Showing papers in "Journal of Computational Chemistry in 1986"
TL;DR: An all atom potential energy function for the simulation of proteins and nucleic acids and the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach is presented.
Abstract: We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.
3,291 citations
TL;DR: In this article, an algorithm for locating transition states designed for use in the ab initio program package GAUSSIAN 82 is presented, which can locate transition states even if started in the wrong region of the energy surface.
Abstract: An algorithm for locating transition states designed for use in the ab initio program package GAUSSIAN 82 is presented. It is capable of locating transition states even if started in the wrong region of the energy surface, and, by incorporating the ideas on hessian mode following due to Cerjan and Miller, can locate transition states for alternative rearrangement/dissociation reactions from the same initial starting point. It can also be used to locate minima.
1,331 citations
TL;DR: In this article, an approach to couple ab initio quantum mechanical geometry optimiuzations with molecular mechanical optimizations is presented, with the added capability to carry out molecular dynamics simulations of the systems to earch for new local minima.
Abstract: We present an approach to couple ab initio quantum mechanical geometry optimiuzations with molecular mechanical optimizations, with the added capability to carry out molecular dynamics simulations of the systems to earch for new local minima. The approach is applied to the aqueous solution CH3Cl + Cl− exchange reaction and the gas phase protonation of polyethers.
1,046 citations
TL;DR: Ghose and Ghose as discussed by the authors showed the necessity of atomic physicochemical parameters in three-dimensional receptor mapping and derived more refined and widely applicable hydrophobicity parameters, including carbon, hydrogen, oxygen, nitrogen, sulfur, and halogens.
Abstract: Earlier we showed (A. K. Ghose and G. M. Crippen, J. Med. Chem., 28, 333, 1985) the necessity of atomic physicochemical parameters in three‐dimensional receptor mapping. Here we derive more refined and widely applicable hydrophobicity parameters. Carbon, hydrogen, oxygen, nitrogen, sulfur, and halogens are classified into 110 atom types. Among these, the hydrophobic contributions of 90 atom types have been evaluated from the log P(water‐octanol) values of 494 molecules, using the additive model and leastsquares technique. It gave a standard deviation of 0.347, a correlation coefficient of 0.962, and an explained variance of 0.908. These atomic values were used to predict the log P values of 69 compounds. The predicted values showed a standard deviation of 0.404 and a correlation coefficient of 0.896. This work has been compared with more conventional approaches.
583 citations
TL;DR: In this article, a split-valence 3-21G basis set for third and fourth-row, main-group elements has been developed for the calculation of equilibrium geometries, normal mode vibrational frequencies, reaction energies, and electric dipole moments involving a variety of normal and hypervalent compounds.
Abstract: Two new series of efficient basis sets for third- and fourth-row, main-group elements have been developed. Split-valence 3-21G basis sets have been formulated from the minimal expansions by Huzinaga, in which each atomic orbital has been represented by a sum of three Gaussians. The original expansions for s− and p−type orbitals (except those for 1s) have been replaced by new combinations in which the two sets of orbitals (of the same n quantum number) share Gaussian exponents. The Huzinaga expansions for 1s, 3d and 4d (fourth-row elements only) have been employed without further alteration. The valence atomic functions 4s, 4p for third-row elements; 5s, 5p for fourth-row elements have been split into two and one Gaussian parts. Supplemented 3-21G(*) representations have been formed from the 3-21G basis sets by the addition of a set of single d−type Gaussian functions.
The performance of 3-21G and 3-21G(*) basis sets is examined with regard to the calculation of equilibrium geometries, normal mode vibrational frequencies, reaction energies, and electric dipole moments involving a variety of normal and hypervalent compounds containing third- and fourth-row, main-group elements. The supplementary functions incorporated into the 3-21G(*) basis sets are generally found to be important, especially for the proper description of equilibrium bond lengths and electric dipole moments. 3-21G(*) representations are recommended for general use in lieu of the unsupplemented 3-21G basis sets.
443 citations
TL;DR: In this paper, an improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems.
Abstract: An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.
237 citations
TL;DR: The MNDO parameters for sulfur have been reoptimized and Calculations for a number of sulfur compounds indicate a very significant improvement.
Abstract: The MNDO parameters for sulfur have been reoptimized. Calculations for a number of sulfur compounds indicate a very significant improvement. Inclusion of d AOs failed to correct the errors for compounds of sulfur in its higher valence states. Since d AOs are not included, the calculations are still confined to compounds of divalent sulfur.
224 citations
TL;DR: In this article, a molecular dynamics program for arbitrary molecular mixtures is presented, where all intramolecular degrees of freedom are treated explicitly, which means that the program is based on central forces only.
Abstract: A molecular dynamics program for arbitrary molecular mixtures is presented. All intramolecular degrees of freedom are treated explicitly, which means that the program is based on central forces only. A double time step technique has been devised in order to separate rapidly varying, covalent forces from slowly varying ones. Typically, the ratio between the different time steps is about 10, with only a minor computational effort spent in the evaluation of the covalent forces. The program source code is arranged so as to obtain maximal efficiency on a vector processor, while still being portable. On a Cray 1A, a typical simulation of an ion-chelate in aqueous solution with 984 atoms requires a total of 29 μs/interaction with a spherical cutoff distance of 10A.
98 citations
TL;DR: The results obtained for the relative energies of the three conformers and the conformation of the side groups were affected by the inclusion of the electrostatic term and, in particular, by the charge assigned to the ionic groups of DMIS.
Abstract: Methods of molecular mechanics were applied to investigate the conformation of the (methyl 2-O-sulfate-4-methyl-α-L-idopyranose) uronic acid (DMIS), in order to correlate the peculiar vicinal proton coupling constants observed in polysaccharides containing the iduronate ring to the conformational characteristics of this sugar ring. We found three conformers with comparable energies, namely the two chair forms 1C4 and 4C1 and the skew-boat form 2S0(L); the latter is separated from each chair form by a barrier of about 9 kcal/mol. Along the pseudorotational path three additional minima (3S1, 1S3, and 1S5) were found, yet at least 4 kcal/mol higher than 2S0. The results obtained for the relative energies of the three conformers and the conformation of the side groups were affected by the inclusion of the electrostatic term and, in particular, by the charge assigned to the ionic groups of DMIS. However, the conformational properties of the idopyranosidic ring in DMIS (and in related compounds) should still be interpreted in terms of equilibrium among these three conformers only.
89 citations
79 citations
TL;DR: The performance of a variety of levels of theory in evaluating molecular electron affinities (EAs) has been systematically examined in this article, and the results appear to be significantly affected by spin contamination in the UHF wavefunctions.
Abstract: The performance of a variety of levels of theory in evaluating molecular electron affinities (EAs) has been systematically examined. Calculations have been carried out for six different basis sets and for nine theoretical procedures including unrestricted (UHF) and restricted (RHF) Hartree‐Fock theory, Møler‐Plesset perturbation theory (UMP2, UMP3, UMP4), configuration interaction (UCISD, RCISD, RCISD(Q)) and equations‐of‐motion (EOM) approaches. Electron affinities were evaluated for CH3, NH2, OH, F, C2H, CN, BO, N3, OCN, and NO2. Very poor results are generally obtained unless diffuse functions are included in the basis set and electron correlation is incorporated. Even with the largest basis set used in the present study (6‐311 + + G(2d, 2p)), there are still residual errors greater than 0.2 eV (UMP4) or 0.6 eV (CISD) in the absolute EAs. However, better results are obtained under certain circumstances for relative EAs. The results appear to be significantly affected by spin contamination in the UHF wave‐functions. For those systems for which spin contamination is small, best absolute values of the EAs generally come from the EOM and UMP2 calculations, whereas the most constant errors (thereby allowing systematic correction) are found at the UMP4, CISD, and RCISD(Q) levels. For the systems for which spin contamination is larger, best results are obtained with the CI‐based procedures (CISD and RCISD(Q)). The errors in calculated EAs for the molecules with differing electronic characteristics can vary quite widely. Caution must therefore be exercised before applying schemes which rely on a constancy of errors to estimate electron affinities. The UMP procedures appear particularly suspect in this regard if spin contamination is significant. The RCISD(Q) approach is recommended under such circumstances.
IBM1
TL;DR: Ab initio molecular orbital theory at the MP4/6‐311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol−1.
Abstract: The proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anion is proposed and applied to CH3-, NH2-, OH-, and CN-.
TL;DR: In this article, the use of gradient techniques for the development of energy-optimized basis sets has been investigated, and the region where the energy surface is approximately quadratic with a positive definite Hessian is found to be very small for large basis sets.
Abstract: The use of gradient techniques for the development of energy-optimized basis sets has been investigated. The region where the energy surface is approximately quadratic with a positive definite Hessian is found to be very small for large basis sets. However, scaled Newton-Raphson methods prove quite effective even when the starting point is outside this region. The analytic calculation of the Hessian is found to be most efficient in terms of computing time.
TL;DR: In this paper, an unconventional SCF method for calculations on large molecules with more than 100 basis functions is described, and compared with conventional SCF calculations, computational times increase by 25% to 75% depending on the basis set and the shape of the molecule.
Abstract: An unconventional SCF method for calculations on large molecules with more than 100 basis functions is described. Storage problems which arise in conventional SCF schemes when storing more than 107 integrals are avoided by repeated calculation of integrals. The resulting increase in computational times is kept at a reasonable level by (a) improving the initial guess, (b) accelerating convergence, (c) employing a recursive construction of the Fock matrix, and (d) eliminating insignificant integrals from the calculation by a density-weighted cutoff criterion. Sample calculations show that, compared with conventional SCF calculations, computational times increase by 25%–75% depending on the basis set and the shape of the molecule.
TL;DR: In this paper, a powerful transfer-matrix method is described for treating graph-theoretic weighted enumeration problems, which is particularly amenable for system graphs which are long in one direction and narrow in transverse directions.
Abstract: A frequently encountered problem in chemical applications is that of a weighted enumeration (or summation over) a class of extended subgraphs of a given system graph, which might represent a chemical structure. Some aspects of a powerful transfer‐matrix method are described for treating such graphtheoretic weighted enumeration problems. This method is seen to be particularly amenable for system graphs which are long in one direction and narrow in transverse directions. When the system graph is uniform (i.e., translationally symmetric) along one extended direction, asymptotic results can be readily extracted.
TL;DR: In this paper, ab initio calculations at the STO 3G level were performed on almost all of the possible isomers for the entire series of closo-carboranes, C2Bn−2Hn, 5 ⩽ n⩽ 12.
Abstract: Ab initio calculations at the STO‐3G level were performed on almost all of the possible isomers for the entire series of closo‐carboranes, C2Bn‐2Hn, 5 ⩽ n ⩽ 12. Geometry optimizations using the gradient method were also included in all calculations. We report here the relative energies obtained for the various isomers as well as the optimized structures. These calculations confirm our previous predictions of relative stabilities obtained from topological charge stabilization. Comparisons of our structures with those from experimental data provide us with a measure of reliability for bond distances obtained using ab initio SCF MO calculations at the STO‐3G level. Results from the geometry optimization substantiated the experimentally known fluxional behavior of the 8 and 11 atom polyhedra.
TL;DR: The complete harmonic force field and dipole moment derivatives have been computed for toluene at the Hartree‐Fock level using a 4‐21G basis set using the six scale factors optimized for benzene to scale the computed harmonic force constants.
Abstract: The complete harmonic force field and dipole moment derivatives have been computed for toluene at the Hartree-Fock level using a 4-21G basis set. The six scale factors optimized for benzene were used to scale the computed harmonic force constants of toluene. The vibrational frequencies of toluene computed from this scaled quantum mechanical force field are quite good. After a correction was made to two previously proposed spectral assignments, the mean deviation from the experimental frequencies is only 7.8 cm-1 except for the frequencies related to the methyl group. Five more scale factors for the vibrational modes of the methyl group were reoptimized. The final comparison showed an overall mean deviation of 7.5 cm-1 between the theoretical spectrum and the experimental spectrum. Computed intensities are qualitatively in agreement with experiments. They are highly useful in the investigation of questionable assignments.
TL;DR: A nonanalytical procedure is proposed to calculate the surface area and cross‐sectional areas of molecules and four ways are proposed to define quantitatively the intuitive notion of «molecular globularity».
Abstract: A nonanalytical procedure is proposed to calculate the surface area and cross-sectional areas of molecules. Results are reviewed for about 70 species comprising alkanes, acyclic and cyclic, alkyl halides, and alcohols. By regression analysis, relationships are detected between surface areas or segment areas and physical properties. Computed cross-sectional areas are confronted with adsorption values. Four ways are proposed to define quantitatively the intuitive notion of «molecular globularity».
TL;DR: A structural minimization procedure which converges rapidly and restricts the atomic shifts is outlined, implemented by adding a harmonic penalty term for the displacements of atomic positions and resetting the reference coordinates with respect to which the constraints are computed during the minimization.
Abstract: A structural minimization procedure which converges rapidly and restricts the atomic shifts is outlined. It is implemented by adding a harmonic penalty term for the displacements of atomic positions and resetting the reference coordinates with respect to which the constraints are computed during the minimization. The resetting serves to reduce the constraint energy of the minimized structure to negligible levels.
TL;DR: A systematic and objective method is developed here to enumerate all theoretically possible SGAL's for a protein, based only on its covalent structure, regardless of whether the three‐dimensional structure is known or unknown.
Abstract: The classification of patterns of the three-dimensional folding of a covalently crosslinked polypeptide chain can be used to introduce long-range interactions into the theoretical search for the native conformation of a protein. This classification into Spatial Geometric Arrangements of Loops (SGAL) had been proposed earlier (H. Meirovitch and H. A. Scheraga, Macromolecules14, 1250, 1981). It is based on the subdivision of the protein molecule into closed loops, defined by covalent crosslinks (such as disulfide bonds). Various SGAL classes correspond to the presence or absence of mutual penetration of loops, called entanglements or thrustings. A systematic and objective method is developed here to enumerate all theoretically possible SGAL's for a protein, based only on its covalent structure, i.e., the pattern of disulfide bonds or other crosslinks, regardless of whether the three-dimensional structure is known or unknown. This information can be of use in structural predictions of folding patterns. Using a modification of the method, it is also possible to determine the SGAL class to which a protein of known structure belongs. Out of 18 proteins with known three-dimensional structure and containing more than two disulfide bonds, five have a native structure with at least one entanglement or thrusting. Thus, threaded SGAL's represent a significant structural feature of native proteins. All five involve neighboring loops in the sequences. Their presence in a protein can suggest restrictions on the possible ways of folding the protein.
TL;DR: In this paper, the relative stabilities of the isomers and the barriers of the 1,3 shift are discussed in terms of proton affinities and bond orders, and the relative barrier heights are quantitatively related to bond orders.
Abstract: Ab initio molecular orbital calculations at SCF level with the 3‐21G, 6‐31G, and 6‐31G** basis sets and CI level with the 6‐31G basis set have been carried out for an isoelectronic series HXCHY and XCHYH, where X, Y can be CH2, NH, and O. Optimized structures (3‐21G and 6‐31G**) for both tautomers and the 1,3 hydrogen shift transition states are reported. The relative stabilities of the isomers and the barriers of the 1,3 shift are discussed in terms of proton affinities and bond orders. It is shown that both the relative stabilities of the tautomers and the relative barrier heights can be explained qualitatively using simple proton affinity arguments and that the barrier heights are quantitatively related to bond orders.
TL;DR: In this article, an algorithm for enumerating all 2-factors of polyhexes is presented, and some properties of 2 -factors and their properties are discussed, as well as their properties in terms of properties of polytopes.
Abstract: An algorithm is developed for enumerating all 2-factors of polyhexes. Some properties of 2-factors of polyhexes are discussed.
TL;DR: In this article, the atomic-atom potentials representing separate contributions to the non-empirical interaction energy have been derived in the SCF decomposition scheme corrected for basis set superposition error by the counterpoise method.
Abstract: Atom-atom potentials representing separate contributions to the nonempirical interaction energy have been derived in the SCF decomposition scheme corrected for basis set superposition error by the counterpoise method. The nontransferable long-range electrostatic multipole and classical induction terms have been evaluated directly from cumulative atomic multipole expansions, whereas the short-range exchange, charge-transfer, and electrostatic penetration contributions have been represented by simplified potentials of the form (β + δR−1) exp(−δR) fitted to the corresponding ab initio results for 336 dimer configurations formed by HF, H2O, NH3, CH4, CO, and CO2. The dominant anisotropic character of electrostatic multipole atom-atom potentials and much more isotropic nature of the potentials representing short-range terms is illustrated in the Appendix for head-on interactions in CO ‥ OC and HF ‥ FH dimers.
TL;DR: Heats of formation of 119 closed‐ and open‐shell carbocations calculated by the semiempirical quantum chemical methods MINDO/3 and MNDO are reported and compared with experimental data to find errors which were found in the calculations of the ions.
Abstract: Heats of formation of 119 closed- and open-shell carbocations calculated by the semiempirical quantum chemical methods MINDO/3 and MNDO are reported and compared with experimental data. With proper consideration of failures in specific areas, both methods can be used for the thermodynamics of carbocations containing C, H, N, and O. MINDO/3 predicts unrealistic values for nitrogen containing cations with nitrogen multiple bonds and is not suited for closed-shell cations containing oxygen. Saturated acyclic hydrocarbon radical cations often are computed with abnormally long CC bonds by MNDO. Otherwise, the standard deviation of the two methods is not very different, being in the range of ±13 kcal/mol. MINDO/3 tends to overestimate the cation stabilities, whereas MNDO calculates cations usually too high in energy. Some of the errors which were found in the calculations of the ions are related to the computed values for the parent neutral structures, but others are not.
TL;DR: The interactive programming system GRAPH, implemented at the Faculty of Electrical Engineering in Belgrade, is described and the applicability of this system in chemical investigations is pointed out.
Abstract: The interactive programming system GRAPH, implemented at the Faculty of Electrical Engineering in Belgrade, is described. This system has been designed to treat a great variety of problems of graph theory. In the present article we point out the applicability of the system GRAPH in chemical investigations and illustrate it by two examples.
TL;DR: This work proposes a full numerical method to calculate analytical matrix elements for Morse oscillators and compares, for the I2 system, the different results given by Gallas, Vasan, and Cross, and the variational method.
Abstract: Many authors have contributed expressions for obtaining analytical matrix elements for Morse oscillators. In this work, we discuss the advantages of using these expressions. At the same time, we propose a full numerical method to calculate these matrix elements and we compare, for the I2 system, the different results given by Gallas, Vasan, and Cross, and the variational method.
TL;DR: In this article, the solvation energies of first-row compounds LiX (X H, Li, BeH, BH2, CH3, NH2, OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito.
Abstract: Solvation energies of lithium first-row compounds LiX (X H, Li, BeH, BH2, CH3, NH2, OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito (MP2/6-31 + G*//6-31G* with zero-point vibrational energy corrections at 3-21G//3-21G). The solvation energies are found to be remarkably constant: −18.0 ± 1.2 and −21.5 ± 1.3 kcal/mol for the hydrates and ammonia solvates, respectively. This independence on the nature of X is due largely to the ionic character of the LiX compounds (dipole moments 4.7–6.6 debye). The unexpectedly high solvation energies of the lithium molecule (−14.3 and −17.8 kcal/mol, respectively) are due to the polarizability of Li2. At the same level, the lithium cation has interaction energies with H2O and NH3 of −34.1 and −39.7 kcal/mol, respectively. For the hydrates of LiOH and LiF cyclic structures with hydrogen bonds and somewhat increased solvation energies also are described.
TL;DR: The interaction of superoxide ion O2− with up to four water molecules [O2−: (H2O)n, n = 1, 2, 4] has been investigated using ab initio molecular orbital theory as discussed by the authors.
Abstract: The interaction of superoxide ion O2− with up to four water molecules [O2−: (H2O)n, n = 1, 2, 4] has been investigated using ab initio molecular orbital theory. The binding energy of O2−: H2O is calculated to be −20.6 kcal/mol in good agreement with gas phase experimental data. At the MP3/6-31G* level the O2−:H2O complex has a C2v structure with a double (cyclic) hydrogen bond between O2− and H2O. A Cs structure with a single hydrogen bond is only 0.7 kcal/mol less stable. Interaction of H2O with the doubly occupied π* orbital of O2− is preferred slightly over interaction with the singly occupied π* orbital. Natural bond orbital analysis suggests that both electrostatic and charge transfer interactions are important in anionic complexes. The charge transfer occurs predominantly in the O2− → H2O direction and is important in determining the relative stabilities of the different structures and states. Singly and doubly hydrogen-bonded structures for the O2−: (H2O)2 and O2−: (H2O)4 clusters were found to be similar in stability and the increase in binding of the cluster becomes smaller as each additional water molecule is added to the cluster.
TL;DR: In this article, it is considered that the formation of the intermediate ammonium carbamate (or the equivalent carbamic acid) takes place through the interaction of neutral species, and that this part of the synthesis is open to ab initio computations.
Abstract: A complete understanding of the synthesis of urea, (NH2)2CO, from NH3, CO2, and H2O remains an unsolved problem. It is considered that the formation of the intermediate ammonium carbamate (or the equivalent carbamic acid) takes place through the interaction of neutral species, and that this part of the synthesis is open to ab initio computations. Such calculations are reported on the formation of carbamic acid from NH3, CO2, and H2O. We have also investigated the formation of carbonic acid from CO2 and H2O showing that the six-membered ring transition state is non-planar, in contradiction with earlier reported calculations.
TL;DR: In this article, Monte Carlo determinations of the intramolecular thermodynamics of the Ala dipeptide in the C7, C5, αR, and PII conformations are reported.
Abstract: Monte Carlo determinations of the intramolecular thermodynamics of the Ala dipeptide in the C7, C5, αR, and PII conformations are reported. The calculations are carried out in the quasiharmonic approximation, with intramolecular entropies determined from the covariance matrix of the atomic displacements. The free energy of transition from C7 to C5, αR, and PII are found to be endergonic and dominated by the intrinsic energy of disrupting the intramolecular hydrogen bond in the C7 conformation. These results are combined with previous estimates of the free energy of hydration of the Ala dipeptide in water computed from liquid state Monte Carlo simulations using the probability ratio method. The net free energy of C7, αR, and PII are found to be similar, and it is thus reasonable to expect that all three forms are thermally populated at ambient temperature. The intermolecular carbonyl-water hydrogen bond in C5, αR, and PII competes successfully with the intramolecular NH…OC interaction in C7.