Calculation of solvation free energy using RISM theory for peptide in salt solution

We developed a robust, highly efficient algorithm for solving the full reference interaction site model (RISM) equations for salt solutions near a solute molecule with many atomic sites. It was obtained as an extension of our previously reported algorithm for pure water near the solute molecule. The algorithm is a judicious hybrid of the Newton–Raphson and Picard methods. The most striking advantage is that the Jacobian matrix is just part of the input data and need not be recalculated at all. To illustrate the algorithm, we solved the full RISM equations for a dipeptide (NH₂(SINGLE BOND)CHCH₃(SINGLE BOND)CONH(SINGLE BOND)CHCH₃(SINGLE BOND)COOH) in a 1 M NaCl solution. The extended simple point charge (SPC/E) model was employed for water molecules. Two different conformations of the dipeptide were considered. It was assumed for each conformation that the dipeptide was present either as an un-ionized form or as a zwitterion. The structure of the salt solution near the dipeptide and salt effects on the solvation free energy were also discussed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1724–1735, 1998     

Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water

Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLS-AA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirms that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.     

A theoretical study of bond energies in model Si–H–Cl molecules using density functional approaches for representing Si surface chemistry

The reliability of density functional theory (DFT) methods for calculating Si(SINGLE BOND)2H, Si(SINGLE BOND)Cl, and Si(SINGLE BOND)Si bond energies is examined in reactions involving molecules and small clusters representing various surface sites appropriate for Si surface chemistry. Results are presented for systematic studies using a valence double-zeta polarization basis for both all-electron calculations and valence–electron calculations employing effective core potentials (ECPs). All-electron DFT results are comparable to much more demanding MP4, G2, and MC–SCF–CI calculations for computed bond energies. Whereas the use of ECPs introduces systematic energy differences of ca. 3–5 kcal/mol compared to AE results, depending on the type of bond involved, the use of ECPs for carrying out calculations on larger clusters is discussed where AE calculations become more computationally demanding. The convergence of Si bond energies as a function of replacing hydrogens with silyl groups is examined. In constructing models to describe etching processes involving Cl species on Si surfaces, the need for incorporating differences in thermochemistries for one-, two-, and three-coordinate Si surface sites is emphasized. Comparisons of semiempirical approaches for thermochemistries of Si-containing species find these methods somewhat less reliable for obtaining reliable bond energies compared to computationally more demanding DFT and ab initio correlated models. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2075–2085, 1997     

G2 ab initio calculations on three-membered rings: Role of hydrogen atoms

G2 ab initio calculations on all ABX three-membered rings (TMRs) that can be derived from cyclopropane by systematic substitution of the (SINGLE BOND)CH₂ groups by (SINGLE BOND)NH or (SINGLE BOND)O groups have been performed. Our results show that the decrease in the A(SINGLE BOND)B bond length as the electronegativity of X increases is significantly larger than that found for the corresponding acyclic analogs. In general, a systematic substitution of the (SINGLE BOND)CH₂ groups of cyclopropane by (SINGLE BOND)NH or (SINGLE BOND)O groups implies significant geometric changes that are not reflected in a parallel change of the corresponding conventional ring strain energy (CRSE). When the electronegativity of the groups forming the TMR increases the effect on the CRSE of the system is small, although the charge delocalization inside the ring decreases. The near constancy of the CRSE along the series can be explained in terms of the charge redistribution of the system where the (SINGLE BOND)CH₂ groups play a crucial role. There are, however, significant changes in the hydrogenation energies of the TMR investigated; our results show that, when in an ABX three-membered ring, the electronegativity of X increases the hydrogenation energy of A(SINGLE BOND)B bond decreases and vice versa. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1072–1086, 1998     

Calculation of bond dissociation energies for oxygen containing molecules by ab initio and density functional theory methods

Two ab initio (ROHF and MP2), one local (SVWN), four hybrid (BHandH, BHandHLYP, Becke3LYP, and Becke3P86), and two nonlocal (BLYP and BP86) density functional theory (DFT) methods are used for calculating the dissociation energies of molecules that contain H(SINGLE BOND)O, O(SINGLE BOND)O and O(SINGLE BOND)C bonds. The sensitivity to the basis set of the prediction of bond dissociation energies with DFT methods was tested with Becke3LYP on the H(SINGLE BOND)O dissociation energy of water. The 6–31 + G(d) methods are chosen as the smallest basis set which produces reasonable results. The calculated values for all other ab initio and DFT methods were performed with these basis sets and then compared with the experimental data. The suitability of DFT methods for computing reliable bond dissociation energies of oxygen containing molecules is discussed. © 1996 John Wiley & Sons, Inc.     

Calculation of solvation and binding free energy differences between VX-478 and its analogs by free energy perturbation and AMSOL methods

Summary VX-478 belongs to a novel class of HIV-1 protease inhibitors that are based on N,N-disubstituted benzene sulfonamides. Force field parameters for the N,N-dialkyl benzene sulfonamide moiety have been assembled from the literature and from our own ab initio calculations. These parameters were employed to calculate solvation and binding free energy differences between VX-478 and two analogs. The free energy perturbation method has been used to determine these differences using two approaches. In the first approach, intergroup interaction terms only were included in the calculation of free energies (as in most reports of free energy calculations using AMBER). In the second approach, both the inter- and intragroup interaction terms were included. The results obtained with the two approaches are in excellent agreement with each other and are also in close agreement with the experimental results. The solvation free energies of N,N-dimethyl benzene sulfonamide derivatives (truncated models of the inhibitors), calculated using continuum solvation (AMSOL) methods, are found to be in qualitative agreement with the experimental and free energy perturbation results. The binding and solvation free energy results are discussed in the context of structure-based drug design to show how physicochemical properties (for example aqueous solubilities and bioavailabilities) of these HIV-1 protease inhibitors were improved, while maintaining their inhibitory potency.     

A density functional study of Fe(SINGLE BOND)N2, Fe(SINGLE BOND)N+2, and Fe(SINGLE BOND)N−2

The interaction of an iron atom with molecular nitrogen was studied using density functional theory. Calculations were of the all-electron type and both conventional local and gradient-dependent models were used. A ground state of linear structure was found for Fe(SINGLE BOND)N₂, with 2S + 1 = 3, whereas the triangular Fe(SINGLE BOND)N₂ geometry, of C_2v symmetry, was located 2.1 kcal/mol higher in energy, at least for the gradient-dependent model. The reversed order was found using the conventional local approximation. In Fe(SINGLE BOND)N₂, the N(SINGLE BOND)N bond is strongly perturbed by the iron atom: It has a bond order of 2.4, a vibrational frequency of 1886 cm⁻¹, and an equilibrium bond length of 1.16 Å: These values are 3.0, 2359 cm⁻¹, and 1.095 Å, respectively, for the free N₂ molecule. With the gradient-dependent model and corrections for nonsphericity of the Fe atom, a very small binding energy, 8.8 kcal/mol, was calculated for Fe(SINGLE BOND)N₂. Quartet ground states were found for both Fe(SINGLE BOND)N⁺₂ and Fe(SINGLE BOND)N⁻₂. The adiabatic ionization potential, electron affinity, and electronegativity were also computed; the predicted values are 7.2, 1.22, and 4.2 eV, respectively. © 1997 John Wiley & Sons, Inc.     

Synthesis and properties of polycarbosilanes with the meta-linkage bending unit by hydrosilylation polymerization

The polycarbosilanes (PCS) with meta-linkage bending unit ((SINGLE BOND)Me₂Si(SINGLE BOND)m(SINGLE BOND)C₆H₄(SINGLE BOND)Me₂Si(SINGLE BOND)CH₂CH₂(SINGLE BOND)) were successfully synthesized in mild conditions by hydrosilylation in the presence of [Pt{(CH₂(DOUBLE BOND)CHSiMe₂)₂O}₂]. The PCS obtained were soluble in various solvents owing to the lowering of the crystallinity. These properties are well compared with those of the PCS [(SINGLE BOND)Me₂Si(SINGLE BOND)p(SINGLE BOND)C₆H₄(SINGLE BOND)Me₂Si(SINGLE BOND)CH₂CH₂(SINGLE BOND)]_n. © 1996 John Wiley & Sons, Inc.     

Molecular structure and binding energies of monosubstituted hexacarbonyls of chromium,molybdenum, and tungsten: Relativistic density functional study

Relativistic density functional calculations have been carried out for the group VI transition metal carbonyls M(CO)₅L (M=Cr, Mo, W; L=OH₂, NH₃, PH₃, PMe₃, N₂, CO, OC (isocarbonyl), CS, CH₂, CF₂, CCl₂, NO⁺). The optimized molecular structures and M(SINGLE BOND)L bond dissociation energies, as well as the metal–carbonyl bond energy of the trans CO group, have been calculated. Besides the marked dependence of the trans M(SINGLE BOND)CO bond length on the type of ligand L, such an effect on the that bond energy is also observed. For the chromium compounds, the trans Cr(SINGLE BOND)CO bond length varies from 184 to 199 pm and its bond energy from 242 to 150 kJ/mol. For the molybdenum compounds, the range is 197 to 216 pm and 253 to 128 kJ/mol and, for tungsten, 198 to 214 pm and 293 to 159 kJ/mol. The observed trends can be explained with the π acceptor strength of the L ligand. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1985–1992, 1997     

Conformational analysis and rotation barriers of 2-aminoethanethiol and 2-aminoethanol: An ab initio study

All the possible rotamers of 2-aminoethanol and 2-amino-ethanethiol were fully optimized at the ab initio level using the 6–31G** basis with correlation energy inclusion and zero-point energy evaluation. Thirteen local minima for the former and 14 for the latter compound were found. In both molecules, the gauche′-gauche-gauche′ (g′Gg′) is the prevailing conformation, but in the sulfurated compound, it is accompanied by relevant percentages of other conformers, owing to the very low ΔE values. The stability of the g′Gg′ accommodation derives mainly from the presence of weak hydrogen bridges (O(SINGLE BOND)H···N and S(SINGLE BOND)H···N, respectively). The rotation barriers around the C(SINGLE BOND)C and C(SINGLE BOND)N bonds are higher than those around the C(SINGLE BOND)O and C(SINGLE BOND)S ones. © 1996 John Wiley & Sons, Inc.     

Ab initio studies of three-membered ring formation through intramolecular nucleophilic substitution

Three-membered ring (3MR) forming processes of ⁻X(SINGLE BOND)CH₂(SINGLE BOND)CH₂(SINGLE BOND)F and ⁻CH₂(SINGLE BOND)C((SINGLE BOND)Y)(SINGLE BOND)CH₂(SINGLE BOND)F (X(DOUBLE BOND)CH₂, O, or S and Y(DOUBLE BOND)0 or S) through a gas phase neighboring group mechanism (S_Ni) are studied theoretically using the ab initio molecular orbital method with the 6–31+G* basis set. When electron correlation effects are considered, the activation (ΔG^≠) and reaction energies (ΔG⁰) are lowered by ca. 10 kcal mol⁻¹, indicating the importance of the electron correlation effect in these reactions. The contribution of entropy of activation (−TΔS^≠) at 298 K to ΔG^≠ is very small, and the reactions are enthalpy controlled. The ΔG^≠ and ΔG⁰ values for these ring closure processes largely depend on the stabilities of the reactants and the heteroatom acting as a nucleophilic center. The Bell–Evans–Polanyi principle applies well to all these reaction series. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1773–1784, 1997     

A comparative study of O2, CO,and NO binding to iron–porphyrin

Minimum-energy structures of O₂, CO, and NO iron–porphyrin (FeP) complexes, computed with the Car–Parrinello molecular dynamics, agree well with the available experimental data for synthetic heme models. The diatomic molecule induces a 0.3–0.4 Å displacement of the Fe atom out of the porphyrin nitrogen (N_p) plane and a doming of the overall porphyrin ring. The energy of the iron–diatomic bond increases in the order Fe(SINGLE BOND)O₂ (9 kcal/mol) < Fe(SINGLE BOND)CO (26 kcal/mol) < Fe(SINGLE BOND)NO (35 kcal/mol). The presence of an imidazole axial ligand increases the strength of the Fe(SINGLE BOND)O₂ and Fe(SINGLE BOND)CO bonds (15 and 35 kcal/mol, respectively), with few structural changes with respect to the FeP(CO) and FeP(O₂) complexes. In contrast, the imidazole ligand does not affect the energy of the Fe(SINGLE BOND)NO bond, but induces significant structural changes with respect to the FeP(NO) complex. Similar variations in the iron–imidazole bond with respect to the addition of CO, O₂, and NO are also discussed. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 31–35, 1998     

Evaluating the relative free energy of hydration of new thrombin inhibitor candidates using the finite difference thermodynamic integration (FDTI) method

Thrombin is a serine protease involved in blood coagulation. Since thrombin inhibitors appear to be effective in the treatment and prevention of thrombotic and embolic disorders, considerable attention has been focused on the structure and interactions of the enzyme. In this work, we calculated the relative free energies of hydration of the new thrombin inhibitor candidates, p‐substituted derivatives of benzamidine, a well‐known noncovalent thrombin inhibitor. We used molecular dynamics and the finite difference thermodynamic integration (FDTI) algorithm within the Discover program of MSI. We have shown that the orthogonality problem that occurs in the calculation of intraperturbed‐group contributions to the free energy is treated adequately by the FDTI method. We have also shown that problems of singularity and convergence in free energy calculations can be properly solved using this method. To conclude, the calculated free energies of hydration gave the following order of solvation for the candidates: p‐(2‐oxo‐1‐propyl)benzamidine > p‐methylbenzamidine > p‐ethylbenzamidine > p‐(1‐propyl)benzamidine > benzamidine. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

An original route to poly[silylene-co-(2,4-disilapentane-2,4-diyl)] oligomers,efficient precursors of silicon carbide-based ceramics with variable C/Si ratios

Novel oligomers possessing a backbone formed of ((TRIPLE BOND)Si(SINGLE BOND)CH₂(SINGLE BOND)Si(TRIPLE BOND)) and (SINGLE BOND)Si(SINGLE BOND)_n units were prepared by the copolycondensation of bis(chlorosilyl)methanes and various dichlorosilanes in the presence of sodium, in refluxing toluene. The effect of the respective molar ratios of comonomers on the yields and the structure of the copolymers was investigated. The role of substituents on silicon atoms in the ability of these materials to provide convenient ceramic precursors upon pyrolysis was examined. When (TRIPLE BOND)Si(SINGLE BOND)H bonds were present, thermal cross-linking was readily performed and ceramics possessing variable C/Si ratios were prepared.     

Benzazole-N(SINGLE BOND)BH3 adducts. Reductive transposition of 2-benzimidazole, 2-benzothiazole,and 2-benzoxazole N(SINGLE BOND)BH3 adducts to 1,3,2-benzimidazaborole, 1,3,2-benzoxaborole,and 1,3,2-benzothiazaborole

1,3,2-Benzimidazaborole, 1,3,2-benzoxaborole, and 1,3,2-benzothiazaborole were synthesized from the corresponding 2-benzazole N(SINGLE BOND)BH₃ and 2-benzazole S(SINGLE BOND)BH₃ adducts through a reductive transposition from the isolobal fragment X(SINGLE BOND)C(sp²) (DOUBLE BOND) N(sp²) (SINGLE BOND) B(sp³) (X (DOUBLE BOND) N, O, S) to the fragment X(SINGLE BOND)B(sp²) (DOUBLE BOND) N(sp²) (SINGLE BOND) C(sp³). N(SINGLE BOND)BH₃ substitution shifts to lower frequencies 4-H, C-3a, and C-7a resonances. The X-ray diffraction analysis of 2-(o-methoxyphenyl)benzothiazole N(SINGLE BOND)BH₃ adduct is reported. Two new tetracyclic boron-bridged compounds were observed as by-products (6,9-(ethyl)-diaza-2-oxa-1-bora[3,4,7,8]-dibenzobycyclo[4.3.0]-nona-3,7-diene, 6d, and 8-aza-9-oxa-2-thia-1-bora-[3,4,7,8]dibenzobycyclo[3.4.0]nona-3,7-diene, 15d, when 2-(o-methoxyphenyl)-1-ethylbenzimidazole-BH₃ 6b and 2-(o-methoxyphenyl)-benzothiazole-BH₃ 15b adducts were heated. © 1996 John Wiley & Sons, Inc.     

Ab initio MO study of the solvent effect on the SN2 reaction of the trimethylsulfonium cation with chloride anion

A recently developed ab initio MO theory including solvent effects has been applied to a typical cation-anion reaction, the S_N2 reaction of the trimethylsulfonium cation with the chloride anion. In the gas phase, the trimethylsulfonium and chloride ions are unstabilized, and the reaction is expected to proceed rapidly. In aqueous solution, the reactant ions are largely stabilized, and the reaction has been predicted to be endothermic, with an activation energy of 30–40 kcal/mol. This potential energy profile, which agrees with experimental results, has been well elucidated by differential solvation at several stages of the reaction path. At the transition state of this reaction, the C and H atoms in the transferring CH₃ group are almost in a plane that is perpendicular to the Cl(SINGLE BOND)C(SINGLE BOND)S line, reflecting the concerted nature of the reaction. The population analysis has shown that the electrons in the C(SINGLE BOND)S bond are mostly withdrawn by the sulfur atom at the transition state and that the electron transfer from Cl to CH₃ occurs after the transition state. The calculated activation energy for the reaction in ethanol is smaller than that in water. This agrees with experiments. © 1996 John Wiley & Sons, Inc.     

Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase

The interactions between biologically important enzymes and drugs are of great interest. In order to address some aspects of these interactions we have initiated a program to investigate enzymedrug interactions. Specifically, the interactions between one of the isozymes of carbonic anhydrase and a family of drugs known as sulfonamides have been studied using computational methods. In particular the electrostatic free energy of binding of carbonic anhydrase II with acetazolamide, methazolamide,p-chlorobenzenesulfonamide,p-aminobenzenesulfonamide and three new compounds (MK1, MK2, and MK3) has been computed using finite-difference Poisson-Boltzmann (FDPB) [1] method and the semimacroscopic version [2, 3] of the protein dipole Langevin dipole (PDLD) method [4]. Both methods, FDPB and PDLD, give similar results for the electrostatic free energy of binding even though different charges and different treatments were used for the protein. The calculated electrostatic binding free energies are in reasonable agreement with the experimental data. The potential and the limitation of electrostatic models for studies of binding energies are discussed.     

Conformers of gaseous protonated glycine

Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller–Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH₃⁺ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)₂⁺. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0–10 and 30–40 kcal mol⁻¹. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1862–1876, 1998     

Estimates of the structure and dimerization energy of polyacetylene from ab initio calculations on finite polyenes

Ab initio calculations at the Hartree-Fock (HF) and the second-order Møller-Plesset (MP2) levels are performed for finite polyenes C_2nH_2n+2 to estimate the structure and dimerization energy (E_dim) of polyacetylene. The effect of electron correlation on the structure of finite polyenes is analyzed in detail. The MP3/6–31G* C(DOUBLE BOND)C and C(SINGLE BOND)C bond lengths in polyacetylene are estimated by a simple extrapolation method using empirical corrections for the MP2 deficiencies, yielding values [C(DOUBLE BOND)C(MP3) ∼ 1.36 Å and C(SINGLE BOND)C(MP3) ∼ 1.44 Å] that are in a good agreement with experiment (C(DOUBLE BOND)C (DOUBLE BOND) 1.36 Å and C(SINGLE BOND)C (DOUBLE BOND) 1.44–1.45 Å). Comparison is also made with other theoretical estimates of polyacetylene structure. E_dim is approximated by the energy difference between the equilibrium and hypothetical polyenic structures. It is estimated that E_dim is ∼ 1.4–1.5 kcal/mol (0.06–0.07 eV) per carbon-carbon bond at the HF level with 4–21G and 6–31G* basis sets and ∼ 0.3–0.5 kcal/mol (0.013–0.022 eV) at the MP2 level with the 6–31G* basis set. It is concluded that E_dim is very sensitive to the level of approximation employed so that a proper treatment of electron correlation is essential to obtain a reliable estimate of the dimerization energy. © 1997 John Wiley & Sons, Inc.     

Silaacetylene: A possible target for experimental studies

The equilibrium geometries and transition states for interconversion of the CSiH₂ isomers in the singlet electronic ground state are optimized at the MP2 and CCSD(T) levels of theory using a TZ2P basis set. The heats of formation, vibrational frequencies, infrared intensities, and rotational constants are also predicted. There are three energy minima on the CSiH₂ potential energy surface. Energy calculations at CCSD(T)/TZ2P(fd) + ZPE predict that the global energy minimum is silavinylidene (1), which is 34.1 kcal mol⁻¹ lower in energy than trans-bent silaacetylene (2) and 84.1 kcal mol⁻¹ more stable than the vinylidene isomer (3). The barrier for rearrangement 2→1 is calculated at the same level of theory to be 5.1 kcal mol⁻¹, while for the rearrangement 3→2 a barrier of 2.7 kcal mol⁻¹ is predicted. The natural bond orbital (NBO) population scheme indicates a clear polarization of the C(SINGLE BOND)Si bonds toward the carbon end. A significant ionic contribution to the C(SINGLE BOND)Si bonds of 1 and 2 is suggested by the NBO analysis. The C(SINGLE BOND)Si bond length of trans-bent silaacetylene (2) is longer than previously calculated [1.665 Å at CCSD(T)/TZ2P)]. The calculated carbon-silicon bond length of 2 is in the middle between the C(SINGLE BOND)Si double bond length of 1 (1.721 Å) and the C(SINGLE BOND)Si triple bond of the linear form HCSiH (4), which is 1.604 Å. Structure 4 is a higher-order saddle point on the potential energy surface. © 1996 by John Wiley & Sons, Inc.