The barrier height of the F+H2 reaction revisited: coupled-cluster and multireference configuration-interaction benchmark calculations

Large scale coupled-cluster benchmark calculations have been carried out to determine the barrier height of the F+H2 reaction as accurately as possible. The best estimates for the barrier height of the linear and bent transition states amount to 2.16 and 1.63 kcal/mol, respectively. These values include corrections for core correlation, scalar-relativistic effects, spin-orbit effects, as well as the diagonal Born-Oppenheimer correction. The CCSD(T) basis-set limits are estimated using extrapolation techniques with augmented quintuple and sextuple-zeta basis sets, and remaining N-electron errors are determined using coupled-cluster singles, doubles, triples, quadruples calculations with up to augmented quintuple-zeta basis sets. The remaining uncertainty is estimated to be less than 0.1 kcal/mol. The coupled-cluster results are used to calibrate multireference configuration-interaction calculations with empirical scaling of the correlation energy.     

MRSDCI STUDIES OF LOW-LYING ELECTRONIC STATES OF THE N_2F~+ MOLECULE

Ab initio electronic structure calculations are reported for low-lying electronic states,X ~1Σ~+andA ~1Π of the N_2F~+ molecule.Geometric parameters for the ground state X ~1Σ~+ are predicted by means of mul-tireference single and double excitation configuration interaction(MRSDCI)calculations with a double zeta pluspolarization(DZ+P)basis set.Vertical excitation energy for these two electronic states is determined usingMRSDCI/DZ+P calculations at the ground state equilibrium geometry.The oscillator strength for the X~1Σ+→A ~1Π transition and the radiative lifetime for the A~1Π state are calculated based on the MRSDCI wavefunc-tions.     

Modeling reaction pathways of low energy particle deposition on polymer surfaces via first principle calculations

The chemical processes that lead to polystyrene surface modification via low energy deposition of C(2)H(+), C(2)F(+), CH(2), CH(2)(+), and H(+) radicals and ions are examined using first principles calculations. Specifically, the reaction mechanisms responsible for products identified in classical molecular dynamics with reactive empirical bond-order potentials are examined using density functional theory. In addition, these calculations consider how the presence of charges on the incident particles changes the result for the CH(2) system through the comparison of barriers, transition states, and final products for CH(2) and CH(2)(+). The structures of the reaction species and energy barriers are determined using the B3LYP hybrid functional. Finally, CCSD/6-31G(d,p) single point energy calculations are carried out to obtain optimized energy barriers. The results indicate that the large variety of reactions occurring on the polystyrene surface are a consequence of complex interactions between the substrate and the deposited particles, which can easily be identified and characterized using advanced computational methodologies, such as first principle calculations.     

Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model

The solution conformation of alpha-conotoxin GI and its two single disulfide analogues are simulated using a polarizable force field in combination with the molecular fragmentation quantum chemical calculation. The polarizability is explicitly described by allowing the partial charges and fragment dipole moments to be variables, with values coming from the linear-scaling energy-based molecular fragmentation calculations at the B3LYP/6-31G(d) level. In comparison with the full quantum chemical calculations, the fragmentation approaches can yield precise ground-state energies, dipole moments, and static polarizabilities for peptides. The B3LYP/6-31G(d) charges and fragment-centered dipole moments are introduced in calculations of electrostatic terms in both AmberFF03 and OPLS force fields. Our test calculations on the gas-phase glucagon (PDB code: 1gcn) and solvated alpha-conotoxin GI (PDB code: 1not) demonstrate that the present polarization model is capable of describing the structural properties (such as the relative conformational energies, intramolecular hydrogen bonds, and disulfide bonds) with accuracy comparable to some other polarizable force fields (ABEEM/MM and OPLS-PFF) and the quantum mechanics/molecular mechanics (QM/MM) hybrid model. The employment of fragment-centered dipole moments in calculations of dipole-dipole interactions can save computational time in comparison with those polarization models using atom-centered dipole moments without much loss of accuracy. The molecular dynamics simulations using the polarizable force field demonstrate that two single disulfide GI analogues are more flexible and less structured than the native alpha-conotoxin GI, in agreement with NMR experiments. The polarization effect is important in simulations of the folding/unfolding process of solvated proteins.     

Si~2Cl~6分子的内旋转能垒和振动基频的理论研究

用从头算方法HF/6-31G^*^*和密度函方法B3LYP/6-31G^*^*,对Si~2Cl~6分子的平衡几何构型进行优化,优化的结果与实验结果吻合得较好.并用上述两种不同的方法计算Si~2Cl~6分子的内旋转能垒,结果分别为8.786和6.694kJ/mol,其中DFT方法的计算结果与实验结果4.18kJ/mol吻合得较好.对Si~2Cl~6分子的振动基频进行计算.用HF/6-31G^*^*SQM力场所计算的频率理论值与实验值的平均误差为7.3cm^-^1,用B3LYP/6-31G^*^*未标度的力场所计算的频率理论值与实验值的平均误差为6.0cm^-^1.该密度泛函方法(B3LYP/~6-31G^*^*)的理论计算值比用HF/6-31G^*^*标度后的SQM力场计算的频率与实验值(除Si--Si键扭转振动基频之外的11条振动基频)吻合得更好.并给出了Si--Si键扭转振动基频的预测值。     

Electronic absorption spectra of amino substituted anthraquinones and their interpretation using the ZINDO/S and AM1 methods

Electronic absorption spectra of 1,2-diamino-9,10-anthraquinone (12DAAQ), 1,4-diamino-9,10-anthraquinone (14DAAQ), 1,5-diamino-9,10-anthraquinone (15DAAQ), and 2,6-diamino-9,10-anthraquinone (26DAAQ) are investigated. Molecular geometries of the amino anthraquinones in the ground state are optimized using the semiempirical ZINDO/1 and AM1 methods without imposing any symmetry constraints. The ground state geometries of all the molecular systems are found to be planar. For interpretation of the spectra, ZINDO/S-CI and AM1-CI calculations employing singly excited configuration using the completely optimized geometry are carried out. Such calculations on the electronic spectra of amino anthraquinones are carried out for the first time. On the basis of these calculations, the assignment of the spectra are successfully made.     

Cope elimination: elucidation of solvent effects from QM/MM simulations

The Cope elimination reactions for threo- and erythro-N,N-dimethyl-3-phenyl-2-butylamine oxide have been investigated using QM/MM calculations in water, THF, and DMSO. The aprotic solvents provide up to million-fold rate accelerations. The effects of solvation on the reactants, transition structures, and rates of reaction are elucidated here using two-dimensional potentials of mean force (PMF) derived from free-energy perturbation calculations in Monte Carlo simulations (MC/FEP). The resultant free energies of activation in solution are in close agreement with experiment. Ab initio calculations at the MP2/6-311+G-(2d,p) level using the PCM continuum solvent model were also carried out; however, only the QM/MM methodology was able to reproduce the large rate increases in proceeding from water to the dipolar aprotic solvents. Solute-solvent interaction energies and radial distribution functions are also analyzed and show that poorer solvation of the reactant in the aprotic solvents is primarily responsible for the observed rate enhancements. It is found that the amine oxide oxygen is the acceptor of three hydrogen bonds from water molecules for the reactant but only one to two weaker ones at the transition state. The overall quantitative success of the computations supports the present QM/MM/MC approach, featuring PDDG/PM3 as the QM method.     

Toward a consistent treatment of polarization in model QM/MM calculations

The concept of model chemistries within hybrid QM/MM calculations has been addressed through analysis of the polarization energy determined by two distinct approaches based on (i) induced charges and (ii) induced dipoles. The quantum mechanical polarization energy for four configurations of the water dimer has been determined for a range of basis sets using Morokuma energy decomposition analysis. This benchmark value has been compared to the fully classical polarization energy determined using the induced dipole approach, and the molecular mechanics polarization energy calculated using induced charges within the MM region of hybrid QM/MM calculations. From the water dimer calculations, it is concluded that the induced charge approach is consistent with medium sized basis set calculations whereas the induced dipole approach is consistent with large basis set calculations. This result is highly relevant to the concept of QM/MM model chemistries.     

Energetics and structural elucidation of mechanisms for gas phase H/D exchange of protonated peptides

Hydrogen/deuterium exchange reactions involving protonated triglycine and deuterated ammonia (ND(3)) have been examined in the gas phase using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Ab initio and density functional theory (DFT) calculations have been carried out to model the exchanges and to obtain energetics and vibrational frequencies for molecules involved in the proposed exchange mechanisms. Structural optimization and frequency calculations have been performed at the B3LYP level of theory with the 6-311+G(d,p) basis set. Transition states have been calculated at the same level of theory and basis set as above using the QST2 and QST3 methods. Single-point energy calculations have been performed at the MP2/6-311+G(d,p) level. Six labile sites of protonated triglycine were found to undergo H/D exchange. Of these six labile hydrogens, two are amide, three are ammonium, and one is carboxyl. Detailed mechanisms for each of these transfers are proposed. Qualitative onium ion and tautomer mechanisms for the exchanges of ammonium and amide hydrogens, respectively, using semiempirical calculations were suggested in previous studies by Beauchamp et al. As shown by the current ab initio and DFT calculations completed during this study, the mechanisms proposed in that study are notionally correct; however, the tautomer mechanisms are shown here to be the result of the fact that a second stable isomer of protonated triglycine exists in which the amide1 carbonyl oxygen is protonated. The exchange of the carboxyl hydrogen is found to proceed via a transition state resembling an ammonium ion interacting with a carboxylate moiety via two hydrogen bonds. The current work thus provides significant mechanistic and structural detail for a considerably more in-depth understanding of the processes involved in gas phase H/D exchange of peptides.     

3-酰基-2,4-吡咯烷二酮及其N-酰基衍生物相对稳定性的理论计算

对 3 酰基 2 ,4 吡咯烷二酮 (1)及其N 酰基衍生物 (2 )的各种异构体 (a -e)分别进行了HF/6 31G和HF/6 31G 水平上的优化计算 ,并考虑电子相关效应 (MP2 /6 31G )对其能量进行了校正 ,探讨了计算水平对体系相对稳定性的影响。HF/6 31G 及MP2 /6 31G 上的计算结果表明 1d和 2a分别为化合物 1和 2的最稳定结构形式 ,与实验观察到的结果一致。同时对N 位取代酰基引起的优势结构的变化给出了较合理的解释。     

Mixing parameters for geometry optimization using the Hamiltonian algorithm

We study the mixing parameters for the search of an optimal geometry using the Hamiltonian algorithm (HA) combined with ab initio molecular orbital calculations. We choose the C?CC?CC?CC dihedral angle of the butane molecule as an example. HF/3-21G level calculations are employed as the molecular orbital calculations. The distributions of the eigenvalues of mixing coefficients are fitted with the linear, quadratic, and quartic functions. Analyses of HA calculations both up to 2,000 and 60,000 iterative calculations show a possibility that the mixing process reduces the number of iterations. The low energy HF/3-21G, B3LYP/6-31G**, and PCM B3LYP/aug-cc-pVDZ optimized structures of the N-acetyl l-histidine N??-methyl amide and four water molecule supermolecule were also determined using the HA optimization method and compared to the recently determined thought to be global minimum energy structure.     

取代基对苯腈类低聚物几何及电子特征的影响

用半经验量化计算研究了一系列苯腈类低聚合物的几何结构及其电子特征。苯腈类低聚合物几何结构的计算采用半经验量子化学计算和分子力学构象分析相结合的方法,而电子特征则的计算采用ＺＩＮＤＯ／Ｓ－ＣＩ方法。取代基包括甲氧基、甲基、羟基、氨基、氟和硝基。它们在苯环上可以采用邻位、间位和对位三个取代位置。计算结果表明,不同的基团在苯环上采用不同的取代位置时,低聚物的构象会存在一定的差别,而且电性会随着基团的得失     

Vertical excitation energies for ribose and deoxyribose nucleosides

Vertical excitation energies for DNA and RNA nucleosides are determined with electron structure calculations using the time-dependent density functional theory (TDDFT) method at the B3LYP/6-311++G(d,p) level for nucleoside structures optimized at the same level of theory. The excitation energies and state assignments are verified using B3LYP/aug-cc-pVDZ level calculations. The nature of the first four excited states of the nucleosides are studied and compared with those of isolated bases. The lowest npi* and pipi* transitions in the nucleoside remain localized on the aromatic rings of the base moiety. New low-energy npi* and pisigma* transitions are introduced in the nucleosides as a result of bonding to the ribose and deoxyribose molecules. The effect on the low-lying excited state transitions of the binding to phosphate groups at the 5'- and 3',5'-hydroxyl sites of the uracil ribose nucleoside are also studied. Some implications of these calculations on the de-excitation dynamics of nucleic acids are discussed.     

Modelling of high-pressure phase equilibria using the Sako–Wu–Prausnitz equation of state: II. Vapour–liquid equilibria and liquid–liquid equilibria in polyolefin systems

Phase equilibria in binary and ternary polyolefin systems are calculated using the cubic equation of state proposed by Sako–Wu–Prausnitz (SWP). Calculations were done for high-pressure phase equilibria in ethylene/polyethylene (LDPE) systems and for liquid–liquid equilibria (LLE) in systems containing either high-density polyethylene or poly(ethylene-co-propylene). The calculations for the copolymer/solvent systems are compared with those using the SAFT EOS. The two equations of state can describe UCST, LCST as well as U-LCST behaviour with similar accuracy. Whereas, the binary interaction parameter is temperature-independent for SAFT, it is found to be a function of temperature for the SWP model. Moreover, the influence of an inert gas on the LCST of the polyethylene/hexane system is investigated using the SWP EOS. The polydispersity of the different polyethylenes is considered in the phase equilibrium calculations using pseudocomponents chosen by the moments of the experimental molecular weight distributions.     

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.     

Molecular orbital study for Na, Mg, and Al adsorption on the Si (111) surface

We investigated the interactions between the Si(111) surface and the Na, Mg, and Al atoms using cluster model calculations. Calculations were performed at levels of complete-active-space self-consistent-field (CASSCF) and multi-reference singly and doubly excited configuration interaction (MRSDCI) calculations using the model core potential method. Our calculations revealed that the most favorable sites of Na, Mg, and Al adsorption on Si(111) are on top (T₁), bridge (B₂), and 3-fold filled (T₄) sites, respectively. The nature of chemical bonds between these metal atoms and the dangling bonds of the surface Si atoms are found to be essentially covalent.     

Ab initio calculations of the vibrational force field and IR intensities of the ammonia dimers

Ab initio SCF calculations using the 4-31G basis set have been carried out to determine the equilibrium geometry, force constants and dipole moment derivatives of the linear (C_s and cylic (C_2h) ammonia dimers. The results are compared with monomer calculations and experimental data.     

A theoretical study on the ionization of H2S with analysis of vibrational structure of the photoelectron spectra

Ab initio calculations were performed to study the molecular structures and the vibrational levels of the low-lying ionic states (²B₁, ²A₁ and ²B₂) of hydrogen sulphide. The equilibrium molecular structure and the vibrational analysis of these states are presented. The normal vibrational calculations at the RHF level and more extensive calculations at the SDCI level using the explicit vibrational Hamiltonians were used for the vibrational analysis. The theoretical ionization intensity curves including the vibrational structures of these ionic states are also presented and compared with the photoelectron spectrum. The results show that the global shape of the potential energy surface has to be taken into consideration in order to analyze the ²A₁ and ²B₂ states. A new assignment of the photoelectron spectra of H₂S is proposed.     

The valence orbitals of NH3 by electron momentum spectroscopy: Quantitative comparisons using Hartree-Fock limit and correlated wavefunctions

The complete valence shell binding energy spectra and valence orbital electron momentum distributions for NH₃ have been measured by high-momentum-resolution electron momentum spectroscopy (EMS). The results are quantitatively compared with theoretical calculations using SCF wavefunctions ranging from DZ quality to a newly developed 126-GTO wavefunction essentially at the Hartree-Fock limit. The 3a₁ and to a lesser extent the 2a₁ valence orbital are not adequately described even at the Hartree-Fock limit with basis set saturation including diffuse functions. The differences between theory and experiment are largely resolved by ion-neutral overlap calculations using CI wavefunctions to incorporate the effects of electron correlation. The 126-G (CI) wavefunctions provide accurate calculation of a wide range of electronic properties of NH₃ and also give good quantitative prediction of the three valence orbital momentum distributions as well as a reasonable prediction of the many-body pole strength distribution observed in the (2a₁)⁻¹ inner valence binding energy spectrum. The present EMS results are compared with recent investigations of wavefunction tails by exterior electron distribution calculations and Penning ionization electron spectroscopy measurements reported by Ohno et al.     

UV spectral changes from rotational and inversion processes at the nitrogen center in aniline molecules

The decoupling of electrons by nuclear distortion and its influence on the UV spectrum are studied using CNDO/S calculations on aniline type molecules. Spectral changes with respect to the rotational angle of the amine group and the degree of hybridization at the nitrogen atom are investigated. The experimental spectrum is discussed on the basis of calculations performed for a variety of nuclear conformations. In particular, changes of the second (charge transfer) band are considered. INDO calculations of potential curves of aniline for the two degrees of freedom yield barriers of 1.2 kcal/ mole for the nitrogen inversion and of 7.5 kcal/mole for the internal amine rotation at the hybridization angle = 39.35°.