HSCH₃ model complex and database analyses of 609 X-ray protein structures. The aromatic-thiol π hydrogen bonding interaction can achieve a stabilization energy of 2.60 kcal mol^?1, and is stronger than the already documented aromatic-hydroxyl and aromatic-amino hydrogen bonds. However, the occurrence of the aromatic-thiol hydrogen bond is rather rare in proteins. This is because most of the thiol groups participate in the formation of either disulphide bonds or stronger S—H…O (or N) ‘normal’ hydrogen bonds in a protein environment. Interactions between the side chains of phenylalanine and cysteine residues are characterized as the phenyl(Phe)(HSCH₂-)(Cys) interaction. The bonding energy for such interactions is approximately 3.71 kcal mol-¹ and is achieved in a geometric arrangement with an optimal phenyl(Phe)-(HS-)(Cys) π-type hydrogen bonding interaction. The interaction is very sensitive to the orientation of the two lone electron pairs on the sulphur atom relative to the π electron cloud of the phenyl ring. Accordingly, the interaction configurations that can accomplish a significant bonding energy exist only within a narrow configurational space. The database analysis of 609 experimental X-ray protein structures demonstrates that only 268 of the 1620 cysteine residues involve such phenylalanine-cysteine side chain interactions. Most of these interactions occur in the form of π (aromatic)-lone pair(sulphur) attractions, and correspond to a bonding energy less than 1.5 kcal mol^?1. A few were identified as the aromatic-thiol hydrogen bond with a bonding energy of 2.0–3.6 kcal mol^?1.     

Computational study on structures,thermochemical properties,and bond energies of disulfide oxygen (S–S–O)‐bridged CH3SSOH and CH3SS(=O)H and radicals

Cleavage of disulfide bonds is a common method used in linking peptides to proteins in biochemical reactions. The structures, internal rotor potentials, bond energies, and thermochemical properties (Δ_fH°, S°, and Cp(T)) of the S–S bridge molecules CH₃SSOH and CH₃SS(=O)H and the radicals CH₃SS?=O and C?H₂SSOH that correspond to H‐atom loss are determined by computational chemistry. Structure and thermochemical parameters (S° and Cp(T)) are determined using density functional Becke, three‐parameter, Lee–Yang–Parr (B3LYP)/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p). The enthalpies of formation for stable species are calculated using the total energies at B3LYP/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p), and the higher level composite CBS–QB3 levels with work reactions that are close to isodesmic in most cases. The enthalpies of formation for CH₃SSOH, CH₃SS(=O)H are ?38.3 and ?16.6 kcal mol^?1, respectively, where the difference is in enthalpy RSO–H versus RS(=O)–H bonding. The C–H bond energy of CH₃SSOH is 99.2 kcal mol^?1, and the O–H bond energy is weaker at 76.9 kcal mol^?1. Cleavage of the weak O–H bond in CH₃SSOH results in an electron rearrangement upon loss of the CH₃SSO–H hydrogen atom; the radical rearranges to form the more stable CH₃SS· = O radical structure. Cleavage of the C–H bond in CH₃SS(=O)H results in an unstable [CH₂SS(=O)H]* intermediate, which decomposes exothermically to lower energy CH₂ = S + HSO. The CH₃SS(=O)–H bond energy is quite weak at 54.8 kcal mol^?1 with the H–C bond estimated at between 91 and 98 kcal mol^?1. Disulfide bond energies for CH₃S–SOH and CH3S–S(=O)H are low: 67.1 and 39.2 kcal mol^?1. Copyright © 2011 John Wiley & Sons, Ltd.     

Accurate ab initio anharmonic force field and heat of formation for silane

From large basis set coupled cluster calculations and a minor empirical adjustment, an anharmonic force field for silane has been derived that is consistently of spectroscopic quality (±1 cm^?1 on vibrational fundamentals) for all isotopomers of silane studied. Inner-shell polarization functions have an appreciable effect on computed properties and even on anharmonic corrections. From large basis set coupled cluster calculations and extrapolations to the infinite-basis set limit, we obtain TAE₀ = 303.80 ± 0.18 kcal mol^?1, which includes an anharmonic zero-point energy (19.59 kcal mol^?1), inner-shell correlation (—0.36 kcal mol^?1), scalar relativistic corrections (— 0.70 kcal mol^?1) and atomic spin-orbit corrections (—0.43 kcal mol^?1). In combination with the recently revised ΔH ^o _{f, o}[Si(g)], we obtain ΔH ^o _f.o[SiH₄(g)] = 9.9 ± 0.4 kcal mol^?1 in between the two established experimental values.     

Ab initio study of synergetic effects of two strong interactions of cation–π interaction and lithium bond in M+ ··· phenyl lithium ··· N (M = Li,Na, K; N = H2O and NH3) complex

Quantum chemical calculations have been performed to investigate the interplay between the cation–π interaction and lithium bonding in the M⁺?···?phenyl lithium?···?OH₂ and M⁺?···?phenyl lithium?···?NH₃ (M?=?Li, Na, K) complexes. The cation–π interaction and lithium bonding in the trimers become stronger relative to the dimers. The interaction energy of cation–π interaction is increased by about 4.4–6.3%, while that of lithium bonding is increased by about 5.2–15.9%. The cooperative energy becomes larger for the stronger cation–π interaction and lithium bond. The F atom and methyl group in the phenyl ring impose a reverse effect on the cation–π interaction and lithium bond. The interaction mechanism in the complexes has been understood with the many-body interaction analysis, electrostatic potentials, and energy decomposition.     

Mass spectrometric and ab initio study of the interaction between 9-methylguanine and amino acid amide group

The temperature dependent field ionization mass spectrometry method combined with ab initio calculations was used to determine the interaction energies and the structures of 9-methylguanine-acrylamide dimers. Acrylamide mimics the side chain amide group of the natural amino acids asparagine and glutamine. The experimental enthalpy of the dimer formation derived from the van't Hoff plot is ?59.5 ± 3.8 kJ mol^?1. The value is higher than interaction energies between acrylamide and other nucleic acid bases which were determined to be ?57.0 for 1-methylcytosine, ?52.0 for 9-methyladenine, and ?40.6 kJ mol^?1 for 1-methyl-uracil. In total, eight hydrogen bonded dimers formed by the three lowest energy 9-methylguanine tautomers and acrylamide were found in the quantum chemical calculations performed at the DFT/B3LYP/6-31++G?? and MP2/6-31++G?? levels of theory. The relative stability and the interaction energies of the dimers were calculated accounting for the basis set superposition error and the zero-point vibrational energy correction. The lowest energy dimer found in the calculations is formed by acrylamide (Ac) with the keto tautomer of 9-methylguanine (Gk). It is stabilized by two intermolecular H bonds, C6=O(Gk) · · · H—N(Ac) and Nl—H(Gk) · · ·O(Ac), and it is more stable than the second lowest energy dimer by ≈ 25 kJ mol^?1. The calculated interaction energies of the lowest energy 9-methylguanine-acrylamide dimer are ?65.0 kJ mol^?1 and ?67.7 kJ mol^?1 at the MP2 and DFT levels of theory, respectively. The experimental enthalpy of the dimer formation is in good agreement with both the calculated interaction energies of the GkAc dimer and much higher than the interaction energies calculated for all other 9-methylguanine-acrylamide dimers. This proved that only one dimer was present in the experimental samples. To verify whether acrylamide is a good model of the amino acid-amide group, we performed direct calculations of the 9-methylguanine-glutamine dimers at the same levels of theory as used for the complexes involving acrylamide. The interaction energies found for the lowest energy 9-methylguanine-glutamine dimer are ?65.1 kJ mon^?1 (MP2/6-31++G??) and ?66.2 kJ mol^?1 (DFT/B3LYP/6-31++G??) and these values are very close (within 0.5 kJ mol^?1) to the interaction energies obtained for the 9-methylguanine-acrylamide dimers.     

Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR,NBO and AIM analyses

Protonation increases the total binding energy of the 8-oxoguanine-cytosine (8OG:C) base pair by 60–70% at the B3LYP/6-311++G(d,?p) level of theory. It changes the individual H-bond energies, estimated from electron charge densities at bond critical points, by 1.16 to ?16.41?kcal?mol^?1. The individual H-bond energies and the two bond X–Y spin–spin coupling constants (^2hJ_X–Y) increase with protonation where 8OG behaves as an H-bond donor; the reverse is true for the H-bonds in which the 8OG unit acts as an H-bond acceptor. Similar to ^2hJ_X–Y, the value of ^1hJ_O–H (a one-bond H?···?Y spin–spin coupling constant) is distance dependent and in linear correlation with the O?···?H distance, but the ^1hJ_N–H values are independent of the N–H distance and the PSO term is the predominant portion in it. The ¹J_X–H spin–spin coupling constant is dominated by the negative FC term for all hydrogen bonds, although the PSO term is the best to investigate the behaviour of ¹J_X–H across the X–H?·?Y H-bond.     

Comparison of the Kinetics of the Exchange Mechanism of the Thallium Ion with 18C6 and with Pentaglyme in Acetonitrile Solutions

Abstract

In acetonitrile solutions, the exchange reaction is bimolecular in the Tl⁺ + 18C6 system, while in the Tl⁺ + pentaglyme system the associative-dissociative and the bimolecular mechanisms coexist at room temperature and the bimolecular exchange reaction dominates at 263° K. For the bimolecular mechanism in the case of Tl⁺ + 18C6 and the associative-dissociative mechanism in the case of Tl⁺ + pentaglyme, the activation energies of the exchange reactions change with temperature. At 298° K, in the Tl⁺ + 18C6 system the activation energy for the bimolecular exchange reaction is ≈ 2 kcal.mol^?1 and exchange rate constant (k₁) is (4.1 ± 0.1) × 10⁷ s^?1mol^?1; in the Tl⁺ + pentaglyme system, the activation energy for the associative-dissociative exchange reaction is ≈ 5 kcal mol^?1 and the decomplexation rate constant (k_?2) is (2.2 ± 0.4) X 10⁵ s^?1. The activation energy for the bimolecular exchange in the Tl⁺ + pentaglyme system was determined to be 3.00 ± 0.05 kcal.mol_?1 and the exchange rate constant (3.0 ± 0.1) X 10⁸ s^?1 mol^?1.     

Metal hydrides as sodium bond acceptors: hydride-sodium bond in the XH ··· NaH (X = HBe,LiBe, NaBe,HMg, LiMg,and NaMg) complexes

New kinds of sodium bonding complexes XH?···?NaH (X?=?HBe, LiBe, NaBe, HMg, LiMg, and NaMg) have been predicted and characterized in the present paper. For each XH?···?NaH complex, the hydride-sodium bond is formed between the negatively charged H atom of XH and the positively charged Na atom of NaH. Due to the formation of the complexes, both the X–H and the Na–H bonds are elongated, and the Na–H stretching vibrational frequency is redshifted. The interaction energies in the XH?···?NaH complexes at the MP2/6-311++G(3df, 3pd) level increased in the order: HBeH?···?NaH (?4.50?kcal/mol)?相似文献   

Cooperativity between the hydrogen bonding and halogen bonding in F3CX ··· NCH(CNH) ··· NCH(CNH) complexes (X=Cl,Br)

MP2 calculations with the cc-pVTZ basis set were used to analyse the intermolecular interactions in F₃CX?···?NCH(CNH)?···?NCH(CNH) triads (X=Cl, Br), which are connected via hydrogen and halogen bonds. Molecular geometries, binding energies, and infrared spectra of the dyads and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention was given to parameters such as the cooperative energies, cooperative dipole moments, and many-body interaction energies. All studied complexes, with the simultaneous presence of a halogen bond and a hydrogen bond, show cooperativity with energy values ranging between ?1.32 and ?2.88?kJ?mol^?1. The electronic properties of the complexes were analysed using the Molecular Electrostatic Potential (MEP), electron density shift maps and the parameters derived from the Atoms in Molecules (AIM) methodology.     

Crystal structure and thermodynamic properties of phase change material bis(1-dodecylammonium) tetrachlorochromate (C12H25NH3)2CdCl4(s)

A novel complex bis(1-dodecylammonium) tetrachlorochromate (C₁₂H₂₅NH₃)₂CdCl₄(s) (abbreviated as C₁₂Cd(s)) was synthesized by liquid phase reaction. Crystal structure and composition of the complex were determined by X-ray crystallography, chemical analysis, and elemental analysis. It is triclinic, the space group is P?1 and Z = 2. Lattice potential energy (LPE) of the complex was calculated to be kJ·mol^?1 from crystallographic data. Low-temperature heat capacities were measured by a precise automatic adiabatic calorimeter over the temperature range from 78 to 370 K. The temperature, molar enthalpy, and entropy of the phase transition of the complex were determined to be 331.88 ± 0.02 K, 55.79 ± 0.46 kJ·mol^?1, and 168.10 ± 1.38 J·K^?1·mol^?1, respectively. Two polynomial equations of the heat capacities as a function of temperature were fitted by least-square method. Smoothed heat capacities and thermodynamic functions of the complex were calculated.     

The 1,2-hydrogen shift reaction for monohalogenophosphanes PH2X and HPX (X = F,Cl)

The aim of the present study was to perform a quantum chemical investigation in the 1,2-hydrogen shift reaction for the PH₂X and HPX molecules (X = F,Cl). Several phosphorus–halogen-bearing molecules were studied, including PH₂F, PH₂Cl, HPF, HPCl, HPFH, HPClH, PFH and PClH. The energies of stationary and saddle points on the ground electronic potential energy surface were investigated with post-Hartree–Fock methods [CCSD(T), MP2, QCISD] and different DFT functionals. The PH₂F 1,2-hydrogen shift energy barrier was 75 kcal mol^?1 at the CCSD(T) level and only a small increase in this value was observed for the HPF isomerisation. In contrast, the HPCl 1,2-hydrogen shift barrier is higher than the PH₂Cl one, which presented a barrier height of 69 kcal mol^?1 among CCSD(T) and composite methods. The rate constants of these unimolecular rearrangements varied from 10^?44 to 10^?38 s^?1, and these isomerisation channels exhibited large half-lives. In addition, the heat of formation of each monohalogenophosphane was also calculated. The Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) analysis were also employed to characterise the differences between the phosphorous–halogen bonds.     

A comparative coupled cluster and density functional theory study of the HOCI → HCIO transition state

The structural features of the HOCl → HClO isomerization mechanism, including all stationary points, and one saddle point, were examined by use of coupled cluster and the B3LYP density functional theory methodology. To improve the results a very large 6–311++G (3df, 3pd) Gaussian-type basis set was employed in the presented calculations. In addition, Gaussian-3 theory was tested against our coupled cluster (with single, double and triple excitations) results, and they were found to correlate closely with one another by around 1–2 kcal mol^?1. The energy change for this isomerization reaction is predicted to be 54.5 kcalmol^?1 and 52.5 kcalmol^?1 with the B3LYP and CCSD (T) methods, respectively, and the activation barrier is 76.1 kcal mol^?1 and 70.1 kcalmol^?1 with the same methods.     

Counter anion effect on structural,opto-electronic and charge transport properties of fused π-conjugated imidazolium compound

The structure–activity relationship of fused π-conjugated imidazolium cation with three counter anion molecules, BF₄^?, CF₃SO₃^? and (CF₃SO₂)₂N^?, was studied using electronic structure calculations. The structural, opto-electronic and charge transport properties of these complexes were studied. The charge transfer from π-conjugated imidazolium(I) to counter anion was confirmed in all the studied complexes. Interaction energy varies significantly depending on the counter anion and the stability was found higher for I-BF₄ complex than both I–CF₃SO₃ and I–(CF₃SO₂)₂N complexes. The strong (C–H)⁺···F^? hydrogen bond of length 1.95 Å between fused π-conjugated imidazolium and BF^?₄ anion is the driving force for the strongest interaction energy in I–BF₄ complex. The energy decomposition analysis confirms that the interaction between imidazolium and counter anion is mainly driven by electrostatic and orbital interaction. It has been observed that the absorption spectra of the complex are independent of anion nature but the influence of anion character is observed on frontier molecular orbital pattern. The charge transport property of I–BF₄ complex was studied by using tight-binding Hamiltonian approach and found that the hole mobility in I–BF₄ is 1.13 × 10^?4 cm² V^?1 s^?1.     

Density functional and spectroscopic studies of nitrogen inversion in substituted dizocilpines

While developing a synthesis towards tagged dizocilpine (MK‐801) analogues, we observed highly restricted inversion of a nitrogen centre in a number hydroxylamines obtained as key intermediates. These compounds are shown to possess some of the structural elements which are expected to significantly hinder the nitrogen inversion, potentially leading to hydroxylamines with a chiral nitrogen centre. Free energy barriers (ΔG^≠) of the nitrogen inversion were estimated to be ca. 22 kcal mol^?1 at temperatures near 420 K using variable temperature NMR measurements in DMSO‐d₆. Further density functional studies of a number model systems were undertaken in order to better rationalize the measured inversion barriers and follow the role of various structural factors in raising the barrier height of the nitrogen inversion process. Copyright © 2008 John Wiley & Sons, Ltd.     

Anharmonic effect of the dissociation rate constant of the unimolecular reactions of CH2XCHFO (X = H,F)

This study examines six unimolecular reactions of CH₂XCHFO (X?=?H,?F). The geometries of the reactions are optimized with Gaussian 03. The calculated barrier heights show that bond C–C′ scission, CH₂XCHFO (X?=?H,?F)?→?CH₂X?+?CHFO (R1), dominates the decomposition of CH₂XCHFO. For X?=?H and X?=?F, the barrier heights of (R1) are 13.37 and 9.67?kcal?mol^?1, respectively. The YL (Yao and Lin) method is used to calculate the anharmonic and harmonic rate constants of the unimolecular reactions. The results clearly demonstrate the anharmonic effect of these reactions. In the microcanonical case, for (R1) (X?=?H), the total energy is from 42.78 to 144.84?kcal?mol^?1. The corresponding anharmonic rate constants are from 1.57?×?10¹² to 2.52?×?10^13?s^?1 and the harmonic rate constants are from 1.52?×?10¹² to 2.52?×?10^13?s^?1.     

Long distance structural consequences of H‐bonding: the case of complexes of para‐substituted phenol derivatives

H‐bonded complexes of p‐X‐PhOH/p‐X‐PhO^? with fluoride and hydrofluoric acid (X = OH, H, NO₂) were subject of optimization (by means of B3LYP/6‐311+G**) for gradually changed O···F distance from d_O···F = 4.0 Å down to (i) the distance of the proton transfer from the hydroxyl group to fluoride leading to O^?···HF interaction and (ii) fully optimized system (O^?···HF type). In this way, we simulate gradual changes of H‐bond strength estimating simultaneously the energy of interaction, E_int, energy of deformation, E_def, and the binding energy, E_tot. The obtained geometrical parameters allow us to show that H‐bond formation causes substantial changes in geometry, even at so distant parts of the system as the ring and bond length in para‐substituents (OH and NO₂). All these changes are monotonically dependent on interaction and deformation energies. Copyright © 2009 John Wiley & Sons, Ltd.     

Conformational analysis of 3‐methyl‐3‐silathiane and 3‐fluoro‐3‐methyl‐3‐silathiane

The conformational equilibria of 3‐methyl‐3‐silathiane 5 , 3‐fluoro‐3‐methyl‐3‐silathiane 6 and 1‐fluoro‐1‐methyl‐1‐silacyclohexane 7 have been studied using low temperature ¹³C NMR spectroscopy and theoretical calculations. The conformer ratio at 103 K was measured to be about 5 _ax: 5 _eq = 15:85, 6 _ax: 6 _eq = 50:50 and 7 _ax: 7 _eq = 25:75. The equatorial preference of the methyl group in 5 (0.35 kcal mol^?1) is much less than in 3‐methylthiane 9 (1.40 kcal mol^?1) but somewhat greater than in 1‐methyl‐1‐silacyclohexane 1 (0.23 kcal mol^?1). Compounds 5–7 have low barriers to ring inversion: 5.65 (ax → eq) and 6.0 (eq → ax) kcal mol^?1 ( 5 ), 4.6 ( 6 ), 5.1 (Me_ax → Me_eq) and 5.4 (Me_eq → Me_ax) kcal mol^?1 ( 7 ). Steric effects cannot explain the observed conformational preferences, like equal population of the two conformers of 6 , or different conformer ratio for 5 and 7 . Actually, by employing the NBO analysis, in particular, considering the second order perturbation energies, vicinal stereoelectronic interactions between the Si–X and adjacent C–H, C–S, and C–C bonds proved responsible. Copyright © 2010 John Wiley & Sons, Ltd.