Predictive Abilities of Scaled Quantum Mechanical Molecular Force Fields: Application to 1,3-Butadiene

The positions of some IR bands of the s-trans-1,3-butadiene-h ₆ and -1,1,2-d ₃ isotopomers in the gas phase have been measured using a Brucker IFS 120 HR spectrometer with a resolution of 2 cm^–1. The structural parameters of the s-trans- and s-gauche-1,3-butadiene conformers were optimized completely at the MP2/6-31G* theoretical level and their MP2/6-31G*//MP2/6-31G* quantum mechanical force fields (QMFFs) were calculated. Using only the experimental vibrational frequencies of s-trans-1,3-butadiene-h ₆ the QMFF of the s-trans conformer was corrected by Pulay's scaling method (eight scale factors were involved). The scaled QMFF was used to calculate the mean vibrational amplitudes and the Coriolis coupling constants of s-trans-1,3-butadiene-h ₆ and the vibrational frequencies of 12 of its deuterated isotopomers. The set of scale factors obtained for correction of the s-trans QMFF was transferred to the QMFF of the s-gauche conformer. Its theoretical vibrational spectrum and those of some deuterated and C¹³ isotopomers were calculated. The ability of this scaling approach (transferring of scale factors) to predict the vibrational frequencies of rotational conformers and their isotopomers, as well as other molecular characteristics, and to permit detection of perturbations of the experimental bands are discussed.     

Vibrational spectra of 1,1,3,3-tetramethyl-2-nitroguanidine and their interpretation with the use of scaling of quantum-chemical force field

The IR (4000–50 cm⁻¹) and Raman (3500–170 cm⁻¹) spectra of solid 1,1,3,3-tetramethyl-2-nitroguanidine (TMNG) were obtained. The spectra were interpreted using the scaling of the TMNG quantum-chemical force field in the B3LYP/6-311G(d,p) approximation. Transferable scale factors necessary for the interpretation of spectra of more complex related compounds were determined. The scaled harmonic force field is supposed to be used in the analysis of the available gas-phase electron diffraction data for TMNG. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 495–498, March, 2008.     

鸟嘌呤红外光谱的密度泛函理论研究──标度量子力学(SQM)力场处理

用密度泛函理论DFT(B3LYP)/6-31G^*方法对鸟嘌呤分子的酮-胺式和醇-胺式异构体的几何结构、振动谐性力场和红外光谱进行了研究.理论力场由迁移自相关分子异胞嘧啶和咪唑的力常数标度因子进行标度.算得振动频率与鸟嘌呤的实验基质隔离IR光谱比较平均偏差对酮-胺式和醇-胺式分别为6.6和6.0cm^-1.根据振动频率的势能分布和DFT计算的光谱强度值对鸟嘌呤分子的实验振动基频进行了理论归属.     

Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs

The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the joint treatment of ab initio and experimental vibrational data of the four primary nucleobases using a new algorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factors in Cartesian coordinates for the considered molecules includes diagonal elements for all atoms of the molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1–3 and some 1–4 interactions). The choice of the model is based on the results of the second-order perturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital (NBO) analysis. The scaling factors obtained within this model as a result of solving the inverse problem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine molecules were used to correct the Hessians of the canonical base pairs: adenine–thymine and cytosine–guanine. The proposed procedure is based on the block structure of the scaling matrix for molecular entities with non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducing internal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field of a compound of a complex structure with non-covalent H-bonds.     

Calculation of Second- and Higher-Order Force Constants Including Electron Correlation Effects and Hartree-Fock Force Constant Scaling

A formalism suitable for practical implementation is suggested for computation of quadratic, cubic, and quartic force constants using the configuration interaction (CI) method. Expressions are compared which involve the Hartree-Fock (HF) harmonic and anharmonic force constants calculated by the HF and CI methods. Also, physical assumptions are formulated to perform scaling of the diagonal harmonic and, which is more important, of anharmonic HF force constants with a common scaling factor. This approach is consistent with the data of ab initio quantum-chemical calculations. A table is presented which compares the results of valence force constant calculations for a series of simple organic molecules.     

Molecular structures of acetylene derivatives of tin

The geometry and force fields of the bis(trimethylstannyl)acetylene molecule (a conformer withD _3d symmetry corresponding to a minimum of the total energy of the molecule) were calculated by the RHF and MP2(fc) methods. The effective core potential in SBK form with the optimized 31G^* valence basis set was employed in the case of Sn atoms. The 6–31G^** and 6–311G^** basis sets were used for carbon and hydrogen atoms. Vibrational spectra of the light and perdeuterated isotopomers of bis(trimethylstannyl)acetylene were interpreted using the procedure of scaling the quantum-chemical force fields. For Part 5, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 616–626, April, 2000.     

Some aspects of scaling factor calculations for quantum-mechanical molecular force fields

Stages of the scaling procedure for correcting molecular force fields obtained in rough quantum chemical calculations are discussed. The procedure includes selection of the number of scaling factors and their determination using experimental vibration frequencies of isotopomers and related molecules. It is stated that the difference in anharmonicity corrections for light molecules and their heavy analogs is to be taken into account along with possible errors in vibration frequency assignments of both isotopomers and more complex related molecules.     

2-氟-5-溴吡啶分子振动光谱的密度泛涵理论研究

用密度泛函理论方法B3LYP以及6-311++G(2df,2pd)基组对2-氟-5-溴吡啶分子 的平衡几何构型进行了优化并计算了该分子的振动谐力场。使用Pulay的标度方法 对理论力场进行了标度。采用Wilson的GF矩阵方法,根据标度后的理论力场进行了 简正坐标分析,对2-氟-5-溴吡啶分子的振动基频进行了理论研究,得到了势能分 布和红外振动频率。与红外频率的实验值相比较,理论频率的均方差为24 cm~(-1) 。此外,根据振动模式的势能分布对此分子的振动基频进行了理论归属,并对前人 的指认进行了修正和补充。     

On the Scaling Behavior of the Force/Extension Relation of a Chain

Applying an extending force F along the end‐to‐end vector r of a chain enlarges the initial size ρ_i ∼ | r _i| leading to a final state with ρ_f larger than ρ_i. Assuming a power law dependence of the size ρ ∼ N^ν of the chain on its length N, at the two different states with different exponents ν_i and ν_f, a scaling relationship is derived between the measure of the extending force F and the extension ρ of the chain. The exponent γ of the force/extension relation, ρ ∼ F^γ, depends on both exponents ν_i and ν_f of the initial and the final states. A relation between γ and the exponents ν_i and ν_f is derived which permits the explanation of previous results and predicts some more. The scaling behavior is checked with the exactly soluble model of a random walk under a force.

     

若干三核羧酸配合物的振动光谱及其与结构的某些相关规律

报导了通式为［Ｆｅ_２Ｍ（μ_３－Ｏ）（μ－Ｏ_２ＣＲ）_６·Ｌ_３］·ＸＨ_２Ｏ［其中Ｍ＝Ｍｎ（Ⅱ），Ｃｏ（Ⅱ），Ｎｉ（Ⅱ），Ｆｅ（Ⅲ）（这时骨架为阳离子）；Ｒ＝ＣＨ_３，Ｃ_２Ｈ_５；Ｌ＝Ｈ_２Ｏ，ｐｙ］的３类１１个配合物的振动光谱。在谱带经验归属及简正坐标分析计算的基础上，分别详细讨论了配体及骨架的振动光谱与结构的某些相关规律。这些规律具有一定的普遍性，因而有其理论和实际应用价值。     

Molecular structure of bismuth trichloride from combined electron diffraction and vibrational spectroscopic study

The results of an electron diffraction reanalysis, augmented with a combined electron diffraction and vibrational spectroscopic elucidation, of the molecular structure of BiCl₃ are reported. The principal parameters arer _g (Bi-Cl)=2.424±0.005 å (r =2.417±0.005 å) and <Cl-Bi-Cl=97.5±0.2. They are in excellent agreement with previous electron diffraction analysis [1], utilizing a more limited data range from the same experiment. They are also fully consistent with the expected trends of geometrical variation in the Group V trihalide series. The force fields of BiCl₃, determined by normal coordinate analysis and by combined analysis, agree within experimental error.     

FC(O)NCS 分子振动光谱的理论研究

采用DFT(B3LYP)方法,以6-3G*为基组对FC(O)NCS的顺式和反式两种构型的几何结构,振动谐性力场和红外光谱进行了研究。B3LYP/6-31G*计算水平和大多数有机分子的一套固定标度因子进行标度。根据标度后的理论力场进行简正坐标分析得到的势能分布(PED)和红外光谱强度值对FC(O)NCS分子的顺式和反式两种构型的振动基频进行了理论归属。     

Scaled Quantum Mechanical Force Fields for the Peroxynitrates. II. Fluorocarbonyl Peroxynitrate and Chlorocarbonyl Peroxynitrate.

The vibrational properties of fluorocarbonyl peroxynitrate, FC(O)OONO₂ and chlorocarbonyl peroxynitrate, ClC(O)OONO₂ were studied by means of density functional theory (DFT) methods. The obtained results served to revise the reported experimental spectra and their corresponding assignments. Subsequently, the revised data were used in the definition of scaled quantum mechanics (SQM) force fields for these peroxynitrates. A set of internal force constants was also calculated from such force fields.     

Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields

Dimerization free energies are fundamental quantities that describe the strength of interaction of different molecules. Obtaining accurate experimental values for small molecules and disentangling the conformations that contribute most to the binding can be extremely difficult, due to the size of the systems and the small energy differences. In many cases, one has to resort to computational methods to calculate such properties. In this work, we used molecular dynamics simulations in conjunction with metadynamics to calculate the free energy of dimerization of small aromatic rings, and compared three models from popular online servers for atomistic force fields, namely G54a7, CHARMM36 and OPLS. We show that, regardless of the force field, the profiles for the dimerization free energy of these compounds are very similar. However, significant care needs to be taken when studying larger molecules, since the deviations from the trends increase with the size of the molecules, resulting in force field dependent preferred stacking modes; for example, in the cases of pyrene and tetracene. Our results provide a useful background study for using topology builders to model systems which rely on stacking of aromatic moieties, and are relevant in areas ranging from drug design to supramolecular assembly.     

Force constant calculations for octahedral complexes of the type M(CO)5L, based on the CO-factored force field

Using the maximum value of the sum of the interaction constants, the CO-factored force field of octahedral M(CO)₅L molecules was solved to give the relations which allow direct calculation of force constants from C---O stretching frequencies of the all-¹²C¹⁶O molecule. The force constants calculated by these relations were used to predict C---O stretching frequencies of isotopically enriched species of some complexes of the type M(CO)₅L. The results obtained showed that there exists a very good agreement between observed and calculated frequencies. This led us to conclude that the solution presented for the force field of M(CO)₅L molecules is a valid solution.     

A new method to evaluate force constants from experimental spectral data

An iterative procedure is proposed to facilitate the determination of molecular vi-brational force constants from the experimental fundamental frequencies. Proper restrictions are introduced to the force constants based on physical considerations for getting reasonable results. The experimental data of Coriolis coupling coefficients and isotopic frequency shifts are utilized to reduce the uncertainty of the calculated force constants when they are available. A series of various kinds of molecules have been calculated by this method and the results are satisfactory.